1
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Cheng L, Sun J, Deustua JE, Bhethanabotla VC, Miller TF. Molecular-orbital-based machine learning for open-shell and multi-reference systems with kernel addition Gaussian process regression. J Chem Phys 2022; 157:154105. [PMID: 36272799 DOI: 10.1063/5.0110886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We introduce a novel machine learning strategy, kernel addition Gaussian process regression (KA-GPR), in molecular-orbital-based machine learning (MOB-ML) to learn the total correlation energies of general electronic structure theories for closed- and open-shell systems by introducing a machine learning strategy. The learning efficiency of MOB-ML(KA-GPR) is the same as the original MOB-ML method for the smallest criegee molecule, which is a closed-shell molecule with multi-reference characters. In addition, the prediction accuracies of different small free radicals could reach the chemical accuracy of 1 kcal/mol by training on one example structure. Accurate potential energy surfaces for the H10 chain (closed-shell) and water OH bond dissociation (open-shell) could also be generated by MOB-ML(KA-GPR). To explore the breadth of chemical systems that KA-GPR can describe, we further apply MOB-ML to accurately predict the large benchmark datasets for closed- (QM9, QM7b-T, and GDB-13-T) and open-shell (QMSpin) molecules.
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Affiliation(s)
- Lixue Cheng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Jiace Sun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - J Emiliano Deustua
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Vignesh C Bhethanabotla
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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2
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Mehta N, Martin JML. Explicitly Correlated Double-Hybrid DFT: A Comprehensive Analysis of the Basis Set Convergence on the GMTKN55 Database. J Chem Theory Comput 2022; 18:5978-5991. [PMID: 36099641 PMCID: PMC9558368 DOI: 10.1021/acs.jctc.2c00426] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Double-hybrid density functional theory (DHDFT) offers
a pathway
to accuracy approaching composite wavefunction approaches such as
G4 theory. However, the Görling–Levy second-order perturbation
theory (GLPT2) term causes them to partially inherit the slow ∝L–3 (with L the maximum
angular momentum) basis set convergence of correlated wavefunction
methods. This could potentially be remedied by introducing F12 explicit
correlation: we investigate the basis set convergence of both DHDFT
and DHDFT-F12 (where GLPT2 is replaced by GLPT2-F12) for the large
and chemically diverse general main-group thermochemistry, kinetics,
and noncovalent interactions (GMTKN55) benchmark suite. The B2GP-PLYP-D3(BJ)
and revDSD-PBEP86-D4 DHDFs are investigated as test cases, together
with orbital basis sets as large as aug-cc-pV5Z and F12 basis sets
as large as cc-pVQZ-F12. We show that F12 greatly accelerates basis
set convergence of DHDFs, to the point that even the modest cc-pVDZ-F12
basis set is closer to the basis set limit than cc-pV(Q+d)Z or def2-QZVPPD
in orbital-based approaches, and in fact comparable in quality to
cc-pV(5+d)Z. Somewhat surprisingly, aug-cc-pVDZ-F12 is not required
even for the anionic subsets. In conclusion, DHDF-F12/VDZ-F12 eliminates
concerns about basis set convergence in both the development and applications
of double-hybrid functionals. Mass storage and I/O bottlenecks for
larger systems can be circumvented by localized pair natural orbital
approximations, which also exhibit much gentler system size scaling.
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Affiliation(s)
- Nisha Mehta
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Jan M L Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
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3
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Sparrow ZM, Ernst BG, Quady TK, DiStasio RA. Uniting Nonempirical and Empirical Density Functional Approximation Strategies Using Constraint-Based Regularization. J Phys Chem Lett 2022; 13:6896-6904. [PMID: 35863751 DOI: 10.1021/acs.jpclett.2c00643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this work, we present a general framework that unites the two primary strategies for constructing density functional approximations (DFAs): nonempirical (NE) constraint satisfaction and empirical (E) data-driven optimization. The proposed method employs B-splines, bell-shaped spline functions with compact support, to construct each inhomogeneity correction factor (ICF). This choice offers several distinct advantages over traditional polynomial expansions by enabling explicit enforcement of linear and nonlinear constraints as well as ICF smoothness using Tikhonov and penalized B-splines (P-splines) regularization. As proof-of-concept, we use the so-called CASE (constrained and smoothed empirical) framework to construct a constraint-satisfying and data-driven global hybrid that exhibits enhanced performance across a diverse set of chemical properties. We argue that the CASE approach can be used to generate DFAs that maintain the physical rigor and transferability of NE-DFAs while leveraging high-quality quantum-mechanical data to remove the arbitrariness of ansatz selection and improve performance.
