Whs File Conflicts Resolver Conjugation
Posted : admin On 07.08.2019Whs File Conflicts Resolver Conjugation 9,1/10 4945 reviews
BROWZ delivers assurance that your business is working with safe, qualified, and socially responsible contractors and suppliers. We provide Contractor Management and prequalication services to the worlds most respected brands. Whs File Conflicts Resolver Spanish Conjugation The more detailed description, yelled. One of the goals of Windows Home Server is to protect you from a hard disk crash. It succeeds because it places copies of a file on the various hard drives that are connected to the Windows Home Server.
- Jon Paul JanetDepartment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Fang LiuDepartment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Aditya NandyDepartment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United StatesDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Chenru DuanDepartment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United StatesDepartment of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Tzuhsiung YangDepartment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Sean LinDepartment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Heather J. Kulik*Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States*E-mail: [email protected]. Phone: 617-253-4584.
Supporting Info (1)»Supporting Information Supporting Information
Download Hi-Res ImageDownload to MS-PowerPointCite This:Inorg. Chem.2019581610592-10606
Abstract
Recent transformative advances in computing power and algorithms have made computational chemistry central to the discovery and design of new molecules and materials. First-principles simulations are increasingly accurate and applicable to large systems with the speed needed for high-throughput computational screening. Despite these strides, the combinatorial challenges associated with the vastness of chemical space mean that more than just fast and accurate computational tools are needed for accelerated chemical discovery. In transition-metal chemistry and catalysis, unique challenges arise. The variable spin, oxidation state, and coordination environments favored by elements with well-localized d or f electrons provide great opportunity for tailoring properties in catalytic or functional (e.g., magnetic) materials but also add layers of uncertainty to any design strategy. We outline five key mandates for realizing computationally driven accelerated discovery in inorganic chemistry: (i) fully automated simulation of new compounds, (ii) knowledge of prediction sensitivity or accuracy, (iii) faster-than-fast property prediction methods, (iv) maps for rapid chemical space traversal, and (v) a means to reveal design rules on the kilocompound scale. Through case studies in open-shell transition-metal chemistry, we describe how advances in methodology and software in each of these areas bring about new chemical insights. We conclude with our outlook on the next steps in this process toward realizing fully autonomous discovery in inorganic chemistry using computational chemistry.
SPECIAL ISSUE
This article is part of the
Synopsis
A unified approach to computational high-throughput screening in open-shell transition-metal chemistry is presented in which challenges in uncertainty associated with modeling are tackled through automating simulation, knowing prediction sensitivity, developing faster-than-fast prediction methods, mapping chemical space, and revealing design rules.
ARTICLE SECTIONSJump To
Thanks to transformative advances in computing power and algorithms,(1−13) computational chemistry has become central to the discovery and design of new molecules(14−18) and materials.(19−25) Fully first-principles simulations of length or time scales that would have been inconceivable a little over a decade ago in the biological(13,26,27) and materials(28,29) sciences are increasingly routine. The hardware and strategies that have enabled these advances are far-ranging but include simplification of the complexity or number of quantum-mechanical electron-repulsion integral evaluations.(1−13) Regardless of the flavor of improvement, the practical effect is profound: a simulation that would have taken a week a little over a decade ago now takes less than an hour.(3) Alongside computational cost reductions, the accuracy of practical first-principles methods has improved dramatically through new functional forms that tackle long-range physics.(30−36) Within widely applied density functional theory (DFT), recent years have brought new insight about the interplay between delocalization (i.e., self-interaction) error(37,38) and static correlation error(39−41) and the relationship between density and energetic errors(42−47) relevant to transition-metal chemistry.(40,48) The same advances that have made widely employed DFT applicable to ever-larger systems have transformed gold standard correlated wave function theory (WFT) methods as well.(9−11,49) WFT methods that were once applicable to only a handful of atoms can now be employed to study hundreds.(12,50) Statistical techniques have also started(51,52) to make these WFT methods as “black box” as DFT.
Despite these great strides, the accelerated discovery of new catalysts(53−57) and materials(58−63) requires a different approach to realize computation’s full potential. The orders of magnitude advance in speed and accuracy has not translated directly to an equivalent acceleration in developing new chemical insight. These observations motivate us to focus on a distinct, larger problem: only a tiny fraction (ca. 1 part in 1050)(64,65) of chemical space has ever been explored. This chemical space contains all of the as-yet unknown catalysts, materials, and therapeutic drugs or otherwise useful molecules. The effort to uncover these molecules and materials unites the efforts of thousands of researchers in chemistry, materials science, and engineering worldwide. However, over the course of the lifetimes of these researchers, only a small dent will likely be made with traditional Edisonian approaches applied to this vast unexplored chemical space. Unique challenges arise in transition-metal chemistry and catalysis. The variable spin, oxidation state, and coordination environments favored by elements with well-localized d or f electrons provide great opportunity for tailoring properties in catalysis(17,66−72) or functional (e.g., magnetic) materials.(73−81) At the same time, this combinatorial challenge increases the uncertainty in how to best explore this vast chemical space to satisfy design objectives.
Although the need for accelerated exploration of chemical space is shared by experimental and computational researchers, the recent advances outlined here have poised computational chemistry to make important contributions to discovery efforts. Over the past few years, our group’s focus on how to tackle inorganic chemistry design challenges through advances in computation has been shaped by addressing five key mandates:
(1) Automate the simulation of new compounds. Until recently, it was not uncommon for new transition-metal complex and catalyst simulation candidates to be built by hand. Accelerated discovery requires tools that enable the automated generation of high-quality structures for rapid simulation, both to eliminate a potential source of human error and to remove bottlenecks to the large-scale discovery of new molecules and materials.
(2) Quantify prediction sensitivity or accuracy. Even as methods become more and more accurate, small changes in a computational method choice can have a substantial effect on the predicted activity of a catalyst or promise of a material. In most practical cases, where systematic improvement to chemical accuracy may be beyond reach, a design effort must operate with an awareness of the prediction sensitivity of the chosen method.
(3) Develop faster-than-fast property predictions. Despite orders-of-magnitude acceleration of first-principles simulation in recent years, direct combinatorial simulation will barely scratch the surface of the vast challenge that is unexplored chemical space. An alternative approach that can predict molecular or materials properties without first-principles computational cost is essential to advancing rapid chemical discovery.
(4) Map and traverse chemical space. To overcome combinatorial challenges, a “map” of where compounds sit with respect to each other in chemical space is needed. This map can help researchers identify what the most promising regions are for a particular target functionality and focus on only a small fraction of an otherwise unexplorable space.
(5) Reveal design rules on the kilocompound scale. The output of any high-throughput screen should never be a single molecule as the only promising candidate to solve an outstanding challenge. There are far too many unforeseen limitations, such as synthesizability, stability, and market-sensitive cost of materials, that cannot be anticipated completely beforehand. Computational high-throughput screening will be most valuable when it reveals the design features that improve a molecule’s performance. As data set sizes get larger, the tools that can reveal and encapsulate design rules will necessarily differ from simpler models that could be used for smaller, narrower data sets studied in the past.
To begin to solve these challenges in inorganic chemistry, we first take inspiration from organic chemistry. Here, machine-readable representations such as the simplified molecular input line entry system(82) (SMILES) string tell us nearly all we need to know about a molecule. With a SMILES string, precise three-dimensional (3D) structures can be generated,(83) leading to routine force-field,(84,85) semiempirical,(86−88) or first-principles characterization with high accuracy.(89) Such representations also lend themselves to quantitative structure–property relationship (QSPR) models(90,91) that enable even more complex mappings between the chemical composition and physicochemical properties (e.g., bioavailability(92,93)). For this reason, it is not surprising that machine learning (ML) models have excelled in encapsulating organic molecule chemical bonding.(94−98) Large multimillion molecule databases of organic compounds(99,100) are an excellent source for chemical discovery. To avoid exhaustive study of that entire space, concepts of molecular similarity may be exploited to identify the most diverse subset of compounds within such databases.(101) Applications in organic chemistry also benefit from all of these concepts being distilled in open-source tools, such as RDkit(102) and OpenBabel.(83,103)
Conversely, in inorganic chemistry, accurate generation of a 3D structure from a SMILES string must be carried out in a spin- and oxidation-state-dependent manner. Few force fields(104,105) or semiempirical methods(106) have been developed to be predictive for inorganic chemistry, mandating more computationally demanding first-principles simulation with results that are very sensitive to method parameters.(107−116) Here, QSPRs are often specific to a single metal, oxidation state, and spin state, thus enabling focus on properties of the ligand rather than metal-specific properties.(58,117−120) Repositories such as the Cambridge Structural Database(121) only have thousands of inorganic complex structures, and these represent compounds that have been characterized, crystallized, and published, limiting their promise as a resource for the discovery of truly new chemistry. Concepts of molecular similarity are less well-defined: a homoleptic manganese(II) ethylenediamine complex and hexaaqua iron(III) behave more similarly to each other than either does to an FeIII(acac) complex, despite the latter two sharing the same metal, oxidation state, and immediate coordination environment (Figure 1). Advances beyond each of these limitations in inorganic chemistry are essential to addressing the broader challenges we have outlined.
We have taken a divide-and-conquer approach to address this challenge: using techniques that work in organic chemistry and devising new syntax and tools where conventional approaches would fail because of the uncertainty of inorganic complex modeling. The rest of this manuscript is as follows. In section 2, we provide the computational details of the calculations employed in this work. In section 3, we present case studies illustrating successes and remaining opportunities for improvement that arise in tackling the five key challenges that we have outlined here. Finally, in section 4, we provide our conclusions and outlook for the most important obstacles that remain toward realizing the goal of fully autonomous, accelerated computational discovery in inorganic chemistry.
ARTICLE SECTIONSJump To
In this work, we carry out original analysis of DFT data sets and trained ML models generated in prior work.(18,122−124) We concisely summarize some of the details of these efforts here but refer the reader to the original work for more detail. The compounds in section 3a are homoleptic complexes generated in ref (124). The 5664 compound space was generated in ref (18), characterized with an artificial neural network (ANN) from ref (123), as well as with DFT, as outlined in sections 3b and 3d. The revised autocorrelation (RAC) feature selection and kernel ridge regression (KRR) models detailed in sections 3c and 3e are from ref (122). ML models introduced in this work include (i) an ANN that separately predicts equatorial and axial metal–ligand (M–L) bond lengths, trained on data from refs (122) and (123), and (ii) ANNs trained on MCDL-25 descriptors that predict the redox and ionization (IP) potentials. These new ML models that facilitate analysis are freely available online as part of the molSimplify(125) code and are detailed further in the Supporting Information (SI). The complete-active-space perturbation theory (CASPT2) benchmarks and Perdew–Burke–Ernzerhof (PBE) functional tuning results are derived from prior work(126) and outlined in the SI.
For all other simulations, a consistent workflow was employed. The molSimplify(125) toolkit was used to generate octahedral transition-metal complex structures from a pool of organic ligands common in inorganic chemistry with enforced equatorial symmetry but allowing up to two distinct axial ligands. DFT geometry optimizations were then carried out using TeraChem(1,127) with the B3LYP(128−130) hybrid DFT functional, occasionally varying the fraction of Hartree–Fock (HF) exchange from its default 20% value, as indicated in the text. The LANL2DZ(131) effective core potential was employed for transition metals with the 6-31G* basis set for all other atoms. The effect of using a modest basis set, which enables larger, using a genetic algorithm for first stage screening and multiple filtering stages for further refinement. An important step forward is to expand our diversity of candidate compds., including both synthetic and property-based measures of diversity. For example, top monomer pairs from our screening are all donor-donor (D-D) combinations, in contrast with the typical donor-acceptor (D-A) motif used in org. photovoltaics. We also find a strong 'sequence effect', in which the av. HOMO-LUMO gap of tetramers changes by ∼0.2 eV as a function of monomer sequence (e.g., ABBA vs. BAAB); this has rarely been explored in conjugated polymers. Beyond such optoelectronic optimization, we discuss other properties needed for high-efficiency org. solar cells, and applications of screening methods to other areas, including non-fullerene n-type materials, tandem cells, and improving charge and exciton transport.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXmsFGktro%253D&md5=85b4807c36484c8ad37cd8d9cd6d8eb817Vogiatzis, K. D.; Polynski, M. V.; Kirkland, J. K.; Townsend, J.; Hashemi, A.; Liu, C.; Pidko, E. A.Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities. Chem. Rev.2018, DOI: 10.1021/acs.chemrev.8b00361[ACS Full Text ], Google ScholarThere is no corresponding record for this reference.
18Janet, J. P.; Chan, L.; Kulik, H. J.Accelerating Chemical Discovery with Machine Learning: Simulated Evolution of Spin Crossover Complexes with an Artificial Neural Network. J. Phys. Chem. Lett.2018, 9, 1064– 1071, DOI: 10.1021/acs.jpclett.8b00170[ACS Full Text ], [CAS], Google Scholar18Accelerating Chemical Discovery with Machine Learning: Simulated Evolution of Spin Crossover Complexes with an Artificial Neural Network
Journal of Physical Chemistry Letters (2018), 9 (5), 1064-1071CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
Machine learning (ML) has emerged as a powerful complement to simulation for materials discovery by reducing time for evaluation of energies and properties at accuracy competitive with first-principles methods. We use genetic algorithm (GA) optimization to discover unconventional spin-crossover complexes in combination with efficient scoring from an artificial neural network (ANN) that predicts spin-state splitting of inorg. complexes. We explore a compd. space of over 5600 candidate materials derived from eight metal/oxidn. state combinations and a 32-ligand pool. We introduce a strategy for error-aware ML-driven discovery by limiting how far the GA travels away from the nearest ANN training points while maximizing property (i.e., spin-splitting) fitness, leading to discovery of 80% of the leads from full chem. space enumeration. Over a 51-complex subset, av. unsigned errors (4.5 kcal/mol) are close to the ANN's baseline 3 kcal/mol error. By obtaining leads from the trained ANN within seconds rather than days from a DFT-driven GA, this strategy demonstrates the power of ML for accelerating inorg. material discovery.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXisFarsr4%253D&md5=a21e7f08b8a407aeeae8ae1b2ae07b9e19Curtarolo, S.; Hart, G. L.; Nardelli, M. B.; Mingo, N.; Sanvito, S.; Levy, O.The High-Throughput Highway to Computational Materials Design. Nat. Mater.2013, 12, 191– 201, DOI: 10.1038/nmat3568[Crossref], [PubMed], [CAS], Google Scholar19The high-throughput highway to computational materials design
Curtarolo, Stefano; Hart, Gus L. W.; Nardelli, Marco Buongiorno; Mingo, Natalio; Sanvito, Stefano; Levy, Ohad
Nature Materials (2013), 12 (3), 191-201CODEN: NMAACR; ISSN:1476-1122. (Nature Publishing Group)
A review. High-throughput computational materials design is an emerging area of materials science. By combining advanced thermodn. and electronic-structure methods with intelligent data mining and database construction, and exploiting the power of current supercomputer architectures, scientists generate, manage and analyze enormous data repositories for the discovery of novel materials. In this Review we provide a current snapshot of this rapidly evolving field, and highlight the challenges and opportunities that lie ahead.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXislWju7c%253D&md5=5e116fbafda8e8437ccd0fdf7304d93920Curtarolo, S.; Setyawan, W.; Hart, G. L.; Jahnatek, M.; Chepulskii, R. V.; Taylor, R. H.; Wang, S.; Xue, J.; Yang, K.; Levy, O.; Mehl, M. J.; Stokes, H. T.; Demchenko, D. O.; Morgan, D.AFLOW: An Automatic Framework for High-Throughput Materials Discovery. Comput. Mater. Sci.2012, 58, 218– 226, DOI: 10.1016/j.commatsci.2012.02.005[Crossref], [CAS], Google Scholar20AFLOW: An automatic framework for high-throughput materials discovery
Curtarolo, Stefano; Setyawan, Wahyu; Hart, Gus L. W.; Jahnatek, Michal; Chepulskii, Roman V.; Taylor, Richard H.; Wang, Shidong; Xue, Junkai; Yang, Kesong; Levy, Ohad; Mehl, Michael J.; Stokes, Harold T.; Demchenko, Denis O.; Morgan, Dane
Computational Materials Science (2012), 58 (), 218-226CODEN: CMMSEM; ISSN:0927-0256. (Elsevier B.V.)
Recent advances in computational materials science present novel opportunities for structure discovery and optimization, including uncovering of unsuspected compds. and metastable structures, electronic structure, surface, and nano-particle properties. The practical realization of these opportunities requires systematic generation and classification of the relevant computational data by high-throughput methods. In this paper we present Aflow (Automatic Flow), a software framework for high-throughput calcn. of crystal structure properties of alloys, intermetallics and inorg. compds. The Aflow software is available for the scientific community on the website of the materials research consortium, aflowlib.org. Its geometric and electronic structure anal. and manipulation tools are addnl. available for online operation at the same website. The combination of automatic methods and user online interfaces provide a powerful tool for efficient quantum computational materials discovery and characterization.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XksVyktL8%253D&md5=8129bab53c054672274b0d6fa64172ef21Ong, S. P.; Richards, W. D.; Jain, A.; Hautier, G.; Kocher, M.; Cholia, S.; Gunter, D.; Chevrier, V. L.; Persson, K. A.; Ceder, G.Python Materials Genomics (Pymatgen): A Robust, Open-Source Python Library for Materials Analysis. Comput. Mater. Sci.2013, 68, 314– 319, DOI: 10.1016/j.commatsci.2012.10.028[Crossref], [CAS], Google Scholar21Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis
Ong, Shyue Ping; Richards, William Davidson; Jain, Anubhav; Hautier, Geoffroy; Kocher, Michael; Cholia, Shreyas; Gunter, Dan; Chevrier, Vincent L.; Persson, Kristin A.; Ceder, Gerbrand
Computational Materials Science (2013), 68 (), 314-319CODEN: CMMSEM; ISSN:0927-0256. (Elsevier B.V.)
We present the Python Materials Genomics (pymatgen) library, a robust, open-source Python library for materials anal. A key enabler in high-throughput computational materials science efforts is a robust set of software tools to perform initial setup for the calcns. (e.g., generation of structures and necessary input files) and post-calcn. anal. to derive useful material properties from raw calcd. data. The pymatgen library aims to meet these needs by (1) defining core Python objects for materials data representation, (2) providing a well-tested set of structure and thermodn. analyses relevant to many applications, and (3) establishing an open platform for researchers to collaboratively develop sophisticated analyses of materials data obtained both from first principles calcns. and expts. The pymatgen library also provides convenient tools to obtain useful materials data via the Materials Project's REpresentational State Transfer (REST) Application Programming Interface (API). As an example, using pymatgen's interface to the Materials Project's RESTful API and phase diagram package, we demonstrate how the phase and electrochem. stability of a recently synthesized material, Li4SnS4, can be analyzed using a min. of computing resources. We find that Li4SnS4 is a stable phase in the Li-Sn-S phase diagram (consistent with the fact that it can be synthesized), but the narrow range of lithium chem. potentials for which it is predicted to be stable would suggest that it is not intrinsically stable against typical electrodes used in lithium-ion batteries.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsVGjt7g%253D&md5=104f567dbd8f4199911ded91bc42100e22Nørskov, J. K.; Bligaard, T.The Catalyst Genome. Angew. Chem., Int. Ed.2013, 52, 776– 777, DOI: 10.1002/anie.201208487[Crossref], [CAS], Google Scholar22Norskov, Jens K.; Bligaard, Thomas
Angewandte Chemie, International Edition (2013), 52 (3), 776-777CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
There is no expanded citation for this reference.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhslymtrzM&md5=ec50826a181c734b9338addfa16a2bfc23Han, S.; Huang, Y.; Watanabe, T.; Dai, Y.; Walton, K. S.; Nair, S.; Sholl, D. S.; Meredith, J. C.High-Throughput Screening of Metal–Organic Frameworks for CO2 Separation. ACS Comb. Sci.2012, 14, 263– 267, DOI: 10.1021/co3000192[ACS Full Text ], [CAS], Google Scholar23High-Throughput Screening of Metal-Organic Frameworks for CO2 Separation
Han, Sangil; Huang, Yougui; Watanabe, Taku; Dai, Ying; Walton, Krista S.; Nair, Sankar; Sholl, David S.; Meredith, J. Carson
ACS Combinatorial Science (2012), 14 (4), 263-267CODEN: ACSCCC; ISSN:2156-8944. (American Chemical Society)
A parallel high-throughput sorption methodol. is described for screening CO2 and N2 adsorption and diffusion selectivity in metal org. frameworks, before and after exposure to H2O vapor and acid gases. The authors illustrate this approach by simultaneously studying 8 candidate Metal-Org. Framework (MOF) materials, of which the best material has a CO2/N2 membrane selectivity of 152 and a CO2 permeability of 60 barrer for Co-NIC. This approach provides a significant increase in efficiency of obtaining the sepn. properties of MOFs. While the authors describe here the identification of novel materials for CO2 capture, the methodol. enables exploration of the performance and stability of novel porous materials for a wide range of applications.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XktFeksL4%253D&md5=d0a02f702ff2490c9b799467f4170ec924Wilmer, C. E.; Leaf, M.; Lee, C. Y.; Farha, O. K.; Hauser, B. G.; Hupp, J. T.; Snurr, R. Q.Large-Scale Screening of Hypothetical Metal–Organic Frameworks. Nat. Chem.2012, 4, 83– 89, DOI: 10.1038/nchem.1192[Crossref], [CAS], Google Scholar24Large-scale screening of hypothetical metal-organic frameworks
Wilmer, Christopher E.; Leaf, Michael; Lee, Chang Yeon; Farha, Omar K.; Hauser, Brad G.; Hupp, Joseph T.; Snurr, Randall Q.
Nature Chemistry (2012), 4 (2), 83-89CODEN: NCAHBB; ISSN:1755-4330. (Nature Publishing Group)
Metal-org. frameworks (MOFs) are porous materials constructed from modular mol. building blocks, typically metal clusters and org. linkers. These can, in principle, be assembled to form an almost unlimited no. of MOFs, yet materials reported to date represent only a tiny fraction of the possible combinations. Here, the authors demonstrate a computational approach to generate all conceivable MOFs from a given chem. library of building blocks (based on the structures of known MOFs) and rapidly screen them to find the best candidates for a specific application. From a library of 102 building blocks the authors generated 137,953 hypothetical MOFs and for each calcd. the pore-size distribution, surface area and methane-storage capacity. The authors identified over 300 MOFs with a predicted methane-storage capacity better than that of any known material, and this approach also revealed structure-property relations. Methyl-functionalized MOFs were frequently top performers, so the authors selected one such promising MOF and exptl. confirmed its predicted capacity.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhsVagtL3K&md5=3becbfed2fdacdb8b58146666da7c03825Witman, M.; Ling, S.; Anderson, S.; Tong, L.; Stylianou, K. C.; Slater, B.; Smit, B.; Haranczyk, M.In Silico Design and Screening of Hypothetical Mof-74 Analogs and Their Experimental Synthesis. Chem. Sci.2016, 7, 6263– 6272, DOI: 10.1039/C6SC01477A[Crossref], [PubMed], [CAS], Google Scholar25In silico design and screening of hypothetical MOF-74 analogs and their experimental synthesis
Witman, Matthew; Ling, Sanliang; Anderson, Samantha; Tong, Lianheng; Stylianou, Kyriakos C.; Slater, Ben; Smit, Berend; Haranczyk, Maciej
Chemical Science (2016), 7 (9), 6263-6272CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)
In this work we present the in silico design of metal-org. frameworks (MOFs) exhibiting 1-dimensional rod topologies. We introduce an algorithm for construction of this family of MOF topologies, and illustrate its application for enumerating MOF-74-type analogs. Furthermore, we perform a broad search for new linkers that satisfy the topol. requirements of MOF-74 and consider the largest database of known chem. space for org. compds., the PubChem database. Our in silico crystal assembly, when combined with dispersion-cor. d. functional theory (DFT) calcns., is demonstrated to generate a hypothetical library of open-metal site contg. MOF-74 analogs in the 1-D rod topol. from which we can simulate the adsorption behavior of CO2. We finally conclude that these hypothetical structures have synthesizable potential through computational identification and exptl. validation of a novel MOF-74 analog, Mg2(olsalazine).
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtVGisrrF&md5=6b0d264eb348a0e5a29b30cd803abf0726Ufimtsev, I. S.; Luehr, N.; Martínez, T. J.Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics. J. Phys. Chem. Lett.2011, 2, 1789– 1793, DOI: 10.1021/jz200697c[ACS Full Text ], [CAS], Google Scholar26Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics
Ufimtsev, Ivan S.; Luehr, Nathan; Martinez, Todd J.
Journal of Physical Chemistry Letters (2011), 2 (14), 1789-1793CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
Charge transfer at the bovine pancreatic trypsin inhibitor (BPTI) protein-water interface was analyzed by means of ab initio Born-Oppenheimer mol. dynamics simulation of the entire protein running on graphical processing units (GPUs). The efficiency of the GPU-based quantum chem. algorithms implemented in our TeraChem program enables us to perform these calcns. on a desktop computer. Mulliken and Voronoi deformation d. (VDD) population anal. reveals that between 2.0 and 3.5 electrons are transferred from surrounding water mols. to the protein over the course of the 8.8 ps simulation. Solving for the electronic structure of BPTI in the absence of surrounding water mols. (i.e., in the gas phase) leads to large intraprotein charge transfer, where approx. one electron in total is transferred from neutral to polar residues. Solvation relieves this polarization stress, leading to a neutralization of the excess pos. charge of the neutral residues.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXosFyktr0%253D&md5=e8f7eae80215597532e8bae205ee358d27Kulik, H. J.Large-Scale QM/MM Free Energy Simulations of Enzyme Catalysis Reveal the Influence of Charge Transfer. Phys. Chem. Chem. Phys.2018, 20, 20650– 20660, DOI: 10.1039/C8CP03871F[Crossref], [CAS], Google Scholar27Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer
Physical Chemistry Chemical Physics (2018), 20 (31), 20650-20660CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
Hybrid quantum mech.-mol. mech. (QM/MM) simulations provide key insights into enzyme structure-function relationships. Numerous studies have demonstrated that large QM regions are needed to systematically converge ground state, zero temp. properties with electrostatic embedding QM/MM. However, it is not well known if ab initio QM/MM free energy simulations have this same dependence, in part due to the hundreds of thousands of energy evaluations required for free energy estns. that in turn limit QM region size. Here, we leverage recent advances in electronic structure efficiency and accuracy to carry out range-sepd. hybrid d. functional theory free energy simulations in a representative methyltransferase. By studying 200 ps of ab initio QM/MM dynamics for each of five QM regions from minimal (64 atoms) to one-sixth of the protein (544 atoms), we identify crit. differences between large and small QM region QM/MM in charge transfer between substrates and active site residues as well as in geometric structure and dynamics that coincide with differences in predicted free energy barriers. Distinct geometric and electronic structure features in the largest QM region indicate that important aspects of enzymic rate enhancement in methyltransferases are identified with large-scale electronic structure.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhtlOgt73F&md5=e179ba52def7e9425a2dcfb4e40c7b9e28Fales, B. S.; Levine, B. G.Nanoscale Multireference Quantum Chemistry: Full Configuration Interaction on Graphical Processing Units. J. Chem. Theory Comput.2015, 11, 4708– 4716, DOI: 10.1021/acs.jctc.5b00634[ACS Full Text ], [CAS], Google Scholar28Nanoscale Multireference Quantum Chemistry: Full Configuration Interaction on Graphical Processing Units
Journal of Chemical Theory and Computation (2015), 11 (10), 4708-4716CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Methods based on a full CI (FCI) expansion in an active space of orbitals are widely used for modeling chem. phenomena such as bond breaking, multiply excited states, and conical intersections in small-to-medium-sized mols., but these phenomena occur in systems of all sizes. To scale such calcns. up to the nanoscale, we have developed an implementation of FCI in which electron repulsion integral transformation and several of the more expensive steps in σ vector formation are performed on graphical processing unit (GPU) hardware. When applied to a 1.7 × 1.4 × 1.4 nm silicon nanoparticle (Si72H64) described with the polarized, all-electron 6-31G** basis set, our implementation can solve for the ground state of the 16-active-electron/16-active-orbital CASCI Hamiltonian (more than 100,000,000 configurations) in 39 min on a single NVidia K40 GPU.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsVyktrjF&md5=0909ca201d7302bfd994d495c552f52429Zhao, Q.; Kulik, H. J.Electronic Structure Origins of Surface-Dependent Growth in III-V Quantum Dots. Chem. Mater.2018, 30, 7154– 7165, DOI: 10.1021/acs.chemmater.8b03125[ACS Full Text ], [CAS], Google Scholar29Electronic Structure Origins of Surface-Dependent Growth in III-V Quantum Dots
Chemistry of Materials (2018), 30 (20), 7154-7165CODEN: CMATEX; ISSN:0897-4756. (American Chemical Society)
Indium phosphide quantum dots (QDs) have emerged as a promising candidate to replace more toxic II-VI CdSe QDs, but prodn. of high-quality III-V InP QDs with targeted properties requires a better understanding of their growth. We develop a first-principles-derived model that unifies InP QD formation from isolated precursor and early stage cluster reactions to 1.3 nm magic sized clusters and rationalize exptl. obsd. properties of full sized >3 nm QDs. Our first-principles study on realistic QD models reveals large surface-dependent reactivity for all elementary growth process steps, including In-ligand bond cleavage and P precursor addn. These thermodn. trends correlate well to kinetic properties at all stages of growth, indicating the presence of labile and stable spots on cluster and QD surfaces. Correlation of electronic or geometric properties to energetics identifies surprising sources for these variations: short In···In sepn. on the surface produces the most reactive sites, at odds with conventional understanding of strain (i.e., sepn.) in bulk metallic surfaces increasing reactivity and models for ionic II-VI QD growth. These differences are rationalized by the covalent, directional nature of bonding in III-V QDs and explained by bond order metrics derived directly from the In-O bond d. The unique constraints of carboxylate and P precursor bonding to In atoms rationalize why all sizes of InP clusters and QDs are In-rich but become less so as QDs mature. These observations support the development of alternate growth recipes that take into account strong surface-dependence of kinetics as well as the shapes of both In and P precursors to control both kinetics and surface morphol. in III-V QDs.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhsleqtL%252FO&md5=58136a35c84f458aa7ef56eca668bc7e30Kümmel, S.; Kronik, L.Orbital-Dependent Density Functionals: Theory and Applications. Rev. Mod. Phys.2008, 80, 3– 60, DOI: 10.1103/RevModPhys.80.3[Crossref], [CAS], Google Scholar30Orbital-dependent density functionals: Theory and applications
Reviews of Modern Physics (2008), 80 (1), 3-60CODEN: RMPHAT; ISSN:0034-6861. (American Physical Society)
This review provides a perspective on the use of orbital-dependent functionals, which is currently considered one of the most promising avenues in modern d.-functional theory. The focus here is on four major themes: the motivation for orbital-dependent functionals in terms of limitations of semilocal functionals; the optimized effective potential as a rigorous approach to incorporating orbital-dependent functionals within the Kohn-Sham framework; the rationale behind and advantages and limitations of four popular classes of orbital-dependent functionals; and the use of orbital-dependent functionals for predicting excited-state properties. For each of these issues, both formal and practical aspects are assessed.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXlslKms74%253D&md5=867b579a9dfef4dfa661a6af35d6d21d31Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H.A Consistent and Accurate Ab Initio Parametrization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu. J. Chem. Phys.2010, 132, 154104, DOI: 10.1063/1.3382344[Crossref], [PubMed], [CAS], Google Scholar31A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
Grimme, Stefan; Antony, Jens; Ehrlich, Stephan; Krieg, Helge
Journal of Chemical Physics (2010), 132 (15), 154104/1-154104/19CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
The method of dispersion correction as an add-on to std. Kohn-Sham d. functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coeffs. and cutoff radii that are both computed from first principles. The coeffs. for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination nos. (CN). They are used to interpolate between dispersion coeffs. of atoms in different chem. environments. The method only requires adjustment of two global parameters for each d. functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of at. forces. Three-body nonadditivity terms are considered. The method has been assessed on std. benchmark sets for inter- and intramol. noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean abs. deviations for the S22 benchmark set of noncovalent interactions for 11 std. d. functionals decrease by 15%-40% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C6 coeffs. also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in mols. and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems. (c) 2010 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXkvVyks7o%253D&md5=2bca89d904579d5565537a0820dc2ae832Livshits, E.; Baer, R.A Well-Tempered Density Functional Theory of Electrons in Molecules. Phys. Chem. Chem. Phys.2007, 9, 2932– 2941, DOI: 10.1039/b617919c[Crossref], [CAS], Google Scholar32A well-tempered density functional theory of electrons in molecules
Physical Chemistry Chemical Physics (2007), 9 (23), 2932-2941CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
This Invited Article reports extensions of a recently developed approach to d. functional theory with correct long-range behavior (R. Baer and D. Neuhauser, Phys. Rev. Lett., 2005, 94, 043002). The central quantities are a splitting functional γ[n] and a complementary exchange-correlation functional EγXC[n]. We give a practical method for detg. the value of γ in mols., assuming an approxn. for EγXC is given. The resulting theory shows good ability to reproduce the ionization potentials for various mols. However it is not of sufficient accuracy for forming a satisfactory framework for studying mol. properties. A somewhat different approach is then adopted, which depends on a d.-independent γ and an addnl. parameter w eliminating part of the local exchange functional. The values of these two parameters are obtained by best-fitting to exptl. atomization energies and bond lengths of the mols. in the G2(1) database. The optimized values are γ = 0.5 a-10 and w = 0.1. We then examine the performance of this slightly semi-empirical functional for a variety of mol. properties, comparing to related works and expt. We show that this approach can be used for describing in a satisfactory manner a broad range of mol. properties, be they static or dynamic. Most satisfactory is the ability to describe valence, Rydberg and inter-mol. charge-transfer excitations.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXmtVylsbY%253D&md5=32a27f5ad7ff5749d93bb6dc0394ae7933Stein, T.; Kronik, L.; Baer, R.Reliable Prediction of Charge Transfer Excitations in Molecular Complexes Using Time-Dependent Density Functional Theory. J. Am. Chem. Soc.2009, 131, 2818– 2820, DOI: 10.1021/ja8087482[ACS Full Text ], [CAS], Google Scholar33Reliable prediction of charge transfer excitations in molecular complexes using time-dependent density functional theory
Journal of the American Chemical Society (2009), 131 (8), 2818-2820CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
We show how charge transfer excitations at mol. complexes can be calcd. quant. using time-dependent d. functional theory. Predictive power is obtained from range-sepd. hybrid functionals using nonempirical tuning of the range-splitting parameter. Excellent performance of this approach is obtained for a series of complexes composed of various arom. donors and the tetracyanoethylene acceptor, paving the way to systematic nonempirical quant. studies of charge-transfer excitations in real systems.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhvVSns7s%253D&md5=b01ac7f2580fdb9495f7e51be1910d5734Körzdörfer, T.; Brédas, J.-L.Organic Electronic Materials: Recent Advances in the DFT Description of the Ground and Excited States Using Tuned Range-Separated Hybrid Functionals. Acc. Chem. Res.2014, 47, 3284– 3291, DOI: 10.1021/ar500021t[ACS Full Text ], [CAS], Google Scholar34Organic electronic materials: recent advances in the DFT description of the ground and excited states using tuned range-separated hybrid functionals
Accounts of chemical research (2014), 47 (11), 3284-91 ISSN:.
CONSPECTUS: Density functional theory (DFT) and its time-dependent extension (TD-DFT) are powerful tools enabling the theoretical prediction of the ground- and excited-state properties of organic electronic materials with reasonable accuracy at affordable computational costs. Due to their excellent accuracy-to-numerical-costs ratio, semilocal and global hybrid functionals such as B3LYP have become the workhorse for geometry optimizations and the prediction of vibrational spectra in modern theoretical organic chemistry. Despite the overwhelming success of these out-of-the-box functionals for such applications, the computational treatment of electronic and structural properties that are of particular interest in organic electronic materials sometimes reveals severe and qualitative failures of such functionals. Important examples include the overestimation of conjugation, torsional barriers, and electronic coupling as well as the underestimation of bond-length alternations or excited-state energies in low-band-gap polymers. In this Account, we highlight how these failures can be traced back to the delocalization error inherent to semilocal and global hybrid functionals, which leads to the spurious delocalization of electron densities and an overestimation of conjugation. The delocalization error for systems and functionals of interest can be quantified by allowing for fractional occupation of the highest occupied molecular orbital. It can be minimized by using long-range corrected hybrid functionals and a nonempirical tuning procedure for the range-separation parameter. We then review the benefits and drawbacks of using tuned long-range corrected hybrid functionals for the description of the ground and excited states of π-conjugated systems. In particular, we show that this approach provides for robust and efficient means of characterizing the electronic couplings in organic mixed-valence systems, for the calculation of accurate torsional barriers at the polymer limit, and for the reliable prediction of the optical absorption spectrum of low-band-gap polymers. We also explain why the use of standard, out-of-the-box range-separation parameters is not recommended for the DFT and/or TD-DFT description of the ground and excited states of extended, pi-conjugated systems. Finally, we highlight a severe drawback of tuned range-separated hybrid functionals by discussing the example of the calculation of bond-length alternation in polyacetylene, which leads us to point out the challenges for future developments in this field.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2cnosFaltg%253D%253D&md5=378dd3ab4b06d00152d606ed0f7c933f35Autschbach, J.; Srebro, M.Delocalization Error and “Functional Tuning” in Kohn–Sham Calculations of Molecular Properties. Acc. Chem. Res.2014, 47, 2592– 2602, DOI: 10.1021/ar500171t[ACS Full Text ], [CAS], Google Scholar35Delocalization Error and 'Functional Tuning' in Kohn-Sham Calculations of Molecular Properties
Accounts of Chemical Research (2014), 47 (8), 2592-2602CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
A review. Kohn-Sham theory (KST) is the 'workhorse' of numerical quantum chem. This is particularly true for first-principles calcns. of ground- and excited-state properties for larger systems, including electronic spectra, electronic dynamic and static linear and higher order response properties (including nonlinear optical (NLO) properties), conformational or dynamic averaging of spectra and response properties, or properties that are affected by the coupling of electron and nuclear motion. This Account explores the sometimes dramatic impact of the delocalization error (DE) and possible benefits from the use of long-range corrections (LC) and 'tuning' of functionals in KST calcns. of mol. ground-state and response properties. Tuning refers to a nonempirical mol.-specific detn. of adjustable parameters in functionals to satisfy known exact conditions, for instance, that the energy of the HOMO should be equal to the neg. vertical ionization potential (IP) or that the energy as a function of fractional electron nos. should afford straight-line segments. The presentation is given from the viewpoint of a chemist interested in computations of a variety of mol. optical and spectroscopic properties and of a theoretician developing methods for computing such properties with KST. In recent years, the use of LC functionals, functional tuning, and quantifying the DE explicitly have provided valuable insight regarding the performance of KST for mol. properties. We discuss a no. of different mol. properties, with examples from recent studies from our lab. and related literature. The selected properties probe different aspects of mol. electronic structure. Elec. field gradients and hyperfine coupling consts. can be exquisitely sensitive to the DE because it affects the ground-state electron d. and spin d. distributions. For π-conjugated mols., it is shown how the DE manifests itself either in too strong or too weak delocalization of localized MOs (LMOs). Optical rotation is an elec.-magnetic linear response property that is calcd. in a similar fashion as the elec. polarizability, but it is more sensitive to approxns. and can benefit greatly from tuning and small DE. Hyperpolarizabilities of π-conjugated 'push-pull' systems are examples of NLO properties that can be greatly improved by tuning of range-sepd. exchange (RSE) functionals, in part due to improved charge-transfer excitation energies. On-going work on band gap predictions is also mentioned. The findings may provide clues for future improvements of KST because different mol. properties exhibit varying sensitivity to approxns. in the electronic structure model. The utility of analyzing mol. properties and the impact of the DE in terms of LMOs, representing 'chemist's orbitals' such as individual lone pairs and bonds, is highlighted.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtVGksbvL&md5=2d587db13d129951b7bef20e57356ba636Dion, M.; Rydberg, H.; Schröder, E.; Langreth, D. C.; Lundqvist, B. I.Van Der Waals Density Functional for General Geometries. Phys. Rev. Lett.2004, 92, 246401, DOI: 10.1103/PhysRevLett.92.246401[Crossref], [PubMed], [CAS], Google Scholar36Van der Waals Density Functional for General Geometries
Dion, M.; Rydberg, H.; Schroeder, E.; Langreth, D. C.; Lundqvist, B. I.
Physical Review Letters (2004), 92 (24), 246401/1-246401/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
A scheme within d. functional theory is proposed that provides a practical way to generalize to unrestricted geometries the method applied with some success to layered geometries [H. Rydberg et al., Phys. Rev. Lett. 91, 126402 (2003)]. It includes van der Waals forces in a seamless fashion. By expansion to second order in a carefully chosen quantity contained in the long-range part of the correlation functional, the nonlocal correlations are expressed in terms of a d.-d. interaction formula. It contains a relatively simple parametrized kernel, with parameters detd. by the local d. and its gradient. The proposed functional is applied to rare gas and benzene dimers, where it is shown to give a realistic description.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXltVerur4%253D&md5=abbf50b023000f126ba66af15c78658337Mori-Sánchez, P.; Cohen, A. J.; Yang, W.Many-Electron Self-Interaction Error in Approximate Density Functionals. J. Chem. Phys.2006, 125, 201102, DOI: 10.1063/1.2403848[Crossref], [PubMed], [CAS], Google Scholar37Many-electron self-interaction error in approximate density functionals
Journal of Chemical Physics (2006), 125 (20), 201102/1-201102/4CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
One of the most important challenges in d. functional theory (DFT) is the proper description of fractional charge systems relating to the self-interaction error (SIE). Traditionally, the SIE has been formulated as a one-electron problem, which has been addressed in several recent functionals. However, these recent one-electron SIE-free functionals, while greatly improving the description of thermochem. and reaction barriers in general, still exhibit many of the difficulties assocd. with SIE. Thus we emphasize the need to surpass this limit and shed light on the many-electron SIE. After identifying the sufficient condition for functionals to be free from SIE, we focus on the symptoms and investigate the performance of most popular functionals. We show that these functionals suffer from many-electron SIE. Finally, we give a SIE classification of d. functionals.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XhtlSlt77E&md5=8de0c410a67a0f7da2a2ef194c21a25b38Cohen, A. J.; Mori-Sánchez, P.; Yang, W.Insights into Current Limitations of Density Functional Theory. Science2008, 321, 792– 794, DOI: 10.1126/science.1158722[Crossref], [PubMed], [CAS], Google Scholar38Insights into Current Limitations of Density Functional Theory
Science (Washington, DC, United States) (2008), 321 (5890), 792-794CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
A review. D. functional theory of electronic structure is widely and successfully applied in simulations throughout engineering and sciences. However, for many predicted properties, there are spectacular failures that can be traced to the delocalization error and static correlation error of commonly used approxns. These errors can be characterized and understood through the perspective of fractional charges and fractional spins introduced recently. Reducing these errors will open new frontiers for applications of d. functional theory.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXptlyhsrg%253D&md5=502dc9289c4a858806549cd769681ac839Bajaj, A.; Janet, J. P.; Kulik, H. J.Communication: Recovering the Flat-Plane Condition in Electronic Structure Theory at Semi-Local DFT Cost. J. Chem. Phys.2017, 147, 191101, DOI: 10.1063/1.5008981[Crossref], [PubMed], [CAS], Google Scholar39Communication: Recovering the flat-plane condition in electronic structure theory at semi-local DFT cost
Journal of Chemical Physics (2017), 147 (19), 191101/1-191101/5CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
The flat-plane condition is the union of two exact constraints in electronic structure theory: (i) energetic piecewise linearity with fractional electron removal or addn. and (ii) invariant energetics with change in electron spin in a half filled orbital. Semi-local d. functional theory (DFT) fails to recover the flat plane, exhibiting convex fractional charge errors (FCE) and concave fractional spin errors (FSE) that are related to delocalization and static correlation errors. We previously showed that DFT+U eliminates FCE but now demonstrate that, like other widely employed corrections (i.e., Hartree-Fock exchange), it worsens FSE. To find an alternative strategy, we examine the shape of semi-local DFT deviations from the exact flat plane and we find this shape to be remarkably consistent across ions and mols. We introduce the judiciously modified DFT (jmDFT) approach, wherein corrections are constructed from few-parameter, low-order functional forms that fit the shape of semi-local DFT errors. We select one such phys. intuitive form and incorporate it self-consistently to correct semi-local DFT. We demonstrate on model systems that jmDFT represents the first easy-to-implement, no-overhead approach to recovering the flat plane from semi-local DFT. (c) 2017 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvVKiur3E&md5=6867200d3110186577eaf90189d384ec40Srebro, M.; Autschbach, J.Does a Molecule-Specific Density Functional Give an Accurate Electron Density? The Challenging Case of the CuCl Electric Field Gradient. J. Phys. Chem. Lett.2012, 3, 576– 581, DOI: 10.1021/jz201685r[ACS Full Text ], [CAS], Google Scholar40Does a Molecule-Specific Density Functional Give an Accurate Electron Density? The Challenging Case of the CuCl Electric Field Gradient
Journal of Physical Chemistry Letters (2012), 3 (5), 576-581CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
In the framework of detg. system-specific long-range cor. d. functionals, the question is addressed whether such functionals, tuned to satisfy the condition -εHOMO = IP or other energetic criteria, provide accurate electron densities. A nonempirical phys. motivated two-dimensional tuning of range-sepd. hybrid functionals is proposed and applied to the particularly challenging case of a mol. property that depends directly on the ground-state d.: the copper elec. field gradient (EFG) in CuCl. From a continuous range of functional parametrizations that closely satisfy -εHOMO = IP and the correct asymptotic behavior of the potential, the one that best fulfills the straight-line behavior of E(N), the energy as a function of a fractional electron no. N, was found to provide the most accurate electron d. as evidenced by calcd. EFGs. The functional also performs well for related Cu systems.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhvVSkurs%253D&md5=03ae2a0685bb16a6eefbc6f8dbd45bae41Brumboiu, I. E.; Prokopiou, G.; Kronik, L.; Brena, B.Valence Electronic Structure of Cobalt Phthalocyanine from an Optimally Tuned Range-Separated Hybrid Functional. J. Chem. Phys.2017, 147, 044301, DOI: 10.1063/1.4993623[Crossref], [PubMed], [CAS], Google Scholar41Valence electronic structure of cobalt phthalocyanine from an optimally tuned range-separated hybrid functional
Brumboiu, Iulia Emilia; Prokopiou, Georgia; Kronik, Leeor; Brena, Barbara
Journal of Chemical Physics (2017), 147 (4), 044301/1-044301/11CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
We analyze the valence electronic structure of cobalt phthalocyanine (CoPc) by means of optimally tuning a range-sepd. hybrid functional. The tuning is performed by modifying both the amt. of short-range exact exchange (α) included in the hybrid functional and the range-sepn. parameter (γ), with two strategies employed for finding the optimal γ for each α. The influence of these two parameters on the structural, electronic, and magnetic properties of CoPc is thoroughly investigated. The electronic structure is found to be very sensitive to the amt. and range in which the exact exchange is included. The electronic structure obtained using the optimal parameters is compared to gas-phase photoelectron data and GW calcns., with the unoccupied states addnl. compared with inverse photo-electron spectroscopy measurements. The calcd. spectrum with tuned γ, detd. for the optimal value of α = 0.1, yields a very good agreement with both exptl. results and with GW calcns. that well-reproduce the exptl. data. (c) 2017 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXht1WltL7N&md5=9395ce64444a63786f5a84a44eced18b42Gani, T. Z. H.; Kulik, H. J.Where Does the Density Localize? Convergent Behavior for Global Hybrids, Range Separation, and DFT+U. J. Chem. Theory Comput.2016, 12, 5931, DOI: 10.1021/acs.jctc.6b00937[ACS Full Text ], [CAS], Google Scholar42Where Does the Density Localize? Convergent Behavior for Global Hybrids, Range Separation, and DFT+U
Journal of Chemical Theory and Computation (2016), 12 (12), 5931-5945CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Approx. d. functional theory (DFT) suffers from many-electron self-interaction error, otherwise known as delocalization error, that may be diagnosed and then cor. through elimination of the deviation from exact piecewise linear behavior between integer electron nos. Although paths to correction of energetic delocalization error are well-established, the impact of these corrections on the electron d. is less well-studied. Here, we compare the effect on d. delocalization of DFT + U (i.e., semilocal DFT augmented with a Hubbard U correction), global hybrid tuning, and range-sepd. hybrid tuning on a diverse test set of 32 transition metal complexes and observe the three methods to have qual. equiv. effects on the ground state d. Regardless of valence orbital diffuseness (i.e., from 2p to 5p), ligand electronegativity (i.e., from Al to O), basis set (i.e., plane wave vs. localized basis set), metal (i.e., Ti, Fe, Ni), and spin state, or tuning method, we consistently observe substantial charge loss at the metal and gain at ligand atoms (∼0.3-0.5 e or more). This charge loss at the metal is preferentially from the minority spin, leading to increasing magnetic moment as well. Using accurate wave function theory refs., we observe that a min. error in partial charges and magnetic moments occurs at higher tuning parameters than typically employed to eliminate energetic delocalization error. These observations motivate the need to develop multifaceted approx.-DFT error correction approaches that sep. treat d. delocalization and energetic errors to recover both correct d. and orbital energy-derived properties.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvVWnur3O&md5=8e8f87defc97835ccb0d6f3a4663e44643Medvedev, M. G.; Bushmarinov, I. S.; Sun, J.; Perdew, J. P.; Lyssenko, K. A.Density Functional Theory Is Straying from the Path toward the Exact Functional. Science2017, 355, 49– 52, DOI: 10.1126/science.aah5975[Crossref], [PubMed], [CAS], Google Scholar43Density functional theory is straying from the path toward the exact functional
Medvedev, Michael G.; Bushmarinov, Ivan S.; Sun, Jianwei; Perdew, John P.; Lyssenko, Konstantin A.
