Towards a density functional theory of molecular fragments. What is the shape of atoms in molecules?
Portada 44 (170) 2020
PDF

How to Cite

Chávez, V. H., & Wasserman, A. (2020). Towards a density functional theory of molecular fragments. What is the shape of atoms in molecules?. Revista De La Academia Colombiana De Ciencias Exactas, Físicas Y Naturales, 44(170), 269–279. https://doi.org/10.18257/raccefyn.960

Downloads

Download data is not yet available.

Métricas Alternativas


Dimensions

Abstract

In 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?

https://doi.org/10.18257/raccefyn.960

Keywords

Density Functional Theory; Chemical Reactivity
PDF

References

Bader, R. F. W. (1990). International Series of Monographs on Chemistry. Atoms in Molecules, A Quantum Theory, 22.

Chen, 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.

Cohen, A. J., Mori-Sánchez, P., Yang, W. (2008a). Fractional spins and static correlation error in density functional theory. J. Chem. Phys. 129: 121104.

Cohen, A. J., Mori-Sánchez, P., Yang, W. (2008b). Insights into current limitations of density functional theory. Science. 321: 792-794.

Cohen, M. H. & Wasserman, A. (2006). On Hardness and Electronegativity Equalization in Chemical Reactivity Theory. J. Stat. Phys. 125: 1121-1139.

Dutoi, 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.

Elliott, P., Burke, K., Cohen, M. H., Wasserman, A. (2010). Partition density-functional theory. Phys. Rev. A. 82: 024501.

Fermi, E. (1927). Statistical method to determine some properties of atoms. Rend. Accad. Naz. Lincei. 6: 5.

Geerlings, P., De Proft, F., Langenaeker, W. (2003). Conceptual density functional theory. Chem. Rev. 103 (5): 1793-1874.

Geerlings, P., Fias, S., Boisdenghien, Z., De Proft, F. (2014). Conceptual DFT: Chemistry from the linear response function. Chem. Soc. Rev. 43 (14): 4989-5008.

Gómez, S., Nafziger, J., Restrepo, A., Wasserman, A. (2017). Partition-DFT on the water dimer. J. Chem. Phys. 146 (7): 074106.

Gómez, S., Oueis, Y., Restrepo, A., Wasserman, A. (2019). Partition potential for hydrogen bonding in formic acid dimers. Int. J. Quantum Chem. 119 (4): e25814.

Gordon, 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: 632-672.

Hegde, G. & Bowen, R. C. (2017). Machine-learned approximations to density functional theory hamiltonians. Sci. Rep. 7: 42669.

Hohenberg, P. & Kohn, W. (1964). Inhomogeneous electron gas. Phys. Rev. 136: B864-B871.

Jacob, C. R. & Neugebauer, J. (2014). Subsystem density-functional theory. Wiley Interdisciplinary Reviews-Computational Molecular Science. 4: 325-362.

Jiang, 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: 164112.

Kohn, W. & Sham, L. J. (1965). Self-consistent equations including exchange and correlation effects. Phys. Rev. 140: A1133.

Komsa, 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.

Kummel, S. & Kronik, L. (2008). Orbital-dependent density functionals: Theory and applications. Rev. Mod. Phys. 80: 3-60.

Lee, S. J., Welborn, M., Manby, F. R., Miller III, T. F. (2019). Projection-based wave function-in-DFT embedding. Accounts of Chemical Research. 52: 1359-1368.

Makmal, 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): 062512.

Mardirossian, 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: 2315-2372.

Mi, W. & Pavanello, M. (2019). Nonlocal Subsystem Density Functional Theory. J. Phys. Chem. Lett. 11 (1): 272-279.

Mori-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: 146401.

Nafziger, J. (2015). Partition density functional theory. Ph.D thesis, Purdue University.

Nafziger, J. & Wasserman, A. (2014). Density-Based Partitioning Methods for Ground-State Molecular Calculations. J. Phys. Chem. A. 118: 7623-7639.

Nafziger, J. & Wasserman, A. (2015). Fragment-based treatment of delocalization and static correlation errors in density-functional theory. J. Chem. Phys. 143: 234105.

Nalewajski, R. F. & Parr, R. G. (2000). Information theory, atoms in molecules, and molecular similarity. Proc. Natl. Acad. Sci. U.S.A. 97 (16): 8879-8882.

Niffenegger, K., Oueis, Y., Nafziger, J., Wasserman, A. (2019). Density embedding with constrained chemical potential. Mol. Phys. 117 (15-16): 2188-2194.

Parr, R. G., Donnelly, R. A., Levy, M., Palke, W. E. (1978). Electronegativity - density functional viewpoint. J. Chem. Phys. 68: 3801-3807.

