1
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Mester D, Nagy PR, Kállay M. Basis-Set Limit CCSD(T) Energies for Large Molecules with Local Natural Orbitals and Reduced-Scaling Basis-Set Corrections. J Chem Theory Comput 2024; 20:7453-7468. [PMID: 39207805 DOI: 10.1021/acs.jctc.4c00777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The calculation of density-based basis-set correction (DBBSC), which remedies the basis-set incompleteness (BSI) error of the correlation energy, is combined with local approximations. Aiming at large-scale applications, the procedure is implemented in our efficient local natural orbital-based coupled-cluster singles and doubles with perturbative triples [LNO-CCSD(T)] scheme. To this end, the range-separation function, which characterizes the one-electron BSI in space, is decomposed into the sum of contributions from individual localized molecular orbitals (LMOs). A compact domain is constructed around each LMO, and the corresponding contributions are evaluated only within these restricted domains. Furthermore, for the calculation of the complementary auxiliary basis set (CABS) correction, which significantly improves the Hartree-Fock (HF) energy, the local density fitting approximation is utilized. The errors arising from the local approximations are examined in detail, efficient prescreening techniques are introduced to compress the numerical quadrature used for DBBSC, and conservative default thresholds are selected for the truncation parameters. The efficiency of the DBBSC-LNO-CCSD(T) method is demonstrated through representative examples of up to 1000 atoms. Based on the numerical results, we conclude that the corrections drastically reduce the BSI error using double-ζ basis sets, often to below 1 kcal/mol compared to the reliable LNO-CCSD(T) complete basis set references, while significant improvements are also achieved with triple-ζ basis sets. Considering that the calculation of the DBBSC and CABS corrections only moderately increases the wall-clock time required for the post-HF steps in practical applications, the proposed DBBSC-LNO-CCSD(T) method offers a highly efficient and robust tool for large-scale calculations.
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Affiliation(s)
- Dávid Mester
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Muegyetem rkp. 3, H-1111 Budapest, Hungary
- HUN-REN-BME Quantum Chemistry Research Group, Muegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME Lendület Quantum Chemistry Research Group, Muegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Péter R Nagy
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Muegyetem rkp. 3, H-1111 Budapest, Hungary
- HUN-REN-BME Quantum Chemistry Research Group, Muegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME Lendület Quantum Chemistry Research Group, Muegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Muegyetem rkp. 3, H-1111 Budapest, Hungary
- HUN-REN-BME Quantum Chemistry Research Group, Muegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME Lendület Quantum Chemistry Research Group, Muegyetem rkp. 3, H-1111 Budapest, Hungary
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2
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Hernández-Segura LI, Olvera-Rubalcava FA, Flores-Moreno R, Calaminici P, Köster AM. Exchange-correlation kernel for perturbation dependent auxiliary functions in auxiliary density perturbation theory. J Mol Model 2024; 30:302. [PMID: 39115689 PMCID: PMC11310252 DOI: 10.1007/s00894-024-06091-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 07/23/2024] [Indexed: 08/11/2024]
Abstract
CONTEXT Analytic exchange-correlation kernel formulations are of the outermost importance for density functional theory (DFT) perturbation calculations. In this paper, the working equation for the exchange-correlation kernel of the generalized gradient approximation (GGA) for perturbation dependent auxiliary functions is derived and discussed in the framework of auxiliary density functional theory (ADFT). The presented new formulation is extended to the unrestricted approach, too. A comprehensive discussion of the implementation of the GGA ADFT kernel, using either the native exchange-correlation functional implementations in deMon2k or the ones from the LibXC library, is given. Calculations with analytic exchange-correlation kernels are compared to their finite difference counterparts. The obtained results are in quantitative agreement. Nevertheless, analytic GGA ADFT kernel implementations show substantial improvement in the computational performance. Similar results are reported for analytic second derivatives of effective core potential (ECP) and model core potential (MCP) matrix elements when compared to their finite difference counterparts in molecular frequency analyses. METHOD All calculations are performed in the framework of ADFT as implemented in deMon2k. In the ADFT analytic frequency calculations, auxiliary density perturbation theory was used. The underlying two-center exchange-correlation kernel matrix elements are calculated by numerical integration either with analytic or finite difference kernel expressions. Validation calculations are performed with the VWN and PBE functionals employing DFT-optimized DZVP basis sets in conjunction with automatically generated GEN-A2 auxiliary density function sets. In the (Pt3Cu)n cluster benchmark calculations, the RPBE functional was used. For Pt atoms, the quasi-relativistic LANL2DZ effective core potential with the corresponding valence basis set was employed, whereas for Cu atoms, the all-electron DFT-optimized TZVP basis was applied. The auxiliary density was expanded by the automatically generated GEN-A2* auxiliary function set. We run all benchmark calculations in parallel on 24 cores.
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Affiliation(s)
- Luis I Hernández-Segura
- Chemistry Department, CINVESTAV, Av. Instituto Politecnico Nacional 2508, Col. San Pedro Zacatenco, Del. Gustavo A. Madero, Mexico City, C.P. 07360, Mexico.
| | - Flor A Olvera-Rubalcava
- Chemistry Department, CINVESTAV, Av. Instituto Politecnico Nacional 2508, Col. San Pedro Zacatenco, Del. Gustavo A. Madero, Mexico City, C.P. 07360, Mexico
| | - Roberto Flores-Moreno
- Departamento de Química, Universidad de Guadalajara, Blvd. Gral. Marcelino García Barragán 1421, Guadalajara, Jal., C.P. 44430, Mexico
| | - Patrizia Calaminici
- Chemistry Department, CINVESTAV, Av. Instituto Politecnico Nacional 2508, Col. San Pedro Zacatenco, Del. Gustavo A. Madero, Mexico City, C.P. 07360, Mexico
| | - Andreas M Köster
- Chemistry Department, CINVESTAV, Av. Instituto Politecnico Nacional 2508, Col. San Pedro Zacatenco, Del. Gustavo A. Madero, Mexico City, C.P. 07360, Mexico.
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3
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Barrios Herrera L, Lourenço MP, Hostaš J, Calaminici P, Köster AM, Tchagang A, Salahub DR. Active-learning for global optimization of Ni-Ceria nanoparticles: The case of Ce 4-xNi xO 8- x (x = 1, 2, 3). J Comput Chem 2024; 45:1643-1656. [PMID: 38551129 DOI: 10.1002/jcc.27346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/15/2024] [Accepted: 03/05/2024] [Indexed: 06/04/2024]
Abstract
Ni-CeO2 nanoparticles (NPs) are promising nanocatalysts for water splitting and water gas shift reactions due to the ability of ceria to temporarily donate oxygen to the catalytic reaction and accept oxygen after the reaction is completed. Therefore, elucidating how different properties of the Ni-Ceria NPs relate to the activity and selectivity of the catalytic reaction, is of crucial importance for the development of novel catalysts. In this work the active learning (AL) method based on machine learning regression and its uncertainty is used for the global optimization of Ce(4-x)NixO(8-x) (x = 1, 2, 3) nanoparticles, employing density functional theory calculations. Additionally, further investigation of the NPs by mass-scaled parallel-tempering Born-Oppenheimer molecular dynamics resulted in the same putative global minimum structures found by AL, demonstrating the robustness of our AL search to learn from small datasets and assist in the global optimization of complex electronic structure systems.
