1
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Neugebauer H, Pinski P, Grimme S, Neese F, Bursch M. Assessment of DLPNO-MP2 Approximations in Double-Hybrid DFT. J Chem Theory Comput 2023; 19:7695-7703. [PMID: 37862406 PMCID: PMC10653103 DOI: 10.1021/acs.jctc.3c00896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Indexed: 10/22/2023]
Abstract
The unfavorable scaling (N5) of the conventional second-order Møller-Plesset theory (MP2) typically prevents the application of double-hybrid (DH) density functionals to large systems with more than 100 atoms. A prominent approach to reduce the computational demand of electron correlation methods is the domain-based local pair natural orbital (DLPNO) approximation that is successfully used in the framework of DLPNO-CCSD(T). Its extension to MP2 [Pinski P.; Riplinger, C.; Valeev, E. F.; Neese, F. J. Chem. Phys. 2015, 143, 034108.] paved the way for DLPNO-based DH (DLPNO-DH) methods. In this work, we assess the accuracy of the DLPNO-DH approximation compared to conventional DHs on a large number of 7925 data points for thermochemistry and 239 data points for structural features, including main-group and transition-metal systems. It is shown that DLPNO-DH-DFT can be applied successfully to perform energy calculations and geometry optimizations for large molecules at a drastically reduced computational cost. Furthermore, PNO space extrapolation is shown to be applicable, similar to its DLPNO-CCSD(T) counterpart, to reduce the remaining error.
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Affiliation(s)
- Hagen Neugebauer
- Mulliken
Center for Theoretical Chemistry, Clausius Institute for Physical
and Theoretical Chemistry, University of
Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - Peter Pinski
- HQS
Quantum Simulations GmbH, Rintheimer Straße 23, D-76131 Karlsruhe, Germany
| | - Stefan Grimme
- Mulliken
Center for Theoretical Chemistry, Clausius Institute for Physical
and Theoretical Chemistry, University of
Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Markus Bursch
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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2
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Rossomme E, Cunha LA, Li W, Chen K, McIsaac AR, Head-Gordon T, Head-Gordon M. The Good, the Bad, and the Ugly: Pseudopotential Inconsistency Errors in Molecular Applications of Density Functional Theory. J Chem Theory Comput 2023; 19:2827-2841. [PMID: 37156013 DOI: 10.1021/acs.jctc.3c00089] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The pseudopotential (PP) approximation is one of the most common techniques in computational chemistry. Despite its long history, the development of custom PPs has not tracked with the explosion of different density functional approximations (DFAs). As a result, the use of PPs with exchange/correlation models for which they were not developed is widespread, although this practice is known to be theoretically unsound. The extent of PP inconsistency errors (PPIEs) associated with this practice has not been systematically explored across the types of energy differences commonly evaluated in chemical applications. We evaluate PPIEs for a number of PPs and DFAs across 196 chemically relevant systems of both transition-metal and main-group elements, as represented by the W4-11, TMC34, and S22 data sets. Near the complete basis set limit, these PPs are found to cleanly approach all-electron (AE) results for noncovalent interactions but introduce root-mean-squared errors (RMSEs) upwards of 15 kcal mol-1 into predictions of covalent bond energies for a number of popular DFAs. We achieve significant improvements through the use of empirical atom- and DFA-specific PP corrections, indicating considerable systematicity of the PPIEs. The results of this work have implications for chemical modeling in both molecular contexts and for DFA design, which we discuss.
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Affiliation(s)
- Elliot Rossomme
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Leonardo A Cunha
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Wanlu Li
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kaixuan Chen
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Alexandra R McIsaac
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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3
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Gasevic T, Stückrath JB, Grimme S, Bursch M. Optimization of the r 2SCAN-3c Composite Electronic-Structure Method for Use with Slater-Type Orbital Basis Sets. J Phys Chem A 2022; 126:3826-3838. [PMID: 35654439 PMCID: PMC9255700 DOI: 10.1021/acs.jpca.2c02951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The "Swiss army knife" composite density functional electronic-structure method r2SCAN-3c (J. Chem. Phys. 2021, 154, 064103) is extended and optimized for the use with Slater-type orbital basis sets. The meta generalized-gradient approximation (meta-GGA) functional r2SCAN by Furness et al. is combined with a tailor-made polarized triple-ζ Slater-type atomic orbital (STO) basis set (mTZ2P), the semiclassical London dispersion correction (D4), and a geometrical counterpoise (gCP) correction. Relativistic effects are treated explicitly with the scalar-relativistic zeroth-order regular approximation (SR-ZORA). The performance of the new implementation is assessed on eight geometry and 74 energy benchmark sets, including the extensive GMTKN55 database as well as recent sets such as ROST61 and IONPI19. In geometry optimizations, the STO-based r2SCAN-3c is either on par with or more accurate than the hybrid density functional approximation M06-2X-D3(0)/TZP. In energy calculations, the overall accuracy is similar to the original implementation of r2SCAN-3c with Gaussian-type atomic orbitals (GTO), but basic properties, intermolecular noncovalent interactions, and barrier heights are better described with the STO approach, resulting in a lower weighted mean absolute deviation (WTMAD-2(STO) = 7.15 vs 7.50 kcal mol-1 with the original method) for the GMTKN55 database. The STO-optimized r2SCAN-3c outperforms many conventional hybrid/QZ approaches in most common applications at a fraction of their cost. The reliable, robust, and accurate r2SCAN-3c implementation with STOs is a promising alternative to the original implementation with GTOs and can be generally used for a broad field of quantum chemical problems.