Parr, R. G. & Yang, W. T. (1984). Density functional-approach to the frontier-electron theory of chemical-reactivity. J. Am. Chem. Soc. 106: 4049-4050.

Parrish, 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.

Perdew, 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: 1691-1694.

Perdew, J. P. & Schmidt, K. (2001). Jacob’s ladder of density functional approximations for the exchange-correlation energy. AIP Conf. Proc. 577: 1-20.

Pribram-Jones, A., Gross, D. A., Burke, K. (2015). DFT: A Theory Full of Holes? Annu. Rev. Phys. Chem. 66: 283-304.

Seidl, A., Gorling, A., Vogl, P., Majewski, J. A., Levy, M. (1996). Generalized Kohn-Sham schemes and the band-gap problem. Phys. Rev. B. 53: 3764-3774.

Seino, 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: 241705.

Smith, 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.

Snyder, J. C., Rupp, M., Hansen, K., Muller, K. R., Burke, K. (2012). Finding density functionals with machine learning. Phys. Rev. Lett. 108: 253002.

Sun, J., Ruzsinszky, A., Perdew, J. P. (2015). Strongly constrained and appropriately normed semilocal density functional. Phys. Rev. Lett. 115: 036402.

Sun, Q. N. & Chan, G. K. L. (2016). Quantum embedding theories. Acc. Chem. Res. 49: 2705-2712.

Thomas, L. H. (1927). The calculation of atomic fields. P. Camb. Philos. Soc. 23: 542-548.

Chávez V.H., Shi Y., Oueis Y., Wasserman. A. (2020). Basis set implementation of partition density functional theory. In progress.

Wasserman, A., Nafziger, J., Jiang, K. L., Kim, M. C., Sim, E., Burke, K. (2017). The importance of being inconsistent. Annu. Rev. Phys. Chem. 68: 555-581.

Weizsäcker, C. F. von. (1935). Zur theorie der kernmassen. Zeitschrift fur Physik A Hadrons and Nuclei. 96: 431-458.

Yang, W., Cohen, A. J., Mori-Sánchez, P. (2012). Derivative discontinuity, bandgap and lowest unoccupied molecular orbital in density functional theory. J. Chem. Phys. 136: 204111.

Yao, Y., Shushkov, P., Miller, T. F., Giapis, K. P. (2019). Direct dioxygen evolution in collisions of carbon dioxide with surfaces. Nat. Commun. 10 (1): 2294.

Yu, H. Y. S., Li, S. H. L., Truhlar, D. G. (2016). Perspective: Kohn-sham density functional theory descending a staircase. J. Chem. Phys. 145: 130901.

Zhang, 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.

Declaration of originality and transfer author's rights

The authors declare:

  1. The published data and reference materials have been duly identified with their respective credits and have been included in the bibliographic notes and citations that have been so identified and that should it be required, I have all releases and permissions from any copyrighted material. 
  2. All material presented is free from any copyright and that I accept full legal responsibility for any legal claims relating to copyrighted intellectual property, fully exonerating from responsibility the Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales.
  3. This work is unpublished and will not be sent to any other journal while waiting for the editorial decision of this journal. I declare that there is no conflict of interest in this manuscript.
  4. In case of publication of this article, all author´s rights are transferred to the Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales, and so cannot be reproduced in any form without the express permission of it.
  5. By means of this document, if the article is accepted for publication by the Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales, the Revista assumes the right to edit and publish the articles in national and international indices or data bases for academic and scientific use in paper, electronic, CD-ROM, internet form either of the complete text or any other known form known or to be known and non-commercial, respecting the rights of the authors.

Transfer of author rights

In case the article is approved for publication, the main author in representation of himself and his co-authors or the main author and his co-authors must cede the author rights of the corresponding article to the Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales, except in the following cases:

The authors and co-authors will retain the right to revise, adapt, prepare derived works, oral presentations, and distribution to some colleagues of reprints of their own published work, if the corresponding credit is given to the Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales. It is also permissible to publish the title of the work, summary, tables, and figures of the work in the corresponding web sites of the authors or their employers, also giving credit to the Revista.

If the work has been realized under contract, the author’s employer has the right to revise, adapt, prepare derivative works, reproduce, or distribute in hard copy the published work, in a secure manner and for the exclusive use of his employees.

If the Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales were approached for permission by a third party for using, printing, or publishing specifically articles already published, the Revista must obtain the express permission of the author and co-authors of the work or of the employer except for use in classrooms, libraries, or reprinted in a collective work. The Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales reserves the possible use in its front cover of figures submitted with the manuscripts.

No other right, other than the author’s right, can be claimed by the Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales.