Density-functional theory with dispersion-correcting potentials for methane: Bridging the efficiency and accuracy gap between high-level wave function and classical molecular mechanics methods

Large clusters of noncovalently bonded molecules can only be efficiently modeled by classical mechanics simulations. One prominent challenge associated with this approach is obtaining force-field parameters that accurately describe noncovalent interactions. High-level correlated wave function method...

Full description

Autores:
Tipo de recurso:
Fecha de publicación:
2013
Institución:
Universidad Tecnológica de Bolívar
Repositorio:
Repositorio Institucional UTB
Idioma:
eng
OAI Identifier:
oai:repositorio.utb.edu.co:20.500.12585/9071
Acceso en línea:
https://hdl.handle.net/20.500.12585/9071
Palabra clave:
Rights
restrictedAccess
License
http://creativecommons.org/licenses/by-nc-nd/4.0/
id UTB2_84c6a7a27509630e67a7a3091a988f24
oai_identifier_str oai:repositorio.utb.edu.co:20.500.12585/9071
network_acronym_str UTB2
network_name_str Repositorio Institucional UTB
repository_id_str
dc.title.none.fl_str_mv Density-functional theory with dispersion-correcting potentials for methane: Bridging the efficiency and accuracy gap between high-level wave function and classical molecular mechanics methods
title Density-functional theory with dispersion-correcting potentials for methane: Bridging the efficiency and accuracy gap between high-level wave function and classical molecular mechanics methods
spellingShingle Density-functional theory with dispersion-correcting potentials for methane: Bridging the efficiency and accuracy gap between high-level wave function and classical molecular mechanics methods
title_short Density-functional theory with dispersion-correcting potentials for methane: Bridging the efficiency and accuracy gap between high-level wave function and classical molecular mechanics methods
title_full Density-functional theory with dispersion-correcting potentials for methane: Bridging the efficiency and accuracy gap between high-level wave function and classical molecular mechanics methods
title_fullStr Density-functional theory with dispersion-correcting potentials for methane: Bridging the efficiency and accuracy gap between high-level wave function and classical molecular mechanics methods
title_full_unstemmed Density-functional theory with dispersion-correcting potentials for methane: Bridging the efficiency and accuracy gap between high-level wave function and classical molecular mechanics methods
title_sort Density-functional theory with dispersion-correcting potentials for methane: Bridging the efficiency and accuracy gap between high-level wave function and classical molecular mechanics methods
description Large clusters of noncovalently bonded molecules can only be efficiently modeled by classical mechanics simulations. One prominent challenge associated with this approach is obtaining force-field parameters that accurately describe noncovalent interactions. High-level correlated wave function methods, such as CCSD(T), are capable of correctly predicting noncovalent interactions, and are widely used to produce reference data. However, high-level correlated methods are generally too computationally costly to generate the critical reference data required for good force-field parameter development. In this work we present an approach to generate Lennard-Jones force-field parameters to accurately account for noncovalent interactions. We propose the use of a computational step that is intermediate to CCSD(T) and classical molecular mechanics, that can bridge the accuracy and computational efficiency gap between them, and demonstrate the efficacy of our approach with methane clusters. On the basis of CCSD(T)-level binding energy data for a small set of methane clusters, we develop methane-specific, atom-centered, dispersion-correcting potentials (DCPs) for use with the PBE0 density-functional and 6-31+G(d,p) basis sets. We then use the PBE0-DCP approach to compute a detailed map of the interaction forces associated with the removal of a single methane molecule from a cluster of eight methane molecules and use this map to optimize the Lennard-Jones parameters for methane. The quality of the binding energies obtained by the Lennard-Jones parameters we obtained is assessed on a set of methane clusters containing from 2 to 40 molecules. Our Lennard-Jones parameters, used in combination with the intramolecular parameters of the CHARMM force field, are found to closely reproduce the results of our dispersion-corrected density-functional calculations. The approach outlined can be used to develop Lennard-Jones parameters for any kind of molecular system. © Published 2013 by the American Chemical Society.