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Affiliation(s)
- Zachary M Sparrow
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Brian G Ernst
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Trine K Quady
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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4
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Zapata Trujillo JC, McKemmish LK. VIBFREQ1295: A New Database for Vibrational Frequency Calculations. J Phys Chem A 2022; 126:4100-4122. [PMID: 35723975 DOI: 10.1021/acs.jpca.2c01438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
High-throughput approaches for producing approximate vibrational spectral data for molecules of astrochemistry interest rely on harmonic frequency calculations using computational quantum chemistry. However, model chemistry recommendations (i.e., a level of theory and basis set pair) for these calculations are not yet available and, thus, thorough benchmarking against comprehensive benchmark databases is needed. Here, we present a new database for vibrational frequency calculations (VIBFREQ1295) storing 1295 experimental fundamental frequencies and CCSD(T)(F12*)/cc-pVDZ-F12 ab initio harmonic frequencies from 141 molecules. VIBFREQ1295's experimental data was complied through a comprehensive review of contemporary experimental data, while the ab initio data was computed here. The chemical space spanned by the molecules chosen is considered in-depth and is shown to have good representation of common organic functional groups and vibrational modes. Scaling factors are routinely used to approximate the effect of anharmonicity and convert computed harmonic frequencies to predicted fundamental frequencies. With our experimental and high-level ab initio data, we find that a single global uniform scaling factor of 0.9617(3) results in median differences of 15.9(5) cm-1. A far superior performance with a median difference of 7.5(5) cm-1 can be obtained, however, by using separate scaling factors (SFs) for three regions: frequencies less than 1000 cm-1 (SF = 0.987(1)), between 1000 and 2000 cm-1 (SF = 0.9727(6)), and above 2000 cm-1 (SF = 0.9564(4)). This sets a lower bound for the performance that could be reliably obtained using scaling of harmonic frequency calculations to predict experimental fundamental frequencies. VIBFREQ1295's most important purpose is to provide a robust database for benchmarking the performance of any vibrational frequency calculations. VIBFREQ1295 data could also be used to train machine-learning models for the prediction of vibrational spectra and as a reference and data starting point for more detailed spectroscopic modeling of particular molecules. The database can be found as part of the Supporting Information for this paper or in the Harvard DataVerse at https://doi.org/10.7910/DVN/VLVNU7.
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Affiliation(s)
| | - Laura K McKemmish
- School of Chemistry, University of New South Wales, 2052 Sydney, Australia
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5
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Trung NQ, Mechler A, Hoa NT, Vo QV. Calculating bond dissociation energies of X-H (X=C, N, O, S) bonds of aromatic systems via density functional theory: a detailed comparison of methods. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220177. [PMID: 35706655 PMCID: PMC9174704 DOI: 10.1098/rsos.220177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/06/2022] [Indexed: 05/03/2023]
Abstract
In this study, the performance of 17 different density functional theory functionals was compared for the calculation of the bond dissociation energy (BDE) values of X-H (X=C, N, O, S) bonds of aromatic compounds. The effect of the size of the basis set (expansions of 6-31(G)) was also assessed for the initial geometry and zero-point energy calculations, followed by the single-point BDE calculations with different model chemistries with the 6-311 + (3df,2p) basis set. It was found that the size of the basis set for geometry optimization has a much smaller effect on the accuracy of BDE than the choice of functional for the following single-point calculations. The M06-2X, M05-2X and M08-HX functionals yielded highly accurate BDE values compared to experimental data (with the average mean unsigned error MUE = 1.2-1.5 kcal mol-1), performing better than any of the other functionals. The results suggest that geometry optimization may be performed with B3LYP functional and a small basis set, whereas the M06-2X, M05-2X and M08-HX density functionals with a suitably large basis set offer the best method for calculating BDEs of ArX-H (X=C, N, O, S) bonds.
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Affiliation(s)
- Nguyen Quang Trung
- Department of Chemistry, The University of Danang - University of Science and Education, Da Nang 550000, Vietnam
- Quality Assurance and Testing Center 2, Danang 550000, Vietnam
| | - Adam Mechler
- Department of Chemistry and Physics, La Trobe University, Victoria 3086, Australia
| | - Nguyen Thi Hoa
- Academic Affairs, The University of Danang - University of Technology and Education, Danang 550000, Vietnam
| | - Quan V. Vo
- Faculty of Chemical Technology – Environment, The University of Danang - University of Technology and Education, Danang 550000, Vietnam
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6
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Zapata Trujillo JC, McKemmish LK. Meta‐analysis of uniform scaling factors for harmonic frequency calculations. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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7
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Gould T, Dale SG. Poisoning density functional theory with benchmark sets of difficult systems. Phys Chem Chem Phys 2022; 24:6398-6403. [PMID: 35244641 DOI: 10.1039/d2cp00268j] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Large benchmark sets like GMTKN55 [Goerigk et al., Phys. Chem. Chem. Phys., 2017, 19, 32184] let us analyse the performance of density functional theory over a diverse range of systems and bonding types. However, assessing over a large and diverse set can miss cases where approaches fail badly, and can give a misleading sense of security. To this end we introduce a series of 'poison' benchmark sets, P30-5, P30-10 and P30-20, comprising systems with up to 5, 10 and 20 atoms, respectively. These sets represent the most difficult-to-model systems in GMTKN55. We expect them to be useful in developing new approximations, identifying weak points in existing ones, and to aid in selecting appropriate DFAs for computational studies involving difficult physics, e.g. catalysis.
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Affiliation(s)
- Tim Gould
- Qld Micro- and Nanotechnology Centre, Griffith University, Nathan, Qld 4111, Australia.
| | - Stephen G Dale
- Qld Micro- and Nanotechnology Centre, Griffith University, Nathan, Qld 4111, Australia.
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8
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Mehta N, Goerigk L. Assessing the Applicability of the Geometric Counterpoise Correction in B2PLYP/Double-ζ Calculations for Thermochemistry, Kinetics, and Noncovalent Interactions. Aust J Chem 2021. [DOI: 10.1071/ch21133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We present a proof-of-concept study of the suitability of Kruse and Grimme’s geometric counterpoise correction (gCP) for basis set superposition errors (BSSEs) in double-hybrid density functional calculations with a double-ζ basis set. The gCP approach only requires geometrical information as an input and no orbital/density information is needed. Therefore, this correction is practically free of any additional cost. gCP is trained against the Boys and Bernardi counterpoise correction across a set of 528 noncovalently bound dimers. We investigate the suitability of the approach for the B2PLYP/def2-SVP level of theory, and reveal error compensation effects—missing London dispersion and the BSSE—associated with B2PLYP/def2-SVP calculations, and present B2PLYP-gCP-D3(BJ)/def2-SVP with the reparametrised DFT-D3(BJ) and gCP corrections as a more balanced alternative. Benchmarking results on the S66x8 benchmark set for noncovalent interactions and the GMTKN55 database for main-group thermochemistry, kinetics, and noncovalent interactions show a statistical improvement of the B2PLYP-gCP-D3(BJ) scheme over plain B2PLYP and B2PLYP-D3(BJ). B2PLYP-D3(BJ) shows significant overestimation of interaction energies, barrier heights with larger deviations from the reference values, and wrong relative stabilities in conformers, all of which can be associated with BSSE. We find that the gCP-corrected method represents a significant improvement over B2PLYP-D3(BJ), particularly for intramolecular noncovalent interactions. These findings encourage future developments of efficient double-hybrid DFT strategies that can be applied when double-hybrid calculations with large basis sets are not feasible due to system size.
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9
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Bartlett RJ, Park YC, Bauman NP, Melnichuk A, Ranasinghe D, Ravi M, Perera A. Index of multi-determinantal and multi-reference character in coupled-cluster theory. J Chem Phys 2020; 153:234103. [PMID: 33353328 DOI: 10.1063/5.0029339] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A full configuration interaction calculation (FCI) ultimately defines the innate molecular orbital description of a molecule. Its density matrix and the natural orbitals obtained from it quantify the difference between having N-dominantly occupied orbitals in a reference determinant for a wavefunction to describe N-correlated electrons and how many of those N-electrons are left to the remaining virtual orbitals. The latter provides a measure of the multi-determinantal character (MDC) required to be in a wavefunction. MDC is further split into a weak correlation part and a part that indicates stronger correlation often called multi-reference character (MRC). If several virtual orbitals have high occupation numbers, then one might argue that these additional orbitals should be allowed to have a larger role in the calculation, as in MR methods, such as MCSCF, MR-CI, or MR-coupled-cluster (MR-CC), to provide adequate approximations toward the FCI. However, there are problems with any of these MR methods that complicate the calculations compared to the uniformity and ease of application of single-reference CC calculations (SR-CC) and their operationally single-reference equation-of-motion (EOM-CC) extensions. As SR-CC theory is used in most of today's "predictive" calculations, an assessment of the accuracy of SR-CC at some truncation of the cluster operator would help to quantify how large an issue MRC actually is in a calculation, and how it might be alleviated while retaining the convenient SR computational character of CC/EOM-CC. This paper defines indices that identify MRC situations and help assess how reliable a given calculation is.
