Publicación:
Towards a density functional theory of molecular fragments. What is the shape of atoms in molecules?

dc.contributor.authorChávez, Victor H.
dc.contributor.authorWasserman, Adam
dc.contributor.corporatenameAcademia Colombiana de Ciencias Exactas, Físicas y Naturalesspa
dc.date.accessioned2021-12-10T08:19:36Z
dc.date.available2021-12-10T08:19:36Z
dc.date.issued2020-03-25
dc.description.abstractEn cierta forma, la mecánica cuántica da solución a todos los problemas de la química, lo único que hay que hacer es resolver las ecuaciones de Schrödinger para las moléculas de interés. Desafortunadamente, el costo computacional de resolver estas ecuaciones crece exponencialmente con el número de electrones y para más de ~100 electrones resulta imposible resolverlas con precisión química (~2 kcal/mol). Las ecuaciones de Kohn-Sham (KS) de la teoría del funcional de la densidad (density functional theory, DFT) permiten reformular las ecuaciones de Schrödinger usando la densidad de probabilidad electrónica como la variable central sin necesidad de calcular las funciones de onda de Schrödinger. El costo de resolver las ecuaciones de Kohn-Sham solo crece como N3, donde N es el número de electrones, lo que ha llevado a la inmensa popularidad de la DFT en química. A pesar de esta popularidad, incluso las aproximaciones más sofisticadas de las KS-DFT llevan a errores que limitan el uso de métodos basados exclusivamente en la densidad electrónica. En este artículo se discute cómo pueden desarrollarse nuevos métodos que escalen linealmente con N usando densidades de fragmentos como las variables principales en lugar de densidades totales, así como la forma en que estos métodos proveen una respuesta atractiva a la pregunta del subtítulo: ¿cuál es la forma de los átomos en las moléculas?.spa
dc.description.abstractIn some sense, quantum mechanics solves all the problems in chemistry: The only thing one has to do is solve the Schrödinger equation for the molecules of interest. Unfortunately, the computational cost of solving this equation grows exponentially with the number of electrons and for more than ~100 electrons, it is impossible to solve it with chemical accuracy (~ 2 kcal/mol). The Kohn-Sham (KS) equations of density functional theory (DFT) allow us to reformulate the Schrödinger equation using the electronic probability density as the central variable without having to calculate the Schrödinger wave functions. The cost of solving the Kohn-Sham equations grows only as N3, where N is the number of electrons, which has led to the immense popularity of DFT in chemistry. Despite this popularity, even the most sophisticated approximations in KS-DFT result in errors that limit the use of methods based exclusively on the electronic density. By using fragment densities (as opposed to total densities) as the main variables, we discuss here how new methods can be developed that scale linearly with N while providing an appealing answer to the subtitle of the article: What is the shape of atoms in molecules?.eng
dc.format.mimetypeapplication/pdfspa
dc.identifier.doihttps://doi.org/10.18257/raccefyn.960
dc.identifier.urihttps://repositorio.accefyn.org.co/handle/001/1197
dc.language.isospaspa
dc.publisherAcademia Colombiana de Ciencias Exactas, Físicas y Naturalesspa
dc.publisher.placeBogotá, Colombiaspa
dc.relation.citationendpage279spa
dc.relation.citationissue170spa
dc.relation.citationstartpage269spa
dc.relation.citationvolume44spa