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Affiliation(s)
- Lizandra Barrios Herrera
- Department of Chemistry, Department of Physics and Astronomy, CMS Centre for Molecular Simulation, IQST Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Calgary, Canada
| | - Maicon Pierre Lourenço
- Departamento de Química e Física, Centro de Ciências Exatas, Naturais e da Saúde (CCENS), Universidade Federal do Espírito Santo, Espírito Santo, Brasil
| | - Jiří Hostaš
- Department of Chemistry, Department of Physics and Astronomy, CMS Centre for Molecular Simulation, IQST Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Calgary, Canada
- Digital Technologies Research Centre, National Research Council of Canada, Ottawa, Canada
| | | | | | - Alain Tchagang
- Digital Technologies Research Centre, National Research Council of Canada, Ottawa, Canada
| | - 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 Calgary, Calgary, Canada
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4
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Hostaš J, Pérez-Becerra KO, Calaminici P, Barrios-Herrera L, Lourenço MP, Tchagang A, Salahub DR, Köster AM. How important is the amount of exact exchange for spin-state energy ordering in DFT? Case study of molybdenum carbide cluster, Mo4C2. J Chem Phys 2023; 159:184301. [PMID: 37947508 DOI: 10.1063/5.0169409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
Since the form of the exact functional in density functional theory is unknown, we must rely on density functional approximations (DFAs). In the past, very promising results have been reported by combining semi-local DFAs with exact, i.e. Hartree-Fock, exchange. However, the spin-state energy ordering and the predictions of global minima structures are particularly sensitive to the choice of the hybrid functional and to the amount of exact exchange. This has been already qualitatively described for single conformations, reactions, and a limited number of conformations. Here, we have analyzed the mixing of exact exchange in exchange functionals for a set of several hundred isomers of the transition metal carbide, Mo4C2. The analysis of the calculated energies and charges using PBE0-type functional with varying amounts of exact exchange yields the following insights: (1) The sensitivity of spin-energy splitting is strongly correlated with the amount of exact exchange mixing. (2) Spin contamination is exacerbated when correlation is omitted from the exchange-correlation functional. (3) There is not one ideal value for the exact exchange mixing which can be used to parametrize or choose among the functionals. Calculated energies and electronic structures are influenced by exact exchange at a different magnitude within a given distribution; therefore, to extend the application range of hybrid functionals to the full periodic table the spin-energy splitting energies should be investigated.
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Affiliation(s)
- Jiří Hostaš
- Department of Chemistry, CMS - Centre for Molecular Simulation, IQST - Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Kevin O Pérez-Becerra
- Departamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, CDMX C.P. 07360, Mexico
| | - Patrizia Calaminici
- Departamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, CDMX C.P. 07360, Mexico
| | - Lizandra Barrios-Herrera
- Department of Chemistry, CMS - Centre for Molecular Simulation, IQST - Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Maicon Pierre Lourenço
- Departamento de Química e Física - Centro de Ciências Exatas, Naturais e da Saúde - CCENS - Universidade Federal do Espírito Santo, 29500-000 Alegre, Espírito Santo, Brazil
| | - Alain Tchagang
- Digital Technologies Research Centre, National Research Council of Canada, 1200 Montréal Road, Ottawa, Ontario K1A 0R6, Canada
| | - Dennis R Salahub
- Department of Chemistry, CMS - Centre for Molecular Simulation, IQST - Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Andreas M Köster
- Departamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, CDMX C.P. 07360, Mexico
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Sepehri A, Li RR, Hoffmann MR. Riemannian Trust Region Method for Minimization of the Fourth Central Moment for Localized Molecular Orbitals. J Phys Chem A 2023. [PMID: 37285307 DOI: 10.1021/acs.jpca.3c01295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The importance of localized molecular orbitals (MOs) in correlation treatments beyond mean-field calculation and in the illustration of chemical bonding (and antibonding) can hardly be overstated. However, the generation of orthonormal localized occupied MOs is significantly more straightforward than obtaining orthonormal localized virtual MOs. Orthonormal MOs allow facile use of highly efficient group theoretical methods (e.g., graphical unitary group approach) for calculation of Hamiltonian matrix elements in multireference configuration interaction calculations (such as MRCISD) and in quasi-degenerate perturbation treatments, such as the Generalized Van Vleck Perturbation Theory. Moreover, localized MOs can elucidate qualitative understanding of bonding in molecules, in addition to high-accuracy quantitative descriptions. We adopt the powers of the fourth moment cost function introduced by Jørgensen and coworkers. Because the fourth moment cost functions are prone to having multiple negative Hessian eigenvalues when starting from easily available canonical (or near-canonical) MOs, standard optimization algorithms can fail to obtain the orbitals of the virtual or partially occupied spaces. To overcome this drawback, we applied a trust region algorithm on an orthonormal Riemannian manifold with an approximate retraction from the tangent space built into the first and second derivatives of the cost function. Moreover, the Riemannian trust region outer iterations were coupled to truncated Conjugate Gradient inner loops, which avoided any costly solutions of simultaneous linear equations or eigenvector/eigenvalue solutions. Numerical examples are provided on model systems, including the high-connectivity H10 set in 1-, 2-, and 3-dimensional arrangements, and on a chemically realistic description of cyclobutadiene (c-C4H4) and the propargyl radical (C3H3). In addition to demonstrating the algorithm on occupied and virtual blocks of orbitals, the method is also shown to work on the active space at the MCSCF level of theory.
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Affiliation(s)
- Aliakbar Sepehri
- Chemistry Department, University of North Dakota, Grand Forks, North Dakota 58202-9024, United States
| | - Run R Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Mark R Hoffmann
- Chemistry Department, University of North Dakota, Grand Forks, North Dakota 58202-9024, United States
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Csóka J, Kállay M. Analytic gradients for local density fitting Hartree-Fock and Kohn-Sham methods. J Chem Phys 2023; 158:024110. [PMID: 36641408 DOI: 10.1063/5.0131683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We present analytic gradients for local density fitting Hartree-Fock (HF) and hybrid Kohn-Sham (KS) density functional methods. Due to the non-variational nature of the local fitting algorithm, the method of Lagrange multipliers is used to avoid the solution of the coupled perturbed HF and KS equations. We propose efficient algorithms for the solution of the arising Z-vector equations and the gradient calculation that preserve the third-order scaling and low memory requirement of the original local fitting algorithm. In order to demonstrate the speed and accuracy of our implementation, gradient calculations and geometry optimizations are presented for various molecular systems. Our results show that significant speedups can be achieved compared to conventional density fitting calculations without sacrificing accuracy.
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Affiliation(s)
- József Csóka
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary
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7
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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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8
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Deviers J, Cailliez F, Gutiérrez BZ, Kattnig DR, de la Lande A. Ab initio derivation of flavin hyperfine interactions for the protein magnetosensor cryptochrome. Phys Chem Chem Phys 2022; 24:16784-16798. [PMID: 35775941 DOI: 10.1039/d1cp05804e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The radicals derived from flavin adenine dinucleotide (FAD) are a corner stone of recent hypotheses about magnetoreception, including the compass of migratory songbirds. These models attribute a magnetic sense to coherent spin dynamics in radical pairs within the flavo-protein cryptochrome. The primary determinant of sensitivity and directionality of this process are the hyperfine interactions of the involved radicals. Here, we present a comprehensive computational study of the hyperfine couplings in the protonated and unprotonated FAD radicals in cryptochrome 4 from C. livia. We combine long (800 ns) molecular dynamics trajectories to accurate quantum chemistry calculations. Hyperfine parameters are derived using auxiliary density functional theory applied to cluster and hybrid QM/MM (Quantum Mechanics/Molecular Mechanics) models comprising the FAD and its significant surrounding environment, as determined by a detailed sensitivity analysis. Thanks to this protocol we elucidate the sensitivity of the hyperfine interaction parameters to structural fluctuations and the polarisation effect of the protein environment. We find that the ensemble-averaged hyperfine interactions are predominantly governed by thermally induced geometric distortions of the flavin. We discuss our results in view of the expected performance of these radicals as part of a magnetoreceptor. Our data could be used to parametrize spin Hamiltonians including not only average values but also standard deviations.