publishDate 2013
dc.date.issued.none.fl_str_mv 2013
dc.date.accessioned.none.fl_str_mv 2020-03-26T16:32:53Z
dc.date.available.none.fl_str_mv 2020-03-26T16:32:53Z
dc.type.coarversion.fl_str_mv http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.coar.fl_str_mv http://purl.org/coar/resource_type/c_2df8fbb1
dc.type.driver.none.fl_str_mv info:eu-repo/semantics/article
dc.type.hasVersion.none.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.spa.none.fl_str_mv Artículo
status_str publishedVersion
dc.identifier.citation.none.fl_str_mv Journal of Chemical Theory and Computation; Vol. 9, Núm. 8; pp. 3342-3349
dc.identifier.issn.none.fl_str_mv 15499618
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/20.500.12585/9071
dc.identifier.doi.none.fl_str_mv 10.1021/ct4003114
dc.identifier.instname.none.fl_str_mv Universidad Tecnológica de Bolívar
dc.identifier.reponame.none.fl_str_mv Repositorio UTB
dc.identifier.orcid.none.fl_str_mv 35094573000
7003322749
identifier_str_mv Journal of Chemical Theory and Computation; Vol. 9, Núm. 8; pp. 3342-3349
15499618
10.1021/ct4003114
Universidad Tecnológica de Bolívar
Repositorio UTB
35094573000
7003322749
url https://hdl.handle.net/20.500.12585/9071
dc.language.iso.none.fl_str_mv eng
language eng
dc.rights.coar.fl_str_mv http://purl.org/coar/access_right/c_16ec
dc.rights.uri.none.fl_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.accessRights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
dc.rights.cc.none.fl_str_mv Atribución-NoComercial 4.0 Internacional
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
Atribución-NoComercial 4.0 Internacional
http://purl.org/coar/access_right/c_16ec
eu_rights_str_mv restrictedAccess
dc.format.medium.none.fl_str_mv Recurso electrónico
dc.format.mimetype.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv https://www.scopus.com/inward/record.uri?eid=2-s2.0-84882440261&doi=10.1021%2fct4003114&partnerID=40&md5=9c96c2dcf6e8e42cbc205c3cca744d1b
institution Universidad Tecnológica de Bolívar
bitstream.url.fl_str_mv https://repositorio.utb.edu.co/bitstream/20.500.12585/9071/1/MiniProdInv.png
bitstream.checksum.fl_str_mv 0cb0f101a8d16897fb46fc914d3d7043
bitstream.checksumAlgorithm.fl_str_mv MD5
repository.name.fl_str_mv Repositorio Institucional UTB
repository.mail.fl_str_mv repositorioutb@utb.edu.co
_version_ 1814021658565935104
spelling 2020-03-26T16:32:53Z2020-03-26T16:32:53Z2013Journal of Chemical Theory and Computation; Vol. 9, Núm. 8; pp. 3342-334915499618https://hdl.handle.net/20.500.12585/907110.1021/ct4003114Universidad Tecnológica de BolívarRepositorio UTB350945730007003322749Large clusters of noncovalently bonded molecules can only be efficiently modeled by classical mechanics simulations. One prominent challenge associated with this approach is obtaining force-field parameters that accurately describe noncovalent interactions. High-level correlated wave function methods, such as CCSD(T), are capable of correctly predicting noncovalent interactions, and are widely used to produce reference data. However, high-level correlated methods are generally too computationally costly to generate the critical reference data required for good force-field parameter development. In this work we present an approach to generate Lennard-Jones force-field parameters to accurately account for noncovalent interactions. We propose the use of a computational step that is intermediate to CCSD(T) and classical molecular mechanics, that can bridge the accuracy and computational efficiency gap between them, and demonstrate the efficacy of our approach with methane clusters. On the basis of CCSD(T)-level binding energy data for a small set of methane clusters, we develop methane-specific, atom-centered, dispersion-correcting potentials (DCPs) for use with the PBE0 density-functional and 6-31+G(d,p) basis sets. We then use the PBE0-DCP approach to compute a detailed map of the interaction forces associated with the removal of a single methane molecule from a cluster of eight methane molecules and use this map to optimize the Lennard-Jones