dc.relation.ispartofjournalRevista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturalesspa
dc.rightsCreative Commons Attribution-NonCommercial-ShareAlike 4.0 Internationalspa
dc.rights.accessrightsinfo:eu-repo/semantics/openAccessspa
dc.rights.coarhttp://purl.org/coar/access_right/c_abf2spa
dc.rights.licenseAtribución-NoComercial 4.0 Internacional (CC BY-NC 4.0)spa
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/spa
dc.sourceRevista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturalesspa
dc.subject.proposalFuncionales de la densidadspa
dc.subject.proposalDensity functionalseng
dc.subject.proposalEstructura electrónicaspa
dc.subject.proposalElectronic structureeng
dc.subject.proposalReactividad químicaspa
dc.subject.proposalChemical reactivityeng
dc.titleTowards a density functional theory of molecular fragments. What is the shape of atoms in molecules?spa
dc.typeArtículo de revistaspa
dc.type.coarhttp://purl.org/coar/resource_type/c_6501spa
dc.type.coarversionhttp://purl.org/coar/version/c_970fb48d4fbd8a85spa
dc.type.contentDataPaperspa
dc.type.driverinfo:eu-repo/semantics/articlespa
dc.type.redcolhttp://purl.org/redcol/resource_type/ARTREVspa
dc.type.versioninfo:eu-repo/semantics/publishedVersionspa
dcterms.audienceEstudiantes, Profesores, Comunidad científica colombianaspa
dcterms.referencesBader, R. F. W. (1990). International Series of Monographs on Chemistry. Atoms in Molecules, A Quantum Theory, 22.spa
dcterms.referencesChen, M., Jiang, X. W., Zhuang, H. L., Wang, L. W., Carter, E. A. (2016). Peta-scale orbital-free density functional theory enabled by small-box algorithms. J. Chem. Theory Comput. 12: 2950-2963.spa
dcterms.referencesCohen, A. J., Mori-Sánchez, P., Yang, W. (2008a). Fractional spins and static correlation error in density functional theory. J. Chem. Phys. 129: 121104.spa
dcterms.referencesCohen, A. J., Mori-Sánchez, P., Yang, W. (2008b). Insights into current limitations of density functional theory. Science. 321: 792-794.spa
dcterms.referencesCohen, M. H. & Wasserman, A. (2006). On Hardness and Electronegativity Equalization in Chemical Reactivity Theory. J. Stat. Phys. 125: 1121-1139spa
dcterms.referencesDutoi, A. D. & Head-Gordon, M. (2006). Self-interaction error of local density functionals for alkali–halide dissociation. Chem. Phys. Lett. 422 (1-3): 230-233.spa
dcterms.referencesElliott, P., Burke, K., Cohen, M. H., Wasserman, A. (2010). Partition density-functional theory. Phys. Rev. A. 82: 024501spa
dcterms.referencesFermi, E. (1927). Statistical method to determine some properties of atoms. Rend. Accad. Naz. Lincei. 6: 5.spa
dcterms.referencesGeerlings, P., De Proft, F., Langenaeker, W. (2003). Conceptual density functional theory. Chem. Rev. 103 (5): 1793-1874spa
dcterms.referencesGeerlings, P., Fias, S., Boisdenghien, Z., De Proft, F. (2014). Conceptual DFT: Chemistry from the linear response function. Chem. Soc. Rev. 43 (14): 4989-5008spa
dcterms.referencesGómez, S., Nafziger, J., Restrepo, A., Wasserman, A. (2017). Partition-DFT on the water dimer. J. Chem. Phys. 146 (7): 074106.spa
dcterms.referencesGómez, S., Oueis, Y., Restrepo, A., Wasserman, A. (2019). Partition potential for hydrogen bonding in formic acid dimers. Int. J. Quantum Chem. 119 (4): e25814spa
dcterms.referencesGordon, M. S., Fedorov, D. G., Pruitt, S. R., Slipchenko, L. V. (2012). Fragmentation Methods: A Route to Accurate Calculations on Large Systems. Chem. Rev. 112: 632-672spa