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Affiliation(s)
- Jean Deviers
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, UK.,Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France.
| | - Fabien Cailliez
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France.
| | - Bernardo Zúñiga Gutiérrez
- Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, C. P. 44430, Guadalajara Jal, Mexico
| | - Daniel R Kattnig
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, UK
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France.
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9
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Delesma FA, Delgado-Venegas RI, Salahub DR, Del Campo JM, Pedroza-Montero JN, Calaminici P, Köster AM. Self-Consistent Auxiliary Density Perturbation Theory. J Chem Theory Comput 2021; 17:6934-6946. [PMID: 34709812 DOI: 10.1021/acs.jctc.1c00713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The working equations for the extension of auxiliary density perturbation theory (ADPT) to hybrid functionals, employing the variational fitting of the Fock potential, are derived. The response equations in the resulting self-consistent ADPT (SC-ADPT) are solved iteratively with an adapted Eirola-Nevanlinna algorithm. As a result, a memory and CPU time efficient implementation of perturbation theory free of four-center electron repulsion integrals (ERIs) is obtained. Our validation calculations of SC-ADPT static and dynamic polarizabilities show quantitative agreement with corresponding coupled perturbed Hartree-Fock and Kohn-Sham results employing four-center ERIs. The comparison of SC-ADPT hybrid functional polarizabilities with coupled cluster reference calculations yield semiquantitative agreement. The presented systematic study of the dynamic polarizabilities of oligothiophenes shows that hybrid functionals can overcome the pathological misplacement of excitation poles by the local density and generalized gradient approximations. Good agreement with experimental dynamic polarizabilities for all studied oligothiophenes is achieved with range-separated hybrid functionals in the framework of SC-ADPT.
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Affiliation(s)
- Francisco A Delesma
- Departamento de Química, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México.,Programa de Doctorado en Nanociencias y Nanotecnología, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México
| | - Rogelio I Delgado-Venegas
- Department of Chemistry, Department of Physics and Astronomy CMS - Centre for Molecular Simulation, IQST - Institute for Quantum Science and Technology and Quantum Alberta, University of Calgary, 2500 University Drive N.W., Calgary, AB Canada T2N 1N4
| | - Dennis R Salahub
- Department of Chemistry, Department of Physics and Astronomy CMS - Centre for Molecular Simulation, IQST - Institute for Quantum Science and Technology and Quantum Alberta, University of Calgary, 2500 University Drive N.W., Calgary, AB Canada T2N 1N4
| | - Jorge M Del Campo
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Jesús N Pedroza-Montero
- Departamento de Química, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México.,Programa de Doctorado en Nanociencias y Nanotecnología, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México
| | - Patrizia Calaminici
- Departamento de Química, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México.,Programa de Doctorado en Nanociencias y Nanotecnología, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México
| | - Andreas M Köster
- Departamento de Química, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México.,Programa de Doctorado en Nanociencias y Nanotecnología, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07000, México
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10
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Diagonalization-free self-consistent field approach with localized molecular orbitals. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02850-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Helmich-Paris B, de Souza B, Neese F, Izsák R. An improved chain of spheres for exchange algorithm. J Chem Phys 2021; 155:104109. [PMID: 34525816 DOI: 10.1063/5.0058766] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In the present work, we describe a more accurate and efficient variant of the chain-of-spheres algorithm (COSX) for exchange matrix computations. Higher accuracy for the numerical integration is obtained with new grids that were developed using global optimization techniques. With our new default grids, the average absolute energy errors are much lower than 0.1 kcal/mol, which is desirable to achieve "chemical accuracy." Although the size of the new grids is increased by roughly a factor of 2.5, the excellent efficiency of the original COSX implementation is still further improved in most cases. The evaluation of the analytic electrostatic potential integrals was significantly accelerated by a new implementation of rolled-out versions of the Dupuis-Rys-King and Head-Gordon-Pople algorithms. Compared to our earlier implementation, a twofold speedup is obtained for the frequently used triple-ζ basis sets, while up to a 16-fold speedup is observed for quadruple-ζ basis sets. These large gains are a consequence of both the more efficient integral evaluation and the intermediate exchange matrix computation in a partially contracted basis when generally contracted shells occur. With our new RIJCOSX implementation, we facilitate accurate self-consistent field (SCF) binding energy calculations on a large supra-molecular complex composed of 320 atoms. The binding-energy errors with respect to the fully analytic results are well below 0.1 kcal/mol for the cc-pV(T/Q)Z basis sets and even smaller than for RIJ with fully analytic exchange. At the same time, our RIJCOSX SCF calculation even with the cc-pVQZ basis and the finest grid is 21 times faster than the fully analytic calculation.
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Affiliation(s)
- Benjamin Helmich-Paris
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | | | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Róbert Izsák
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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12
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Reliability and performances of real-time time-dependent auxiliary density functional theory. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02819-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Geudtner G. Parallelization of deMon2k: an overview. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02786-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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G0W0 based on time-dependent auxiliary density perturbation theory. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02755-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Csóka J, Kállay M. Speeding up Hartree-Fock and Kohn-Sham calculations with first-order corrections. J Chem Phys 2021; 154:164114. [PMID: 33940810 DOI: 10.1063/5.0041276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Several approaches are presented to improve the efficiency of Hartree-Fock and Kohn-Sham self-consistent field (SCF) calculations relying on a simple first-order energy correction reminiscent of the scheme used in dual-basis SCF methods. The basic idea is to perform an initial SCF calculation computing approximate Fock-matrices and, in the final iteration step, to use a more complete Fock-matrix builder together with the energy correction to diminish the error. The approximation is tested for conventional and local density fitting (DF) SCF approaches combining various auxiliary basis sets, fitting metrics, and Fock-matrix construction algorithms in the initial and final iterations as well as for seminumerical SCF methods combining integration grids of different qualities. We also report the implementation of the occupied orbital resolution of identity exchange construction algorithm with local DF approximations. Benchmark calculations are presented for total energies, reaction energies, and molecular geometries. Our results show that speedups of up to 80% can be expected utilizing the new approaches without significant loss of accuracy.
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Affiliation(s)
- József Csóka
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
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16
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Omar KA, Hasnaoui K, de la Lande A. First-Principles Simulations of Biological Molecules Subjected to Ionizing Radiation. Annu Rev Phys Chem 2021; 72:445-465. [PMID: 33878897 DOI: 10.1146/annurev-physchem-101419-013639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ionizing rays cause damage to genomes, proteins, and signaling pathways that normally regulate cell activity, with harmful consequences such as accelerated aging, tumors, and cancers but also with beneficial effects in the context of radiotherapies. While the great pace of research in the twentieth century led to the identification of the molecular mechanisms for chemical lesions on the building blocks of biomacromolecules, the last two decades have brought renewed questions, for example, regarding the formation of clustered damage or the rich chemistry involving the secondary electrons produced by radiolysis. Radiation chemistry is now meeting attosecond science, providing extraordinary opportunities to unravel the very first stages of biological matter radiolysis. This review provides an overview of the recent progress made in this direction, focusing mainly on the atto- to femto- to picosecond timescales. We review promising applications of time-dependent density functional theory in this context.
