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Hu F, Wang Y, Zeng J, Deng X, Xia F, Xu X. Unveiling the State Transition Mechanisms of Ras Proteins through Enhanced Sampling and QM/MM Simulations. J Phys Chem B 2024; 128:1418-1427. [PMID: 38323538 DOI: 10.1021/acs.jpcb.3c07666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
In cells, wild-type RasGTP complexes exist in two distinct states: active State 2 and inactive State 1. These complexes regulate their functions by transitioning between the two states. However, the mechanisms underlying this state transition have not been clearly elucidated. To address this, we conducted a detailed simulation study to characterize the energetics of the stable states involved in the state transitions of the HRasGTP complex, specifically from State 2 to State 1. This was achieved by employing multiscale quantum mechanics/molecular mechanics and enhanced sampling molecular dynamics methods. Based on the simulation results, we constructed the two-dimensional free energy landscapes that provide crucial information about the conformational changes of the HRasGTP complex from State 2 to State 1. Furthermore, we also explored the conformational changes from the intermediate state to the product state during guanosine triphosphate hydrolysis. This study on the conformational changes involved in the HRas state transitions serves as a valuable reference for understanding the corresponding events of both KRas and NRas as well.
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Affiliation(s)
- Fangchen Hu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Yiqiu Wang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Juan Zeng
- School of Biomedical Engineering, Guangdong Medical University, Dongguan 523808, China
| | - Xianming Deng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Fei Xia
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai 200433, China
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Hersh WH, Chan TY. Improving the accuracy of 31P NMR chemical shift calculations by use of scaling methods. Beilstein J Org Chem 2023; 19:36-56. [PMID: 36726479 PMCID: PMC9843238 DOI: 10.3762/bjoc.19.4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/14/2022] [Indexed: 01/12/2023] Open
Abstract
Calculation of 31P NMR chemical shifts for a series of tri- and tetracoordinate phosphorus compounds using several basis sets and density functional theory (DFT) functionals gave a modest fit to experimental chemical shifts, but an excellent linear fit when plotted against the experimental values. The resultant scaling methods were then applied to a variety of "large" compounds previously selected by Latypov et al. and a set of stereoisomeric and unusual compounds selected here. No one method was best for all structural types. For compounds that contain P-P bonds and P-C multiple bonds, the Latypov et al. method using the PBE0 functional was best (mean absolute deviation/root mean square deviation (MAD/RMSD) = 6.9/8.5 ppm and 6.6/8.2 ppm, respectively), but for the full set of compounds gave higher deviations (MAD/RMSD = 8.2/12.3 ppm), and failed by over 60 ppm for a three-membered phosphorus heterocycle. Use of the M06-2X functional for both the structural optimization and NMR chemical shift calculation was best overall for the compounds without P-C multiple bonds (MAD/RMSD = 5.4/7.1 ppm), but failed by 30-49 ppm for compounds having any P-C multiple-bond character. Failures of these magnitudes have not been reported previously for these widely used functionals. These failures were then used to screen a variety of recommended functionals, leading to better overall methods for calculation of these chemical shifts: optimization with the M06-2X functional and NMR calculation with the PBE0 or ωB97x-D functionals gave values for MAD/RMSD = 6.9/8.5 ppm and 6.8/9.1 ppm, respectively, over an experimental chemical shift range of -181 to 356 ppm. Due to the unexplained failures observed, we recommend use of more than one method when looking at novel structures.
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Affiliation(s)
- William H Hersh
- Department of Chemistry and Biochemistry, Queens College, Queens, NY 11367-1597, USA,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Tsz-Yeung Chan
- Department of Chemistry and Biochemistry, Queens College, Queens, NY 11367-1597, USA,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
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3
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Accuracy of electronic density calculated using an optimally tuned range-separated hybrid functional. Theor Chem Acc 2023. [DOI: 10.1007/s00214-022-02952-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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4
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Teale AM, Helgaker T, Savin A, Adamo C, Aradi B, Arbuznikov AV, Ayers PW, Baerends EJ, Barone V, Calaminici P, Cancès E, Carter EA, Chattaraj PK, Chermette H, Ciofini I, Crawford TD, De Proft F, Dobson JF, Draxl C, Frauenheim T, Fromager E, Fuentealba P, Gagliardi L, Galli G, Gao J, Geerlings P, Gidopoulos N, Gill PMW, Gori-Giorgi P, Görling A, Gould T, Grimme S, Gritsenko O, Jensen HJA, Johnson ER, Jones RO, Kaupp M, Köster AM, Kronik L, Krylov AI, Kvaal S, Laestadius A, Levy M, Lewin M, Liu S, Loos PF, Maitra NT, Neese F, Perdew JP, Pernal K, Pernot P, Piecuch P, Rebolini E, Reining L, Romaniello P, Ruzsinszky A, Salahub DR, Scheffler M, Schwerdtfeger P, Staroverov VN, Sun J, Tellgren E, Tozer DJ, Trickey SB, Ullrich CA, Vela A, Vignale G, Wesolowski TA, Xu X, Yang W. DFT exchange: sharing perspectives on the workhorse of quantum chemistry and materials science. Phys Chem Chem Phys 2022; 24:28700-28781. [PMID: 36269074 PMCID: PMC9728646 DOI: 10.1039/d2cp02827a] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/09/2022] [Indexed: 12/13/2022]
Abstract
In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format of the paper is that of a roundtable discussion, in which the participants express and exchange views on DFT in the form of 302 individual contributions, formulated as responses to a preset list of 26 questions. Supported by a bibliography of 777 entries, the paper represents a broad snapshot of DFT, anno 2022.
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Affiliation(s)
- Andrew M. Teale
- School of Chemistry, University of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Trygve Helgaker
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - Andreas Savin
- Laboratoire de Chimie Théorique, CNRS and Sorbonne University, 4 Place Jussieu, CEDEX 05, 75252 Paris, France.
| | - Carlo Adamo
- PSL University, CNRS, ChimieParisTech-PSL, Institute of Chemistry for Health and Life Sciences, i-CLeHS, 11 rue P. et M. Curie, 75005 Paris, France.
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, University of Bremen, P.O. Box 330440, D-28334 Bremen, Germany.
| | - Alexei V. Arbuznikov
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7Straße des 17. Juni 13510623Berlin
| | | | - Evert Jan Baerends
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands.
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy.
| | - Patrizia Calaminici
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), CDMX, 07360, Mexico.
| | - Eric Cancès
- CERMICS, Ecole des Ponts and Inria Paris, 6 Avenue Blaise Pascal, 77455 Marne-la-Vallée, France.
| | - Emily A. Carter
- Department of Mechanical and Aerospace Engineering and the Andlinger Center for Energy and the Environment, Princeton UniversityPrincetonNJ 08544-5263USA
| | | | - Henry Chermette
- Institut Sciences Analytiques, Université Claude Bernard Lyon1, CNRS UMR 5280, 69622 Villeurbanne, France.
| | - Ilaria Ciofini
- PSL University, CNRS, ChimieParisTech-PSL, Institute of Chemistry for Health and Life Sciences, i-CLeHS, 11 rue P. et M. Curie, 75005 Paris, France.
| | - T. Daniel Crawford
- Department of Chemistry, Virginia TechBlacksburgVA 24061USA,Molecular Sciences Software InstituteBlacksburgVA 24060USA
| | - Frank De Proft
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium.
| | | | - Claudia Draxl
- Institut für Physik and IRIS Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany. .,Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - Thomas Frauenheim
- Bremen Center for Computational Materials Science, University of Bremen, P.O. Box 330440, D-28334 Bremen, Germany. .,Beijing Computational Science Research Center (CSRC), 100193 Beijing, China.,Shenzhen JL Computational Science and Applied Research Institute, 518110 Shenzhen, China
| | - Emmanuel Fromager
- Laboratoire de Chimie Quantique, Institut de Chimie, CNRS/Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France.
| | - Patricio Fuentealba
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile.
| | - Laura Gagliardi
- Department of Chemistry, Pritzker School of Molecular Engineering, The James Franck Institute, and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.
| | - Giulia Galli
- Pritzker School of Molecular Engineering and Department of Chemistry, The University of Chicago, Chicago, IL, USA.
| | - Jiali Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China. .,Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paul Geerlings
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Nikitas Gidopoulos
- Department of Physics, Durham University, South Road, Durham DH1 3LE, UK.
| | - Peter M. W. Gill
- School of Chemistry, University of SydneyCamperdown NSW 2006Australia
| | - Paola Gori-Giorgi
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands.
| | - Andreas Görling
- Chair of Theoretical Chemistry, University of Erlangen-Nuremberg, Egerlandstrasse 3, 91058 Erlangen, Germany.
| | - Tim Gould
- Qld Micro- and Nanotechnology Centre, Griffith University, Gold Coast, Qld 4222, Australia.
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany.
| | - Oleg Gritsenko
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands.
| | - Hans Jørgen Aagaard Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark.
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie UniversityHalifaxNova ScotiaB3H 4R2Canada
| | - Robert O. Jones
- Peter Grünberg Institut PGI-1, Forschungszentrum Jülich52425 JülichGermany
| | - Martin Kaupp
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Straße des 17. Juni 135, 10623, Berlin.
| | - Andreas M. Köster
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav)CDMX07360Mexico
| | - Leeor Kronik
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovoth, 76100, Israel.
| | - Anna I. Krylov
- Department of Chemistry, University of Southern CaliforniaLos AngelesCalifornia 90089USA
| | - Simen Kvaal
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - Andre Laestadius
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - Mel Levy
- Department of Chemistry, Tulane University, New Orleans, Louisiana, 70118, USA.
| | - Mathieu Lewin
- CNRS & CEREMADE, Université Paris-Dauphine, PSL Research University, Place de Lattre de Tassigny, 75016 Paris, France.
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, NC 27599-3420, USA. .,Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, France.
| | - Neepa T. Maitra
- Department of Physics, Rutgers University at Newark101 Warren StreetNewarkNJ 07102USA
| | - Frank Neese
- Max Planck Institut für Kohlenforschung, Kaiser Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany.
| | - John P. Perdew
- Departments of Physics and Chemistry, Temple UniversityPhiladelphiaPA 19122USA
| | - Katarzyna Pernal
- Institute of Physics, Lodz University of Technology, ul. Wolczanska 219, 90-924 Lodz, Poland.
| | - Pascal Pernot
- Institut de Chimie Physique, UMR8000, CNRS and Université Paris-Saclay, Bât. 349, Campus d'Orsay, 91405 Orsay, France.
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA. .,Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - Elisa Rebolini
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France.
| | - Lucia Reining
- Laboratoire des Solides Irradiés, CNRS, CEA/DRF/IRAMIS, École Polytechnique, Institut Polytechnique de Paris, F-91120 Palaiseau, France. .,European Theoretical Spectroscopy Facility
| | - Pina Romaniello
- Laboratoire de Physique Théorique (UMR 5152), Université de Toulouse, CNRS, UPS, France.
| | - Adrienn Ruzsinszky
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA.
| | - Dennis R. Salahub
- Department of Chemistry, Department of Physics and Astronomy, CMS – Centre for Molecular Simulation, IQST – Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary2500 University Drive NWCalgaryAlbertaT2N 1N4Canada
| | - Matthias Scheffler
- The NOMAD Laboratory at the FHI of the Max-Planck-Gesellschaft and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Faradayweg 4-6, D-14195, Germany.
| | - Peter Schwerdtfeger
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study, Massey University Auckland, 0632 Auckland, New Zealand.
| | - Viktor N. Staroverov
- Department of Chemistry, The University of Western OntarioLondonOntario N6A 5B7Canada
| | - Jianwei Sun
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA.
| | - Erik Tellgren
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - David J. Tozer
- Department of Chemistry, Durham UniversitySouth RoadDurhamDH1 3LEUK
| | - Samuel B. Trickey
- Quantum Theory Project, Deptartment of Physics, University of FloridaGainesvilleFL 32611USA
| | - Carsten A. Ullrich
- Department of Physics and Astronomy, University of MissouriColumbiaMO 65211USA
| | - Alberto Vela
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), CDMX, 07360, Mexico.
| | - Giovanni Vignale
- Department of Physics, University of Missouri, Columbia, MO 65203, USA.
| | - Tomasz A. Wesolowski
- Department of Physical Chemistry, Université de Genève30 Quai Ernest-Ansermet1211 GenèveSwitzerland
| | - Xin Xu
- Shanghai Key Laboratory of Molecular Catalysis and Innovation Materials, Collaborative Innovation Centre of Chemistry for Energy Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China.
| | - Weitao Yang
- Department of Chemistry and Physics, Duke University, Durham, NC 27516, USA.
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Domagała M, Jabłoński M, Dubis AT, Zabel M, Pfitzner A, Palusiak M. Testing of Exchange-Correlation Functionals of DFT for a Reliable Description of the Electron Density Distribution in Organic Molecules. Int J Mol Sci 2022; 23:ijms232314719. [PMID: 36499046 PMCID: PMC9740346 DOI: 10.3390/ijms232314719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022] Open
Abstract
Researchers carrying out calculations using the DFT method face the problem of the correct choice of the exchange-correlation functional to describe the quantities they are interested in. This article deals with benchmark calculations aimed at testing various exchange-correlation functionals in terms of a reliable description of the electron density distribution in molecules. For this purpose, 30 functionals representing all rungs of Jacob's Ladder are selected and then the values of some QTAIM-based parameters are compared with their reference equivalents obtained at the CCSD/aug-cc-pVTZ level of theory. The presented results show that the DFT method undoubtedly has the greatest problems with a reliable description of the electron density distribution in multiple strongly polar bonds, such as C=O, and bonds associated with large electron charge delocalization. The performance of the tested functionals turned out to be unsystematic. Nevertheless, in terms of a reliable general description of QTAIM-based parameters, the M11, SVWN, BHHLYP, M06-HF, and, to a slightly lesser extent, also BLYP, B3LYP, and X3LYP functionals turned out to be the worst. It is alarming to find the most popular B3LYP functional in this group. On the other hand, in the case of the electron density at the bond critical point, being the most important QTAIM-based parameter, the M06-HF functional is especially discouraged due to the very poor description of the C=O bond. On the contrary, the VSXC, M06-L, SOGGA11-X, M06-2X, MN12-SX, and, to a slightly lesser extent, also TPSS, TPSSh, and B1B95 perform well in this respect. Particularly noteworthy is the overwhelming performance of double hybrids in terms of reliable values of bond delocalization indices. The results show that there is no clear improvement in the reliability of describing the electron density distribution with climbing Jacob's Ladder, as top-ranked double hybrids are also, in some cases, able to produce poor values compared to CCSD.
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Affiliation(s)
- Małgorzata Domagała
- Faculty of Chemistry, University of Lodz, Pomorska 163/165, 90-236 Lodz, Poland
| | - Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
- Correspondence: ; Tel.: +48-056-611-4695
| | - Alina T. Dubis
- Faculty of Chemistry, University of Białystok, Ciołkowskiego 1K, 15-245 Białystok, Poland
| | - Manfred Zabel
- Institute of Inorganic Chemistry, University of Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
| | - Arno Pfitzner
- Institute of Inorganic Chemistry, University of Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
| | - Marcin Palusiak
- Faculty of Chemistry, University of Lodz, Pomorska 163/165, 90-236 Lodz, Poland
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6
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Wang F, Cheng J. Automated Workflow for Computation of Redox Potentials, Acidity Constants and Solvation Free Energies Accelerated by Machine Learning. J Chem Phys 2022; 157:024103. [DOI: 10.1063/5.0098330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Fast evolution of modern society stimulates intense development of new materials with novel functionalities in energy and environmental applications. Due to rapid progress of computer science, computational design of materials with target properties has recently attracted lots of interests. Accurate and efficient calculation of fundamental thermodynamic properties, including redox potentials, acidity constants, and solvation free energies, is of great importance for selection and design of desirable materials. Free energy calculation based on ab initio molecular dynamics (AIMD) can predict these properties with high accuracy at complex environments, however being impeded by high computational costs. To address this issue, this work develops an automated scheme that combines iterative training of machine learning potentials (MLPs) and free energy calculation, and deomonstrates that these thermodynamic properties can be computed by ML accelerated MD with ab initio accuracy and much longer time scale at cheaper costs, improving poor statistics and convergence of numerical integration by AIMD. Our automated scheme lays the foundation for computational chemistry-assisted materials design.
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7
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Brémond E, Li H, Sancho-García JC, Adamo C. Double Hybrids and Noncovalent Interactions: How Far Can We Go? J Phys Chem A 2022; 126:2590-2599. [PMID: 35438491 DOI: 10.1021/acs.jpca.2c01193] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The accurate evaluation of weak noncovalent interactions in large, that is those containing up to thousand atoms, molecular systems represents a difficult challenge for any quantum chemical method. Indeed, some approximations are often introduced to render affordable these calculations. Here, we consider the PBE-QIDH/DH-SVPD protocol, combining a nonempirical double hybrid functional (PBE-QIDH) with a small basis set (DH-SVPD) tailored for noncovalent interactions with a double aim: (i) explore the robustness and accuracy of this protocol with respect to other Density Functional Approximations; (ii) illustrate how its performances are affected by the computational parameters underlying the calculation of the exact exchange and the Coulomb contribution, as well as the perturbative term. To this end, we consider three data sets, namely S66, L7, and CiM13, incorporating molecules of increasing size. On the bright side, our results suggest that the PBE-QIDH/DH-SVPD protocol is particularly accurate for large systems such as those contained in the CiM13 set (up to more than 1000 atoms and 14 000 basis functions), for which the DLPNO approximation leads to a significant speed-up for the evaluation of the perturbative correlation term. However, our analysis also points out the limit of this statistical exercise, when the quality of the reference data cannot be easily assessed, due to the size of the molecular complexes involved, and when the number of molecules is limited.
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Affiliation(s)
- Eric Brémond
- Université de Paris, ITODYS, CNRS, F-75006 Paris, France
| | - Hanwei Li
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France
| | | | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France.,Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
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8
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Yan W, Xu X. Accurate Prediction of Nuclear Magnetic Resonance Parameters via the XYG3 Type of Doubly Hybrid Density Functionals. J Chem Theory Comput 2022; 18:2931-2946. [PMID: 35467852 DOI: 10.1021/acs.jctc.2c00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful and versatile tools in elucidating molecular structures. To eliminate ambiguities of experimental assignments, accurate calculations of NMR spectra are of great importance. Here, a method for theoretical evaluation of the NMR shielding constants by analytic derivatives using gauge including atomic orbitals (GIAO) has been implemented for the XYG3 type of doubly hybrid density functionals (xDH), namely, the GIAO-xDH method. Benchmark calculations on shielding constants and chemical shifts demonstrate the remarkable accuracy of the GIAO-xDH method, compared to the accurate CCSD(T) references. It is shown here that the XYGJ-OS functional is able to give a mean absolute deviation (MAD) of ∼3.0 ppm in the calculated shielding constants for 13C, 15N, 17O, 19F, while both XYGJ-OS and xDH-PBE0 functionals are able to provide a satisfactory estimation of chemical shifts with MADs of ∼0.03 and 1.0 ppm for 1H and 13C, respectively. The basis set influence upon the method has been examined and a computational scheme considering both accuracy and efficiency has been proposed and tested to predict the experimental 13C chemical shifts of five medium-sized natural product molecules, yielding a MAD of ∼1.0 ppm, which demonstrates the practical feasibility of the GIAO-xDH method.
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Affiliation(s)
- Wenjie Yan
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
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Jha R, Jana G, Chattaraj PK. Possible catalytic activity of N,N-coordinated mono-cationic copper bound Pyrazol-1-yl(1H-pyrrol-2-yl)methanone complex: a computational study. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [DOI: 10.1007/s43538-022-00072-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Prokopiou G, Hartstein M, Govind N, Kronik L. Optimal Tuning Perspective of Range-Separated Double Hybrid Functionals. J Chem Theory Comput 2022; 18:2331-2340. [PMID: 35369687 PMCID: PMC9009176 DOI: 10.1021/acs.jctc.2c00082] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Indexed: 11/29/2022]
Abstract
We study the optimal tuning of the free parameters in range-separated double hybrid functionals, based on enforcing the exact conditions of piecewise linearity and spin constancy. We find that introducing the range separation in both the exchange and the correlation terms allows for the minimization of both fractional charge and fractional spin errors for singlet atoms. The optimal set of parameters is system specific, underlining the importance of the tuning procedure. We test the performance of the resulting optimally tuned functionals for the dissociation curves of diatomic molecules. We find that they recover the correct dissociation curve for the one-electron system, H2+, and improve the dissociation curves of many-electron molecules such as H2 and Li2, but they also yield a nonphysical maximum and only converge to the correct dissociation limit at very large distances.
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Affiliation(s)
- Georgia Prokopiou
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovoth 76100, Israel
| | - Michal Hartstein
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovoth 76100, Israel
| | - Niranjan Govind
- Physical
and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Leeor Kronik
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovoth 76100, Israel
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11
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Hong P, Song X, Huang Z, Tan K, Wu A, Lu X. Insights into the Mechanism of Metal-Catalyzed Transformation of Oxime Esters: Metal-Bound Radical Pathway vs Free Radical Pathway. J Org Chem 2022; 87:6014-6024. [PMID: 35389656 DOI: 10.1021/acs.joc.2c00273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Controlling of radical reactivity by binding a radical to the metal center is an elegant strategy to overcome the challenge that radical intermediates are "too reactive to be selective". Yet, its application has seemingly been limited to a few strained-ring substrates, azide compounds, and diazo compounds. Meanwhile, first-row transition-metal-catalyzed (mainly, Fe, Ni, Cu) transformations of oxime esters have been reported recently in which the activation processes are assumed to follow free-radical mechanisms. In this work, we show by means of density functional theory calculations that the activation of oxime esters catalyzed by Fe(II) and Cu(I) catalysts more likely affords a metal-bound iminyl radical, rather than the presumed free iminyl radical, and the whole process follows a metal-bound radical mechanism. The as-formed metal-bound radical intermediates are an Fe(III)-iminyl radical (Stotal = 2, SFe = 5/2, and Siminyl = -1/2) and a Cu(II)-iminyl radical (Stotal = 0, SCu = 1/2, and Siminyl = -1/2). The discovery of such novel substrates affording metal-bound radical intermediates may facilitate the experimental design of metal-catalyzed asymmetric synthesis using oxime esters to achieve the desired enantioselectivity.
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Affiliation(s)
- Pan Hong
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory for Theoretical and Computational Chemistry, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiaolin Song
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory for Theoretical and Computational Chemistry, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhengqi Huang
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory for Theoretical and Computational Chemistry, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Kai Tan
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory for Theoretical and Computational Chemistry, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Anan Wu
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory for Theoretical and Computational Chemistry, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xin Lu
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory for Theoretical and Computational Chemistry, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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12
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Tran LN. Can second-order perturbation theory accurately predict electron density of open-shell molecules? The importance of self-consistency. Phys Chem Chem Phys 2022; 24:19393-19400. [DOI: 10.1039/d2cp01495e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron density plays an essential role in predicting molecular properties.
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Affiliation(s)
- Lan Nguyen Tran
- National Institute of Applied Mechanics and Informatics, Vietnam Academy of Science and Technology, Ho Chi Minh City 700000, Vietnam
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13
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Theoretical Description of Water from Single-Molecule to Condensed Phase: a Review of Recent Progress on Potential Energy Surfaces and Molecular Dynamics. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2201005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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14
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Brémond É, Tognetti V, Chermette H, Sancho-García JC, Joubert L, Adamo C. Electronic Energy and Local Property Errors at QTAIM Critical Points while Climbing Perdew's Ladder of Density-Functional Approximations. J Chem Theory Comput 2021; 18:293-308. [PMID: 34958205 DOI: 10.1021/acs.jctc.1c00981] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate the relationships between electron-density and electronic-energy errors produced by modern exchange-correlation density-functional approximations belonging to all of the rungs of Perdew's ladder. To this aim, a panel of relevant (semi)local properties evaluated at critical points of the electron-density field (as defined within the framework of Bader's atoms-in-molecules theory) are computed on a large selection of molecular systems involved in thermodynamic, kinetic, and noncovalent interaction chemical databases using density functionals developed in a nonempirical and minimally and highly parametrized fashion. The comparison of their density- and energy-based performance, also discussed in terms of density-driven errors, casts light on the strengths and weaknesses of the most recent and efficient density-functional approximations.
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Affiliation(s)
- Éric Brémond
- Université de Paris, ITODYS, CNRS, F-75006 Paris, France
| | - Vincent Tognetti
- Normandy University, COBRA UMR 6014 and FR 3038, Université de Rouen INSA Rouen, CNRS, F-76821 Mont St Aignan, France
| | - Henry Chermette
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, 5 rue de la Doua, F-69100 Villeurbanne, France
| | | | - Laurent Joubert
- Normandy University, COBRA UMR 6014 and FR 3038, Université de Rouen INSA Rouen, CNRS, F-76821 Mont St Aignan, France
| | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences (i-CLeHS), UMR 8060, F-75005 Paris, France.,Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
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15
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Ramos C, Muehlbrad J, Janesko BG. Density functionals with full nonlocal exchange, nonlocal rung-3.5 correlation, and D3 dispersion: Combined accuracy for general main-group thermochemistry, kinetics, and noncovalent interactions. J Comput Chem 2021; 42:1974-1981. [PMID: 34387364 DOI: 10.1002/jcc.26728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/25/2021] [Indexed: 11/11/2022]
Abstract
We introduce the HF-R35-D3(BJ) functional combining full nonlocal exact (Hartree-Fock-like, HF) exchange, inexpensive rung-3.5 correlation constructed from nonlocal one-electron operators, and nonlocal D3 dispersion corrections. HF-R35-D3(BJ) is among the first full-exact-exchange functionals offering competitive accuracy for general main-group thermochemistry, kinetics, and noncovalent interactions. HF-R35-D3(BJ) gives weighted mean absolute deviation WTMAD-2 8.5 kcal/mol across the entire GMTKN55 dataset, outperforming most dispersion-corrected semilocal functionals and approaching the accuracy of dispersion-corrected global hybrids. This requires six fitted parameters, three each in the nonlocal correlation and dispersion corrections. Full nonlocal exchange appears to help give accurate binding energies and reasonable energy orderings for water hexamers. These results motivate continued exploration of inexpensive nonlocal correlation corrections to nonlocal exchange.
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Affiliation(s)
- Chloe Ramos
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas, USA
| | - Jeremiah Muehlbrad
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas, USA
| | - Benjamin G Janesko
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas, USA
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16
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Li H, Brémond E, Sancho-García JC, Adamo C. Pairing double hybrid functionals with a tailored basis set for an accurate thermochemistry of hydrocarbons. RSC Adv 2021; 11:26073-26082. [PMID: 35479441 PMCID: PMC9037073 DOI: 10.1039/d1ra04108h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/19/2021] [Indexed: 11/21/2022] Open
Abstract
A collection of five challenging datasets, including noncovalent interactions, reaction barriers and electronic rearrangements of medium-sized hydrocarbons, has been selected to verify the robustness of double-hybrid functionals used in conjunction with the small DH-SVPD basis set, especially developed for noncovalent interactions. The analysis is completed by other, more standard functionals, for a total of 17 models, including also empirical corrections for dispersion. The obtained results show that the chemical accuracy threshold, that is an error lower than 1.0 kcal mol−1, can be obtained by pairing the nonempirical PBE-QIDH functional with the DH-SVPD basis set, as well as by other semi-empirical functionals, such as DSD-PBEP86, using larger basis sets and empirical corrections. More in general, a significant improvement can be obtained using the DH-SVPD basis set with DHs, without resorting to any empirical corrections. This choice leads to a fast computational protocol that, avoiding any empirical potential, remains on a fully quantum ground. The pairing of the PBE-QIDH double-hybrid functional with a tailored split-valence basis set leads to a fast computational protocol for the accurate evaluation of hydrocarbon thermochemistry, without resorting to any empirical correction.![]()
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Affiliation(s)
- Hanwei Li
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences F-75005 Paris France
| | - Eric Brémond
- Université de Paris, ITODYS, CNRS F-75006 Paris France
| | | | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences F-75005 Paris France .,Institut Universitaire de France 103 Boulevard Saint Michel F-75005 Paris France
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17
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Janesko BG. Replacing hybrid density functional theory: motivation and recent advances. Chem Soc Rev 2021; 50:8470-8495. [PMID: 34060549 DOI: 10.1039/d0cs01074j] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Density functional theory (DFT) is the most widely-used electronic structure approximation across chemistry, physics, and materials science. Every year, thousands of papers report hybrid DFT simulations of chemical structures, mechanisms, and spectra. Unfortunately, hybrid DFT's accuracy is ultimately limited by tradeoffs between over-delocalization and under-binding. This review summarizes these tradeoffs, and introduces six modern attempts to go beyond them while maintaining hybrid DFT's relatively low computational cost: DFT+U, self-interaction corrections, localized orbital scaling corrections, local hybrid functionals, real-space nondynamical correlation, and our rung-3.5 approach. The review concludes with practical suggestions for DFT users to identify and mitigate these tradeoffs' impact on their simulations.
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Affiliation(s)
- Benjamin G Janesko
- Department of Chemistry & Biochemistry, Texas Christian University, 2800 S. University Dr, Fort Worth, TX 76129, USA.
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18
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Li H, Tirri B, Brémond E, Sancho-García JC, Adamo C. Beyond Chemical Accuracy for Alkane Thermochemistry: The DH thermo Approach. J Org Chem 2021; 86:5538-5545. [PMID: 33822605 DOI: 10.1021/acs.joc.1c00058] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The so-called protobranching phenomenon, that is the greater stability of branched alkanes with respect to their linear isomers, represents an interesting challenge for approaches based on density functional theory (DFT), since it requires a balanced description of several electronic effects, including (intramolecular) dispersion forces. Here, we investigate this problem using a protocol recently developed based on double-hybrid functionals and a small basis set, DH-SVPD, suited for noncovalent interactions. The energies of bond separation reactions (BSR), defined on the basis of an isodesmic principle, are taken as reference properties for the evaluation of 15 DFT approaches. The obtained results show that error lower than the so-called "chemical accuracy" (<1.0 kcal/mol) can be obtained by the proposed protocol on both relative reaction energies and enthalpies. These results are then verified on the standard BSR36 data set and support the proposition of our computational protocol, named DHthermo, where any DH functional, such as PBE-QIDH or B2PLYP, provides accurate results when coupled to an empirical dispersion correction and the DH-SVPD basis set. This protocol not only gives subchemical accuracy on the thermochemistry of alkanes but it is extremely easy to use with common quantum-chemistry codes.
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Affiliation(s)
- Hanwei Li
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France
| | - Bernardino Tirri
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France
| | - Eric Brémond
- Université de Paris, ITODYS, CNRS, F-75006 Paris, France
| | | | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France.,Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
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19
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Bircher MP, Villard J, Rothlisberger U. Efficient Treatment of Correlation Energies at the Basis-Set Limit by Monte Carlo Summation of Continuum States. J Chem Theory Comput 2020; 16:6550-6559. [PMID: 32915565 PMCID: PMC7584365 DOI: 10.1021/acs.jctc.0c00724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Indexed: 11/28/2022]
Abstract
The calculation of electron correlation is vital for the description of atomistic phenomena in physics, chemistry, and biology. However, accurate wavefunction-based methods exhibit steep scaling and often sluggish convergence with respect to the basis set at hand. Because of their delocalization and ease of extrapolation to the basis-set limit, plane waves would be ideally suited for the calculation of basis-set limit correlation energies. However, the routine use of correlated wavefunction approaches in a plane-wave basis set is hampered by prohibitive scaling due to a large number of virtual continuum states and has not been feasible for all but the smallest systems, even if substantial computational resources are available and methods with comparably beneficial scaling, such as the Møller-Plesset perturbation theory to second order (MP2), are used. Here, we introduce a stochastic sampling of the MP2 integrand based on Monte Carlo summation over continuum orbitals, which allows for speedups of up to a factor of 1000. Given a fixed number of sampling points, the resulting algorithm is dominated by a flat scaling of ∼ O ( N 2 ) . Absolute correlation energies are accurate to <0.1 kcal/mol with respect to conventional calculations for several hundreds of electrons. This allows for the calculation of unbiased basis-set limit correlation energies for systems containing hundreds of electrons with unprecedented efficiency gains based on a straightforward treatment of continuum contributions.
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Affiliation(s)
- Martin P. Bircher
- Computational
and Soft Matter Physics, Universität
Wien, Sensengasse 8/9, A-1090 Wien, Austria
| | - Justin Villard
- Laboratory
of Computational Chemistry and Biochemistry, Institut des Sciences
et Ingénierie Chimiques, Ecole Polytechnique
Fédérale de Lausanne (EPFL), Av. F.A. Forel 2, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Institut des Sciences
et Ingénierie Chimiques, Ecole Polytechnique
Fédérale de Lausanne (EPFL), Av. F.A. Forel 2, CH-1015 Lausanne, Switzerland
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20
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Grotjahn R, Lauter GJ, Haasler M, Kaupp M. Evaluation of Local Hybrid Functionals for Electric Properties: Dipole Moments and Static and Dynamic Polarizabilities. J Phys Chem A 2020; 124:8346-8358. [DOI: 10.1021/acs.jpca.0c06939] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Robin Grotjahn
- Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Institut für Chemie, Sekr. C7, Straße des 17. Juni 135, D-10623, Berlin, Germany
| | - Gregor J. Lauter
- Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Institut für Chemie, Sekr. C7, Straße des 17. Juni 135, D-10623, Berlin, Germany
| | - Matthias Haasler
- Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Institut für Chemie, Sekr. C7, Straße des 17. Juni 135, D-10623, Berlin, Germany
| | - Martin Kaupp
- Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Institut für Chemie, Sekr. C7, Straße des 17. Juni 135, D-10623, Berlin, Germany
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21
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Mayorov AV, Krisyuk BE, Sokolova N. Kinetics and mechanisms of the first step of ozonolysis of trans-isoprene. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Liu Z, Chen Z, Xi J, Xu X. An accurate single descriptor for ion-π interactions. Natl Sci Rev 2020; 7:1036-1045. [PMID: 34692123 PMCID: PMC8288966 DOI: 10.1093/nsr/nwaa051] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/18/2019] [Accepted: 03/23/2020] [Indexed: 11/24/2022] Open
Abstract
Non-covalent interactions between ions and π systems play an important role in molecular recognition, catalysis and biology. To guide the screen and design for artificial hosts, catalysts and drug delivery, understanding the physical nature of ion-π complexes via descriptors is indispensable. However, even with multiple descriptors that contain the leading term of electrostatic and polarized interactions, the quantitative description for the binding energies (BEs) of ion-π complexes is still lacking because of the intrinsic shortcomings of the commonly used descriptors. Here, we have shown that the impartment of orbital details into the electrostatic energy (coined as OEE) makes an excellent single descriptor for BEs of not only spherical, but also multiply-shaped, ion-π systems, highlighting the importance of an accurate description of the electrostatic interactions. Our results have further demonstrated that OEEs from a low-level method could be calibrated to BEs from a high-level method, offering a powerful practical strategy for an accurate prediction of a set of ion-π interactions.
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Affiliation(s)
- Zhangyun Liu
- Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Zheng Chen
- Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Jinyang Xi
- Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai 200433, China
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23
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Witwicki M, Walencik PK, Jezierska J. How accurate is density functional theory in predicting spin density? An insight from the prediction of hyperfine coupling constants. J Mol Model 2019; 26:10. [PMID: 31834497 DOI: 10.1007/s00894-019-4268-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/25/2019] [Indexed: 01/30/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy has been proven to be an important technique for studying paramagnetic systems. Probably, the most accessible EPR parameter and the one that provides a significant amount of information about molecular structure and spin density is the hyperfine coupling constant (HFCC). Hence, accurate quantum-chemical modeling of HFCCs is frequently essential to the adequate interpretation of EPR spectra. It requires the precise spin density, which is the difference between the densities of α- and β-electrons, and thus, its quality is expected to reflect the quality of the total electron density. The question of which approximate exchange-correlation density functional yields sufficiently accurate HFCCs, and thus, the spin density remains open. To assess the performance of well-established density functionals for calculating HFCCs, we used a series of 26 small paramagnetic species and compared the obtained results to the CCSD reference values. The performance of DFT was also tested on EPR-studied o-semiquinone radical interacting with water molecules and Mg2+ cation. The HFCCs were additionally calculated by the DLPNO-CCSD method, and this wave function-based technique was found superior to all functionals we tested. Although some functionals were found, on average, to be fairly efficient, we found that the most accurate functional is system-dependent, and therefore, the DLPNO-CCSD method should be preferred for theoretical investigations of the HFCCs and spin density.