dcterms.referencesHegde, G. & Bowen, R. C. (2017). Machine-learned approximations to density functional theory hamiltonians. Sci. Rep. 7: 42669spa
dcterms.referencesHohenberg, P. & Kohn, W. (1964). Inhomogeneous electron gas. Phys. Rev. 136: B864-B871spa
dcterms.referencesJacob, C. R. & Neugebauer, J. (2014). Subsystem density-functional theory. Wiley Interdisciplinary Reviews-Computational Molecular Science. 4: 325-362spa
dcterms.referencesJiang, K., Nafziger, J., Wasserman, A. (2018). Constructing a non-additive noninteracting kinetic energy functional approximation for covalent bonds from exact conditions. The Journal of chemical physics. 149: 164112spa
dcterms.referencesKohn, W. & Sham, L. J. (1965). Self-consistent equations including exchange and correlation effects. Phys. Rev. 140: A1133spa
dcterms.referencesKomsa, D. N. & Staroverov, V. N. (2016). Elimination of spurious fractional charges in dissociating molecules by correcting the shape of approximate Kohn–Sham potentials. J. Chem. Theory Comput. 12 (11): 5361-5366.spa
dcterms.referencesKummel, S. & Kronik, L. (2008). Orbital-dependent density functionals: Theory and applications. Rev. Mod. Phys. 80: 3-60spa
dcterms.referencesLee, S. J., Welborn, M., Manby, F. R., Miller III, T. F. (2019). Projection-based wave function-in- DFT embedding. Accounts of Chemical Research. 52: 1359-1368spa
dcterms.referencesMakmal, A., Kuemmel, S., Kronik, L. (2011). Dissociation of diatomic molecules and the exactexchange Kohn-Sham potential: The case of LiF. Phys. Rev. A. 83 (6): 062512spa
dcterms.referencesMardirossian, N. & Head-Gordon, M. (2017). Thirty years of density functional theory in computational chemistry: An overview and extensive assessment of 200 density functionals. Mol. Phys. 115: 2315-2372spa
dcterms.referencesMi, W. & Pavanello, M. (2019). Nonlocal Subsystem Density Functional Theory. J. Phys. Chem. Lett. 11 (1): 272-279.spa
dcterms.referencesMori-Sánchez, P., Cohen, A. J., Yang, W. (2008). Localization and delocalization errors in density functional theory and implications for band-gap prediction. Phys. Rev. Lett. 100: 146401spa
dcterms.referencesNafziger, J. (2015). Partition density functional theory. Ph.D thesis, Purdue Universityspa
dcterms.referencesNafziger, J. & Wasserman, A. (2014). Density-Based Partitioning Methods for Ground-State Molecular Calculations. J. Phys. Chem. A. 118: 7623-7639.spa
dcterms.referencesNafziger, J. & Wasserman, A. (2015). Fragment-based treatment of delocalization and static correlation errors in density-functional theory. J. Chem. Phys. 143: 234105spa
dcterms.referencesNalewajski, R. F. & Parr, R. G. (2000). Information theory, atoms in molecules, and molecular similarity. Proc. Natl. Acad. Sci. U.S.A. 97 (16): 8879-8882spa
dcterms.referencesNiffenegger, K., Oueis, Y., Nafziger, J., Wasserman, A. (2019). Density embedding with constrained chemical potential. Mol. Phys. 117 (15-16): 2188-2194spa
dcterms.referencesParr, R. G., Donnelly, R. A., Levy, M., Palke, W. E. (1978). Electronegativity - density functional viewpoint. J. Chem. Phys. 68: 3801-3807spa
dcterms.referencesParr, R. G. & Yang, W. T. (1984). Density functional-approach to the frontier-electron theory of chemical-reactivity. J. Am. Chem. Soc. 106: 4049-4050spa