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Affiliation(s)
- Karwan Ali Omar
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France; .,Department of Chemistry, College of Education, University of Sulaimani, 41005 Kurdistan, Iraq
| | - Karim Hasnaoui
- High Performance Computing User Support Team, Institut du Développement et des Ressources en Informatique Scientifique (IDRIS), 91403 Orsay, France.,Maison de la Simulation, CNRS, Commissariat à l'Energie Atomique et aux Énergies Alternatives (CEA), Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France;
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17
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Hostaš J, Tchagang A, Lourenço MP, Köster AM, Salahub DR. Global optimization of ~ 1 nm MoS2 and CaCO3 nanoparticles. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02743-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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18
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Symmetry-adapted density fitting in auxiliary density functional theory. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02729-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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Förster A, Visscher L. Low-Order Scaling G0W0 by Pair Atomic Density Fitting. J Chem Theory Comput 2020; 16:7381-7399. [PMID: 33174743 PMCID: PMC7726916 DOI: 10.1021/acs.jctc.0c00693] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Indexed: 12/18/2022]
Abstract
We derive a low-scaling G0W0 algorithm for molecules using pair atomic density fitting (PADF) and an imaginary time representation of the Green's function and describe its implementation in the Slater type orbital (STO)-based Amsterdam density functional (ADF) electronic structure code. We demonstrate the scalability of our algorithm on a series of water clusters with up to 432 atoms and 7776 basis functions and observe asymptotic quadratic scaling with realistic threshold qualities controlling distance effects and basis sets of triple-ζ (TZ) plus double polarization quality. Also owing to a very small prefactor, a G0W0 calculation for the largest of these clusters takes only 240 CPU hours with these settings. We assess the accuracy of our algorithm for HOMO and LUMO energies in the GW100 database. With errors of 0.24 eV for HOMO energies on the quadruple-ζ level, our implementation is less accurate than canonical all-electron implementations using the larger def2-QZVP GTO-type basis set. Apart from basis set errors, this is related to the well-known shortcomings of the GW space-time method using analytical continuation techniques as well as to numerical issues of the PADF approach of accurately representing diffuse atomic orbital (AO) products. We speculate that these difficulties might be overcome by using optimized auxiliary fit sets with more diffuse functions of higher angular momenta. Despite these shortcomings, for subsets of medium and large molecules from the GW5000 database, the error of our approach using basis sets of TZ and augmented double-ζ (DZ) quality is decreasing with system size. On the augmented DZ level, we reproduce canonical, complete basis set limit extrapolated reference values with an accuracy of 80 meV on average for a set of 20 large organic molecules. We anticipate our algorithm, in its current form, to be very useful in the study of single-particle properties of large organic systems such as chromophores and acceptor molecules.
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Affiliation(s)
- Arno Förster
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
| | - Lucas Visscher
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
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20
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Pedroza-Montero JN, Delesma FA, Morales JL, Calaminici P, Köster AM. Variational fitting of the Fock exchange potential with modified Cholesky decomposition. J Chem Phys 2020; 153:134112. [DOI: 10.1063/5.0020084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Jesús Naín Pedroza-Montero
- Programa de Doctorado en Nanociencias y Nanotecnología, Cinvestav, Av. Instituto Politécnico Nacional, 2508, A.P. 14740, Ciudad de México 07000, Mexico
| | - Francisco Antonio Delesma
- Programa de Doctorado en Nanociencias y Nanotecnología, Cinvestav, Av. Instituto Politécnico Nacional, 2508, A.P. 14740, Ciudad de México 07000, Mexico
| | - José Luis Morales
- Departamento de Química, Cinvestav, Av. Instituto Politécnico Nacional, 2508, A.P. 14740, Ciudad de México 07000, Mexico
| | - Patrizia Calaminici
- Programa de Doctorado en Nanociencias y Nanotecnología, Cinvestav, Av. Instituto Politécnico Nacional, 2508, A.P. 14740, Ciudad de México 07000, Mexico
- Departamento de Química, Cinvestav, Av. Instituto Politécnico Nacional, 2508, A.P. 14740, Ciudad de México 07000, Mexico
| | - Andreas M. Köster
- Programa de Doctorado en Nanociencias y Nanotecnología, Cinvestav, Av. Instituto Politécnico Nacional, 2508, A.P. 14740, Ciudad de México 07000, Mexico
- Departamento de Química, Cinvestav, Av. Instituto Politécnico Nacional, 2508, A.P. 14740, Ciudad de México 07000, Mexico
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21
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Patterson CH. Density fitting in periodic systems: Application to TDHF in diamond and oxides. J Chem Phys 2020; 153:064107. [DOI: 10.1063/5.0014106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- C. H. Patterson
- School of Physics, Trinity College Dublin, Dublin 2, Ireland
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22
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Csóka J, Kállay M. Speeding up density fitting Hartree–Fock calculations with multipole approximations. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1769213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- József Csóka
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest, Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest, Hungary
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23
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Pedroza-Montero JN, Morales JL, Geudtner G, Álvarez-Ibarra A, Calaminici P, Köster AM. Variational Density Fitting with a Krylov Subspace Method. J Chem Theory Comput 2020; 16:2965-2974. [PMID: 32223134 DOI: 10.1021/acs.jctc.9b01212] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we present the implementation of a variational density fitting methodology that uses iterative linear algebra for solving the associated system of linear equations. It is well known that most difficulties with this system arise from the fact that the coefficient matrix is in general ill-conditioned and, due to finite precision round-off errors, it may not be positive definite. The dimensionality, given by the number of auxiliary functions, also poses a challenge in terms of memory and time demand since the coefficient matrix is dense. The methodology presented is based on a preconditioned Krylov subspace method able to deal with indefinite ill-conditioned equation systems. To assess its potential, it has been combined with double asymptotic electron repulsion integral expansions as implemented in the deMon2k package. A numerical study on a set of problems with up to 130,000 auxiliary functions shows its effectiveness to alleviate the abovementioned problematic. A comparison with the default methodology used in deMon2k based on a truncated eigenvalue decomposition of the coefficient matrix indicates that the proposed method exhibits excellent robustness and scalability when implemented in a parallel setting.
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Affiliation(s)
- Jesús N Pedroza-Montero
- Programa de Doctorado de Nanociencias y Nanotecnologı́as, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico
| | - José Luis Morales
- Departamento de Quı́mica, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico
| | - Gerald Geudtner
- Departamento de Quı́mica, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico
| | - Aurelio Álvarez-Ibarra
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS, Université Paris Saclay. 15 avenue Jean Perrin, F91405 Orsay, France
| | - Patrizia Calaminici
- Programa de Doctorado de Nanociencias y Nanotecnologı́as, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico.,Departamento de Quı́mica, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico
| | - Andreas M Köster
- Programa de Doctorado de Nanociencias y Nanotecnologı́as, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico.,Departamento de Quı́mica, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico
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24
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Lew-Yee JFH, Flores-Moreno R, Morales JL, M Del Campo J. Asymmetric Density Fitting with Modified Cholesky Decomposition Applied to Second-Order Electron Propagator. J Chem Theory Comput 2020; 16:1597-1605. [PMID: 31967819 DOI: 10.1021/acs.jctc.9b01215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computation of molecular orbital electron repulsion integrals (MO-ERIs) as a transformation from atomic orbital ERIs (AO-ERIs) is the bottleneck of second-order electron propagator calculations when a single orbital is studied. In this contribution, asymmetric density fitting is combined with modified Cholesky decomposition to generate efficiently the required MO-ERIs. The key point of the presented algorithms is to keep track of integrals through partial contractions performed on three-center AO-ERIs; these contractions are stored in RAM instead of the AO-ERIs. Two implementations are provided, an in-core, which reduces the arithmetic and memory scaling factors as compared to the four-center AO-ERIs contraction method, and a semidirect, which overcomes memory limitations by evaluating antisymmetrized MO-ERIs in batches. On the numerical side, the proposed approach is fast and stable. The bad effects due to ill conditioning, namely, several negative and close to zero eigenvalues due to machine round off errors of the matrix associated with the density fitting process, are effectively controlled by means of a modified Cholesky factorization that avoids the matrix inversion needed to perform the asymmetrical density fitting implementation. The numerical experience presented shows that the in-core implementation is highly competitive to perform calculations on medium and large basis sets, while the semidirect implementation has small variations in time by changes in the available memory. The general applicability is illustrated on a set of selected relatively large-size molecules.