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Affiliation(s)
- Thomas Gasevic
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Julius B Stückrath
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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4
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Bursch M, Neugebauer H, Ehlert S, Grimme S. Dispersion corrected r 2SCAN based global hybrid functionals: r 2SCANh, r 2SCAN0, and r 2SCAN50. J Chem Phys 2022; 156:134105. [PMID: 35395897 DOI: 10.1063/5.0086040] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The regularized and restored semilocal meta-generalized gradient approximation (meta-GGA) exchange-correlation functional r2SCAN [Furness et al., J. Phys. Chem. Lett. 11, 8208-8215 (2020)] is used to create three global hybrid functionals with varying admixtures of Hartree-Fock "exact" exchange (HFX). The resulting functionals r2SCANh (10% HFX), r2SCAN0 (25% HFX), and r2SCAN50 (50% HFX) are combined with the semi-classical D4 London dispersion correction. The new functionals are assessed for the calculation of molecular geometries, main-group, and metalorganic thermochemistry at 26 comprehensive benchmark sets. These include the extensive GMTKN55 database, ROST61, and IONPI19 sets. It is shown that a moderate admixture of HFX leads to relative improvements of the mean absolute deviations for thermochemistry of 11% (r2SCANh-D4), 16% (r2SCAN0-D4), and 1% (r2SCAN50-D4) compared to the parental semi-local meta-GGA. For organometallic reaction energies and barriers, r2SCAN0-D4 yields an even larger mean improvement of 35%. The computation of structural parameters (geometry optimization) does not systematically profit from the HFX admixture. Overall, the best variant r2SCAN0-D4 performs well for both main-group and organometallic thermochemistry and is better or on par with well-established global hybrid functionals, such as PW6B95-D4 or PBE0-D4. Regarding systems prone to self-interaction errors (SIE4x4), r2SCAN0-D4 shows reasonable performance, reaching the quality of the range-separated ωB97X-V functional. Accordingly, r2SCAN0-D4 in combination with a sufficiently converged basis set [def2-QZVP(P)] represents a robust and reliable choice for general use in the calculation of thermochemical properties of both main-group and organometallic chemistry.
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Affiliation(s)
- Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Hagen Neugebauer
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
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5
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Gueci L, Ferrante F, Prestianni A, Arena F, Duca D. Benzyl alcohol to benzaldehyde oxidation on MnOx clusters: Unraveling atomistic features. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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6
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Bao JL, Welch BK, Ulusoy IS, Zhang X, Xu X, Wilson AK, Truhlar DG. Predicting Bond Dissociation Energies and Bond Lengths of Coordinatively Unsaturated Vanadium-Ligand Bonds. J Phys Chem A 2020; 124:9757-9770. [PMID: 33180508 DOI: 10.1021/acs.jpca.0c06519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the electronic structure of coordinatively unsaturated transition-metal compounds and predicting their physical properties are of great importance for catalyst design. Bond dissociation energy De and bond length re are two of the fundamental quantities for which good predictions are important for a successful design strategy. In the present work, recent experimentally measured bond energies and bond lengths of VX diatomic molecules (X = C, N, S) are used as a gauge to consider the utility of a number of electronic structure methods. Single-reference methods are one focus because of their efficiency and utility in practical calculations, and multireference configuration interaction (MRCISD) methods and a composite coupled cluster (CCC) method are a second focus because of their potential high accuracy. The comparison is especially challenging because of the large multireference M diagnostics of these molecules, in the range 0.15-0.19. For the single-reference methods, Kohn-Sham density functional theory (KS-DFT) has been tested with a variety of approximate exchange-correlation functionals. Of these, MOHLYP provides the bond dissociation energies in best agreement with experiments, and BLYP provides the bond lengths that are in best agreement with experiments; but by requiring good performance for both the De and re of the vanadium compounds, MOHLYP, MN12-L, MGGA_MS1, MGGA_MS0, O3LYP, and M06-L are the most highly recommended functionals. The CCC calculations include up to connected pentuple excitations for the valence electrons and up to connected quadruple excitations for the core-valence terms; this results in highly accurate dissociation energies and good bond lengths. Averaged over the three molecules, the mean unsigned deviation of CCC bond energies from experimental ones is only 0.4 kcal/mol, demonstrating excellent convergence of theory and experiments.
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Affiliation(s)
- Junwei Lucas Bao
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Bradley K Welch
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Inga S Ulusoy
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824-1322, United States.,Theoretical Chemistry, Institute of Physical Chemistry, Heidelberg University, Im Neuenheimer Feld 229, Heidelberg 69120, Germany
| | - Xin Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China.,Department of Chemistry, Chemical Theory Center, Inorganometallic Catalyst Design Center, and Minnesota Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Xuefei Xu
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Angela K Wilson
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, Inorganometallic Catalyst Design Center, and Minnesota Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
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7
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DFT insights into the oxygen-assisted selective oxidation of benzyl alcohol on manganese dioxide catalysts. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119812] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Förster A, Visscher L. Double hybrid DFT calculations with Slater type orbitals. J Comput Chem 2020; 41:1660-1684. [PMID: 32297682 PMCID: PMC7317772 DOI: 10.1002/jcc.26209] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 12/14/2022]
Abstract
On a comprehensive database with 1,644 datapoints, covering several aspects of main-group as well as of transition metal chemistry, we assess the performance of 60 density functional approximations (DFA), among them 36 double hybrids (DH). All calculations are performed using a Slater type orbital (STO) basis set of triple-ζ (TZ) quality and the highly efficient pair atomic resolution of the identity approach for the exchange- and Coulomb-term of the KS matrix (PARI-K and PARI-J, respectively) and for the evaluation of the MP2 energy correction (PARI-MP2). Employing the quadratic scaling SOS-AO-PARI-MP2 algorithm, DHs based on the spin-opposite-scaled (SOS) MP2 approximation are benchmarked against a database of large molecules. We evaluate the accuracy of STO/PARI calculations for B3LYP as well as for the DH B2GP-PLYP and show that the combined basis set and PARI-error is comparable to the one obtained using the well-known def2-TZVPP Gaussian-type basis set in conjunction with global density fitting. While quadruple-ζ (QZ) calculations are currently not feasible for PARI-MP2 due to numerical issues, we show that, on the TZ level, Jacob's ladder for classifying DFAs is reproduced. However, while the best DHs are more accurate than the best hybrids, the improvements are less pronounced than the ones commonly found on the QZ level. For conformers of organic molecules and noncovalent interactions where very high accuracy is required for qualitatively correct results, DHs provide only small improvements over hybrids, while they still excel in thermochemistry, kinetics, transition metal chemistry and the description of strained organic systems.
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Affiliation(s)
- Arno Förster
- Theoretical ChemistryVrije UniversiteitAmsterdamThe Netherlands
| | - Lucas Visscher
- Theoretical ChemistryVrije UniversiteitAmsterdamThe Netherlands
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9
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Wang Y, Verma P, Zhang L, Li Y, Liu Z, Truhlar DG, He X. M06-SX screened-exchange density functional for chemistry and solid-state physics. Proc Natl Acad Sci U S A 2020; 117:2294-2301. [PMID: 31953258 PMCID: PMC7007546 DOI: 10.1073/pnas.1913699117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Screened-exchange hybrid density functionals are especially recommended for solid-state systems because they combine the advantages of hybrid functionals with the correct physics and lower computational cost associated with the attenuation of Hartree-Fock exchange at long range. We present a screened-exchange hybrid functional, M06-SX, that combines the functional form of the local revM06-L functional with a percentage of short-range nonlocal Hartree-Fock exchange. The M06-SX functional gives good results not only for a large set of training data but also for several databases quite different from the training data. The mean unsigned error (MUE) of the M06-SX functional is 2.85 kcal/mol for 418 atomic and molecular energies (AME418) in Minnesota Database 2019, which is better than all five other screened-exchange hybrid functionals tested in this work. The M06-SX functional also gives especially good results for semiconductor band gaps, molecular dissociation energies, noncovalent interactions, barrier heights, and electronic excitation energies excluding long-range charge transfer excitations. For the LC18 lattice constants database, the M06-SX functional gives an MUE of only 0.034 Å. Therefore, the M06-SX functional is well suited for studying molecular chemistry as well as solid-state physics.
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Affiliation(s)
- Ying Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410006, China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Pragya Verma
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455-0431
- Chemical Theory Center, University of Minnesota, Minneapolis, MN 55455-0431
- Nanoporous Materials Genome Center, University of Minnesota, Minneapolis, MN 55455-0431
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431
| | - Lujia Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200062, China
| | - Yaqi Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410006, China
| | - Zhonghua Liu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410006, China
| | - Donald G Truhlar
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455-0431;
- Chemical Theory Center, University of Minnesota, Minneapolis, MN 55455-0431
- Nanoporous Materials Genome Center, University of Minnesota, Minneapolis, MN 55455-0431
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431
| | - 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;
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200062, China
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10
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Zhang L, Wang Y, Yang Y, Zhang P, Wang C. Rhenium-catalyzed alkylarylation of alkenes with PhI(O2CR)2via decarboxylation to access indolinones and dihydroquinolinones. Org Chem Front 2020. [DOI: 10.1039/d0qo00953a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rhenium-catalyzed alkylarylation of alkenes with hypervalent iodine(iii) reagents (HIRs) via decarboxylation to access various 3,3-disubstituted indolinones and trans-3,4-dihydroquinolinones is described.
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Affiliation(s)
- Lei Zhang
- National Demonstration Center for Experimental Chemistry Education
- Hebei Key Laboratory of Organic Functional Molecules
- College of Chemistry and Material Science
- Hebei Normal University
- Shijiazhuang 050024
| | - Yin Wang
- Beijing National Laboratory for Molecular Sciences
- CAS Key Laboratory of Molecular Recognition and Function
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Yunhui Yang
- Beijing National Laboratory for Molecular Sciences
- CAS Key Laboratory of Molecular Recognition and Function
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Ping Zhang
- National Demonstration Center for Experimental Chemistry Education
- Hebei Key Laboratory of Organic Functional Molecules
- College of Chemistry and Material Science
- Hebei Normal University
- Shijiazhuang 050024
| | - Congyang Wang
- Beijing National Laboratory for Molecular Sciences
- CAS Key Laboratory of Molecular Recognition and Function
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
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11
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Verma P, Janesko BG, Wang Y, He X, Scalmani G, Frisch MJ, Truhlar DG. M11plus: A Range-Separated Hybrid Meta Functional with Both Local and Rung-3.5 Correlation Terms and High Across-the-Board Accuracy for Chemical Applications. J Chem Theory Comput 2019; 15:4804-4815. [DOI: 10.1021/acs.jctc.9b00411] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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
| | - Benjamin G. Janesko
- Department of Chemistry and Biochemistry, Texas Christian University, Fort Worth, Texas 76110, 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
| | - 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 at NYU 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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12
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Jia B, Yang Y, Jin X, Mao G, Wang C. Rhenium-Catalyzed Phthalide Synthesis from Benzamides and Aldehydes via C–H Bond Activation. Org Lett 2019; 21:6259-6263. [DOI: 10.1021/acs.orglett.9b02142] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bing Jia
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- Provincial Key Laboratory of Oil & Gas Chemical Technology, College of Chemistry and Chemical Engineering, Northeast Petroleum University, Daqing 163318, China
| | - Yunhui Yang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101400, China
| | - Xiqing Jin
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Guoliang Mao
- Provincial Key Laboratory of Oil & Gas Chemical Technology, College of Chemistry and Chemical Engineering, Northeast Petroleum University, Daqing 163318, China
| | - Congyang Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101400, China
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13
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Chan B, Gill PMW, Kimura M. Assessment of DFT Methods for Transition Metals with the TMC151 Compilation of Data Sets and Comparison with Accuracies for Main-Group Chemistry. J Chem Theory Comput 2019; 15:3610-3622. [PMID: 31150234 DOI: 10.1021/acs.jctc.9b00239] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In the present study, we have gathered a collection (that we term TMC151) of accurate reference data for transition-metal reactions for the assessment of quantum chemistry methods. It comprises diatomic dissociation energies and reaction energies and barriers for prototypical transition-metal reactions. Our assessment of a diverse range of different types of DFT methods shows that the most accurate functionals include ωB97M-V, ωB97X-V, MN15, and B97M-rV. Notably, they have also been previously validated to be highly robust for main-group chemistry. Nevertheless, even these methods show substantially worse accuracies for transition metals than for main-group chemistry. For less accurate methods, there is not a good correlation between their accuracies for main-group and transition-metal chemistries. Thus, in the development of new DFT, it is important to assess the accuracies for both types of data. In this regard, we have formulated the TMC34 model for efficient assessment of the performance for transition metals, which complements our previously developed MG8 model for main-group chemistry. Together, they provide a cost-effective means for initial assessment of new methodologies.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering , Nagasaki University , Bunkyo 1-14 , Nagasaki 852-8521 , Japan
| | - Peter M W Gill
- Research School of Chemistry , Australian National University , Canberra , Australian Capital Territory 2601 , Australia
| | - Masanari Kimura
- Graduate School of Engineering , Nagasaki University , Bunkyo 1-14 , Nagasaki 852-8521 , Japan
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14
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Re‐Catalyzed Annulations of Weakly Coordinating
N
‐Carbamoyl Indoles/Indolines with Alkynes via C−H/C−N Bond Cleavage. Chemistry 2019; 25:8245-8248. [DOI: 10.1002/chem.201901518] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Indexed: 11/07/2022]
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15
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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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16
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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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17
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Ibeji CU, Tolufashe GF, Ntombela T, Govender T, Maguire GEM, Lamichhane G, Kruger HG, Honarparvar B. The catalytic role of water in the binding site of l,d-transpeptidase 2 within acylation mechanism: A QM/MM (ONIOM) modelling. Tuberculosis (Edinb) 2018; 113:222-230. [PMID: 30514506 DOI: 10.1016/j.tube.2018.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/11/2018] [Accepted: 10/14/2018] [Indexed: 01/13/2023]
Abstract
Mycobacterium tuberculosis is the causative agent of Tuberculosis. Formation of 3 → 3 crosslinks in the peptidoglycan layer of M. tuberculosis is catalyzed by l,d-transpeptidases. These enzymes can confer resistance against classical β-lactams that inhibit enzymes that generate 4 → 3 peptidoglycan crosslinks. The focus of this study is to investigate the catalytic role of water molecules in the acylation mechanism of the β-lactam ring within two models; 4- and 6-membered ring systems using two-layered our Own N-layer integrated Molecular Mechanics ONIOM (B3LYP/6-311++G(2d,2p): AMBER) model. The obtained thermochemical parameters revealed that the 6-membered ring model best describes the inhibition mechanism of acylation which indicates the role of water in the preference of 6-membered ring reaction pathway. This finding is in accordance with experimental data for the rate-limiting step of cysteine protease with the same class of inhibitor and binding affinity for both inhibitors. As expected, the ΔG# results also reveal that the 6-membered ring reaction pathway is the most favourable. The electrostatic potential (ESP) and the natural bond orbital analysis (NBO) showed stronger interactions in 6-membered ring transition state (TS-6) mechanism involving water in the active site of the enzyme. This study could be helpful in the development of novel antibiotics against l,d-transpeptidase.
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Affiliation(s)
- Collins U Ibeji
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa; Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
| | - Gideon F Tolufashe
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa; School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Gyanu Lamichhane
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.
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18
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Revised M06 density functional for main-group and transition-metal chemistry. Proc Natl Acad Sci U S A 2018; 115:10257-10262. [PMID: 30237285 DOI: 10.1073/pnas.1810421115] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We present a hybrid metageneralized-gradient-approximation functional, revM06, which is based on adding Hartree-Fock exchange to the revM06-L functional form. Compared with the original M06 suite of density functionals, the resulting revM06 functional has significantly improved across-the-board accuracy for both main-group and transition-metal chemistry. The revM06 functional improves on the M06-2X functional for main-group and transition-metal bond energies, atomic excitation energies, isomerization energies of large molecules, molecular structures, and both weakly and strongly correlated atomic and molecular data, and it shows a clear improvement over M06 and M06-2X for noncovalent interactions, including smoother potential curves for rare-gas dimers. The revM06 functional also predicts more accurate results than M06 and M06-2X for most of the outside-the-training-set test sets examined in this study. Therefore, the revM06 functional is well-suited for a broad range of chemical applications for both main-group and transition-metal elements.
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19
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Hu L, Chen H. Comparative computational study on C-C/C-N/C-Br bond formations in Rh(III)-catalyzed C-H functionalizations: Stepwise versus concerted mechanisms. J Organomet Chem 2018. [DOI: 10.1016/j.jorganchem.2018.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Engkvist O, Norrby PO, Selmi N, Lam YH, Peng Z, Sherer EC, Amberg W, Erhard T, Smyth LA. Computational prediction of chemical reactions: current status and outlook. Drug Discov Today 2018; 23:1203-1218. [PMID: 29510217 DOI: 10.1016/j.drudis.2018.02.014] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/31/2018] [Accepted: 02/26/2018] [Indexed: 01/05/2023]
Abstract
Over the past few decades, various computational methods have become increasingly important for discovering and developing novel drugs. Computational prediction of chemical reactions is a key part of an efficient drug discovery process. In this review, we discuss important parts of this field, with a focus on utilizing reaction data to build predictive models, the existing programs for synthesis prediction, and usage of quantum mechanics and molecular mechanics (QM/MM) to explore chemical reactions. We also outline potential future developments with an emphasis on pre-competitive collaboration opportunities.
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Affiliation(s)
- Ola Engkvist
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, SE-43183 Mölndal, Sweden.
| | - Per-Ola Norrby
- Pharmaceutical Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, SE-43183 Mölndal, Sweden
| | - Nidhal Selmi
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, SE-43183 Mölndal, Sweden
| | - Yu-Hong Lam
- Modeling and Informatics, MRL, Merck & Co., Rahway, NJ 07065, USA
| | - Zhengwei Peng
- Modeling and Informatics, MRL, Merck & Co., Rahway, NJ 07065, USA
| | - Edward C Sherer
- Modeling and Informatics, MRL, Merck & Co., Rahway, NJ 07065, USA
| | - Willi Amberg
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Medicinal Chemistry, Knollstrasse, 67061 Ludwigshafen, Germany
| | - Thomas Erhard
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Medicinal Chemistry, Knollstrasse, 67061 Ludwigshafen, Germany
| | - Lynette A Smyth
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Medicinal Chemistry, Knollstrasse, 67061 Ludwigshafen, Germany
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21
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Jacobson LD, Bochevarov AD, Watson MA, Hughes TF, Rinaldo D, Ehrlich S, Steinbrecher TB, Vaitheeswaran S, Philipp DM, Halls MD, Friesner RA. Automated Transition State Search and Its Application to Diverse Types of Organic Reactions. J Chem Theory Comput 2017; 13:5780-5797. [PMID: 28957627 DOI: 10.1021/acs.jctc.7b00764] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Transition state search is at the center of multiple types of computational chemical predictions related to mechanistic investigations, reactivity and regioselectivity predictions, and catalyst design. The process of finding transition states in practice is, however, a laborious multistep operation that requires significant user involvement. Here, we report a highly automated workflow designed to locate transition states for a given elementary reaction with minimal setup overhead. The only essential inputs required from the user are the structures of the separated reactants and products. The seamless workflow combining computational technologies from the fields of cheminformatics, molecular mechanics, and quantum chemistry automatically finds the most probable correspondence between the atoms in the reactants and the products, generates a transition state guess, launches a transition state search through a combined approach involving the relaxing string method and the quadratic synchronous transit, and finally validates the transition state via the analysis of the reactive chemical bonds and imaginary vibrational frequencies as well as by the intrinsic reaction coordinate method. Our approach does not target any specific reaction type, nor does it depend on training data; instead, it is meant to be of general applicability for a wide variety of reaction types. The workflow is highly flexible, permitting modifications such as a choice of accuracy, level of theory, basis set, or solvation treatment. Successfully located transition states can be used for setting up transition state guesses in related reactions, saving computational time and increasing the probability of success. The utility and performance of the method are demonstrated in applications to transition state searches in reactions typical for organic chemistry, medicinal chemistry, and homogeneous catalysis research. In particular, applications of our code to Michael additions, hydrogen abstractions, Diels-Alder cycloadditions, carbene insertions, and an enzyme reaction model involving a molybdenum complex are shown and discussed.
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Affiliation(s)
- Leif D Jacobson
- Schrödinger, Inc. , 120 West 45th St., New York, New York 10036, United States
| | - Art D Bochevarov
- Schrödinger, Inc. , 120 West 45th St., New York, New York 10036, United States
| | - Mark A Watson
- Schrödinger, Inc. , 120 West 45th St., New York, New York 10036, United States
| | - Thomas F Hughes
- Schrödinger, Inc. , 120 West 45th St., New York, New York 10036, United States
| | - David Rinaldo
- Schrödinger GmbH , Dynamostrasse 13, D-68165 Mannheim, Germany
| | - Stephan Ehrlich
- Schrödinger GmbH , Dynamostrasse 13, D-68165 Mannheim, Germany
| | | | - S Vaitheeswaran
- Schrödinger, Inc. , 222 Third St., Suite 2230, Cambridge, Massachusetts 02142, United States
| | - Dean M Philipp
- Schrödinger, Inc. , 101 SW Main St., Suite 1300, Portland, Oregon 97204, United States
| | - Mathew D Halls
- Schrödinger, Inc. , 5820 Oberlin Dr., Suite 203, San Diego, California 92121, United States
| | - Richard A Friesner
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
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22
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Revised M06-L functional for improved accuracy on chemical reaction barrier heights, noncovalent interactions, and solid-state physics. Proc Natl Acad Sci U S A 2017; 114:8487-8492. [PMID: 28739954 DOI: 10.1073/pnas.1705670114] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present the revM06-L functional, which we designed by optimizing against a larger database than had been used for Minnesota 2006 local functional (M06-L) and by using smoothness restraints. The optimization strategy reduced the number of parameters from 34 to 31 because we removed some large terms that increased the required size of the quadrature grid and the number of self-consistent-field iterations. The mean unsigned error (MUE) of revM06-L on 422 chemical energies is 3.07 kcal/mol, which is improved from 3.57 kcal/mol calculated by M06-L. The MUE of revM06-L for the chemical reaction barrier height database (BH76) is 1.98 kcal/mol, which is improved by more than a factor of 2 with respect to the M06-L functional. The revM06-L functional gives the best result among local functionals tested for the noncovalent interaction database (NC51), with an MUE of only 0.36 kcal/mol, and the MUE of revM06-L for the solid-state lattice constant database (LC17) is half that for M06-L. The revM06-L functional also yields smoother potential curves, and it predicts more-accurate results than M06-L for seven out of eight diversified test sets not used for parameterization. We conclude that the revM06-L functional is well suited for a broad range of applications in chemistry and condensed-matter physics.
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23
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Affiliation(s)
- Guoliang Mao
- Provincial Key Laboratory of Oil and Gas Chemical Technology; College of Chemistry and Chemical Engineering; Northeast Petroleum University; 163318 Daqing China
| | - Qiang Huang
- Provincial Key Laboratory of Oil and Gas Chemical Technology; College of Chemistry and Chemical Engineering; Northeast Petroleum University; 163318 Daqing China
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Molecular Recognition and Function; CAS Research/Education Center for Excellence in Molecular Sciences; Institute of Chemistry, Chinese Academy of Sciences; 100190 Beijing China
| | - Congyang Wang
- Beijing National Laboratory for Molecular Sciences; CAS Key Laboratory of Molecular Recognition and Function; CAS Research/Education Center for Excellence in Molecular Sciences; Institute of Chemistry, Chinese Academy of Sciences; 100190 Beijing China
- University of Chinese Academy of Sciences; 100049 Beijing China
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24
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Minenkov Y, Sliznev VV, Cavallo L. Accurate Gas Phase Formation Enthalpies of Alloys and Refractories Decomposition Products. Inorg Chem 2017; 56:1386-1401. [DOI: 10.1021/acs.inorgchem.6b02441] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yury Minenkov
- Physical Sciences
and Engineering Division, King Abdullah University of Science and Technology, KAUST Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Valery V. Sliznev
- Ivanovo State University of Chemistry and Technology, Research Institute for Thermodynamics
and Kinetics of Chemical Processes, 153460 Ivanovo, Russian Federation
| | - Luigi Cavallo
- Physical Sciences
and Engineering Division, King Abdullah University of Science and Technology, KAUST Catalysis Center, Thuwal 23955-6900, Saudi Arabia
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25
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Bao JL, Zhang X, Xu X, Truhlar DG. Predicting bond dissociation energy and bond length for bimetallic diatomic molecules: a challenge for electronic structure theory. Phys Chem Chem Phys 2017; 19:5839-5854. [DOI: 10.1039/c6cp08896a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We test the accuracy of Kohn–Sham density functional theory for strongly correlated metal–metal bonds that occur in catalytically active sites and intermediates and examine the orbitals and configurations involved to analyze the results.
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Affiliation(s)
- Junwei Lucas Bao
- Department of Chemistry
- Chemical Theory Center, and Supercomputing Institute
- University of Minnesota
- Minneapolis
- USA
| | - Xin Zhang
- State Key Laboratory of Chemical Resource Engineering
- Institute of Materia Medica
- College of Science
- Beijing University of Chemical Technology
- Beijing
| | - Xuefei Xu
- Center for Combustion Energy
- Tsinghua University
- Beijing 100084
- China
| | - Donald G. Truhlar
- Department of Chemistry
- Chemical Theory Center, and Supercomputing Institute
- University of Minnesota
- Minneapolis
- USA
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26
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Hu L, Chen H. What Factors Control the Reactivity of Cobalt–Imido Complexes in C–H Bond Activation via Hydrogen Abstraction? ACS Catal 2016. [DOI: 10.1021/acscatal.6b02694] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lianrui Hu
- Beijing
National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Hui Chen
- Beijing
National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
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27
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Attia AAA, Silaghi-Dumitrescu R. A mononuclear non-heme-iron dioxygen-carrying protein? J Mol Graph Model 2016; 69:103-10. [PMID: 27607306 DOI: 10.1016/j.jmgm.2016.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 10/21/2022]
Abstract
The ability of mononuclear non-heme iron complexes to function as molecular oxygen transporters is investigated by density functional theory. The factors governing the efficiency of the reversible binding of dioxygen at the active site of the dinuclear non-heme iron enzyme hemerythrin, including antiferromagnetic coupling and the conversion of dioxygen to hydroperoxo by a proton coupled 2-electron transfer mechanism, are revisited and considered as possible tools in mononuclear non-heme complexes. Several mononuclear non-heme model complexes, including active sites of enzymes already known to interact with dioxgenic ligands, are constructed and the molecular oxygen transportation capabilities of these complexes are examined computationally. The high-spin nature of the ground state of these complexes implies an intrinsic kinetic lability of the oxy structures, as also evident from potential energy surface calculations towards iron-dioxygen cleavage. Proton affinities as calibrated with reference compounds showed that these complexes are highly unlikely to undergo protonation to form hydroperoxo-like adducts. Mixed superoxo descriptions of the dissociated dioxygenic ligands in all complexes add to the overall conclusion that these model structures are significantly disadvantaged in any attempt to be employed for molecular oxygen transportation.
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Affiliation(s)
- Amr A A Attia
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania.
| | - Radu Silaghi-Dumitrescu
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania.
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28
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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: 694] [Impact Index Per Article: 86.8] [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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29
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Sun Y, Chen H. DFT Methods to Study the Reaction Mechanism of Iridium-Catalyzed Hydrogenation of Olefins: Which Functional Should be Chosen? Chemphyschem 2015; 17:119-27. [DOI: 10.1002/cphc.201500817] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Yihua Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS); CAS Key Laboratory of Photochemistry; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
| | - Hui Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS); CAS Key Laboratory of Photochemistry; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
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30
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Hu L, Chen H. Assessment of DFT Methods for Computing Activation Energies of Mo/W-Mediated Reactions. J Chem Theory Comput 2015; 11:4601-14. [DOI: 10.1021/acs.jctc.5b00373] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lianrui Hu
- Beijing National Laboratory
for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hui Chen
- Beijing National Laboratory
for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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31
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Goldsmith BR, Hwang T, Seritan S, Peters B, Scott SL. Rate-Enhancing Roles of Water Molecules in Methyltrioxorhenium-Catalyzed Olefin Epoxidation by Hydrogen Peroxide. J Am Chem Soc 2015; 137:9604-16. [DOI: 10.1021/jacs.5b03750] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bryan R. Goldsmith
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Taeho Hwang
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Stefan Seritan
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Baron Peters
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Susannah L. Scott
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
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32
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Tang H, Huang XR, Yao J, Chen H. Understanding the Effects of Bidentate Directing Groups: A Unified Rationale for sp2 and sp3 C–H Bond Activations. J Org Chem 2015; 80:4672-82. [DOI: 10.1021/acs.joc.5b00580] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hao Tang
- Beijing
National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- Institute
of Theoretical Chemistry, State Key Laboratory of Theoretical and
Computational Chemistry, Jilin University, Changchun, 130023, China
| | - Xu-Ri Huang
- Institute
of Theoretical Chemistry, State Key Laboratory of Theoretical and
Computational Chemistry, Jilin University, Changchun, 130023, China
| | - Jiannian Yao
- Beijing
National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Hui Chen
- Beijing
National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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Sun Y, Hu L, Chen H. Comparative Assessment of DFT Performances in Ru- and Rh-Promoted σ-Bond Activations. J Chem Theory Comput 2015; 11:1428-38. [PMID: 26574354 DOI: 10.1021/ct5009119] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, the performances of 19 density functional theory (DFT) methods are calibrated comparatively on Ru- and Rh-promoted σ-bond (C-H, O-H, and H-H) activations. DFT calibration reference is generated from explicitly correlated coupled cluster CCSD(T)-F12 calculations, and the 4s4p core-valence correlation effect of the two 4d platinum group transition metals is also included. Generally, the errors of DFT methods for calculating energetics of Ru-/Rh-mediated reactions appear to correlate more with the magnitude of energetics itself than other factors such as metal identity. For activation energy calculations, the best performing functionals for both Ru and Rh systems are MN12SX < CAM-B3LYP < M06-L < MN12L < M06 < ωB97X < B3LYP < LC-ωPBE (in the order of increasing mean unsigned deviations, MUDs, of less than 2 kcal/mol). For reaction energy calculations, best functionals with MUDs less than 2 kcal/mol are PBE0 < CAM-B3LYP ≈ N12SX. The effect of the DFT empirical dispersion correction on the performance of the DFT methods is beneficial for most density functionals tested in this work, reducing their MUDs to different extents. After including empirical dispersion correction, ωB97XD, B3LYP-D3, and CAM-B3LYP-D3 (PBE0-D3, B3LYP-D3, and ωB97XD) are the three best performing DFs for activation energy (reaction energy) calculations, from which B3LYP-D3 and ωB97XD can notably be recommended uniformly for both the reaction energy and reaction barrier calculations. The good performance of B3LYP-D3 in quantitative description of the energetic trends further adds value to B3LYP-D3 and singles this functional out as a reasonable choice in the Ru/Rh-promoted σ-bond activation processes.
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Affiliation(s)
- Yuanyuan Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Lianrui Hu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Hui Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
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Sokołowski K, Bury W, Tulewicz A, Cieślak AM, Justyniak I, Kubicki D, Krajewska E, Milet A, Moszyński R, Lewiński J. Experimental and Computational Insights into Carbon Dioxide Fixation by RZnOH Species. Chemistry 2015; 21:5496-503. [DOI: 10.1002/chem.201406271] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Indexed: 11/05/2022]
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O'Hair RAJ, Canale V, Zavras A, Khairallah GN, d'Alessandro N. Gas-phase reactions of the rhenium oxide anions, [ReOx]- (x = 2 - 4) with the neutral organic substrates methane, ethene, methanol and acetic acid. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:557-568. [PMID: 26307735 DOI: 10.1255/ejms.1332] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The ion-molecule reactions of the rhenium oxide anions, [ReOx](-) (x = 2 - 4) with the organic substrates methane, ethene, methanol and acetic acid have been examined in a linear ion trap mass spectrometer. The only reactivity observed was between [ReO(2)](-) and acetic acid. Isotope labelled experiments and high-resolution mass spectrometry measurements were used to assign the formulas of the ionic products. Collision-induced dissociation and ion-molecule reactions with acetic acid were used to probe the structures of the mass-selected primary product ions. Density functional theory calculations [PBE0/LanL2DZ6-311+G(d)] were used to suggest possible structures. The three primary product channels observed are likely to arise from the formation of: the metallalactone [ReO(2)(CH(2)CO(2))](-) (m/z 277) and H(2); [CH(3)ReO(2)(OH)](-) (m/z 251) and CO; and [ReO(3)](-) (m/z 235), H(2) and CH(2)CO.
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Affiliation(s)
- Richard A J O'Hair
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3010, Australia. ARC Centre of Excellence for Free Radical Chemistry and Biotechnology.
| | - Valentino Canale
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3010, Australia. ARC Centre of Excellence for Free Radical Chemistry and Biotechnology. Department of Engineering and Geology (INGEO), "G. d'Annunzio" University of Chieti and Pescara, Viale Pindaro, 42, I- 65127 Pescara, Italy.
| | - Athanasios Zavras
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3010, Australia. ARC Centre of Excellence for Free Radical Chemistry and Biotechnology.
| | - George N Khairallah
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3010, Australia. ARC Centre of Excellence for Free Radical Chemistry and Biotechnology.
| | - Nicola d'Alessandro
- Department of Engineering and Geology (INGEO), "G. d'Annunzio" University of Chieti and Pescara, Viale Pindaro, 42, I- 65127 Pescara, Italy.
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Luo G, Luo Y, Maeda S, Qu J, Hou Z, Ohno K. Theoretical Mechanistic Studies on Methyltrioxorhenium-Catalyzed Olefin Cyclopropanation: Stepwise Transfer of a Terminal Methylene Group. Organometallics 2014. [DOI: 10.1021/om500560f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gen Luo
- State Key Laboratory of Fine Chemicals,
School
of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian 116024, People’s Republic of China
| | - Yi Luo
- State Key Laboratory of Fine Chemicals,
School
of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian 116024, People’s Republic of China
| | - Satoshi Maeda
- Department of Chemistry,
Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Jingping Qu
- State Key Laboratory of Fine Chemicals,
School
of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian 116024, People’s Republic of China
| | - Zhaomin Hou
- State Key Laboratory of Fine Chemicals,
School
of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian 116024, People’s Republic of China
- Organometallic Chemistry
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Koichi Ohno
- Department of Chemistry, Graduate School of
Science, Tohoku University, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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Ciancaleoni G, Rampino S, Zuccaccia D, Tarantelli F, Belanzoni P, Belpassi L. An ab Initio Benchmark and DFT Validation Study on Gold(I)-Catalyzed Hydroamination of Alkynes. J Chem Theory Comput 2014; 10:1021-34. [PMID: 26580180 DOI: 10.1021/ct400980w] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
High level ab initio calculations have been carried out on an archetypal gold(I)-catalyzed reaction: hydroamination of ethyne. We studied up to 12 structures of possible gold(I)-coordinated species modeling different intermediates potentially present in a catalytic cycle for the addition of a protic nucleophile to an alkyne. The benchmark is used to evaluate the performances of some popular density functionals for describing geometries and relative energies of stationary points along the reaction profile. Most functionals (including hybrid or meta-hybrid) give accurate structures but large nonsystematic errors (4-12 kcal/mol) along the reaction energy profile. The double hybrid functional B2PLYP outperforms all considered functionals and compares very nicely with our reference ab initio benchmark energies. Moreover, we present an assessment of the accuracy of commonly used approaches to include relativistic effects, such as relativistic effective potentials and a scalar ZORA Hamiltonian, by a comparison with the results obtained using a relativistic all-electron four-component Dirac-Kohn-Sham method. The contribution of nonscalar relativistic effects in gold(I)-catalyzed reactions, as we investigated here, is expected to be on the order of 1 kcal/mol.
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Affiliation(s)
- Gianluca Ciancaleoni
- Istituto di Scienze e Tecnologie Molecolari del CNR c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia , 06123, Italy
| | - Sergio Rampino
- Istituto di Scienze e Tecnologie Molecolari del CNR c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia , 06123, Italy
| | - Daniele Zuccaccia
- Dipartimento di Chimica, Fisica e Ambiente, Università di Udine , Via Cotonificio 108, I-33100 Udine, Italy
| | - Francesco Tarantelli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia , 06123, Italy
| | - Paola Belanzoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia , 06123, Italy
| | - Leonardo Belpassi
- Istituto di Scienze e Tecnologie Molecolari del CNR c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia , 06123, Italy
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