Science (Washington, DC, United States) (2017), 355 (6320), 49-52CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
The theorems at the core of d. functional theory (DFT) state that the energy of a many-electron system in its ground state is fully defined by its electron d. distribution. This connection is made via the exact functional for the energy, which minimizes at the exact d. For years, DFT development focused on energies, implicitly assuming that functionals producing better energies become better approxns. of the exact functional. We examd. the other side of the coin: the energy-minimizing electron densities for at. species, as produced by 128 historical and modern DFT functionals. We found that these densities became closer to the exact ones, reflecting theor. advances, until the early 2000s, when this trend was reversed by unconstrained functionals sacrificing phys. rigor for the flexibility of empirical fitting.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhs1SqtQ%253D%253D&md5=670a71b442b1bd30abf15abc9bb15d9044Kulik, H. J.Perspective: Treating Electron over-Delocalization with the DFT+U Method. J. Chem. Phys.2015, 142, 240901, DOI: 10.1063/1.4922693[Crossref], [PubMed], [CAS], Google Scholar44Perspective: Treating electron over-delocalization with the DFT+U method
Journal of Chemical Physics (2015), 142 (24), 240901/1-240901/10CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
A review. Many people in the materials science and solid-state community are familiar with the acronym 'DFT+U.'. For those less familiar, this technique uses ideas from model Hamiltonians that permit the description of both metals and insulators to address problems of electron over-delocalization in practical implementations of d. functional theory (DFT). Exchange-correlation functionals in DFT are often described as belonging to a hierarchical 'Jacob's ladder' of increasing accuracy in moving from local to non-local descriptions of exchange and correlation. DFT+U is not on this 'ladder' but rather acts as an 'elevator' because it systematically tunes relative energetics, typically on a localized subshell (e.g., d or f electrons), regardless of the underlying functional employed. However, this tuning is based on a metric of the local electron d. of the subshells being addressed, thus necessitating phys. or chem. or intuition about the system of interest. I will provide a brief overview of the history of how DFT+U came to be starting from the origin of the Hubbard and Anderson model Hamiltonians. This history lesson is necessary because it permits us to make the connections between the 'Hubbard U' and fundamental outstanding challenges in electronic structure theory, and it helps to explain why this method is so widely applied to transition-metal oxides and organometallic complexes alike. (c) 2015 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtFSltbbE&md5=55b110113e6648e8cad7287fd4faf0f145Zhao, Q.; Kulik, H. J.Where Does the Density Localize in the Solid State? Divergent Behavior for Hybrids and DFT+U. J. Chem. Theory Comput.2018, 14, 670– 683, DOI: 10.1021/acs.jctc.7b01061[ACS Full Text ], [CAS], Google Scholar45Where Does the Density Localize in the Solid State? Divergent Behavior for Hybrids and DFT+U
Journal of Chemical Theory and Computation (2018), 14 (2), 670-683CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Approx. d. functional theory (DFT) is widely used in chem. and physics, despite delocalization errors that affect energetic and d. properties. DFT+U (i.e., semi-local DFT augmented with a Hubbard U correction) and global hybrid functionals are two commonly employed practical methods to address delocalization error. Recent work demonstrated that in transition metal complexes both methods localize d. away from the metal and onto surrounding ligands, regardless of metal or ligand identity. In this work, we compare d. localization trends with DFT+U and global hybrids on a diverse set of 34 transition-metal-contg. solids with varying magnetic state, electron configuration and valence shell, and coordinating-atom orbital diffuseness (i.e., O, S, Se). We also study open-framework solids in which the metal is coordinated by mol. ligands, i.e., MCO3, M(OH)2, M(NCNH)2, K3M(CN)6 (M = V-Ni). As in transition metal complexes, incorporation of Hartree-Fock exchange consistently localizes d. away from the metal, but DFT+U exhibits diverging behavior, localizing d. (i) onto the metal in low-spin and late transition metals and (ii) away from the metal in other cases in agreement with hybrids. To isolate the effect of the crystal environment, we ext. mol. analogs from open-framework transition metal solids and observe consistent localization of the d. away from the metal in all cases with both DFT+U and hybrid exchange. These observations highlight the limited applicability of trends established for functional tuning on transition metal complexes even to equiv. coordination environments in the solid state.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXjsVKiug%253D%253D&md5=91c357b4180519bb06c1ad1a63c3760946Kim, M.-C.; Sim, E.; Burke, K.Understanding and Reducing Errors in Density Functional Calculations. Phys. Rev. Lett.2013, 111, 073003, DOI: 10.1103/PhysRevLett.111.073003[Crossref], [PubMed], [CAS], Google Scholar46Understanding and reducing errors in density functional calculations
Physical Review Letters (2013), 111 (7), 073003/1-073003/5CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
We decomp. the energy error of any variational d. functional theory calcn. into a contribution due to the approx. functional and that due to the approx. d. Typically, the functional error dominates, but in many interesting situations the d.-driven error dominates. Examples range from calcns. of electron affinities to preferred geometries of ions and radicals in soln. In these abnormal cases, the error in d. functional theory can be greatly reduced by using a more accurate d. A small orbital gap often indicates a substantial d.-driven error.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsVehtb7F&md5=320723a5e50d94d975df04c25c53aded47Kim, M.-C.; Park, H.; Son, S.; Sim, E.; Burke, K.Improved DFT Potential Energy Surfaces via Improved Densities. J. Phys. Chem. Lett.2015, 6, 3802– 3807, DOI: 10.1021/acs.jpclett.5b01724[ACS Full Text ], [CAS], Google Scholar47Improved DFT Potential Energy Surfaces via Improved Densities
Kim, Min-Cheol; Park, Hansol; Son, Suyeon; Sim, Eunji; Burke, Kieron
Journal of Physical Chemistry Letters (2015), 6 (19), 3802-3807CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
D.-cor. DFT is a method that cures several failures of self-consistent semilocal DFT calcns. by using a more accurate d. instead. A novel procedure employs the Hartree-Fock d. to bonds that are more severely stretched than ever before. This substantially increases the range of accurate potential energy surfaces obtainable from semilocal DFT for many heteronuclear mols. We show that this works for both neutral and charged mols. We explain why and explore more difficult cases, for example, CH+, where d.-cor. DFT results are even better than sophisticated methods like CCSD. We give a simple criterion for when DC-DFT should be more accurate than self-consistent DFT that can be applied for most cases.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsVKlsLfJ&md5=59839f8600a934c5d2990f3802059fa748Duignan, T. J.; Autschbach, J.Impact of the Kohn–Sham Delocalization Error on the 4f Shell Localization and Population in Lanthanide Complexes. J. Chem. Theory Comput.2016, 12, 3109– 3121, DOI: 10.1021/acs.jctc.6b00238[ACS Full Text ], [CAS], Google Scholar48Impact of the Kohn-Sham Delocalization Error on the 4f Shell Localization and Population in Lanthanide Complexes
Journal of Chemical Theory and Computation (2016), 12 (7), 3109-3121CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
The extent of ligand to metal donation bonding and mixing of 4f (and 5d) orbitals with ligand orbitals is studied by Kohn-Sham (KS) calcns. for LaX3 (X = F, Cl, Br, I), GdX3, and LuX3 model complexes, CeCl62-, YbCp3, and selected lanthanide complexes with larger ligands. The KS delocalization error (DE) is quantified via the curvature of the energy for noninteger electron nos. The extent of donation bonding and 4f-ligand mixing correlates well with the DE. For Lu complexes, the DE also correlates with the extent of mixing of ligand and 4f orbitals in the canonical MOs (MOs). However, the localized set of MOs and population analyses indicate that the closed 4f shell is localized. Attempts to create situations where mixing of 4f and ligand orbitals occurs due to a degeneracy of fragment orbitals were unsuccessful. For La(III) and, in particular, for Ce(IV), Hartree-Fock, KS, and coupled cluster singles and doubles calcns. are in agreement in that excess 4f populations arise from ligand donation, along with donation into the 5d shell. Likewise, KS calcns. for all systems with incompletely filled 4f shells, even those with 'optimally tuned' functionals affording a small DE, produce varying degrees of excess 4f populations which may be only partially attributed to 5d polarization.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xos1Slu7s%253D&md5=85e82e44072d8d26b9247afc4510f10749Riplinger, C.; Neese, F.An Efficient and near Linear Scaling Pair Natural Orbital Based Local Coupled Cluster Method. J. Chem. Phys.2013, 138, 034106, DOI: 10.1063/1.4773581[Crossref], [PubMed], [CAS], Google Scholar49An efficient and near linear scaling pair natural orbital based local coupled cluster method
Journal of Chemical Physics (2013), 138 (3), 034106/1-034106/18CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
In previous publications, it was shown that an efficient local coupled cluster method with single- and double excitations can be based on the concept of pair natural orbitals (PNOs) . The resulting local pair natural orbital-coupled-cluster single double (LPNO-CCSD) method has since been proven to be highly reliable and efficient. For large mols., the no. of amplitudes to be detd. is reduced by a factor of 105-106 relative to a canonical CCSD calcn. on the same system with the same basis set. In the original method, the PNOs were expanded in the set of canonical virtual orbitals and single excitations were not truncated. This led to a no. of fifth order scaling steps that eventually rendered the method computationally expensive for large mols. (e.g., >100 atoms). In the present work, these limitations are overcome by a complete redesign of the LPNO-CCSD method. The new method is based on the combination of the concepts of PNOs and projected AOs (PAOs). Thus, each PNO is expanded in a set of PAOs that in turn belong to a given electron pair specific domain. In this way, it is possible to fully exploit locality while maintaining the extremely high compactness of the original LPNO-CCSD wavefunction. No terms are dropped from the CCSD equations and domains are chosen conservatively. The correlation energy loss due to the domains remains below <0.05%, which implies typically 15-20 but occasionally up to 30 atoms per domain on av. The new method has been given the acronym DLPNO-CCSD ('domain based LPNO-CCSD'). The method is nearly linear scaling with respect to system size. The original LPNO-CCSD method had three adjustable truncation thresholds that were chosen conservatively and do not need to be changed for actual applications. In the present treatment, no addnl. truncation parameters have been introduced. Any addnl. truncation is performed on the basis of the three original thresholds. There are no real-space cutoffs. Single excitations are truncated using singles-specific natural orbitals. Pairs are prescreened according to a multipole expansion of a pair correlation energy est. based on local orbital specific virtual orbitals (LOSVs). Like its LPNO-CCSD predecessor, the method is completely of black box character and does not require any user adjustments. It is shown here that DLPNO-CCSD is as accurate as LPNO-CCSD while leading to computational savings exceeding one order of magnitude for larger systems. The largest calcns. reported here featured >8800 basis functions and >450 atoms. In all larger test calcns. done so far, the LPNO-CCSD step took less time than the preceding Hartree-Fock calcn., provided no approxns. have been introduced in the latter. Thus, based on the present development reliable CCSD calcns. on large mols. with unprecedented efficiency and accuracy are realized. (c) 2013 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXpslOqtw%253D%253D&md5=4327115b95524107245acb44ff4aaa7b50Saitow, M.; Becker, U.; Riplinger, C.; Valeev, E. F.; Neese, F.A New Near-Linear Scaling, Efficient and Accurate, Open-Shell Domain-Based Local Pair Natural Orbital Coupled Cluster Singles and Doubles Theory. J. Chem. Phys.2017, 146, 164105, DOI: 10.1063/1.4981521[Crossref], [PubMed], [CAS], Google ScholarWhs File Conflicts Resolver Conjugations
50A new near-linear scaling, efficient and accurate, open-shell domain-based local pair natural orbital coupled cluster singles and doubles theory
Saitow, Masaaki; Becker, Ute; Riplinger, Christoph; Valeev, Edward F.; Neese, Frank
Journal of Chemical Physics (2017), 146 (16), 164105/1-164105/31CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
The Coupled-Cluster expansion, truncated after single and double excitations (CCSD), provides accurate and reliable mol. electronic wave functions and energies for many mol. systems around their equil. geometries. However, the high computational cost, which is well-known to scale as O(N6) with system size N, has limited its practical application to small systems consisting of not more than approx. 20-30 atoms. To overcome these limitations, low-order scaling approxns. to CCSD have been intensively investigated over the past few years. In our previous work, we have shown that by combining the pair natural orbital (PNO) approach and the concept of orbital domains it is possible to achieve fully linear scaling CC implementations (DLPNO-CCSD and DLPNO-CCSD(T)) that recover around 99.9% of the total correlation energy [C. Riplinger et al., J. Chem. Phys. 144, 024109 (2016)]. The prodn. level implementations of the DLPNO-CCSD and DLPNO-CCSD(T) methods were shown to be applicable to realistic systems composed of a few hundred atoms in a routine, black-box fashion on relatively modest hardware. In 2011, a reduced-scaling CCSD approach for high-spin open-shell UHF ref. wave functions was proposed (UHF-LPNO-CCSD) [A. Hansen et al., J. Chem. Phys. 135, 214102 (2011)]. After a few years of experience with this method, a few shortcomings of UHF-LPNO-CCSD were noticed that required a redesign of the method, which is the subject of this paper. To this end, we employ the high-spin open-shell variant of the N-electron valence perturbation theory formalism to define the initial guess wave function, and consequently also the open-shell PNOs. The new PNO ansatz properly converges to the closed-shell limit since all truncations and approxns. have been made in strict analogy to the closed-shell case. Furthermore, given the fact that the formalism uses a single set of orbitals, only a single PNO integral transformation is necessary, which offers large computational savings. We show that, with the default PNO truncation parameters, approx. 99.9% of the total CCSD correlation energy is recovered for open-shell species, which is comparable to the performance of the method for closed-shells. UHF-DLPNO-CCSD shows a linear scaling behavior for closed-shell systems, while linear to quadratic scaling is obtained for open-shell systems. The largest systems we have considered contain more than 500 atoms and feature more than 10 000 basis functions with a triple-ζ quality basis set. (c) 2017 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXmvVeqsL8%253D&md5=898703521d990dfd299c935e34adbfa651Stein, C. J.; Reiher, M.Automated Selection of Active Orbital Spaces. J. Chem. Theory Comput.2016, 12, 1760– 1771, DOI: 10.1021/acs.jctc.6b00156[ACS Full Text ], [CAS], Google Scholar51Stein, Christopher J.; Reiher, Markus
Journal of Chemical Theory and Computation (2016), 12 (4), 1760-1771CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
One of the key challenges of quantum-chem. multi-configuration methods is the necessity to manually select orbitals for the active space. This selection requires both expertise and experience and can therefore impose severe limitations on the applicability of this most general class of ab initio methods. A poor choice of the active orbital space may yield even qual. wrong results. This is obviously a severe problem, esp. for wave function methods that are designed to be systematically improvable. Here, we show how the iterative nature of the d. matrix renormalization group combined with its capability to include up to about 100 orbitals in the active space can be exploited for a systematic assessment and selection of active orbitals. These benefits allow us to implement an automated approach for active orbital space selection, which can turn multi-configuration models into black box approaches.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XjvFyltLs%253D&md5=c46ae44d10c10dfa409cf8807a77930852Sayfutyarova, E. R.; Sun, Q.; Chan, G. K.-L.; Knizia, G.Automated Construction of Molecular Active Spaces from Atomic Valence Orbitals. J. Chem. Theory Comput.2017, 13, 4063– 4078, DOI: 10.1021/acs.jctc.7b00128[ACS Full Text ], [CAS], Google Scholar52Automated Construction of Molecular Active Spaces from Atomic Valence Orbitals
Sayfutyarova, Elvira R.; Sun, Qiming; Chan, Garnet Kin-Lic; Knizia, Gerald
Journal of Chemical Theory and Computation (2017), 13 (9), 4063-4078CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
We introduce the at. valence active space (AVAS), a simple and well-defined automated technique for constructing active orbital spaces for use in multi-configuration and multi-ref. (MR) electronic structure calcns. Concretely, the technique constructs active MOs capable of describing all relevant electronic configurations emerging from a targeted set of at. valence orbitals (e.g., the metal d orbitals in a redcoordination complex). This is achieved via a linear transformation of the occupied and unoccupied orbital spaces from an easily obtainable single-ref. wavefunction (such as from a Hartree-Fock or Kohn-Sham calcns.) based on projectors to targeted at. valence orbitals. We discuss the premises, theory, and implementation of the idea, and several of its variations are tested. To investigate the performance and accuracy, we calc. the excitation energies for various transition metal complexes in typical application scenarios. Addnl., we follow the homolytic bond breaking process of a Fenton reaction along its reaction coordinate. While the described AVAS technique is not an universal soln. to the active space problem, its premises are fulfilled in many application scenarios of transition metal chem. and bond dissocn. processes. In these cases the technique makes MR calcns. easier to execute, easier to reproduce by any user, and simplifies the detn. of the appropriate size of the active space required for accurate results.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXht1WmtL7L&md5=2c8d3c8062fa13f4f4e68c6432bb65b153Xiao, D.; Martini, L. A.; Snoeberger, R. C., III; Crabtree, R. H.; Batista, V. S.Inverse Design and Synthesis of Acac-Coumarin Anchors for Robust TiO2 Sensitization. J. Am. Chem. Soc.2011, 133, 9014– 9022, DOI: 10.1021/ja2020313[ACS Full Text ], [CAS], Google Scholar53Inverse Design and Synthesis of acac-Coumarin Anchors for Robust TiO2 Sensitization
Xiao, Dequan; Martini, Lauren A.; Snoeberger, Robert C., III; Crabtree, Robert H.; Batista, Victor S.
Journal of the American Chemical Society (2011), 133 (23), 9014-9022CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
An inverse design methodol. suitable to assist the synthesis and optimization of mol. sensitizers for dye-sensitized solar cells is introduced. The method searches for mol. adsorbates with suitable photoabsorption properties through continuous optimization of alchem. structures in the vicinity of a ref. mol. framework. The approach is illustrated as applied to the design and optimization of linker chromophores for TiO2 sensitization, using the recently developed phenyl-acetylacetonate (i.e., phenyl-acac) anchor [McNamara et al. J. Am. Chem. Soc.2008, 130, 14329-14338] as a ref. framework. A novel anchor (3-acac-pyran-2-one) is a local optimum, with improved sensitization properties when compared to phenyl-acac. Its mol. structure is related to known coumarin dyes that could be used as lead chromophore anchors for practical applications in dye-sensitized solar cells. Synthesis and spectroscopic characterization confirms that the linker provides robust attachment to TiO2, even in aq. conditions, yielding improved sensitization to solar light and ultrafast interfacial electron injection. The findings are particularly relevant to the design of sensitizers for dye-sensitized solar cells because of the wide variety of structures that are possible but they should be equally useful for other applications such as ligand design for homogeneous catalysis.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXmsVWlsbg%253D&md5=fa04c6e57f5290bac149a6448e8fb70854Weymuth, T.; Reiher, M.Gradient-Driven Molecule Construction: An Inverse Approach Applied to the Design of Small-Molecule Fixating Catalysts. Int. J. Quantum Chem.2014, 114, 838– 850, DOI: 10.1002/qua.24686[Crossref], [CAS], Google Scholar54Gradient-driven molecule construction: An inverse approach applied to the design of small-molecule fixating catalysts
International Journal of Quantum Chemistry (2014), 114 (13), 838-850CODEN: IJQCB2; ISSN:0020-7608. (John Wiley & Sons, Inc.)
A review. Rational design of mols. and materials usually requires extensive screening of mol. structures for the desired property. The inverse approach to deduce a structure for a predefined property would be highly desirable, but is, unfortunately, not well defined. However, feasible strategies for such an inverse design process may be successfully developed for specific purposes. We discuss options for calcg. 'jacket' potentials that fulfill a predefined target requirement-a concept that we recently introduced (Weymuth and Reiher, MRS Proceedings 2013, 1524, DOI:10.1557/opl.2012.1764). We consider the case of small-mol. activating transition metal catalysts. As a target requirement we choose the vanishing geometry gradients on all atoms of a subsystem consisting of a metal center binding the small mol. to be activated. The jacket potential can be represented within a full quantum model or by a sequence of approxns. of which a field of electrostatic point charges is the simplest. In a second step, the jacket potential needs to be replaced by a chem. viable chelate-ligand structure for which the geometry gradients on all of its atoms are also required to vanish. To analyze the feasibility of this approach, we dissect a known dinitrogen-fixating catalyst to study possible design strategies that must eventually produce the known catalyst. © 2014 Wiley Periodicals, Inc.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXmvVSntro%253D&md5=09e6116d6ed6fa3a3a9f2cdfa0296ab055Krausbeck, F.; Sobez, J.-G.; Reiher, M.Stabilization of Activated Fragments by Shell-Wise Construction of an Embedding Environment. J. Comput. Chem.2017, 38, 1023– 1038, DOI: 10.1002/jcc.24749[Crossref], [PubMed], [CAS], Google Scholar55Stabilization of activated fragments by shell-wise construction of an embedding environment
Krausbeck, Florian; Sobez, Jan-Grimo; Reiher, Markus
Journal of Computational Chemistry (2017), 38 (14), 1023-1038CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
An activated fragment which is structurally unstable when considered isolated can be stabilized through binding to a suitable mol. environment; for instance, to a transition-metal fragment. The metal fragment may be designed in a shell-wise build-up of a surrounding mol. environment. However, adding more and more atoms in a consecutive fashion soon leads to a combinatorial explosion of structures, which is unfeasible to handle without automation. Here, we present a fully automated and parallelized framework that constructs such an embedding environment atom-wise. Mol. realizations of such an environment are constructed based on simple heuristic rules intended to screen a sufficiently large portion of the possible compd. space and are then subsequently optimized by electronic structure methods. (Constrained-optimized) structures are then evaluated with respect to a scoring function, for which we choose here the concept of gradient-driven mol. construction. This concept searches for structure modifications that reduce the forces on all atoms. We develop and analyze our approach at the example of CO2 activation by reproducing a known compd. and mapping out possible alternative structures and their effect on the stabilization of a (bent) CO2 ligand. For all generated structures, the nuclear gradient on the activated fragment and its coordination energy are evaluated to steer the design process. © 2017 Wiley Periodicals, Inc.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXjtl2jsbc%253D&md5=c4091c40e34bb8a4150cae60d8aa3d7b56Kim, J. Y.; Kulik, H. J.When Is Ligand pKa a Good Descriptor for Catalyst Energetics? In Search of Optimal CO2 Hydration Catalysts. J. Phys. Chem. A2018, 122, 4579– 4590, DOI: 10.1021/acs.jpca.8b03301[ACS Full Text ], [CAS], Google Scholar56When Is Ligand pKa a Good Descriptor for Catalyst Energetics? In Search of Optimal CO2 Hydration Catalysts
Journal of Physical Chemistry A (2018), 122 (18), 4579-4590CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
The authors present a detailed study of nearly 70 Zn mol. catalysts for CO2 hydration from four diverse ligand classes ranging from well-studied carbonic anhydrase mimics (e.g., cyclen) to new structures the authors obtain by leveraging diverse hits from large org. libraries. Using microkinetic anal. and establishing linear free energy relations, turnover is sensitive to the relative thermodn. stability of reactive hydroxyl and bound bicarbonate moieties. The authors observe a wide range of thermodn. stabilities for these intermediates, showing up to 6 kcal/mol improvement over well-studied cyclen catalysts. The authors observe a good correlation between the pKa of the Zn-OH2 moiety and the resulting relative stability of hydroxyl moieties over bicarbonate, which may be rationalized by the dominant effect of the difference in higher Zn-OH bond order in comparison to weaker bonding in bicarbonate and H2O. A direct relation is identified between isolated org. ligand pKa and the pKa of a bound H2O mol. on the catalyst. Thus, org. ligand pKa, which is intuitive, easy to compute or tabulate, and much less sensitive to electronic structure method choice than whole-catalyst properties, is a good quant. descriptor for predicting the effect of through-bond electronic effects on relative CO2 hydration energetics. The authors expect this to be applicable to other reactions where is it essential to stabilize turnover-detg. hydroxyl species with respect to more weakly bound moieties. Finally, the authors note exceptions for rigid ligands (e.g., porphyrins) that preferentially stabilize hydroxyl over bicarbonate without reducing pKa values as substantially. The authors expect the strategy outlined here, to (i) curate diverse ligands from large org. libraries and (ii) identify when ligand-only properties can det. catalyst energetics, to be broadly useful for both exptl. and computational catalyst design.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXns12gu78%253D&md5=b543453a77cf44993940ec72254f01e957Gani, T. Z. H.; Kulik, H. J.Understanding and Breaking Scaling Relations in Single-Site Catalysis: Methane-to-Methanol Conversion by Fe(IV)═O. ACS Catal.2018, 8, 975– 986, DOI: 10.1021/acscatal.7b03597[ACS Full Text ], [CAS], Google Scholar57Understanding and Breaking Scaling Relations in Single-Site Catalysis: Methane to Methanol Conversion by FeIV=O
ACS Catalysis (2018), 8 (2), 975-986CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)
Computational high-throughput screening is an essential tool for catalyst design, limited primarily by the efficiency with which accurate predictions can be made. In bulk heterogeneous catalysis, linear free energy relationships (LFERs) have been extensively developed to relate elementary step activation energies, and thus overall catalytic activity, back to the adsorption energies of key intermediates, dramatically reducing the computational cost of screening. The applicability of these LFERs to single-site catalysts remains unclear, owing to the directional, covalent metal-ligand bonds and the broader chem. space of accessible ligand scaffolds. Through a computational screen of nearly 500 model Fe(II) complexes for CH4 hydroxylation, we observe that (1) tuning ligand field strength yields LFERs by comparably shifting energetics of the metal 3d levels that govern the stability of different intermediates and (2) distortion of the metal coordination geometry breaks these LFERs by increasing the splitting between the dxz/dyz and dz2 metal states that govern reactivity. Thus, in single-site catalysts, low Bronsted-Evans-Polanyi slopes for oxo formation, which would limit peak turnover frequency achievable through ligand field tuning alone, can be overcome through structural distortions achievable in exptl. characterized compds. Observations from this screen also motivate the placement of strong HB donors in targeted positions as a scaffold-agnostic strategy for further activity improvement. More generally, our findings motivate broader variation of coordination geometries in reactivity studies with single-site catalysts.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvFCkt7bL&md5=4a77acfe70ad49658dd437ff91ff959958Chu, Y.; Heyndrickx, W.; Occhipinti, G.; Jensen, V. R.; Alsberg, B. K.An Evolutionary Algorithm for De Novo Optimization of Functional Transition Metal Compounds. J. Am. Chem. Soc.2012, 134, 8885– 8895, DOI: 10.1021/ja300865u[ACS Full Text ], [CAS], Google Scholar58An Evolutionary Algorithm for de Novo Optimization of Functional Transition Metal Compounds
Chu, Yunhan; Heyndrickx, Wouter; Occhipinti, Giovanni; Jensen, Vidar R.; Alsberg, Bjoern K.
Journal of the American Chemical Society (2012), 134 (21), 8885-8895CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
A review; development of functional inorg. and transition metal compds. is usually based on ad hoc qualified guesses, with computational methods playing a lesser role than in drug discovery. A de novo evolutionary algorithm (EA) is presented that automatically generates transition metal complexes using a search space constrained around chem. meaningful structures assembled from three kinds of fragments: a part shared by all structures and typically contg. the metal center itself, one or several parts consisting of ligand skeletons, and unconstrained parts that may grow and vary freely. In EA optimizations, using a cost-efficient fitness function based on a linear quant. structure-activity relationship model for catalytic activity, we demonstrate the capabilities of the method by retracing the transition from the first-generation, phosphine-based Grubbs olefin metathesis catalysts to second-generation catalysts contg. N-heterocyclic carbene ligands instead of phosphines. Moreover, DFT calcns. on selected high-fitness, last-generation structures from these evolutionary expts. suggest that, in terms of catalytic activity, the structures arrived at by virtual evolution alone compare favorably with existing, highly active catalysts. The structures from the evolution expts. are, however, complex and probably difficult to synthesize, but a set of manually simplified variations thereof might form the leads for a new generation of Grubbs catalysts.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XlvV2ksrk%253D&md5=fa77234d830c2480eaf04344860f0c6559Keinan, S.; Hu, X.; Beratan, D. N.; Yang, W.Designing Molecules with Optimal Properties Using the Linear Combination of Atomic Potentials Approach in an AM1 Semiempirical Framework. J. Phys. Chem. A2007, 111, 176– 181, DOI: 10.1021/jp0646168[ACS Full Text ], [CAS], Google Scholar59Designing Molecules with Optimal Properties Using the Linear Combination of Atomic Potentials Approach in an AM1 Semiempirical Framework
Keinan, Shahar; Hu, Xiangqian; Beratan, David N.; Yang, Weitao
Journal of Physical Chemistry A (2007), 111 (1), 176-181CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
The linear combination of at. potentials (LCAP) approach is implemented in the AM1 semiempirical framework and is used to design mol. structures with optimized properties. The optimization procedure uses property deriv. information to search mol. space and thus avoid direct enumeration and evaluation of each mol. in a library. Two tests are described: the optimization of first hyperpolarizabilities of substituted aroms. and the optimization of a figure of merit for n-type org. semiconductors.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XhtlSgs73F&md5=49c9371eb6842d1482db01962a263e6d60Keinan, S.; Therien, M. J.; Beratan, D. N.; Yang, W.Molecular Design of Porphyrin-Based Nonlinear Optical Materials. J. Phys. Chem. A2008, 112, 12203– 12207, DOI: 10.1021/jp806351d[ACS Full Text ], [CAS], Google Scholar60Molecular Design of Porphyrin-Based Nonlinear Optical Materials
Keinan, Shahar; Therien, Michael J.; Beratan, David N.; Yang, Weitao
Journal of Physical Chemistry A (2008), 112 (47), 12203-12207CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
Nonlinear optical chromophores contg. (porphyrinato)Zn(II), proquinoid, and (terpyridyl)metal(II) building blocks were optimized in a library contg. ∼106 structures using the linear combination of at. potentials (LCAP) methodol. The authors report here the library design and mol. property optimizations. Two basic structural types of large β0 chromophores were examd.: linear and T-shaped motifs. These T-shaped geometries suggest a promising NLO chromophoric architecture for exptl. study and further support the value of performing LCAP searches in large chem. spaces.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhtlWqtL3K&md5=9ba87f84a22d6642b40a4cb0c01abff961Wang, M.; Hu, X.; Beratan, D. N.; Yang, W.Designing Molecules by Optimizing Potentials. J. Am. Chem. Soc.2006, 128, 3228– 3232, DOI: 10.1021/ja0572046[ACS Full Text ], [CAS], Google Scholar61Wang, Mingliang; Hu, Xiangqian; Beratan, David N.; Yang, Weitao
Journal of the American Chemical Society (2006), 128 (10), 3228-3232CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The astronomical no. of accessible discrete chem. structures makes rational mol. design extremely challenging. We formulate the design of mols. with specific tailored properties as performing a continuous optimization in the space of electron-nuclear attraction potentials. The optimization is facilitated by using a linear combination of at. potentials (LCAP), a general framework that creates a continuous property landscape from an otherwise unlinked set of discrete mol.-property values. A demonstration of this approach is given for the optimization of mol. electronic polarizability and hyperpolarizability. We show that the optimal structures can be detd. without enumerating and sep. evaluating the characteristics of the combinatorial no. of possible structures, a process that would be much slower. The LCAP approach may be used with quantum or classical Hamiltonians, suggesting possible applications to drug design and new materials discovery.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XhsVOmtLw%253D&md5=3197d3966132f37386fc4b8c0d01adfe62Gani, T. Z. H.; Ioannidis, E. I.; Kulik, H. J.Computational Discovery of Hydrogen Bond Design Rules for Electrochemical Ion Separation. Chem. Mater.2016, 28, 6207– 6218, DOI: 10.1021/acs.chemmater.6b02378[ACS Full Text ], [CAS], Google Scholar62Computational Discovery of Hydrogen Bond Design Rules for Electrochemical Ion Separation
Gani, Terry Z. H.; Ioannidis, Efthymios I.; Kulik, Heather J.
Chemistry of Materials (2016), 28 (17), 6207-6218CODEN: CMATEX; ISSN:0897-4756. (American Chemical Society)
Selective ion sepn. is a major challenge with far-ranging impact from H2O desalination to product sepn. in catalysis. Recently introduced ferrocene (Fc)/ferrocenium (Fc+) polymer electrode materials were demonstrated exptl. and theor. to selectively bind carboxylates over perchlorate through weak C-H···O H bond (HB) interactions that favor carboxylates, despite the comparable size and charge of the two species. However, practical application of this technol. in aq. environments requires further selectivity enhancement. Using a 1st-principles discovery approach, the authors study the effect of Fc/Fc+ functional groups (FGs) on the selectivity and reversibility of formate-Fc+ adsorption with respect to perchlorate in aq. soln. The authors' wide design space of 44 FGs enables identification of FGs with higher selectivity and rationalization of trends through electronic energy decompn. anal. or geometric H bonding anal. Overall, the authors observe weaker, longer HBs for perchlorate as compared to formate with Fc+. The authors further identify Fc+ functionalizations that simultaneously increase selectivity for formate in aq. environments but permit rapid release from neutral Fc. The authors introduce the materiaphore, a 3-dimensional abstraction of these design rules, to help guide next-generation material optimization for selective ion sorption. This approach is expected to have broad relevance in computational discovery for mol. recognition, sensing, sepns., and catalysis.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtlOqurrK&md5=b39b5e18e93adbf41d47f688141ff18463Kim, J. Y.; Steeves, A. H.; Kulik, H. J.Harnessing Organic Ligand Libraries for First-Principles Inorganic Discovery: Indium Phosphide Quantum Dot Precursor Design Strategies. Chem. Mater.2017, 29, 3632– 3643, DOI: 10.1021/acs.chemmater.7b00472[ACS Full Text ], [CAS], Google Scholar63Harnessing Organic Ligand Libraries for First-Principles Inorganic Discovery: Indium Phosphide Quantum Dot Precursor Design Strategies
Kim, Jeong Yun; Steeves, Adam H.; Kulik, Heather J.
Chemistry of Materials (2017), 29 (8), 3632-3643CODEN: CMATEX; ISSN:0897-4756. (American Chemical Society)
Indium phosphide quantum dots (QDs) represent promising replacements for more toxic QDs, but InP QD prodn. lags behind other QD materials due to limited understanding of how to tune InP QD growth. We carry out a first-principles, computational screen of the tuning of In carboxylate precursor chem. to alter the kinetics of elementary steps in InP QD growth. We employ a large database normally used for discovery of therapeutic drug-like mols. to discover design rules for these inorg. complexes while maintaining realism (i.e., stable, synthetically accessible substituents) and providing diversity in a 210-mol. test set. We show the In-O bond cleavage energy, which is tuned through ligand functionalization, to be a useful proxy for In-P bond formation energetics in InP QD synthesis. Energy decompn. anal. on a 32-mol. subset reveals that lower activation energies correlate to later transition states, due to stabilization from greater In-P bond formation and more favorable reaction energetics. Our simulations suggest that altering ligand nucleophilicity tunes the reaction barrier over a 10 kcal/mol range, providing the conjugate acid's pKa as an exptl. handle to lead to better control of growth conditions and to improve synthesized InP QD quality. Importantly, these trends hold regardless of phosphorus precursor chemistries and in the longer chain length ligands typically used in synthesis.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXltlWgsrg%253D&md5=c8f7471512784618b9c19c24f08b918c64Virshup, A. M.; Contreras-García, J.; Wipf, P.; Yang, W.; Beratan, D. N.Stochastic Voyages into Uncharted Chemical Space Produce a Representative Library of All Possible Drug-Like Compounds. J. Am. Chem. Soc.2013, 135, 7296– 7303, DOI: 10.1021/ja401184g[ACS Full Text ], [CAS], Google Scholar64Stochastic Voyages into Uncharted Chemical Space Produce a Representative Library of All Possible Drug-Like Compounds
Virshup, Aaron M.; Contreras-Garcia, Julia; Wipf, Peter; Yang, Weitao; Beratan, David N.
Journal of the American Chemical Society (2013), 135 (19), 7296-7303CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The 'small mol. universe' (SMU), the set of all synthetically feasible org. mols. of 500 Da mol. wt. or less, is estd. to contain over 1060 structures, making exhaustive searches for structures of interest impractical. Here, we describe the construction of a 'representative universal library' spanning the SMU that samples the full extent of feasible small mol. chemistries. This library was generated using the newly developed Algorithm for Chem. Space Exploration with Stochastic Search (ACSESS). ACSESS makes two important contributions to chem. space exploration: it allows the systematic search of the unexplored regions of the small mol. universe, and it facilitates the mining of chem. libraries that do not yet exist, providing a near-infinite source of diverse novel compds.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXltV2ntbc%253D&md5=503aa28914b01850b36487ce7ef41ad865Bohacek, R. S.; McMartin, C.; Guida, W. C.The Art and Practice of Structure-Based Drug Design: A Molecular Modeling Perspective. Med. Res. Rev.1996, 16, 3– 50, DOI: 10.1002/(SICI)1098-1128(199601)16:1<3::AID-MED1>3.0.CO;2-6[Crossref], [PubMed], [CAS], Google Scholar65The art and practice of structure-based drug design: a molecular modeling perspective
Bohacek, Regine S.; McMartin, Colin; Guida, Wayne C.
Medicinal Research Reviews (1996), 16 (1), 3-50CODEN: MRREDD; ISSN:0198-6325. (Wiley)
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XhtFyls78%253D&md5=edfa592791c111479117feed600dead666Grajciar, L.; Heard, C. J.; Bondarenko, A. A.; Polynski, M. V.; Meeprasert, J.; Pidko, E. A.; Nachtigall, P.Towards Operando Computational Modeling in Heterogeneous Catalysis. Chem. Soc. Rev.2018, 47, 8307– 8348, DOI: 10.1039/C8CS00398J[Crossref], [PubMed], [CAS], Google Scholar66Towards operando computational modeling in heterogeneous catalysis
Grajciar, Lukas; Heard, Christopher J.; Bondarenko, Anton A.; Polynski, Mikhail V.; Meeprasert, Jittima; Pidko, Evgeny A.; Nachtigall, Petr
Chemical Society Reviews (2018), 47 (22), 8307-8348CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
An increased synergy between exptl. and theor. investigations in heterogeneous catalysis has become apparent during the last decade. Exptl. work has extended from ultra-high vacuum and low temp. towards operando conditions. These developments have motivated the computational community to move from std. descriptive computational models, based on inspection of the potential energy surface at 0 K and low reactant concns. (0 K/UHV model), to more realistic conditions. The transition from 0 K/UHV to operando models has been backed by significant developments in computer hardware and software over the past few decades. New methodol. developments, designed to overcome part of the gap between 0 K/UHV and operando conditions, include (i) global optimization techniques, (ii) ab initio constrained thermodn., (iii) biased mol. dynamics, (iv) microkinetic models of reaction networks and (v) machine learning approaches. The importance of the transition is highlighted by discussing how the mol. level picture of catalytic sites and the assocd. reaction mechanisms changes when the chem. environment, pressure and temp. effects are correctly accounted for in mol. simulations. It is the purpose of this review to discuss each method on an equal footing, and to draw connections between methods, particularly where they may be applied in combination.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhs1yntL%252FF&md5=e3daa236843cf11a45226cf9a9b39ebb67Arockiam, P. B.; Bruneau, C.; Dixneuf, P. H.Ruthenium(II)-Catalyzed C-H Bond Activation and Functionalization. Chem. Rev.2012, 112, 5879– 5918, DOI: 10.1021/cr300153j[ACS Full Text ], [CAS], Google Scholar67Ruthenium(II)-Catalyzed C-H Bond Activation and Functionalization
Arockiam, Percia Beatrice; Bruneau, Christian; Dixneuf, Pierre H.
Chemical Reviews (Washington, DC, United States) (2012), 112 (11), 5879-5918CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
A review of chem. of ruthenium catalysts in C-H bond activation and functionalization is presented.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xht1yrtrvN&md5=b403adaa5692ec97d2b81d92ddb4dbba68Prier, C. K.; Rankic, D. A.; MacMillan, D. W. C.Visible Light Photoredox Catalysis with Transition Metal Complexes: Applications in Organic Synthesis. Chem. Rev.2013, 113, 5322– 5363, DOI: 10.1021/cr300503r[ACS Full Text ], [CAS], Google Scholar68Visible Light Photoredox Catalysis with Transition Metal Complexes: Applications in Organic Synthesis
Prier, Christopher K.; Rankic, Danica A.; MacMillan, David W. C.
Chemical Reviews (Washington, DC, United States) (2013), 113 (7), 5322-5363CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
A review. This review will highlight the early work on the use of transition metal complexes as photoredox catalysts to promote reactions of org. compds. (prior to 2008), as well as cover the surge of work that has appeared since 2008. We have for the most part grouped reactions according to whether the org. substrate undergoes redn., oxidn., or a redox neutral reaction and throughout have sought to highlight the variety of reactive intermediates that may be accessed via this general reaction manifold.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXktFKgtLc%253D&md5=e09e6cf6a4c64fd3e8f21d55e151266e69Rouquet, G.; Chatani, N.Catalytic Functionalization of C(sp2)-H and C(sp3)-H Bonds by Using Bidentate Directing Groups. Angew. Chem., Int. Ed.2013, 52, 11726– 11743, DOI: 10.1002/anie.201301451[Crossref], [CAS], Google Scholar69Catalytic functionalization of C(sp2)-H and C(sp3)-H bonds by using bidentate directing groups
Angewandte Chemie, International Edition (2013), 52 (45), 11726-11743CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
A review. C-H bonds are ubiquitous in org. compds. It would, therefore, appear that direct functionalization of substrates by activation of C-H bonds would eliminate the multiple steps and limitations assocd. with the prepn. of functionalized starting materials. Regioselectivity is an important issue because org. mols. can contain a wide variety of C-H bonds. The use of a directing group can largely overcome the issue of regiocontrol by allowing the catalyst to come into proximity with the targeted C-H bonds. A wide variety of functional groups have been evaluated for use as directing groups in the transformation of C-H bonds. In 2005, Daugulis reported the arylation of unactivated C(sp3)-H bonds by using 8-aminoquinoline and picolinamide as bidentate directing groups, with Pd(OAc)2 as the catalyst. Encouraged by these promising results, a no. of transformations of C-H bonds have since been developed by using systems based on bidentate directing groups. In this review, recent advances in this area are discussed.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsF2ntLrF&md5=70cf2067c1f766af742178dc5e04341f70Schultz, D. M.; Yoon, T. P.Solar Synthesis: Prospects in Visible Light Photocatalysis. Science2014, 343, 1239176, DOI: 10.1126/science.1239176[Crossref], [PubMed], [CAS], Google Scholar70Solar synthesis: prospects in visible light photocatalysis
Science (New York, N.Y.) (2014), 343 (6174), 1239176 ISSN:.
Chemists have long aspired to synthesize molecules the way that plants do-using sunlight to facilitate the construction of complex molecular architectures. Nevertheless, the use of visible light in photochemical synthesis is fundamentally challenging because organic molecules tend not to interact with the wavelengths of visible light that are most strongly emitted in the solar spectrum. Recent research has begun to leverage the ability of visible light-absorbing transition metal complexes to catalyze a broad range of synthetically valuable reactions. In this review, we highlight how an understanding of the mechanisms of photocatalytic activation available to these transition metal complexes, and of the general reactivity patterns of the intermediates accessible via visible light photocatalysis, has accelerated the development of this diverse suite of reactions.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2cvovFejsg%253D%253D&md5=3c1c0a23eea300c9dbe2c46f9736eb8771Shaffer, D. W.; Bhowmick, I.; Rheingold, A. L.; Tsay, C.; Livesay, B. N.; Shores, M. P.; Yang, J. Y.Spin-State Diversity in a Series of Co(II) PNP Pincer Bromide Complexes. Dalton Trans.2016, 45, 17910– 17917, DOI: 10.1039/C6DT03461F[Crossref], [PubMed], [CAS], Google Scholar71Spin-state diversity in a series of Co(II) PNP pincer bromide complexes
Shaffer, David W.; Bhowmick, Indrani; Rheingold, Arnold L.; Tsay, Charlene; Livesay, Brooke N.; Shores, Matthew P.; Yang, Jenny Y.
Dalton Transactions (2016), 45 (44), 17910-17917CODEN: DTARAF; ISSN:1477-9226. (Royal Society of Chemistry)
The authors describe the structural and electronic impacts of modifying the bridging atom in a family of Co(II) pincer complexes Co(t-Bu)2PEPyEP(t-Bu)2Br2 (Py = pyridine, E = CH2, NH, and O for compds. 1-3, resp.). Structural characterization by single crystal x-ray diffraction indicates that compds. 1 and 3 are 5-coordinate complexes with both bromides bound to the Co ion, while compd. 2 is square planar with one bromide in the outer coordination sphere. The redn. potentials of 1-3, characterized by cyclic voltammetry, are consistent with the increasing electron-withdrawing character of the pincer ligand as the linker (E) between the pyridine and phosphine arms becomes more electroneg. Magnetic property studies of compds. 1 and 2 confirm high- and low-spin behavior, resp., through a broad temp. range. However, complex 3 features an unusual combination of high spin S = 3/2 Co(II) and temp. dependent spin-crossover between S = 3/2 and S = 1/2 states. The different magnetic behaviors obsd. among the three CoBr2 pincer complexes reflects the importance of small ligand perturbations on overall coordination geometry and resulting spin state properties.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xhs1ygtL%252FO&md5=9e0d26504b056b61c90c2e54d395998472Tsay, C.; Yang, J. Y.Electrocatalytic Hydrogen Evolution under Acidic Aqueous Conditions and Mechanistic Studies of a Highly Stable Molecular Catalyst. J. Am. Chem. Soc.2016, 138, 14174– 14177, DOI: 10.1021/jacs.6b05851[ACS Full Text ], [CAS], Google Scholar72Electrocatalytic Hydrogen Evolution under Acidic Aqueous Conditions and Mechanistic Studies of a Highly Stable Molecular Catalyst
Journal of the American Chemical Society (2016), 138 (43), 14174-14177CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
Electrocatalytic activity of a water-sol. nickel complex, [Ni(DHMPE)2]2+ (DHMPE = 2-bis(di(hydroxymethyl)phosphino)ethane), for the hydrogen evolution reaction (HER) at pH 1 is reported. The catalyst functions at a rate of ∼103 s-1 (kobs) with high Faradaic efficiency. Quantification of the complex before and after 18+ hours of electrolysis reveals negligible decompn. under catalytic conditions. Although highly acidic conditions are common in electrolytic cells, this is a rare example of a homogeneous catalyst for HER that functions with high stability at low pH. The stability of the compd. and proposed catalytic intermediates enabled detailed mechanistic studies. The thermodn. parameters governing electron and proton transfer were used to det. the appropriate reductants and acids to access the catalytic cycle in a stepwise fashion, permitting direct spectroscopic identification of intermediates. These studies support a mechanism for proton redn. that proceeds through two-electron redn. of the nickel(II) complex, protonation to generate [HNi(DHMPE)2]+, and further protonation to initiate hydrogen bond formation.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtFKms7%252FL&md5=b314b82c3f0e9110a5b1b69f6d9ea14973Ashley, D. C.; Jakubikova, E.Ironing out the Photochemical and Spin-Crossover Behavior of Fe (II) Coordination Compounds with Computational Chemistry. Coord. Chem. Rev.2017, 337, 97– 111, DOI: 10.1016/j.ccr.2017.02.005[Crossref], [CAS], Google Scholar73Ironing out the photochemical and spin-crossover behavior of Fe(II) coordination compounds with computational chemistry
Coordination Chemistry Reviews (2017), 337 (), 97-111CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)
Effective strategies for designing Fe(II) coordination complexes with specifically tailored spin-state energetics can lead to advances in many areas of inorg. and materials chem. These include, but are not limited to, rational development of novel spin crossover complexes, efficient chromophores for photosensitization of dye-sensitized solar cells, and multifunctional materials. As the spin-state ordering of transition metal complexes is strongly rooted in their electronic structures, computational chem. has naturally played an important role in assisting exptl. work in this area. Unfortunately, despite many advances, accurate detn. of the spin-state energetics of Fe(II) complexes still poses a remarkable challenge for virtually all applicable forms of electronic structure theory due to being controlled by a delicate balancing between correlation and exchange effects. This review focuses on some of the more notable successes and failures of modern electronic structure theory in properly describing these systems in the absence of solid-state effects. The strengths and weaknesses of using traditional wavefunction based methods and d. functional theory are considered, and illustrative examples are provided to demonstrate that the modern computational chemist should make use of exptl. data whenever possible and expect to utilize a combination of methods to obtain the best results. The review closes by briefly surveying some of the many interesting combined computational and exptl. studies of Fe(II) chem. that have lead to greater fundamental insight and practical understanding of this challenging class of systems.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXjt1Kjsrw%253D&md5=a6ae75e9fd6d88060425623023792b9e74Bowman, D. N.; Bondarev, A.; Mukherjee, S.; Jakubikova, E.Tuning the Electronic Structure of Fe(II) Polypyridines via Donor Atom and Ligand Scaffold Modifications: A Computational Study. Inorg. Chem.2015, 54, 8786– 8793, DOI: 10.1021/acs.inorgchem.5b01409[ACS Full Text ], [CAS], Google Scholar74Tuning the Electronic Structure of Fe(II) Polypyridines via Donor Atom and Ligand Scaffold Modifications: A Computational Study
Bowman, David N.; Bondarev, Alexey; Mukherjee, Sriparna; Jakubikova, Elena
Inorganic Chemistry (2015), 54 (17), 8786-8793CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
Fe(II) polypyridines are an important class of pseudo-octahedral metal complexes known for their potential applications in mol. electronic switches, data storage and display devices, sensors, and dye-sensitized solar cells. Fe(II) polypyridines have a d6 electronic configuration and pseudo-octahedral geometry and can therefore possess either a high-spin (quintet) or a low-spin (singlet) ground state. In this study, we investigate a series of complexes based on [Fe(tpy)2]2+ (tpy = 2,2';6',2'-terpyridine) and [Fe(dcpp)2]2+ (dcpp = 2,6-bis(2-carboxypyridyl)pyridine). The ligand field strength in these complexes is systematically tuned by replacing the central pyridine with five-membered (N-heterocyclic carbene, pyrrole, furan) or six-membered (aryl, thiazine-1,1-dioxide, 4-pyrone) moieties. To det. the impact of ligand substitutions on the relative energies of metal-centered states, the singlet, triplet, and quintet states of the Fe(II) complexes were optimized in water (PCM) using d. functional theory at the B3LYP+D2 level with 6-311G* (nonmetals) and SDD (Fe) basis sets. It was found that the dcpp ligand scaffold allows for a more ideal octahedral coordination environment in comparison to the tpy ligand scaffold. The presence of six-membered central rings also allows for a more ideally octahedral coordination environment relative to five-membered central rings, regardless of the ligand scaffold. We find that the ligand field strength in the Fe(II) polypyridines can be tuned by altering the donor atom identity, with C donor atoms providing the strongest ligand field.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtlOrsLbN&md5=d57d2f7ec920f5dba73a68df25bded3475Yella, A.; Lee, H. W.; Tsao, H. N.; Yi, C. Y.; Chandiran, A. K.; Nazeeruddin, M. K.; Diau, E. W. G.; Yeh, C. Y.; Zakeeruddin, S. M.; Gratzel, M.Porphyrin-Sensitized Solar Cells with Cobalt (II/III)-Based Redox Electrolyte Exceed 12% Efficiency. Science2011, 334, 629– 634, DOI: 10.1126/science.1209688[Crossref], [PubMed], [CAS], Google Scholar75Porphyrin-Sensitized Solar Cells with Cobalt (II/III)-Based Redox Electrolyte Exceed 12% Efficiency
Yella, Aswani; Lee, Hsuan-Wei; Tsao, Hoi Nok; Yi, Chenyi; Chandiran, Aravind Kumar; Nazeeruddin, Md. Khaja; Diau, Eric Wei-Guang; Yeh, Chen-Yu; Zakeeruddin, Shaik M.; Graetzel, Michael
Science (Washington, DC, United States) (2011), 334 (6056), 629-634CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
The iodide/triiodide redox shuttle has limited the efficiencies accessible in dye-sensitized solar cells. Here, the authors report mesoscopic solar cells that incorporate a Co(II/III)tris(bipyridyl)-based redox electrolyte in conjunction with a custom synthesized donor-π-bridge-acceptor zinc porphyrin dye as sensitizer (designated YD2-o-C8). The specific mol. design of YD2-o-C8 greatly retards the rate of interfacial back electron transfer from the conduction band of the nanocryst. titanium dioxide film to the oxidized cobalt mediator, which enables attainment of strikingly high photovoltages approaching 1 V. Because the YD2-o-C8 porphyrin harvests sunlight across the visible spectrum, large photocurrents are generated. Cosensitization of YD2-o-C8 with another org. dye further enhances the performance of the device, leading to a measured power conversion efficiency of 12.3% under simulated air mass 1.5 global sunlight.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtlyqu7nI&md5=23304b8a38934e2a776cba498b05fd2176Czerwieniec, R.; Yu, J. B.; Yersin, H.Blue-Light Emission of Cu(I) Complexes and Singlet Harvesting. Inorg. Chem.2011, 50, 8293– 8301, DOI: 10.1021/ic200811a[ACS Full Text ], [CAS], Google Scholar76Blue-Light Emission of Cu(I) Complexes and Singlet Harvesting
Inorganic Chemistry (2011), 50 (17), 8293-8301CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
Strongly luminescent neutral copper(I) complexes of the type Cu(pop)(NN), with pop = bis(2-(diphenylphosphanyl)phenyl)ether and NN = bis(pyrazol-1-yl)borohydrate (pz2BH2), tetrakis(pyrazol-1-yl)borate (pz4B), or bis(pyrazol-1-yl)-biphenyl-borate (pz2Bph2), are readily accessible in reactions of Cu(acetonitrile)4+ with equimolar amts. of the pop and NN ligands at ambient temp. All products were characterized by means of single crystal x-ray diffractometry. The compds. exhibit very strong blue/white luminescence with emission quantum yields of up to 90%. Investigations of spectroscopic properties and the emission decay behavior in the temp. range between 1.6 K and ambient temp. allow us to assign the emitting electronic states. Below 100 K, the emission decay times are in the order of many hundreds of microseconds. Therefore, it is concluded that the emission stems from the lowest triplet state. This state is assigned to a metal-to-ligand charge-transfer state (3MLCT) involving Cu-3d and pop-π* orbitals. With temp. increase, the emission decay time is drastically reduced to e.g. to 13 μs (Cu(pop)(pz2Bph2)) at ambient temp. At this temp., the complexes exhibit high emission quantum yields, as neat material or doped into poly(Me methacrylate) (PMMA). This behavior is assigned to an efficient thermal population of a singlet state (being classified as 1MLCT), which lies only 800 to 1300 cm-1 above the triplet state, depending on the individual complex. Thus, the resulting emission at ambient temp. largely represents a fluorescence. For applications in OLEDs and LEECs, for example, this type of thermally activated delayed fluorescence (TADF) creates a new mechanism that allows to harvest both singlet and triplet excitons (excitations) in the lowest singlet state. This effect of singlet harvesting leads to drastically higher radiative rates than obtainable for emissions from triplet states of Cu(I) complexes. Crystallog. data are given.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXpslaju78%253D&md5=ff8a63e35a70c801bc3a4bdd0f60db5f77Dias, F. B.; Bourdakos, K. N.; Jankus, V.; Moss, K. C.; Kamtekar, K. T.; Bhalla, V.; Santos, J.; Bryce, M. R.; Monkman, A. P.Triplet Harvesting with 100% Efficiency by Way of Thermally Activated Delayed Fluorescence in Charge Transfer OLED Emitters. Adv. Mater.2013, 25, 3707– 3714, DOI: 10.1002/adma.201300753[Crossref], [PubMed], [CAS], Google Scholar77Triplet Harvesting with 100% Efficiency by Way of Thermally Activated Delayed Fluorescence in Charge Transfer OLED Emitters
Dias, Fernando B.; Bourdakos, Konstantinos N.; Jankus, Vygintas; Moss, Kathryn C.; Kamtekar, Kiran T.; Bhalla, Vandana; Santos, Jose; Bryce, Martin R.; Monkman, Andrew P.
Advanced Materials (Weinheim, Germany) (2013), 25 (27), 3707-3714CODEN: ADVMEW; ISSN:0935-9648. (Wiley-VCH Verlag GmbH & Co. KGaA)
Org. light-emitting diodes (OLEDs) have their performance limited by the no. of emissive singlet states created upon charge recombination (25%). Recently, a novel strategy has been proposed, based on thermally activated up-conversion of triplet to singlet states, yielding delayed fluorescence (TADF), which greatly enhances electroluminescence. The energy barrier for this reverse intersystem crossing mechanism is proportional to the exchange energy (ΔEST) between the singlet and triplet states; therefore, materials with intramol. charge transfer (ICT) states, where it is known that the exchange energy is small, are perfect candidates. However, here it is shown that triplet states can be harvested with 100% efficiency via TADF, even in materials with ΔEST of more than 20 kT (where k is the Boltzmann const. and T is the temp.) at room temp. The key role played by lone pair electrons in achieving this high efficiency in a series of ICT mols. is elucidated. The results show the complex photophysics of efficient TADF materials and give clear guidelines for designing new emitters.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXotFSmtrg%253D&md5=c5afb072b044a1bde2416f129952f4a178Kuttipillai, P. S.; Zhao, Y. M.; Traverse, C. J.; Staples, R. J.; Levine, B. G.; Lunt, R. R.Phosphorescent Nanocluster Light-Emitting Diodes. Adv. Mater.2016, 28, 320– 326, DOI: 10.1002/adma.201504548[Crossref], [PubMed], [CAS], Google Scholar78Kuttipillai, Padmanaban S.; Zhao, Yimu; Traverse, Christopher J.; Staples, Richard J.; Levine, Benjamin G.; Lunt, Richard R.
Advanced Materials (Weinheim, Germany) (2016), 28 (2), 320-326CODEN: ADVMEW; ISSN:0935-9648. (Wiley-VCH Verlag GmbH & Co. KGaA)
Inorg. phosphorescent metal halide nanoclusters are demonstrated as an entirely new platform for tunable and efficient light-emitting diodes. Here, we report the integration of molybdenum halide nanocluster salts into optically and elec. pumped nanocluster light-emitting devices and demonstrate tunable emission by means of varying cation substitution. Here, we report the integration of molybdenum halide nanocluster salts into optically and elec. pumped nanocluster light-emitting devices and demonstrate tunable emission by means of varying cation substitution. While the efficiencies of the proof-of-principle elec. pumped devices are not fully optimized, the optically pumped nanocluster devices show quantum efficiencies of 2.5% for peak emission at 800 nm. We utilize both luminescent and electroluminescent transient dynamics to understand the nanocluster photophysics and analyze time-dependent d. functional theory (TDDFT) calcns. performed on the core cluster to gain insights about the nature of the phosphorescent emitting state.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhvVaqu7rM&md5=2a4d02cf90ed075fdab8acd8901e677579Leitl, M. J.; Kuchle, F. R.; Mayer, H. A.; Wesemann, L.; Yersin, H.Brightly Blue and Green Emitting Cu(I) Dimers for Singlet Harvesting in Oleds. J. Phys. Chem. A2013, 117, 11823– 11836, DOI: 10.1021/jp402975d[ACS Full Text ], [CAS], Google Scholar79Brightly Blue and Green Emitting Cu(I) Dimers for Singlet Harvesting in OLEDs
Leitl, Markus J.; Kuechle, Fritz-Robert; Mayer, Hermann A.; Wesemann, Lars; Yersin, Hartmut
Journal of Physical Chemistry A (2013), 117 (46), 11823-11836CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
With the chelating aminophosphane ligands Ph2P-(o-C6H4)-NMe2 (PNMe2) and Ph2P-(o-C6H4)-NC4H8 (PNpy), the 4 halide (Cl, Br, I)-bridged Cu coordination compds. [Cu(μ-Cl)(PNMe2)]2 (1), [Cu(μ-Br)(PNMe2)]2 (2), [Cu(μ-I)(PNMe2)]2 (3), and [Cu(μ-I)(PNpy)]2 (4) were synthesized and structurally characterized. Their photophys. properties were studied. The complexes exhibit strong blue (λmax = 464 (3) and 465 nm (4)) and green (λmax = 506 (1) and 490 nm (2)) luminescence as powders with quantum yields of ≤65% at decay times of ≥4.1 μs. A study of the emission decay behavior at 1.3-300 K gives insight into the nature of the emitting states. At temps. T .ltorsim. 60 K, the decay times of the studied compds. are several hundred μs long, which indicates that the emission originates from a triplet state (T1 state). DFT calcns. show that this state is of (metal+halide)-to-ligand charge transfer 3(M+X)-LCT character. Studies at 1.3 K allow gaining insight into the 3 triplet substates, in particular, to det. the individual substate decay times being as long as a few ms. The zero-field splittings are < 1 or 2 cm-1. With an anal. of these data, conclusions about the effectiveness of spin-orbit coupling (SOC) can be drawn. The large differences of SOC consts. of the halides are not obviously displayed in the triplet state properties. With a temp. increase from T ≈ 60 to 300 K, a significant decrease of the emission decay time by almost 2 orders of magnitude is obsd., and at ambient temp., the decay times amt. only to ∼4-7 μs without a significant redn. of the emission quantum yields. This drastic decrease of the (radiative) decay time is a result of the thermal population of a short-lived singlet state (S1 state) that lies energetically only a few hundred wavenos. (460-630 cm-1) higher than the T1 state. Such an emission mechanism corresponds to a thermally-activated delayed fluorescence (TADF). At ambient temp., almost only a delayed fluorescence (∼98%) is obsd. Compds. showing this mechanism are highly attractive for applications in OLEDs or LEECs as, in principle, it is possible to harvest all singlet and triplet excitons for the generation of light in the lowest excited singlet state. This effect represents the singlet harvesting mechanism.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhtlaisbnM&md5=0c0994b85d6f4a0c0f42671ef32df80680Linfoot, C. L.; Leitl, M. J.; Richardson, P.; Rausch, A. F.; Chepelin, O.; White, F. J.; Yersin, H.; Robertson, N.Thermally Activated Delayed Fluorescence (TADF) and Enhancing Photoluminescence Quantum Yields of Cu-I(Diimine)(Diphosphine)(+) Complexes-Photophysical, Structural, and Computational Studies. Inorg. Chem.2014, 53, 10854– 10861, DOI: 10.1021/ic500889s[ACS Full Text ], [CAS], Google Scholar80Thermally Activated Delayed Fluorescence (TADF) and Enhancing Photoluminescence Quantum Yields of [CuI(diimine)(diphosphine)]+ Complexes-Photophysical, Structural, and Computational Studies
Linfoot, Charlotte L.; Leitl, Markus J.; Richardson, Patricia; Rausch, Andreas F.; Chepelin, Oleg; White, Fraser J.; Yersin, Hartmut; Robertson, Neil
Inorganic Chemistry (2014), 53 (20), 10854-10861CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
[Cu(I)(POP)(dmbpy)][BF4] and [Cu(I)(POP)(tmbpy)][BF4] (dmbpy = 4,4'-dimethyl-2,2'-bipyridyl; tmbpy = 4,4',6,6'-tetramethyl-2,2'-bipyridyl; POP = bis[2-(diphenylphosphino)-phenyl]ether) were studied in a wide temp. range by steady-state and time-resolved emission spectroscopy in fluid soln., frozen soln., and as solid powders. Emission quantum yields of up to 74% were obsd. for 2 in a rigid matrix (powder), substantially higher than for 1 of ∼9% under the same conditions. Importantly, the emission of 2 at ambient temp. represents a thermally activated delayed fluorescence (TADF) which renders the compd. to be a good candidate for singlet harvesting in OLEDs. The role of steric constraints within the complexes, in particular their influences on the emission quantum yields, were studied by hybrid-DFT calcns. for the excited triplet state of 1 and 2 while manipulating the torsion angle between the bipyridyl and POP ligands. Both complexes showed similar flexibility within a ±10° range of the torsion angle; however, 2 appeared limited to this range, whereas 1 could be further twisted with little energy demand. A restricted flexibility leads to a redn. of nonradiative deactivation and thus an increase of emission quantum yield.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXht1SqsbfE&md5=59f450a82d6fc5cf172c8a80c6f6d91e81Zink, D. M.; Bachle, M.; Baumann, T.; Nieger, M.; Kuhn, M.; Wang, C.; Klopper, W.; Monkowius, U.; Hofbeck, T.; Yersin, H.; Brase, S.Synthesis, Structure, and Characterization of Dinuclear Copper(I) Halide Complexes with PAN Ligands Featuring Exciting Photoluminescence Properties. Inorg. Chem.2013, 52, 2292– 2305, DOI: 10.1021/ic300979c[ACS Full Text ], [CAS], Google Scholar81Synthesis, Structure, and Characterization of Dinuclear Copper(I) Halide Complexes with P%N Ligands Featuring Exciting Photoluminescence Properties
Zink, Daniel M.; Baechle, Michael; Baumann, Thomas; Nieger, Martin; Kuehn, Michael; Wang, Cong; Klopper, Wim; Monkowius, Uwe; Hofbeck, Thomas; Yersin, Hartmut; Brase, Stefan
Inorganic Chemistry (2013), 52 (5), 2292-2305CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
Highly luminescent dinuclear Cu(I) complexes were synthesized in good yields using a modular ligand system of easily accessible diphenylphosphinopyridine-type P%N ligands. Characterization of these complexes via x-ray crystallog. studies and elemental anal. revealed a dinuclear complex structure with a butterfly-shaped metal-halide core. The complexes feature emission covering the visible spectrum from blue to red together with high quantum yields up to 96%. D. functional theory calcns. show that the HOMO consists mainly of orbitals of both the metal core and the bridging halides, while the LUMO resides dominantly on the heterocyclic part of the P%N ligands. Therefore, modification of the heterocyclic moiety of the bridging ligand allows for systematic tuning of the luminescence wavelength. By increasing the arom. system of the N-heterocycle or through functionalization of the pyridyl moiety, complexes with emission maxima from 481 to 713 nm were obtained. For a representative compd., the ambient-temp. emission can be assigned as a thermally activated delayed fluorescence, featuring an attractively short emission decay time of only 6.5 μs at φPL = 0.8. It is proposed to apply these compds. for singlet harvesting in OLEDs.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhsV2ru7bE&md5=7bbf16d7368c5ae6819aa4f308e2de2982Weininger, D.Smiles, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules. J. Chem. Inf. Model.1988, 28, 31– 36, DOI: 10.1021/ci00057a005[ACS Full Text ], [CAS], Google Scholar82SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
Journal of Chemical Information and Computer Sciences (1988), 28 (1), 31-6CODEN: JCISD8; ISSN:0095-2338.
The SMILES (simplified mol. input line entry system) chem. notation system is described for information processing. The system is based on principles of mol. graph theory and it allows structure specification by use of a very small and natural grammar well suited for high-speed machine processing. The system is easy to use, has high machine compatibility, and allows many computer applications, including notation generation, const. speed database retrieval, substructure searching, and property prediction models.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL1cXnsVeqsA%253D%253D&md5=04592975f9dd3c0ce3c1ad618ba2b17d83O’Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R.Open Babel: An Open Chemical Toolbox. J. Cheminf.2011, 3, 33, DOI: 10.1186/1758-2946-3-33[Crossref], [PubMed], [CAS], Google Scholar83O'Boyle, Noel M.; Banck, Michael; James, Craig A.; Morley, Chris; Vandermeersch, Tim; Hutchison, Geoffrey R.
Journal of Cheminformatics (2011), 3 (), 33CODEN: JCOHB3; ISSN:1758-2946. (Chemistry Central Ltd.)
Background: A frequent problem in computational modeling is the interconversion of chem. structures between different formats. While std. interchange formats exist (for example, Chem. Markup Language) and de facto stds. have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chem. data, differences in the data stored by different formats (0D vs. 3D, for example), and competition between software along with a lack of vendor-neutral formats. Results: We discuss, for the first time, Open Babel, an open-source chem. toolbox that speaks the many languages of chem. data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chem. and mol. data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions: Open Babel presents a soln. to the proliferation of multiple chem. file formats. In addn., it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chem. data in areas such as org. chem., drug design, materials science, and computational chem. It is freely available under an open-source license.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhsVWjurbF&md5=74e4f19b7f87417f916d57f7abcfb76184Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J.Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc.1996, 118, 11225– 11236, DOI: 10.1021/ja9621760[ACS Full Text ], [CAS], Google Scholar84Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
Jorgensen, William L.; Maxwell, David S.; Tirado-Rives, Julian
Journal of the American Chemical Society (1996), 118 (45), 11225-11236CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The parametrization and testing of the OPLS all-atom force field for org. mols. and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER all-atom force field. The torsional parameters were detd. by fitting to rotational energy profiles obtained from ab initio MO calcns. at the RHF/6-31G*//RHF/6-31G* level for more than 50 org. mols. and ions. The quality of the fits was high with av. errors for conformational energies of less than 0.2 kcal/mol. The force-field results for mol. structures are also demonstrated to closely match the ab initio predictions. The nonbonded parameters were developed in conjunction with Monte Carlo statistical mechanics simulations by computing thermodn. and structural properties for 34 pure org. liqs. including alkanes, alkenes, alcs., ethers, acetals, thiols, sulfides, disulfides, aldehydes, ketones, and amides. Av. errors in comparison with exptl. data are 2% for heats of vaporization and densities. The Monte Carlo simulations included sampling all internal and intermol. degrees of freedom. It is found that such non-polar and monofunctional systems do not show significant condensed-phase effects on internal energies in going from the gas phase to the pure liqs.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XmtlOitrs%253D&md5=fef2924a69421881390282aa309ae91b85Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A.Development and Testing of a General Amber Force Field. J. Comput. Chem.2004, 25, 1157– 1174, DOI: 10.1002/jcc.20035[Crossref], [PubMed], [CAS], Google Scholar85Development and testing of a general Amber force field
Wang, Junmei; Wolf, Romain M.; Caldwell, James W.; Kollman, Peter A.; Case, David A.
Journal of Computational Chemistry (2004), 25 (9), 1157-1174CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
We describe here a general Amber force field (GAFF) for org. mols. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most org. and pharmaceutical mols. that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited no. of atom types, but incorporates both empirical and heuristic models to est. force consts. and partial at. charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallog. structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 Å, which is comparable to that of the Tripos 5.2 force field (0.25 Å) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 Å, resp.). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermol. energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 Å and 1.2 kcal/mol, resp. These data are comparable to results from Parm99/RESP (0.16 Å and 1.18 kcal/mol, resp.), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to expt.) is about 0.5 kcal/mol. GAFF can be applied to wide range of mols. in an automatic fashion, making it suitable for rational drug design and database searching.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXksFakurc%253D&md5=2992017a8cf51f89290ae2562403b11586Brandenburg, J. G.; Grimme, S.Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB). J. Phys. Chem. Lett.2014, 5, 1785– 1789, DOI: 10.1021/jz500755u[ACS Full Text ], [CAS], Google Scholar86Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB)
Journal of Physical Chemistry Letters (2014), 5 (11), 1785-1789CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
The ambitious goal of org. crystal structure prediction challenges theor. methods regarding their accuracy and efficiency. Dispersion-cor. d. functional theory (DFT-D) in principle is applicable, but the computational demands, for example, to compute a huge no. of polymorphs, are too high. Here, we demonstrate that this task can be carried out by a dispersion-cor. d. functional tight binding (DFTB) method. The semiempirical Hamiltonian with the D3 correction can accurately and efficiently model both solid- and gas-phase inter- and intramol. interactions at a speed up of 2 orders of magnitude compared to DFT-D. The mean abs. deviations for interaction (lattice) energies for various databases are typically 2-3 kcal/mol (10-20%), i.e., only about two times larger than those for DFT-D. For zero-point phonon energies, small deviations of <0.5 kcal/mol compared to DFT-D are obtained.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXnsVegsbk%253D&md5=7c4e54ca1b8d5ed35fba996028a06f5887Gaus, M.; Cui, Q.; Elstner, M.DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB). J. Chem. Theory Comput.2011, 7, 931– 948, DOI: 10.1021/ct100684s[ACS Full Text ], [CAS], Google Scholar87DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)
Journal of Chemical Theory and Computation (2011), 7 (4), 931-948CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
The self-consistent-charge d.-functional tight-binding method (SCC-DFTB) is an approx. quantum chem. method derived from d. functional theory (DFT) based on a second-order expansion of the DFT total energy around a ref. d. In the present study, we combine earlier extensions and improve them consistently with, first, an improved Coulomb interaction between at. partial charges and, second, the complete third-order expansion of the DFT total energy. These modifications lead us to the next generation of the DFTB methodol. called DFTB3, which substantially improves the description of charged systems contg. elements C, H, N, O, and P, esp. regarding hydrogen binding energies and proton affinities. As a result, DFTB3 is particularly applicable to biomol. systems. Remaining challenges and possible solns. are also briefly discussed.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXjtVKgu74%253D&md5=179659060fa503023375266a674d02e788Korth, M.; Thiel, W.Benchmarking Semiempirical Methods for Thermochemistry, Kinetics, and Noncovalent Interactions: OMx Methods Are Almost as Accurate and Robust as DFT-GGA Methods for Organic Molecules. J. Chem. Theory Comput.2011, 7, 2929– 2936, DOI: 10.1021/ct200434a[ACS Full Text ], [CAS], Google Scholar88Benchmarking Semiempirical Methods for Thermochemistry, Kinetics, and Noncovalent Interactions: OMx Methods Are Almost As Accurate and Robust As DFT-GGA Methods for Organic Molecules
Journal of Chemical Theory and Computation (2011), 7 (9), 2929-2936CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Semiempirical quantum mech. (SQM) methods offer a fast approx. treatment of the electronic structure and the properties of large mols. Careful benchmarks are required to establish their accuracy. Here, we report a validation of std. SQM methods using a subset of the comprehensive GMTKN24 database for general main group thermochem., kinetics, and noncovalent interactions, which has recently been introduced to evaluate d. functional theory (DFT) methods. For all SQM methods considered presently, parameters are available for the elements H, C, N, and O, and consequently, we have extd. from the GMTKN24 database all species contg. only these four elements (excluding multireference cases). The resulting GMTKN24-hcno database has 370 entries (derived from 593 energies) compared with 715 entries (derived from 1033 energies) in the original GMTKN24 database. The current benchmark covers established std. SQM methods (AM1, PM6), more recent approaches with orthogonalization corrections (OM1, OM2, OM3), and the self-consistent-charge d. functional tight binding method (SCC-DFTB). The results are compared against each other and against DFT results using std. functionals. We find that the OMx methods outperform AM1, PM6, and SCC-DFTB by a significant margin, with a substantial gain in accuracy esp. for OM2 and OM3. These latter methods are quite accurate even in comparison with DFT, with an overall mean abs. deviation of 6.6 kcal/mol for PBE and 7.9 kcal/mol for OM3. The OMx methods are also remarkably robust with regard to the unusual bonding situations encountered in the 'mindless' MB08-165 test set, for which all other SQM methods fail badly.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtVagsLnP&md5=0079e95651d673b00b4643413218490f89Gallandi, L.; Marom, N.; Rinke, P.; Körzdörfer, T.Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules II: Non-Empirically Tuned Long-Range Corrected Hybrid Functionals. J. Chem. Theory Comput.2016, 12, 605– 614, DOI: 10.1021/acs.jctc.5b00873[ACS Full Text ], [CAS], Google Scholar89Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules II: Non-Empirically Tuned Long-Range Corrected Hybrid Functionals
Gallandi, Lukas; Marom, Noa; Rinke, Patrick; Koerzdoerfer, Thomas
Journal of Chemical Theory and Computation (2016), 12 (2), 605-614CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
The performance of non-empirically tuned long-range cor. hybrid functionals for the prediction of vertical ionization potentials (IPs) and electron affinities (EAs) is assessed for a set of 24 org. acceptor mols. Basis set-extrapolated coupled cluster singles, doubles, and perturbative triples [CCSD(T)] calcns. serve as a ref. for this study. Compared to std. exchange-correlation functionals, tuned long-range cor. hybrid functionals produce highly reliable results for vertical IPs and EAs, yielding mean abs. errors on par with computationally more demanding GW calcns. In particular, it is demonstrated that long-range cor. hybrid functionals serve as ideal starting points for non-self-consistent GW calcns.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xis1GisQ%253D%253D&md5=1c32cfab4c7179be6a885866297b108990Kubinyi, H.QSAR and 3D QSAR in Drug Design Part 1: Methodology. Drug Discovery Today1997, 2, 457– 467, DOI: 10.1016/S1359-6446(97)01079-9[Crossref], [CAS], Google Scholar90QSAR and 3D QSAR in drug design. Part 1: methodology
Drug Discovery Today (1997), 2 (11), 457-467CODEN: DDTOFS; ISSN:1359-6446. (Elsevier)
A review with 45 refs. Classical QSAR methods describe structure-activity relationships in terms of physicochem. parameters and steric properties (Hansch anal., extrathermodynamic approach), or certain structural features (Free Wilson anal.). 3D QSAR methods, esp. comparative mol. field anal., consider the three-dimensional structures and the binding modes of protein ligands. Quant. similarity-activity relationships derive correlations between the similarities of individual compds. and their biol. activities. Theory and methodol. of these approaches are described here, together with the proper use of regression and partial least squares analyses for deriving quant. structure-activity relationships. Part 2, to be published in the Dec. issue, will address applications and problems.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXns1CqtL4%253D&md5=4eac3be8867dda8d65d68385b4e73a6591Jorgensen, W. L.; Duffy, E. M.Prediction of Drug Solubility from Structure. Adv. Drug Delivery Rev.2002, 54, 355– 366, DOI: 10.1016/S0169-409X(02)00008-X[Crossref], [PubMed], [CAS], Google Scholar91Jorgensen, William L.; Duffy, Erin M.
Advanced Drug Delivery Reviews (2002), 54 (3), 355-366CODEN: ADDREP; ISSN:0169-409X. (Elsevier Science Ireland Ltd.)
A review with refs. The aq. soly. of a drug is an important factor affecting its bioavailability. Numerous computational methods have been developed for the prediction of aq. soly. from a compd.'s structure. A review is provided of the methodol. and quality of results for the most useful procedures including the model implemented in the QikProp program. Viable methods now exist for predictions with <1 log unit uncertainty, which is adequate for prescreening synthetic candidates or design of combinatorial libraries. Further progress with predictive methods would require an exptl. database of highly accurate solubilities for a large, diverse collection of drug-like mols.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38Xitlartbc%253D&md5=bc749286d56bf55c26d25b70806217e192Turner, J. V.; Glass, B. D.; Agatonovic-Kustrin, S.Prediction of Drug Bioavailability Based on Molecular Structure. Anal. Chim. Acta2003, 485, 89– 102, DOI: 10.1016/S0003-2670(03)00406-9[Crossref], [CAS], Google Scholar92Prediction of drug bioavailability based on molecular structure
Turner, Joseph V.; Glass, Beverly D.; Agatonovic-Kustrin, Snezana
Analytica Chimica Acta (2003), 485 (1), 89-102CODEN: ACACAM; ISSN:0003-2670. (Elsevier Science B.V.)
Oral dosing is the most common method of drug administration, and final plasma concns. of the drug depend upon its bioavailability. In the current study, a quant. structure-pharmacokinetic relation (QSPR) was developed for a diverse range of compds. to allow prediction of drug bioavailability. Bioavailability data for 169 compds. was taken from the literature, and from the mol. structures 94 theor. descriptors were generated. Stepwise regression was employed to develop a regression equation based on 159 training compds., and predictive ability was tested on 10 compds. reserved for that purpose. The final regression equation included eight descriptors that represented electronic, steric, hydrophobic and constituent parameters of the drug mols., all of which could be related to soly. and partitioning properties. Predicted bioavailability for the training set agreed more closely for drugs exhibiting mid-range literature bioavailability values. A correlation of 0.72 was achieved for test set bioavailability predictions when compared with literature values. The structure-pharmacokinetic relation developed in the current study highlighted soly. and partitioning characteristics that may be useful in designing drugs with appropriate bioavailability.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXjvVClsrs%253D&md5=3b84cf48b6a181d16e1b48dd5e38740d93Sliwoski, G.; Kothiwale, S.; Meiler, J.; Lowe, E. W.Computational Methods in Drug Discovery. Pharmacol. Rev.2014, 66, 334– 395, DOI: 10.1124/pr.112.007336[Crossref], [PubMed], [CAS], Google Scholar93Sliwoski, Gregory; Kothiwale, Sandeepkumar; Meiler, Jens; Lowe Edward, W.
Pharmacological Reviews (2014), 66 (1), 334-395, 62 pp.CODEN: PAREAQ; ISSN:1521-0081. (American Society for Pharmacology and Experimental Therapeutics)
A review. Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small mols. for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, mol. descriptors, and quant. structure-activity relationships. In addn., important tools such as target/ligand data bases, homol. modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiol. properties are discussed with successful examples from literature.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsVGnu7nL&md5=3dde38a0b60c583f832c688c2d27819f94Smith, J. S.; Isayev, O.; Roitberg, A. E.ANI-1: An Extensible Neural Network Potential with DFT Accuracy at Force Field Computational Cost. Chem. Sci.2017, 8, 3192– 3203, DOI: 10.1039/C6SC05720A[Crossref], [PubMed], [CAS], Google Scholar94ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost
Chemical Science (2017), 8 (4), 3192-3203CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)
Deep learning is revolutionizing many areas of science and technol., esp. image, text, and speech recognition. In this paper, we demonstrate how a deep neural network (NN) trained on quantum mech. (QM) DFT calcns. can learn an accurate and transferable potential for org. mols. We introduce ANAKIN-ME (Accurate NeurAl networK engINe for Mol. Energies) or ANI for short. ANI is a new method designed with the intent of developing transferable neural network potentials that utilize a highly-modified version of the Behler and Parrinello symmetry functions to build single-atom at. environment vectors (AEV) as a mol. representation. AEVs provide the ability to train neural networks to data that spans both configurational and conformational space, a feat not previously accomplished on this scale. We utilized ANI to build a potential called ANI-1, which was trained on a subset of the GDB databases with up to 8 heavy atoms in order to predict total energies for org. mols. contg. four atom types: H, C, N, and O. To obtain an accelerated but phys. relevant sampling of mol. potential surfaces, we also proposed a Normal Mode Sampling (NMS) method for generating mol. conformations. Through a series of case studies, we show that ANI-1 is chem. accurate compared to ref. DFT calcns. on much larger mol. systems (up to 54 atoms) than those included in the training data set.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXitlGnsrs%253D&md5=95b2f5106c620c6f09560966dba3559e95Faber, F. A.; Hutchison, L.; Huang, B.; Gilmer, J.; Schoenholz, S. S.; Dahl, G. E.; Vinyals, O.; Kearnes, S.; Riley, P. F.; von Lilienfeld, O. A.Prediction Errors of Molecular Machine Learning Models Lower Than Hybrid DFT Error. J. Chem. Theory Comput.2017, 13, 5255– 5264, DOI: 10.1021/acs.jctc.7b00577[ACS Full Text ], [CAS], Google Scholar95Prediction Errors of Molecular Machine Learning Models Lower than Hybrid DFT Error
Faber, Felix A.; Hutchison, Luke; Huang, Bing; Gilmer, Justin; Schoenholz, Samuel S.; Dahl, George E.; Vinyals, Oriol; Kearnes, Steven; Riley, Patrick F.; von Lilienfeld, O. Anatole
Journal of Chemical Theory and Computation (2017), 13 (11), 5255-5264CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
We investigate the impact of choosing regressors and mol. representations for the construction of fast machine learning (ML) models of thirteen electronic ground-state properties of org. mols. The performance of each regressor/representation/property combination is assessed using learning curves which report out-of-sample errors as a function of training set size with up to ∼118k distinct mols. Mol. structures and properties at hybrid d. functional theory (DFT) level of theory come from the QM9 database [Ramakrishnan et al, Scientific Data 1 140022 (2014)] and include enthalpies and free energies of atomization , HOMO/LUMO energies and gap, dipole moment, polarizability, zero point vibrational energy, heat capacity and the highest fundamental vibrational frequency. Various mol. representations have been studied (Coulomb matrix, bag of bonds, BAML and ECFP4, mol. graphs (MG)), as well as newly developed distribution based variants including histograms of distances (HD), and angles (HDA/MARAD), and dihedrals (HDAD). Regressors include linear models (Bayesian ridge regression (BR) and linear regression with elastic net regularization (EN)), random forest (RF), kernel ridge regression (KRR) and two types of neural networks, graph convolutions (GC) and gated graph networks (GG). Out-of sample errors are strongly dependent on the choice of representation and regressor and mol. property. Electronic properties are typically best accounted for by MG and GC, while energetic properties are better described by HDAD and KRR. The specific combinations with the lowest out-of-sample errors in the ∼118k training set size limit are (free) energies and enthalpies of atomization (HDAD/KRR), HOMO/LUMO eigenvalue and gap (MG/GC), dipole moment (MG/GC), static polarizability (MG/GG), zero point vibrational energy (HDAD/KRR), heat capacity at room temp. (HDAD/KRR), and highest fundamental vibrational frequency (BAML/RF). We present numerical evidence that ML model predictions deviate from DFT (B3LYP) less than DFT (B3LYP) deviates from expt. for all properties. Furthermore, out-of-sample prediction errors with respect to hybrid DFT ref. are on par with, or close to, chem. accuracy. The results suggest that ML models could be more accurate than hybrid DFT if explicitly electron correlated quantum (or exptl.) data was available.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhsFWhu7vL&md5=c1cd87e50b04558c403a92184f4d017b96Ramakrishnan, R.; Dral, P. O.; Rupp, M.; von Lilienfeld, O. A.Big Data Meets Quantum Chemistry Approximations: The Delta-Machine Learning Approach. J. Chem. Theory Comput.2015, 11, 2087– 96, DOI: 10.1021/acs.jctc.5b00099[ACS Full Text ], [CAS], Google Scholar96Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning Approach
Ramakrishnan, Raghunathan; Dral, Pavlo O.; Rupp, Matthias; von Lilienfeld, O. Anatole
Journal of Chemical Theory and Computation (2015), 11 (5), 2087-2096CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Chem. accurate and comprehensive studies of the virtual space of all possible mols. are severely limited by the computational cost of quantum chem. We introduce a composite strategy that adds machine learning corrections to computationally inexpensive approx. legacy quantum methods. After training, highly accurate predictions of enthalpies, free energies, entropies, and electron correlation energies are possible, for significantly larger mol. sets than used for training. For thermochem. properties of up to 16k isomers of C7H10O2 we present numerical evidence that chem. accuracy can be reached. We also predict electron correlation energy in post Hartree-Fock methods, at the computational cost of Hartree-Fock, and we establish a qual. relationship between mol. entropy and electron correlation. The transferability of our approach is demonstrated, using semiempirical quantum chem. and machine learning models trained on 1 and 10% of 134k org. mols., to reproduce enthalpies of all remaining mols. at d. functional theory level of accuracy.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXmtlams7Y%253D&md5=a59b33f51a9dd6dbad95290f2642c30697Yao, K.; Herr, J. E.; Toth, D. W.; Mckintyre, R.; Parkhill, J.The Tensormol-0.1 Model Chemistry: A Neural Network Augmented with Long-Range Physics. Chem. Sci.2018, 9, 2261– 2269, DOI: 10.1039/C7SC04934J[Crossref], [PubMed], [CAS], Google Scholar97The TensorMol-0.1 model chemistry: a neural network augmented with long-range physics
Yao, Kun; Herr, John E.; Toth, David W.; McKintyre, Ryker; Parkhill, John
Chemical Science (2018), 9 (8), 2261-2269CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)
Traditional force fields cannot model chem. reactivity, and suffer from low generality without re-fitting. Neural network potentials promise to address these problems, offering energies and forces with near ab initio accuracy at low cost. However a, is offered in an open-source Python package capable of many of the simulation types commonly used to study chem.: geometry optimizations, harmonic spectra, open or periodic mol. dynamics, Monte Carlo, and nudged elastic band calcns. We describe the robustness and speed of the package, demonstrating its millihartree accuracy and scalability to tens-of-thousands of atoms on ordinary laptops. We demonstrate the performance of the model by reproducing vibrational spectra, and simulating the mol. dynamics of a protein. Our comparisons with electronic structure theory and exptl. data demonstrate that neural network mol. dynamics is poised to become an important tool for mol. simulation, lowering the resource barrier to simulating chem.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhtFOitLY%253D&md5=6c4d95e1748fd3dabb87c862297bdc4b98Gómez-Bombarelli, R.; Wei, J. N.; Duvenaud, D.; Hernández-Lobato, J. M.; Sánchez-Lengeling, B.; Sheberla, D.; Aguilera-Iparraguirre, J.; Hirzel, T. D.; Adams, R. P.; Aspuru-Guzik, A.Automatic Chemical Design Using a systems.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XptV2hsA%253D%253D&md5=c67aac0ca496cfadb199ba000fb9a7d7110Ganzenmüller, G.; Berkaïne, N.; Fouqueau, A.; Casida, M. E.; Reiher, M.Comparison of Density Functionals for Differences between the High- (T2g5) and Low- (A1g1) Spin States of Iron(II) Compounds. IV. Results for the Ferrous Complexes [Fe(L)(‘NHS4’)]. J. Chem. Phys.2005, 122, 234321, DOI: 10.1063/1.1927081[Crossref], [PubMed], [CAS], Google Scholar110Comparison of density functionals for differences between the high-(5T2g) and low-(1A1g) spin states of iron(II) compounds. IV. Results for the ferrous complexes [Fe(L)('NHS4')]
Ganzenmuller, Georg; Berkaine, Nabil; Fouqueau, Antony; Casida, Mark E.; Reiher, Markus
Journal of Chemical Physics (2005), 122 (23), 234321/1-234321/12CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
Previous work testing d. functionals for use in calcg. high-spin-low-spin energy differences, ΔEHL, for iron(II) spin-crossover transitions has tended to conclude that only properly reparametrized hybrid functionals can predict ΔEHL since it seems to depend critically on a correct description of the electron pairing energy governed by the exchange term. Exceptions to this rule are the previous three papers (I, II, and III in the present series of papers) where it was found that modern generalized gradient approxns. (GGAs) and meta-GGAs could do as well as hybrid functionals, if not better, for this type of problem. In the present paper, we extend these previous studies to five more mols. which are too large to treat with high-quality ab initio calcns., namely, the series [Fe(L)( NHS4')], where NHS4 = 2.2'-bis(2-mercaptophenylthio)diethylamine dianion, and L = NH3, N2H4, PMe3, CO, and NO+. Since we know of no reliable exptl. est. of ΔEHL, we content ourselves with a comparison against the exptl. detd. ground-state spin symmetry including, in so far as possible, finite-temp. effects. Together with the results of Papers I, II, and III, this paper provides a test of a large no. of functionals against the high-spin/low-spin properties of a diverse set of Fe(II) compds., making it possible to draw some particularly interesting conclusions. Trends among different classes of functionals are discussed and it is pointed out that there is at least one functional, namely, the OLYP generalized gradient approxn., which is able to give a reasonably good description of the delicate spin energetics of Fe(II) coordination compds. without resorting to hybrid functionals which require the relatively more expensive calcn. of a Hartree-Fock-type exchange term.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXlvVers7w%253D&md5=2db2dbbfd9e5b9872d33799ddd4145df111Fouqueau, A.; Casida, M. E.; Daku, L. M. L.; Hauser, A.; Neese, F.Comparison of Density Functionals for Energy and Structural Differences between the High-[5t2g:(T2g) 4 (Eg) 2] and Low-[1a1g:(T2g) 6 (Eg) 0] Spin States of Iron (II) Coordination Compounds. II. More Functionals and the Hexaminoferrous Cation,[Fe (NH3) 6] 2. J. Chem. Phys.2005, 122, 044110, DOI: 10.1063/1.1839854[Crossref], [PubMed], [CAS], Google Scholar111Comparison of density functionals for energy and structural differences between the high- [5T2g:(t2g)4(eg)2] and low- [1A1g:(t2g)6(eg)0] spin states of iron (II) coordination compounds. II. More functionals and the hexaminoferrous cation, [Fe(NH3)6]2+
Fouqueau, Antony; Casida, Mark E.; Daku, Latevi Max Lawson; Hauser, Andreas; Neese, Frank
Journal of Chemical Physics (2005), 122 (4), 044110/1-044110/13CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
The ability of different d. functionals to describe the structural and energy differences between the high- [5T2g:(t2g)4(eg)2] and low- [1A1g:(t2g)6(eg)0] spin states of small octahedral ferrous compds. is studied. This work is an extension of our previous study of the hexaquoferrous cation, [Fe(H2O)6]2+, to include a second compd.-namely, the hexaminoferrous cation, [Fe(NH3)6]2+-and several addnl. functionals. In particular, the present study includes the highly parametrized generalized gradient approxns. (GGAs) known as HCTH and the meta-GGA VSXC [which together we refer to as highly parametrized d. functionals (HPDFs)], now readily available in the GAUSSIAN03 program, as well as the hybrid functional PBE0. Since there are very few exptl. results for these mols. with which to compare, comparison is made with best ests. obtained from second-order perturbation theory-cor. complete active space SCF (CASPT2) calcns., with spectroscopy oriented CI (SORCI) calcns., and with ligand field theory (LFT) estns. While CASPT2 and SORCI are among the most reliable ab initio methods available for this type of problem, LFT embodies many decades of empirical experience. These three methods are found to give coherent results and provide best ests. of the adiabatic low-spin-high-spin energy difference, ΔELHadia, of 12 000-13 000 cm-1 for [Fe(H2O)6]2+ and 9 000-11 000 cm-1 for [Fe(NH3)6]2+. All functionals beyond the purely local approxn. produce reasonably good geometries, so long as adequate basis sets are used. In contrast, the energy splitting, ΔELHadia, is much more sensitive to the choice of functional. The local d. approxn. severely over stabilizes the low-spin state with respect to the high-spin state. This 'd. functional theory (DFT) spin pairing-energy problem' persists, but is reduced, for traditional GGAs. In contrast the hybrid functional B3LYP underestimates ΔELHadia by a few thousands of wave nos. The RPBE GGA of Hammer, Hansen, and Norskov gives good results for ΔELHadia as do the HPDFs, esp. the VSXC functional. Surprisingly the HCTH functionals actually over correct the DFT spin pairing-energy problem, destabilizing the low-spin state relative to the high-spin state. Best agreement is found for the hybrid functional PBE0.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXht12gs78%253D&md5=35804dbc0bc4ee59241e818f13e2883f112Droghetti, A.; Alfè, D.; Sanvito, S.Assessment of Density Functional Theory for Iron (II) Molecules across the Spin-Crossover Transition. J. Chem. Phys.2012, 137, 124303, DOI: 10.1063/1.4752411[Crossref], [PubMed], [CAS], Google Scholar112Assessment of density functional theory for iron(II) molecules across the spin-crossover transition
Journal of Chemical Physics (2012), 137 (12), 124303/1-124303/12CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
Octahedral Fe2+ mols. are particularly interesting as they often exhibit a spin-crossover transition. In spite of the many efforts aimed at assessing the performances of d. functional theory for such systems, an exchange-correlation functional able to account accurately for the energetic of the various possible spin-states has not been identified yet. Here, we critically discuss the issues related to the theor. description of this class of mols. from first principles. In particular, we present a comparison between different d. functionals for four ions, namely, Fe(H2O)62+, Fe(NH3)62+, Fe(NCH)62+, and Fe(CO)62+. These are characterized by different ligand-field splittings and ground state spin multiplicities. Since no exptl. data are available for the gas phase, the d. functional theory results are benchmarked against those obtained with diffusion Monte Carlo, one of the most accurate methods available to compute ground state total energies of quantum systems. On the one hand, we show that most of the functionals considered provide a good description of the geometry and of the shape of the potential energy surfaces. On the other hand, the same functionals fail badly in predicting the energy differences between the various spin states. In the case of Fe(H2O)62+, Fe(NH3)62+, Fe(NCH)62+, this failure is related to the drastic underestimation of the exchange energy. Therefore, quite accurate results can be achieved with hybrid functionals including about 50% of Hartree-Fock exchange. In contrast, in the case of Fe(CO)62+, the failure is likely to be caused by the multiconfigurational character of the ground state wave-function and no suitable exchange and correlation functional has been identified. (c) 2012 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xhtl2kur3P&md5=f2531095b13d0df7a15c8a8df36ee6c7113Gani, T. Z. H.; Kulik, H. J.Unifying Exchange Sensitivity in Transition Metal Spin-State Ordering and Catalysis through Bond Valence Metrics. J. Chem. Theory Comput.2017, 13, 5443– 5457, DOI: 10.1021/acs.jctc.7b00848[ACS Full Text ], [CAS], Google Scholar113Unifying Exchange Sensitivity in Transition-Metal Spin-State Ordering and Catalysis through Bond Valence Metrics
Journal of Chemical Theory and Computation (2017), 13 (11), 5443-5457CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Accurate predictions of spin-state ordering, reaction energetics, and barrier heights are crit. for the computational discovery of open-shell transition-metal (TM) catalysts. Semilocal approxns. in d. functional theory, such as the generalized gradient approxn. (GGA), suffer from delocalization error that causes them to overstabilize strongly bonded states. Descriptions of energetics and bonding are often improved by introducing a fraction of exact exchange (e.g., erroneous low-spin GGA ground states are instead correctly predicted as high-spin with a hybrid functional). The degree of spin-splitting sensitivity to exchange can be understood based on the chem. compn. of the complex, but the effect of exchange on reaction energetics within a single spin state is less well-established. Across a no. of model iron complexes, we observe strong exchange sensitivities of reaction barriers and energies that are of the same magnitude as those for spin splitting energies. We rationalize trends in both reaction and spin energetics by introducing a measure of delocalization, the bond valence of the metal-ligand bonds in each complex. The bond valence thus represents a simple-to-compute property that unifies understanding of exchange sensitivity for catalytic properties and spin-state ordering in TM complexes. Close agreement of the resulting per-metal-org.-bond sensitivity ests., together with failure of alternative descriptors demonstrates the utility of the bond valence as a robust descriptor of how differences in metal-ligand delocalization produce differing relative energetics with exchange tuning. Our unified description explains the overall effect of exact exchange tuning on the paradigmatic two-state FeO+/CH4 reaction that combines challenges of spin-state and reactivity predictions. This new descriptor-sensitivity relationship provides a path to quantifying how predictions in transition-metal complex screening are sensitive to the method used.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhs1yhsbvM&md5=0b3666cf2f06530da16efaed7230ded7114Cramer, C. J.; Truhlar, D. G.Density Functional Theory for Transition Metals and Transition Metal Chemistry. Phys. Chem. Chem. Phys.2009, 11, 10757– 10816, DOI: 10.1039/b907148b[Crossref], [PubMed], [CAS], Google Scholar114Density functional theory for transition metals and transition metal chemistry
Physical Chemistry Chemical Physics (2009), 11 (46), 10757-10816CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
A review. We introduce d. functional theory and review recent progress in its application to transition metal chem. Topics covered include local, meta, hybrid, hybrid meta, and range-sepd. functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including mols., clusters, nanoparticles, surfaces, and solids.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhsVentrfK&md5=3bb9a3202e5d1493390a1ad863f60c4c115Ioannidis, E. I.; Kulik, H. J.Ligand-Field-Dependent Behavior of Meta-GGA Exchange in Transition-Metal Complex Spin-State Ordering. J. Phys. Chem. A2017, 121, 874– 884, DOI: 10.1021/acs.jpca.6b11930[ACS Full Text ], [CAS], Google Scholar115Ligand-Field-Dependent Behavior of Meta-GGA Exchange in Transition-Metal Complex Spin-State Ordering
Journal of Physical Chemistry A (2017), 121 (4), 874-884CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
Prediction of spin-state ordering in transition metal complexes is essential for understanding catalytic activity and designing functional materials. Semi-local approxns. in d. functional theory, such as the generalized-gradient approxn. (GGA), suffer from delocalization error that gives rise to systematic bias for low-spin electronic states. Incorporation of exact exchange is known to counteract this bias, instead favoring high-spin states, in a manner that has recently been identified to be ligand-field dependent. In this work, we introduce a tuning strategy to identify the effect of incorporating the Laplacian of the d. (i.e., a meta-GGA) in exchange on spin-state ordering. We employ a diverse test set of M(II) and M(III) first-row transition metal ions from Ti to Cu as well as octahedral complexes of these ions with ligands of increasing field strength (i.e., H2O, NH3, and CO). We show that the sensitivity of spin-state ordering to meta-GGA exchange is highly ligand-field dependent, stabilizing high-spin states in strong-field (i.e., CO) cases and stabilizing low-spin states in weak-field (i.e., H2O, NH3, and isolated ions) cases. This diverging behavior leads to generally improved treatment of isolated ions and strong field complexes over a std. GGA but worsened treatment for the hexa-aqua or hexa-ammine complexes. These observations highlight the sensitivity of functional performance to subtle changes in chem. bonding.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXkvVKluw%253D%253D&md5=24bab166153fdb361bc4d2c248d08257116Ioannidis, E. I.; Kulik, H. J.Towards Quantifying the Role of Exact Exchange in Predictions of Transition Metal Complex Properties. J. Chem. Phys.2015, 143, 034104, DOI: 10.1063/1.4926836[Crossref], [PubMed], [CAS], Google Scholar116Towards quantifying the role of exact exchange in predictions of transition metal complex properties
Journal of Chemical Physics (2015), 143 (3), 034104/1-034104/11CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
We est. the prediction sensitivity with respect to Hartree-Fock exchange in approx. d. functionals for representative Fe(II) and Fe(III) octahedral complexes. Based on the observation that the range of parameters spanned by the most widely employed functionals is relatively narrow, we compute electronic structure property and spin-state orderings across a relatively broad range of Hartree-Fock exchange (0%-50%) ratios. For the entire range considered, we consistently observe linear relationships between spin-state ordering that differ only based on the element of the direct ligand and thus may be broadly employed as measures of functional sensitivity in predictions of organometallic compds. The role Hartree-Fock exchange in hybrid functionals is often assumed to play is to correct self-interaction error-driven electron delocalization (e.g., from transition metal centers to neighboring ligands). Surprisingly, we instead observe that increasing Hartree-Fock exchange reduces charge on iron centers, corresponding to effective delocalization of charge to ligands, thus challenging notions of the role of Hartree-Fock exchange in shifting predictions of spin-state ordering. (c) 2015 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtFOksLrJ&md5=049f548f340da52dbbfdf01985bb9149117Tortorella, S.; Marotta, G.; Cruciani, G.; De Angelis, F.Quantitative Structure-Property Relationship Modeling of Ruthenium Sensitizers for Solar Cells Applications: Novel Tools for Designing Promising Candidates. RSC Adv.2015, 5, 23865– 23873, DOI: 10.1039/C5RA01906K[Crossref], [CAS], Google Scholar117Quantitative structure-property relationship modeling of ruthenium sensitizers for solar cells applications: novel tools for designing promising candidates
Tortorella, Sara; Marotta, Gabriele; Cruciani, Gabriele; De Angelis, Filippo
RSC Advances (2015), 5 (30), 23865-23873CODEN: RSCACL; ISSN:2046-2069. (Royal Society of Chemistry)
To date, the most common way of screening new potential sensitizers for dye sensitized solar cells is via the traditional time and money consuming trial and error approach. In this study we explore the possibility of extending drug discovery and cheminformatic approaches to the field of material science with the aim of a quant. structure-property relationship elucidation that could lead to a fast and inexpensive in silico screening of new ruthenium sensitizers for third generation solar cells. Starting from the building of a database of already tested candidates used to train the predictive models, appropriate descriptors extd. from images of 3D mol. interaction fields (GRID/MIFs), as well as semi-empirical calcd. descriptors, were chosen to describe the target structures. Then, structure-performance (Jsc, Voc and PCE) models were built and analyzed in order to elucidate structure-property relationships and interesting results were obtained. In particular, we were able to find the mol. descriptors that more contribute to enhance the performance investigated, thus finding directives for the design of potentially high-performing candidates. We also proposed an efficient correction of the exptl. Jsc and Voc based on the quantity of the LiI additive for electrolyte used to build the devices. In the early stage of this project, we demonstrated that mol. modeling methods could be successfully extended to the field of material science as alternative to the traditional expensive and time-consuming trial and error approach.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXjtlWnt78%253D&md5=17b9f7325749b253c92d6404d0d6c813118Cruz, V. L.; Martinez, S.; Ramos, J.; Martinez-Salazar, J.3D-QSAR as a Tool for Understanding and Improving Single-Site Polymerization Catalysts. A Review. Organometallics2014, 33, 2944– 2959, DOI: 10.1021/om400721v[ACS Full Text ], [CAS], Google Scholar1183D-QSAR as a Tool for Understanding and Improving Single-Site Polymerization Catalysts. A Review
Cruz, Victor L.; Martinez, Sonia; Ramos, Javier; Martinez-Salazar, Javier
Organometallics (2014), 33 (12), 2944-2959CODEN: ORGND7; ISSN:0276-7333. (American Chemical Society)
A review. This paper reviews the findings of quant. structure-activity relationship (QSAR) studies focusing on single-site polymn. catalysts, with special attention paid to the use of 3D-QSAR tools. Such tools reveal the fine details of catalyst structure that may be correlated with polymn. activity or the properties of the synthesized polymer. The introduction of effective single-site polymn. catalysts, in addn. to allowing scientists to synthesize new tailor-made polymers, has enabled a detailed theor. anal. of the synthesis process. The benefits of single-site polymn. for theor. studies include easy elucidation of the catalyst structure, a well-defined mechanism of action, and the fact that expts. can be systematically conducted on catalyst series featuring different substitution patterns. Using QSAR methods, exptl. results can be related to theor. measurements through statistical or chemometric tools. These tools have been extensively and successfully used in the field of drug design.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXpsFejsLw%253D&md5=90097f911091bd4c45e7ae17b418901b119Fey, N.; Orpen, A. G.; Harvey, J. N.Building Ligand Knowledge Bases for Organometallic Chemistry: Computational Description of Phosphorus (III)-Donor Ligands and the Metal–Phosphorus Bond. Coord. Chem. Rev.2009, 253, 704– 722, DOI: 10.1016/j.ccr.2008.04.017[Crossref], [CAS], Google Scholar119Building ligand knowledge bases for organometallic chemistry: Computational description of phosphorus(III)-donor ligands and the metal-phosphorus bond
Coordination Chemistry Reviews (2009), 253 (5+6), 704-722CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)
A review. Changing the coordinated ligands is a powerful and synthetically convenient way of modifying and fine-tuning the properties of transition metal complexes, esp. those active in homogeneous catalysis. Parameters capturing such changes in the steric and electronic characteristics of complexes have played a key role in improving the authors' understanding of ligand effects on the kinetic, thermodn., spectroscopic and structural behavior of such species. Such ligand parameters can be useful for interpreting expts., but they can also guide the discovery of novel ligands from ligand maps and allow the prediction of ligand effects before further experimentation. The latter aims esp. are best served if such parameters can be detd. before ligands and complexes were synthesized, and here the authors review calcd. descriptors for P(III) ligands as widely used in organometallic and coordination chem. The authors also discuss the application of such ligand descriptors in models, maps and predictions of ligand effects, describe related computational studies of the metal-P bond, and provide an overview of the statistical methods used.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXisFSksL8%253D&md5=0880c3e55c8f1594b2dabde2abced6d7120Venkatraman, V.; Abburu, S.; Alsberg, B. K.Artificial Evolution of Coumarin Dyes for Dye Sensitized Solar Cells. Phys. Chem. Chem. Phys.2015, 17, 27672– 27682, DOI: 10.1039/C5CP04624F[Crossref], [CAS], Google Scholar120Artificial evolution of coumarin dyes for dye sensitized solar cells
Venkatraman, Vishwesh; Abburu, Sailesh; Alsberg, Bjoern Kaare
Physical Chemistry Chemical Physics (2015), 17 (41), 27672-27682CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
The design and discovery of novel mol. structures with optimal properties has been an ongoing effort for materials scientists. This field has in general been dominated by expt. driven trial-and-error approaches that are often expensive and time-consuming. Here, it is investigated if a de novo computational design methodol. can be applied to the design of coumarin-based dye sensitizers with improved properties for use in Gratzel solar cells. To address the issue of synthetic accessibility of the designed compds., a fragment-based assembly is employed, wherein the combination of chem. motifs (derived from the existing databases of structures) is carried out with respect to user-adaptable set of rules. Rather than using computationally intensive d. functional theory (DFT)/ab initio methods to screen candidate dyes, quant. structure-property relationship (QSPR) models (calibrated from empirical data) are employed for rapid estn. of the property of interest, which in this case is the product of short circuit current (Jsc) and open circuit voltage (Voc). Since QSPR models have limited validity, pre-detd. applicability domain criteria are used to prevent unacceptable extrapolation. DFT anal. of the top-ranked structures provides supporting evidence of their potential for dye sensitized solar cell applications.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsFamsb%252FI&md5=efe96c9e44d82e09bbb1e7df317c5caa121Allen, F. H.The Cambridge Structural Database: A Quarter of a Million Crystal Structures and Rising. Acta Crystallogr., Sect. B: Struct. Sci.2002, 58, 380– 388, DOI: 10.1107/S0108768102003890[Crossref], [PubMed], [CAS], Google Scholar121The Cambridge Structural Database: a quarter of a million crystal structures and rising
Acta Crystallographica, Section B: Structural Science (2002), B58 (3, No. 1), 380-388CODEN: ASBSDK; ISSN:0108-7681. (Blackwell Munksgaard)
The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-mol. crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chem. information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500000 crystal structures by the year 2010.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XktVOqu74%253D&md5=406cd0df6ea9035a0ebf8dd9eccbd1f8122Janet, J. P.; Kulik, H. J.Resolving Transition Metal Chemical Space: Feature Selection for Machine Learning and Structure-Property Relationships. J. Phys. Chem. A2017, 121, 8939– 8954, DOI: 10.1021/acs.jpca.7b08750[ACS Full Text ], [CAS], Google Scholar122Resolving Transition Metal Chemical Space: Feature Selection for Machine Learning and Structure-Property Relationships
Journal of Physical Chemistry A (2017), 121 (46), 8939-8954CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
Machine learning (ML) of quantum mech. properties shows promise for accelerating chem. discovery. For transition metal chem. where accurate calcns. are computationally costly and available training data sets are small, the mol. representation becomes a crit. ingredient in ML model predictive accuracy. We introduce a series of revised autocorrelation functions (RACs) that encode relationships of the heuristic at. properties (e.g., size, connectivity, and electronegativity) on a mol. graph. We alter the starting point, scope, and nature of the quantities evaluated in std. ACs to make these RACs amenable to inorg. chem. On an org. mol. set, we first demonstrate superior std. AC performance to other presently available topol. descriptors for ML model training, with mean unsigned errors (MUEs) for atomization energies on set-aside test mols. as low as 6 kcal/mol. For inorg. chem., our RACs yield 1 kcal/mol ML MUEs on set-aside test mols. in spin-state splitting in comparison to 15-20× higher errors for feature sets that encode whole-mol. structural information. Systematic feature selection methods including univariate filtering, recursive feature elimination, and direct optimization (e.g., random forest and LASSO) are compared. Random-forest- or LASSO-selected subsets 4-5× smaller than the full RAC set produce sub- to 1 kcal/mol spin-splitting MUEs, with good transferability to metal-ligand bond length prediction (0.004-5 Å MUE) and redox potential on a smaller data set (0.2-0.3 eV MUE). Evaluation of feature selection results across property sets reveals the relative importance of local, electronic descriptors (e.g., electronegativity, at. no.) in spin-splitting and distal, steric effects in redox potential and bond lengths.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhslGhsLnL&md5=5da87c7a2084fd54de3d4ebe1bf9330c123Janet, J. P.; Kulik, H. J.Predicting Electronic Structure Properties of Transition Metal Complexes with Neural Networks. Chem. Sci.2017, 8, 5137– 5152, DOI: 10.1039/C7SC01247K[Crossref], [PubMed], [CAS], Google Scholar123Predicting electronic structure properties of transition metal complexes with neural networks
Chemical Science (2017), 8 (7), 5137-5152CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)
High-throughput computational screening has emerged as a crit. component of materials discovery. Direct d. functional theory (DFT) simulation of inorg. materials and mol. transition metal complexes is often used to describe subtle trends in inorg. bonding and spin-state ordering, but these calcns. are computationally costly and properties are sensitive to the exchange-correlation functional employed. To begin to overcome these challenges, we trained artificial neural networks (ANNs) to predict quantum-mech.-derived properties, including spin-state ordering, sensitivity to Hartree-Fock exchange, and spin-state specific bond lengths in transition metal complexes. Our ANN is trained on a small set of inorg.-chem.-appropriate empirical inputs that are both maximally transferable and do not require precise three-dimensional structural information for prediction. Using these descriptors, our ANN predicts spin-state splittings of single-site transition metal complexes (i.e., Cr-Ni) at arbitrary amts. of Hartree-Fock exchange to within 3 kcal mol-1 accuracy of DFT calcns. Our exchange-sensitivity ANN enables improved predictions on a diverse test set of exptl.-characterized transition metal complexes by extrapolation from semi-local DFT to hybrid DFT. The ANN also outperforms other machine learning models (i.e., support vector regression and kernel ridge regression), demonstrating particularly improved performance in transferability, as measured by prediction errors on the diverse test set. We establish the value of new uncertainty quantification tools to est. ANN prediction uncertainty in computational chem., and we provide addnl. heuristics for identification of when a compd. of interest is likely to be poorly predicted by the ANN. The ANNs developed in this work provide a strategy for screening transition metal complexes both with direct ANN prediction and with improved structure generation for validation with first principles simulation.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXotVCgsrY%253D&md5=83fb0e4026c680b8e68e63a374dd0358124Nandy, A.; Duan, C.; Janet, J. P.; Gugler, S.; Kulik, H. J.Strategies and Software for Machine Learning Accelerated Discovery in Transition Metal Chemistry. Ind. Eng. Chem. Res.2018, 57, 13973– 13986, DOI: 10.1021/acs.iecr.8b04015[ACS Full Text ], [CAS], Google Scholar124Strategies and Software for Machine Learning Accelerated Discovery in Transition Metal Chemistry
Nandy, Aditya; Duan, Chenru; Janet, Jon Paul; Gugler, Stefan; Kulik, Heather J.
Industrial & Engineering Chemistry Research (2018), 57 (42), 13973-13986CODEN: IECRED; ISSN:0888-5885. (American Chemical Society)
Machine learning the electronic structure of open shell transition metal complexes presents unique challenges, including robust and automated data set generation. Here, we introduce tools that simplify data acquisition from d. functional theory (DFT) and validation of trained machine learning models using the molSimplify automatic design (mAD) workflow. We demonstrate this workflow by training and comparing the performance of LASSO, kernel ridge regression (KRR), and artificial neural network (ANN) models using heuristic, topol. revised autocorrelation (RAC) descriptors we have recently introduced for machine learning inorg. chem. On a series of open shell transition metal complexes, we evaluate set aside test errors of these models for predicting the HOMO level and HOMO-LUMO gap. The best performing models are ANNs, which show 0.15 and 0.25 eV test set mean abs. errors on the HOMO level and HOMO-LUMO gap, resp. Poor performing KRR models using the full 153-feature RAC set are improved to nearly the same performance as the ANNs when trained on down-selected subsets of 20-30 features. Anal. of the essential descriptors for HOMO level and HOMO-LUMO gap prediction as well as comparison to subsets previously obtained for other properties reveal the paramount importance of nonlocal, steric properties in detg. frontier MO energetics. We demonstrate our model performance on diverse complexes and in the discovery of mols. with target HOMO-LUMO gaps from a large 15,000 mol. design space in minutes rather than days that full DFT evaluation would require.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhslOqsr3I&md5=23e996b0a37eadc2588a104a17ba5470125Ioannidis, E. I.; Gani, T. Z. H.; Kulik, H. J.molSimplify: A Toolkit for Automating Discovery in Inorganic Chemistry. J. Comput. Chem.2016, 37, 2106– 2117, DOI: 10.1002/jcc.24437[Crossref], [PubMed], [CAS], Google Scholar125molSimplify: A toolkit for automating discovery in inorganic chemistry
Ioannidis, Efthymios I.; Gani, Terry Z. H.; Kulik, Heather J.
Journal of Computational Chemistry (2016), 37 (22), 2106-2117CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
We present an automated, open source toolkit for the first-principles screening and discovery of new inorg. mols. and intermol. complexes. Challenges remain in the automatic generation of candidate inorg. mol. structures due to the high variability in coordination and bonding, which we overcome through a divide-and-conquer tactic that flexibly combines force-field preoptimization of org. fragments with alignment to first-principles-trained metal-ligand distances. Exploration of chem. space is enabled through random generation of ligands and intermol. complexes from large chem. databases. We validate the generated structures with the root mean squared (RMS) gradients evaluated from d. functional theory (DFT), which are around 0.02 Ha/au across a large 150 mol. test set. Comparison of molSimplify results to full optimization with the universal force field reveals that RMS DFT gradients are improved by 40%. Seamless generation of input files, prepn. and execution of electronic structure calcns., and post-processing for each generated structure aids interpretation of underlying chem. and energetic trends. © 2016 Wiley Periodicals, Inc.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtV2gu7bN&md5=8963dad8dc0f6da848871be864ef7e09126Liu, F.; Yang, T.; Yang, J.; Xu, E.; Bajaj, A.; Kulik, H. J., Bridging the Homogeneous–Heterogeneous Divide: Modeling Spin and Reactivity in Single Atom Catalysis. Submitted.Google ScholarThere is no corresponding record for this reference.