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Affiliation(s)
- Rodney J Bartlett
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, USA
| | - Young Choon Park
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, USA
| | - Nicholas P Bauman
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, USA
| | - Ann Melnichuk
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, USA
| | - Duminda Ranasinghe
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Moneesha Ravi
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, USA
| | - Ajith Perera
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, USA
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10
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Capsaicin, a Powerful •OH-Inactivating Ligand. Antioxidants (Basel) 2020; 9:antiox9121247. [PMID: 33302572 PMCID: PMC7763808 DOI: 10.3390/antiox9121247] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 11/28/2020] [Accepted: 12/03/2020] [Indexed: 12/16/2022] Open
Abstract
Oxidative conditions are frequently enhanced by the presence of redox metal ions. In this study, the role of capsaicin (8-methyl-N-vanillyl-6-nonenamide, CAP) in copper-induced oxidative stress was investigated using density functional theory simulations. It was found that CAP has the capability to chelate Cu(II), leading to complexes that are harder to reduce than free Cu(II). CAP fully turns off the Cu(II) reduction by Asc−, and slows down the reduction in this cation by O2•−. Therefore, CAP is proposed as an •OH-inactivating ligand by impeding the reduction in metal ions (OIL-1), hindering the production of •OH via Fenton-like reactions, at physiological pH. CAP is also predicted to be an excellent antioxidant as a scavenger of •OH, yielded through Fenton-like reactions (OIL-2). The reactions between CAP-Cu(II) chelates and •OH were estimated to be diffusion-limited. Thus, these chelates are capable of deactivating this dangerous radical immediately after being formed by Fenton-like reactions.
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11
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Williams ZM, Wiles TC, Manby FR. Accurate Hybrid Density Functionals with UW12 Correlation. J Chem Theory Comput 2020; 16:6176-6194. [PMID: 32820918 DOI: 10.1021/acs.jctc.0c00442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In previous work, we suggested a single-parameter hybrid functional containing a novel correlation contribution based on the Unsöld approximation, UW12. This model resembles the explicitly correlated part of MP2-F12 theory and can be written as an explicit formula in terms of the single-particle reduced density matrix. Here, we further investigate hybrid functionals containing UW12 correlation and in particular look at functionals with a large fraction of exact exchange to reduce the self-interaction error. We suggest two new hybrid functionals B-LYP-osUW12 and fB-LYP-osUW12. On the test sets we use, our best hybrid functional overall (B-LYP-osUW12) is of similar accuracy to the best double hybrids considered while eliminating the need for virtual orbitals.
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Affiliation(s)
- Zack M Williams
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Timothy C Wiles
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
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12
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13
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Wappett DA, Goerigk L. Toward a Quantum-Chemical Benchmark Set for Enzymatically Catalyzed Reactions: Important Steps and Insights. J Phys Chem A 2019; 123:7057-7074. [DOI: 10.1021/acs.jpca.9b05088] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
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14
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Vogiatzis KD, Polynski MV, Kirkland JK, Townsend J, Hashemi A, Liu C, Pidko EA. Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities. Chem Rev 2019; 119:2453-2523. [PMID: 30376310 PMCID: PMC6396130 DOI: 10.1021/acs.chemrev.8b00361] [Citation(s) in RCA: 212] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Indexed: 12/28/2022]
Abstract
Computational chemistry provides a versatile toolbox for studying mechanistic details of catalytic reactions and holds promise to deliver practical strategies to enable the rational in silico catalyst design. The versatile reactivity and nontrivial electronic structure effects, common for systems based on 3d transition metals, introduce additional complexity that may represent a particular challenge to the standard computational strategies. In this review, we discuss the challenges and capabilities of modern electronic structure methods for studying the reaction mechanisms promoted by 3d transition metal molecular catalysts. Particular focus will be placed on the ways of addressing the multiconfigurational problem in electronic structure calculations and the role of expert bias in the practical utilization of the available methods. The development of density functionals designed to address transition metals is also discussed. Special emphasis is placed on the methods that account for solvation effects and the multicomponent nature of practical catalytic systems. This is followed by an overview of recent computational studies addressing the mechanistic complexity of catalytic processes by molecular catalysts based on 3d metals. Cases that involve noninnocent ligands, multicomponent reaction systems, metal-ligand and metal-metal cooperativity, as well as modeling complex catalytic systems such as metal-organic frameworks are presented. Conventionally, computational studies on catalytic mechanisms are heavily dependent on the chemical intuition and expert input of the researcher. Recent developments in advanced automated methods for reaction path analysis hold promise for eliminating such human-bias from computational catalysis studies. A brief overview of these approaches is presented in the final section of the review. The paper is closed with general concluding remarks.