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Affiliation(s)
- Juan Felipe Huan Lew-Yee
- Departamento de Fı́sica y Quı́mica Teórica, Facultad de Quı́mica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Roberto Flores-Moreno
- Departamento de Quı́mica, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, Guadalajara Jalisco 44430, Mexico
| | - José Luis Morales
- Facultad de Quı́mica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Jorge M Del Campo
- Departamento de Fı́sica y Quı́mica Teórica, Facultad de Quı́mica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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25
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Kállay M, Nagy PR, Mester D, Rolik Z, Samu G, Csontos J, Csóka J, Szabó PB, Gyevi-Nagy L, Hégely B, Ladjánszki I, Szegedy L, Ladóczki B, Petrov K, Farkas M, Mezei PD, Ganyecz Á. The MRCC program system: Accurate quantum chemistry from water to proteins. J Chem Phys 2020; 152:074107. [DOI: 10.1063/1.5142048] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Mihály Kállay
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Péter R. Nagy
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Dávid Mester
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Zoltán Rolik
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Gyula Samu
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - József Csontos
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - József Csóka
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - P. Bernát Szabó
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - László Gyevi-Nagy
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Bence Hégely
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - István Ladjánszki
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Lóránt Szegedy
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Bence Ladóczki
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Klára Petrov
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Máté Farkas
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Pál D. Mezei
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Ádám Ganyecz
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
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26
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Förster A, Franchini M, van Lenthe E, Visscher L. A Quadratic Pair Atomic Resolution of the Identity Based SOS-AO-MP2 Algorithm Using Slater Type Orbitals. J Chem Theory Comput 2020; 16:875-891. [PMID: 31930915 PMCID: PMC7027358 DOI: 10.1021/acs.jctc.9b00854] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Indexed: 01/04/2023]
Abstract
We report a production level implementation of pair atomic resolution of the identity (PARI) based second-order Møller-Plesset perturbation theory (MP2) in the Slater type orbital (STO) based Amsterdam Density Functional (ADF) code. As demonstrated by systematic benchmarks, dimerization and isomerization energies obtained with our code using STO basis sets of triple-ζ-quality show mean absolute deviations from Gaussian type orbital, canonical, basis set limit extrapolated, global density fitting (DF)-MP2 results of less than 1 kcal/mol. Furthermore, we introduce a quadratic scaling atomic orbital based spin-opposite-scaled (SOS)-MP2 approach with a very small prefactor. Due to a worst-case scaling of [Formula: see text], our implementation is very fast already for small systems and shows an exceptionally early crossover to canonical SOS-PARI-MP2. We report computational wall time results for linear as well as for realistic three-dimensional molecules and show that triple-ζ quality calculations on molecules of several hundreds of atoms are only a matter of a few hours on a single compute node, the bottleneck of the computations being the SCF rather than the post-SCF energy correction.
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Affiliation(s)
- Arno Förster
- Theoretical Chemistry, Vrije
Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The
Netherlands
| | - Mirko Franchini
- Theoretical Chemistry, Vrije
Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The
Netherlands
- Scientific Computing & Modelling
NV, De Boelelaan 1083, NL-1081 HV Amsterdam, The
Netherlands
| | - Erik van Lenthe
- Scientific Computing & Modelling
NV, De Boelelaan 1083, NL-1081 HV Amsterdam, The
Netherlands
| | - Lucas Visscher
- Theoretical Chemistry, Vrije
Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The
Netherlands
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27
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Böning née Pfennig M, Dongol KG, Romero Boston GM, Schmitz S, Wartchow R, Samaniego-Rojas JD, Köster AM, Butenschön H. Trifluoromethyl-Substituted Benzocyclobutenone and Benzocyclobutenedione: The Structure Anomaly of (Benzocyclobutenedione)tricarbonylchromium Complexes. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Monika Böning née Pfennig
- Institut für Organische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 1B, D-30167 Hannover, Germany
| | - Krishna Gopal Dongol
- Institut für Organische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 1B, D-30167 Hannover, Germany
| | - Geanne Marize Romero Boston
- Institut für Organische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 1B, D-30167 Hannover, Germany
| | - Stefan Schmitz
- Institut für Organische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 1B, D-30167 Hannover, Germany
| | - Rudolf Wartchow
- Institut für Anorganische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 9, D-30167 Hannover, Germany
| | - Juan D. Samaniego-Rojas
- Departamento de Química, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508,
Col. San Pedro Zacatenco, CDMX, C.P. 07360, México
| | - Andreas M. Köster
- Departamento de Química, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508,
Col. San Pedro Zacatenco, CDMX, C.P. 07360, México
| | - Holger Butenschön
- Institut für Organische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 1B, D-30167 Hannover, Germany
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28
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Pérez-Figueroa SE, Calaminici P, Köster AM. Hybrid ADFT Study of the C 104 and C 106 IPR Isomers. J Phys Chem A 2019; 123:4565-4574. [PMID: 31021089 DOI: 10.1021/acs.jpca.9b00665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work presents a hybrid auxiliary density functional theory (ADFT) study of the neutral and hexaanionic C104 and C106 fullerenes with the aim to determine their ground state structures. To this end, all C104 and C106 fullerene structures that obey the isolated pentagon rule (IPR) were optimized with the Perdew-Burke-Ernzerhof generalized gradient approximation followed by a single-point energy calculation with the PBE0 hybrid functional. Our studies show that this composite approach yields relative energies of giant fullerenes that are accurate to around 1 kcal/mol. As a result, the ground states of C104, C1046-, and C1066- can be assigned to the isomers 234:Cs, 821:D2, and 891:Cs, respectively. On the other hand, the energetically lowest lying IPR isomers of C106, 331:Cs, 1194:C2, 534:C1 are separated by less than 1 kcal/mol which makes an unequivocal ground state assignment by hybrid DFT methods impossible. To guide future experiments, we also report the simulated IR and Raman spectra of the most stable neutral and hexaanionic C104 and C106 fullerenes.
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29
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Mejía-Rodríguez D, de la Lande A. Multicomponent density functional theory with density fitting. J Chem Phys 2019; 150:174115. [DOI: 10.1063/1.5078596] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daniel Mejía-Rodríguez
- Laboratoire de Chimie Physique, Université Paris Sud/CNRS, Université Paris Saclay, 15 Avenue Jean Perrin, 91405 Orsay, France
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique, Université Paris Sud/CNRS, Université Paris Saclay, 15 Avenue Jean Perrin, 91405 Orsay, France
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30
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de la Lande A, Alvarez-Ibarra A, Hasnaoui K, Cailliez F, Wu X, Mineva T, Cuny J, Calaminici P, López-Sosa L, Geudtner G, Navizet I, Garcia Iriepa C, Salahub DR, Köster AM. Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review. Molecules 2019; 24:molecules24091653. [PMID: 31035516 PMCID: PMC6539060 DOI: 10.3390/molecules24091653] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/18/2022] Open
Abstract
deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born-Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.
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Affiliation(s)
- Aurélien de la Lande
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Aurelio Alvarez-Ibarra
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Karim Hasnaoui
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Fabien Cailliez
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
| | - Xiaojing Wu
- Laboratoire de Chimie Physique, CNRS, Université Paris Sud, Université Paris Saclay, 15 avenue Jean Perrin, 91405 Orsay, France.
