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dc.creatorTorres E.
dc.creatorDilabio G.A.
dc.date.accessioned2020-03-26T16:32:53Z
dc.date.available2020-03-26T16:32:53Z
dc.date.issued2013
dc.identifier.citationJournal of Chemical Theory and Computation; Vol. 9, Núm. 8; pp. 3342-3349
dc.identifier.issn15499618
dc.identifier.urihttps://hdl.handle.net/20.500.12585/9071
dc.description.abstractLarge 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.eng
dc.format.mediumRecurso electrónico
dc.format.mimetypeapplication/pdf
dc.language.isoeng
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.sourcehttps://www.scopus.com/inward/record.uri?eid=2-s2.0-84882440261&doi=10.1021%2fct4003114&partnerID=40&md5=9c96c2dcf6e8e42cbc205c3cca744d1b
dc.titleDensity-functional theory with dispersion-correcting potentials for methane: Bridging the efficiency and accuracy gap between high-level wave function and classical molecular mechanics methods
dcterms.bibliographicCitationPatchkoskii, 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. 10439-10444
dcterms.bibliographicCitationPatchkoskii, S., Tse, J.S., Thermodynamic stability of hydrogen clathrates (2003) Proc. Natl. Acad. Sci. U.S.A, 100, pp. 14645-14650
dcterms.bibliographicCitationAngell, C.A., Formation of Glasses from Liquids and Biopolymers (1995) Science, 267, pp. 1924-1935
dcterms.bibliographicCitationWang, 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. 1157-1174
dcterms.bibliographicCitationJorgensen, 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. 1657-1666
dcterms.bibliographicCitationKaminski, 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. 6474-6487
dcterms.bibliographicCitationWu, 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. 8748-8757
dcterms.bibliographicCitationWu, Q., Yang, W., Empirical correction to density functional theory for van der Waals interactions (2002) J. Chem. Phys., 116, pp. 515-524
dcterms.bibliographicCitationGrimme, S., Accurate description of van der Waals complexes by density functional theory including empirical corrections (2004) J. Comput. Chem., 25, pp. 1463-1473
dcterms.bibliographicCitationGrimme, S., Semiempirical GGA-Type Density Functional Constructed with a Long-Range Dispersion Correction (2006) J. Comput. Chem., 27, pp. 1787-1799
dcterms.bibliographicCitationGrimme, 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. 154104
dcterms.bibliographicCitationJohnson, E.R., Becke, A.D., A post-Hartree-Fock model of intermolecular interactions (2005) J. Chem. Phys., 123, p. 024101
dcterms.bibliographicCitationBecke, A.D., Arabi, A.A., Kannemann, F.O., Nonempirical density-functional theory for van der Waals interactions. Can (2010) J. Chem., 88, pp. 1057-1062
dcterms.bibliographicCitationOtero-De-La-Roza, A., Johnson, E.R., A benchmark for non-covalent interactions in solids (2012) J. Chem. Phys., 137, p. 054103
dcterms.bibliographicCitationTkatchenko, 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. 073005
dcterms.bibliographicCitationMarom, 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. 3944-3951
dcterms.bibliographicCitationTorres, E., Dilabio, G.A., A (Nearly) Universally Applicable Method for Modeling Noncovalent Interactions Using B3LYP (2012) J. Phys. Chem. Lett., 3, pp. 1738-1744
dcterms.bibliographicCitationVon 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. 153004
dcterms.bibliographicCitationVon 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. 195119
dcterms.bibliographicCitationLin, 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. 205131
dcterms.bibliographicCitationZang, 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. See
dcterms.bibliographicCitationLi, 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. 094312
dcterms.bibliographicCitationAdamo, C., Barone, V., Toward reliable density functional methods without adjustable parameters: The PBE0 model (1999) J. Chem. Phys., 110, pp. 6158-6169
dcterms.bibliographicCitationChristiansen, P.A., Lee, Y.S., Pitzer, K.S., Improved ab initio effective core potentials for molecular calculations (1979) J. Chem. Phys., 71, p. 4445
dcterms.bibliographicCitationJohnson, 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. See
dcterms.bibliographicCitationMacKie, I.D., Dilabio, G.A., Approximations to complete basis set-extrapolated, highly correlated non-covalent interaction energies (2011) J. Chem. Phys., 135, p. 134318
dcterms.bibliographicCitationTkatchenko, 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. 045116
dcterms.bibliographicCitationFrisch, 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, PA
dcterms.bibliographicCitationFrisch, 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.01
dcterms.bibliographicCitationGaussian, Inc. Wallingford, CT
dcterms.bibliographicCitationTakeuchi, H., The structural investigation on small methane clusters described by two different potentials (2012) Comput. Theor. Chem., 986, pp. 48-56
dcterms.bibliographicCitationTodorov, 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. 1911-1918
dcterms.bibliographicCitationAl-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. 660-668
dcterms.bibliographicCitationBoys, 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. 553-566
dcterms.bibliographicCitationChai, J.-D., Head-Gordon, M., Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections (2008) Phys. Chem. Chem. Phys., 10, pp. 6615-6620
dcterms.bibliographicCitationZhao, 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. 215-241
dcterms.bibliographicCitationDilabio, 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. 348-353
dcterms.bibliographicCitationMacKie, 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. 10968-10976
dcterms.bibliographicCitationMacKie, 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. 6092-6098
datacite.rightshttp://purl.org/coar/access_right/c_16ec
oaire.resourceTypehttp://purl.org/coar/resource_type/c_6501
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.driverinfo:eu-repo/semantics/article
dc.type.hasversioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doi10.1021/ct4003114
dc.rights.accessrightsinfo:eu-repo/semantics/restrictedAccess
dc.rights.ccAtribución-NoComercial 4.0 Internacional
dc.identifier.instnameUniversidad Tecnológica de Bolívar
dc.identifier.reponameRepositorio UTB
dc.type.spaArtículo
dc.identifier.orcid35094573000
dc.identifier.orcid7003322749


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