127Pritchard, B.; Autschbach, J.Theoretical Investigation of Paramagnetic NMR Shifts in Transition Metal Acetylacetonato Complexes: Analysis of Signs, Magnitudes, and the Role of the Covalency of Ligand–Metal Bonding. Inorg. Chem.2012, 51, 8340– 8351, DOI: 10.1021/ic300868v[ACS Full Text ], [CAS], Google Scholar127Theoretical Investigation of Paramagnetic NMR Shifts in Transition Metal Acetylacetonato Complexes: Analysis of Signs, Magnitudes, and the Role of the Covalency of Ligand-Metal Bonding
Inorganic Chemistry (2012), 51 (15), 8340-8351CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
Ligand chem. shifts are calcd. and analyzed for three paramagnetic transition metal tris-acetylacetonato (acac) complexes, high-spin Fe(III) and Cr(III), and low-spin Ru(III), using scalar relativistic d. functional theory (DFT). The signs and magnitudes of the paramagnetic NMR ligand chem. shifts are directly related to the extent of covalent acac oxygen-to-metal σ donation involving unoccupied metal valence dσ acceptor orbitals. The role of delocalization of metal-centered spin d. over the ligand atoms plays a minor secondary role. Of particular interest is the origin of the sign and magnitude of the Me carbon chem. shift in the acac ligands, and the role played by the DFT delocalization error when calcg. such shifts. The α vs. β spin balance of oxygen σ donation to metal valence d acceptor orbitals is responsible for the sign and the magnitude of the ligand Me carbon chem. shift. A problematic case is the Me carbon shift of Fe(acac)3. Most functionals produce shifts >1400 ppm, whereas the exptl. shift is ∼279 ppm. Range-sepd. hybrid functionals that are optimally tuned for Fe(acac)3 based on DFT energetic criteria predict a lower limit of ∼2000 ppm for the Me carbon shift of the high-spin electronic configuration. Since the exptl. value is based on a very strongly broadened signal it is possibly unreliable.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtV2gsrrM&md5=f32b42adf95295c8e605888e154e0417128Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J.Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields. J. Phys. Chem.1994, 98, 11623– 11627, DOI: 10.1021/j100096a001[ACS Full Text ], [CAS], Google Scholar128Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields
Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J.
Journal of Physical Chemistry (1994), 98 (45), 11623-7CODEN: JPCHAX; ISSN:0022-3654.
The unpolarized absorption and CD spectra of the fundamental vibrational transitions of the chiral mol. 4-methyl-2-oxetanone are calcd. ab initio. Harmonic force fields are obtained using d. functional theory (DFT), MP2 and SCF methodologies, and a [5s4p2d/3s2p] (TZ2P) basis set. DFT calcns. use the LSDA, BLYP, and Becke3LYP (B3LYP) d. functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with expt. The MP2 force field yields spectra in slightly worse agreement with expt. than the B3LYP force field. The SCF force field yields spectra in poor agreement with expt. The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreement with expt.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2cXmvVSitbY%253D&md5=93486da1864d900b4527d020cf36171f129Becke, A. D.Density-Functional Thermochemistry. III. The Role of Exact Exchange. J. Chem. Phys.1993, 98, 5648– 5652, DOI: 10.1063/1.464913[Crossref], [CAS], Google Scholar129Density-functional thermochemistry. III. The role of exact exchange
Journal of Chemical Physics (1993), 98 (7), 5648-52CODEN: JCPSA6; ISSN:0021-9606.
Despite the remarkable thermochem. accuracy of Kohn-Sham d.-functional theories with gradient corrections for exchange-correlation, the author believes that further improvements are unlikely unless exact-exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange-correlation functional (contg. local-spin-d., gradient, and exact-exchange terms) is tested for 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total at. energies of first- and second-row systems. This functional performs better than previous functionals with gradient corrections only, and fits expt. atomization energies with an impressively small av. abs. deviation of 2.4 kcal/mol.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK3sXisVWgtrw%253D&md5=291bbfc119095338bb1624f0c21c7ca8130Lee, C.; Yang, W.; Parr, R. G.Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density. Phys. Rev. B: Condens. Matter Mater. Phys.1988, 37, 785– 789, DOI: 10.1103/PhysRevB.37.785[Crossref], [PubMed], [CAS], Google Scholar130Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
Physical Review B: Condensed Matter and Materials Physics (1988), 37 (2), 785-9CODEN: PRBMDO; ISSN:0163-1829.
A correlation-energy formula due to R. Colle and D. Salvetti (1975), in which the correlation energy d. is expressed in terms of the electron d. and a Laplacian of the 2nd-order Hartree-Fock d. matrix, is restated as a formula involving the d. and local kinetic-energy d. On insertion of gradient expansions for the local kinetic-energy d., d.-functional formulas for the correlation energy and correlation potential are then obtained. Through numerical calcns. on a no. of atoms, pos. ions, and mols., of both open- and closed-shell type, it is demonstrated that these formulas, like the original Colle-Salvetti formulas, give correlation energies within a few percent.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL1cXktFWrtbw%253D&md5=ee7b59267a2ff72e15171a481819ccf8131Hay, P. J.; Wadt, W. R.Ab Initio Effective Core Potentials for Molecular Calculations. Potentials for the Transition Metal Atoms Sc to Hg. J. Chem. Phys.1985, 82, 270– 283, DOI: 10.1063/1.448799[Crossref], [CAS], Google Scholar131Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms scandium to mercury
Journal of Chemical Physics (1985), 82 (1), 270-83CODEN: JCPSA6; ISSN:0021-9606.
Ab initio effective core potentials (ECP's) were generated to replace the Coulomb, exchange, and core-orthogonality effects of the chem. inert core electron in the transition metal atoms Sc to Hg. For the second and third transition series relative ECP's were generated which also incorporate the mass-velocity and Darwin relativistic effects into the potential. The ab initio ECP's should facilitate valence electron calcns. on mols. contg. transition-metal atoms with accuracies approaching all-electron calcns. at a fraction of the computational cost. Analytic fits to the potentials are presented for use in multicenter integral evaluation. Gaussian orbital valence basis sets are developed for the (3d,4s,4p), (4d,5s,5p), and (5d,6s,6p) orbitals of the first, second, and third transition series atoms, resp. All-electron and valence-electron at. excitation energies are also compared for the low-lying states of Sc-Hg, and the valence-electron calcns. reproduce the all-electron excitation energies (typically within a few tenths of an eV).
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2MXhtlyju70%253D&md5=29271d2a54b5c81acd19762c570e64d7132Janet, J. P.; Gani, T. Z. H.; Steeves, A. H.; Ioannidis, E. I.; Kulik, H. J.Leveraging Cheminformatics Strategies for Inorganic Discovery: Application to Redox Potential Design. Ind. Eng. Chem. Res.2017, 56, 4898– 4910, DOI: 10.1021/acs.iecr.7b00808[ACS Full Text ], [CAS], Google Scholar132Leveraging Cheminformatics Strategies for Inorganic Discovery: Application to Redox Potential Design
Janet, Jon Paul; Gani, Terry Z. H.; Steeves, Adam H.; Ioannidis, Efthymios I.; Kulik, Heather J.
Industrial & Engineering Chemistry Research (2017), 56 (17), 4898-4910CODEN: IECRED; ISSN:0888-5885. (American Chemical Society)
Virtual high throughput screening, typically driven by first-principles, d. functional theory calcns., has emerged as a powerful tool for the discovery of new materials. Although the computational materials science community has benefited from open source tools for the rapid structure generation, calcn., and anal. of cryst. inorg. materials, software and strategies to address the unique challenges of inorg. complex discovery have not been as widely available. We present a unified view of our recent developments in the open source molSimplify code for inorg. discovery. Building on our previous efforts in the automated generation of highly accurate inorg. mol. structures, first-principles simulation, and property anal. to accelerate high-throughput screening, we have recently incorporated a neural network that both improves structure generation and predicts electronic properties prior to first-principles calcn. We also provide an overview of how multimillion mol. org. libraries can be leveraged for inorg. discovery alongside cheminformatics concepts of mol. diversity in order to efficiently traverse chem. space. We demonstrate all of these tools on the discovery of design rules for octahedral Fe(II/III) redox couples with nitrogen ligands. Over a search of only approx. 40 new mols., we obtain redox potentials relative to the Fc/Fc+ couple ranging from -1 to 4.5 V in aq. soln. Our new automated correlation anal. reveals heteroatom identity and the degree of structural branching to be key ligand descriptors in detg. redox potential. This inorg. discovery toolkit provides a promising approach to advancing transition metal complex design.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXls1Snsrg%253D&md5=e3fd8c1374593e68ef94838197ff73a4133Klamt, A.; Schuurmann, G.Cosmo: A New Approach to Dielectric Screening in Solvents with Explicit Expressions for the Screening Energy and Its Gradient. J. Chem. Soc., Perkin Trans. 21993, 2, 799– 805, DOI: 10.1039/P29930000799[Crossref], Google ScholarThere is no corresponding record for this reference.
134Liu, F.; Luehr, N.; Kulik, H. J.; Martínez, T. J.Quantum Chemistry for Solvated Molecules on Graphical Processing Units Using Polarizable Continuum Models. J. Chem. Theory Comput.2015, 11, 3131– 3144, DOI: 10.1021/acs.jctc.5b00370[ACS Full Text ], [CAS], Google Scholar134Quantum Chemistry for Solvated Molecules on Graphical Processing Units Using Polarizable Continuum Models
Liu, Fang; Luehr, Nathan; Kulik, Heather J.; Martinez, Todd J.
Journal of Chemical Theory and Computation (2015), 11 (7), 3131-3144CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chem. simulations. However, its application in quantum mech. calcns. of large-scale biomol. systems can be limited by computational expense of both the gas phase electronic structure and the solvation interaction. The authors have previously used graphical processing units (GPUs) to accelerate the first of these steps. Here, the authors extend the use of GPUs to accelerate electronic structure calcns. including C-PCM solvation. Implementation on the GPU leads to significant acceleration of the generation of the required integrals for C-PCM. The authors further propose two strategies to improve the soln. of the required linear equations: a dynamic convergence threshold and a randomized block-Jacobi preconditioner. These strategies are not specific to GPUs and are expected to be beneficial for both CPU and GPU implementations. The authors benchmark the performance of the new implementation using over 20 small proteins in solvent environment. Using a single GPU, the authors' method evaluates the C-PCM related integrals and their derivs. >10× faster than that with a conventional CPU-based implementation. The authors' improvements to the linear solver provide a further 3× acceleration. The overall calcns. including C-PCM solvation require, typically, 20-40% more effort than that for their gas phase counterparts for a moderate basis set and mol. surface discretization level. The relative cost of the C-PCM solvation correction decreases as the basis sets and/or cavity radii increase. Therefore, description of solvation with this model should be routine. The authors also discuss applications to the study of the conformational landscape of an amyloid fibril.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtVaksbvL&md5=5ae2f3b82c19a302b7cae538cf623a72135Konezny, S. J.; Doherty, M. D.; Luca, O. R.; Crabtree, R. H.; Soloveichik, G. L.; Batista, V. S.Reduction of Systematic Uncertainty in DFT Redox Potentials of Transition-Metal Complexes. J. Phys. Chem. C2012, 116, 6349– 6356, DOI: 10.1021/jp300485t[ACS Full Text ], [CAS], Google Scholar135Reduction of Systematic Uncertainty in DFT Redox Potentials of Transition-Metal Complexes
Konezny, Steven J.; Doherty, Mark D.; Luca, Oana R.; Crabtree, Robert H.; Soloveichik, Grigorii L.; Batista, Victor S.
Journal of Physical Chemistry C (2012), 116 (10), 6349-6356CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
Reliable calcns. of redox potentials could provide valuable insight into catalytic mechanisms of electrochem. active transition-metal complexes as well as guidelines for the design of new electrocatalysts. However, the correlation between theor. and exptl. data is often uncertain, since redox properties depend strongly on exptl. conditions of electrochem. measurements, including the nature of the solvent, electrolyte, and working electrode. Here, the use of internal refs. allows for quant. theor. predictions of redox potentials with std. deviations σ comparable to typical exptl. errors of cyclic voltammetry measurements. Agreement for 1st-, 2nd-, and 3rd-row transition-metal complexes is demonstrated even at a rather modest level of d. functional theory (σ = 64 mV for the UB3LYP/6-311G* level). This is shown for benchmark redox couples, including ([MCp2]0/+ (Cp = η5-cyclopentadienyl), [MCp*2]0/+ (Cp* = η5-1,2,3,4,5-pentamethylcyclopentadienyl), [M(bpy)3]2+/3+ (bpy =2,2'-bipyridine), and [Ir(acac)3]0/+ (acac = acetylacetonate), with M = Fe, Co, Ni, Ru, Os, or Ir) in various nonaq. solvents [acetonitrile (MeCN), DMSO, and CH2Cl2 (DCM)].
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XisFShs7Y%253D&md5=d6404b1f8351da6d38f54369a715d1b3136Roy, L. E.; Jakubikova, E.; Guthrie, M. G.; Batista, E. R.Calculation of One-Electron Redox Potentials Revisited. Is It Possible to Calculate Accurate Potentials with Density Functional Methods?. J. Phys. Chem. A2009, 113, 6745– 6750, DOI: 10.1021/jp811388w[ACS Full Text ], [CAS], Google Scholar136Calculation of One-Electron Redox Potentials Revisited. Is It Possible to Calculate Accurate Potentials with Density Functional Methods?
Roy, Lindsay E.; Jakubikova, Elena; Guthrie, M. Graham; Batista, Enrique R.
Journal of Physical Chemistry A (2009), 113 (24), 6745-6750CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
D. Functional calcns. have been performed to calc. the one-electron oxidn. potential for ferrocene and the redox couples for a series of small transition metal compds. of the first-, second-, and third-row elements. The solvation effects are incorporated via a self-consistent reaction field (SCRF), using the polarized continuum model (PCM). From our study of seven different d. functionals combined with three different basis sets for ferrocene, we find that no d. functional method can reproduce the redox trends from expt. when referencing our results to the exptl. abs. std. hydrogen electrode (SHE) potential. Including addnl. necessary assumptions such as solvation effects does not lead to any conclusion regarding the appropriate functional. However, we propose that if one refs. their transition metal compds. results to the calcd. abs. half-cell potential of ferrocene, they can circumvent the addnl. assumptions necessary to predict a redox couple. Upon employing this method on several organometallic and inorg. complexes, we obtained very good correlation between calcd. and exptl. values (R2 = 0.97), making it possible to predict trends with a high level of confidence. The hybrid functional B3LYP systematically underestimates the redox potential; however, the linear correlation between DFT and expt. is good (R2 = 0.96) when including a baseline shift. This protocol is a powerful tool that allows theor. chemists to predict the redox potential in soln. of several transition metal complexes a priori and aids in the rational design of redox-active catalysts.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXmtF2ktbw%253D&md5=d745a07128c9c61744e10400a62a6ef3137Baik, M.-H.; Friesner, R. A.Computing Redox Potentials in Solution: Density Functional Theory as a Tool for Rational Design of Redox Agents. J. Phys. Chem. A2002, 106, 7407– 7412, DOI: 10.1021/jp025853n[ACS Full Text ], [CAS], Google Scholar137Computing Redox Potentials in Solution: Density Functional Theory as A Tool for Rational Design of Redox Agents
Journal of Physical Chemistry A (2002), 106 (32), 7407-7412CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
High-level d. functional theory in combination with a continuum solvation model was employed to compute std. redox potentials in soln. phase for three different classes of electrochem. active mols.: small org. mols., metallocenes, and M(bpy)3x (M = Fe, Ru, Os; x = +3, +2, +1, 0, -1). Excellent agreement with exptl. detd. redox potentials is found with an av. deviation of ∼150 mV when four different solvents commonly in use for electrochem. measurements were included. To obtain quant. agreement between theory and expt., the use of a large basis set is crucial esp. when the redox couple includes anionic species. Whereas the addn. of diffuse functions improved the results notably, vibrational zero-point-energy corrections and addn. of entropy effects are less important. The computational protocol for computing redox potentials in soln., which was benchmarked, is a powerful and novel tool that will allow a mol.-level understanding of the features dictating the properties of redox-active species.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XltlCntbw%253D&md5=8bb4d98b7e856f3692ac99345090f341138Janet, J. P.; Zhao, Q.; Ioannidis, E. I.; Kulik, H. J.Density Functional Theory for Modeling Large Molecular Adsorbate-Surface Interactions: A Mini-Review and Worked Example. Mol. Simul.2017, 43, 327– 345, DOI: 10.1080/08927022.2016.1258465[Crossref], [CAS], Google Scholar138Density functional theory for modelling large molecular adsorbate-surface interactions: a mini-review and worked example
Janet, Jon Paul; Zhao, Qing; Ioannidis, Efthymios I.; Kulik, Heather J.
Molecular Simulation (2017), 43 (5-6), 327-345CODEN: MOSIEA; ISSN:0892-7022. (Taylor & Francis Ltd.)
First-principles simulation has played an ever-increasing role in the discovery and interpretation of the chem. properties of surface-adsorbate interactions. Nevertheless, key challenges remain for the computational chemist wishing to study surface chem.: modeling the full extent of exptl. conditions, managing computational cost, minimising human effort in simulation set-up and maximising accuracy. This article introduces new tools for streamlining surface chem. simulation set-up and reviews some of the challenges in first-principles, d. functional theory (DFT) simulation of surface phenomena. Furthermore, we provide a worked example of Co tetraphenylporphyrin on Au(1 1 1) in which we analyze electronic and energetic properties with semi-local DFT and compare to predictions made from hybrid functional and the so-called DFT+U correction. Through both review and the worked example, we aim to provide a pedagogical introduction to the challenges and the insight that first-principles simulation can provide in surface chem.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvFKjtLfN&md5=c67fdcedeb2e116dfe3bf04e49ec41e2139Halgren, T. A.Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94. J. Comput. Chem.1996, 17, 490– 519, DOI: 10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P[Crossref], [CAS], Google Scholar139Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
Journal of Computational Chemistry (1996), 17 (5 & 6), 490-519CODEN: JCCHDD; ISSN:0192-8651. (Wiley)
This article introduces MMFF94, the initial published version of the Merck mol. force field (MMFF). It describes the objectives set for MMFF, the form it takes, and the range of systems to which it applies. This study also outlines the methodol. employed in parameterizing MMFF94 and summarizes its performance in reproducing computational and exptl. data. Though similar to MM3 in some respects, MMFF94 differs in ways intended to facilitate application to condensed-phase processes in mol.-dynamics simulations. Indeed, MMFF94 seeks to achieve MM3-like accuracy for small mols. in a combined 'org./protein' force field that is equally applicable to proteins and other systems of biol. significance. A second distinguishing feature is that the core protion of MMFF94 has primarily been derived from high-quality computational approach, nearly all MMFF parameters have been detd. in a mutually consistent fashion from the full set of available computational data. MMFF94 reproduces the computational data used in its parameterization very well. In addn., MMFF94 reproduces exptl. bond lengths (0.014 Å root mean square [rms]), bond angles (1.2° rms), vibrational frequencies (61 cm-1 rms), conformational energies (0.38 kcal/mol rms), and rotational barriers (0.39 kcal/mol rms) very nearly as well as does MM3 for comparable systems. MMFF94 also describes intermol. interactions in hydrogen-bonded systems in a way that closely parallels that given by the highly regarded OPLS force field.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XhvVGmsbk%253D&md5=56fb073477b4f49d1dfbd786fc56a480140Reiher, M.Theoretical Study of the Fe (Phen) 2 (NCS) 2 Spin-Crossover Complex with Reparametrized Density Functionals. Inorg. Chem.2002, 41, 6928– 6935, DOI: 10.1021/ic025891l[ACS Full Text ], [CAS], Google Scholar140Theoretical Study of the Fe(phen)2(NCS)2 Spin-Crossover Complex with Reparametrized Density Functionals
Inorganic Chemistry (2002), 41 (25), 6928-6935CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
The theor. study of spin-crossover compds. is very challenging as those parts of the exptl. findings that concern the electronic structure of these compds. can currently hardly be reproduced because of either tech. limitations of highly accurate ab initio methods or because of inaccuracies of d. functional methods in the prediction of low-spin/high-spin energy splitting. However, calcns. with reparametrized d. functionals on mols. of the thermal spin-crossover type can give improved results when compared with expt. for close-lying states of different spin and are therefore important for, e.g., transition metal catalysis. A classification of transition metal compds. within hybrid d. functional theory is given to distinguish std., crit., and complicated cases. From the class of complicated cases we choose the prominent spin-crossover compd. Fe(phen)2(NCS)2 and show in a first step how the electronic contribution to the energy splitting can be calcd. In a second step, the vibrational effects on the spin flip are investigated within the harmonic force-field approxn. of the isolated-mol. approach. A main result of the study is the necessity of exact-exchange redn. in hybrid d. functionals to arrive at reasonable electronic energy splittings. The study resolves problems that originated from the use of std. d. functionals, which are not able to reproduce the electronic contribution to the low-spin/high-spin splitting correctly, and demonstrates to which extent reparametrized d. functionals can be used for the prediction of the spin-crossover effect.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38Xoslaqtbw%253D&md5=ebc3252d68752bf1a679792f21010774141Fouqueau, A.; Mer, S.; Casida, M. E.; Lawson Daku, L. M.; Hauser, A.; Mineva, T.; Neese, F.Comparison of Density Functionals for Energy and Structural Differences between the High- [5t2g: (T2g)4(Eg)2] and Low- [1a1g: (T2g)6(Eg)0] Spin States of the Hexaquoferrous Cation [Fe(H2O)6]2. J. Chem. Phys.2004, 120, 9473– 9486, DOI: 10.1063/1.1710046[Crossref], [PubMed], [CAS], Google Scholar141Comparison of density functionals for energy and structural differences between the high- [5T2g: (t2g)4(eg)2] and low- [1A1g: (t2g)6(eg)0] spin states of the hexaquoferrous cation [Fe(H2O)6]2+
Fouqueau, Antony; Mer, Sebastien; Casida, Mark E.; Lawson Daku, Latevi Max; Hauser, Andreas; Mineva, Tsonka; Neese, Frank
Journal of Chemical Physics (2004), 120 (20), 9473-9486CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
A comparison of d. functionals is made for the calcn. of energy and geometry differences for the high- [5T2g: (t2g)4(eg)2] and low- [1A1g: (t2g)6(eg)0] spin states of the hexaquoferrous cation [Fe(H2O)6]2+. Since very little exptl. results are available (except for crystal structures involving the cation in its high-spin state), the primary comparison is with our own complete active-space SCF (CASSCF), second-order perturbation theory-cor. complete active-space SCF (CASPT2), and spectroscopy-oriented CI (SORCI) calcns. We find that generalized gradient approxns. (GGAs) and the B3LYP hybrid functional provide geometries in good agreement with expt. and with our CASSCF calcns. provided sufficiently extended basis sets are used (i.e., polarization functions on the iron and polarization and diffuse functions on the water mols.). In contrast, CASPT2 calcns. of the low-spin-high-spin energy difference ΔELH = ELS-EHS appear to be significantly overestimated due to basis set limitations in the sense that the energy difference of the at. asymptotes (5D → 1I excitation of Fe2+) are overestimated by about 3000 cm-1. An empirical shift of the mol. ΔELH based upon at. calcns. provides a best est. of 12 000-13 000 cm-1. Our unshifted SORCI result is 13 300 cm-1, consistent with previous comparisons between SORCI and exptl. excitation energies which suggest that no such empirical shift is needed in conjunction with this method. In contrast, after estn. of incomplete basis set effects, GGAs with one exception underestimate this value by 3000-4000 cm-1 while the B3LYP functional underestimates it by only about 1000 cm-1. The exception is the GGA functional RPBE which appears to perform as well as or better than the B3LYP functional for the properties studied here. In order to obtain a best est. of the mol. ΔELH within the context of d. functional theory (DFT) calcns. we have also performed at. excitation energy calcns. using the multiplet sum method. These at. DFT calcns. suggest that no empirical correction is needed for the DFT calcns.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXjvVSqsrc%253D&md5=d7a26c0ba7db2cabc63d79d461e24d2f142Mortensen, J. J.; Kaasbjerg, K.; Frederiksen, S. L.; Nørskov, J. K.; Sethna, J. P.; Jacobsen, K. W.Bayesian Error Estimation in Density-Functional Theory. Phys. Rev. Lett.2005, 95, 216401, DOI: 10.1103/PhysRevLett.95.216401[Crossref], [PubMed], [CAS], Google Scholar142Bayesian Error Estimation in Density-Functional Theory
Mortensen, J. J.; Kaasbjerg, K.; Frederiksen, S. L.; Noerskov, J. K.; Sethna, J. P.; Jacobsen, K. W.
Physical Review Letters (2005), 95 (21), 216401/1-216401/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
We present a practical scheme for performing error ests. for d.-functional theory calcns. The approach, which is based on ideas from Bayesian statistics, involves creating an ensemble of exchange-correlation functionals by comparing with an exptl. database of binding energies for mols. and solids. Fluctuations within the ensemble can then be used to est. errors relative to expt. on calcd. quantities such as binding energies, bond lengths, and vibrational frequencies. It is demonstrated that the error bars on energy differences may vary by orders of magnitude for different systems in good agreement with existing experience.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXht1ejt77M&md5=7608c3d1ac63b52a40e025c3196b1890143Proppe, J.; Reiher, M.Reliable Estimation of Prediction Uncertainty for Physicochemical Property Models. J. Chem. Theory Comput.2017, 13, 3297– 3317, DOI: 10.1021/acs.jctc.7b00235[ACS Full Text ], [CAS], Google Scholar143Reliable Estimation of Prediction Uncertainty for Physicochemical Property Models
Journal of Chemical Theory and Computation (2017), 13 (7), 3297-3317CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
One of the major challenges in computational science is to det. the uncertainty of a virtual measurement, that is the prediction of an observable based on calcns. As highly accurate first-principles calcns. are in general unfeasible for most phys. systems, one usually resorts to parameteric property models of observables, which require calibration by incorporating ref. data. The resulting predictions and their uncertainties are sensitive to systematic errors such as inconsistent ref. data, parametric model assumptions, or inadequate computational methods. Here, we discuss the calibration of property models in the light of bootstrapping, a sampling method that can be employed for identifying systematic errors and for reliable estn. of the prediction uncertainty. We apply bootstrapping to assess a linear property model linking the 57Fe Mossbauer isomer shift to the contact electron d. at the iron nucleus for a diverse set of 44 mol. iron compds. The contact electron d. is calcd. with 12 d. functionals across Jacob's ladder (PWLDA, BP86, BLYP, PW91, PBE, M06-L, TPSS, B3LYP, B3PW91, PBE0, M06, TPSSh). We provide systematic-error diagnostics and reliable, locally resolved uncertainties for isomer-shift predictions. Pure and hybrid d. functionals yield av. prediction uncertainties of 0.06-0.08 mm s-1 and 0.04-0.05 mm s-1, resp., the latter being close to the av. exptl. uncertainty of 0.02 mm s-1. Furthermore, we show that both model parameters and prediction uncertainty depend significantly on the compn. and no. of ref. data points. Accordingly, we suggest that rankings of d. functionals based on performance measures (e.g., the squared coeff. of correlation, r2, or the root-mean-square error, RMSE) should not be inferred from a single data set. This study presents the first statistically rigorous calibration anal. for theor. Mossbauer spectroscopy, which is of general applicability for physicochem. property models and not restricted to isomer-shift predictions. We provide the statistically meaningful ref. data set MIS39 and a new calibration of the isomer shift based on the PBE0 functional.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXpt1ykt7w%253D&md5=41bb917d7e3707ab9c6308a00dd056c9144Simm, G. N.; Reiher, M.Error-Controlled Exploration of Chemical Reaction Networks with Gaussian Processes. J. Chem. Theory Comput.2018, 14, 5238– 5248, DOI: 10.1021/acs.jctc.8b00504[ACS Full Text ], [CAS], Google Scholar144Error-Controlled Exploration of Chemical Reaction Networks with Gaussian Processes
Journal of Chemical Theory and Computation (2018), 14 (10), 5238-5248CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
For a theor. understanding of the reactivity of complex chem. systems, relative energies of stationary points on potential energy hypersurfaces need to be calcd. to high accuracy. Due to the large no. of intermediates present in all but the simplest chem. processes, approx. quantum chem. methods are required that allow for fast evaluations of the relative energies but at the expense of accuracy. Despite the plethora of benchmark studies, the accuracy of a quantum chem. method is often difficult to assess. Moreover, a significant improvement of a method's accuracy (e.g., through reparameterization or systematic model extension) is rarely possible. Here, we present a new approach that allows for the systematic, problem-oriented, and rolling improvement of quantum chem. results through the application of Gaussian processes. Due to its Bayesian nature, reliable error ests. are provided for each prediction. A ref. method of high accuracy can be employed if the uncertainty assocd. with a particular calcn. is above a given threshold. The new data point is then added to a growing data set in order to continuously improve the model and, as a result, all subsequent predictions. Previous predictions are validated by the updated model to ensure that uncertainties remain within the given confidence bound, which we call backtracking. We demonstrate our approach with the example of a complex chem. reaction network.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhs1Gmt7vK&md5=116ed9b1481210ec5564eb6e1d0157f8145Cailliez, F.; Pernot, P.Statistical Approaches to Forcefield Calibration and Prediction Uncertainty in Molecular Simulation. J. Chem. Phys.2011, 134, 054124, DOI: 10.1063/1.3545069[Crossref], [PubMed], [CAS], Google Scholar145Statistical approaches to forcefield calibration and prediction uncertainty in molecular simulation
Journal of Chemical Physics (2011), 134 (5), 054124/1-054124/14CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
Calibration of force fields for mol. simulation should account for the measurement uncertainty of the ref. dataset and for the model inadequacy, i.e., the inability of the force-field/simulation pair to reproduce exptl. data within their uncertainty range. In all rigor, the resulting uncertainty of calibrated force-field parameters is a source of uncertainty for simulation predictions. Various calibration strategies and calibration models within the Bayesian calibration/prediction framework are explored in the present article. In the case of Lennard-Jones potential for Argon, we show that prediction uncertainty for thermodynamical and transport properties, albeit very small, is larger than statistical simulation uncertainty. (c) 2011 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhsF2jtrw%253D&md5=cb127efab49b9b1eb06abe50c1872588146Pernot, P.; Civalleri, B.; Presti, D.; Savin, A.Prediction Uncertainty of Density Functional Approximations for Properties of Crystals with Cubic Symmetry. J. Phys. Chem. A2015, 119, 5288– 5304, DOI: 10.1021/jp509980w[ACS Full Text ], [CAS], Google Scholar146Prediction Uncertainty of Density Functional Approximations for Properties of Crystals with Cubic Symmetry
Pernot, Pascal; Civalleri, Bartolomeo; Presti, Davide; Savin, Andreas
Journal of Physical Chemistry A (2015), 119 (21), 5288-5304CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
The performance of a method is generally measured by an assessment of the errors between the method's results and a set of ref. data. The prediction uncertainty is a measure of the confidence that can be attached to a method's prediction. Its estn. is based on the random part of the errors not explained by ref. data uncertainty, which implies an evaluation of the systematic component(s) of the errors. As the predictions of most d. functional approxns. (DFA) present systematic errors, the std. performance statistics, such as the mean of the abs. errors (MAE or MUE), cannot be directly used to infer prediction uncertainty. We investigate here an a posteriori calibration method to est. the prediction uncertainty of DFAs for properties of solids. A linear model is shown to be adequate to address the systematic trend in the errors. The applicability of this approach to modest-size ref. sets (28 systems) is evaluated for the prediction of band gaps, bulk moduli, and lattice consts. with a wide panel of DFAs.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsF2gsrk%253D&md5=bf61ac91c6e79665c5009483c411f921147Pernot, P.; Savin, A.Probabilistic Performance Estimators for Computational Chemistry Methods: The Empirical Cumulative Distribution Function of Absolute Errors. J. Chem. Phys.2018, 148, 241707, DOI: 10.1063/1.5016248[Crossref], [PubMed], [CAS], Google Scholar147Probabilistic performance estimators for computational chemistry methods: The empirical cumulative distribution function of absolute errors
Journal of Chemical Physics (2018), 148 (24), 241707/1-241707/15CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
Benchmarking studies in computational chem. use ref. datasets to assess the accuracy of a method through error statistics. The commonly used error statistics, such as the mean signed and mean unsigned errors, do not inform end-users on the expected amplitude of prediction errors attached to these methods. We show that, the distributions of model errors being neither normal nor zero-centered, these error statistics cannot be used to infer prediction error probabilities. To overcome this limitation, we advocate for the use of more informative statistics, based on the empirical cumulative distribution function of unsigned errors, namely, (1) the probability for a new calcn. to have an abs. error below a chosen threshold and (2) the maximal amplitude of errors one can expect with a chosen high confidence level. Those statistics are also shown to be well suited for benchmarking and ranking studies. Moreover, the std. error on all benchmarking statistics depends on the size of the ref. dataset. Systematic publication of these std. errors would be very helpful to assess the statistical reliability of benchmarking conclusions. (c) 2018 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXkslahsLc%253D&md5=545f83770372feeffae51431c4b2b3ec148Weymuth, T.; Proppe, J.; Reiher, M.Statistical Analysis of Semiclassical Dispersion Corrections. J. Chem. Theory Comput.2018, 14, 2480– 2494, DOI: 10.1021/acs.jctc.8b00078[ACS Full Text ], [CAS], Google Scholar148Statistical Analysis of Semiclassical Dispersion Corrections
Journal of Chemical Theory and Computation (2018), 14 (5), 2480-2494CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Semiclassical dispersion corrections developed by Grimme and co-workers have become indispensable in applications of Kohn-Sham d. functional theory. A deeper understanding of the underlying parametrization might be crucial for well-founded further improvements of this successful approach. To this end, we present an in-depth assessment of the fit parameters present in semiclassical (D3-type) dispersion corrections by means of a statistically rigorous anal. We find that the choice of the cost function generally has a small effect on the empirical parameters of D3-type dispersion corrections with respect to the ref. set under consideration. Only in a few cases, the choice of cost function has a surprisingly large effect on the total dispersion energies. In particular, the weighting scheme in the cost function can significantly affect the reliability of predictions. In order to obtain unbiased (data-independent) uncertainty ests. for both the empirical fit parameters and the corresponding predictions, we carried out a nonparametric bootstrap anal. This anal. reveals that the std. deviation of the mean of the empirical D3 parameters is small. Moreover, the mean prediction uncertainty obtained by bootstrapping is not much larger than previously reported error measures. On the basis of a jackknife anal., we find that the original ref. set is slightly skewed, but our results also suggest that this feature hardly affects the prediction of dispersion energies. Furthermore, we find that the introduction of small uncertainties to the ref. data does not change the conclusions drawn in this work. However, a rigorous anal. of error accumulation arising from different parametrizations reveals that error cancellation does not necessarily occur, leading to a monotonically increasing deviation in the dispersion energy with increasing mol. size. We discuss this issue in detail at the prominent example of the C60 'buckycatcher'. We find deviations between individual parametrizations of several tens of kilocalories per mol in some cases. Hence, in combination with any calcn. of dispersion energies, we recommend to always det. the assocd. uncertainties for which we will provide a software tool.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXmvVaqsL4%253D&md5=723d9ba5398927668bdedd0141a9b508149Bowman, D. N.; Jakubikova, E.Low-Spin Versus High-Spin Ground State in Pseudo-Octahedral Iron Complexes. Inorg. Chem.2012, 51, 6011– 6019, DOI: 10.1021/ic202344w[ACS Full Text ], [CAS], Google Scholar149Low-Spin versus High-Spin Ground State in Pseudo-Octahedral Iron Complexes
Inorganic Chemistry (2012), 51 (11), 6011-6019CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
Pseudo-octahedral complexes of iron find applications as switches in mol. electronic devices, materials for data storage, and, more recently, as candidates for dye-sensitizers in dye-sensitized solar cells. Iron, as a first row transition metal, provides a weak ligand-field splitting in an octahedral environment. This results in the presence of low-lying 5T excited states that, depending on the identity of iron ligands, can become the ground state of the complex. The small energy difference between the low-spin, 1A, and high-spin, 5T, states presents a challenge for accurate prediction of their ground state using d. functional theory. In this work, we investigate the applicability of the B3LYP functional to the ground state detn. of first row transition metal complexes, focusing mainly on Fe(II) polypyridine complexes with ligands of varying ligand field strength. It has been shown previously that B3LYP artificially favors the 5T state as the ground state of Fe(II) complexes, and the error in the energy differences between the 1A and 5T states is systematic for a set of structurally related complexes. We demonstrate that structurally related complexes can be defined as pseudo-octahedral complexes that undergo similar distortion in the metal-ligand coordination environment between the high-spin and low-spin states. The systematic behavior of complexes with similar distortion can be exploited, and the ground state of an arbitrary Fe(II) complex can be detd. by comparing the calcd. energy differences between the singlet and quintet electronic states of a complex to the energy differences of structurally related complexes with a known, exptl. detd. ground state.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XnsVKrsLc%253D&md5=b025afcba2cc19000a9165657fcce3ee150Salomon, O.; Reiher, M.; Hess, B. A.Assertion and Validation of the Performance of the B3LYP* Functional for the First Transition Metal Row and the G2 Test Set. J. Chem. Phys.2002, 117, 4729– 4737, DOI: 10.1063/1.1493179[Crossref], [CAS], Google Scholar150Assertion and validation of the performance of the B3LYP* functional for the first transition metal row and the G2 test set
Salomon, Oliver; Reiher, Markus; Hess, Bernd Artur
Journal of Chemical Physics (2002), 117 (10), 4729-4737CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
The exact exchange part in hybrid d. functionals is analyzed with respect to the prediction of ground state multiplicities. It has been found [M. Reiher, O. Salomon, and B. A. Hess, Theor. Chem. Acc., 107, 48 (2001)] that pure and hybrid d. functionals yield energy splittings between high-spin and low-spin states of Fe-sulfur complexes that differ by more than 100 kJ/mol and thus fail to reliably predict the correct multiplicity of the ground state. This deviation can lead to meaningless reaction energetics for metal-catalyzed reactions. The finding that the energy splitting depends linearly on the exact exchange admixt. parameter led to a new parametrization of the B3LYP functional which was dubbed B3LYP*. In the present paper we investigate the generality and transferability of this functional. We study the extent to which the exact exchange admixt. affects the thermochem. validated with respect to the ref. data set of mols. from the G2 test set. Metallocenes and bis(benzene) metal complexes of the first transition metal period are chosen to test the transferability of the findings for Fe-sulfur complexes. Moreover, the slope of the linear dependence of the energy splitting of high-spin and low-spin states on the amt. of admixt. of exact exchange is studied in detail.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XmsVWnurc%253D&md5=6a81456831ecdf8113eaf6b8cf10e579151Duignan, T.; Autschbach, J.; Batista, E.; Yang, P.Assessment of Tuned Range Separated Exchange Functionals for Spectroscopies and Properties of Uranium Complexes. J. Chem. Theory Comput.2017, 13, 3614– 3625, DOI: 10.1021/acs.jctc.7b00526[ACS Full Text ], [CAS], Google Scholar151Assessment of Tuned Range Separated Exchange Functionals for Spectroscopies and Properties of Uranium Complexes
Duignan, Thomas J.; Autschbach, Jochen; Batista, Enrique; Yang, Ping
Journal of Chemical Theory and Computation (2017), 13 (8), 3614-3625CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
The Kohn-Sham delocalization error (DE) is quantified in select uranium compds. for various functionals and shown to correlate with the magnitude of dative ligand donation into the 5f shell. Range sepd. exchange functionals are reparametrized to minimize the DE and analyzed for their spectroscopic predictive capabilities. Valence excitation spectra of occupied 5f systems exhibit noticeable improvement upon reparametrization, e.g. UCl6-, UCl62-, and UO2+. Less sensitivity to the reparameterization was obsd. for closed shell 5f systems and core excitation spectra. A general parametrization is proposed to perform well for valence excitation spectra with small DE.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtFGntr7M&md5=e9266fb8c8dce67cee153fea825f5c3a152van der Maaten, L.; Hinton, G.Visualizing Data Using t-SNE. J. Mach. Learn. Res.2008, 9, 2579– 2605Google ScholarThere is no corresponding record for this reference.
153Wilbraham, L.; Verma, P.; Truhlar, D. G.; Gagliardi, L.; Ciofini, I.Multiconfiguration Pair-Density Functional Theory Predicts Spin-State Ordering in Iron Complexes with the Same Accuracy as Complete Active Space Second-Order Perturbation Theory at a Significantly Reduced Computational Cost. J. Phys. Chem. Lett.2017, 8, 2026– 2030, DOI: 10.1021/acs.jpclett.7b00570[ACS Full Text ], [CAS], Google Scholar153Multiconfiguration Pair-Density Functional Theory Predicts Spin-State Ordering in Iron Complexes with the Same Accuracy as Complete Active Space Second-Order Perturbation Theory at a Significantly Reduced Computational Cost
Wilbraham, Liam; Verma, Pragya; Truhlar, Donald G.; Gagliardi, Laura; Ciofini, Ilaria
Journal of Physical Chemistry Letters (2017), 8 (9), 2026-2030CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
The spin-state orderings in nine Fe(II) and Fe(III) complexes with ligands of diverse ligand-field strength were investigated with multiconfiguration pair-d. functional theory (MC-PDFT). The performance of this method was compared to that of complete active space second-order perturbation theory (CASPT2) and Kohn-Sham d. functional theory. We also investigated the dependence of CASPT2 and MC-PDFT results on the size of the active-space. MC-PDFT reproduces the CASPT2 spin-state ordering, the dependence on the ligand field strength, and the dependence on active space at a computational cost that is significantly reduced as compared to CASPT2.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXls1Sntrg%253D&md5=c15ddb19af9f96bb1445e0bda0ebf45b154Mahler, A.; Janesko, B. G.; Moncho, S.; Brothers, E. N.When Hartree-Fock Exchange Admixture Lowers DFT-Predicted Barrier Heights: Natural Bond Orbital Analyses and Implications for Catalysis. J. Chem. Phys.2018, 148, 244106, DOI: 10.1063/1.5032218[Crossref], [PubMed], [CAS], Google Scholar154When Hartree-Fock exchange admixture lowers DFT-predicted barrier heights: Natural bond orbital analyses and implications for catalysis
Mahler, Andrew; Janesko, Benjamin G.; Moncho, Salvador; Brothers, Edward N.
Journal of Chemical Physics (2018), 148 (24), 244106/1-244106/9CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
The conventional wisdom in d. functional theory (DFT) is that std. approxns. systematically underestimate chem. reaction barrier heights and that exact (Hartree-Fock-like, HF) exchange admixt. improves this. This conventional wisdom is inconsistent with the good performance of functionals without HF exchange for many reactions on metal catalyst surfaces. We have studied several 'anomalous' gas-phase reactions where this conventional wisdom is upended, and a HF exchange admixt. decreases or does not affect the predicted barrier heights [Mahler et al., J. Chem. Phys. 146, 234103 (2017)]. Here we show how natural bond orbital analyses can help identify and explain some factors that produce anomalous barriers. Applications to pnictogen inversion, std. benchmark reaction barrier datasets, and a model Grubbs catalyst illustrate the utility of this approach. This approach is expected to aid DFT users in choosing appropriate functionals, and aid DFT developers in devising DFT approxns. generally applicable to catalysis. (c) 2018 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXht1aksbvJ&md5=0feaebe27c8d317355b5a6e0b73eb3f5155Ramakrishnan, R.; Dral, P. O.; Rupp, M.; von Lilienfeld, O. A., Quantum Chemistry Structures and Properties of 134 Kilo Molecules. 2014, 1, 140022.Google ScholarThere is no corresponding record for this reference.
156Kier, L. B.A Shape Index from Molecular Graphs. Quant. Struct.-Act. Relat.1985, 4, 109– 116, DOI: 10.1002/qsar.19850040303[Crossref], [CAS], Google Scholar156Kier, Lemont B.
Quantitative Structure-Activity Relationships (1985), 4 (3), 109-16CODEN: QSARDI; ISSN:0722-3676.
A numerical index of mol. shape was derived from the graph of the nonhydrogen mol. skeleton. The index is based on the count of 2-bond fragments in a graph relative to the max. no. possible in the isomeric star graph and the min. no. in the isomeric linear graph. In this initial study all nonhydrogen atoms and all bonds are considered equal. The 2K index describes the mol. shape in relation to the star and linear graph and is normalized to the no. of atoms. Applications are presented for shape similarity estn., cavity filling ability, and QSAR analyses.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL28Xhs1Wmsb0%253D&md5=1aab51ef350cc6b074980626f3011dee157Herr, J. E.; Yao, K.; McIntyre, R.; Toth, D. W.; Parkhill, J.Metadynamics for Training Neural Network Model Chemistries: A Competitive Assessment. J. Chem. Phys.2018, 148, 241710, DOI: 10.1063/1.5020067[Crossref], [PubMed], [CAS], Google Scholar157Metadynamics for training neural network model chemistries: A competitive assessment
Herr, John E.; Yao, Kun; McIntyre, Ryker; Toth, David W.; Parkhill, John
Journal of Chemical Physics (2018), 148 (24), 241710/1-241710/9CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
Neural network model chemistries (NNMCs) promise to facilitate the accurate exploration of chem. space and simulation of large reactive systems. One important path to improving these models is to add layers of phys. detail, esp. long-range forces. At short range, however, these models are data driven and data limited. Little is systematically known about how data should be sampled, and 'test data' chosen randomly from some sampling techniques can provide poor information about generality. If the sampling method is narrow, 'test error' can appear encouragingly tiny while the model fails catastrophically elsewhere. In this manuscript, we competitively evaluate two common sampling methods: mol. dynamics (MD), normal-mode sampling, and one uncommon alternative, Metadynamics (MetaMD), for prepg. training geometries. We show that MD is an inefficient sampling method in the sense that addnl. samples do not improve generality. We also show that MetaMD is easily implemented in any NNMC software package with cost that scales linearly with the no. of atoms in a sample mol. MetaMD is a black-box way to ensure samples always reach out to new regions of chem. space, while remaining relevant to chem. near kbT. It is a cheap tool to address the issue of generalization. (c) 2018 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXkslaht7s%253D&md5=5d3b9f188e3df8fe0e6f381da1eee5a6158Broto, P.; Moreau, G.; Vandycke, C.Molecular Structures: Perception, Autocorrelation Descriptor and Sar Studies: System of Atomic Contributions for the Calculation of the N-Octanol/Water Partition Coefficients. Eur. J. Med. Chem.1984, 19, 71– 78[CAS], Google Scholar158Molecular structures: perception, autocorrelation descriptor and SAR studies. System of atomic contributions for the calculation of the n-octanol/water partition coefficients
European Journal of Medicinal Chemistry (1984), 19 (1), 71-8CODEN: EJMCA5; ISSN:0009-4374.
A system of additive and constitutive at. contributions to log P (partition coeff.) is proposed. The contributions to log P take into account the nature of atoms and their environment. Numerical values of 222 contributions were derived from a set of 1868 exptl. log P values. This system allows calcn. of log P for most org. mols. with a precision of 0.4 log P units, and gives an estn. of the distribution of lipophilicity on mol. structures.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2cXitVyksLc%253D&md5=179a4663f68bb04c76b00c658a81b7d9This article is cited by 5 publications.
- Carlo Alberto Gaggioli, Samuel J. Stoneburner, Christopher J. Cramer, Laura Gagliardi. Beyond Density Functional Theory: The Multiconfigurational Approach To Model Heterogeneous Catalysis. ACS Catalysis2019, Article ASAP.
- Aditya Nandy, Jiazhou Zhu, Jon Paul Janet, Chenru Duan, Rachel B. Getman, Heather J. Kulik. Machine Learning Accelerates the Discovery of Design Rules and Exceptions in Stable Metal–Oxo Intermediate Formation. ACS Catalysis2019, Article ASAP.
- John E. Herr, Kevin Koh, Kun Yao, John Parkhill. Compressing physics with an autoencoder: Creating an atomic species representation to improve machine learning models in the chemical sciences. The Journal of Chemical Physics2019,151 (8) , 084103. DOI: 10.1063/1.5108803.
- Heather J. Kulik. Making machine learning a useful tool in the accelerated discovery of transition metal complexes. Wiley Interdisciplinary Reviews: Computational Molecular Science2019,119 DOI: 10.1002/wcms.1439.
- Stefan Gugler, Jon Paul Janet, Heather J. Kulik. Enumeration of de novo inorganic complexes for chemical discovery and machine learning. Molecular Systems Design & Engineering2019,58 DOI: 10.1039/C9ME00069K.
- ARTICLE SECTIONSJump To
This article references 158 other publications.
- 1Ufimtsev, I. S.; Martinez, T. J.Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics. J. Chem. Theory Comput.2009, 5, 2619– 2628, DOI: 10.1021/ct9003004[ACS Full Text ], [CAS], Google Scholar1https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtVelurvJ&md5=f4e320ac3479e4b566a6b8bdb9e5add8Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular DynamicsJournal of Chemical Theory and Computation (2009), 5 (10), 2619-2628CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)We demonstrate that a video gaming machine contg. two consumer graphical cards can outpace a state-of-the-art quad-core processor workstation by a factor of more than 180× in Hartree-Fock energy + gradient calcns. Such performance makes it possible to run large scale Hartree-Fock and D. Functional Theory calcns., which typically require hundreds of traditional processor cores, on a single workstation. Benchmark Born-Oppenheimer mol. dynamics simulations are performed on two mol. systems using the 3-21G basis set - a hydronium ion solvated by 30 waters (94 atoms, 405 basis functions) and an aspartic acid mol. solvated by 147 waters (457 atoms, 2014 basis functions). Our GPU implementation can perform 27 ps/day and 0.7 ps/day of ab initio mol. dynamics simulation on a single desktop computer for these systems.
- 2Ufimtsev, I. S.; Martínez, T. J.Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation. J. Chem. Theory Comput.2008, 4, 222– 231, DOI: 10.1021/ct700268q[ACS Full Text ], [CAS], Google Scholar2https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXps1KhsA%253D%253D&md5=6859acd25ffaf6e16fa28dc82b556806Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral EvaluationJournal of Chemical Theory and Computation (2008), 4 (2), 222-231CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)Modern videogames place increasing demands on the computational and graphical hardware, leading to novel architectures that have great potential in the context of high performance computing and mol. simulation. We demonstrate that Graphical Processing Units (GPUs) can be used very efficiently to calc. two-electron repulsion integrals over Gaussian basis functions - the first step in most quantum chem. calcns. A benchmark test performed for the evaluation of approx. 106 (ss ss) integrals over contracted s-orbitals showed that a naive algorithm implemented on the GPU achieves up to 130-fold speedup over a traditional CPU implementation on an AMD Opteron. Subsequent calcns. of the Coulomb operator for a 256-atom DNA strand show that the GPU advantage is maintained for basis sets including higher angular momentum functions.
- 3Ufimtsev, I. S.; Martínez, T. J.Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation. J. Chem. Theory Comput.2009, 5, 1004– 1015, DOI: 10.1021/ct800526s[ACS Full Text ], [CAS], Google Scholar3https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXislKqtbY%253D&md5=80ec2283f6e8a85c3aff2cb0fa4dee4aQuantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field ImplementationJournal of Chemical Theory and Computation (2009), 5 (4), 1004-1015CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)We demonstrate the use of graphical processing units (GPUs) to carry out complete self-consistent-field calcns. for mols. with as many as 453 atoms (2131 basis functions). Speedups ranging from 28× to 650× are achieved as compared to a mature third-party quantum chem. program (GAMESS) running on a traditional CPU. The computational organization used to construct the Coulomb and exchange operators is discussed. We also present results using three GPUs in parallel, combining coarse and fine-grained parallelism.
- 4Ochsenfeld, C.; Kussmann, J.; Lambrecht, D. S.Linear-Scaling Methods in Quantum Chemistry. Rev. Comput. Chem.2007, 23, 1, DOI: 10.1002/9780470116449.ch1[Crossref], [CAS], Google Scholar4https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXisFWqtbc%253D&md5=2ec0d1cbda81fd7310d2c8fcf4ca452bOchsenfeld, Christian; Kussmann, Joerg; Lambrecht, Daniel S.Reviews in Computational Chemistry (2007), 23 (), 1-82CODEN: RCCHEY; ISSN:1069-3599. (Wiley-VCH)A review. The following topics are discussed: some basics of SCF theory; direct SCF methods and two-electron integral screening; calcn. of integrals via multipole expansion; exchange type contractors; exchange-correlation matrix of KS-DFT;d. matrix based SCF; tensor formalism; energy minimization; outlook on electron correlation methods for large systems.
- 5Eichkorn, K.; Weigend, F.; Treutler, O.; Ahlrichs, R.Auxiliary Basis Sets for Main Row Atoms and Transition Metals and Their Use to Approximate Coulomb Potentials. Theor. Chem. Acc.1997, 97, 119– 124, DOI: 10.1007/s002140050244[Crossref], [CAS], Google Scholar5https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXmvFCisbg%253D&md5=d6af66738d1910b99d1f86310d315e46Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentialsEichkorn, Karin; Weigend, Florian; Treutler, Oliver; Ahlrichs, ReinhartTheoretical Chemistry Accounts (1997), 97 (1-4), 119-124CODEN: TCACFW; ISSN:1432-881X. (Springer)We present auxiliary basis sets for the atoms H to At - excluding the lanthanides - optimized for an efficient treatment of mol. electronic Coulomb interactions. For atoms beyond Kr our approach is based on effective core potentials to describe core electrons. The approx. representation of the electron d. in terms of the auxiliary basis has virtually no effect on computed structures and affects the energy by <10-4 a.u. per atom. Efficiency is demonstrated in applications for mols. with ≤300 atoms and 2500 basis functions.
- 6Eichkorn, K.; Treutler, O.; Öhm, H.; Häser, M.; Ahlrichs, R.Auxiliary Basis Sets to Approximate Coulomb Potentials. Chem. Phys. Lett.1995, 240, 283– 290, DOI: 10.1016/0009-2614(95)00621-A[Crossref], [CAS], Google Scholar6https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2MXms1ylu74%253D&md5=2ccc5127a1afa8c7626fe8dad7fa71daAuxiliary basis sets to approximate Coulomb potentialsEichkorn, Karin; Treutler, Oliver; Oehm, Holger; Haeser, Marco; Ahlrichs, ReinhartChemical Physics Letters (1995), 240 (4), 283-90CODEN: CHPLBC; ISSN:0009-2614. (Elsevier)We demonstrate accuracy and computational efficiency resulting from an approx. treatment of Coulomb operators which is based on the expansion of mol. electron densities in atom-centered auxiliary basis sets. This is of special importance in d. functional methods which sep. the treatment of Coulomb and exchange-correlation terms. Auxiliary basis sets are optimized as much as possible for isolated atoms and then augmented for use in mol. electronic structure calcns. For mols. involving atoms up to Br this typically affects energies by only 10-4 au per atom, and computed structure consts. by less than 0.1 pm in bond distances and 0.1° in bond angles.
- 7Libisch, F.; Huang, C.; Carter, E. A.Embedded Correlated Wavefunction Schemes: Theory and Applications. Acc. Chem. Res.2014, 47, 2768– 2775, DOI: 10.1021/ar500086h[ACS Full Text ], [CAS], Google Scholar7https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXptVahu7c%253D&md5=c38754b2218f3584b29849f2d7c4bb1dEmbedded Correlated Wavefunction Schemes: Theory and ApplicationsAccounts of Chemical Research (2014), 47 (9), 2768-2775CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)A review. Ab initio modeling of matter has become a pillar of chem. research: with ever-increasing computational power, simulations can be used to accurately predict, for example, chem. reaction rates, electronic and mech. properties of materials, and dynamical properties of liqs. Many competing quantum mech. methods have been developed over the years that vary in computational cost, accuracy, and scalability: d. functional theory (DFT), the workhorse of solid-state electronic structure calcns., features a good compromise between accuracy and speed. However, approx. exchange-correlation functionals limit DFT's ability to treat certain phenomena or states of matter, such as charge-transfer processes or strongly correlated materials. Furthermore, conventional DFT is purely a ground-state theory: electronic excitations are beyond its scope. Excitations in mols. are routinely calcd. using time-dependent DFT linear response; however applications to condensed matter are still limited. By contrast, many-electron wavefunction methods aim for a very accurate treatment of electronic exchange and correlation. Unfortunately, the assocd. computational cost renders treatment of more than a handful of heavy atoms challenging. On the other side of the accuracy spectrum, parametrized approaches like tight-binding can treat millions of atoms. In view of the different (dis-)advantages of each method, the simulation of complex systems seems to force a compromise: one is limited to the most accurate method that can still handle the problem size. For many interesting problems, however, compromise proves insufficient. A possible soln. is to break up the system into manageable subsystems that may be treated by different computational methods. The interaction between subsystems may be handled by an embedding formalism. In this Account, we review embedded correlated wavefunction (CW) approaches and some applications. We first discuss our d. functional embedding theory, which is formally exact. We show how to det. the embedding potential, which replaces the interaction between subsystems, at the DFT level. CW calcns. are performed using a fixed embedding potential, i.e., a non-self-consistent embedding scheme. We demonstrate this embedding theory for two challenging electron transfer phenomena: (1) initial oxidn. of an aluminum surface and (2) hot-electron-mediated dissocn. of hydrogen mols. on a gold surface. In both cases, the interaction between gas mols. and metal surfaces were treated by sophisticated CW techniques, with the remainder of the extended metal surface being treated by DFT. Our embedding approach overcomes the limitations of conventional Kohn-Sham DFT in describing charge transfer, multiconfigurational character, and excited states. From these embedding simulations, we gained important insights into fundamental processes that are crucial aspects of fuel cell catalysis (i.e., O2 redn. at metal surfaces) and plasmon-mediated photocatalysis by metal nanoparticles. Moreover, our findings agree very well with exptl. observations, while offering new views into the chem. We finally discuss our recently formulated potential-functional embedding theory that provides a seamless, first-principles way to include back-action onto the environment from the embedded region.