parameters for methane. The quality of the binding energies obtained by the Lennard-Jones parameters we obtained is assessed on a set of methane clusters containing from 2 to 40 molecules. Our Lennard-Jones parameters, used in combination with the intramolecular parameters of the CHARMM force field, are found to closely reproduce the results of our dispersion-corrected density-functional calculations. The approach outlined can be used to develop Lennard-Jones parameters for any kind of molecular system. © Published 2013 by the American Chemical Society.Recurso electrónicoapplication/pdfenghttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/restrictedAccessAtribución-NoComercial 4.0 Internacionalhttp://purl.org/coar/access_right/c_16echttps://www.scopus.com/inward/record.uri?eid=2-s2.0-84882440261&doi=10.1021%2fct4003114&partnerID=40&md5=9c96c2dcf6e8e42cbc205c3cca744d1bDensity-functional theory with dispersion-correcting potentials for methane: Bridging the efficiency and accuracy gap between high-level wave function and classical molecular mechanics methodsinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArtículohttp://purl.org/coar/version/c_970fb48d4fbd8a85http://purl.org/coar/resource_type/c_2df8fbb1Torres E.Dilabio G.A.Patchkoskii, S., Tse, J.S., Yurchenko, S.N., Zhechkov, L., Heine, T., Seifert, G., Graphene nanostructures as tunable storage media for molecular hydrogen (2005) Proc. Natl. Acad. Sci. U.S.A, 102, pp. 10439-10444Patchkoskii, S., Tse, J.S., Thermodynamic stability of hydrogen clathrates (2003) Proc. Natl. Acad. Sci. U.S.A, 100, pp. 14645-14650Angell, C.A., Formation of Glasses from Liquids and Biopolymers (1995) Science, 267, pp. 1924-1935Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., Case, D.A., Development and testing of a general amber force field (2004) J. Comput. Chem., 25, pp. 1157-1174Jorgensen, W.L., Tirado-Rives, J., The OPLS Force Field for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin (1988) J. Am. Chem. Soc., 110, pp. 1657-1666Kaminski, G.A., Friesner, R.A., Tirado-Rives, J., Jorgensen, W.L., Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides (2001) J. Phys. Chem. B, 105, pp. 6474-6487Wu, X., Vargas, M.C., Nayak, S., Lotrich, V., Scoles, G., Towards extending the applicability of density functional theory to weakly bound systems (2001) J. Chem. Phys., 115, pp. 8748-8757Wu, Q., Yang, W., Empirical correction to density functional theory for van der Waals interactions (2002) J. Chem. Phys., 116, pp. 515-524Grimme, S., Accurate description of van der Waals complexes by density functional theory including empirical corrections (2004) J. Comput. Chem., 25, pp. 1463-1473Grimme, S., Semiempirical GGA-Type Density Functional Constructed with a Long-Range Dispersion Correction (2006) J. Comput. Chem., 27, pp. 1787-1799Grimme, S., Antony, J., Ehrlich, S., Krieg, H., A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu (2010) J. Chem. Phys., 132, p. 154104Johnson, E.R., Becke, A.D., A post-Hartree-Fock model of intermolecular interactions (2005) J. Chem. Phys., 123, p. 024101Becke, A.D., Arabi, A.A., Kannemann, F.O., Nonempirical density-functional theory for van der Waals interactions. Can (2010) J. Chem., 88, pp. 1057-1062Otero-De-La-Roza, A., Johnson, E.R., A benchmark for non-covalent interactions in solids (2012) J. Chem. Phys., 137, p. 054103Tkatchenko, A., Scheffler, M., Accurate Molecular Van der Waals Interactions from Ground-State Electron Density and Free-Atom Reference Data. Phys (2009) Rev. Lett., 102, p. 073005Marom, N., Tkatchenko, A., Rossi, M., Gobre, V.V., Hod, O., Scheffler, M., Kronik, L., Dispersion Interactions with Density-Functional Theory: Benchmarking Semiempirical and Interatomic Pairwise Corrected Density Functionals (2011) J. Chem. Theory Comput., 7, pp. 3944-3951Torres, E., Dilabio, G.A., A (Nearly) Universally Applicable Method for Modeling Noncovalent Interactions Using B3LYP (2012) J. Phys. Chem. Lett., 3, pp. 1738-1744Von Lilienfeld, O.A., Tavernelli, I., Rothlisberger, U., Optimization of Effective Atom Centered Potentials for London Dispersion Forces in Density Functional Theory (2004) Phys. Rev. Lett., 93, p. 153004Von Lilienfeld, O.A., Tavernelli, I., Rothlisberger, U., Performance of optimized atom-centered potentials for weakly bonded systems using density functional theory (2005) Phys. Rev. B, 71, p. 195119Lin, I.