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Affiliation(s)
| | | | - Justin K. Kirkland
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jacob Townsend
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Ali Hashemi
- Inorganic
Systems Engineering group, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Chong Liu
- Inorganic
Systems Engineering group, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Evgeny A. Pidko
- TheoMAT
group, ITMO University, Lomonosova 9, St. Petersburg 191002, Russia
- Inorganic
Systems Engineering group, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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15
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Bao JJ, Gagliardi L, Truhlar DG. Weak Interactions in Alkaline Earth Metal Dimers by Pair-Density Functional Theory. J Phys Chem Lett 2019; 10:799-805. [PMID: 30715896 DOI: 10.1021/acs.jpclett.8b03846] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Alkaline earth dimers have small bond energies (less than 5 kcal/mol) that provide a difficult challenge for electronic structure calculations. They are especially challenging for Kohn-Sham density functional theory (KS-DFT) using generalized gradient approximations (GGAs) as the exchange-correlation density functional because GGAs often do not provide accurate results for weak interactions. Here we treat alkaline earth dimers from six different rows of the periodic table. We show that the dominant correlating configurations are the same in all six dimers. We also show that multiconfiguration pair-density functional theory (MC-PDFT) using a fully translated GGA as the on-top density functional not only performs much better than KS-DFT with GGAs in predicting equilibrium distances and dissociation energies but also performs better than the more computationally demanding complete active space second-order perturbation theory (CASPT2) with large basis sets and performs even better than CASPT2 with smaller basis sets.
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Affiliation(s)
- Jie J Bao
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute , University of Minnesota , Minneapolis Minnesota 55455-0431 , United States
| | - Laura Gagliardi
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute , University of Minnesota , Minneapolis Minnesota 55455-0431 , United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute , University of Minnesota , Minneapolis Minnesota 55455-0431 , United States
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16
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Verma P, Wang Y, Ghosh S, He X, Truhlar DG. Revised M11 Exchange-Correlation Functional for Electronic Excitation Energies and Ground-State Properties. J Phys Chem A 2019; 123:2966-2990. [DOI: 10.1021/acs.jpca.8b11499] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Pragya Verma
- Department of Chemistry, Chemical Theory Center, Nanoporous Materials Genome Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Ying Wang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410006, China
| | - Soumen Ghosh
- Department of Chemistry, Chemical Theory Center, Nanoporous Materials Genome Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry, New York University, Shanghai, Shanghai 200062, China
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, Nanoporous Materials Genome Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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17
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Morgante P, Peverati R. ACCDB: A collection of chemistry databases for broad computational purposes. J Comput Chem 2018; 40:839-848. [DOI: 10.1002/jcc.25761] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/09/2018] [Accepted: 11/11/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Pierpaolo Morgante
- Chemistry Program; Florida Institute of Technology, 150 W. University Blvd.; Melbourne Florida, 32901
| | - Roberto Peverati
- Chemistry Program; Florida Institute of Technology, 150 W. University Blvd.; Melbourne Florida, 32901
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18
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Najibi A, Goerigk L. The Nonlocal Kernel in van der Waals Density Functionals as an Additive Correction: An Extensive Analysis with Special Emphasis on the B97M-V and ωB97M-V Approaches. J Chem Theory Comput 2018; 14:5725-5738. [DOI: 10.1021/acs.jctc.8b00842] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Asim Najibi
- School of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
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19
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Mehta N, Casanova-Páez M, Goerigk L. Semi-empirical or non-empirical double-hybrid density functionals: which are more robust? Phys Chem Chem Phys 2018; 20:23175-23194. [PMID: 30062343 DOI: 10.1039/c8cp03852j] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of non-empirical double-hybrid density functionals (DHDFs) is a very active research area with the number of approaches in this field having increased rapidly. At the same time, there is a lack of published work that provides a fair assessment and comparison between non-empirical and semi-empirical DHDFs on an equal footing. Herein, we close this gap and present a thorough analysis of both classes of DHDFs on the large GMTKN55 benchmark database for general main-group thermochemistry, kinetics, and noncovalent interactions [Goerigk et al., Phys. Chem. Chem. Phys., 2017, 19, 32184-32215]. In total, 115 variations of dispersion-corrected and -uncorrected DHDFs are tested, which will be condensed to an in-depth assessment of 31 methods: 19 non-empirical and 12 semi-empirical DHDFs. As such, our study represents the largest DHDF study ever conducted and can serve as an important benchmark informing method developers and users alike. Our results show that semi-empirical DHDFs are the most robust density functional approximations and more reliable and accurate than non-empirical ones. In fact, some non-empirical approaches are even outperformed by hybrid approaches or even dispersion-corrected and -uncorrected MP2 and SCS-MP2. SOS0-PBE0-2-D3(BJ) is the only exception and the only non-empirical DHDF that we can safely recommend for general applicability. However, it is still outperformed by six semi-empirical DHDFs, of which we would like to particularly recommend the following five: ωB97X-2-D3(BJ), DSD-BLYP-D3(BJ), DSD-PBEP86-D3(BJ), B2NC-PLYP-D3(BJ), and B2GPPLYP-D3(BJ). Our findings seriously question current trends in the field and they highlight that novel strategies have to be found in order to outperform the currently best density functional theory methods on the market. We hope that our study can function as an important cornerstone inspiring such a change of direction in the field.