- 8Challacombe, M.; Schwegler, E.Linear Scaling Computation of the Fock Matrix. J. Chem. Phys.1997, 106, 5526– 5536, DOI: 10.1063/1.473575[Crossref], [CAS], Google Scholar8https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXitFGqur0%253D&md5=49e5027d4943a29e22834fbe6a4ab1c2Challacombe, Matt; Schwegler, EricJournal of Chemical Physics (1997), 106 (13), 5526-5536CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)Computation of the Fock matrix is currently the limiting factor in the application of Hartree-Fock and hybrid Hartree-Fock/d. functional theories to larger systems. Computation of the Fock matrix is dominated by calcn. of the Coulomb and exchange matrixes. With conventional Gaussian-based methods, computation of the Fock matrix typically scales as ∼N2.7, where N is the no. of basis functions. A hierarchical multipole method is developed for fast computation of the Coulomb matrix. This method, together with a recently described approach to computing the Hartree-Fock exchange matrix of insulators [J. Chem. Phys. 105, 2726 (1900)], leads to a linear scaling algorithm for calcn. of the Fock matrix. Linear scaling computation of the Fock matrix is demonstrated for a sequence of water clusters at the RHF/3-21G level of theory, and corresponding accuracies in converged total energies are shown to be comparable with those obtained from std. quantum chem. programs. RHF/3-21G calcns. on several proteins of current interest are documented, including endothelin, charybdotoxin, and the tetramerization monomer of P53. The P53 calcn., involving 698 atoms and 3836 basis functions, may be the largest Hartree-Fock calcn. to date. The electrostatic potentials of charybdotoxin and the tetramerization monomer of P53 are visualized and the results are related to mol. function.
- 9Hampel, C.; Werner, H. J.Local Treatment of Electron Correlation in Coupled Cluster Theory. J. Chem. Phys.1996, 104, 6286– 6297, DOI: 10.1063/1.471289[Crossref], [CAS], Google Scholar9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XisVertLk%253D&md5=af5ce4613fc863ce6d87d87aa113d113Local treatment of electron correlation in coupled cluster theoryJournal of Chemical Physics (1996), 104 (16), 6286-97CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)The closed-shell coupled cluster theory restricted to single and double excitation operators (CCSD) is formulated in a basis of nonorthogonal local correlation functions. Excitations are made from localized MOs into subspaces (domains) of the local basis, which strongly reduces the no. of amplitudes to be optimized. Furthermore, the correlation of distant electrons can be treated in a simplified way (e.g., by MP2) or entirely neglected. It is demonstrated for 20 mols. that the local correlation treatment recovers 98%-99% of the correlation energy obtained in the corresponding full CCSD calcn. Singles-doubles CI (CISD), quadratic CI (QCISD), and Moeller-Plesset perturbation theory [MP2, MP3, MP4(SDQ)] are treated as special cases.
- 10Schütz, M.; Hetzer, G.; Werner, H.-J.Low-Order Scaling Local Electron Correlation Methods. I. Linear Scaling Local MP2. J. Chem. Phys.1999, 111, 5691– 5705, DOI: 10.1063/1.479957[Crossref], [CAS], Google Scholar10https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1MXlvFWgtL4%253D&md5=bb229e7d159a61407c34c2dcdbf820d0Low-order scaling local electron correlation methods. I. Linear scaling local MP2Schutz, Martin; Hetzer, Georg; Werner, Hans-JoachimJournal of Chemical Physics (1999), 111 (13), 5691-5705CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)A new implementation of local second-order Moeller-Plesset perturbation theory (LMP2) is presented for which asymptotically all computational resources (CPU, memory, and disk) scale only linearly with the mol. size. This is achieved by (1) using orbital domains for each electron pair that are independent of mol. size; (2) classifying the pairs according to a distance criterion and neglecting very distant pairs; (3) treating distant pairs by a multipole approxn., and (4) using efficient pre-screening algorithms in the integral transformation. The errors caused by the various approxns. are negligible. LMP2 calcns. on mols. including up to 500 correlated electrons and over 1500 basis functions in C1 symmetry are reported, all carried out on a single low-cost personal computer.
- 11Hohenstein, E. G.; Parrish, R. M.; Martínez, T. J.Tensor Hypercontraction Density Fitting. I. Quartic Scaling Second-and Third-Order Møller-Plesset Perturbation Theory. J. Chem. Phys.2012, 137, 044103, DOI: 10.1063/1.4732310[Crossref], [PubMed], [CAS], Google Scholar11https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtVOgtb7M&md5=5ce6ce5cd9f7915a7d02ed5bc5fed4f2Tensor hypercontraction density fitting. I. Quartic scaling second- and third-order Moller-Plesset perturbation theoryHohenstein, Edward G.; Parrish, Robert M.; Martinez, Todd J.Journal of Chemical Physics (2012), 137 (4), 044103/1-044103/10CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)Many approxns. have been developed to help deal with the O(N4) growth of the electron repulsion integral (ERI) tensor, where N is the no. of one-electron basis functions used to represent the electronic wavefunction. Of these, the d. fitting (DF) approxn. is currently the most widely used despite the fact that it is often incapable of altering the underlying scaling of computational effort with respect to mol. size. We present a method for exploiting sparsity in three-center overlap integrals through tensor decompn. to obtain a low-rank approxn. to d. fitting (tensor hypercontraction d. fitting or THC-DF). This new approxn. reduces the 4th-order ERI tensor to a product of five matrixes, simultaneously reducing the storage requirement as well as increasing the flexibility to regroup terms and reduce scaling behavior. As an example, we demonstrate such a scaling redn. for second- and third-order perturbation theory (MP2 and MP3), showing that both can be carried out in O(N4) operations. This should be compared to the usual scaling behavior of O(N5) and O(N6) for MP2 and MP3, resp. The THC-DF technique can also be applied to other methods in electronic structure theory, such as coupled-cluster and CI, promising significant gains in computational efficiency and storage redn. (c) 2012 American Institute of Physics.
- 12Song, C.; Martínez, T. J.Reduced Scaling CASPT2 Using Supporting Subspaces and Tensor Hyper-Contraction. J. Chem. Phys.2018, 149, 044108, DOI: 10.1063/1.5037283[Crossref], [PubMed], [CAS], Google Scholar12https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhtl2jtrvL&md5=1761b7dd2d04b400e20480e53ba52d72Reduced scaling CASPT2 using supporting subspaces and tensor hyper-contractionJournal of Chemical Physics (2018), 149 (4), 044108/1-044108/21CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)We present a reduced scaling formulation of the state specific complete active space second-order perturbation method (CASPT2) requiring O(N4) operations and O(N2) memory for a fixed active space, where N is proportional to system size. Motivated by the properties of the Kronecker sum, we introduce the supporting subspace technique (SST), which decomps. the CASPT2 linear equations into two parts: a single-ref. MP2 energy term using dressed orbitals, plus a reduced linear system with dimension scaling as O(N2). Together with Laplace quadrature, the SST allows us to reformulate CASPT2 using a MP2 energy computation and Fock builds. By further applying the tensor hyper-contraction (THC) approxn., the MP2-like term can be computed with O(N4) operations, and the remainder can be solved with O(N3) operations using the preconditioned conjugate gradient method. This is the first application of THC in the context of multi-ref. methods. We also developed an efficient implementation of the method by utilizing graphical processing units and exploiting spatial sparsity in tensor operations. We benchmark the accuracy of the new method against conventional CASPT2 for reactions in the gas phase. We apply the new method to Menshutkin SN2 reactions in carbon nanotubes, demonstrating the feasibility of CASPT2 calcns. with O(100) atoms. (c) 2018 American Institute of Physics.
- 13Andermatt, S.; Cha, J.; Schiffmann, F.; VandeVondele, J.Combining Linear-Scaling DFT with Subsystem DFT in Born–Oppenheimer and Ehrenfest Molecular Dynamics Simulations: From Molecules to a Virus in Solution. J. Chem. Theory Comput.2016, 12, 3214– 3227, DOI: 10.1021/acs.jctc.6b00398[ACS Full Text ], [CAS], Google Scholar13https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XptVSiu7c%253D&md5=500805f7da3d1e24f859154380247243Combining Linear-Scaling DFT with Subsystem DFT in Born-Oppenheimer and Ehrenfest Molecular Dynamics Simulations: From Molecules to a Virus in SolutionAndermatt, Samuel; Cha, Jinwoong; Schiffmann, Florian; VandeVondele, JoostJournal of Chemical Theory and Computation (2016), 12 (7), 3214-3227CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)In this work, methods for the efficient simulation of large systems embedded in a mol. environment are presented. These methods combine linear-scaling (LS) Kohn-Sham (KS) d. functional theory (DFT) with subsystem (SS) DFT. LS DFT is efficient for large subsystems, while SS DFT is linear scaling with a smaller prefactor for large sets of small mols. The combination of SS and LS, which is an embedding approach, can result in a 10-fold speedup over a pure LS simulation for large systems in aq. soln. In addn. to a ground-state Born-Oppenheimer SS + LS implementation, a time-dependent d. functional theory-based Ehrenfest mol. dynamics (EMD) using d. matrix propagation is presented that allows for performing nonadiabatic dynamics. D. matrix-based EMD in the SS framework is naturally linear scaling and appears suitable to study the electronic dynamics of mols. in soln. In the LS framework, linear scaling results as long as the d. matrix remains sparse during time propagation. However, we generally find a less than exponential decay of the d. matrix after a sufficiently long EMD run, preventing LS EMD simulations with arbitrary accuracy. The methods are tested on various systems, including spectroscopy on dyes, the electronic structure of TiO2 nanoparticles, electronic transport in carbon nanotubes, and the satellite tobacco mosaic virus in explicit soln.
- 14Shu, Y.; Levine, B. G.Simulated Evolution of Fluorophores for Light Emitting Diodes. J. Chem. Phys.2015, 142, 104104, DOI: 10.1063/1.4914294[Crossref], [PubMed], [CAS], Google Scholar14https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXksVahtbs%253D&md5=5d8036df01a30de456d5ae8f4525603bSimulated evolution of fluorophores for light emitting diodesJournal of Chemical Physics (2015), 142 (10), 104104/1-104104/11CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)Org. light emitting diodes based on fluorophores with a propensity for thermally activated delayed fluorescence (TADF) are able to circumvent limitations imposed on device efficiency by spin statistics. Mols. with a propensity for TADF necessarily have 2 properties: a small gap between the lowest lying singlet and triplet excited states and a large transition dipole moment for fluorescence. The authors demonstrate the use of a genetic algorithm to search a region of chem. space for mols. with these properties. This algorithm is based on a flexible and intuitive representation of the mol. as a tree data structure, in which the nodes correspond to mol. fragments. The implementation takes advantage of hybrid parallel graphics processing unit accelerated computer clusters to allow efficient sampling while retaining a reasonably accurate description of the electronic structure (in this case, CAM-B3LYP/6-31G**). In total, the authors have identified 3792 promising candidate fluorophores from a chem. space contg. 1.26 × 106 mols. This required performing electronic structure calcns. on only 7518 mols., a small fraction of the full space. Several novel classes of mols. which show promise as fluorophores are presented. (c) 2015 American Institute of Physics.
- 15Gomez-Bombarelli, R.; Aguilera-Iparraguirre, J.; Hirzel, T. D.; Duvenaud, D.; Maclaurin, D.; Blood-Forsythe, M. A.; Chae, H. S.; Einzinger, M.; Ha, D. G.; Wu, T.; Markopoulos, G.; Jeon, S.; Kang, H.; Miyazaki, H.; Numata, M.; Kim, S.; Huang, W. L.; Hong, S. I.; Baldo, M.; Adams, R. P.; Aspuru-Guzik, A.Design of Efficient Molecular Organic Light-Emitting Diodes by a High-Throughput Virtual Screening and Experimental Approach. Nat. Mater.2016, 15, 1120, DOI: 10.1038/nmat4717[Crossref], [PubMed], [CAS], Google Scholar15https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtlSgt7%252FP&md5=03fcd094e3e5ac872e0f56fb6576eb28Design of efficient molecular organic light-emitting diodes by a high-throughput virtual screening and experimental approachGomez-Bombarelli, Rafael; Aguilera-Iparraguirre, Jorge; Hirzel, Timothy D.; Duvenaud, David; MacLaurin, Dougal; Blood-Forsythe, Martin A.; Chae, Hyun Sik; Einzinger, Markus; Ha, Dong-Gwang; Wu, Tony; Markopoulos, Georgios; Jeon, Soonok; Kang, Hosuk; Miyazaki, Hiroshi; Numata, Masaki; Kim, Sunghan; Huang, Wenliang; Hong, Seong Ik; Baldo, Marc; Adams, Ryan P.; Aspuru-Guzik, AlanNature Materials (2016), 15 (10), 1120-1127CODEN: NMAACR; ISSN:1476-1122. (Nature Publishing Group)Virtual screening is becoming a ground-breaking tool for mol. discovery due to the exponential growth of available computer time and const. improvement of simulation and machine learning techniques. An integrated org. functional material design process that incorporates theor. insight, quantum chem., cheminformatics, machine learning, industrial expertise, org. synthesis, mol. characterization, device fabrication and optoelectronic testing is reported. After exploring a search space of 1.6 × 106 mols. and screening >400,000 of them using time-dependent d. functional theory, thousands of promising novel org. LED mols. across the visible spectrum were identified. The team collaboratively selected the best candidates from this set. The exptl. detd. external quantum efficiencies for these synthesized candidates were ≤22%.
- 16Kanal, I. Y.; Owens, S. G.; Bechtel, J. S.; Hutchison, G. R.Efficient Computational Screening of Organic Polymer Photovoltaics. J. Phys. Chem. Lett.2013, 4, 1613– 1623, DOI: 10.1021/jz400215j[ACS Full Text ], [CAS], Google Scholar16https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXmsFGktro%253D&md5=85b4807c36484c8ad37cd8d9cd6d8eb8Efficient computational screening of organic polymer photovoltaicsKanal, Ilana Y.; Owens, Steven G.; Bechtel, Jonathon S.; Hutchison, Geoffrey R.Journal of Physical Chemistry Letters (2013), 4 (10), 1613-1623CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)Review. There has been increasing interest in rational, computationally driven design methods for materials, including org. photovoltaics (OPVs). Our approach focuses on a screening 'pipeline', using a genetic algorithm for first stage screening and multiple filtering stages for further refinement. An important step forward is to expand our diversity of candidate compds., including both synthetic and property-based measures of diversity. For example, top monomer pairs from our screening are all donor-donor (D-D) combinations, in contrast with the typical donor-acceptor (D-A) motif used in org. photovoltaics. We also find a strong 'sequence effect', in which the av. HOMO-LUMO gap of tetramers changes by ∼0.2 eV as a function of monomer sequence (e.g., ABBA vs. BAAB); this has rarely been explored in conjugated polymers. Beyond such optoelectronic optimization, we discuss other properties needed for high-efficiency org. solar cells, and applications of screening methods to other areas, including non-fullerene n-type materials, tandem cells, and improving charge and exciton transport.
- 17Vogiatzis, K. D.; Polynski, M. V.; Kirkland, J. K.; Townsend, J.; Hashemi, A.; Liu, C.; Pidko, E. A.Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities. Chem. Rev.2018, DOI: 10.1021/acs.chemrev.8b00361[ACS Full Text ], Google ScholarThere is no corresponding record for this reference.
- 18Janet, J. P.; Chan, L.; Kulik, H. J.Accelerating Chemical Discovery with Machine Learning: Simulated Evolution of Spin Crossover Complexes with an Artificial Neural Network. J. Phys. Chem. Lett.2018, 9, 1064– 1071, DOI: 10.1021/acs.jpclett.8b00170[ACS Full Text ], [CAS], Google Scholar18https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXisFarsr4%253D&md5=a21e7f08b8a407aeeae8ae1b2ae07b9eAccelerating Chemical Discovery with Machine Learning: Simulated Evolution of Spin Crossover Complexes with an Artificial Neural NetworkJournal of Physical Chemistry Letters (2018), 9 (5), 1064-1071CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)Machine learning (ML) has emerged as a powerful complement to simulation for materials discovery by reducing time for evaluation of energies and properties at accuracy competitive with first-principles methods. We use genetic algorithm (GA) optimization to discover unconventional spin-crossover complexes in combination with efficient scoring from an artificial neural network (ANN) that predicts spin-state splitting of inorg. complexes. We explore a compd. space of over 5600 candidate materials derived from eight metal/oxidn. state combinations and a 32-ligand pool. We introduce a strategy for error-aware ML-driven discovery by limiting how far the GA travels away from the nearest ANN training points while maximizing property (i.e., spin-splitting) fitness, leading to discovery of 80% of the leads from full chem. space enumeration. Over a 51-complex subset, av. unsigned errors (4.5 kcal/mol) are close to the ANN's baseline 3 kcal/mol error. By obtaining leads from the trained ANN within seconds rather than days from a DFT-driven GA, this strategy demonstrates the power of ML for accelerating inorg. material discovery.
- 19Curtarolo, S.; Hart, G. L.; Nardelli, M. B.; Mingo, N.; Sanvito, S.; Levy, O.The High-Throughput Highway to Computational Materials Design. Nat. Mater.2013, 12, 191– 201, DOI: 10.1038/nmat3568[Crossref], [PubMed], [CAS], Google Scholar19https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXislWju7c%253D&md5=5e116fbafda8e8437ccd0fdf7304d939The high-throughput highway to computational materials designCurtarolo, Stefano; Hart, Gus L. W.; Nardelli, Marco Buongiorno; Mingo, Natalio; Sanvito, Stefano; Levy, OhadNature Materials (2013), 12 (3), 191-201CODEN: NMAACR; ISSN:1476-1122. (Nature Publishing Group)A review. High-throughput computational materials design is an emerging area of materials science. By combining advanced thermodn. and electronic-structure methods with intelligent data mining and database construction, and exploiting the power of current supercomputer architectures, scientists generate, manage and analyze enormous data repositories for the discovery of novel materials. In this Review we provide a current snapshot of this rapidly evolving field, and highlight the challenges and opportunities that lie ahead.
- 20Curtarolo, S.; Setyawan, W.; Hart, G. L.; Jahnatek, M.; Chepulskii, R. V.; Taylor, R. H.; Wang, S.; Xue, J.; Yang, K.; Levy, O.; Mehl, M. J.; Stokes, H. T.; Demchenko, D. O.; Morgan, D.AFLOW: An Automatic Framework for High-Throughput Materials Discovery. Comput. Mater. Sci.2012, 58, 218– 226, DOI: 10.1016/j.commatsci.2012.02.005[Crossref], [CAS], Google Scholar20https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XksVyktL8%253D&md5=8129bab53c054672274b0d6fa64172efAFLOW: An automatic framework for high-throughput materials discoveryCurtarolo, Stefano; Setyawan, Wahyu; Hart, Gus L. W.; Jahnatek, Michal; Chepulskii, Roman V.; Taylor, Richard H.; Wang, Shidong; Xue, Junkai; Yang, Kesong; Levy, Ohad; Mehl, Michael J.; Stokes, Harold T.; Demchenko, Denis O.; Morgan, DaneComputational Materials Science (2012), 58 (), 218-226CODEN: CMMSEM; ISSN:0927-0256. (Elsevier B.V.)Recent advances in computational materials science present novel opportunities for structure discovery and optimization, including uncovering of unsuspected compds. and metastable structures, electronic structure, surface, and nano-particle properties. The practical realization of these opportunities requires systematic generation and classification of the relevant computational data by high-throughput methods. In this paper we present Aflow (Automatic Flow), a software framework for high-throughput calcn. of crystal structure properties of alloys, intermetallics and inorg. compds. The Aflow software is available for the scientific community on the website of the materials research consortium, aflowlib.org. Its geometric and electronic structure anal. and manipulation tools are addnl. available for online operation at the same website. The combination of automatic methods and user online interfaces provide a powerful tool for efficient quantum computational materials discovery and characterization.
- 21Ong, S. P.; Richards, W. D.; Jain, A.; Hautier, G.; Kocher, M.; Cholia, S.; Gunter, D.; Chevrier, V. L.; Persson, K. A.; Ceder, G.Python Materials Genomics (Pymatgen): A Robust, Open-Source Python Library for Materials Analysis. Comput. Mater. Sci.2013, 68, 314– 319, DOI: 10.1016/j.commatsci.2012.10.028[Crossref], [CAS], Google Scholar21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsVGjt7g%253D&md5=104f567dbd8f4199911ded91bc42100ePython Materials Genomics (pymatgen): A robust, open-source python library for materials analysisOng, Shyue Ping; Richards, William Davidson; Jain, Anubhav; Hautier, Geoffroy; Kocher, Michael; Cholia, Shreyas; Gunter, Dan; Chevrier, Vincent L.; Persson, Kristin A.; Ceder, GerbrandComputational Materials Science (2013), 68 (), 314-319CODEN: CMMSEM; ISSN:0927-0256. (Elsevier B.V.)We present the Python Materials Genomics (pymatgen) library, a robust, open-source Python library for materials anal. A key enabler in high-throughput computational materials science efforts is a robust set of software tools to perform initial setup for the calcns. (e.g., generation of structures and necessary input files) and post-calcn. anal. to derive useful material properties from raw calcd. data. The pymatgen library aims to meet these needs by (1) defining core Python objects for materials data representation, (2) providing a well-tested set of structure and thermodn. analyses relevant to many applications, and (3) establishing an open platform for researchers to collaboratively develop sophisticated analyses of materials data obtained both from first principles calcns. and expts. The pymatgen library also provides convenient tools to obtain useful materials data via the Materials Project's REpresentational State Transfer (REST) Application Programming Interface (API). As an example, using pymatgen's interface to the Materials Project's RESTful API and phase diagram package, we demonstrate how the phase and electrochem. stability of a recently synthesized material, Li4SnS4, can be analyzed using a min. of computing resources. We find that Li4SnS4 is a stable phase in the Li-Sn-S phase diagram (consistent with the fact that it can be synthesized), but the narrow range of lithium chem. potentials for which it is predicted to be stable would suggest that it is not intrinsically stable against typical electrodes used in lithium-ion batteries.
- 22Nørskov, J. K.; Bligaard, T.The Catalyst Genome. Angew. Chem., Int. Ed.2013, 52, 776– 777, DOI: 10.1002/anie.201208487[Crossref], [CAS], Google Scholar22https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhslymtrzM&md5=ec50826a181c734b9338addfa16a2bfcNorskov, Jens K.; Bligaard, ThomasAngewandte Chemie, International Edition (2013), 52 (3), 776-777CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)There is no expanded citation for this reference.
- 23Han, S.; Huang, Y.; Watanabe, T.; Dai, Y.; Walton, K. S.; Nair, S.; Sholl, D. S.; Meredith, J. C.High-Throughput Screening of Metal–Organic Frameworks for CO2 Separation. ACS Comb. Sci.2012, 14, 263– 267, DOI: 10.1021/co3000192[ACS Full Text ], [CAS], Google Scholar23https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XktFeksL4%253D&md5=d0a02f702ff2490c9b799467f4170ec9High-Throughput Screening of Metal-Organic Frameworks for CO2 SeparationHan, Sangil; Huang, Yougui; Watanabe, Taku; Dai, Ying; Walton, Krista S.; Nair, Sankar; Sholl, David S.; Meredith, J. CarsonACS Combinatorial Science (2012), 14 (4), 263-267CODEN: ACSCCC; ISSN:2156-8944. (American Chemical Society)A parallel high-throughput sorption methodol. is described for screening CO2 and N2 adsorption and diffusion selectivity in metal org. frameworks, before and after exposure to H2O vapor and acid gases. The authors illustrate this approach by simultaneously studying 8 candidate Metal-Org. Framework (MOF) materials, of which the best material has a CO2/N2 membrane selectivity of 152 and a CO2 permeability of 60 barrer for Co-NIC. This approach provides a significant increase in efficiency of obtaining the sepn. properties of MOFs. While the authors describe here the identification of novel materials for CO2 capture, the methodol. enables exploration of the performance and stability of novel porous materials for a wide range of applications.
- 24Wilmer, C. E.; Leaf, M.; Lee, C. Y.; Farha, O. K.; Hauser, B. G.; Hupp, J. T.; Snurr, R. Q.Large-Scale Screening of Hypothetical Metal–Organic Frameworks. Nat. Chem.2012, 4, 83– 89, DOI: 10.1038/nchem.1192[Crossref], [CAS], Google Scholar24https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhsVagtL3K&md5=3becbfed2fdacdb8b58146666da7c038Large-scale screening of hypothetical metal-organic frameworksWilmer, Christopher E.; Leaf, Michael; Lee, Chang Yeon; Farha, Omar K.; Hauser, Brad G.; Hupp, Joseph T.; Snurr, Randall Q.Nature Chemistry (2012), 4 (2), 83-89CODEN: NCAHBB; ISSN:1755-4330. (Nature Publishing Group)Metal-org. frameworks (MOFs) are porous materials constructed from modular mol. building blocks, typically metal clusters and org. linkers. These can, in principle, be assembled to form an almost unlimited no. of MOFs, yet materials reported to date represent only a tiny fraction of the possible combinations. Here, the authors demonstrate a computational approach to generate all conceivable MOFs from a given chem. library of building blocks (based on the structures of known MOFs) and rapidly screen them to find the best candidates for a specific application. From a library of 102 building blocks the authors generated 137,953 hypothetical MOFs and for each calcd. the pore-size distribution, surface area and methane-storage capacity. The authors identified over 300 MOFs with a predicted methane-storage capacity better than that of any known material, and this approach also revealed structure-property relations. Methyl-functionalized MOFs were frequently top performers, so the authors selected one such promising MOF and exptl. confirmed its predicted capacity.
- 25Witman, M.; Ling, S.; Anderson, S.; Tong, L.; Stylianou, K. C.; Slater, B.; Smit, B.; Haranczyk, M.In Silico Design and Screening of Hypothetical Mof-74 Analogs and Their Experimental Synthesis. Chem. Sci.2016, 7, 6263– 6272, DOI: 10.1039/C6SC01477A[Crossref], [PubMed], [CAS], Google Scholar25https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtVGisrrF&md5=6b0d264eb348a0e5a29b30cd803abf07In silico design and screening of hypothetical MOF-74 analogs and their experimental synthesisWitman, Matthew; Ling, Sanliang; Anderson, Samantha; Tong, Lianheng; Stylianou, Kyriakos C.; Slater, Ben; Smit, Berend; Haranczyk, MaciejChemical Science (2016), 7 (9), 6263-6272CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)In this work we present the in silico design of metal-org. frameworks (MOFs) exhibiting 1-dimensional rod topologies. We introduce an algorithm for construction of this family of MOF topologies, and illustrate its application for enumerating MOF-74-type analogs. Furthermore, we perform a broad search for new linkers that satisfy the topol. requirements of MOF-74 and consider the largest database of known chem. space for org. compds., the PubChem database. Our in silico crystal assembly, when combined with dispersion-cor. d. functional theory (DFT) calcns., is demonstrated to generate a hypothetical library of open-metal site contg. MOF-74 analogs in the 1-D rod topol. from which we can simulate the adsorption behavior of CO2. We finally conclude that these hypothetical structures have synthesizable potential through computational identification and exptl. validation of a novel MOF-74 analog, Mg2(olsalazine).
- 26Ufimtsev, I. S.; Luehr, N.; Martínez, T. J.Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics. J. Phys. Chem. Lett.2011, 2, 1789– 1793, DOI: 10.1021/jz200697c[ACS Full Text ], [CAS], Google Scholar26https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXosFyktr0%253D&md5=e8f7eae80215597532e8bae205ee358dCharge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular DynamicsUfimtsev, Ivan S.; Luehr, Nathan; Martinez, Todd J.Journal of Physical Chemistry Letters (2011), 2 (14), 1789-1793CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)Charge transfer at the bovine pancreatic trypsin inhibitor (BPTI) protein-water interface was analyzed by means of ab initio Born-Oppenheimer mol. dynamics simulation of the entire protein running on graphical processing units (GPUs). The efficiency of the GPU-based quantum chem. algorithms implemented in our TeraChem program enables us to perform these calcns. on a desktop computer. Mulliken and Voronoi deformation d. (VDD) population anal. reveals that between 2.0 and 3.5 electrons are transferred from surrounding water mols. to the protein over the course of the 8.8 ps simulation. Solving for the electronic structure of BPTI in the absence of surrounding water mols. (i.e., in the gas phase) leads to large intraprotein charge transfer, where approx. one electron in total is transferred from neutral to polar residues. Solvation relieves this polarization stress, leading to a neutralization of the excess pos. charge of the neutral residues.
- 27Kulik, H. J.Large-Scale QM/MM Free Energy Simulations of Enzyme Catalysis Reveal the Influence of Charge Transfer. Phys. Chem. Chem. Phys.2018, 20, 20650– 20660, DOI: 10.1039/C8CP03871F[Crossref], [CAS], Google Scholar27https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhtlOgt73F&md5=e179ba52def7e9425a2dcfb4e40c7b9eLarge-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transferPhysical Chemistry Chemical Physics (2018), 20 (31), 20650-20660CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)Hybrid quantum mech.-mol. mech. (QM/MM) simulations provide key insights into enzyme structure-function relationships. Numerous studies have demonstrated that large QM regions are needed to systematically converge ground state, zero temp. properties with electrostatic embedding QM/MM. However, it is not well known if ab initio QM/MM free energy simulations have this same dependence, in part due to the hundreds of thousands of energy evaluations required for free energy estns. that in turn limit QM region size. Here, we leverage recent advances in electronic structure efficiency and accuracy to carry out range-sepd. hybrid d. functional theory free energy simulations in a representative methyltransferase. By studying 200 ps of ab initio QM/MM dynamics for each of five QM regions from minimal (64 atoms) to one-sixth of the protein (544 atoms), we identify crit. differences between large and small QM region QM/MM in charge transfer between substrates and active site residues as well as in geometric structure and dynamics that coincide with differences in predicted free energy barriers. Distinct geometric and electronic structure features in the largest QM region indicate that important aspects of enzymic rate enhancement in methyltransferases are identified with large-scale electronic structure.
- 28Fales, B. S.; Levine, B. G.Nanoscale Multireference Quantum Chemistry: Full Configuration Interaction on Graphical Processing Units. J. Chem. Theory Comput.2015, 11, 4708– 4716, DOI: 10.1021/acs.jctc.5b00634[ACS Full Text ], [CAS], Google Scholar28https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsVyktrjF&md5=0909ca201d7302bfd994d495c552f524Nanoscale Multireference Quantum Chemistry: Full Configuration Interaction on Graphical Processing UnitsJournal of Chemical Theory and Computation (2015), 11 (10), 4708-4716CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)Methods based on a full CI (FCI) expansion in an active space of orbitals are widely used for modeling chem. phenomena such as bond breaking, multiply excited states, and conical intersections in small-to-medium-sized mols., but these phenomena occur in systems of all sizes. To scale such calcns. up to the nanoscale, we have developed an implementation of FCI in which electron repulsion integral transformation and several of the more expensive steps in σ vector formation are performed on graphical processing unit (GPU) hardware. When applied to a 1.7 × 1.4 × 1.4 nm silicon nanoparticle (Si72H64) described with the polarized, all-electron 6-31G** basis set, our implementation can solve for the ground state of the 16-active-electron/16-active-orbital CASCI Hamiltonian (more than 100,000,000 configurations) in 39 min on a single NVidia K40 GPU.
- 29Zhao, Q.; Kulik, H. J.Electronic Structure Origins of Surface-Dependent Growth in III-V Quantum Dots. Chem. Mater.2018, 30, 7154– 7165, DOI: 10.1021/acs.chemmater.8b03125[ACS Full Text ], [CAS], Google Scholar29https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhsleqtL%252FO&md5=58136a35c84f458aa7ef56eca668bc7eElectronic Structure Origins of Surface-Dependent Growth in III-V Quantum DotsChemistry of Materials (2018), 30 (20), 7154-7165CODEN: CMATEX; ISSN:0897-4756. (American Chemical Society)Indium phosphide quantum dots (QDs) have emerged as a promising candidate to replace more toxic II-VI CdSe QDs, but prodn. of high-quality III-V InP QDs with targeted properties requires a better understanding of their growth. We develop a first-principles-derived model that unifies InP QD formation from isolated precursor and early stage cluster reactions to 1.3 nm magic sized clusters and rationalize exptl. obsd. properties of full sized >3 nm QDs. Our first-principles study on realistic QD models reveals large surface-dependent reactivity for all elementary growth process steps, including In-ligand bond cleavage and P precursor addn. These thermodn. trends correlate well to kinetic properties at all stages of growth, indicating the presence of labile and stable spots on cluster and QD surfaces. Correlation of electronic or geometric properties to energetics identifies surprising sources for these variations: short In···In sepn. on the surface produces the most reactive sites, at odds with conventional understanding of strain (i.e., sepn.) in bulk metallic surfaces increasing reactivity and models for ionic II-VI QD growth. These differences are rationalized by the covalent, directional nature of bonding in III-V QDs and explained by bond order metrics derived directly from the In-O bond d. The unique constraints of carboxylate and P precursor bonding to In atoms rationalize why all sizes of InP clusters and QDs are In-rich but become less so as QDs mature. These observations support the development of alternate growth recipes that take into account strong surface-dependence of kinetics as well as the shapes of both In and P precursors to control both kinetics and surface morphol. in III-V QDs.
- 30Kümmel, S.; Kronik, L.Orbital-Dependent Density Functionals: Theory and Applications. Rev. Mod. Phys.2008, 80, 3– 60, DOI: 10.1103/RevModPhys.80.3[Crossref], [CAS], Google Scholar30https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXlslKms74%253D&md5=867b579a9dfef4dfa661a6af35d6d21dOrbital-dependent density functionals: Theory and applicationsReviews of Modern Physics (2008), 80 (1), 3-60CODEN: RMPHAT; ISSN:0034-6861. (American Physical Society)This review provides a perspective on the use of orbital-dependent functionals, which is currently considered one of the most promising avenues in modern d.-functional theory. The focus here is on four major themes: the motivation for orbital-dependent functionals in terms of limitations of semilocal functionals; the optimized effective potential as a rigorous approach to incorporating orbital-dependent functionals within the Kohn-Sham framework; the rationale behind and advantages and limitations of four popular classes of orbital-dependent functionals; and the use of orbital-dependent functionals for predicting excited-state properties. For each of these issues, both formal and practical aspects are assessed.
- 31Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H.A Consistent and Accurate Ab Initio Parametrization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu. J. Chem. Phys.2010, 132, 154104, DOI: 10.1063/1.3382344[Crossref], [PubMed], [CAS], Google Scholar31https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXkvVyks7o%253D&md5=2bca89d904579d5565537a0820dc2ae8A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-PuGrimme, Stefan; Antony, Jens; Ehrlich, Stephan; Krieg, HelgeJournal of Chemical Physics (2010), 132 (15), 154104/1-154104/19CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)The method of dispersion correction as an add-on to std. Kohn-Sham d. functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coeffs. and cutoff radii that are both computed from first principles. The coeffs. for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination nos. (CN). They are used to interpolate between dispersion coeffs. of atoms in different chem. environments. The method only requires adjustment of two global parameters for each d. functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of at. forces. Three-body nonadditivity terms are considered. The method has been assessed on std. benchmark sets for inter- and intramol. noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean abs. deviations for the S22 benchmark set of noncovalent interactions for 11 std. d. functionals decrease by 15%-40% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C6 coeffs. also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in mols. and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems. (c) 2010 American Institute of Physics.
- 32Livshits, E.; Baer, R.A Well-Tempered Density Functional Theory of Electrons in Molecules. Phys. Chem. Chem. Phys.2007, 9, 2932– 2941, DOI: 10.1039/b617919c[Crossref], [CAS], Google Scholar32https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXmtVylsbY%253D&md5=32a27f5ad7ff5749d93bb6dc0394ae79A well-tempered density functional theory of electrons in moleculesPhysical Chemistry Chemical Physics (2007), 9 (23), 2932-2941CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)This Invited Article reports extensions of a recently developed approach to d. functional theory with correct long-range behavior (R. Baer and D. Neuhauser, Phys. Rev. Lett., 2005, 94, 043002). The central quantities are a splitting functional γ[n] and a complementary exchange-correlation functional EγXC[n]. We give a practical method for detg. the value of γ in mols., assuming an approxn. for EγXC is given. The resulting theory shows good ability to reproduce the ionization potentials for various mols. However it is not of sufficient accuracy for forming a satisfactory framework for studying mol. properties. A somewhat different approach is then adopted, which depends on a d.-independent γ and an addnl. parameter w eliminating part of the local exchange functional. The values of these two parameters are obtained by best-fitting to exptl. atomization energies and bond lengths of the mols. in the G2(1) database. The optimized values are γ = 0.5 a-10 and w = 0.1. We then examine the performance of this slightly semi-empirical functional for a variety of mol. properties, comparing to related works and expt. We show that this approach can be used for describing in a satisfactory manner a broad range of mol. properties, be they static or dynamic. Most satisfactory is the ability to describe valence, Rydberg and inter-mol. charge-transfer excitations.
- 33Stein, T.; Kronik, L.; Baer, R.Reliable Prediction of Charge Transfer Excitations in Molecular Complexes Using Time-Dependent Density Functional Theory. J. Am. Chem. Soc.2009, 131, 2818– 2820, DOI: 10.1021/ja8087482[ACS Full Text ], [CAS], Google Scholar33https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhvVSns7s%253D&md5=b01ac7f2580fdb9495f7e51be1910d57Reliable prediction of charge transfer excitations in molecular complexes using time-dependent density functional theoryJournal of the American Chemical Society (2009), 131 (8), 2818-2820CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)We show how charge transfer excitations at mol. complexes can be calcd. quant. using time-dependent d. functional theory. Predictive power is obtained from range-sepd. hybrid functionals using nonempirical tuning of the range-splitting parameter. Excellent performance of this approach is obtained for a series of complexes composed of various arom. donors and the tetracyanoethylene acceptor, paving the way to systematic nonempirical quant. studies of charge-transfer excitations in real systems.
- 34Körzdörfer, T.; Brédas, J.-L.Organic Electronic Materials: Recent Advances in the DFT Description of the Ground and Excited States Using Tuned Range-Separated Hybrid Functionals. Acc. Chem. Res.2014, 47, 3284– 3291, DOI: 10.1021/ar500021t[ACS Full Text ], [CAS], Google Scholar34https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2cnosFaltg%253D%253D&md5=378dd3ab4b06d00152d606ed0f7c933fOrganic electronic materials: recent advances in the DFT description of the ground and excited states using tuned range-separated hybrid functionalsAccounts of chemical research (2014), 47 (11), 3284-91 ISSN:.CONSPECTUS: Density functional theory (DFT) and its time-dependent extension (TD-DFT) are powerful tools enabling the theoretical prediction of the ground- and excited-state properties of organic electronic materials with reasonable accuracy at affordable computational costs. Due to their excellent accuracy-to-numerical-costs ratio, semilocal and global hybrid functionals such as B3LYP have become the workhorse for geometry optimizations and the prediction of vibrational spectra in modern theoretical organic chemistry. Despite the overwhelming success of these out-of-the-box functionals for such applications, the computational treatment of electronic and structural properties that are of particular interest in organic electronic materials sometimes reveals severe and qualitative failures of such functionals. Important examples include the overestimation of conjugation, torsional barriers, and electronic coupling as well as the underestimation of bond-length alternations or excited-state energies in low-band-gap polymers. In this Account, we highlight how these failures can be traced back to the delocalization error inherent to semilocal and global hybrid functionals, which leads to the spurious delocalization of electron densities and an overestimation of conjugation. The delocalization error for systems and functionals of interest can be quantified by allowing for fractional occupation of the highest occupied molecular orbital. It can be minimized by using long-range corrected hybrid functionals and a nonempirical tuning procedure for the range-separation parameter. We then review the benefits and drawbacks of using tuned long-range corrected hybrid functionals for the description of the ground and excited states of π-conjugated systems. In particular, we show that this approach provides for robust and efficient means of characterizing the electronic couplings in organic mixed-valence systems, for the calculation of accurate torsional barriers at the polymer limit, and for the reliable prediction of the optical absorption spectrum of low-band-gap polymers. We also explain why the use of standard, out-of-the-box range-separation parameters is not recommended for the DFT and/or TD-DFT description of the ground and excited states of extended, pi-conjugated systems. Finally, we highlight a severe drawback of tuned range-separated hybrid functionals by discussing the example of the calculation of bond-length alternation in polyacetylene, which leads us to point out the challenges for future developments in this field.
- 35Autschbach, J.; Srebro, M.Delocalization Error and “Functional Tuning” in Kohn–Sham Calculations of Molecular Properties. Acc. Chem. Res.2014, 47, 2592– 2602, DOI: 10.1021/ar500171t[ACS Full Text ], [CAS], Google Scholar35https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtVGksbvL&md5=2d587db13d129951b7bef20e57356ba6Delocalization Error and 'Functional Tuning' in Kohn-Sham Calculations of Molecular PropertiesAccounts of Chemical Research (2014), 47 (8), 2592-2602CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)A review. Kohn-Sham theory (KST) is the 'workhorse' of numerical quantum chem. This is particularly true for first-principles calcns. of ground- and excited-state properties for larger systems, including electronic spectra, electronic dynamic and static linear and higher order response properties (including nonlinear optical (NLO) properties), conformational or dynamic averaging of spectra and response properties, or properties that are affected by the coupling of electron and nuclear motion. This Account explores the sometimes dramatic impact of the delocalization error (DE) and possible benefits from the use of long-range corrections (LC) and 'tuning' of functionals in KST calcns. of mol. ground-state and response properties. Tuning refers to a nonempirical mol.-specific detn. of adjustable parameters in functionals to satisfy known exact conditions, for instance, that the energy of the HOMO should be equal to the neg. vertical ionization potential (IP) or that the energy as a function of fractional electron nos. should afford straight-line segments. The presentation is given from the viewpoint of a chemist interested in computations of a variety of mol. optical and spectroscopic properties and of a theoretician developing methods for computing such properties with KST. In recent years, the use of LC functionals, functional tuning, and quantifying the DE explicitly have provided valuable insight regarding the performance of KST for mol. properties. We discuss a no. of different mol. properties, with examples from recent studies from our lab. and related literature. The selected properties probe different aspects of mol. electronic structure. Elec. field gradients and hyperfine coupling consts. can be exquisitely sensitive to the DE because it affects the ground-state electron d. and spin d. distributions. For π-conjugated mols., it is shown how the DE manifests itself either in too strong or too weak delocalization of localized MOs (LMOs). Optical rotation is an elec.-magnetic linear response property that is calcd. in a similar fashion as the elec. polarizability, but it is more sensitive to approxns. and can benefit greatly from tuning and small DE. Hyperpolarizabilities of π-conjugated 'push-pull' systems are examples of NLO properties that can be greatly improved by tuning of range-sepd. exchange (RSE) functionals, in part due to improved charge-transfer excitation energies. On-going work on band gap predictions is also mentioned. The findings may provide clues for future improvements of KST because different mol. properties exhibit varying sensitivity to approxns. in the electronic structure model. The utility of analyzing mol. properties and the impact of the DE in terms of LMOs, representing 'chemist's orbitals' such as individual lone pairs and bonds, is highlighted.
- 36Dion, M.; Rydberg, H.; Schröder, E.; Langreth, D. C.; Lundqvist, B. I.Van Der Waals Density Functional for General Geometries. Phys. Rev. Lett.2004, 92, 246401, DOI: 10.1103/PhysRevLett.92.246401[Crossref], [PubMed], [CAS], Google Scholar36https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXltVerur4%253D&md5=abbf50b023000f126ba66af15c786583Van der Waals Density Functional for General GeometriesDion, M.; Rydberg, H.; Schroeder, E.; Langreth, D. C.; Lundqvist, B. I.Physical Review Letters (2004), 92 (24), 246401/1-246401/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)A scheme within d. functional theory is proposed that provides a practical way to generalize to unrestricted geometries the method applied with some success to layered geometries [H. Rydberg et al., Phys. Rev. Lett. 91, 126402 (2003)]. It includes van der Waals forces in a seamless fashion. By expansion to second order in a carefully chosen quantity contained in the long-range part of the correlation functional, the nonlocal correlations are expressed in terms of a d.-d. interaction formula. It contains a relatively simple parametrized kernel, with parameters detd. by the local d. and its gradient. The proposed functional is applied to rare gas and benzene dimers, where it is shown to give a realistic description.
- 37Mori-Sánchez, P.; Cohen, A. J.; Yang, W.Many-Electron Self-Interaction Error in Approximate Density Functionals. J. Chem. Phys.2006, 125, 201102, DOI: 10.1063/1.2403848[Crossref], [PubMed], [CAS], Google Scholar37https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XhtlSlt77E&md5=8de0c410a67a0f7da2a2ef194c21a25bMany-electron self-interaction error in approximate density functionalsJournal of Chemical Physics (2006), 125 (20), 201102/1-201102/4CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)One of the most important challenges in d. functional theory (DFT) is the proper description of fractional charge systems relating to the self-interaction error (SIE). Traditionally, the SIE has been formulated as a one-electron problem, which has been addressed in several recent functionals. However, these recent one-electron SIE-free functionals, while greatly improving the description of thermochem. and reaction barriers in general, still exhibit many of the difficulties assocd. with SIE. Thus we emphasize the need to surpass this limit and shed light on the many-electron SIE. After identifying the sufficient condition for functionals to be free from SIE, we focus on the symptoms and investigate the performance of most popular functionals. We show that these functionals suffer from many-electron SIE. Finally, we give a SIE classification of d. functionals.
- 38Cohen, A. J.; Mori-Sánchez, P.; Yang, W.Insights into Current Limitations of Density Functional Theory. Science2008, 321, 792– 794, DOI: 10.1126/science.1158722[Crossref], [PubMed], [CAS], Google Scholar38https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXptlyhsrg%253D&md5=502dc9289c4a858806549cd769681ac8Insights into Current Limitations of Density Functional TheoryScience (Washington, DC, United States) (2008), 321 (5890), 792-794CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)A review. D. functional theory of electronic structure is widely and successfully applied in simulations throughout engineering and sciences. However, for many predicted properties, there are spectacular failures that can be traced to the delocalization error and static correlation error of commonly used approxns. These errors can be characterized and understood through the perspective of fractional charges and fractional spins introduced recently. Reducing these errors will open new frontiers for applications of d. functional theory.
- 39Bajaj, A.; Janet, J. P.; Kulik, H. J.Communication: Recovering the Flat-Plane Condition in Electronic Structure Theory at Semi-Local DFT Cost. J. Chem. Phys.2017, 147, 191101, DOI: 10.1063/1.5008981[Crossref], [PubMed], [CAS], Google Scholar39https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvVKiur3E&md5=6867200d3110186577eaf90189d384ecCommunication: Recovering the flat-plane condition in electronic structure theory at semi-local DFT costJournal of Chemical Physics (2017), 147 (19), 191101/1-191101/5CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)The flat-plane condition is the union of two exact constraints in electronic structure theory: (i) energetic piecewise linearity with fractional electron removal or addn. and (ii) invariant energetics with change in electron spin in a half filled orbital. Semi-local d. functional theory (DFT) fails to recover the flat plane, exhibiting convex fractional charge errors (FCE) and concave fractional spin errors (FSE) that are related to delocalization and static correlation errors. We previously showed that DFT+U eliminates FCE but now demonstrate that, like other widely employed corrections (i.e., Hartree-Fock exchange), it worsens FSE. To find an alternative strategy, we examine the shape of semi-local DFT deviations from the exact flat plane and we find this shape to be remarkably consistent across ions and mols. We introduce the judiciously modified DFT (jmDFT) approach, wherein corrections are constructed from few-parameter, low-order functional forms that fit the shape of semi-local DFT errors. We select one such phys. intuitive form and incorporate it self-consistently to correct semi-local DFT. We demonstrate on model systems that jmDFT represents the first easy-to-implement, no-overhead approach to recovering the flat plane from semi-local DFT. (c) 2017 American Institute of Physics.
- 40Srebro, M.; Autschbach, J.Does a Molecule-Specific Density Functional Give an Accurate Electron Density? The Challenging Case of the CuCl Electric Field Gradient. J. Phys. Chem. Lett.2012, 3, 576– 581, DOI: 10.1021/jz201685r[ACS Full Text ], [CAS], Google Scholar40https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhvVSkurs%253D&md5=03ae2a0685bb16a6eefbc6f8dbd45baeDoes a Molecule-Specific Density Functional Give an Accurate Electron Density? The Challenging Case of the CuCl Electric Field GradientJournal of Physical Chemistry Letters (2012), 3 (5), 576-581CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)In the framework of detg. system-specific long-range cor. d. functionals, the question is addressed whether such functionals, tuned to satisfy the condition -εHOMO = IP or other energetic criteria, provide accurate electron densities. A nonempirical phys. motivated two-dimensional tuning of range-sepd. hybrid functionals is proposed and applied to the particularly challenging case of a mol. property that depends directly on the ground-state d.: the copper elec. field gradient (EFG) in CuCl. From a continuous range of functional parametrizations that closely satisfy -εHOMO = IP and the correct asymptotic behavior of the potential, the one that best fulfills the straight-line behavior of E(N), the energy as a function of a fractional electron no. N, was found to provide the most accurate electron d. as evidenced by calcd. EFGs. The functional also performs well for related Cu systems.
- 41Brumboiu, I. E.; Prokopiou, G.; Kronik, L.; Brena, B.Valence Electronic Structure of Cobalt Phthalocyanine from an Optimally Tuned Range-Separated Hybrid Functional. J. Chem. Phys.2017, 147, 044301, DOI: 10.1063/1.4993623[Crossref], [PubMed], [CAS], Google Scholar41https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXht1WltL7N&md5=9395ce64444a63786f5a84a44eced18bValence electronic structure of cobalt phthalocyanine from an optimally tuned range-separated hybrid functionalBrumboiu, Iulia Emilia; Prokopiou, Georgia; Kronik, Leeor; Brena, BarbaraJournal of Chemical Physics (2017), 147 (4), 044301/1-044301/11CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)We analyze the valence electronic structure of cobalt phthalocyanine (CoPc) by means of optimally tuning a range-sepd. hybrid functional. The tuning is performed by modifying both the amt. of short-range exact exchange (α) included in the hybrid functional and the range-sepn. parameter (γ), with two strategies employed for finding the optimal γ for each α. The influence of these two parameters on the structural, electronic, and magnetic properties of CoPc is thoroughly investigated. The electronic structure is found to be very sensitive to the amt. and range in which the exact exchange is included. The electronic structure obtained using the optimal parameters is compared to gas-phase photoelectron data and GW calcns., with the unoccupied states addnl. compared with inverse photo-electron spectroscopy measurements. The calcd. spectrum with tuned γ, detd. for the optimal value of α = 0.1, yields a very good agreement with both exptl. results and with GW calcns. that well-reproduce the exptl. data. (c) 2017 American Institute of Physics.
- 42Gani, T. Z. H.; Kulik, H. J.Where Does the Density Localize? Convergent Behavior for Global Hybrids, Range Separation, and DFT+U. J. Chem. Theory Comput.2016, 12, 5931, DOI: 10.1021/acs.jctc.6b00937[ACS Full Text ], [CAS], Google Scholar42https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvVWnur3O&md5=8e8f87defc97835ccb0d6f3a4663e446Where Does the Density Localize? Convergent Behavior for Global Hybrids, Range Separation, and DFT+UJournal of Chemical Theory and Computation (2016), 12 (12), 5931-5945CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)Approx. d. functional theory (DFT) suffers from many-electron self-interaction error, otherwise known as delocalization error, that may be diagnosed and then cor. through elimination of the deviation from exact piecewise linear behavior between integer electron nos. Although paths to correction of energetic delocalization error are well-established, the impact of these corrections on the electron d. is less well-studied. Here, we compare the effect on d. delocalization of DFT + U (i.e., semilocal DFT augmented with a Hubbard U correction), global hybrid tuning, and range-sepd. hybrid tuning on a diverse test set of 32 transition metal complexes and observe the three methods to have qual. equiv. effects on the ground state d. Regardless of valence orbital diffuseness (i.e., from 2p to 5p), ligand electronegativity (i.e., from Al to O), basis set (i.e., plane wave vs. localized basis set), metal (i.e., Ti, Fe, Ni), and spin state, or tuning method, we consistently observe substantial charge loss at the metal and gain at ligand atoms (∼0.3-0.5 e or more). This charge loss at the metal is preferentially from the minority spin, leading to increasing magnetic moment as well. Using accurate wave function theory refs., we observe that a min. error in partial charges and magnetic moments occurs at higher tuning parameters than typically employed to eliminate energetic delocalization error. These observations motivate the need to develop multifaceted approx.-DFT error correction approaches that sep. treat d. delocalization and energetic errors to recover both correct d. and orbital energy-derived properties.
- 43Medvedev, M. G.; Bushmarinov, I. S.; Sun, J.; Perdew, J. P.; Lyssenko, K. A.Density Functional Theory Is Straying from the Path toward the Exact Functional. Science2017, 355, 49– 52, DOI: 10.1126/science.aah5975[Crossref], [PubMed], [CAS], Google Scholar43https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhs1SqtQ%253D%253D&md5=670a71b442b1bd30abf15abc9bb15d90Density functional theory is straying from the path toward the exact functionalMedvedev, Michael G.; Bushmarinov, Ivan S.; Sun, Jianwei; Perdew, John P.; Lyssenko, Konstantin A.Science (Washington, DC, United States) (2017), 355 (6320), 49-52CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)The theorems at the core of d. functional theory (DFT) state that the energy of a many-electron system in its ground state is fully defined by its electron d. distribution. This connection is made via the exact functional for the energy, which minimizes at the exact d. For years, DFT development focused on energies, implicitly assuming that functionals producing better energies become better approxns. of the exact functional. We examd. the other side of the coin: the energy-minimizing electron densities for at. species, as produced by 128 historical and modern DFT functionals. We found that these densities became closer to the exact ones, reflecting theor. advances, until the early 2000s, when this trend was reversed by unconstrained functionals sacrificing phys. rigor for the flexibility of empirical fitting.
- 44Kulik, H. J.Perspective: Treating Electron over-Delocalization with the DFT+U Method. J. Chem. Phys.2015, 142, 240901, DOI: 10.1063/1.4922693[Crossref], [PubMed], [CAS], Google Scholar44https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtFSltbbE&md5=55b110113e6648e8cad7287fd4faf0f1Perspective: Treating electron over-delocalization with the DFT+U methodJournal of Chemical Physics (2015), 142 (24), 240901/1-240901/10CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)A review. Many people in the materials science and solid-state community are familiar with the acronym 'DFT+U.'. For those less familiar, this technique uses ideas from model Hamiltonians that permit the description of both metals and insulators to address problems of electron over-delocalization in practical implementations of d. functional theory (DFT). Exchange-correlation functionals in DFT are often described as belonging to a hierarchical 'Jacob's ladder' of increasing accuracy in moving from local to non-local descriptions of exchange and correlation. DFT+U is not on this 'ladder' but rather acts as an 'elevator' because it systematically tunes relative energetics, typically on a localized subshell (e.g., d or f electrons), regardless of the underlying functional employed. However, this tuning is based on a metric of the local electron d. of the subshells being addressed, thus necessitating phys. or chem. or intuition about the system of interest. I will provide a brief overview of the history of how DFT+U came to be starting from the origin of the Hubbard and Anderson model Hamiltonians. This history lesson is necessary because it permits us to make the connections between the 'Hubbard U' and fundamental outstanding challenges in electronic structure theory, and it helps to explain why this method is so widely applied to transition-metal oxides and organometallic complexes alike. (c) 2015 American Institute of Physics.