-C., Coutinho-Neto, M.D., Felsenheimer, C., Von Lilienfeld, O.A., Tavernelli, I., Rothlisberger, U., Library of dispersion-corrected atom-centered potentials for generalized gradient approximation functionals: Elements H, C, N, O, He, Ne, Ar, and Kr (2007) Phys. Rev. B, 75, p. 205131Zang, J., Nair, S., Sholl, D.S., (2013) J. Phys. Chem. A, , For example, Zang et al. use force-fields derived from density-functional theory methods corrected for dispersion using general (and older generation) pair-wise dispersion terms. SeeLi, A.H., Chao, S.D., Intermolecular potentials of the methane dimer calculated with Møller-Plesset perturbation theory and density functional theory (2006) J. Chem. Phys., 125, p. 094312Adamo, C., Barone, V., Toward reliable density functional methods without adjustable parameters: The PBE0 model (1999) J. Chem. Phys., 110, pp. 6158-6169Christiansen, P.A., Lee, Y.S., Pitzer, K.S., Improved ab initio effective core potentials for molecular calculations (1979) J. Chem. Phys., 71, p. 4445Johnson, E.R., Dilabio, G.A., Theoretical Study of Dispersion Binding of Hydrocarbon Molecules to Hydrogen-Terminated Silicon(100)-2 × 1 (2009) J. Phys. Chem. C, 113, pp. 5681-5689. , DCPs were also developed for the silicon atom. SeeMacKie, I.D., Dilabio, G.A., Approximations to complete basis set-extrapolated, highly correlated non-covalent interaction energies (2011) J. Chem. Phys., 135, p. 134318Tkatchenko, A., Von Lilienfeld, O.A., Popular Kohn-Sham density functionals strongly overestimate many-body interactions in van der Waals systems (2008) Phys. Rev. B., 78, p. 045116Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Montgomery, Jr.J.A., Pople, J.A., (2004), Gaussian 03, Revision D.01. Gaussian Inc. Pittsburgh, PAFrisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Fox, D.J., (2009), Gaussian 09, Revision C.01Gaussian, Inc. Wallingford, CTTakeuchi, H., The structural investigation on small methane clusters described by two different potentials (2012) Comput. Theor. Chem., 986, pp. 48-56Todorov, I.T., Smith, W., Trachenko, K., Dove, M.T., DL-POLY-3: New dimensions in molecular dynamics simulations via massive parallelism (2006) J. Mater. Chem., 16, pp. 1911-1918Al-Matar, A.K., Rockstraw, D.A., A generating equation for mixing rules and two new mixing rules for interatomic potential energy parameters (2004) J. Comput. Chem., 25, pp. 660-668Boys, S.F., Bernardi, F., The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors (1970) Mol. Phys., 19, pp. 553-566Chai, J.-D., Head-Gordon, M., Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections (2008) Phys. Chem. Chem. Phys., 10, pp. 6615-6620Zhao, Y., Truhlar, D.G., The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06-class functionals and 12 other functionals (2008) Theor. Chem. Acc., 120, pp. 215-241Dilabio, G.A., Accurate Treatment of van der Waals Interactions using Standard Density Functional Theory with Effective Core-Type Potentials: Application to Carbon-Containing Dimers (2008) Chem. Phys. Lett., 455, pp. 348-353MacKie, I.D., Dilabio, G.A., Interactions in Large, Polyaromatic Hydrocarbons Dimers: Application of Density Functional Theory with Dispersion Corrections (2008) J. Phys. Chem. A, 112, pp. 10968-10976MacKie, I.D., Dilabio, G.A., Accurate dispersion interactions from standard density-functional theory methods with small basis sets (2010) Phys. Chem. Chem. Phys., 12, pp. 6092-6098http://purl.org/coar/resource_type/c_6501THUMBNAILMiniProdInv.pngMiniProdInv.pngimage/png23941https://repositorio.utb.edu.co/bitstream/20.500.12585/9071/1/MiniProdInv.png0cb0f101a8d16897fb46fc914d3d7043MD5120.500.12585/9071oai:repositorio.utb.edu.co:20.500.12585/90712021-02-02 14:53:05.525Repositorio Institucional UTBrepositorioutb@utb.edu.co