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Affiliation(s)
- Nisha Mehta
- School of Chemistry, The University of Melbourne, Parkville, Australia.
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20
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Green ML, Jean P, Heaven MC. Dative Bonding between Closed-Shell Atoms: The BeF - Anion. J Phys Chem Lett 2018; 9:1999-2002. [PMID: 29613801 DOI: 10.1021/acs.jpclett.8b00784] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Beryllium can exhibit unusually strong attractive interactions under conditions where it is nominally a closed-shell atom. Two prominent examples are the Be2 dimer and the He-BeO complex. In the present study, we examine the bonding of the closed-shell Be-F- anion. This molecule preserves the closed-shell character of the individual atoms as the electron affinity of F is high (328.16 kJ mol-1) while that of Be is negative. Photodetachment spectroscopy was used to determine the vibrational frequency for BeF- and the electron affinity of BeF (104.2 kJ mol-1). The latter has been used to determine a lower bound of 343 kJ mol-1 for the bond energy of BeF-. Electronic structure calculations yielded predictions that were in good agreement with the observed data. A natural bond orbital analysis shows that BeF- is primarily bound by a dative interaction.
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Affiliation(s)
- Mallory L Green
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Pearl Jean
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Michael C Heaven
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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21
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Gould T. ‘Diet GMTKN55’ offers accelerated benchmarking through a representative subset approach. Phys Chem Chem Phys 2018; 20:27735-27739. [DOI: 10.1039/c8cp05554h] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The GMTKN55 benchmarking protocol allows comprehensive analysis and ranking of density functional approximations with diverse chemical behaviours. This work reports diet versions of GMTKN55 which reproduce key properties of the full protocol at substantially reduced numerical cost. ‘Diet GMTKN55’ can thus be used for benchmarking expensive methods, or in combination with solid state benchmarks.
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Affiliation(s)
- Tim Gould
- Qld Micro- and Nanotechnology Centre, Griffith University
- Nathan
- Australia
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22
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Wang Y, Wang X, Truhlar DG, He X. How Well Can the M06 Suite of Functionals Describe the Electron Densities of Ne, Ne6+, and Ne8+? J Chem Theory Comput 2017; 13:6068-6077. [DOI: 10.1021/acs.jctc.7b00865] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ying Wang
- State
Key Laboratory of Precision Spectroscopy, School of Chemistry and
Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Xianwei Wang
- State
Key Laboratory of Precision Spectroscopy, School of Chemistry and
Molecular Engineering, East China Normal University, Shanghai, 200062, China
- Center for Optics & Optoelectronics Research, College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310023, China
| | - Donald G. Truhlar
- Department
of Chemistry, Chemical Theory Center, Nanoporous Materials Genome
Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Xiao He
- State
Key Laboratory of Precision Spectroscopy, School of Chemistry and
Molecular Engineering, East China Normal University, Shanghai, 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
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23
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Alvarez-Thon L, Mammino L. Information on Gas-Phase Diatomic Molecules from Magnetically Induced Current Densities. J Comput Chem 2017; 39:52-60. [DOI: 10.1002/jcc.25083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 09/20/2017] [Accepted: 09/22/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Luis Alvarez-Thon
- Facultad de Ingeniería, Universidad Central de Chile; Toesca 1783 Santiago Chile
| | - Liliana Mammino
- Department of Chemistry; University of Venda, P/bag X5050; Thohoyandou 0950 South Africa
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24
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Ariyarathna IR, Miliordos E. The Versatile Personality of Beryllium: Be(O2)1–2 vs Be(CO)1–2. J Phys Chem A 2017; 121:7051-7058. [DOI: 10.1021/acs.jpca.7b06519] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Isuru R. Ariyarathna
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Evangelos Miliordos
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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25
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Goerigk L, Hansen A, Bauer C, Ehrlich S, Najibi A, Grimme S. A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions. Phys Chem Chem Phys 2017; 19:32184-32215. [DOI: 10.1039/c7cp04913g] [Citation(s) in RCA: 854] [Impact Index Per Article: 122.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We present the updated and extended GMTKN55 benchmark database for more accurate and extensive energetic evaluation of density functionals and other electronic structure methods with detailed guidelines for method users.