dcterms.referencesParrish, R. M., Burns, L. A., Smith, D. G. A., Simmonett, A. C., DePrince III, A. E., Hohenstein, E. G., Bozkaya U., Sokilov A. Y., Di Remigio R., Richard R. M., Gonthier J. F., James A. M., McAlexander H. R., Kumar A., Saitow M., Wang X., Pritchard B. P., Verma P., Shaefer H. F., Patkowski K., King R. A., Valeev E. F., Evangelista F. A., Turney J. M., Crawford T. D., Sherrill C. D. (2017). Psi4 1.1: An open-source electronic structure program emphasizing automation, advanced libraries, and interoperability. J. Chem. Theory Comput. 13 (7): 3185-3197.spa
dcterms.referencesPerdew, J. P., Parr, R. G., Levy, M., Balduz Jr, J. L. (1982). Density-functional theory for fractional particle number: Derivative discontinuities of the energy. Phys. Rev. Lett. 49: 1691-1694spa
dcterms.referencesPerdew, J. P. & Schmidt, K. (2001). Jacob’s ladder of density functional approximations for the exchange-correlation energy. AIP Conf. Proc. 577: 1-20.spa
dcterms.referencesPribram-Jones, A., Gross, D. A., Burke, K. (2015). DFT: A Theory Full of Holes? Annu. Rev. Phys. Chem. 66: 283-304spa
dcterms.referencesSeidl, A., Gorling, A., Vogl, P., Majewski, J. A., Levy, M. (1996). Generalized Kohn-Sham schemes and the band-gap problem. Phys. Rev. B. 53: 3764-3774spa
dcterms.referencesSeino, J., Kageyama, R., Fujinami, M., Ikabata, Y., Nakai, H. (2018). Semi-local machinelearned kinetic energy density functional with third-order gradients of electron density. J. Chem. Phys. 148: 241705spa
dcterms.referencesSmith, D.G., Burns, L.A., Sirianni, D.A., Nascimento, D.R., Kumar, A., James, A.M., Schriber, J.B., Zhang, T., Zhang, B., Abbott, A.S., Berquist, E.J. (2018). Psi4numpy: An interactive quantum chemistry programming environment for reference implementations and rapid development. Journal of chemical theory and computation. 14: 3504-3511.spa
dcterms.referencesSnyder, J. C., Rupp, M., Hansen, K., Muller, K. R., Burke, K. (2012). Finding density functionals with machine learning. Phys. Rev. Lett. 108: 253002spa
dcterms.referencesSun, J., Ruzsinszky, A., Perdew, J. P. (2015). Strongly constrained and appropriately normed semilocal density functional. Phys. Rev. Lett. 115: 036402spa
dcterms.referencesSun, Q. N. & Chan, G. K. L. (2016). Quantum embedding theories. Acc. Chem. Res. 49: 2705-2712spa
dcterms.referencesThomas, L. H. (1927). The calculation of atomic fields. P. Camb. Philos. Soc. 23: 542-548.spa
dcterms.referencesChávez V.H., Shi Y., Oueis Y., Wasserman. A. (2020). Basis set implementation of partition density functional theory. In progressspa
dcterms.referencesWasserman, A., Nafziger, J., Jiang, K. L., Kim, M. C., Sim, E., Burke, K. (2017). The importance of being inconsistent. Annu. Rev. Phys. Chem. 68: 555-581spa
dcterms.referencesWeizsäcker, C. F. von. (1935). Zur theorie der kernmassen. Zeitschrift fur Physik A Hadrons and Nuclei. 96: 431-458spa
dcterms.referencesYang, W., Cohen, A. J., Mori-Sánchez, P. (2012). Derivative discontinuity, bandgap and lowest unoccupied molecular orbital in density functional theory. J. Chem. Phys. 136: 204111spa
dcterms.referencesYao, Y., Shushkov, P., Miller, T. F., Giapis, K. P. (2019). Direct dioxygen evolution in collisions of carbon dioxide with surfaces. Nat. Commun. 10 (1): 2294spa
dcterms.referencesYu, H. Y. S., Li, S. H. L., Truhlar, D. G. (2016). Perspective: Kohn-sham density functional theory descending a staircase. J. Chem. Phys. 145: 130901spa
dcterms.referencesZhang, Y., Kitchaev, D.A., Yang, J., Chen, T., Dacek, S.T., Sarmiento-Pérez, R.A., Márques, M.A., Peng, H., Ceder, G., Perdew, J.P., Sun, J. (2018). Efficient first-principles prediction of solid stability: Towards chemical accuracy. NPJ Comput. Mater. 4: 9.spa
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