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, 75005 Paris, France.
| | - Tzonka Mineva
- Matériaux Avancés pour la Catalyse et la Santé, UMR 5253 CNRS/UM/ENSCM, Institut Charles Gerhardt de Montpellier (ICGM) Montpellier CEDEX 5, 34090 Montpellier, France.
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse CEDEX 4, France.
| | - Patrizia Calaminici
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, Mexico.
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
| | - Luis López-Sosa
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
| | - Gerald Geudtner
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
| | - Isabelle Navizet
- Laboratoire Modélisation et Simulation Multi Échelle, Université Paris-Est, MSME, UMR 8208 CNRS, UPEM, 5 bd Descartes, 77454 Marne-la-Vallée, France.
| | - Cristina Garcia Iriepa
- Laboratoire Modélisation et Simulation Multi Échelle, Université Paris-Est, MSME, UMR 8208 CNRS, UPEM, 5 bd Descartes, 77454 Marne-la-Vallée, France.
| | - Dennis R Salahub
- Department of Chemistry, Centre for Molecular Simulation, Institute for Quantum Science and Technology and Quantum Alberta, University of Calgary, 2500 University Drive N.W., Calgary, AB T2N 1N4, Canada.
- College of Chemistry and Chemical Engineering, Henan University of Technology, No. 100, Lian Hua Street, High-Tech Development Zone, Zhengzhou 450001, China.
| | - Andreas M Köster
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, Mexico.
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México.
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31
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Mester D, Kállay M. Reduced-Scaling Approach for Configuration Interaction Singles and Time-Dependent Density Functional Theory Calculations Using Hybrid Functionals. J Chem Theory Comput 2019; 15:1690-1704. [DOI: 10.1021/acs.jctc.8b01199] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Dávid Mester
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box
91, H-1521 Budapest, Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box
91, H-1521 Budapest, Hungary
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32
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Delesma FA, Geudtner G, Mejía-Rodríguez D, Calaminici P, Köster AM. Range-Separated Hybrid Functionals with Variational Fitted Exact Exchange. J Chem Theory Comput 2018; 14:5608-5616. [DOI: 10.1021/acs.jctc.8b00436] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Francisco A. Delesma
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México
| | - Gerald Geudtner
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México
| | - Daniel Mejía-Rodríguez
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México
| | - Patrizia Calaminici
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México
| | - Andreas M. Köster
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, México
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33
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Samu G, Kállay M. Efficient evaluation of the geometrical first derivatives of three-center Coulomb integrals. J Chem Phys 2018; 149:124101. [DOI: 10.1063/1.5049529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Gyula Samu
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Mihály Kállay
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
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34
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Gómez-Pérez JR, Delesma FA, Calaminici P, Köster AM. Accuracy of auxiliary density functional theory hybrid calculations for activation and reaction enthalpies of pericyclic reactions. J Mol Model 2018; 24:223. [PMID: 30078124 DOI: 10.1007/s00894-018-3759-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/24/2018] [Indexed: 11/28/2022]
Abstract
Auxiliary density functional theory (ADFT) hybrid calculations are based on the variational fitting of the Coulomb and Fock potential and, therefore, are free of four-center electron repulsion integrals. So far, ADFT hybrid calculations have been validated successfully for standard enthalpies of formation. In this work the accuracy of ADFT hybrid calculations for the description of pericyclic reactions was quantitatively validated at the B3LYP/6-31G*/GEN-A2* level of theory. Our comparison with conventional Kohn-Sham density functional theory (DFT) results shows that the DFT and ADFT activation and reaction enthalpies are practically indistinguishable. A systematic study of various functionals (PBE, B3LYP, PBE0, CAMB3LYP, CAMPBE0 and HSE06) and basis sets (6-31G*, DZVP-GGA and aug-cc-pVXZ; X = D, T and Q) revealed that the ADFT HSE06/aug-cc-pVTZ/GEN-A2* level of theory yields best balanced accuracy for the activation and reaction enthalpies of the studied pericyclic reactions. With the successfully validate ADFT composite approach consisting of PBE/DZVP-GGA/GEN-A2* structure and transition state optimizations and single-point HSE06/aug-cc-pVTZ/GEN-A2* energy calculations, an accurate, reliable and efficient computational approach for the study of pericyclic reactions in systems at the nanometer scale is proposed.
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Affiliation(s)
- José R Gómez-Pérez
- Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508, A.P. 14-740, 07000, México D.F, Mexico
| | - Francisco A Delesma
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Instituto Politécnico Nacional 2508, A.P. 14-740, 07000, Ciudad de México, Mexico
| | - Patrizia Calaminici
- Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508, A.P. 14-740, 07000, México D.F, Mexico. .,Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Instituto Politécnico Nacional 2508, A.P. 14-740, 07000, Ciudad de México, Mexico.
| | - Andreas M Köster
- Departamento de Química, CINVESTAV, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508, A.P. 14-740, 07000, México D.F, Mexico. .,Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Instituto Politécnico Nacional 2508, A.P. 14-740, 07000, Ciudad de México, Mexico.
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35
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Local density fitting applied to second order propagator equations for core electron binding energies. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Wu X, Clavaguera C, Lagardère L, Piquemal JP, de la Lande A. AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms. J Chem Theory Comput 2018; 14:2705-2720. [PMID: 29630819 DOI: 10.1021/acs.jctc.7b01128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We report the first parameters of the heme redox cofactors for the polarizable AMOEBA force field in both the ferric and ferrous forms. We consider two types of complexes, one with two histidine side chains as axial ligands and one with a histidine and a methionine side chain as ligands. We have derived permanent multipoles from second-order Møller-Plesset perturbation theory (MP2). The sets of parameters have been validated in a first step by comparison of AMOEBA interaction energies of heme and a collection of biologically relevant molecules with MP2 and Density Functional Theory (DFT) calculations. In a second validation step, we consider interaction energies with large aggregates comprising around 80 H2O molecules. These calculations are repeated for 30 structures extracted from semiempirical PM7 DM simulations. Very encouraging agreement is found between DFT and the AMOEBA force field, which results from an accurate treatment of electrostatic interactions. We finally report long (10 ns) MD simulations of cytochromes in two redox states with AMOEBA testing both the 2003 and 2014 AMOEBA water models. These simulations have been carried out with the TINKER-HP (High Performance) program. In conclusion, owing to their ubiquity in biology, we think the present work opens a wide array of applications of the polarizable AMOEBA force field on hemeproteins.
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Affiliation(s)
- Xiaojing Wu
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
| | - Carine Clavaguera
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
| | - Louis Lagardère
- Sorbonne Université, CNRS , Institut Parisien de Chimie Physique et Théorique (IP2CT) , 4 Place Jussieu , F-75005 , Paris , France.,Sorbonne Université , Institut des Sciences du Calcul et des Données (ISCD) , 4 place Jussieu , F-75005 , Paris , France
| | - Jean-Philip Piquemal
- Sorbonne Université, CNRS , Laboratoire de Chimie Théorique (LCT) , 4 Place Jussieu , F-75005 , Paris , France.,Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States.,Institut Universitaire de France , 75005 , Paris , France
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
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37
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Delesma FA, Van den Bossche M, Grönbeck H, Calaminici P, Köster AM, Pettersson LGM. A Chemical View on X-ray Photoelectron Spectroscopy: the ESCA Molecule and Surface-to-Bulk XPS Shifts. Chemphyschem 2017; 19:169-174. [DOI: 10.1002/cphc.201701135] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/04/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Francisco A. Delesma
- Programa de Doctorado en Nanociencias y Nanotecnología; CINVESTAV; Instituto Politécnico Nacional 2508; A.P. 14-740, Ciudad de México 07000 México
| | - Maxime Van den Bossche
- Department of Physics and Competence Centre for Catalysis; Chalmers University of Technology; 412 96 Göteborg Sweden
- Science Institute and Faculty of Physical Sciences; University of Iceland; 107 Reykjavik Iceland
| | - Henrik Grönbeck
- Department of Physics and Competence Centre for Catalysis; Chalmers University of Technology; 412 96 Göteborg Sweden
| | - Patrizia Calaminici
- Programa de Doctorado en Nanociencias y Nanotecnología; CINVESTAV; Instituto Politécnico Nacional 2508; A.P. 14-740, Ciudad de México 07000 México
- Departamento de Química; CINVESTAV; Instituto Politécnico Nacional 2508; A.P. 14-740 Ciudad de México 07000 México
| | - Andreas M. Köster
- Programa de Doctorado en Nanociencias y Nanotecnología; CINVESTAV; Instituto Politécnico Nacional 2508; A.P. 14-740, Ciudad de México 07000 México
- Departamento de Química; CINVESTAV; Instituto Politécnico Nacional 2508; A.P. 14-740 Ciudad de México 07000 México
| | - Lars G. M. Pettersson
- Department of Physics; AlbaNova University Center; Stockholm University; 106 91 Stockholm Sweden
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38
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Wirz LN, Reine SS, Pedersen TB. On Resolution-of-the-Identity Electron Repulsion Integral Approximations and Variational Stability. J Chem Theory Comput 2017; 13:4897-4906. [DOI: 10.1021/acs.jctc.7b00801] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lukas N. Wirz
- Hylleraas Centre for Quantum
Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033
Blindern, N-0315 Oslo, Norway
| | - Simen S. Reine
- Hylleraas Centre for Quantum
Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033
Blindern, N-0315 Oslo, Norway
| | - Thomas Bondo Pedersen
- Hylleraas Centre for Quantum
Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033
Blindern, N-0315 Oslo, Norway
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39
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Hollman DS, Schaefer HF, Valeev EF. Fast construction of the exchange operator in an atom-centred basis with concentric atomic density fitting. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1346312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- David S. Hollman
- Center for Computing Research, Sandia National Laboratories, Livermore, CA, USA
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA, USA
- Department of Chemistry, Virginia Tech, Blacksburg, VA, USA
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA, USA
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40
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Samu G, Kállay M. Efficient evaluation of three-center Coulomb integrals. J Chem Phys 2017; 146:204101. [PMID: 28571354 PMCID: PMC5440237 DOI: 10.1063/1.4983393] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 04/28/2017] [Indexed: 11/14/2022] Open
Abstract
In this study we pursue the most efficient paths for the evaluation of three-center electron repulsion integrals (ERIs) over solid harmonic Gaussian functions of various angular momenta. First, the adaptation of the well-established techniques developed for four-center ERIs, such as the Obara-Saika, McMurchie-Davidson, Gill-Head-Gordon-Pople, and Rys quadrature schemes, and the combinations thereof for three-center ERIs is discussed. Several algorithmic aspects, such as the order of the various operations and primitive loops as well as prescreening strategies, are analyzed. Second, the number of floating point operations (FLOPs) is estimated for the various algorithms derived, and based on these results the most promising ones are selected. We report the efficient implementation of the latter algorithms invoking automated programming techniques and also evaluate their practical performance. We conclude that the simplified Obara-Saika scheme of Ahlrichs is the most cost-effective one in the majority of cases, but the modified Gill-Head-Gordon-Pople and Rys algorithms proposed herein are preferred for particular shell triplets. Our numerical experiments also show that even though the solid harmonic transformation and the horizontal recurrence require significantly fewer FLOPs if performed at the contracted level, this approach does not improve the efficiency in practical cases. Instead, it is more advantageous to carry out these operations at the primitive level, which allows for more efficient integral prescreening and memory layout.
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Affiliation(s)
- Gyula Samu
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Mihály Kállay
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
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41
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Golze D, Iannuzzi M, Hutter J. Local Fitting of the Kohn–Sham Density in a Gaussian and Plane Waves Scheme for Large-Scale Density Functional Theory Simulations. J Chem Theory Comput 2017; 13:2202-2214. [DOI: 10.1021/acs.jctc.7b00148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dorothea Golze
- Department
of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
- COMP/Department
of Applied Physics, Aalto University, P.O. Box 11100, Aalto FI-00076, Finland
| | - Marcella Iannuzzi
- Department
of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jürg Hutter
- Department
of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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42
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Duchemin I, Li J, Blase X. Hybrid and Constrained Resolution-of-Identity Techniques for Coulomb Integrals. J Chem Theory Comput 2017; 13:1199-1208. [DOI: 10.1021/acs.jctc.6b01215] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ivan Duchemin
- INAC, SP2M/L_Sim,
CEA/UJF Cedex 09, Université Grenoble Alpes, 38054 Grenoble, France
| | - Jing Li
- Université Grenoble Alpes, CNRS, Inst NEEL, F-38042 Grenoble, France
| | - Xavier Blase
- Université Grenoble Alpes, CNRS, Inst NEEL, F-38042 Grenoble, France
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43
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Gillet N, Berstis L, Wu X, Gajdos F, Heck A, de la Lande A, Blumberger J, Elstner M. Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level. J Chem Theory Comput 2016; 12:4793-4805. [DOI: 10.1021/acs.jctc.6b00564] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Natacha Gillet
- Institute
of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Laura Berstis
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Xiaojing Wu
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, Université Paris Saclay, Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Fruzsina Gajdos
- Department
of Physics and Astronomy, University College London, Gower Street, London WCIE 6BT, United Kingdom
| | - Alexander Heck
- Institute
of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Aurélien de la Lande
- Laboratoire
de Chimie-Physique, Université Paris Sud, CNRS, Université Paris Saclay, Campus d’Orsay. 15, avenue Jean Perrin, 91405 Cedex Orsay, France
| | - Jochen Blumberger
- Department
of Physics and Astronomy, University College London, Gower Street, London WCIE 6BT, United Kingdom
| | - Marcus Elstner
- Institute
of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
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44
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Nagy PR, Samu G, Kállay M. An Integral-Direct Linear-Scaling Second-Order Møller-Plesset Approach. J Chem Theory Comput 2016; 12:4897-4914. [PMID: 27618512 DOI: 10.1021/acs.jctc.6b00732] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An integral-direct, iteration-free, linear-scaling, local second-order Møller-Plesset (MP2) approach is presented, which is also useful for spin-scaled MP2 calculations as well as for the efficient evaluation of the perturbative terms of double-hybrid density functionals. The method is based on a fragmentation approximation: the correlation contributions of the individual electron pairs are evaluated in domains constructed for the corresponding localized orbitals, and the correlation energies of distant electron pairs are computed with multipole expansions. The required electron repulsion integrals are calculated directly invoking the density fitting approximation; the storage of integrals and intermediates is avoided. The approach also utilizes natural auxiliary functions to reduce the size of the auxiliary basis of the domains and thereby the operation count and memory requirement. Our test calculations show that the approach recovers 99.9% of the canonical MP2 correlation energy and reproduces reaction energies with an average (maximum) error below 1 kJ/mol (4 kJ/mol). Our benchmark calculations demonstrate that the new method enables MP2 calculations for molecules with more than 2300 atoms and 26000 basis functions on a single processor.
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Affiliation(s)
- Péter R Nagy
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics , P.O. Box 91, Budapest H-1521, Hungary
| | - Gyula Samu
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics , P.O. Box 91, Budapest H-1521, Hungary
| | - Mihály Kállay
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics , P.O. Box 91, Budapest H-1521, Hungary
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45
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46
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Köppl C, Werner HJ. Parallel and Low-Order Scaling Implementation of Hartree–Fock Exchange Using Local Density Fitting. J Chem Theory Comput 2016; 12:3122-34. [DOI: 10.1021/acs.jctc.6b00251] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph Köppl
- Institut
für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring
55, 70569 Stuttgart, Germany
| | - Hans-Joachim Werner
- Institut
für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring
55, 70569 Stuttgart, Germany
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47
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Cailliez F, Müller P, Firmino T, Pernot P, de la Lande A. Energetics of Photoinduced Charge Migration within the Tryptophan Tetrad of an Animal (6–4) Photolyase. J Am Chem Soc 2016; 138:1904-15. [DOI: 10.1021/jacs.5b10938] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Fabien Cailliez
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - Pavel Müller
- Institute
for Integrative Biology of the Cell (I2BC), CEA, CNRS, University
Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette
cedex, France
| | - Thiago Firmino
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - Pascal Pernot
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
| | - Aurélien de la Lande
- Laboratoire
de Chimie Physique, UMR 8000 CNRS/University Paris-Sud, University Paris-Saclay, 91405 Orsay, France
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48
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Firmino T, Mangaud E, Cailliez F, Devolder A, Mendive-Tapia D, Gatti F, Meier C, Desouter-Lecomte M, de la Lande A. Quantum effects in ultrafast electron transfers within cryptochromes. Phys Chem Chem Phys 2016; 18:21442-57. [DOI: 10.1039/c6cp02809h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cryptochromes and photolyases are flavoproteins that may undergo ultrafast charge separation upon electronic excitation of their flavin cofactors.
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Affiliation(s)
- Thiago Firmino
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | - Etienne Mangaud
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | - Fabien Cailliez
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | - Adrien Devolder
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | | | - Fabien Gatti
- CTMM
- Institut Charles Gerhardt UMR 5253
- CNRS/Université de Montpellier
- France
| | - Christoph Meier
- Laboratoire Collisions Agrégats Réactivité
- UMR 5589
- IRSAMC
- Université Toulouse III Paul Sabatier
- Toulouse
| | | | - Aurélien de la Lande
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
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49
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Mangaud E, de la Lande A, Meier C, Desouter-Lecomte M. Electron transfer within a reaction path model calibrated by constrained DFT calculations: application to mixed-valence organic compounds. Phys Chem Chem Phys 2015; 17:30889-903. [PMID: 26041466 DOI: 10.1039/c5cp01194a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The quantum dynamics of electron transfer in mixed-valence organic compounds is investigated using a reaction path model calibrated by constrained density functional theory (cDFT). Constrained DFT is used to define diabatic states relevant for describing the electron transfer, to obtain equilibrium structures for each of these states and to estimate the electronic coupling between them. The harmonic analysis at the diabatic minima yields normal modes forming the dissipative bath coupled to the electronic states. In order to decrease the system-bath coupling, an effective one dimensional vibronic Hamiltonian is constructed by partitioning the modes into a linear reaction path which connects both equilibrium positions and a set of secondary vibrational modes, coupled to this reaction coordinate. Using this vibronic model Hamiltonian, dissipative quantum dynamics is carried out using Redfield theory, based on a spectral density which is determined from the cDFT results. In a first benchmark case, the model is applied to a series of mixed-valence organic compounds formed by two 1,4-dimethoxy-3-methylphenylene fragments linked by an increasing number of phenylene bridges. This allows us to examine the coherent electron transfer in extreme situations leading to a ground adiabatic state with or without a barrier and therefore to the trapping of the charge or to an easy delocalization.
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Affiliation(s)
- E Mangaud
- Laboratoire Collisions Agrégats Réactivité, UMR 5589, IRSAMC, Université Toulouse III Paul Sabatier, Bât. 3R1b4, 118 route de Narbonne, F-31062, Toulouse, France. and Laboratoire de Chimie Physique, UMR 8000, Université Paris-Sud, Bât. 349, 15 avenue Jean Perrin, F-91405 Orsay, France
| | - A de la Lande
- Laboratoire de Chimie Physique, UMR 8000, Université Paris-Sud, Bât. 349, 15 avenue Jean Perrin, F-91405 Orsay, France
| | - C Meier
- Laboratoire Collisions Agrégats Réactivité, UMR 5589, IRSAMC, Université Toulouse III Paul Sabatier, Bât. 3R1b4, 118 route de Narbonne, F-31062, Toulouse, France.
| | - M Desouter-Lecomte
- Laboratoire de Chimie Physique, UMR 8000, Université Paris-Sud, Bât. 349, 15 avenue Jean Perrin, F-91405 Orsay, France and Département de Chimie, Université de Liège, Sart Tilman, B6, B-4000 Liège, Belgium
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50
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Zuniga-Gutierrez B, Camacho-Gonzalez M, Bendana-Castillo A, Simon-Bastida P, Calaminici P, Köster AM. Efficient calculation of nuclear spin-rotation constants from auxiliary density functional theory. J Chem Phys 2015; 143:104103. [PMID: 26374014 DOI: 10.1063/1.4929999] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The computation of the spin-rotation tensor within the framework of auxiliary density functional theory (ADFT) in combination with the gauge including atomic orbital (GIAO) scheme, to treat the gauge origin problem, is presented. For the spin-rotation tensor, the calculation of the magnetic shielding tensor represents the most demanding computational task. Employing the ADFT-GIAO methodology, the central processing unit time for the magnetic shielding tensor calculation can be dramatically reduced. In this work, the quality of spin-rotation constants obtained with the ADFT-GIAO methodology is compared with available experimental data as well as with other theoretical results at the Hartree-Fock and coupled-cluster level of theory. It is found that the agreement between the ADFT-GIAO results and the experiment is good and very similar to the ones obtained by the coupled-cluster single-doubles-perturbative triples-GIAO methodology. With the improved computational performance achieved, the computation of the spin-rotation tensors of large systems or along Born-Oppenheimer molecular dynamics trajectories becomes feasible in reasonable times. Three models of carbon fullerenes containing hundreds of atoms and thousands of basis functions are used for benchmarking the performance. Furthermore, a theoretical study of temperature effects on the structure and spin-rotation tensor of the H(12)C-(12)CH-DF complex is presented. Here, the temperature dependency of the spin-rotation tensor of the fluorine nucleus can be used to identify experimentally the so far unknown bent isomer of this complex. To the best of our knowledge this is the first time that temperature effects on the spin-rotation tensor are investigated.
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Affiliation(s)
- Bernardo Zuniga-Gutierrez
- Departamento de Ciencias Computacionales, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, C.P. 44430 Guadalajara, Jalisco, Mexico
| | - Monica Camacho-Gonzalez
- Universidad Tecnológica de Tecámac, División A2, Procesos Industriales, Carretera Federal México Pachuca Km 37.5, Col. Sierra Hermosa, C.P. 55740 Tecámac, Estado de México, Mexico
| | - Alfonso Bendana-Castillo
- Universidad Tecnológica de Tecámac, División A3, Tecnologías de la Información y Comunicaciones, Carretera Federal México Pachuca Km 37.5, Col. Sierra Hermosa, C.P. 55740 Tecámac, Estado de México, Mexico
| | - Patricia Simon-Bastida
- Universidad Tecnlógica de Tulancingo, División Electromecánica, Camino a Ahuehuetitla No. 301, Col. Las Presas, C.P. 43642 Tulancingo, Hidalgo, Mexico
| | - Patrizia Calaminici
- Departamento de Química, CINVESTAV, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, México D.F. 07000, Mexico
| | - Andreas M Köster
- Departamento de Química, CINVESTAV, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, México D.F. 07000, Mexico
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