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Affiliation(s)
- Lars Goerigk
- School of Chemistry
- The University of Melbourne
- Parkville
- Australia
| | - Andreas Hansen
- Universität Bonn
- Mulliken Center for Theoretical Chemistry
- Bonn
- Germany
| | - Christoph Bauer
- Universität Bonn
- Mulliken Center for Theoretical Chemistry
- Bonn
- Germany
| | - Stephan Ehrlich
- Universität Bonn
- Mulliken Center for Theoretical Chemistry
- Bonn
- Germany
| | - Asim Najibi
- School of Chemistry
- The University of Melbourne
- Parkville
- Australia
| | - Stefan Grimme
- Universität Bonn
- Mulliken Center for Theoretical Chemistry
- Bonn
- Germany
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26
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Yu HS, He X, Li SL, Truhlar DG. MN15: A Kohn-Sham global-hybrid exchange-correlation density functional with broad accuracy for multi-reference and single-reference systems and noncovalent interactions. Chem Sci 2016; 7:5032-5051. [PMID: 30155154 PMCID: PMC6018516 DOI: 10.1039/c6sc00705h] [Citation(s) in RCA: 701] [Impact Index Per Article: 87.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/06/2016] [Indexed: 01/12/2023] Open
Abstract
Kohn-Sham density functionals are widely used; however, no currently available exchange-correlation functional can predict all chemical properties with chemical accuracy. Here we report a new functional, called MN15, that has broader accuracy than any previously available one. The properties considered in the parameterization include bond energies, atomization energies, ionization potentials, electron affinities, proton affinities, reaction barrier heights, noncovalent interactions, hydrocarbon thermochemistry, isomerization energies, electronic excitation energies, absolute atomic energies, and molecular structures. When compared with 82 other density functionals that have been defined in the literature, MN15 gives the second smallest mean unsigned error (MUE) for 54 data on inherently multiconfigurational systems, the smallest MUE for 313 single-reference chemical data, and the smallest MUE on 87 noncovalent data, with MUEs for these three categories of 4.75, 1.85, and 0.25 kcal mol-1, respectively, as compared to the average MUEs of the other 82 functionals of 14.0, 4.63, and 1.98 kcal mol-1. The MUE for 17 absolute atomic energies is 7.4 kcal mol-1 as compared to an average MUE of the other 82 functionals of 34.6 kcal mol-1. We further tested MN15 for 10 transition-metal coordination energies, the entire S66x8 database of noncovalent interactions, 21 transition-metal reaction barrier heights, 69 electronic excitation energies of organic molecules, 31 semiconductor band gaps, seven transition-metal dimer bond lengths, and 193 bond lengths of 47 organic molecules. The MN15 functional not only performs very well for our training set, which has 481 pieces of data, but also performs very well for our test set, which has 823 data that are not in our training set. The test set includes both ground-state properties and molecular excitation energies. For the latter MN15 achieves simultaneous accuracy for both valence and Rydberg electronic excitations when used with linear-response time-dependent density functional theory, with an MUE of less than 0.3 eV for both types of excitations.
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Affiliation(s)
- Haoyu S Yu
- Department of Chemistry , Chemical Theory Center , Inorganometallic Catalyst Design Center , Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , USA .
| | - Xiao He
- Department of Chemistry , Chemical Theory Center , Inorganometallic Catalyst Design Center , Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , USA .