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Affiliation(s)
- Maciej Witwicki
- Faculty of Chemistry, Wrocław University, ul. F. Joliot-Curie 14, 50-383, Wrocław, Poland.
| | - Paulina K Walencik
- Faculty of Chemistry, Wrocław University, ul. F. Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Julia Jezierska
- Faculty of Chemistry, Wrocław University, ul. F. Joliot-Curie 14, 50-383, Wrocław, Poland
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24
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Su NQ, Xu X. Insights into Direct Methods for Predictions of Ionization Potential and Electron Affinity in Density Functional Theory. J Phys Chem Lett 2019; 10:2692-2699. [PMID: 31059262 DOI: 10.1021/acs.jpclett.9b01052] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Vertical ionization potential (IP) and electron affinity (EA) are fundamental molecular properties, while the Δ method and the direct method are the widely used approaches to compute these properties. The Δ method is calculated by taking the total energy difference of the initial and final states, whose reliability is seriously affected by the issue associated with the imbalanced treatment of these two states. The direct method based on the derivatives involving only one single-state calculation can yield a quasi-particle spectrum whose accuracy, on the other hand, is mostly affected by the levels of approximate molecular structure theories. Because of the aforementioned issues, EA prediction can be particularly problematic. Here we present, for the first time, an analytic theory on the derivation and realization of generalized Kohn-Sham (KS) eigenvalues of doubly hybrid (DH) functionals that depend on both occupied and unoccupied orbitals. The method based on the KS eigenvalues of neutral systems, termed the NKS method, is found to suffer little from the imbalance issue, while it is only the NKS method that can offer accurate EA prediction from a good functional approximation, such as the XYG3 type of DH functionals. Being less sensitive to the size of basis sets, the NKS method is of great significance for its application to large systems. The insights gained in this work are useful for the calculation of properties associated with small energy differences while emphasizing the importance of the development of generalized functionals that rely on both occupied and unoccupied orbitals.
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Affiliation(s)
- Neil Qiang Su
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry , Fudan University , Shanghai 200433 , China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry , Fudan University , Shanghai 200433 , China
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25
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Santra G, Sylvetsky N, Martin JML. Minimally Empirical Double-Hybrid Functionals Trained against the GMTKN55 Database: revDSD-PBEP86-D4, revDOD-PBE-D4, and DOD-SCAN-D4. J Phys Chem A 2019; 123:5129-5143. [PMID: 31136709 PMCID: PMC9479158 DOI: 10.1021/acs.jpca.9b03157] [Citation(s) in RCA: 231] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
We
present a family of minimally empirical double-hybrid DFT functionals
parametrized against the very large and diverse GMTKN55 benchmark.
The very recently proposed ωB97M(2) empirical double hybrid
(with 16 adjustable parameters) has the lowest WTMAD2 (weighted mean
absolute deviation over GMTKN55) ever reported at 2.19 kcal/mol. However,
refits of the DSD-BLYP and DSD-PBEP86 spin-component-scaled, dispersion-corrected
double hybrids can achieve WTMAD2 values as low as 2.33 with the very
recent D4 dispersion correction (2.42 kcal/mol with the D3(BJ) dispersion
term) using just a handful of adjustable parameters. If we use full
DFT correlation in the initial orbital evaluation, the xrevDSD-PBEP86-D4
functional reaches WTMAD2 = 2.23 kcal/mol, statistically indistinguishable
from ωB97M(2) but using just four nonarbitrary adjustable parameters
(and three semiarbitrary ones). The changes from the original DSD
parametrizations are primarily due to noncovalent interaction energies
for large systems, which were undersampled in the original parametrization
set. With the new parametrization, same-spin correlation can be eliminated
at minimal cost in performance, which permits revDOD-PBEP86-D4 and
revDOD-PBE-D4 functionals that scale as N4 or even N3 with the size of the system.
Dependence of WTMAD2 for DSD functionals on the percentage of HF exchange
is roughly quadratic; it is sufficiently weak that any reasonable
value in the 64% to 72% range can be chosen semiarbitrarily. DSD-SCAN
and DOD-SCAN double hybrids involving the SCAN nonempirical meta-GGA
as the semilocal component have also been considered and offer a good
alternative if one wishes to eliminate either the empirical dispersion
correction or the same-spin correlation component. noDispSD-SCAN66
achieves WTMAD2 = 3.0 kcal/mol, compared to 2.7 kcal/mol for DOD-SCAN66-D4.
However, the best performance without dispersion corrections (WTMAD2
= 2.8 kcal/mol) is reached by revωB97X-2, a slight reparametrization
of the Chai–Head-Gordon range-separated double hybrid. Finally,
in the context of double-hybrid functionals, the very recent D4 dispersion
correction is clearly superior over D3(BJ).
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Affiliation(s)
- Golokesh Santra
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Nitai Sylvetsky
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Jan M. L. Martin
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001 Reḥovot, Israel
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26
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Interplay between test sets and statistical procedures in ranking DFT methods: The case of electron density studies. MENDELEEV COMMUNICATIONS 2018. [DOI: 10.1016/j.mencom.2018.05.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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