- 45Zhao, Q.; Kulik, H. J.Where Does the Density Localize in the Solid State? Divergent Behavior for Hybrids and DFT+U. J. Chem. Theory Comput.2018, 14, 670– 683, DOI: 10.1021/acs.jctc.7b01061[ACS Full Text ], [CAS], Google Scholar45https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXjsVKiug%253D%253D&md5=91c357b4180519bb06c1ad1a63c37609Where Does the Density Localize in the Solid State? Divergent Behavior for Hybrids and DFT+UJournal of Chemical Theory and Computation (2018), 14 (2), 670-683CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)Approx. d. functional theory (DFT) is widely used in chem. and physics, despite delocalization errors that affect energetic and d. properties. DFT+U (i.e., semi-local DFT augmented with a Hubbard U correction) and global hybrid functionals are two commonly employed practical methods to address delocalization error. Recent work demonstrated that in transition metal complexes both methods localize d. away from the metal and onto surrounding ligands, regardless of metal or ligand identity. In this work, we compare d. localization trends with DFT+U and global hybrids on a diverse set of 34 transition-metal-contg. solids with varying magnetic state, electron configuration and valence shell, and coordinating-atom orbital diffuseness (i.e., O, S, Se). We also study open-framework solids in which the metal is coordinated by mol. ligands, i.e., MCO3, M(OH)2, M(NCNH)2, K3M(CN)6 (M = V-Ni). As in transition metal complexes, incorporation of Hartree-Fock exchange consistently localizes d. away from the metal, but DFT+U exhibits diverging behavior, localizing d. (i) onto the metal in low-spin and late transition metals and (ii) away from the metal in other cases in agreement with hybrids. To isolate the effect of the crystal environment, we ext. mol. analogs from open-framework transition metal solids and observe consistent localization of the d. away from the metal in all cases with both DFT+U and hybrid exchange. These observations highlight the limited applicability of trends established for functional tuning on transition metal complexes even to equiv. coordination environments in the solid state.
- 46Kim, M.-C.; Sim, E.; Burke, K.Understanding and Reducing Errors in Density Functional Calculations. Phys. Rev. Lett.2013, 111, 073003, DOI: 10.1103/PhysRevLett.111.073003[Crossref], [PubMed], [CAS], Google Scholar46https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsVehtb7F&md5=320723a5e50d94d975df04c25c53adedUnderstanding and reducing errors in density functional calculationsPhysical Review Letters (2013), 111 (7), 073003/1-073003/5CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)We decomp. the energy error of any variational d. functional theory calcn. into a contribution due to the approx. functional and that due to the approx. d. Typically, the functional error dominates, but in many interesting situations the d.-driven error dominates. Examples range from calcns. of electron affinities to preferred geometries of ions and radicals in soln. In these abnormal cases, the error in d. functional theory can be greatly reduced by using a more accurate d. A small orbital gap often indicates a substantial d.-driven error.
- 47Kim, M.-C.; Park, H.; Son, S.; Sim, E.; Burke, K.Improved DFT Potential Energy Surfaces via Improved Densities. J. Phys. Chem. Lett.2015, 6, 3802– 3807, DOI: 10.1021/acs.jpclett.5b01724[ACS Full Text ], [CAS], Google Scholar47https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsVKlsLfJ&md5=59839f8600a934c5d2990f3802059fa7Improved DFT Potential Energy Surfaces via Improved DensitiesKim, Min-Cheol; Park, Hansol; Son, Suyeon; Sim, Eunji; Burke, KieronJournal of Physical Chemistry Letters (2015), 6 (19), 3802-3807CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)D.-cor. DFT is a method that cures several failures of self-consistent semilocal DFT calcns. by using a more accurate d. instead. A novel procedure employs the Hartree-Fock d. to bonds that are more severely stretched than ever before. This substantially increases the range of accurate potential energy surfaces obtainable from semilocal DFT for many heteronuclear mols. We show that this works for both neutral and charged mols. We explain why and explore more difficult cases, for example, CH+, where d.-cor. DFT results are even better than sophisticated methods like CCSD. We give a simple criterion for when DC-DFT should be more accurate than self-consistent DFT that can be applied for most cases.
- 48Duignan, T. J.; Autschbach, J.Impact of the Kohn–Sham Delocalization Error on the 4f Shell Localization and Population in Lanthanide Complexes. J. Chem. Theory Comput.2016, 12, 3109– 3121, DOI: 10.1021/acs.jctc.6b00238[ACS Full Text ], [CAS], Google Scholar48https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xos1Slu7s%253D&md5=85e82e44072d8d26b9247afc4510f107Impact of the Kohn-Sham Delocalization Error on the 4f Shell Localization and Population in Lanthanide ComplexesJournal of Chemical Theory and Computation (2016), 12 (7), 3109-3121CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)The extent of ligand to metal donation bonding and mixing of 4f (and 5d) orbitals with ligand orbitals is studied by Kohn-Sham (KS) calcns. for LaX3 (X = F, Cl, Br, I), GdX3, and LuX3 model complexes, CeCl62-, YbCp3, and selected lanthanide complexes with larger ligands. The KS delocalization error (DE) is quantified via the curvature of the energy for noninteger electron nos. The extent of donation bonding and 4f-ligand mixing correlates well with the DE. For Lu complexes, the DE also correlates with the extent of mixing of ligand and 4f orbitals in the canonical MOs (MOs). However, the localized set of MOs and population analyses indicate that the closed 4f shell is localized. Attempts to create situations where mixing of 4f and ligand orbitals occurs due to a degeneracy of fragment orbitals were unsuccessful. For La(III) and, in particular, for Ce(IV), Hartree-Fock, KS, and coupled cluster singles and doubles calcns. are in agreement in that excess 4f populations arise from ligand donation, along with donation into the 5d shell. Likewise, KS calcns. for all systems with incompletely filled 4f shells, even those with 'optimally tuned' functionals affording a small DE, produce varying degrees of excess 4f populations which may be only partially attributed to 5d polarization.
- 49Riplinger, C.; Neese, F.An Efficient and near Linear Scaling Pair Natural Orbital Based Local Coupled Cluster Method. J. Chem. Phys.2013, 138, 034106, DOI: 10.1063/1.4773581[Crossref], [PubMed], [CAS], Google Scholar49https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXpslOqtw%253D%253D&md5=4327115b95524107245acb44ff4aaa7bAn efficient and near linear scaling pair natural orbital based local coupled cluster methodJournal of Chemical Physics (2013), 138 (3), 034106/1-034106/18CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)In previous publications, it was shown that an efficient local coupled cluster method with single- and double excitations can be based on the concept of pair natural orbitals (PNOs) . The resulting local pair natural orbital-coupled-cluster single double (LPNO-CCSD) method has since been proven to be highly reliable and efficient. For large mols., the no. of amplitudes to be detd. is reduced by a factor of 105-106 relative to a canonical CCSD calcn. on the same system with the same basis set. In the original method, the PNOs were expanded in the set of canonical virtual orbitals and single excitations were not truncated. This led to a no. of fifth order scaling steps that eventually rendered the method computationally expensive for large mols. (e.g., >100 atoms). In the present work, these limitations are overcome by a complete redesign of the LPNO-CCSD method. The new method is based on the combination of the concepts of PNOs and projected AOs (PAOs). Thus, each PNO is expanded in a set of PAOs that in turn belong to a given electron pair specific domain. In this way, it is possible to fully exploit locality while maintaining the extremely high compactness of the original LPNO-CCSD wavefunction. No terms are dropped from the CCSD equations and domains are chosen conservatively. The correlation energy loss due to the domains remains below <0.05%, which implies typically 15-20 but occasionally up to 30 atoms per domain on av. The new method has been given the acronym DLPNO-CCSD ('domain based LPNO-CCSD'). The method is nearly linear scaling with respect to system size. The original LPNO-CCSD method had three adjustable truncation thresholds that were chosen conservatively and do not need to be changed for actual applications. In the present treatment, no addnl. truncation parameters have been introduced. Any addnl. truncation is performed on the basis of the three original thresholds. There are no real-space cutoffs. Single excitations are truncated using singles-specific natural orbitals. Pairs are prescreened according to a multipole expansion of a pair correlation energy est. based on local orbital specific virtual orbitals (LOSVs). Like its LPNO-CCSD predecessor, the method is completely of black box character and does not require any user adjustments. It is shown here that DLPNO-CCSD is as accurate as LPNO-CCSD while leading to computational savings exceeding one order of magnitude for larger systems. The largest calcns. reported here featured >8800 basis functions and >450 atoms. In all larger test calcns. done so far, the LPNO-CCSD step took less time than the preceding Hartree-Fock calcn., provided no approxns. have been introduced in the latter. Thus, based on the present development reliable CCSD calcns. on large mols. with unprecedented efficiency and accuracy are realized. (c) 2013 American Institute of Physics.
- 50Saitow, M.; Becker, U.; Riplinger, C.; Valeev, E. F.; Neese, F.A New Near-Linear Scaling, Efficient and Accurate, Open-Shell Domain-Based Local Pair Natural Orbital Coupled Cluster Singles and Doubles Theory. J. Chem. Phys.2017, 146, 164105, DOI: 10.1063/1.4981521[Crossref], [PubMed], [CAS], Google Scholar50https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXmvVeqsL8%253D&md5=898703521d990dfd299c935e34adbfa6A new near-linear scaling, efficient and accurate, open-shell domain-based local pair natural orbital coupled cluster singles and doubles theorySaitow, Masaaki; Becker, Ute; Riplinger, Christoph; Valeev, Edward F.; Neese, FrankJournal of Chemical Physics (2017), 146 (16), 164105/1-164105/31CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)The Coupled-Cluster expansion, truncated after single and double excitations (CCSD), provides accurate and reliable mol. electronic wave functions and energies for many mol. systems around their equil. geometries. However, the high computational cost, which is well-known to scale as O(N6) with system size N, has limited its practical application to small systems consisting of not more than approx. 20-30 atoms. To overcome these limitations, low-order scaling approxns. to CCSD have been intensively investigated over the past few years. In our previous work, we have shown that by combining the pair natural orbital (PNO) approach and the concept of orbital domains it is possible to achieve fully linear scaling CC implementations (DLPNO-CCSD and DLPNO-CCSD(T)) that recover around 99.9% of the total correlation energy [C. Riplinger et al., J. Chem. Phys. 144, 024109 (2016)]. The prodn. level implementations of the DLPNO-CCSD and DLPNO-CCSD(T) methods were shown to be applicable to realistic systems composed of a few hundred atoms in a routine, black-box fashion on relatively modest hardware. In 2011, a reduced-scaling CCSD approach for high-spin open-shell UHF ref. wave functions was proposed (UHF-LPNO-CCSD) [A. Hansen et al., J. Chem. Phys. 135, 214102 (2011)]. After a few years of experience with this method, a few shortcomings of UHF-LPNO-CCSD were noticed that required a redesign of the method, which is the subject of this paper. To this end, we employ the high-spin open-shell variant of the N-electron valence perturbation theory formalism to define the initial guess wave function, and consequently also the open-shell PNOs. The new PNO ansatz properly converges to the closed-shell limit since all truncations and approxns. have been made in strict analogy to the closed-shell case. Furthermore, given the fact that the formalism uses a single set of orbitals, only a single PNO integral transformation is necessary, which offers large computational savings. We show that, with the default PNO truncation parameters, approx. 99.9% of the total CCSD correlation energy is recovered for open-shell species, which is comparable to the performance of the method for closed-shells. UHF-DLPNO-CCSD shows a linear scaling behavior for closed-shell systems, while linear to quadratic scaling is obtained for open-shell systems. The largest systems we have considered contain more than 500 atoms and feature more than 10 000 basis functions with a triple-ζ quality basis set. (c) 2017 American Institute of Physics.
- 51Stein, C. J.; Reiher, M.Automated Selection of Active Orbital Spaces. J. Chem. Theory Comput.2016, 12, 1760– 1771, DOI: 10.1021/acs.jctc.6b00156[ACS Full Text ], [CAS], Google Scholar51https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XjvFyltLs%253D&md5=c46ae44d10c10dfa409cf8807a779308Stein, Christopher J.; Reiher, MarkusJournal of Chemical Theory and Computation (2016), 12 (4), 1760-1771CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)One of the key challenges of quantum-chem. multi-configuration methods is the necessity to manually select orbitals for the active space. This selection requires both expertise and experience and can therefore impose severe limitations on the applicability of this most general class of ab initio methods. A poor choice of the active orbital space may yield even qual. wrong results. This is obviously a severe problem, esp. for wave function methods that are designed to be systematically improvable. Here, we show how the iterative nature of the d. matrix renormalization group combined with its capability to include up to about 100 orbitals in the active space can be exploited for a systematic assessment and selection of active orbitals. These benefits allow us to implement an automated approach for active orbital space selection, which can turn multi-configuration models into black box approaches.
- 52Sayfutyarova, E. R.; Sun, Q.; Chan, G. K.-L.; Knizia, G.Automated Construction of Molecular Active Spaces from Atomic Valence Orbitals. J. Chem. Theory Comput.2017, 13, 4063– 4078, DOI: 10.1021/acs.jctc.7b00128[ACS Full Text ], [CAS], Google Scholar52https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXht1WmtL7L&md5=2c8d3c8062fa13f4f4e68c6432bb65b1Automated Construction of Molecular Active Spaces from Atomic Valence OrbitalsSayfutyarova, Elvira R.; Sun, Qiming; Chan, Garnet Kin-Lic; Knizia, GeraldJournal of Chemical Theory and Computation (2017), 13 (9), 4063-4078CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)We introduce the at. valence active space (AVAS), a simple and well-defined automated technique for constructing active orbital spaces for use in multi-configuration and multi-ref. (MR) electronic structure calcns. Concretely, the technique constructs active MOs capable of describing all relevant electronic configurations emerging from a targeted set of at. valence orbitals (e.g., the metal d orbitals in a redcoordination complex). This is achieved via a linear transformation of the occupied and unoccupied orbital spaces from an easily obtainable single-ref. wavefunction (such as from a Hartree-Fock or Kohn-Sham calcns.) based on projectors to targeted at. valence orbitals. We discuss the premises, theory, and implementation of the idea, and several of its variations are tested. To investigate the performance and accuracy, we calc. the excitation energies for various transition metal complexes in typical application scenarios. Addnl., we follow the homolytic bond breaking process of a Fenton reaction along its reaction coordinate. While the described AVAS technique is not an universal soln. to the active space problem, its premises are fulfilled in many application scenarios of transition metal chem. and bond dissocn. processes. In these cases the technique makes MR calcns. easier to execute, easier to reproduce by any user, and simplifies the detn. of the appropriate size of the active space required for accurate results.
- 53Xiao, D.; Martini, L. A.; Snoeberger, R. C., III; Crabtree, R. H.; Batista, V. S.Inverse Design and Synthesis of Acac-Coumarin Anchors for Robust TiO2 Sensitization. J. Am. Chem. Soc.2011, 133, 9014– 9022, DOI: 10.1021/ja2020313[ACS Full Text ], [CAS], Google Scholar53https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXmsVWlsbg%253D&md5=fa04c6e57f5290bac149a6448e8fb708Inverse Design and Synthesis of acac-Coumarin Anchors for Robust TiO2 SensitizationXiao, Dequan; Martini, Lauren A.; Snoeberger, Robert C., III; Crabtree, Robert H.; Batista, Victor S.Journal of the American Chemical Society (2011), 133 (23), 9014-9022CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)An inverse design methodol. suitable to assist the synthesis and optimization of mol. sensitizers for dye-sensitized solar cells is introduced. The method searches for mol. adsorbates with suitable photoabsorption properties through continuous optimization of alchem. structures in the vicinity of a ref. mol. framework. The approach is illustrated as applied to the design and optimization of linker chromophores for TiO2 sensitization, using the recently developed phenyl-acetylacetonate (i.e., phenyl-acac) anchor [McNamara et al. J. Am. Chem. Soc.2008, 130, 14329-14338] as a ref. framework. A novel anchor (3-acac-pyran-2-one) is a local optimum, with improved sensitization properties when compared to phenyl-acac. Its mol. structure is related to known coumarin dyes that could be used as lead chromophore anchors for practical applications in dye-sensitized solar cells. Synthesis and spectroscopic characterization confirms that the linker provides robust attachment to TiO2, even in aq. conditions, yielding improved sensitization to solar light and ultrafast interfacial electron injection. The findings are particularly relevant to the design of sensitizers for dye-sensitized solar cells because of the wide variety of structures that are possible but they should be equally useful for other applications such as ligand design for homogeneous catalysis.
- 54Weymuth, T.; Reiher, M.Gradient-Driven Molecule Construction: An Inverse Approach Applied to the Design of Small-Molecule Fixating Catalysts. Int. J. Quantum Chem.2014, 114, 838– 850, DOI: 10.1002/qua.24686[Crossref], [CAS], Google Scholar54https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXmvVSntro%253D&md5=09e6116d6ed6fa3a3a9f2cdfa0296ab0Gradient-driven molecule construction: An inverse approach applied to the design of small-molecule fixating catalystsInternational Journal of Quantum Chemistry (2014), 114 (13), 838-850CODEN: IJQCB2; ISSN:0020-7608. (John Wiley & Sons, Inc.)A review. Rational design of mols. and materials usually requires extensive screening of mol. structures for the desired property. The inverse approach to deduce a structure for a predefined property would be highly desirable, but is, unfortunately, not well defined. However, feasible strategies for such an inverse design process may be successfully developed for specific purposes. We discuss options for calcg. 'jacket' potentials that fulfill a predefined target requirement-a concept that we recently introduced (Weymuth and Reiher, MRS Proceedings 2013, 1524, DOI:10.1557/opl.2012.1764). We consider the case of small-mol. activating transition metal catalysts. As a target requirement we choose the vanishing geometry gradients on all atoms of a subsystem consisting of a metal center binding the small mol. to be activated. The jacket potential can be represented within a full quantum model or by a sequence of approxns. of which a field of electrostatic point charges is the simplest. In a second step, the jacket potential needs to be replaced by a chem. viable chelate-ligand structure for which the geometry gradients on all of its atoms are also required to vanish. To analyze the feasibility of this approach, we dissect a known dinitrogen-fixating catalyst to study possible design strategies that must eventually produce the known catalyst. © 2014 Wiley Periodicals, Inc.
- 55Krausbeck, F.; Sobez, J.-G.; Reiher, M.Stabilization of Activated Fragments by Shell-Wise Construction of an Embedding Environment. J. Comput. Chem.2017, 38, 1023– 1038, DOI: 10.1002/jcc.24749[Crossref], [PubMed], [CAS], Google Scholar55https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXjtl2jsbc%253D&md5=c4091c40e34bb8a4150cae60d8aa3d7bStabilization of activated fragments by shell-wise construction of an embedding environmentKrausbeck, Florian; Sobez, Jan-Grimo; Reiher, MarkusJournal of Computational Chemistry (2017), 38 (14), 1023-1038CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)An activated fragment which is structurally unstable when considered isolated can be stabilized through binding to a suitable mol. environment; for instance, to a transition-metal fragment. The metal fragment may be designed in a shell-wise build-up of a surrounding mol. environment. However, adding more and more atoms in a consecutive fashion soon leads to a combinatorial explosion of structures, which is unfeasible to handle without automation. Here, we present a fully automated and parallelized framework that constructs such an embedding environment atom-wise. Mol. realizations of such an environment are constructed based on simple heuristic rules intended to screen a sufficiently large portion of the possible compd. space and are then subsequently optimized by electronic structure methods. (Constrained-optimized) structures are then evaluated with respect to a scoring function, for which we choose here the concept of gradient-driven mol. construction. This concept searches for structure modifications that reduce the forces on all atoms. We develop and analyze our approach at the example of CO2 activation by reproducing a known compd. and mapping out possible alternative structures and their effect on the stabilization of a (bent) CO2 ligand. For all generated structures, the nuclear gradient on the activated fragment and its coordination energy are evaluated to steer the design process. © 2017 Wiley Periodicals, Inc.
- 56Kim, J. Y.; Kulik, H. J.When Is Ligand pKa a Good Descriptor for Catalyst Energetics? In Search of Optimal CO2 Hydration Catalysts. J. Phys. Chem. A2018, 122, 4579– 4590, DOI: 10.1021/acs.jpca.8b03301[ACS Full Text ], [CAS], Google Scholar56https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXns12gu78%253D&md5=b543453a77cf44993940ec72254f01e9When Is Ligand pKa a Good Descriptor for Catalyst Energetics? In Search of Optimal CO2 Hydration CatalystsJournal of Physical Chemistry A (2018), 122 (18), 4579-4590CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)The authors present a detailed study of nearly 70 Zn mol. catalysts for CO2 hydration from four diverse ligand classes ranging from well-studied carbonic anhydrase mimics (e.g., cyclen) to new structures the authors obtain by leveraging diverse hits from large org. libraries. Using microkinetic anal. and establishing linear free energy relations, turnover is sensitive to the relative thermodn. stability of reactive hydroxyl and bound bicarbonate moieties. The authors observe a wide range of thermodn. stabilities for these intermediates, showing up to 6 kcal/mol improvement over well-studied cyclen catalysts. The authors observe a good correlation between the pKa of the Zn-OH2 moiety and the resulting relative stability of hydroxyl moieties over bicarbonate, which may be rationalized by the dominant effect of the difference in higher Zn-OH bond order in comparison to weaker bonding in bicarbonate and H2O. A direct relation is identified between isolated org. ligand pKa and the pKa of a bound H2O mol. on the catalyst. Thus, org. ligand pKa, which is intuitive, easy to compute or tabulate, and much less sensitive to electronic structure method choice than whole-catalyst properties, is a good quant. descriptor for predicting the effect of through-bond electronic effects on relative CO2 hydration energetics. The authors expect this to be applicable to other reactions where is it essential to stabilize turnover-detg. hydroxyl species with respect to more weakly bound moieties. Finally, the authors note exceptions for rigid ligands (e.g., porphyrins) that preferentially stabilize hydroxyl over bicarbonate without reducing pKa values as substantially. The authors expect the strategy outlined here, to (i) curate diverse ligands from large org. libraries and (ii) identify when ligand-only properties can det. catalyst energetics, to be broadly useful for both exptl. and computational catalyst design.
- 57Gani, T. Z. H.; Kulik, H. J.Understanding and Breaking Scaling Relations in Single-Site Catalysis: Methane-to-Methanol Conversion by Fe(IV)═O. ACS Catal.2018, 8, 975– 986, DOI: 10.1021/acscatal.7b03597[ACS Full Text ], [CAS], Google Scholar57https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhvFCkt7bL&md5=4a77acfe70ad49658dd437ff91ff9599Understanding and Breaking Scaling Relations in Single-Site Catalysis: Methane to Methanol Conversion by FeIV=OACS Catalysis (2018), 8 (2), 975-986CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)Computational high-throughput screening is an essential tool for catalyst design, limited primarily by the efficiency with which accurate predictions can be made. In bulk heterogeneous catalysis, linear free energy relationships (LFERs) have been extensively developed to relate elementary step activation energies, and thus overall catalytic activity, back to the adsorption energies of key intermediates, dramatically reducing the computational cost of screening. The applicability of these LFERs to single-site catalysts remains unclear, owing to the directional, covalent metal-ligand bonds and the broader chem. space of accessible ligand scaffolds. Through a computational screen of nearly 500 model Fe(II) complexes for CH4 hydroxylation, we observe that (1) tuning ligand field strength yields LFERs by comparably shifting energetics of the metal 3d levels that govern the stability of different intermediates and (2) distortion of the metal coordination geometry breaks these LFERs by increasing the splitting between the dxz/dyz and dz2 metal states that govern reactivity. Thus, in single-site catalysts, low Bronsted-Evans-Polanyi slopes for oxo formation, which would limit peak turnover frequency achievable through ligand field tuning alone, can be overcome through structural distortions achievable in exptl. characterized compds. Observations from this screen also motivate the placement of strong HB donors in targeted positions as a scaffold-agnostic strategy for further activity improvement. More generally, our findings motivate broader variation of coordination geometries in reactivity studies with single-site catalysts.
- 58Chu, Y.; Heyndrickx, W.; Occhipinti, G.; Jensen, V. R.; Alsberg, B. K.An Evolutionary Algorithm for De Novo Optimization of Functional Transition Metal Compounds. J. Am. Chem. Soc.2012, 134, 8885– 8895, DOI: 10.1021/ja300865u[ACS Full Text ], [CAS], Google Scholar58https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XlvV2ksrk%253D&md5=fa77234d830c2480eaf04344860f0c65An Evolutionary Algorithm for de Novo Optimization of Functional Transition Metal CompoundsChu, Yunhan; Heyndrickx, Wouter; Occhipinti, Giovanni; Jensen, Vidar R.; Alsberg, Bjoern K.Journal of the American Chemical Society (2012), 134 (21), 8885-8895CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)A review; development of functional inorg. and transition metal compds. is usually based on ad hoc qualified guesses, with computational methods playing a lesser role than in drug discovery. A de novo evolutionary algorithm (EA) is presented that automatically generates transition metal complexes using a search space constrained around chem. meaningful structures assembled from three kinds of fragments: a part shared by all structures and typically contg. the metal center itself, one or several parts consisting of ligand skeletons, and unconstrained parts that may grow and vary freely. In EA optimizations, using a cost-efficient fitness function based on a linear quant. structure-activity relationship model for catalytic activity, we demonstrate the capabilities of the method by retracing the transition from the first-generation, phosphine-based Grubbs olefin metathesis catalysts to second-generation catalysts contg. N-heterocyclic carbene ligands instead of phosphines. Moreover, DFT calcns. on selected high-fitness, last-generation structures from these evolutionary expts. suggest that, in terms of catalytic activity, the structures arrived at by virtual evolution alone compare favorably with existing, highly active catalysts. The structures from the evolution expts. are, however, complex and probably difficult to synthesize, but a set of manually simplified variations thereof might form the leads for a new generation of Grubbs catalysts.
- 59Keinan, S.; Hu, X.; Beratan, D. N.; Yang, W.Designing Molecules with Optimal Properties Using the Linear Combination of Atomic Potentials Approach in an AM1 Semiempirical Framework. J. Phys. Chem. A2007, 111, 176– 181, DOI: 10.1021/jp0646168[ACS Full Text ], [CAS], Google Scholar59https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XhtlSgs73F&md5=49c9371eb6842d1482db01962a263e6dDesigning Molecules with Optimal Properties Using the Linear Combination of Atomic Potentials Approach in an AM1 Semiempirical FrameworkKeinan, Shahar; Hu, Xiangqian; Beratan, David N.; Yang, WeitaoJournal of Physical Chemistry A (2007), 111 (1), 176-181CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)The linear combination of at. potentials (LCAP) approach is implemented in the AM1 semiempirical framework and is used to design mol. structures with optimized properties. The optimization procedure uses property deriv. information to search mol. space and thus avoid direct enumeration and evaluation of each mol. in a library. Two tests are described: the optimization of first hyperpolarizabilities of substituted aroms. and the optimization of a figure of merit for n-type org. semiconductors.
- 60Keinan, S.; Therien, M. J.; Beratan, D. N.; Yang, W.Molecular Design of Porphyrin-Based Nonlinear Optical Materials. J. Phys. Chem. A2008, 112, 12203– 12207, DOI: 10.1021/jp806351d[ACS Full Text ], [CAS], Google Scholar60https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhtlWqtL3K&md5=9ba87f84a22d6642b40a4cb0c01abff9Molecular Design of Porphyrin-Based Nonlinear Optical MaterialsKeinan, Shahar; Therien, Michael J.; Beratan, David N.; Yang, WeitaoJournal of Physical Chemistry A (2008), 112 (47), 12203-12207CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)Nonlinear optical chromophores contg. (porphyrinato)Zn(II), proquinoid, and (terpyridyl)metal(II) building blocks were optimized in a library contg. ∼106 structures using the linear combination of at. potentials (LCAP) methodol. The authors report here the library design and mol. property optimizations. Two basic structural types of large β0 chromophores were examd.: linear and T-shaped motifs. These T-shaped geometries suggest a promising NLO chromophoric architecture for exptl. study and further support the value of performing LCAP searches in large chem. spaces.
- 61Wang, M.; Hu, X.; Beratan, D. N.; Yang, W.Designing Molecules by Optimizing Potentials. J. Am. Chem. Soc.2006, 128, 3228– 3232, DOI: 10.1021/ja0572046[ACS Full Text ], [CAS], Google Scholar61https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XhsVOmtLw%253D&md5=3197d3966132f37386fc4b8c0d01adfeWang, Mingliang; Hu, Xiangqian; Beratan, David N.; Yang, WeitaoJournal of the American Chemical Society (2006), 128 (10), 3228-3232CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)The astronomical no. of accessible discrete chem. structures makes rational mol. design extremely challenging. We formulate the design of mols. with specific tailored properties as performing a continuous optimization in the space of electron-nuclear attraction potentials. The optimization is facilitated by using a linear combination of at. potentials (LCAP), a general framework that creates a continuous property landscape from an otherwise unlinked set of discrete mol.-property values. A demonstration of this approach is given for the optimization of mol. electronic polarizability and hyperpolarizability. We show that the optimal structures can be detd. without enumerating and sep. evaluating the characteristics of the combinatorial no. of possible structures, a process that would be much slower. The LCAP approach may be used with quantum or classical Hamiltonians, suggesting possible applications to drug design and new materials discovery.
- 62Gani, T. Z. H.; Ioannidis, E. I.; Kulik, H. J.Computational Discovery of Hydrogen Bond Design Rules for Electrochemical Ion Separation. Chem. Mater.2016, 28, 6207– 6218, DOI: 10.1021/acs.chemmater.6b02378[ACS Full Text ], [CAS], Google Scholar62https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtlOqurrK&md5=b39b5e18e93adbf41d47f688141ff184Computational Discovery of Hydrogen Bond Design Rules for Electrochemical Ion SeparationGani, Terry Z. H.; Ioannidis, Efthymios I.; Kulik, Heather J.Chemistry of Materials (2016), 28 (17), 6207-6218CODEN: CMATEX; ISSN:0897-4756. (American Chemical Society)Selective ion sepn. is a major challenge with far-ranging impact from H2O desalination to product sepn. in catalysis. Recently introduced ferrocene (Fc)/ferrocenium (Fc+) polymer electrode materials were demonstrated exptl. and theor. to selectively bind carboxylates over perchlorate through weak C-H···O H bond (HB) interactions that favor carboxylates, despite the comparable size and charge of the two species. However, practical application of this technol. in aq. environments requires further selectivity enhancement. Using a 1st-principles discovery approach, the authors study the effect of Fc/Fc+ functional groups (FGs) on the selectivity and reversibility of formate-Fc+ adsorption with respect to perchlorate in aq. soln. The authors' wide design space of 44 FGs enables identification of FGs with higher selectivity and rationalization of trends through electronic energy decompn. anal. or geometric H bonding anal. Overall, the authors observe weaker, longer HBs for perchlorate as compared to formate with Fc+. The authors further identify Fc+ functionalizations that simultaneously increase selectivity for formate in aq. environments but permit rapid release from neutral Fc. The authors introduce the materiaphore, a 3-dimensional abstraction of these design rules, to help guide next-generation material optimization for selective ion sorption. This approach is expected to have broad relevance in computational discovery for mol. recognition, sensing, sepns., and catalysis.
- 63Kim, J. Y.; Steeves, A. H.; Kulik, H. J.Harnessing Organic Ligand Libraries for First-Principles Inorganic Discovery: Indium Phosphide Quantum Dot Precursor Design Strategies. Chem. Mater.2017, 29, 3632– 3643, DOI: 10.1021/acs.chemmater.7b00472[ACS Full Text ], [CAS], Google Scholar63https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXltlWgsrg%253D&md5=c8f7471512784618b9c19c24f08b918cHarnessing Organic Ligand Libraries for First-Principles Inorganic Discovery: Indium Phosphide Quantum Dot Precursor Design StrategiesKim, Jeong Yun; Steeves, Adam H.; Kulik, Heather J.Chemistry of Materials (2017), 29 (8), 3632-3643CODEN: CMATEX; ISSN:0897-4756. (American Chemical Society)Indium phosphide quantum dots (QDs) represent promising replacements for more toxic QDs, but InP QD prodn. lags behind other QD materials due to limited understanding of how to tune InP QD growth. We carry out a first-principles, computational screen of the tuning of In carboxylate precursor chem. to alter the kinetics of elementary steps in InP QD growth. We employ a large database normally used for discovery of therapeutic drug-like mols. to discover design rules for these inorg. complexes while maintaining realism (i.e., stable, synthetically accessible substituents) and providing diversity in a 210-mol. test set. We show the In-O bond cleavage energy, which is tuned through ligand functionalization, to be a useful proxy for In-P bond formation energetics in InP QD synthesis. Energy decompn. anal. on a 32-mol. subset reveals that lower activation energies correlate to later transition states, due to stabilization from greater In-P bond formation and more favorable reaction energetics. Our simulations suggest that altering ligand nucleophilicity tunes the reaction barrier over a 10 kcal/mol range, providing the conjugate acid's pKa as an exptl. handle to lead to better control of growth conditions and to improve synthesized InP QD quality. Importantly, these trends hold regardless of phosphorus precursor chemistries and in the longer chain length ligands typically used in synthesis.
- 64Virshup, A. M.; Contreras-García, J.; Wipf, P.; Yang, W.; Beratan, D. N.Stochastic Voyages into Uncharted Chemical Space Produce a Representative Library of All Possible Drug-Like Compounds. J. Am. Chem. Soc.2013, 135, 7296– 7303, DOI: 10.1021/ja401184g[ACS Full Text ], [CAS], Google Scholar64https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXltV2ntbc%253D&md5=503aa28914b01850b36487ce7ef41ad8Stochastic Voyages into Uncharted Chemical Space Produce a Representative Library of All Possible Drug-Like CompoundsVirshup, Aaron M.; Contreras-Garcia, Julia; Wipf, Peter; Yang, Weitao; Beratan, David N.Journal of the American Chemical Society (2013), 135 (19), 7296-7303CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)The 'small mol. universe' (SMU), the set of all synthetically feasible org. mols. of 500 Da mol. wt. or less, is estd. to contain over 1060 structures, making exhaustive searches for structures of interest impractical. Here, we describe the construction of a 'representative universal library' spanning the SMU that samples the full extent of feasible small mol. chemistries. This library was generated using the newly developed Algorithm for Chem. Space Exploration with Stochastic Search (ACSESS). ACSESS makes two important contributions to chem. space exploration: it allows the systematic search of the unexplored regions of the small mol. universe, and it facilitates the mining of chem. libraries that do not yet exist, providing a near-infinite source of diverse novel compds.
- 65Bohacek, R. S.; McMartin, C.; Guida, W. C.The Art and Practice of Structure-Based Drug Design: A Molecular Modeling Perspective. Med. Res. Rev.1996, 16, 3– 50, DOI: 10.1002/(SICI)1098-1128(199601)16:1<3::AID-MED1>3.0.CO;2-6[Crossref], [PubMed], [CAS], Google Scholar65https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XhtFyls78%253D&md5=edfa592791c111479117feed600dead6The art and practice of structure-based drug design: a molecular modeling perspectiveBohacek, Regine S.; McMartin, Colin; Guida, Wayne C.Medicinal Research Reviews (1996), 16 (1), 3-50CODEN: MRREDD; ISSN:0198-6325. (Wiley)
- 66Grajciar, L.; Heard, C. J.; Bondarenko, A. A.; Polynski, M. V.; Meeprasert, J.; Pidko, E. A.; Nachtigall, P.Towards Operando Computational Modeling in Heterogeneous Catalysis. Chem. Soc. Rev.2018, 47, 8307– 8348, DOI: 10.1039/C8CS00398J[Crossref], [PubMed], [CAS], Google Scholar66https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhs1yntL%252FF&md5=e3daa236843cf11a45226cf9a9b39ebbTowards operando computational modeling in heterogeneous catalysisGrajciar, Lukas; Heard, Christopher J.; Bondarenko, Anton A.; Polynski, Mikhail V.; Meeprasert, Jittima; Pidko, Evgeny A.; Nachtigall, PetrChemical Society Reviews (2018), 47 (22), 8307-8348CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)An increased synergy between exptl. and theor. investigations in heterogeneous catalysis has become apparent during the last decade. Exptl. work has extended from ultra-high vacuum and low temp. towards operando conditions. These developments have motivated the computational community to move from std. descriptive computational models, based on inspection of the potential energy surface at 0 K and low reactant concns. (0 K/UHV model), to more realistic conditions. The transition from 0 K/UHV to operando models has been backed by significant developments in computer hardware and software over the past few decades. New methodol. developments, designed to overcome part of the gap between 0 K/UHV and operando conditions, include (i) global optimization techniques, (ii) ab initio constrained thermodn., (iii) biased mol. dynamics, (iv) microkinetic models of reaction networks and (v) machine learning approaches. The importance of the transition is highlighted by discussing how the mol. level picture of catalytic sites and the assocd. reaction mechanisms changes when the chem. environment, pressure and temp. effects are correctly accounted for in mol. simulations. It is the purpose of this review to discuss each method on an equal footing, and to draw connections between methods, particularly where they may be applied in combination.
- 67Arockiam, P. B.; Bruneau, C.; Dixneuf, P. H.Ruthenium(II)-Catalyzed C-H Bond Activation and Functionalization. Chem. Rev.2012, 112, 5879– 5918, DOI: 10.1021/cr300153j[ACS Full Text ], [CAS], Google Scholar67https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xht1yrtrvN&md5=b403adaa5692ec97d2b81d92ddb4dbbaRuthenium(II)-Catalyzed C-H Bond Activation and FunctionalizationArockiam, Percia Beatrice; Bruneau, Christian; Dixneuf, Pierre H.Chemical Reviews (Washington, DC, United States) (2012), 112 (11), 5879-5918CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review of chem. of ruthenium catalysts in C-H bond activation and functionalization is presented.
- 68Prier, C. K.; Rankic, D. A.; MacMillan, D. W. C.Visible Light Photoredox Catalysis with Transition Metal Complexes: Applications in Organic Synthesis. Chem. Rev.2013, 113, 5322– 5363, DOI: 10.1021/cr300503r[ACS Full Text ], [CAS], Google Scholar68https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXktFKgtLc%253D&md5=e09e6cf6a4c64fd3e8f21d55e151266eVisible Light Photoredox Catalysis with Transition Metal Complexes: Applications in Organic SynthesisPrier, Christopher K.; Rankic, Danica A.; MacMillan, David W. C.Chemical Reviews (Washington, DC, United States) (2013), 113 (7), 5322-5363CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. This review will highlight the early work on the use of transition metal complexes as photoredox catalysts to promote reactions of org. compds. (prior to 2008), as well as cover the surge of work that has appeared since 2008. We have for the most part grouped reactions according to whether the org. substrate undergoes redn., oxidn., or a redox neutral reaction and throughout have sought to highlight the variety of reactive intermediates that may be accessed via this general reaction manifold.
- 69Rouquet, G.; Chatani, N.Catalytic Functionalization of C(sp2)-H and C(sp3)-H Bonds by Using Bidentate Directing Groups. Angew. Chem., Int. Ed.2013, 52, 11726– 11743, DOI: 10.1002/anie.201301451[Crossref], [CAS], Google Scholar69https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsF2ntLrF&md5=70cf2067c1f766af742178dc5e04341fCatalytic functionalization of C(sp2)-H and C(sp3)-H bonds by using bidentate directing groupsAngewandte Chemie, International Edition (2013), 52 (45), 11726-11743CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)A review. C-H bonds are ubiquitous in org. compds. It would, therefore, appear that direct functionalization of substrates by activation of C-H bonds would eliminate the multiple steps and limitations assocd. with the prepn. of functionalized starting materials. Regioselectivity is an important issue because org. mols. can contain a wide variety of C-H bonds. The use of a directing group can largely overcome the issue of regiocontrol by allowing the catalyst to come into proximity with the targeted C-H bonds. A wide variety of functional groups have been evaluated for use as directing groups in the transformation of C-H bonds. In 2005, Daugulis reported the arylation of unactivated C(sp3)-H bonds by using 8-aminoquinoline and picolinamide as bidentate directing groups, with Pd(OAc)2 as the catalyst. Encouraged by these promising results, a no. of transformations of C-H bonds have since been developed by using systems based on bidentate directing groups. In this review, recent advances in this area are discussed.
- 70Schultz, D. M.; Yoon, T. P.Solar Synthesis: Prospects in Visible Light Photocatalysis. Science2014, 343, 1239176, DOI: 10.1126/science.1239176[Crossref], [PubMed], [CAS], Google Scholar70https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2cvovFejsg%253D%253D&md5=3c1c0a23eea300c9dbe2c46f9736eb87Solar synthesis: prospects in visible light photocatalysisScience (New York, N.Y.) (2014), 343 (6174), 1239176 ISSN:.Chemists have long aspired to synthesize molecules the way that plants do-using sunlight to facilitate the construction of complex molecular architectures. Nevertheless, the use of visible light in photochemical synthesis is fundamentally challenging because organic molecules tend not to interact with the wavelengths of visible light that are most strongly emitted in the solar spectrum. Recent research has begun to leverage the ability of visible light-absorbing transition metal complexes to catalyze a broad range of synthetically valuable reactions. In this review, we highlight how an understanding of the mechanisms of photocatalytic activation available to these transition metal complexes, and of the general reactivity patterns of the intermediates accessible via visible light photocatalysis, has accelerated the development of this diverse suite of reactions.
- 71Shaffer, D. W.; Bhowmick, I.; Rheingold, A. L.; Tsay, C.; Livesay, B. N.; Shores, M. P.; Yang, J. Y.Spin-State Diversity in a Series of Co(II) PNP Pincer Bromide Complexes. Dalton Trans.2016, 45, 17910– 17917, DOI: 10.1039/C6DT03461F[Crossref], [PubMed], [CAS], Google Scholar71https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xhs1ygtL%252FO&md5=9e0d26504b056b61c90c2e54d3959984Spin-state diversity in a series of Co(II) PNP pincer bromide complexesShaffer, David W.; Bhowmick, Indrani; Rheingold, Arnold L.; Tsay, Charlene; Livesay, Brooke N.; Shores, Matthew P.; Yang, Jenny Y.Dalton Transactions (2016), 45 (44), 17910-17917CODEN: DTARAF; ISSN:1477-9226. (Royal Society of Chemistry)The authors describe the structural and electronic impacts of modifying the bridging atom in a family of Co(II) pincer complexes Co(t-Bu)2PEPyEP(t-Bu)2Br2 (Py = pyridine, E = CH2, NH, and O for compds. 1-3, resp.). Structural characterization by single crystal x-ray diffraction indicates that compds. 1 and 3 are 5-coordinate complexes with both bromides bound to the Co ion, while compd. 2 is square planar with one bromide in the outer coordination sphere. The redn. potentials of 1-3, characterized by cyclic voltammetry, are consistent with the increasing electron-withdrawing character of the pincer ligand as the linker (E) between the pyridine and phosphine arms becomes more electroneg. Magnetic property studies of compds. 1 and 2 confirm high- and low-spin behavior, resp., through a broad temp. range. However, complex 3 features an unusual combination of high spin S = 3/2 Co(II) and temp. dependent spin-crossover between S = 3/2 and S = 1/2 states. The different magnetic behaviors obsd. among the three CoBr2 pincer complexes reflects the importance of small ligand perturbations on overall coordination geometry and resulting spin state properties.
- 72Tsay, C.; Yang, J. Y.Electrocatalytic Hydrogen Evolution under Acidic Aqueous Conditions and Mechanistic Studies of a Highly Stable Molecular Catalyst. J. Am. Chem. Soc.2016, 138, 14174– 14177, DOI: 10.1021/jacs.6b05851[ACS Full Text ], [CAS], Google Scholar72https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtFKms7%252FL&md5=b314b82c3f0e9110a5b1b69f6d9ea149Electrocatalytic Hydrogen Evolution under Acidic Aqueous Conditions and Mechanistic Studies of a Highly Stable Molecular CatalystJournal of the American Chemical Society (2016), 138 (43), 14174-14177CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Electrocatalytic activity of a water-sol. nickel complex, [Ni(DHMPE)2]2+ (DHMPE = 2-bis(di(hydroxymethyl)phosphino)ethane), for the hydrogen evolution reaction (HER) at pH 1 is reported. The catalyst functions at a rate of ∼103 s-1 (kobs) with high Faradaic efficiency. Quantification of the complex before and after 18+ hours of electrolysis reveals negligible decompn. under catalytic conditions. Although highly acidic conditions are common in electrolytic cells, this is a rare example of a homogeneous catalyst for HER that functions with high stability at low pH. The stability of the compd. and proposed catalytic intermediates enabled detailed mechanistic studies. The thermodn. parameters governing electron and proton transfer were used to det. the appropriate reductants and acids to access the catalytic cycle in a stepwise fashion, permitting direct spectroscopic identification of intermediates. These studies support a mechanism for proton redn. that proceeds through two-electron redn. of the nickel(II) complex, protonation to generate [HNi(DHMPE)2]+, and further protonation to initiate hydrogen bond formation.
- 73Ashley, D. C.; Jakubikova, E.Ironing out the Photochemical and Spin-Crossover Behavior of Fe (II) Coordination Compounds with Computational Chemistry. Coord. Chem. Rev.2017, 337, 97– 111, DOI: 10.1016/j.ccr.2017.02.005[Crossref], [CAS], Google Scholar73https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXjt1Kjsrw%253D&md5=a6ae75e9fd6d88060425623023792b9eIroning out the photochemical and spin-crossover behavior of Fe(II) coordination compounds with computational chemistryCoordination Chemistry Reviews (2017), 337 (), 97-111CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)Effective strategies for designing Fe(II) coordination complexes with specifically tailored spin-state energetics can lead to advances in many areas of inorg. and materials chem. These include, but are not limited to, rational development of novel spin crossover complexes, efficient chromophores for photosensitization of dye-sensitized solar cells, and multifunctional materials. As the spin-state ordering of transition metal complexes is strongly rooted in their electronic structures, computational chem. has naturally played an important role in assisting exptl. work in this area. Unfortunately, despite many advances, accurate detn. of the spin-state energetics of Fe(II) complexes still poses a remarkable challenge for virtually all applicable forms of electronic structure theory due to being controlled by a delicate balancing between correlation and exchange effects. This review focuses on some of the more notable successes and failures of modern electronic structure theory in properly describing these systems in the absence of solid-state effects. The strengths and weaknesses of using traditional wavefunction based methods and d. functional theory are considered, and illustrative examples are provided to demonstrate that the modern computational chemist should make use of exptl. data whenever possible and expect to utilize a combination of methods to obtain the best results. The review closes by briefly surveying some of the many interesting combined computational and exptl. studies of Fe(II) chem. that have lead to greater fundamental insight and practical understanding of this challenging class of systems.
- 74Bowman, D. N.; Bondarev, A.; Mukherjee, S.; Jakubikova, E.Tuning the Electronic Structure of Fe(II) Polypyridines via Donor Atom and Ligand Scaffold Modifications: A Computational Study. Inorg. Chem.2015, 54, 8786– 8793, DOI: 10.1021/acs.inorgchem.5b01409[ACS Full Text ], [CAS], Google Scholar74https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtlOrsLbN&md5=d57d2f7ec920f5dba73a68df25bded34Tuning the Electronic Structure of Fe(II) Polypyridines via Donor Atom and Ligand Scaffold Modifications: A Computational StudyBowman, David N.; Bondarev, Alexey; Mukherjee, Sriparna; Jakubikova, ElenaInorganic Chemistry (2015), 54 (17), 8786-8793CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)Fe(II) polypyridines are an important class of pseudo-octahedral metal complexes known for their potential applications in mol. electronic switches, data storage and display devices, sensors, and dye-sensitized solar cells. Fe(II) polypyridines have a d6 electronic configuration and pseudo-octahedral geometry and can therefore possess either a high-spin (quintet) or a low-spin (singlet) ground state. In this study, we investigate a series of complexes based on [Fe(tpy)2]2+ (tpy = 2,2';6',2'-terpyridine) and [Fe(dcpp)2]2+ (dcpp = 2,6-bis(2-carboxypyridyl)pyridine). The ligand field strength in these complexes is systematically tuned by replacing the central pyridine with five-membered (N-heterocyclic carbene, pyrrole, furan) or six-membered (aryl, thiazine-1,1-dioxide, 4-pyrone) moieties. To det. the impact of ligand substitutions on the relative energies of metal-centered states, the singlet, triplet, and quintet states of the Fe(II) complexes were optimized in water (PCM) using d. functional theory at the B3LYP+D2 level with 6-311G* (nonmetals) and SDD (Fe) basis sets. It was found that the dcpp ligand scaffold allows for a more ideal octahedral coordination environment in comparison to the tpy ligand scaffold. The presence of six-membered central rings also allows for a more ideally octahedral coordination environment relative to five-membered central rings, regardless of the ligand scaffold. We find that the ligand field strength in the Fe(II) polypyridines can be tuned by altering the donor atom identity, with C donor atoms providing the strongest ligand field.
- 75Yella, A.; Lee, H. W.; Tsao, H. N.; Yi, C. Y.; Chandiran, A. K.; Nazeeruddin, M. K.; Diau, E. W. G.; Yeh, C. Y.; Zakeeruddin, S. M.; Gratzel, M.Porphyrin-Sensitized Solar Cells with Cobalt (II/III)-Based Redox Electrolyte Exceed 12% Efficiency. Science2011, 334, 629– 634, DOI: 10.1126/science.1209688[Crossref], [PubMed], [CAS], Google Scholar75https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtlyqu7nI&md5=23304b8a38934e2a776cba498b05fd21Porphyrin-Sensitized Solar Cells with Cobalt (II/III)-Based Redox Electrolyte Exceed 12% EfficiencyYella, Aswani; Lee, Hsuan-Wei; Tsao, Hoi Nok; Yi, Chenyi; Chandiran, Aravind Kumar; Nazeeruddin, Md. Khaja; Diau, Eric Wei-Guang; Yeh, Chen-Yu; Zakeeruddin, Shaik M.; Graetzel, MichaelScience (Washington, DC, United States) (2011), 334 (6056), 629-634CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)The iodide/triiodide redox shuttle has limited the efficiencies accessible in dye-sensitized solar cells. Here, the authors report mesoscopic solar cells that incorporate a Co(II/III)tris(bipyridyl)-based redox electrolyte in conjunction with a custom synthesized donor-π-bridge-acceptor zinc porphyrin dye as sensitizer (designated YD2-o-C8). The specific mol. design of YD2-o-C8 greatly retards the rate of interfacial back electron transfer from the conduction band of the nanocryst. titanium dioxide film to the oxidized cobalt mediator, which enables attainment of strikingly high photovoltages approaching 1 V. Because the YD2-o-C8 porphyrin harvests sunlight across the visible spectrum, large photocurrents are generated. Cosensitization of YD2-o-C8 with another org. dye further enhances the performance of the device, leading to a measured power conversion efficiency of 12.3% under simulated air mass 1.5 global sunlight.
- 76Czerwieniec, R.; Yu, J. B.; Yersin, H.Blue-Light Emission of Cu(I) Complexes and Singlet Harvesting. Inorg. Chem.2011, 50, 8293– 8301, DOI: 10.1021/ic200811a[ACS Full Text ], [CAS], Google Scholar76https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXpslaju78%253D&md5=ff8a63e35a70c801bc3a4bdd0f60db5fBlue-Light Emission of Cu(I) Complexes and Singlet HarvestingInorganic Chemistry (2011), 50 (17), 8293-8301CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)Strongly luminescent neutral copper(I) complexes of the type Cu(pop)(NN), with pop = bis(2-(diphenylphosphanyl)phenyl)ether and NN = bis(pyrazol-1-yl)borohydrate (pz2BH2), tetrakis(pyrazol-1-yl)borate (pz4B), or bis(pyrazol-1-yl)-biphenyl-borate (pz2Bph2), are readily accessible in reactions of Cu(acetonitrile)4+ with equimolar amts. of the pop and NN ligands at ambient temp. All products were characterized by means of single crystal x-ray diffractometry. The compds. exhibit very strong blue/white luminescence with emission quantum yields of up to 90%. Investigations of spectroscopic properties and the emission decay behavior in the temp. range between 1.6 K and ambient temp. allow us to assign the emitting electronic states. Below 100 K, the emission decay times are in the order of many hundreds of microseconds. Therefore, it is concluded that the emission stems from the lowest triplet state. This state is assigned to a metal-to-ligand charge-transfer state (3MLCT) involving Cu-3d and pop-π* orbitals. With temp. increase, the emission decay time is drastically reduced to e.g. to 13 μs (Cu(pop)(pz2Bph2)) at ambient temp. At this temp., the complexes exhibit high emission quantum yields, as neat material or doped into poly(Me methacrylate) (PMMA). This behavior is assigned to an efficient thermal population of a singlet state (being classified as 1MLCT), which lies only 800 to 1300 cm-1 above the triplet state, depending on the individual complex. Thus, the resulting emission at ambient temp. largely represents a fluorescence. For applications in OLEDs and LEECs, for example, this type of thermally activated delayed fluorescence (TADF) creates a new mechanism that allows to harvest both singlet and triplet excitons (excitations) in the lowest singlet state. This effect of singlet harvesting leads to drastically higher radiative rates than obtainable for emissions from triplet states of Cu(I) complexes. Crystallog. data are given.
- 77Dias, F. B.; Bourdakos, K. N.; Jankus, V.; Moss, K. C.; Kamtekar, K. T.; Bhalla, V.; Santos, J.; Bryce, M. R.; Monkman, A. P.Triplet Harvesting with 100% Efficiency by Way of Thermally Activated Delayed Fluorescence in Charge Transfer OLED Emitters. Adv. Mater.2013, 25, 3707– 3714, DOI: 10.1002/adma.201300753[Crossref], [PubMed], [CAS], Google Scholar77https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXotFSmtrg%253D&md5=c5afb072b044a1bde2416f129952f4a1Triplet Harvesting with 100% Efficiency by Way of Thermally Activated Delayed Fluorescence in Charge Transfer OLED EmittersDias, Fernando B.; Bourdakos, Konstantinos N.; Jankus, Vygintas; Moss, Kathryn C.; Kamtekar, Kiran T.; Bhalla, Vandana; Santos, Jose; Bryce, Martin R.; Monkman, Andrew P.Advanced Materials (Weinheim, Germany) (2013), 25 (27), 3707-3714CODEN: ADVMEW; ISSN:0935-9648. (Wiley-VCH Verlag GmbH & Co. KGaA)Org. light-emitting diodes (OLEDs) have their performance limited by the no. of emissive singlet states created upon charge recombination (25%). Recently, a novel strategy has been proposed, based on thermally activated up-conversion of triplet to singlet states, yielding delayed fluorescence (TADF), which greatly enhances electroluminescence. The energy barrier for this reverse intersystem crossing mechanism is proportional to the exchange energy (ΔEST) between the singlet and triplet states; therefore, materials with intramol. charge transfer (ICT) states, where it is known that the exchange energy is small, are perfect candidates. However, here it is shown that triplet states can be harvested with 100% efficiency via TADF, even in materials with ΔEST of more than 20 kT (where k is the Boltzmann const. and T is the temp.) at room temp. The key role played by lone pair electrons in achieving this high efficiency in a series of ICT mols. is elucidated. The results show the complex photophysics of efficient TADF materials and give clear guidelines for designing new emitters.
- 78Kuttipillai, P. S.; Zhao, Y. M.; Traverse, C. J.; Staples, R. J.; Levine, B. G.; Lunt, R. R.Phosphorescent Nanocluster Light-Emitting Diodes. Adv. Mater.2016, 28, 320– 326, DOI: 10.1002/adma.201504548[Crossref], [PubMed], [CAS], Google Scholar78https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhvVaqu7rM&md5=2a4d02cf90ed075fdab8acd8901e6775Kuttipillai, Padmanaban S.; Zhao, Yimu; Traverse, Christopher J.; Staples, Richard J.; Levine, Benjamin G.; Lunt, Richard R.Advanced Materials (Weinheim, Germany) (2016), 28 (2), 320-326CODEN: ADVMEW; ISSN:0935-9648. (Wiley-VCH Verlag GmbH & Co. KGaA)Inorg. phosphorescent metal halide nanoclusters are demonstrated as an entirely new platform for tunable and efficient light-emitting diodes. Here, we report the integration of molybdenum halide nanocluster salts into optically and elec. pumped nanocluster light-emitting devices and demonstrate tunable emission by means of varying cation substitution. Here, we report the integration of molybdenum halide nanocluster salts into optically and elec. pumped nanocluster light-emitting devices and demonstrate tunable emission by means of varying cation substitution. While the efficiencies of the proof-of-principle elec. pumped devices are not fully optimized, the optically pumped nanocluster devices show quantum efficiencies of 2.5% for peak emission at 800 nm. We utilize both luminescent and electroluminescent transient dynamics to understand the nanocluster photophysics and analyze time-dependent d. functional theory (TDDFT) calcns. performed on the core cluster to gain insights about the nature of the phosphorescent emitting state.
- 79Leitl, M. J.; Kuchle, F. R.; Mayer, H. A.; Wesemann, L.; Yersin, H.Brightly Blue and Green Emitting Cu(I) Dimers for Singlet Harvesting in Oleds. J. Phys. Chem. A2013, 117, 11823– 11836, DOI: 10.1021/jp402975d[ACS Full Text ], [CAS], Google Scholar79https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhtlaisbnM&md5=0c0994b85d6f4a0c0f42671ef32df806Brightly Blue and Green Emitting Cu(I) Dimers for Singlet Harvesting in OLEDsLeitl, Markus J.; Kuechle, Fritz-Robert; Mayer, Hermann A.; Wesemann, Lars; Yersin, HartmutJournal of Physical Chemistry A (2013), 117 (46), 11823-11836CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)With the chelating aminophosphane ligands Ph2P-(o-C6H4)-NMe2 (PNMe2) and Ph2P-(o-C6H4)-NC4H8 (PNpy), the 4 halide (Cl, Br, I)-bridged Cu coordination compds. [Cu(μ-Cl)(PNMe2)]2 (1), [Cu(μ-Br)(PNMe2)]2 (2), [Cu(μ-I)(PNMe2)]2 (3), and [Cu(μ-I)(PNpy)]2 (4) were synthesized and structurally characterized. Their photophys. properties were studied. The complexes exhibit strong blue (λmax = 464 (3) and 465 nm (4)) and green (λmax = 506 (1) and 490 nm (2)) luminescence as powders with quantum yields of ≤65% at decay times of ≥4.1 μs. A study of the emission decay behavior at 1.3-300 K gives insight into the nature of the emitting states. At temps. T .ltorsim. 60 K, the decay times of the studied compds. are several hundred μs long, which indicates that the emission originates from a triplet state (T1 state). DFT calcns. show that this state is of (metal+halide)-to-ligand charge transfer 3(M+X)-LCT character. Studies at 1.3 K allow gaining insight into the 3 triplet substates, in particular, to det. the individual substate decay times being as long as a few ms. The zero-field splittings are < 1 or 2 cm-1. With an anal. of these data, conclusions about the effectiveness of spin-orbit coupling (SOC) can be drawn. The large differences of SOC consts. of the halides are not obviously displayed in the triplet state properties. With a temp. increase from T ≈ 60 to 300 K, a significant decrease of the emission decay time by almost 2 orders of magnitude is obsd., and at ambient temp., the decay times amt. only to ∼4-7 μs without a significant redn. of the emission quantum yields. This drastic decrease of the (radiative) decay time is a result of the thermal population of a short-lived singlet state (S1 state) that lies energetically only a few hundred wavenos. (460-630 cm-1) higher than the T1 state. Such an emission mechanism corresponds to a thermally-activated delayed fluorescence (TADF). At ambient temp., almost only a delayed fluorescence (∼98%) is obsd. Compds. showing this mechanism are highly attractive for applications in OLEDs or LEECs as, in principle, it is possible to harvest all singlet and triplet excitons for the generation of light in the lowest excited singlet state. This effect represents the singlet harvesting mechanism.
- 80Linfoot, C. L.; Leitl, M. J.; Richardson, P.; Rausch, A. F.; Chepelin, O.; White, F. J.; Yersin, H.; Robertson, N.Thermally Activated Delayed Fluorescence (TADF) and Enhancing Photoluminescence Quantum Yields of Cu-I(Diimine)(Diphosphine)(+) Complexes-Photophysical, Structural, and Computational Studies. Inorg. Chem.2014, 53, 10854– 10861, DOI: 10.1021/ic500889s[ACS Full Text ], [CAS], Google Scholar80https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXht1SqsbfE&md5=59f450a82d6fc5cf172c8a80c6f6d91eThermally Activated Delayed Fluorescence (TADF) and Enhancing Photoluminescence Quantum Yields of [CuI(diimine)(diphosphine)]+ Complexes-Photophysical, Structural, and Computational StudiesLinfoot, Charlotte L.; Leitl, Markus J.; Richardson, Patricia; Rausch, Andreas F.; Chepelin, Oleg; White, Fraser J.; Yersin, Hartmut; Robertson, NeilInorganic Chemistry (2014), 53 (20), 10854-10861CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)[Cu(I)(POP)(dmbpy)][BF4] and [Cu(I)(POP)(tmbpy)][BF4] (dmbpy = 4,4'-dimethyl-2,2'-bipyridyl; tmbpy = 4,4',6,6'-tetramethyl-2,2'-bipyridyl; POP = bis[2-(diphenylphosphino)-phenyl]ether) were studied in a wide temp. range by steady-state and time-resolved emission spectroscopy in fluid soln., frozen soln., and as solid powders. Emission quantum yields of up to 74% were obsd. for 2 in a rigid matrix (powder), substantially higher than for 1 of ∼9% under the same conditions. Importantly, the emission of 2 at ambient temp. represents a thermally activated delayed fluorescence (TADF) which renders the compd. to be a good candidate for singlet harvesting in OLEDs. The role of steric constraints within the complexes, in particular their influences on the emission quantum yields, were studied by hybrid-DFT calcns. for the excited triplet state of 1 and 2 while manipulating the torsion angle between the bipyridyl and POP ligands. Both complexes showed similar flexibility within a ±10° range of the torsion angle; however, 2 appeared limited to this range, whereas 1 could be further twisted with little energy demand. A restricted flexibility leads to a redn. of nonradiative deactivation and thus an increase of emission quantum yield.
- 81Zink, D. M.; Bachle, M.; Baumann, T.; Nieger, M.; Kuhn, M.; Wang, C.; Klopper, W.; Monkowius, U.; Hofbeck, T.; Yersin, H.; Brase, S.Synthesis, Structure, and Characterization of Dinuclear Copper(I) Halide Complexes with PAN Ligands Featuring Exciting Photoluminescence Properties. Inorg. Chem.2013, 52, 2292– 2305, DOI: 10.1021/ic300979c[ACS Full Text ], [CAS], Google Scholar81https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhsV2ru7bE&md5=7bbf16d7368c5ae6819aa4f308e2de29Synthesis, Structure, and Characterization of Dinuclear Copper(I) Halide Complexes with P%N Ligands Featuring Exciting Photoluminescence PropertiesZink, Daniel M.; Baechle, Michael; Baumann, Thomas; Nieger, Martin; Kuehn, Michael; Wang, Cong; Klopper, Wim; Monkowius, Uwe; Hofbeck, Thomas; Yersin, Hartmut; Brase, StefanInorganic Chemistry (2013), 52 (5), 2292-2305CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)Highly luminescent dinuclear Cu(I) complexes were synthesized in good yields using a modular ligand system of easily accessible diphenylphosphinopyridine-type P%N ligands. Characterization of these complexes via x-ray crystallog. studies and elemental anal. revealed a dinuclear complex structure with a butterfly-shaped metal-halide core. The complexes feature emission covering the visible spectrum from blue to red together with high quantum yields up to 96%. D. functional theory calcns. show that the HOMO consists mainly of orbitals of both the metal core and the bridging halides, while the LUMO resides dominantly on the heterocyclic part of the P%N ligands. Therefore, modification of the heterocyclic moiety of the bridging ligand allows for systematic tuning of the luminescence wavelength. By increasing the arom. system of the N-heterocycle or through functionalization of the pyridyl moiety, complexes with emission maxima from 481 to 713 nm were obtained. For a representative compd., the ambient-temp. emission can be assigned as a thermally activated delayed fluorescence, featuring an attractively short emission decay time of only 6.5 μs at φPL = 0.8. It is proposed to apply these compds. for singlet harvesting in OLEDs.
- 82Weininger, D.Smiles, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules. J. Chem. Inf. Model.1988, 28, 31– 36, DOI: 10.1021/ci00057a005[ACS Full Text ], [CAS], Google Scholar82https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL1cXnsVeqsA%253D%253D&md5=04592975f9dd3c0ce3c1ad618ba2b17dSMILES, a chemical language and information system. 1. Introduction to methodology and encoding rulesJournal of Chemical Information and Computer Sciences (1988), 28 (1), 31-6CODEN: JCISD8; ISSN:0095-2338.The SMILES (simplified mol. input line entry system) chem. notation system is described for information processing. The system is based on principles of mol. graph theory and it allows structure specification by use of a very small and natural grammar well suited for high-speed machine processing. The system is easy to use, has high machine compatibility, and allows many computer applications, including notation generation, const. speed database retrieval, substructure searching, and property prediction models.
- 83O’Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R.Open Babel: An Open Chemical Toolbox. J. Cheminf.2011, 3, 33, DOI: 10.1186/1758-2946-3-33[Crossref], [PubMed], [CAS], Google Scholar83https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhsVWjurbF&md5=74e4f19b7f87417f916d57f7abcfb761O'Boyle, Noel M.; Banck, Michael; James, Craig A.; Morley, Chris; Vandermeersch, Tim; Hutchison, Geoffrey R.Journal of Cheminformatics (2011), 3 (), 33CODEN: JCOHB3; ISSN:1758-2946. (Chemistry Central Ltd.)Background: A frequent problem in computational modeling is the interconversion of chem. structures between different formats. While std. interchange formats exist (for example, Chem. Markup Language) and de facto stds. have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chem. data, differences in the data stored by different formats (0D vs. 3D, for example), and competition between software along with a lack of vendor-neutral formats. Results: We discuss, for the first time, Open Babel, an open-source chem. toolbox that speaks the many languages of chem. data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chem. and mol. data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions: Open Babel presents a soln. to the proliferation of multiple chem. file formats. In addn., it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chem. data in areas such as org. chem., drug design, materials science, and computational chem. It is freely available under an open-source license.
- 84Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J.Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc.1996, 118, 11225– 11236, DOI: 10.1021/ja9621760[ACS Full Text ], [CAS], Google Scholar84https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XmtlOitrs%253D&md5=fef2924a69421881390282aa309ae91bDevelopment and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic LiquidsJorgensen, William L.; Maxwell, David S.; Tirado-Rives, JulianJournal of the American Chemical Society (1996), 118 (45), 11225-11236CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)The parametrization and testing of the OPLS all-atom force field for org. mols. and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER all-atom force field. The torsional parameters were detd. by fitting to rotational energy profiles obtained from ab initio MO calcns. at the RHF/6-31G*//RHF/6-31G* level for more than 50 org. mols. and ions. The quality of the fits was high with av. errors for conformational energies of less than 0.2 kcal/mol. The force-field results for mol. structures are also demonstrated to closely match the ab initio predictions. The nonbonded parameters were developed in conjunction with Monte Carlo statistical mechanics simulations by computing thermodn. and structural properties for 34 pure org. liqs. including alkanes, alkenes, alcs., ethers, acetals, thiols, sulfides, disulfides, aldehydes, ketones, and amides. Av. errors in comparison with exptl. data are 2% for heats of vaporization and densities. The Monte Carlo simulations included sampling all internal and intermol. degrees of freedom. It is found that such non-polar and monofunctional systems do not show significant condensed-phase effects on internal energies in going from the gas phase to the pure liqs.
- 85Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A.Development and Testing of a General Amber Force Field. J. Comput. Chem.2004, 25, 1157– 1174, DOI: 10.1002/jcc.20035[Crossref], [PubMed], [CAS], Google Scholar85https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXksFakurc%253D&md5=2992017a8cf51f89290ae2562403b115Development and testing of a general Amber force fieldWang, Junmei; Wolf, Romain M.; Caldwell, James W.; Kollman, Peter A.; Case, David A.Journal of Computational Chemistry (2004), 25 (9), 1157-1174CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)We describe here a general Amber force field (GAFF) for org. mols. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most org. and pharmaceutical mols. that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited no. of atom types, but incorporates both empirical and heuristic models to est. force consts. and partial at. charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallog. structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 Å, which is comparable to that of the Tripos 5.2 force field (0.25 Å) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 Å, resp.). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermol. energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 Å and 1.2 kcal/mol, resp. These data are comparable to results from Parm99/RESP (0.16 Å and 1.18 kcal/mol, resp.), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to expt.) is about 0.5 kcal/mol. GAFF can be applied to wide range of mols. in an automatic fashion, making it suitable for rational drug design and database searching.
- 86Brandenburg, J. G.; Grimme, S.Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB). J. Phys. Chem. Lett.2014, 5, 1785– 1789, DOI: 10.1021/jz500755u[ACS Full Text ], [CAS], Google Scholar86https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXnsVegsbk%253D&md5=7c4e54ca1b8d5ed35fba996028a06f58Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB)Journal of Physical Chemistry Letters (2014), 5 (11), 1785-1789CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)The ambitious goal of org. crystal structure prediction challenges theor. methods regarding their accuracy and efficiency. Dispersion-cor. d. functional theory (DFT-D) in principle is applicable, but the computational demands, for example, to compute a huge no. of polymorphs, are too high. Here, we demonstrate that this task can be carried out by a dispersion-cor. d. functional tight binding (DFTB) method. The semiempirical Hamiltonian with the D3 correction can accurately and efficiently model both solid- and gas-phase inter- and intramol. interactions at a speed up of 2 orders of magnitude compared to DFT-D. The mean abs. deviations for interaction (lattice) energies for various databases are typically 2-3 kcal/mol (10-20%), i.e., only about two times larger than those for DFT-D. For zero-point phonon energies, small deviations of <0.5 kcal/mol compared to DFT-D are obtained.
- 87Gaus, M.; Cui, Q.; Elstner, M.DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB). J. Chem. Theory Comput.2011, 7, 931– 948, DOI: 10.1021/ct100684s[ACS Full Text ], [CAS], Google Scholar87https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXjtVKgu74%253D&md5=179659060fa503023375266a674d02e7DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)Journal of Chemical Theory and Computation (2011), 7 (4), 931-948CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)The self-consistent-charge d.-functional tight-binding method (SCC-DFTB) is an approx. quantum chem. method derived from d. functional theory (DFT) based on a second-order expansion of the DFT total energy around a ref. d. In the present study, we combine earlier extensions and improve them consistently with, first, an improved Coulomb interaction between at. partial charges and, second, the complete third-order expansion of the DFT total energy. These modifications lead us to the next generation of the DFTB methodol. called DFTB3, which substantially improves the description of charged systems contg. elements C, H, N, O, and P, esp. regarding hydrogen binding energies and proton affinities. As a result, DFTB3 is particularly applicable to biomol. systems. Remaining challenges and possible solns. are also briefly discussed.
- 88Korth, M.; Thiel, W.Benchmarking Semiempirical Methods for Thermochemistry, Kinetics, and Noncovalent Interactions: OMx Methods Are Almost as Accurate and Robust as DFT-GGA Methods for Organic Molecules. J. Chem. Theory Comput.2011, 7, 2929– 2936, DOI: 10.1021/ct200434a[ACS Full Text ], [CAS], Google Scholar88https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtVagsLnP&md5=0079e95651d673b00b4643413218490fBenchmarking Semiempirical Methods for Thermochemistry, Kinetics, and Noncovalent Interactions: OMx Methods Are Almost As Accurate and Robust As DFT-GGA Methods for Organic MoleculesJournal of Chemical Theory and Computation (2011), 7 (9), 2929-2936CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)Semiempirical quantum mech. (SQM) methods offer a fast approx. treatment of the electronic structure and the properties of large mols. Careful benchmarks are required to establish their accuracy. Here, we report a validation of std. SQM methods using a subset of the comprehensive GMTKN24 database for general main group thermochem., kinetics, and noncovalent interactions, which has recently been introduced to evaluate d. functional theory (DFT) methods. For all SQM methods considered presently, parameters are available for the elements H, C, N, and O, and consequently, we have extd. from the GMTKN24 database all species contg. only these four elements (excluding multireference cases). The resulting GMTKN24-hcno database has 370 entries (derived from 593 energies) compared with 715 entries (derived from 1033 energies) in the original GMTKN24 database. The current benchmark covers established std. SQM methods (AM1, PM6), more recent approaches with orthogonalization corrections (OM1, OM2, OM3), and the self-consistent-charge d. functional tight binding method (SCC-DFTB). The results are compared against each other and against DFT results using std. functionals. We find that the OMx methods outperform AM1, PM6, and SCC-DFTB by a significant margin, with a substantial gain in accuracy esp. for OM2 and OM3. These latter methods are quite accurate even in comparison with DFT, with an overall mean abs. deviation of 6.6 kcal/mol for PBE and 7.9 kcal/mol for OM3. The OMx methods are also remarkably robust with regard to the unusual bonding situations encountered in the 'mindless' MB08-165 test set, for which all other SQM methods fail badly.
- 89Gallandi, L.; Marom, N.; Rinke, P.; Körzdörfer, T.Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules II: Non-Empirically Tuned Long-Range Corrected Hybrid Functionals. J. Chem. Theory Comput.2016, 12, 605– 614, DOI: 10.1021/acs.jctc.5b00873[ACS Full Text ], [CAS], Google Scholar89https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xis1GisQ%253D%253D&md5=1c32cfab4c7179be6a885866297b1089Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules II: Non-Empirically Tuned Long-Range Corrected Hybrid FunctionalsGallandi, Lukas; Marom, Noa; Rinke, Patrick; Koerzdoerfer, ThomasJournal of Chemical Theory and Computation (2016), 12 (2), 605-614CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)The performance of non-empirically tuned long-range cor. hybrid functionals for the prediction of vertical ionization potentials (IPs) and electron affinities (EAs) is assessed for a set of 24 org. acceptor mols. Basis set-extrapolated coupled cluster singles, doubles, and perturbative triples [CCSD(T)] calcns. serve as a ref. for this study. Compared to std. exchange-correlation functionals, tuned long-range cor. hybrid functionals produce highly reliable results for vertical IPs and EAs, yielding mean abs. errors on par with computationally more demanding GW calcns. In particular, it is demonstrated that long-range cor. hybrid functionals serve as ideal starting points for non-self-consistent GW calcns.
- 90Kubinyi, H.QSAR and 3D QSAR in Drug Design Part 1: Methodology. Drug Discovery Today1997, 2, 457– 467, DOI: 10.1016/S1359-6446(97)01079-9[Crossref], [CAS], Google Scholar90https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2sXns1CqtL4%253D&md5=4eac3be8867dda8d65d68385b4e73a65QSAR and 3D QSAR in drug design. Part 1: methodologyDrug Discovery Today (1997), 2 (11), 457-467CODEN: DDTOFS; ISSN:1359-6446. (Elsevier)A review with 45 refs. Classical QSAR methods describe structure-activity relationships in terms of physicochem. parameters and steric properties (Hansch anal., extrathermodynamic approach), or certain structural features (Free Wilson anal.). 3D QSAR methods, esp. comparative mol. field anal., consider the three-dimensional structures and the binding modes of protein ligands. Quant. similarity-activity relationships derive correlations between the similarities of individual compds. and their biol. activities. Theory and methodol. of these approaches are described here, together with the proper use of regression and partial least squares analyses for deriving quant. structure-activity relationships. Part 2, to be published in the Dec. issue, will address applications and problems.
- 91Jorgensen, W. L.; Duffy, E. M.Prediction of Drug Solubility from Structure. Adv. Drug Delivery Rev.2002, 54, 355– 366, DOI: 10.1016/S0169-409X(02)00008-X[Crossref], [PubMed], [CAS], Google Scholar91https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38Xitlartbc%253D&md5=bc749286d56bf55c26d25b70806217e1Jorgensen, William L.; Duffy, Erin M.Advanced Drug Delivery Reviews (2002), 54 (3), 355-366CODEN: ADDREP; ISSN:0169-409X. (Elsevier Science Ireland Ltd.)A review with refs. The aq. soly. of a drug is an important factor affecting its bioavailability. Numerous computational methods have been developed for the prediction of aq. soly. from a compd.'s structure. A review is provided of the methodol. and quality of results for the most useful procedures including the model implemented in the QikProp program. Viable methods now exist for predictions with <1 log unit uncertainty, which is adequate for prescreening synthetic candidates or design of combinatorial libraries. Further progress with predictive methods would require an exptl. database of highly accurate solubilities for a large, diverse collection of drug-like mols.
- 92Turner, J. V.; Glass, B. D.; Agatonovic-Kustrin, S.Prediction of Drug Bioavailability Based on Molecular Structure. Anal. Chim. Acta2003, 485, 89– 102, DOI: 10.1016/S0003-2670(03)00406-9[Crossref], [CAS], Google Scholar92https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXjvVClsrs%253D&md5=3b84cf48b6a181d16e1b48dd5e38740dPrediction of drug bioavailability based on molecular structureTurner, Joseph V.; Glass, Beverly D.; Agatonovic-Kustrin, SnezanaAnalytica Chimica Acta (2003), 485 (1), 89-102CODEN: ACACAM; ISSN:0003-2670. (Elsevier Science B.V.)Oral dosing is the most common method of drug administration, and final plasma concns. of the drug depend upon its bioavailability. In the current study, a quant. structure-pharmacokinetic relation (QSPR) was developed for a diverse range of compds. to allow prediction of drug bioavailability. Bioavailability data for 169 compds. was taken from the literature, and from the mol. structures 94 theor. descriptors were generated. Stepwise regression was employed to develop a regression equation based on 159 training compds., and predictive ability was tested on 10 compds. reserved for that purpose. The final regression equation included eight descriptors that represented electronic, steric, hydrophobic and constituent parameters of the drug mols., all of which could be related to soly. and partitioning properties. Predicted bioavailability for the training set agreed more closely for drugs exhibiting mid-range literature bioavailability values. A correlation of 0.72 was achieved for test set bioavailability predictions when compared with literature values. The structure-pharmacokinetic relation developed in the current study highlighted soly. and partitioning characteristics that may be useful in designing drugs with appropriate bioavailability.
- 93Sliwoski, G.; Kothiwale, S.; Meiler, J.; Lowe, E. W.Computational Methods in Drug Discovery. Pharmacol. Rev.2014, 66, 334– 395, DOI: 10.1124/pr.112.007336[Crossref], [PubMed], [CAS], Google Scholar93https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsVGnu7nL&md5=3dde38a0b60c583f832c688c2d27819fSliwoski, Gregory; Kothiwale, Sandeepkumar; Meiler, Jens; Lowe Edward, W.Pharmacological Reviews (2014), 66 (1), 334-395, 62 pp.CODEN: PAREAQ; ISSN:1521-0081. (American Society for Pharmacology and Experimental Therapeutics)A review. Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small mols. for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, mol. descriptors, and quant. structure-activity relationships. In addn., important tools such as target/ligand data bases, homol. modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiol. properties are discussed with successful examples from literature.
- 94Smith, J. S.; Isayev, O.; Roitberg, A. E.ANI-1: An Extensible Neural Network Potential with DFT Accuracy at Force Field Computational Cost. Chem. Sci.2017, 8, 3192– 3203, DOI: 10.1039/C6SC05720A[Crossref], [PubMed], [CAS], Google Scholar94https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXitlGnsrs%253D&md5=95b2f5106c620c6f09560966dba3559eANI-1: an extensible neural network potential with DFT accuracy at force field computational costChemical Science (2017), 8 (4), 3192-3203CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)Deep learning is revolutionizing many areas of science and technol., esp. image, text, and speech recognition. In this paper, we demonstrate how a deep neural network (NN) trained on quantum mech. (QM) DFT calcns. can learn an accurate and transferable potential for org. mols. We introduce ANAKIN-ME (Accurate NeurAl networK engINe for Mol. Energies) or ANI for short. ANI is a new method designed with the intent of developing transferable neural network potentials that utilize a highly-modified version of the Behler and Parrinello symmetry functions to build single-atom at. environment vectors (AEV) as a mol. representation. AEVs provide the ability to train neural networks to data that spans both configurational and conformational space, a feat not previously accomplished on this scale. We utilized ANI to build a potential called ANI-1, which was trained on a subset of the GDB databases with up to 8 heavy atoms in order to predict total energies for org. mols. contg. four atom types: H, C, N, and O. To obtain an accelerated but phys. relevant sampling of mol. potential surfaces, we also proposed a Normal Mode Sampling (NMS) method for generating mol. conformations. Through a series of case studies, we show that ANI-1 is chem. accurate compared to ref. DFT calcns. on much larger mol. systems (up to 54 atoms) than those included in the training data set.
- 95Faber, F. A.; Hutchison, L.; Huang, B.; Gilmer, J.; Schoenholz, S. S.; Dahl, G. E.; Vinyals, O.; Kearnes, S.; Riley, P. F.; von Lilienfeld, O. A.Prediction Errors of Molecular Machine Learning Models Lower Than Hybrid DFT Error. J. Chem. Theory Comput.2017, 13, 5255– 5264, DOI: 10.1021/acs.jctc.7b00577[ACS Full Text ], [CAS], Google Scholar95https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhsFWhu7vL&md5=c1cd87e50b04558c403a92184f4d017bPrediction Errors of Molecular Machine Learning Models Lower than Hybrid DFT ErrorFaber, Felix A.; Hutchison, Luke; Huang, Bing; Gilmer, Justin; Schoenholz, Samuel S.; Dahl, George E.; Vinyals, Oriol; Kearnes, Steven; Riley, Patrick F.; von Lilienfeld, O. AnatoleJournal of Chemical Theory and Computation (2017), 13 (11), 5255-5264CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)We investigate the impact of choosing regressors and mol. representations for the construction of fast machine learning (ML) models of thirteen electronic ground-state properties of org. mols. The performance of each regressor/representation/property combination is assessed using learning curves which report out-of-sample errors as a function of training set size with up to ∼118k distinct mols. Mol. structures and properties at hybrid d. functional theory (DFT) level of theory come from the QM9 database [Ramakrishnan et al, Scientific Data 1 140022 (2014)] and include enthalpies and free energies of atomization , HOMO/LUMO energies and gap, dipole moment, polarizability, zero point vibrational energy, heat capacity and the highest fundamental vibrational frequency. Various mol. representations have been studied (Coulomb matrix, bag of bonds, BAML and ECFP4, mol. graphs (MG)), as well as newly developed distribution based variants including histograms of distances (HD), and angles (HDA/MARAD), and dihedrals (HDAD). Regressors include linear models (Bayesian ridge regression (BR) and linear regression with elastic net regularization (EN)), random forest (RF), kernel ridge regression (KRR) and two types of neural networks, graph convolutions (GC) and gated graph networks (GG). Out-of sample errors are strongly dependent on the choice of representation and regressor and mol. property. Electronic properties are typically best accounted for by MG and GC, while energetic properties are better described by HDAD and KRR. The specific combinations with the lowest out-of-sample errors in the ∼118k training set size limit are (free) energies and enthalpies of atomization (HDAD/KRR), HOMO/LUMO eigenvalue and gap (MG/GC), dipole moment (MG/GC), static polarizability (MG/GG), zero point vibrational energy (HDAD/KRR), heat capacity at room temp. (HDAD/KRR), and highest fundamental vibrational frequency (BAML/RF). We present numerical evidence that ML model predictions deviate from DFT (B3LYP) less than DFT (B3LYP) deviates from expt. for all properties. Furthermore, out-of-sample prediction errors with respect to hybrid DFT ref. are on par with, or close to, chem. accuracy. The results suggest that ML models could be more accurate than hybrid DFT if explicitly electron correlated quantum (or exptl.) data was available.
- 96Ramakrishnan, R.; Dral, P. O.; Rupp, M.; von Lilienfeld, O. A.Big Data Meets Quantum Chemistry Approximations: The Delta-Machine Learning Approach. J. Chem. Theory Comput.2015, 11, 2087– 96, DOI: 10.1021/acs.jctc.5b00099[ACS Full Text ], [CAS], Google Scholar96https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXmtlams7Y%253D&md5=a59b33f51a9dd6dbad95290f2642c306Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning ApproachRamakrishnan, Raghunathan; Dral, Pavlo O.; Rupp, Matthias; von Lilienfeld, O. AnatoleJournal of Chemical Theory and Computation (2015), 11 (5), 2087-2096CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)Chem. accurate and comprehensive studies of the virtual space of all possible mols. are severely limited by the computational cost of quantum chem. We introduce a composite strategy that adds machine learning corrections to computationally inexpensive approx. legacy quantum methods. After training, highly accurate predictions of enthalpies, free energies, entropies, and electron correlation energies are possible, for significantly larger mol. sets than used for training. For thermochem. properties of up to 16k isomers of C7H10O2 we present numerical evidence that chem. accuracy can be reached. We also predict electron correlation energy in post Hartree-Fock methods, at the computational cost of Hartree-Fock, and we establish a qual. relationship between mol. entropy and electron correlation. The transferability of our approach is demonstrated, using semiempirical quantum chem. and machine learning models trained on 1 and 10% of 134k org. mols., to reproduce enthalpies of all remaining mols. at d. functional theory level of accuracy.
- 97Yao, K.; Herr, J. E.; Toth, D. W.; Mckintyre, R.; Parkhill, J.The Tensormol-0.1 Model Chemistry: A Neural Network Augmented with Long-Range Physics. Chem. Sci.2018, 9, 2261– 2269, DOI: 10.1039/C7SC04934J[Crossref], [PubMed], [CAS], Google Scholar97https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhtFOitLY%253D&md5=6c4d95e1748fd3dabb87c862297bdc4bThe TensorMol-0.1 model chemistry: a neural network augmented with long-range physicsYao, Kun; Herr, John E.; Toth, David W.; McKintyre, Ryker; Parkhill, JohnChemical Science (2018), 9 (8), 2261-2269CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)Traditional force fields cannot model chem. reactivity, and suffer from low generality without re-fitting. Neural network potentials promise to address these problems, offering energies and forces with near ab initio accuracy at low cost. However a, is offered in an open-source Python package capable of many of the simulation types commonly used to study chem.: geometry optimizations, harmonic spectra, open or periodic mol. dynamics, Monte Carlo, and nudged elastic band calcns. We describe the robustness and speed of the package, demonstrating its millihartree accuracy and scalability to tens-of-thousands of atoms on ordinary laptops. We demonstrate the performance of the model by reproducing vibrational spectra, and simulating the mol. dynamics of a protein. Our comparisons with electronic structure theory and exptl. data demonstrate that neural network mol. dynamics is poised to become an important tool for mol. simulation, lowering the resource barrier to simulating chem.
- 98https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XptV2hsA%253D%253D&md5=c67aac0ca496cfadb199ba000fb9a7d7Gómez-Bombarelli, R.; Wei, J. N.; Duvenaud, D.; Hernández-Lobato, J. M.; Sánchez-Lengeling, B.; Sheberla, D.; Aguilera-Iparraguirre, J.; Hirzel, T. D.; Adams, R. P.; Aspuru-Guzik, A.Automatic Chemical Design Using a systems.
Comparison of density functionals for differences between the high-(5T2g) and low-(1A1g) spin states of iron(II) compounds. IV. Results for the ferrous complexes [Fe(L)('NHS4')]
Ganzenmuller, Georg; Berkaine, Nabil; Fouqueau, Antony; Casida, Mark E.; Reiher, Markus
Journal of Chemical Physics (2005), 122 (23), 234321/1-234321/12CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
Previous work testing d. functionals for use in calcg. high-spin-low-spin energy differences, ΔEHL, for iron(II) spin-crossover transitions has tended to conclude that only properly reparametrized hybrid functionals can predict ΔEHL since it seems to depend critically on a correct description of the electron pairing energy governed by the exchange term. Exceptions to this rule are the previous three papers (I, II, and III in the present series of papers) where it was found that modern generalized gradient approxns. (GGAs) and meta-GGAs could do as well as hybrid functionals, if not better, for this type of problem. In the present paper, we extend these previous studies to five more mols. which are too large to treat with high-quality ab initio calcns., namely, the series [Fe(L)( NHS4')], where NHS4 = 2.2'-bis(2-mercaptophenylthio)diethylamine dianion, and L = NH3, N2H4, PMe3, CO, and NO+. Since we know of no reliable exptl. est. of ΔEHL, we content ourselves with a comparison against the exptl. detd. ground-state spin symmetry including, in so far as possible, finite-temp. effects. Together with the results of Papers I, II, and III, this paper provides a test of a large no. of functionals against the high-spin/low-spin properties of a diverse set of Fe(II) compds., making it possible to draw some particularly interesting conclusions. Trends among different classes of functionals are discussed and it is pointed out that there is at least one functional, namely, the OLYP generalized gradient approxn., which is able to give a reasonably good description of the delicate spin energetics of Fe(II) coordination compds. without resorting to hybrid functionals which require the relatively more expensive calcn. of a Hartree-Fock-type exchange term.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXlvVers7w%253D&md5=2db2dbbfd9e5b9872d33799ddd4145df111Fouqueau, A.; Casida, M. E.; Daku, L. M. L.; Hauser, A.; Neese, F.Comparison of Density Functionals for Energy and Structural Differences between the High-[5t2g:(T2g) 4 (Eg) 2] and Low-[1a1g:(T2g) 6 (Eg) 0] Spin States of Iron (II) Coordination Compounds. II. More Functionals and the Hexaminoferrous Cation,[Fe (NH3) 6] 2. J. Chem. Phys.2005, 122, 044110, DOI: 10.1063/1.1839854[Crossref], [PubMed], [CAS], Google Scholar111Comparison of density functionals for energy and structural differences between the high- [5T2g:(t2g)4(eg)2] and low- [1A1g:(t2g)6(eg)0] spin states of iron (II) coordination compounds. II. More functionals and the hexaminoferrous cation, [Fe(NH3)6]2+
Fouqueau, Antony; Casida, Mark E.; Daku, Latevi Max Lawson; Hauser, Andreas; Neese, Frank
Journal of Chemical Physics (2005), 122 (4), 044110/1-044110/13CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
The ability of different d. functionals to describe the structural and energy differences between the high- [5T2g:(t2g)4(eg)2] and low- [1A1g:(t2g)6(eg)0] spin states of small octahedral ferrous compds. is studied. This work is an extension of our previous study of the hexaquoferrous cation, [Fe(H2O)6]2+, to include a second compd.-namely, the hexaminoferrous cation, [Fe(NH3)6]2+-and several addnl. functionals. In particular, the present study includes the highly parametrized generalized gradient approxns. (GGAs) known as HCTH and the meta-GGA VSXC [which together we refer to as highly parametrized d. functionals (HPDFs)], now readily available in the GAUSSIAN03 program, as well as the hybrid functional PBE0. Since there are very few exptl. results for these mols. with which to compare, comparison is made with best ests. obtained from second-order perturbation theory-cor. complete active space SCF (CASPT2) calcns., with spectroscopy oriented CI (SORCI) calcns., and with ligand field theory (LFT) estns. While CASPT2 and SORCI are among the most reliable ab initio methods available for this type of problem, LFT embodies many decades of empirical experience. These three methods are found to give coherent results and provide best ests. of the adiabatic low-spin-high-spin energy difference, ΔELHadia, of 12 000-13 000 cm-1 for [Fe(H2O)6]2+ and 9 000-11 000 cm-1 for [Fe(NH3)6]2+. All functionals beyond the purely local approxn. produce reasonably good geometries, so long as adequate basis sets are used. In contrast, the energy splitting, ΔELHadia, is much more sensitive to the choice of functional. The local d. approxn. severely over stabilizes the low-spin state with respect to the high-spin state. This 'd. functional theory (DFT) spin pairing-energy problem' persists, but is reduced, for traditional GGAs. In contrast the hybrid functional B3LYP underestimates ΔELHadia by a few thousands of wave nos. The RPBE GGA of Hammer, Hansen, and Norskov gives good results for ΔELHadia as do the HPDFs, esp. the VSXC functional. Surprisingly the HCTH functionals actually over correct the DFT spin pairing-energy problem, destabilizing the low-spin state relative to the high-spin state. Best agreement is found for the hybrid functional PBE0.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXht12gs78%253D&md5=35804dbc0bc4ee59241e818f13e2883f112Whs File Conflicts Resolver Conjugation Chart
Droghetti, A.; Alfè, D.; Sanvito, S.Assessment of Density Functional Theory for Iron (II) Molecules across the Spin-Crossover Transition. J. Chem. Phys.2012, 137, 124303, DOI: 10.1063/1.4752411[Crossref], [PubMed], [CAS], Google Scholar112Assessment of density functional theory for iron(II) molecules across the spin-crossover transition
Journal of Chemical Physics (2012), 137 (12), 124303/1-124303/12CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
Octahedral Fe2+ mols. are particularly interesting as they often exhibit a spin-crossover transition. In spite of the many efforts aimed at assessing the performances of d. functional theory for such systems, an exchange-correlation functional able to account accurately for the energetic of the various possible spin-states has not been identified yet. Here, we critically discuss the issues related to the theor. description of this class of mols. from first principles. In particular, we present a comparison between different d. functionals for four ions, namely, Fe(H2O)62+, Fe(NH3)62+, Fe(NCH)62+, and Fe(CO)62+. These are characterized by different ligand-field splittings and ground state spin multiplicities. Since no exptl. data are available for the gas phase, the d. functional theory results are benchmarked against those obtained with diffusion Monte Carlo, one of the most accurate methods available to compute ground state total energies of quantum systems. On the one hand, we show that most of the functionals considered provide a good description of the geometry and of the shape of the potential energy surfaces. On the other hand, the same functionals fail badly in predicting the energy differences between the various spin states. In the case of Fe(H2O)62+, Fe(NH3)62+, Fe(NCH)62+, this failure is related to the drastic underestimation of the exchange energy. Therefore, quite accurate results can be achieved with hybrid functionals including about 50% of Hartree-Fock exchange. In contrast, in the case of Fe(CO)62+, the failure is likely to be caused by the multiconfigurational character of the ground state wave-function and no suitable exchange and correlation functional has been identified. (c) 2012 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xhtl2kur3P&md5=f2531095b13d0df7a15c8a8df36ee6c7113Gani, T. Z. H.; Kulik, H. J.Unifying Exchange Sensitivity in Transition Metal Spin-State Ordering and Catalysis through Bond Valence Metrics. J. Chem. Theory Comput.2017, 13, 5443– 5457, DOI: 10.1021/acs.jctc.7b00848[ACS Full Text ], [CAS], Google Scholar113Unifying Exchange Sensitivity in Transition-Metal Spin-State Ordering and Catalysis through Bond Valence Metrics
Journal of Chemical Theory and Computation (2017), 13 (11), 5443-5457CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Accurate predictions of spin-state ordering, reaction energetics, and barrier heights are crit. for the computational discovery of open-shell transition-metal (TM) catalysts. Semilocal approxns. in d. functional theory, such as the generalized gradient approxn. (GGA), suffer from delocalization error that causes them to overstabilize strongly bonded states. Descriptions of energetics and bonding are often improved by introducing a fraction of exact exchange (e.g., erroneous low-spin GGA ground states are instead correctly predicted as high-spin with a hybrid functional). The degree of spin-splitting sensitivity to exchange can be understood based on the chem. compn. of the complex, but the effect of exchange on reaction energetics within a single spin state is less well-established. Across a no. of model iron complexes, we observe strong exchange sensitivities of reaction barriers and energies that are of the same magnitude as those for spin splitting energies. We rationalize trends in both reaction and spin energetics by introducing a measure of delocalization, the bond valence of the metal-ligand bonds in each complex. The bond valence thus represents a simple-to-compute property that unifies understanding of exchange sensitivity for catalytic properties and spin-state ordering in TM complexes. Close agreement of the resulting per-metal-org.-bond sensitivity ests., together with failure of alternative descriptors demonstrates the utility of the bond valence as a robust descriptor of how differences in metal-ligand delocalization produce differing relative energetics with exchange tuning. Our unified description explains the overall effect of exact exchange tuning on the paradigmatic two-state FeO+/CH4 reaction that combines challenges of spin-state and reactivity predictions. This new descriptor-sensitivity relationship provides a path to quantifying how predictions in transition-metal complex screening are sensitive to the method used.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhs1yhsbvM&md5=0b3666cf2f06530da16efaed7230ded7114Cramer, C. J.; Truhlar, D. G.Density Functional Theory for Transition Metals and Transition Metal Chemistry. Phys. Chem. Chem. Phys.2009, 11, 10757– 10816, DOI: 10.1039/b907148b[Crossref], [PubMed], [CAS], Google Scholar114Density functional theory for transition metals and transition metal chemistry
Physical Chemistry Chemical Physics (2009), 11 (46), 10757-10816CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
A review. We introduce d. functional theory and review recent progress in its application to transition metal chem. Topics covered include local, meta, hybrid, hybrid meta, and range-sepd. functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including mols., clusters, nanoparticles, surfaces, and solids.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhsVentrfK&md5=3bb9a3202e5d1493390a1ad863f60c4c115Ioannidis, E. I.; Kulik, H. J.Ligand-Field-Dependent Behavior of Meta-GGA Exchange in Transition-Metal Complex Spin-State Ordering. J. Phys. Chem. A2017, 121, 874– 884, DOI: 10.1021/acs.jpca.6b11930[ACS Full Text ], [CAS], Google Scholar115Ligand-Field-Dependent Behavior of Meta-GGA Exchange in Transition-Metal Complex Spin-State Ordering
Journal of Physical Chemistry A (2017), 121 (4), 874-884CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
Prediction of spin-state ordering in transition metal complexes is essential for understanding catalytic activity and designing functional materials. Semi-local approxns. in d. functional theory, such as the generalized-gradient approxn. (GGA), suffer from delocalization error that gives rise to systematic bias for low-spin electronic states. Incorporation of exact exchange is known to counteract this bias, instead favoring high-spin states, in a manner that has recently been identified to be ligand-field dependent. In this work, we introduce a tuning strategy to identify the effect of incorporating the Laplacian of the d. (i.e., a meta-GGA) in exchange on spin-state ordering. We employ a diverse test set of M(II) and M(III) first-row transition metal ions from Ti to Cu as well as octahedral complexes of these ions with ligands of increasing field strength (i.e., H2O, NH3, and CO). We show that the sensitivity of spin-state ordering to meta-GGA exchange is highly ligand-field dependent, stabilizing high-spin states in strong-field (i.e., CO) cases and stabilizing low-spin states in weak-field (i.e., H2O, NH3, and isolated ions) cases. This diverging behavior leads to generally improved treatment of isolated ions and strong field complexes over a std. GGA but worsened treatment for the hexa-aqua or hexa-ammine complexes. These observations highlight the sensitivity of functional performance to subtle changes in chem. bonding.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXkvVKluw%253D%253D&md5=24bab166153fdb361bc4d2c248d08257116Ioannidis, E. I.; Kulik, H. J.Towards Quantifying the Role of Exact Exchange in Predictions of Transition Metal Complex Properties. J. Chem. Phys.2015, 143, 034104, DOI: 10.1063/1.4926836[Crossref], [PubMed], [CAS], Google Scholar116Towards quantifying the role of exact exchange in predictions of transition metal complex properties
Journal of Chemical Physics (2015), 143 (3), 034104/1-034104/11CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
We est. the prediction sensitivity with respect to Hartree-Fock exchange in approx. d. functionals for representative Fe(II) and Fe(III) octahedral complexes. Based on the observation that the range of parameters spanned by the most widely employed functionals is relatively narrow, we compute electronic structure property and spin-state orderings across a relatively broad range of Hartree-Fock exchange (0%-50%) ratios. For the entire range considered, we consistently observe linear relationships between spin-state ordering that differ only based on the element of the direct ligand and thus may be broadly employed as measures of functional sensitivity in predictions of organometallic compds. The role Hartree-Fock exchange in hybrid functionals is often assumed to play is to correct self-interaction error-driven electron delocalization (e.g., from transition metal centers to neighboring ligands). Surprisingly, we instead observe that increasing Hartree-Fock exchange reduces charge on iron centers, corresponding to effective delocalization of charge to ligands, thus challenging notions of the role of Hartree-Fock exchange in shifting predictions of spin-state ordering. (c) 2015 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtFOksLrJ&md5=049f548f340da52dbbfdf01985bb9149117Tortorella, S.; Marotta, G.; Cruciani, G.; De Angelis, F.Quantitative Structure-Property Relationship Modeling of Ruthenium Sensitizers for Solar Cells Applications: Novel Tools for Designing Promising Candidates. RSC Adv.2015, 5, 23865– 23873, DOI: 10.1039/C5RA01906K[Crossref], [CAS], Google Scholar117Quantitative structure-property relationship modeling of ruthenium sensitizers for solar cells applications: novel tools for designing promising candidates
Tortorella, Sara; Marotta, Gabriele; Cruciani, Gabriele; De Angelis, Filippo
RSC Advances (2015), 5 (30), 23865-23873CODEN: RSCACL; ISSN:2046-2069. (Royal Society of Chemistry)
To date, the most common way of screening new potential sensitizers for dye sensitized solar cells is via the traditional time and money consuming trial and error approach. In this study we explore the possibility of extending drug discovery and cheminformatic approaches to the field of material science with the aim of a quant. structure-property relationship elucidation that could lead to a fast and inexpensive in silico screening of new ruthenium sensitizers for third generation solar cells. Starting from the building of a database of already tested candidates used to train the predictive models, appropriate descriptors extd. from images of 3D mol. interaction fields (GRID/MIFs), as well as semi-empirical calcd. descriptors, were chosen to describe the target structures. Then, structure-performance (Jsc, Voc and PCE) models were built and analyzed in order to elucidate structure-property relationships and interesting results were obtained. In particular, we were able to find the mol. descriptors that more contribute to enhance the performance investigated, thus finding directives for the design of potentially high-performing candidates. We also proposed an efficient correction of the exptl. Jsc and Voc based on the quantity of the LiI additive for electrolyte used to build the devices. In the early stage of this project, we demonstrated that mol. modeling methods could be successfully extended to the field of material science as alternative to the traditional expensive and time-consuming trial and error approach.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXjtlWnt78%253D&md5=17b9f7325749b253c92d6404d0d6c813118Cruz, V. L.; Martinez, S.; Ramos, J.; Martinez-Salazar, J.3D-QSAR as a Tool for Understanding and Improving Single-Site Polymerization Catalysts. A Review. Organometallics2014, 33, 2944– 2959, DOI: 10.1021/om400721v[ACS Full Text ], [CAS], Google Scholar1183D-QSAR as a Tool for Understanding and Improving Single-Site Polymerization Catalysts. A Review
Cruz, Victor L.; Martinez, Sonia; Ramos, Javier; Martinez-Salazar, Javier
Organometallics (2014), 33 (12), 2944-2959CODEN: ORGND7; ISSN:0276-7333. (American Chemical Society)
A review. This paper reviews the findings of quant. structure-activity relationship (QSAR) studies focusing on single-site polymn. catalysts, with special attention paid to the use of 3D-QSAR tools. Such tools reveal the fine details of catalyst structure that may be correlated with polymn. activity or the properties of the synthesized polymer. The introduction of effective single-site polymn. catalysts, in addn. to allowing scientists to synthesize new tailor-made polymers, has enabled a detailed theor. anal. of the synthesis process. The benefits of single-site polymn. for theor. studies include easy elucidation of the catalyst structure, a well-defined mechanism of action, and the fact that expts. can be systematically conducted on catalyst series featuring different substitution patterns. Using QSAR methods, exptl. results can be related to theor. measurements through statistical or chemometric tools. These tools have been extensively and successfully used in the field of drug design.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXpsFejsLw%253D&md5=90097f911091bd4c45e7ae17b418901b119Fey, N.; Orpen, A. G.; Harvey, J. N.Building Ligand Knowledge Bases for Organometallic Chemistry: Computational Description of Phosphorus (III)-Donor Ligands and the Metal–Phosphorus Bond. Coord. Chem. Rev.2009, 253, 704– 722, DOI: 10.1016/j.ccr.2008.04.017[Crossref], [CAS], Google Scholar119Building ligand knowledge bases for organometallic chemistry: Computational description of phosphorus(III)-donor ligands and the metal-phosphorus bond
Coordination Chemistry Reviews (2009), 253 (5+6), 704-722CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)
A review. Changing the coordinated ligands is a powerful and synthetically convenient way of modifying and fine-tuning the properties of transition metal complexes, esp. those active in homogeneous catalysis. Parameters capturing such changes in the steric and electronic characteristics of complexes have played a key role in improving the authors' understanding of ligand effects on the kinetic, thermodn., spectroscopic and structural behavior of such species. Such ligand parameters can be useful for interpreting expts., but they can also guide the discovery of novel ligands from ligand maps and allow the prediction of ligand effects before further experimentation. The latter aims esp. are best served if such parameters can be detd. before ligands and complexes were synthesized, and here the authors review calcd. descriptors for P(III) ligands as widely used in organometallic and coordination chem. The authors also discuss the application of such ligand descriptors in models, maps and predictions of ligand effects, describe related computational studies of the metal-P bond, and provide an overview of the statistical methods used.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXisFSksL8%253D&md5=0880c3e55c8f1594b2dabde2abced6d7120Venkatraman, V.; Abburu, S.; Alsberg, B. K.Artificial Evolution of Coumarin Dyes for Dye Sensitized Solar Cells. Phys. Chem. Chem. Phys.2015, 17, 27672– 27682, DOI: 10.1039/C5CP04624F[Crossref], [CAS], Google Scholar120Artificial evolution of coumarin dyes for dye sensitized solar cells
Venkatraman, Vishwesh; Abburu, Sailesh; Alsberg, Bjoern Kaare
Physical Chemistry Chemical Physics (2015), 17 (41), 27672-27682CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
The design and discovery of novel mol. structures with optimal properties has been an ongoing effort for materials scientists. This field has in general been dominated by expt. driven trial-and-error approaches that are often expensive and time-consuming. Here, it is investigated if a de novo computational design methodol. can be applied to the design of coumarin-based dye sensitizers with improved properties for use in Gratzel solar cells. To address the issue of synthetic accessibility of the designed compds., a fragment-based assembly is employed, wherein the combination of chem. motifs (derived from the existing databases of structures) is carried out with respect to user-adaptable set of rules. Rather than using computationally intensive d. functional theory (DFT)/ab initio methods to screen candidate dyes, quant. structure-property relationship (QSPR) models (calibrated from empirical data) are employed for rapid estn. of the property of interest, which in this case is the product of short circuit current (Jsc) and open circuit voltage (Voc). Since QSPR models have limited validity, pre-detd. applicability domain criteria are used to prevent unacceptable extrapolation. DFT anal. of the top-ranked structures provides supporting evidence of their potential for dye sensitized solar cell applications.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsFamsb%252FI&md5=efe96c9e44d82e09bbb1e7df317c5caa121Allen, F. H.The Cambridge Structural Database: A Quarter of a Million Crystal Structures and Rising. Acta Crystallogr., Sect. B: Struct. Sci.2002, 58, 380– 388, DOI: 10.1107/S0108768102003890[Crossref], [PubMed], [CAS], Google Scholar121The Cambridge Structural Database: a quarter of a million crystal structures and rising
Acta Crystallographica, Section B: Structural Science (2002), B58 (3, No. 1), 380-388CODEN: ASBSDK; ISSN:0108-7681. (Blackwell Munksgaard)
The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-mol. crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chem. information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500000 crystal structures by the year 2010.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XktVOqu74%253D&md5=406cd0df6ea9035a0ebf8dd9eccbd1f8122Janet, J. P.; Kulik, H. J.Resolving Transition Metal Chemical Space: Feature Selection for Machine Learning and Structure-Property Relationships. J. Phys. Chem. A2017, 121, 8939– 8954, DOI: 10.1021/acs.jpca.7b08750[ACS Full Text ], [CAS], Google Scholar122Resolving Transition Metal Chemical Space: Feature Selection for Machine Learning and Structure-Property Relationships
Journal of Physical Chemistry A (2017), 121 (46), 8939-8954CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
Machine learning (ML) of quantum mech. properties shows promise for accelerating chem. discovery. For transition metal chem. where accurate calcns. are computationally costly and available training data sets are small, the mol. representation becomes a crit. ingredient in ML model predictive accuracy. We introduce a series of revised autocorrelation functions (RACs) that encode relationships of the heuristic at. properties (e.g., size, connectivity, and electronegativity) on a mol. graph. We alter the starting point, scope, and nature of the quantities evaluated in std. ACs to make these RACs amenable to inorg. chem. On an org. mol. set, we first demonstrate superior std. AC performance to other presently available topol. descriptors for ML model training, with mean unsigned errors (MUEs) for atomization energies on set-aside test mols. as low as 6 kcal/mol. For inorg. chem., our RACs yield 1 kcal/mol ML MUEs on set-aside test mols. in spin-state splitting in comparison to 15-20× higher errors for feature sets that encode whole-mol. structural information. Systematic feature selection methods including univariate filtering, recursive feature elimination, and direct optimization (e.g., random forest and LASSO) are compared. Random-forest- or LASSO-selected subsets 4-5× smaller than the full RAC set produce sub- to 1 kcal/mol spin-splitting MUEs, with good transferability to metal-ligand bond length prediction (0.004-5 Å MUE) and redox potential on a smaller data set (0.2-0.3 eV MUE). Evaluation of feature selection results across property sets reveals the relative importance of local, electronic descriptors (e.g., electronegativity, at. no.) in spin-splitting and distal, steric effects in redox potential and bond lengths.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhslGhsLnL&md5=5da87c7a2084fd54de3d4ebe1bf9330c123Janet, J. P.; Kulik, H. J.Predicting Electronic Structure Properties of Transition Metal Complexes with Neural Networks. Chem. Sci.2017, 8, 5137– 5152, DOI: 10.1039/C7SC01247K[Crossref], [PubMed], [CAS], Google Scholar123Predicting electronic structure properties of transition metal complexes with neural networks
Chemical Science (2017), 8 (7), 5137-5152CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)
High-throughput computational screening has emerged as a crit. component of materials discovery. Direct d. functional theory (DFT) simulation of inorg. materials and mol. transition metal complexes is often used to describe subtle trends in inorg. bonding and spin-state ordering, but these calcns. are computationally costly and properties are sensitive to the exchange-correlation functional employed. To begin to overcome these challenges, we trained artificial neural networks (ANNs) to predict quantum-mech.-derived properties, including spin-state ordering, sensitivity to Hartree-Fock exchange, and spin-state specific bond lengths in transition metal complexes. Our ANN is trained on a small set of inorg.-chem.-appropriate empirical inputs that are both maximally transferable and do not require precise three-dimensional structural information for prediction. Using these descriptors, our ANN predicts spin-state splittings of single-site transition metal complexes (i.e., Cr-Ni) at arbitrary amts. of Hartree-Fock exchange to within 3 kcal mol-1 accuracy of DFT calcns. Our exchange-sensitivity ANN enables improved predictions on a diverse test set of exptl.-characterized transition metal complexes by extrapolation from semi-local DFT to hybrid DFT. The ANN also outperforms other machine learning models (i.e., support vector regression and kernel ridge regression), demonstrating particularly improved performance in transferability, as measured by prediction errors on the diverse test set. We establish the value of new uncertainty quantification tools to est. ANN prediction uncertainty in computational chem., and we provide addnl. heuristics for identification of when a compd. of interest is likely to be poorly predicted by the ANN. The ANNs developed in this work provide a strategy for screening transition metal complexes both with direct ANN prediction and with improved structure generation for validation with first principles simulation.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXotVCgsrY%253D&md5=83fb0e4026c680b8e68e63a374dd0358124Nandy, A.; Duan, C.; Janet, J. P.; Gugler, S.; Kulik, H. J.Strategies and Software for Machine Learning Accelerated Discovery in Transition Metal Chemistry. Ind. Eng. Chem. Res.2018, 57, 13973– 13986, DOI: 10.1021/acs.iecr.8b04015[ACS Full Text ], [CAS], Google Scholar124Strategies and Software for Machine Learning Accelerated Discovery in Transition Metal Chemistry
Nandy, Aditya; Duan, Chenru; Janet, Jon Paul; Gugler, Stefan; Kulik, Heather J.
Industrial & Engineering Chemistry Research (2018), 57 (42), 13973-13986CODEN: IECRED; ISSN:0888-5885. (American Chemical Society)
Machine learning the electronic structure of open shell transition metal complexes presents unique challenges, including robust and automated data set generation. Here, we introduce tools that simplify data acquisition from d. functional theory (DFT) and validation of trained machine learning models using the molSimplify automatic design (mAD) workflow. We demonstrate this workflow by training and comparing the performance of LASSO, kernel ridge regression (KRR), and artificial neural network (ANN) models using heuristic, topol. revised autocorrelation (RAC) descriptors we have recently introduced for machine learning inorg. chem. On a series of open shell transition metal complexes, we evaluate set aside test errors of these models for predicting the HOMO level and HOMO-LUMO gap. The best performing models are ANNs, which show 0.15 and 0.25 eV test set mean abs. errors on the HOMO level and HOMO-LUMO gap, resp. Poor performing KRR models using the full 153-feature RAC set are improved to nearly the same performance as the ANNs when trained on down-selected subsets of 20-30 features. Anal. of the essential descriptors for HOMO level and HOMO-LUMO gap prediction as well as comparison to subsets previously obtained for other properties reveal the paramount importance of nonlocal, steric properties in detg. frontier MO energetics. We demonstrate our model performance on diverse complexes and in the discovery of mols. with target HOMO-LUMO gaps from a large 15,000 mol. design space in minutes rather than days that full DFT evaluation would require.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhslOqsr3I&md5=23e996b0a37eadc2588a104a17ba5470125Ioannidis, E. I.; Gani, T. Z. H.; Kulik, H. J.molSimplify: A Toolkit for Automating Discovery in Inorganic Chemistry. J. Comput. Chem.2016, 37, 2106– 2117, DOI: 10.1002/jcc.24437[Crossref], [PubMed], [CAS], Google Scholar125molSimplify: A toolkit for automating discovery in inorganic chemistry
Ioannidis, Efthymios I.; Gani, Terry Z. H.; Kulik, Heather J.
Journal of Computational Chemistry (2016), 37 (22), 2106-2117CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
We present an automated, open source toolkit for the first-principles screening and discovery of new inorg. mols. and intermol. complexes. Challenges remain in the automatic generation of candidate inorg. mol. structures due to the high variability in coordination and bonding, which we overcome through a divide-and-conquer tactic that flexibly combines force-field preoptimization of org. fragments with alignment to first-principles-trained metal-ligand distances. Exploration of chem. space is enabled through random generation of ligands and intermol. complexes from large chem. databases. We validate the generated structures with the root mean squared (RMS) gradients evaluated from d. functional theory (DFT), which are around 0.02 Ha/au across a large 150 mol. test set. Comparison of molSimplify results to full optimization with the universal force field reveals that RMS DFT gradients are improved by 40%. Seamless generation of input files, prepn. and execution of electronic structure calcns., and post-processing for each generated structure aids interpretation of underlying chem. and energetic trends. © 2016 Wiley Periodicals, Inc.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtV2gu7bN&md5=8963dad8dc0f6da848871be864ef7e09126Liu, F.; Yang, T.; Yang, J.; Xu, E.; Bajaj, A.; Kulik, H. J., Bridging the Homogeneous–Heterogeneous Divide: Modeling Spin and Reactivity in Single Atom Catalysis. Submitted.Google ScholarThere is no corresponding record for this reference.
127Pritchard, B.; Autschbach, J.Theoretical Investigation of Paramagnetic NMR Shifts in Transition Metal Acetylacetonato Complexes: Analysis of Signs, Magnitudes, and the Role of the Covalency of Ligand–Metal Bonding. Inorg. Chem.2012, 51, 8340– 8351, DOI: 10.1021/ic300868v[ACS Full Text ], [CAS], Google Scholar127Theoretical Investigation of Paramagnetic NMR Shifts in Transition Metal Acetylacetonato Complexes: Analysis of Signs, Magnitudes, and the Role of the Covalency of Ligand-Metal Bonding
Inorganic Chemistry (2012), 51 (15), 8340-8351CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
Ligand chem. shifts are calcd. and analyzed for three paramagnetic transition metal tris-acetylacetonato (acac) complexes, high-spin Fe(III) and Cr(III), and low-spin Ru(III), using scalar relativistic d. functional theory (DFT). The signs and magnitudes of the paramagnetic NMR ligand chem. shifts are directly related to the extent of covalent acac oxygen-to-metal σ donation involving unoccupied metal valence dσ acceptor orbitals. The role of delocalization of metal-centered spin d. over the ligand atoms plays a minor secondary role. Of particular interest is the origin of the sign and magnitude of the Me carbon chem. shift in the acac ligands, and the role played by the DFT delocalization error when calcg. such shifts. The α vs. β spin balance of oxygen σ donation to metal valence d acceptor orbitals is responsible for the sign and the magnitude of the ligand Me carbon chem. shift. A problematic case is the Me carbon shift of Fe(acac)3. Most functionals produce shifts >1400 ppm, whereas the exptl. shift is ∼279 ppm. Range-sepd. hybrid functionals that are optimally tuned for Fe(acac)3 based on DFT energetic criteria predict a lower limit of ∼2000 ppm for the Me carbon shift of the high-spin electronic configuration. Since the exptl. value is based on a very strongly broadened signal it is possibly unreliable.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtV2gsrrM&md5=f32b42adf95295c8e605888e154e0417128Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J.Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields. J. Phys. Chem.1994, 98, 11623– 11627, DOI: 10.1021/j100096a001[ACS Full Text ], [CAS], Google Scholar128Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields
Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J.
Journal of Physical Chemistry (1994), 98 (45), 11623-7CODEN: JPCHAX; ISSN:0022-3654.
The unpolarized absorption and CD spectra of the fundamental vibrational transitions of the chiral mol. 4-methyl-2-oxetanone are calcd. ab initio. Harmonic force fields are obtained using d. functional theory (DFT), MP2 and SCF methodologies, and a [5s4p2d/3s2p] (TZ2P) basis set. DFT calcns. use the LSDA, BLYP, and Becke3LYP (B3LYP) d. functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with expt. The MP2 force field yields spectra in slightly worse agreement with expt. than the B3LYP force field. The SCF force field yields spectra in poor agreement with expt. The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreement with expt.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2cXmvVSitbY%253D&md5=93486da1864d900b4527d020cf36171f129Becke, A. D.Density-Functional Thermochemistry. III. The Role of Exact Exchange. J. Chem. Phys.1993, 98, 5648– 5652, DOI: 10.1063/1.464913[Crossref], [CAS], Google Scholar129Density-functional thermochemistry. III. The role of exact exchange
Journal of Chemical Physics (1993), 98 (7), 5648-52CODEN: JCPSA6; ISSN:0021-9606.
Despite the remarkable thermochem. accuracy of Kohn-Sham d.-functional theories with gradient corrections for exchange-correlation, the author believes that further improvements are unlikely unless exact-exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange-correlation functional (contg. local-spin-d., gradient, and exact-exchange terms) is tested for 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total at. energies of first- and second-row systems. This functional performs better than previous functionals with gradient corrections only, and fits expt. atomization energies with an impressively small av. abs. deviation of 2.4 kcal/mol.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK3sXisVWgtrw%253D&md5=291bbfc119095338bb1624f0c21c7ca8130Lee, C.; Yang, W.; Parr, R. G.Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density. Phys. Rev. B: Condens. Matter Mater. Phys.1988, 37, 785– 789, DOI: 10.1103/PhysRevB.37.785[Crossref], [PubMed], [CAS], Google Scholar130Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
Physical Review B: Condensed Matter and Materials Physics (1988), 37 (2), 785-9CODEN: PRBMDO; ISSN:0163-1829.
A correlation-energy formula due to R. Colle and D. Salvetti (1975), in which the correlation energy d. is expressed in terms of the electron d. and a Laplacian of the 2nd-order Hartree-Fock d. matrix, is restated as a formula involving the d. and local kinetic-energy d. On insertion of gradient expansions for the local kinetic-energy d., d.-functional formulas for the correlation energy and correlation potential are then obtained. Through numerical calcns. on a no. of atoms, pos. ions, and mols., of both open- and closed-shell type, it is demonstrated that these formulas, like the original Colle-Salvetti formulas, give correlation energies within a few percent.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL1cXktFWrtbw%253D&md5=ee7b59267a2ff72e15171a481819ccf8131Hay, P. J.; Wadt, W. R.Ab Initio Effective Core Potentials for Molecular Calculations. Potentials for the Transition Metal Atoms Sc to Hg. J. Chem. Phys.1985, 82, 270– 283, DOI: 10.1063/1.448799[Crossref], [CAS], Google Scholar131Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms scandium to mercury
Journal of Chemical Physics (1985), 82 (1), 270-83CODEN: JCPSA6; ISSN:0021-9606.
Ab initio effective core potentials (ECP's) were generated to replace the Coulomb, exchange, and core-orthogonality effects of the chem. inert core electron in the transition metal atoms Sc to Hg. For the second and third transition series relative ECP's were generated which also incorporate the mass-velocity and Darwin relativistic effects into the potential. The ab initio ECP's should facilitate valence electron calcns. on mols. contg. transition-metal atoms with accuracies approaching all-electron calcns. at a fraction of the computational cost. Analytic fits to the potentials are presented for use in multicenter integral evaluation. Gaussian orbital valence basis sets are developed for the (3d,4s,4p), (4d,5s,5p), and (5d,6s,6p) orbitals of the first, second, and third transition series atoms, resp. All-electron and valence-electron at. excitation energies are also compared for the low-lying states of Sc-Hg, and the valence-electron calcns. reproduce the all-electron excitation energies (typically within a few tenths of an eV).
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2MXhtlyju70%253D&md5=29271d2a54b5c81acd19762c570e64d7132Janet, J. P.; Gani, T. Z. H.; Steeves, A. H.; Ioannidis, E. I.; Kulik, H. J.Leveraging Cheminformatics Strategies for Inorganic Discovery: Application to Redox Potential Design. Ind. Eng. Chem. Res.2017, 56, 4898– 4910, DOI: 10.1021/acs.iecr.7b00808[ACS Full Text ], [CAS], Google Scholar132Leveraging Cheminformatics Strategies for Inorganic Discovery: Application to Redox Potential Design
Janet, Jon Paul; Gani, Terry Z. H.; Steeves, Adam H.; Ioannidis, Efthymios I.; Kulik, Heather J.
Industrial & Engineering Chemistry Research (2017), 56 (17), 4898-4910CODEN: IECRED; ISSN:0888-5885. (American Chemical Society)
Virtual high throughput screening, typically driven by first-principles, d. functional theory calcns., has emerged as a powerful tool for the discovery of new materials. Although the computational materials science community has benefited from open source tools for the rapid structure generation, calcn., and anal. of cryst. inorg. materials, software and strategies to address the unique challenges of inorg. complex discovery have not been as widely available. We present a unified view of our recent developments in the open source molSimplify code for inorg. discovery. Building on our previous efforts in the automated generation of highly accurate inorg. mol. structures, first-principles simulation, and property anal. to accelerate high-throughput screening, we have recently incorporated a neural network that both improves structure generation and predicts electronic properties prior to first-principles calcn. We also provide an overview of how multimillion mol. org. libraries can be leveraged for inorg. discovery alongside cheminformatics concepts of mol. diversity in order to efficiently traverse chem. space. We demonstrate all of these tools on the discovery of design rules for octahedral Fe(II/III) redox couples with nitrogen ligands. Over a search of only approx. 40 new mols., we obtain redox potentials relative to the Fc/Fc+ couple ranging from -1 to 4.5 V in aq. soln. Our new automated correlation anal. reveals heteroatom identity and the degree of structural branching to be key ligand descriptors in detg. redox potential. This inorg. discovery toolkit provides a promising approach to advancing transition metal complex design.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXls1Snsrg%253D&md5=e3fd8c1374593e68ef94838197ff73a4133Klamt, A.; Schuurmann, G.Cosmo: A New Approach to Dielectric Screening in Solvents with Explicit Expressions for the Screening Energy and Its Gradient. J. Chem. Soc., Perkin Trans. 21993, 2, 799– 805, DOI: 10.1039/P29930000799[Crossref], Google ScholarThere is no corresponding record for this reference.
134Liu, F.; Luehr, N.; Kulik, H. J.; Martínez, T. J.Quantum Chemistry for Solvated Molecules on Graphical Processing Units Using Polarizable Continuum Models. J. Chem. Theory Comput.2015, 11, 3131– 3144, DOI: 10.1021/acs.jctc.5b00370[ACS Full Text ], [CAS], Google Scholar134Quantum Chemistry for Solvated Molecules on Graphical Processing Units Using Polarizable Continuum Models
Liu, Fang; Luehr, Nathan; Kulik, Heather J.; Martinez, Todd J.
Journal of Chemical Theory and Computation (2015), 11 (7), 3131-3144CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chem. simulations. However, its application in quantum mech. calcns. of large-scale biomol. systems can be limited by computational expense of both the gas phase electronic structure and the solvation interaction. The authors have previously used graphical processing units (GPUs) to accelerate the first of these steps. Here, the authors extend the use of GPUs to accelerate electronic structure calcns. including C-PCM solvation. Implementation on the GPU leads to significant acceleration of the generation of the required integrals for C-PCM. The authors further propose two strategies to improve the soln. of the required linear equations: a dynamic convergence threshold and a randomized block-Jacobi preconditioner. These strategies are not specific to GPUs and are expected to be beneficial for both CPU and GPU implementations. The authors benchmark the performance of the new implementation using over 20 small proteins in solvent environment. Using a single GPU, the authors' method evaluates the C-PCM related integrals and their derivs. >10× faster than that with a conventional CPU-based implementation. The authors' improvements to the linear solver provide a further 3× acceleration. The overall calcns. including C-PCM solvation require, typically, 20-40% more effort than that for their gas phase counterparts for a moderate basis set and mol. surface discretization level. The relative cost of the C-PCM solvation correction decreases as the basis sets and/or cavity radii increase. Therefore, description of solvation with this model should be routine. The authors also discuss applications to the study of the conformational landscape of an amyloid fibril.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtVaksbvL&md5=5ae2f3b82c19a302b7cae538cf623a72135Konezny, S. J.; Doherty, M. D.; Luca, O. R.; Crabtree, R. H.; Soloveichik, G. L.; Batista, V. S.Reduction of Systematic Uncertainty in DFT Redox Potentials of Transition-Metal Complexes. J. Phys. Chem. C2012, 116, 6349– 6356, DOI: 10.1021/jp300485t[ACS Full Text ], [CAS], Google Scholar135Reduction of Systematic Uncertainty in DFT Redox Potentials of Transition-Metal Complexes
Konezny, Steven J.; Doherty, Mark D.; Luca, Oana R.; Crabtree, Robert H.; Soloveichik, Grigorii L.; Batista, Victor S.
Journal of Physical Chemistry C (2012), 116 (10), 6349-6356CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
Reliable calcns. of redox potentials could provide valuable insight into catalytic mechanisms of electrochem. active transition-metal complexes as well as guidelines for the design of new electrocatalysts. However, the correlation between theor. and exptl. data is often uncertain, since redox properties depend strongly on exptl. conditions of electrochem. measurements, including the nature of the solvent, electrolyte, and working electrode. Here, the use of internal refs. allows for quant. theor. predictions of redox potentials with std. deviations σ comparable to typical exptl. errors of cyclic voltammetry measurements. Agreement for 1st-, 2nd-, and 3rd-row transition-metal complexes is demonstrated even at a rather modest level of d. functional theory (σ = 64 mV for the UB3LYP/6-311G* level). This is shown for benchmark redox couples, including ([MCp2]0/+ (Cp = η5-cyclopentadienyl), [MCp*2]0/+ (Cp* = η5-1,2,3,4,5-pentamethylcyclopentadienyl), [M(bpy)3]2+/3+ (bpy =2,2'-bipyridine), and [Ir(acac)3]0/+ (acac = acetylacetonate), with M = Fe, Co, Ni, Ru, Os, or Ir) in various nonaq. solvents [acetonitrile (MeCN), DMSO, and CH2Cl2 (DCM)].
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XisFShs7Y%253D&md5=d6404b1f8351da6d38f54369a715d1b3136Roy, L. E.; Jakubikova, E.; Guthrie, M. G.; Batista, E. R.Calculation of One-Electron Redox Potentials Revisited. Is It Possible to Calculate Accurate Potentials with Density Functional Methods?. J. Phys. Chem. A2009, 113, 6745– 6750, DOI: 10.1021/jp811388w[ACS Full Text ], [CAS], Google Scholar136Calculation of One-Electron Redox Potentials Revisited. Is It Possible to Calculate Accurate Potentials with Density Functional Methods?
Roy, Lindsay E.; Jakubikova, Elena; Guthrie, M. Graham; Batista, Enrique R.
Journal of Physical Chemistry A (2009), 113 (24), 6745-6750CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
D. Functional calcns. have been performed to calc. the one-electron oxidn. potential for ferrocene and the redox couples for a series of small transition metal compds. of the first-, second-, and third-row elements. The solvation effects are incorporated via a self-consistent reaction field (SCRF), using the polarized continuum model (PCM). From our study of seven different d. functionals combined with three different basis sets for ferrocene, we find that no d. functional method can reproduce the redox trends from expt. when referencing our results to the exptl. abs. std. hydrogen electrode (SHE) potential. Including addnl. necessary assumptions such as solvation effects does not lead to any conclusion regarding the appropriate functional. However, we propose that if one refs. their transition metal compds. results to the calcd. abs. half-cell potential of ferrocene, they can circumvent the addnl. assumptions necessary to predict a redox couple. Upon employing this method on several organometallic and inorg. complexes, we obtained very good correlation between calcd. and exptl. values (R2 = 0.97), making it possible to predict trends with a high level of confidence. The hybrid functional B3LYP systematically underestimates the redox potential; however, the linear correlation between DFT and expt. is good (R2 = 0.96) when including a baseline shift. This protocol is a powerful tool that allows theor. chemists to predict the redox potential in soln. of several transition metal complexes a priori and aids in the rational design of redox-active catalysts.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXmtF2ktbw%253D&md5=d745a07128c9c61744e10400a62a6ef3137Baik, M.-H.; Friesner, R. A.Computing Redox Potentials in Solution: Density Functional Theory as a Tool for Rational Design of Redox Agents. J. Phys. Chem. A2002, 106, 7407– 7412, DOI: 10.1021/jp025853n[ACS Full Text ], [CAS], Google Scholar137Computing Redox Potentials in Solution: Density Functional Theory as A Tool for Rational Design of Redox Agents
Journal of Physical Chemistry A (2002), 106 (32), 7407-7412CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
High-level d. functional theory in combination with a continuum solvation model was employed to compute std. redox potentials in soln. phase for three different classes of electrochem. active mols.: small org. mols., metallocenes, and M(bpy)3x (M = Fe, Ru, Os; x = +3, +2, +1, 0, -1). Excellent agreement with exptl. detd. redox potentials is found with an av. deviation of ∼150 mV when four different solvents commonly in use for electrochem. measurements were included. To obtain quant. agreement between theory and expt., the use of a large basis set is crucial esp. when the redox couple includes anionic species. Whereas the addn. of diffuse functions improved the results notably, vibrational zero-point-energy corrections and addn. of entropy effects are less important. The computational protocol for computing redox potentials in soln., which was benchmarked, is a powerful and novel tool that will allow a mol.-level understanding of the features dictating the properties of redox-active species.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XltlCntbw%253D&md5=8bb4d98b7e856f3692ac99345090f341138Janet, J. P.; Zhao, Q.; Ioannidis, E. I.; Kulik, H. J.Density Functional Theory for Modeling Large Molecular Adsorbate-Surface Interactions: A Mini-Review and Worked Example. Mol. Simul.2017, 43, 327– 345, DOI: 10.1080/08927022.2016.1258465[Crossref], [CAS], Google Scholar138Density functional theory for modelling large molecular adsorbate-surface interactions: a mini-review and worked example
Janet, Jon Paul; Zhao, Qing; Ioannidis, Efthymios I.; Kulik, Heather J.
Molecular Simulation (2017), 43 (5-6), 327-345CODEN: MOSIEA; ISSN:0892-7022. (Taylor & Francis Ltd.)
First-principles simulation has played an ever-increasing role in the discovery and interpretation of the chem. properties of surface-adsorbate interactions. Nevertheless, key challenges remain for the computational chemist wishing to study surface chem.: modeling the full extent of exptl. conditions, managing computational cost, minimising human effort in simulation set-up and maximising accuracy. This article introduces new tools for streamlining surface chem. simulation set-up and reviews some of the challenges in first-principles, d. functional theory (DFT) simulation of surface phenomena. Furthermore, we provide a worked example of Co tetraphenylporphyrin on Au(1 1 1) in which we analyze electronic and energetic properties with semi-local DFT and compare to predictions made from hybrid functional and the so-called DFT+U correction. Through both review and the worked example, we aim to provide a pedagogical introduction to the challenges and the insight that first-principles simulation can provide in surface chem.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvFKjtLfN&md5=c67fdcedeb2e116dfe3bf04e49ec41e2139Halgren, T. A.Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94. J. Comput. Chem.1996, 17, 490– 519, DOI: 10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P[Crossref], [CAS], Google Scholar139Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
Journal of Computational Chemistry (1996), 17 (5 & 6), 490-519CODEN: JCCHDD; ISSN:0192-8651. (Wiley)
This article introduces MMFF94, the initial published version of the Merck mol. force field (MMFF). It describes the objectives set for MMFF, the form it takes, and the range of systems to which it applies. This study also outlines the methodol. employed in parameterizing MMFF94 and summarizes its performance in reproducing computational and exptl. data. Though similar to MM3 in some respects, MMFF94 differs in ways intended to facilitate application to condensed-phase processes in mol.-dynamics simulations. Indeed, MMFF94 seeks to achieve MM3-like accuracy for small mols. in a combined 'org./protein' force field that is equally applicable to proteins and other systems of biol. significance. A second distinguishing feature is that the core protion of MMFF94 has primarily been derived from high-quality computational approach, nearly all MMFF parameters have been detd. in a mutually consistent fashion from the full set of available computational data. MMFF94 reproduces the computational data used in its parameterization very well. In addn., MMFF94 reproduces exptl. bond lengths (0.014 Å root mean square [rms]), bond angles (1.2° rms), vibrational frequencies (61 cm-1 rms), conformational energies (0.38 kcal/mol rms), and rotational barriers (0.39 kcal/mol rms) very nearly as well as does MM3 for comparable systems. MMFF94 also describes intermol. interactions in hydrogen-bonded systems in a way that closely parallels that given by the highly regarded OPLS force field.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK28XhvVGmsbk%253D&md5=56fb073477b4f49d1dfbd786fc56a480140Reiher, M.Theoretical Study of the Fe (Phen) 2 (NCS) 2 Spin-Crossover Complex with Reparametrized Density Functionals. Inorg. Chem.2002, 41, 6928– 6935, DOI: 10.1021/ic025891l[ACS Full Text ], [CAS], Google Scholar140Theoretical Study of the Fe(phen)2(NCS)2 Spin-Crossover Complex with Reparametrized Density Functionals
Inorganic Chemistry (2002), 41 (25), 6928-6935CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
The theor. study of spin-crossover compds. is very challenging as those parts of the exptl. findings that concern the electronic structure of these compds. can currently hardly be reproduced because of either tech. limitations of highly accurate ab initio methods or because of inaccuracies of d. functional methods in the prediction of low-spin/high-spin energy splitting. However, calcns. with reparametrized d. functionals on mols. of the thermal spin-crossover type can give improved results when compared with expt. for close-lying states of different spin and are therefore important for, e.g., transition metal catalysis. A classification of transition metal compds. within hybrid d. functional theory is given to distinguish std., crit., and complicated cases. From the class of complicated cases we choose the prominent spin-crossover compd. Fe(phen)2(NCS)2 and show in a first step how the electronic contribution to the energy splitting can be calcd. In a second step, the vibrational effects on the spin flip are investigated within the harmonic force-field approxn. of the isolated-mol. approach. A main result of the study is the necessity of exact-exchange redn. in hybrid d. functionals to arrive at reasonable electronic energy splittings. The study resolves problems that originated from the use of std. d. functionals, which are not able to reproduce the electronic contribution to the low-spin/high-spin splitting correctly, and demonstrates to which extent reparametrized d. functionals can be used for the prediction of the spin-crossover effect.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38Xoslaqtbw%253D&md5=ebc3252d68752bf1a679792f21010774141Fouqueau, A.; Mer, S.; Casida, M. E.; Lawson Daku, L. M.; Hauser, A.; Mineva, T.; Neese, F.Comparison of Density Functionals for Energy and Structural Differences between the High- [5t2g: (T2g)4(Eg)2] and Low- [1a1g: (T2g)6(Eg)0] Spin States of the Hexaquoferrous Cation [Fe(H2O)6]2. J. Chem. Phys.2004, 120, 9473– 9486, DOI: 10.1063/1.1710046[Crossref], [PubMed], [CAS], Google Scholar141Comparison of density functionals for energy and structural differences between the high- [5T2g: (t2g)4(eg)2] and low- [1A1g: (t2g)6(eg)0] spin states of the hexaquoferrous cation [Fe(H2O)6]2+
Fouqueau, Antony; Mer, Sebastien; Casida, Mark E.; Lawson Daku, Latevi Max; Hauser, Andreas; Mineva, Tsonka; Neese, Frank
Journal of Chemical Physics (2004), 120 (20), 9473-9486CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
A comparison of d. functionals is made for the calcn. of energy and geometry differences for the high- [5T2g: (t2g)4(eg)2] and low- [1A1g: (t2g)6(eg)0] spin states of the hexaquoferrous cation [Fe(H2O)6]2+. Since very little exptl. results are available (except for crystal structures involving the cation in its high-spin state), the primary comparison is with our own complete active-space SCF (CASSCF), second-order perturbation theory-cor. complete active-space SCF (CASPT2), and spectroscopy-oriented CI (SORCI) calcns. We find that generalized gradient approxns. (GGAs) and the B3LYP hybrid functional provide geometries in good agreement with expt. and with our CASSCF calcns. provided sufficiently extended basis sets are used (i.e., polarization functions on the iron and polarization and diffuse functions on the water mols.). In contrast, CASPT2 calcns. of the low-spin-high-spin energy difference ΔELH = ELS-EHS appear to be significantly overestimated due to basis set limitations in the sense that the energy difference of the at. asymptotes (5D → 1I excitation of Fe2+) are overestimated by about 3000 cm-1. An empirical shift of the mol. ΔELH based upon at. calcns. provides a best est. of 12 000-13 000 cm-1. Our unshifted SORCI result is 13 300 cm-1, consistent with previous comparisons between SORCI and exptl. excitation energies which suggest that no such empirical shift is needed in conjunction with this method. In contrast, after estn. of incomplete basis set effects, GGAs with one exception underestimate this value by 3000-4000 cm-1 while the B3LYP functional underestimates it by only about 1000 cm-1. The exception is the GGA functional RPBE which appears to perform as well as or better than the B3LYP functional for the properties studied here. In order to obtain a best est. of the mol. ΔELH within the context of d. functional theory (DFT) calcns. we have also performed at. excitation energy calcns. using the multiplet sum method. These at. DFT calcns. suggest that no empirical correction is needed for the DFT calcns.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXjvVSqsrc%253D&md5=d7a26c0ba7db2cabc63d79d461e24d2f142Mortensen, J. J.; Kaasbjerg, K.; Frederiksen, S. L.; Nørskov, J. K.; Sethna, J. P.; Jacobsen, K. W.Bayesian Error Estimation in Density-Functional Theory. Phys. Rev. Lett.2005, 95, 216401, DOI: 10.1103/PhysRevLett.95.216401[Crossref], [PubMed], [CAS], Google Scholar142Bayesian Error Estimation in Density-Functional Theory
Mortensen, J. J.; Kaasbjerg, K.; Frederiksen, S. L.; Noerskov, J. K.; Sethna, J. P.; Jacobsen, K. W.
Physical Review Letters (2005), 95 (21), 216401/1-216401/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
We present a practical scheme for performing error ests. for d.-functional theory calcns. The approach, which is based on ideas from Bayesian statistics, involves creating an ensemble of exchange-correlation functionals by comparing with an exptl. database of binding energies for mols. and solids. Fluctuations within the ensemble can then be used to est. errors relative to expt. on calcd. quantities such as binding energies, bond lengths, and vibrational frequencies. It is demonstrated that the error bars on energy differences may vary by orders of magnitude for different systems in good agreement with existing experience.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXht1ejt77M&md5=7608c3d1ac63b52a40e025c3196b1890143Proppe, J.; Reiher, M.Reliable Estimation of Prediction Uncertainty for Physicochemical Property Models. J. Chem. Theory Comput.2017, 13, 3297– 3317, DOI: 10.1021/acs.jctc.7b00235[ACS Full Text ], [CAS], Google Scholar143Reliable Estimation of Prediction Uncertainty for Physicochemical Property Models
Journal of Chemical Theory and Computation (2017), 13 (7), 3297-3317CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
One of the major challenges in computational science is to det. the uncertainty of a virtual measurement, that is the prediction of an observable based on calcns. As highly accurate first-principles calcns. are in general unfeasible for most phys. systems, one usually resorts to parameteric property models of observables, which require calibration by incorporating ref. data. The resulting predictions and their uncertainties are sensitive to systematic errors such as inconsistent ref. data, parametric model assumptions, or inadequate computational methods. Here, we discuss the calibration of property models in the light of bootstrapping, a sampling method that can be employed for identifying systematic errors and for reliable estn. of the prediction uncertainty. We apply bootstrapping to assess a linear property model linking the 57Fe Mossbauer isomer shift to the contact electron d. at the iron nucleus for a diverse set of 44 mol. iron compds. The contact electron d. is calcd. with 12 d. functionals across Jacob's ladder (PWLDA, BP86, BLYP, PW91, PBE, M06-L, TPSS, B3LYP, B3PW91, PBE0, M06, TPSSh). We provide systematic-error diagnostics and reliable, locally resolved uncertainties for isomer-shift predictions. Pure and hybrid d. functionals yield av. prediction uncertainties of 0.06-0.08 mm s-1 and 0.04-0.05 mm s-1, resp., the latter being close to the av. exptl. uncertainty of 0.02 mm s-1. Furthermore, we show that both model parameters and prediction uncertainty depend significantly on the compn. and no. of ref. data points. Accordingly, we suggest that rankings of d. functionals based on performance measures (e.g., the squared coeff. of correlation, r2, or the root-mean-square error, RMSE) should not be inferred from a single data set. This study presents the first statistically rigorous calibration anal. for theor. Mossbauer spectroscopy, which is of general applicability for physicochem. property models and not restricted to isomer-shift predictions. We provide the statistically meaningful ref. data set MIS39 and a new calibration of the isomer shift based on the PBE0 functional.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXpt1ykt7w%253D&md5=41bb917d7e3707ab9c6308a00dd056c9144Simm, G. N.; Reiher, M.Error-Controlled Exploration of Chemical Reaction Networks with Gaussian Processes. J. Chem. Theory Comput.2018, 14, 5238– 5248, DOI: 10.1021/acs.jctc.8b00504[ACS Full Text ], [CAS], Google Scholar144Error-Controlled Exploration of Chemical Reaction Networks with Gaussian Processes
Journal of Chemical Theory and Computation (2018), 14 (10), 5238-5248CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
For a theor. understanding of the reactivity of complex chem. systems, relative energies of stationary points on potential energy hypersurfaces need to be calcd. to high accuracy. Due to the large no. of intermediates present in all but the simplest chem. processes, approx. quantum chem. methods are required that allow for fast evaluations of the relative energies but at the expense of accuracy. Despite the plethora of benchmark studies, the accuracy of a quantum chem. method is often difficult to assess. Moreover, a significant improvement of a method's accuracy (e.g., through reparameterization or systematic model extension) is rarely possible. Here, we present a new approach that allows for the systematic, problem-oriented, and rolling improvement of quantum chem. results through the application of Gaussian processes. Due to its Bayesian nature, reliable error ests. are provided for each prediction. A ref. method of high accuracy can be employed if the uncertainty assocd. with a particular calcn. is above a given threshold. The new data point is then added to a growing data set in order to continuously improve the model and, as a result, all subsequent predictions. Previous predictions are validated by the updated model to ensure that uncertainties remain within the given confidence bound, which we call backtracking. We demonstrate our approach with the example of a complex chem. reaction network.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhs1Gmt7vK&md5=116ed9b1481210ec5564eb6e1d0157f8145Cailliez, F.; Pernot, P.Statistical Approaches to Forcefield Calibration and Prediction Uncertainty in Molecular Simulation. J. Chem. Phys.2011, 134, 054124, DOI: 10.1063/1.3545069[Crossref], [PubMed], [CAS], Google Scholar145Statistical approaches to forcefield calibration and prediction uncertainty in molecular simulation
Journal of Chemical Physics (2011), 134 (5), 054124/1-054124/14CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
Calibration of force fields for mol. simulation should account for the measurement uncertainty of the ref. dataset and for the model inadequacy, i.e., the inability of the force-field/simulation pair to reproduce exptl. data within their uncertainty range. In all rigor, the resulting uncertainty of calibrated force-field parameters is a source of uncertainty for simulation predictions. Various calibration strategies and calibration models within the Bayesian calibration/prediction framework are explored in the present article. In the case of Lennard-Jones potential for Argon, we show that prediction uncertainty for thermodynamical and transport properties, albeit very small, is larger than statistical simulation uncertainty. (c) 2011 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhsF2jtrw%253D&md5=cb127efab49b9b1eb06abe50c1872588146Pernot, P.; Civalleri, B.; Presti, D.; Savin, A.Prediction Uncertainty of Density Functional Approximations for Properties of Crystals with Cubic Symmetry. J. Phys. Chem. A2015, 119, 5288– 5304, DOI: 10.1021/jp509980w[ACS Full Text ], [CAS], Google Scholar146Prediction Uncertainty of Density Functional Approximations for Properties of Crystals with Cubic Symmetry
Pernot, Pascal; Civalleri, Bartolomeo; Presti, Davide; Savin, Andreas
Journal of Physical Chemistry A (2015), 119 (21), 5288-5304CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
The performance of a method is generally measured by an assessment of the errors between the method's results and a set of ref. data. The prediction uncertainty is a measure of the confidence that can be attached to a method's prediction. Its estn. is based on the random part of the errors not explained by ref. data uncertainty, which implies an evaluation of the systematic component(s) of the errors. As the predictions of most d. functional approxns. (DFA) present systematic errors, the std. performance statistics, such as the mean of the abs. errors (MAE or MUE), cannot be directly used to infer prediction uncertainty. We investigate here an a posteriori calibration method to est. the prediction uncertainty of DFAs for properties of solids. A linear model is shown to be adequate to address the systematic trend in the errors. The applicability of this approach to modest-size ref. sets (28 systems) is evaluated for the prediction of band gaps, bulk moduli, and lattice consts. with a wide panel of DFAs.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsF2gsrk%253D&md5=bf61ac91c6e79665c5009483c411f921147Pernot, P.; Savin, A.Probabilistic Performance Estimators for Computational Chemistry Methods: The Empirical Cumulative Distribution Function of Absolute Errors. J. Chem. Phys.2018, 148, 241707, DOI: 10.1063/1.5016248[Crossref], [PubMed], [CAS], Google Scholar147Probabilistic performance estimators for computational chemistry methods: The empirical cumulative distribution function of absolute errors
Journal of Chemical Physics (2018), 148 (24), 241707/1-241707/15CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
Benchmarking studies in computational chem. use ref. datasets to assess the accuracy of a method through error statistics. The commonly used error statistics, such as the mean signed and mean unsigned errors, do not inform end-users on the expected amplitude of prediction errors attached to these methods. We show that, the distributions of model errors being neither normal nor zero-centered, these error statistics cannot be used to infer prediction error probabilities. To overcome this limitation, we advocate for the use of more informative statistics, based on the empirical cumulative distribution function of unsigned errors, namely, (1) the probability for a new calcn. to have an abs. error below a chosen threshold and (2) the maximal amplitude of errors one can expect with a chosen high confidence level. Those statistics are also shown to be well suited for benchmarking and ranking studies. Moreover, the std. error on all benchmarking statistics depends on the size of the ref. dataset. Systematic publication of these std. errors would be very helpful to assess the statistical reliability of benchmarking conclusions. (c) 2018 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXkslahsLc%253D&md5=545f83770372feeffae51431c4b2b3ec148Weymuth, T.; Proppe, J.; Reiher, M.Statistical Analysis of Semiclassical Dispersion Corrections. J. Chem. Theory Comput.2018, 14, 2480– 2494, DOI: 10.1021/acs.jctc.8b00078[ACS Full Text ], [CAS], Google Scholar148Statistical Analysis of Semiclassical Dispersion Corrections
Journal of Chemical Theory and Computation (2018), 14 (5), 2480-2494CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Semiclassical dispersion corrections developed by Grimme and co-workers have become indispensable in applications of Kohn-Sham d. functional theory. A deeper understanding of the underlying parametrization might be crucial for well-founded further improvements of this successful approach. To this end, we present an in-depth assessment of the fit parameters present in semiclassical (D3-type) dispersion corrections by means of a statistically rigorous anal. We find that the choice of the cost function generally has a small effect on the empirical parameters of D3-type dispersion corrections with respect to the ref. set under consideration. Only in a few cases, the choice of cost function has a surprisingly large effect on the total dispersion energies. In particular, the weighting scheme in the cost function can significantly affect the reliability of predictions. In order to obtain unbiased (data-independent) uncertainty ests. for both the empirical fit parameters and the corresponding predictions, we carried out a nonparametric bootstrap anal. This anal. reveals that the std. deviation of the mean of the empirical D3 parameters is small. Moreover, the mean prediction uncertainty obtained by bootstrapping is not much larger than previously reported error measures. On the basis of a jackknife anal., we find that the original ref. set is slightly skewed, but our results also suggest that this feature hardly affects the prediction of dispersion energies. Furthermore, we find that the introduction of small uncertainties to the ref. data does not change the conclusions drawn in this work. However, a rigorous anal. of error accumulation arising from different parametrizations reveals that error cancellation does not necessarily occur, leading to a monotonically increasing deviation in the dispersion energy with increasing mol. size. We discuss this issue in detail at the prominent example of the C60 'buckycatcher'. We find deviations between individual parametrizations of several tens of kilocalories per mol in some cases. Hence, in combination with any calcn. of dispersion energies, we recommend to always det. the assocd. uncertainties for which we will provide a software tool.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXmvVaqsL4%253D&md5=723d9ba5398927668bdedd0141a9b508149Bowman, D. N.; Jakubikova, E.Low-Spin Versus High-Spin Ground State in Pseudo-Octahedral Iron Complexes. Inorg. Chem.2012, 51, 6011– 6019, DOI: 10.1021/ic202344w[ACS Full Text ], [CAS], Google Scholar149Low-Spin versus High-Spin Ground State in Pseudo-Octahedral Iron Complexes
Inorganic Chemistry (2012), 51 (11), 6011-6019CODEN: INOCAJ; ISSN:0020-1669. (American Chemical Society)
Pseudo-octahedral complexes of iron find applications as switches in mol. electronic devices, materials for data storage, and, more recently, as candidates for dye-sensitizers in dye-sensitized solar cells. Iron, as a first row transition metal, provides a weak ligand-field splitting in an octahedral environment. This results in the presence of low-lying 5T excited states that, depending on the identity of iron ligands, can become the ground state of the complex. The small energy difference between the low-spin, 1A, and high-spin, 5T, states presents a challenge for accurate prediction of their ground state using d. functional theory. In this work, we investigate the applicability of the B3LYP functional to the ground state detn. of first row transition metal complexes, focusing mainly on Fe(II) polypyridine complexes with ligands of varying ligand field strength. It has been shown previously that B3LYP artificially favors the 5T state as the ground state of Fe(II) complexes, and the error in the energy differences between the 1A and 5T states is systematic for a set of structurally related complexes. We demonstrate that structurally related complexes can be defined as pseudo-octahedral complexes that undergo similar distortion in the metal-ligand coordination environment between the high-spin and low-spin states. The systematic behavior of complexes with similar distortion can be exploited, and the ground state of an arbitrary Fe(II) complex can be detd. by comparing the calcd. energy differences between the singlet and quintet electronic states of a complex to the energy differences of structurally related complexes with a known, exptl. detd. ground state.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XnsVKrsLc%253D&md5=b025afcba2cc19000a9165657fcce3ee150Salomon, O.; Reiher, M.; Hess, B. A.Assertion and Validation of the Performance of the B3LYP* Functional for the First Transition Metal Row and the G2 Test Set. J. Chem. Phys.2002, 117, 4729– 4737, DOI: 10.1063/1.1493179[Crossref], [CAS], Google Scholar150Assertion and validation of the performance of the B3LYP* functional for the first transition metal row and the G2 test set
Salomon, Oliver; Reiher, Markus; Hess, Bernd Artur
Journal of Chemical Physics (2002), 117 (10), 4729-4737CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
The exact exchange part in hybrid d. functionals is analyzed with respect to the prediction of ground state multiplicities. It has been found [M. Reiher, O. Salomon, and B. A. Hess, Theor. Chem. Acc., 107, 48 (2001)] that pure and hybrid d. functionals yield energy splittings between high-spin and low-spin states of Fe-sulfur complexes that differ by more than 100 kJ/mol and thus fail to reliably predict the correct multiplicity of the ground state. This deviation can lead to meaningless reaction energetics for metal-catalyzed reactions. The finding that the energy splitting depends linearly on the exact exchange admixt. parameter led to a new parametrization of the B3LYP functional which was dubbed B3LYP*. In the present paper we investigate the generality and transferability of this functional. We study the extent to which the exact exchange admixt. affects the thermochem. validated with respect to the ref. data set of mols. from the G2 test set. Metallocenes and bis(benzene) metal complexes of the first transition metal period are chosen to test the transferability of the findings for Fe-sulfur complexes. Moreover, the slope of the linear dependence of the energy splitting of high-spin and low-spin states on the amt. of admixt. of exact exchange is studied in detail.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XmsVWnurc%253D&md5=6a81456831ecdf8113eaf6b8cf10e579151Duignan, T.; Autschbach, J.; Batista, E.; Yang, P.Assessment of Tuned Range Separated Exchange Functionals for Spectroscopies and Properties of Uranium Complexes. J. Chem. Theory Comput.2017, 13, 3614– 3625, DOI: 10.1021/acs.jctc.7b00526[ACS Full Text ], [CAS], Google Scholar151Assessment of Tuned Range Separated Exchange Functionals for Spectroscopies and Properties of Uranium Complexes
Duignan, Thomas J.; Autschbach, Jochen; Batista, Enrique; Yang, Ping
Journal of Chemical Theory and Computation (2017), 13 (8), 3614-3625CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
The Kohn-Sham delocalization error (DE) is quantified in select uranium compds. for various functionals and shown to correlate with the magnitude of dative ligand donation into the 5f shell. Range sepd. exchange functionals are reparametrized to minimize the DE and analyzed for their spectroscopic predictive capabilities. Valence excitation spectra of occupied 5f systems exhibit noticeable improvement upon reparametrization, e.g. UCl6-, UCl62-, and UO2+. Less sensitivity to the reparameterization was obsd. for closed shell 5f systems and core excitation spectra. A general parametrization is proposed to perform well for valence excitation spectra with small DE.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtFGntr7M&md5=e9266fb8c8dce67cee153fea825f5c3a152van der Maaten, L.; Hinton, G.Visualizing Data Using t-SNE. J. Mach. Learn. Res.2008, 9, 2579– 2605Google ScholarThere is no corresponding record for this reference.
153Wilbraham, L.; Verma, P.; Truhlar, D. G.; Gagliardi, L.; Ciofini, I.Multiconfiguration Pair-Density Functional Theory Predicts Spin-State Ordering in Iron Complexes with the Same Accuracy as Complete Active Space Second-Order Perturbation Theory at a Significantly Reduced Computational Cost. J. Phys. Chem. Lett.2017, 8, 2026– 2030, DOI: 10.1021/acs.jpclett.7b00570[ACS Full Text ], [CAS], Google Scholar153Multiconfiguration Pair-Density Functional Theory Predicts Spin-State Ordering in Iron Complexes with the Same Accuracy as Complete Active Space Second-Order Perturbation Theory at a Significantly Reduced Computational Cost
Wilbraham, Liam; Verma, Pragya; Truhlar, Donald G.; Gagliardi, Laura; Ciofini, Ilaria
Journal of Physical Chemistry Letters (2017), 8 (9), 2026-2030CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
The spin-state orderings in nine Fe(II) and Fe(III) complexes with ligands of diverse ligand-field strength were investigated with multiconfiguration pair-d. functional theory (MC-PDFT). The performance of this method was compared to that of complete active space second-order perturbation theory (CASPT2) and Kohn-Sham d. functional theory. We also investigated the dependence of CASPT2 and MC-PDFT results on the size of the active-space. MC-PDFT reproduces the CASPT2 spin-state ordering, the dependence on the ligand field strength, and the dependence on active space at a computational cost that is significantly reduced as compared to CASPT2.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXls1Sntrg%253D&md5=c15ddb19af9f96bb1445e0bda0ebf45b154Mahler, A.; Janesko, B. G.; Moncho, S.; Brothers, E. N.When Hartree-Fock Exchange Admixture Lowers DFT-Predicted Barrier Heights: Natural Bond Orbital Analyses and Implications for Catalysis. J. Chem. Phys.2018, 148, 244106, DOI: 10.1063/1.5032218[Crossref], [PubMed], [CAS], Google Scholar154When Hartree-Fock exchange admixture lowers DFT-predicted barrier heights: Natural bond orbital analyses and implications for catalysis
Mahler, Andrew; Janesko, Benjamin G.; Moncho, Salvador; Brothers, Edward N.
Journal of Chemical Physics (2018), 148 (24), 244106/1-244106/9CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
The conventional wisdom in d. functional theory (DFT) is that std. approxns. systematically underestimate chem. reaction barrier heights and that exact (Hartree-Fock-like, HF) exchange admixt. improves this. This conventional wisdom is inconsistent with the good performance of functionals without HF exchange for many reactions on metal catalyst surfaces. We have studied several 'anomalous' gas-phase reactions where this conventional wisdom is upended, and a HF exchange admixt. decreases or does not affect the predicted barrier heights [Mahler et al., J. Chem. Phys. 146, 234103 (2017)]. Here we show how natural bond orbital analyses can help identify and explain some factors that produce anomalous barriers. Applications to pnictogen inversion, std. benchmark reaction barrier datasets, and a model Grubbs catalyst illustrate the utility of this approach. This approach is expected to aid DFT users in choosing appropriate functionals, and aid DFT developers in devising DFT approxns. generally applicable to catalysis. (c) 2018 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXht1aksbvJ&md5=0feaebe27c8d317355b5a6e0b73eb3f5155Ramakrishnan, R.; Dral, P. O.; Rupp, M.; von Lilienfeld, O. A., Quantum Chemistry Structures and Properties of 134 Kilo Molecules. 2014, 1, 140022.Google ScholarThere is no corresponding record for this reference.
156Kier, L. B.A Shape Index from Molecular Graphs. Quant. Struct.-Act. Relat.1985, 4, 109– 116, DOI: 10.1002/qsar.19850040303[Crossref], [CAS], Google Scholar156Kier, Lemont B.
Quantitative Structure-Activity Relationships (1985), 4 (3), 109-16CODEN: QSARDI; ISSN:0722-3676.
A numerical index of mol. shape was derived from the graph of the nonhydrogen mol. skeleton. The index is based on the count of 2-bond fragments in a graph relative to the max. no. possible in the isomeric star graph and the min. no. in the isomeric linear graph. In this initial study all nonhydrogen atoms and all bonds are considered equal. The 2K index describes the mol. shape in relation to the star and linear graph and is normalized to the no. of atoms. Applications are presented for shape similarity estn., cavity filling ability, and QSAR analyses.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL28Xhs1Wmsb0%253D&md5=1aab51ef350cc6b074980626f3011dee157Herr, J. E.; Yao, K.; McIntyre, R.; Toth, D. W.; Parkhill, J.Metadynamics for Training Neural Network Model Chemistries: A Competitive Assessment. J. Chem. Phys.2018, 148, 241710, DOI: 10.1063/1.5020067[Crossref], [PubMed], [CAS], Google Scholar157Metadynamics for training neural network model chemistries: A competitive assessment
Herr, John E.; Yao, Kun; McIntyre, Ryker; Toth, David W.; Parkhill, John
Journal of Chemical Physics (2018), 148 (24), 241710/1-241710/9CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
Neural network model chemistries (NNMCs) promise to facilitate the accurate exploration of chem. space and simulation of large reactive systems. One important path to improving these models is to add layers of phys. detail, esp. long-range forces. At short range, however, these models are data driven and data limited. Little is systematically known about how data should be sampled, and 'test data' chosen randomly from some sampling techniques can provide poor information about generality. If the sampling method is narrow, 'test error' can appear encouragingly tiny while the model fails catastrophically elsewhere. In this manuscript, we competitively evaluate two common sampling methods: mol. dynamics (MD), normal-mode sampling, and one uncommon alternative, Metadynamics (MetaMD), for prepg. training geometries. We show that MD is an inefficient sampling method in the sense that addnl. samples do not improve generality. We also show that MetaMD is easily implemented in any NNMC software package with cost that scales linearly with the no. of atoms in a sample mol. MetaMD is a black-box way to ensure samples always reach out to new regions of chem. space, while remaining relevant to chem. near kbT. It is a cheap tool to address the issue of generalization. (c) 2018 American Institute of Physics.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXkslaht7s%253D&md5=5d3b9f188e3df8fe0e6f381da1eee5a6158Broto, P.; Moreau, G.; Vandycke, C.Molecular Structures: Perception, Autocorrelation Descriptor and Sar Studies: System of Atomic Contributions for the Calculation of the N-Octanol/Water Partition Coefficients. Eur. J. Med. Chem.1984, 19, 71– 78[CAS], Google Scholar158Molecular structures: perception, autocorrelation descriptor and SAR studies. System of atomic contributions for the calculation of the n-octanol/water partition coefficients
European Journal of Medicinal Chemistry (1984), 19 (1), 71-8CODEN: EJMCA5; ISSN:0009-4374.
A system of additive and constitutive at. contributions to log P (partition coeff.) is proposed. The contributions to log P take into account the nature of atoms and their environment. Numerical values of 222 contributions were derived from a set of 1868 exptl. log P values. This system allows calcn. of log P for most org. mols. with a precision of 0.4 log P units, and gives an estn. of the distribution of lipophilicity on mol. structures.
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2cXitVyksLc%253D&md5=179a4663f68bb04c76b00c658a81b7d9Supporting Information
ARTICLE SECTIONSJump To
The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.inorgchem.9b00109.
Structural properties of 66 octahedral transition-metal complexes with water, carbonyl, misc, furan, and pyridine ligands obtained from DFT geometry optimization, ANN predictions, and UFF or MMFF94 force fields, errors of the force fields or ANN with respect to DFT geometry optimization, tuning of DFT functionals to reproduce CASPT2 results, MCDL-25 descriptors, MCDL-25 errors averaged by an exchange fraction, hyperparameters of additional ML models, feature selected subsets for KRR comparisons, comparison of SCO leads with varying metal and oxidation states using both ANN and DFT, redox potential and spin-splitting RAC featuring subset characteristics, and spin and redox properties of representative complexes (PDF)
#Minecraft ID Resolver - A modpack creators best friend!
Welcome! I have created a tool which I believe both normal users and modpack creators will be able to utilize. It is written in Java and therefore will work on every OS and is designed to find and fix Minecraft ID conflicts.
#Usage
- Select the configuration directory
- Search for conflicts
- Manually resolve conflicts by using the list of conflicts the program provides
Please note that the unknown IDs tab is an attempt to support unsupported configuration files (aka any non-forge configuration file) and is most likely always going to be a false positive. Because of this, this tool will not attempt to resolve unknown ID conflicts.
Or if you want to resolve ID conflicts automatically,
- Select the configuration directory
- Search for conflicts
- Provide an NEI ID dump
- For Minecraft 1.5.2 and below:2. Start Minecraft with NEI installed3. Open any world4. Open your inventory5. Click 'Options'6. Click 'Block/Item ID Settings'7. Make sure that item IDs are dumped! It will not dump item IDs by default!8. Click 'Dump ID Map Now'. This will dump the ID map to your
.minecraftfolder. Now just browse to the file when asked to provide a NEI ID dump. - For Minecraft 1.6.2 and above:
- Start Minecraft with NEI installed
- Open any world
- Open your inventory
- Click 'Options'
- Click 'Tools'
- Click 'Data Dumps'
- Make sure that all the block/item IDs or the free block/item IDs are dumped! Do not dump the already used IDs!
- Click 'Dump'. This will dump the ID map to your
.minecraft/dumpsfolder. Now just browse to the file when asked to provide a NEI ID dump.
- For Minecraft 1.5.2 and below:2. Start Minecraft with NEI installed3. Open any world4. Open your inventory5. Click 'Options'6. Click 'Block/Item ID Settings'7. Make sure that item IDs are dumped! It will not dump item IDs by default!8. Click 'Dump ID Map Now'. This will dump the ID map to your
- Allow the program to resolve conflicts automatically
If for whatever reason your configuration is messed up afterwards, there will be a backup in your .minecraft directory named config_bak.
As of version 1.0.5, there is now command line support. The basic usage goes as follows:
Also, do note that the -s argument is not necessary unless you want to set it to true, in which case the conflicts will be displayed and you will be asked if you want to resolve them, rather than them being resolved without user input.
A basic example also goes as follows:
#Building from source
If you just want a stable build, grab the latest version from the releases page.
However, if you want the bleeding edge build first clone the repository. Then you are going to need to add MiG Layout, Apache Commons Collections, Appache Commons IO, and JSAP to the build path. Finally, make sure that the classpath is set to WindowMain and then compile.
#Contributing
Contributing is a great way to help me and the community out. Everything helps!
##Donating
Donating is one way to express your thanks for the work I do in my free time. You can donate any amount here.
##Pull requests
Contirbuting to my code is another wonderful way to help me out. I will accept just about any pull requests.
However, I do ask that:
- Don't make any readme changes unless its of vast importance
- Don't just change a variable or function name and call it a pull request. Please only commit changes that add new content or changes something that is very important
- Follow my coding style
###My coding style
When making a pull request, I ask that you follow a few simple format rules that I use so that even in the future the code still flows nicely.
Rules:
- Keep the first brace on the opening line
e.g.
not
- Separate actions/variable manipulations that are different
- However, breaks, continues, etc. can stay directly under any action.
e.g.
not
- Spaces with if-else blocks (and basically spaces in general)
e.g.
not
- Just be smart and look at some of my code if you have a question
#Using my code in your program
If you want to use my code in your program, that's great! I do ask that you please give me credit. To start off, your going to need to add Apache Commons Collections, and Appache Commons IO to your build path. Then you can add my developer jar to your build path. From there, my 'libraries' are pretty straightforward (most of the time..), but I've still included a (poorly written) Javadoc which is avliable here. In addition, below is a basic example of how to find and resolve ID conflicts.
You will first want to call:
This will populate MultiValueMaps (one for blocks, items, and unknown IDs [IDs that may or may not be blocks/items]) with every item ID found in the configuration directory, and ArrayLists containing the IDs corrosponding name(s), and which configuration file(s) it was found in.
It can be visualized somewhat like this:
So, the ID 1337 has 2 (in this case) blocks mapped to it.
From there, you can retrieve these maps by doing:
By iterating through one of these maps, you can then determine if an ID is conflicting or not by doing:
The above method will return true or false respectively. You can also optionally pass the type parameter (either BLOCK or ITEM. This is case sensitive!) and ConflictHelper will store the conflicting IDs in thier respective ArrayLists.
If you want conflicts to automatically be resolved, we now need to populate more ArrayLists that will contain the unused block and item IDs. It's as simple as calling:
You can also get the unused block/item IDs by calling:
Finally, to resolve the conflicts it's as easy as calling:
#License
This software is licensed under the GNU General Public License v3.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/