- State Key Laboratory of Precision Spectroscopy and Department of Physics , East China Normal University , Shanghai , 200062 , China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai , 200062 , China
| | - Shaohong L Li
- Department of Chemistry , Chemical Theory Center , Inorganometallic Catalyst Design Center , Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , USA .
| | - Donald G Truhlar
- Department of Chemistry , Chemical Theory Center , Inorganometallic Catalyst Design Center , Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , USA .
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27
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Huang W, Xing DH, Lu JB, Long B, Schwarz WHE, Li J. How Much Can Density Functional Approximations (DFA) Fail? The Extreme Case of the FeO4 Species. J Chem Theory Comput 2016; 12:1525-33. [PMID: 26938575 DOI: 10.1021/acs.jctc.5b01040] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A thorough theoretical study of the relative energies of various molecular Fe·4O isomers with different oxidation states of both Fe and O atoms is presented, comparing simple Hartree-Fock through many Kohn-Sham approximations up to extended coupled cluster and DMRG multiconfiguration benchmark methods. The ground state of Fe·4O is a singlet, hexavalent iron(VI) complex (1)C2v-[Fe(VI)O2](2+)(O2)(2-), with isomers of oxidation states Fe(II), Fe(III), Fe(IV), Fe(V), and Fe(VIII) all lying slightly higher within the range of 1 eV. The disputed existence of oxidation state Fe(VIII) is discussed for isolated FeO4 molecules. Density functional theory (DFT) at various DF approximation (DFA) levels of local and gradient approaches, Hartree-Fock exchange and meta hybrids, range dependent, DFT-D and DFT+U models do not perform better for the relative stabilities of the geometric and electronic Fe·4O isomers than within 1-5 eV. The Fe·4O isomeric species are an excellent testing and validation ground for the development of density functional and wave function methods for strongly correlated multireference states, which do not seem to always follow chemical intuition.
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Affiliation(s)
- Wei Huang
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Tsinghua University , Beijing 100084, China
| | - Deng-Hui Xing
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Tsinghua University , Beijing 100084, China
| | - Jun-Bo Lu
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Tsinghua University , Beijing 100084, China
| | - Bo Long
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Tsinghua University , Beijing 100084, China
| | - W H Eugen Schwarz
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Tsinghua University , Beijing 100084, China
| | - Jun Li
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Tsinghua University , Beijing 100084, China
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28
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Yu HS, He X, Truhlar DG. MN15-L: A New Local Exchange-Correlation Functional for Kohn-Sham Density Functional Theory with Broad Accuracy for Atoms, Molecules, and Solids. J Chem Theory Comput 2016; 12:1280-93. [PMID: 26722866 DOI: 10.1021/acs.jctc.5b01082] [Citation(s) in RCA: 300] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kohn-Sham density functional theory is widely used for applications of electronic structure theory in chemistry, materials science, and condensed-matter physics, but the accuracy depends on the quality of the exchange-correlation functional. Here, we present a new local exchange-correlation functional called MN15-L that predicts accurate results for a broad range of molecular and solid-state properties including main-group bond energies, transition metal bond energies, reaction barrier heights, noncovalent interactions, atomic excitation energies, ionization potentials, electron affinities, total atomic energies, hydrocarbon thermochemistry, and lattice constants of solids. The MN15-L functional has the same mathematical form as a previous meta-nonseparable gradient approximation exchange-correlation functional, MN12-L, but it is improved because we optimized it against a larger database, designated 2015A, and included smoothness restraints; the optimization has a much better representation of transition metals. The mean unsigned error on 422 chemical energies is 2.32 kcal/mol, which is the best among all tested functionals, with or without nonlocal exchange. The MN15-L functional also provides good results for test sets that are outside the training set. A key issue is that the functional is local (no nonlocal exchange or nonlocal correlation), which makes it relatively economical for treating large and complex systems and solids. Another key advantage is that medium-range correlation energy is built in so that one does not need to add damped dispersion by molecular mechanics in order to predict accurate noncovalent binding energies. We believe that the MN15-L functional should be useful for a wide variety of applications in chemistry, physics, materials science, and molecular biology.
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Affiliation(s)
- Haoyu S Yu
- Department of Chemistry, Chemical Theory Center, Inorganometallic Catalyst Design Center, and Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455-0431, United States
| | - Xiao He
- Department of Chemistry, Chemical Theory Center, Inorganometallic Catalyst Design Center, and Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455-0431, United States.,State Key Laboratory of Precision Spectroscopy, East China Normal University , Shanghai 200062, China
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, Inorganometallic Catalyst Design Center, and Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455-0431, United States
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