Approximating Electrostatic Potential of Molecules with Point Charges Mimicking the Electron Pairs

Authors

  • T.Yu. Nikolaienko Taras Shevchenko National University of Kyiv
  • L.A. Bulavin Taras Shevchenko National University of Kyiv

DOI:

https://doi.org/10.15407/ujpe68.10.673

Keywords:

electrostatic interaction energy, electron charge density, molecular electrostatic potential, atomic charges

Abstract

The electrostatic component used in the traditional force fields significantly impacts their accuracy in modelling the noncovalent interactions peculiar to biomolecular systems, including hydrogen bonding. In this contribution, we present a physical model for approximating the electrostatic potential of a molecule (MEP) based on the first-principle decomposition of its charge density distribution into the localized components. In contrast to conventional schemes, which typically use atom-centered charges to approximate MEP, the proposed approach locates such charges in the positions selected so as to mimic the anisotropy of the electron density distributions related to the electron pairs of atoms or covalent bonds. This peculiarity leads to a more accurate representation of the overall electrostatic potential, as verified by applying the proposed model to approximate the electrostatic component of the intermolecular interaction energy in 145 noncovalently bound molecular complexes from GMTKN55 database. This benchmark showed the root-mean-square difference between the true and approximated values of the electrostatic component of 2.7 kcal/mol, which is 2.2 times lower as compared to the traditional RESP charges method used as a baseline.

References

J.A. Lemkul. Chapter one - pairwise-additive and polarizable atomistic force fields for molecular dynamics simulations of proteins. In: Progress in Molecular Biology and Translational Science, Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly. Edited by B. Strodel, B. Barz (Academic Press, 2020).

https://doi.org/10.1016/bs.pmbts.2019.12.009

L. Monticelli, D.P. Tieleman. Force fields for classical molecular dynamics. In: Biomolecular Simulations: Methods and Protocols, Methods in Molecular Biology. Edited by L. Monticelli, E. Salonen (Humana Press, 2013).

https://doi.org/10.1007/978-1-62703-017-5

T.Y. Nikolaienko. Interaction of anticancer drug doxorubicin with sodium oleate bilayer: Insights from molecular dynamics simulations. J. Mol. Liq. 235, 31 (2017).

https://doi.org/10.1016/j.molliq.2016.11.065

G.A. Cisneros, M. Karttunen, P. Ren, C. Sagui. Classical electrostatics for biomolecular simulations. Chem. Rev. 114 (1), 779 (2014).

https://doi.org/10.1021/cr300461d

G.M.A. Junqueira, M.Y. Ballester, M.A.C. Nascimento. Reactivity properties of the hoso and hso2 isomers in liquid medium: a sequential monte carlo/quantum mechanics study. J. Mol. Model. 29 (6), 189 (2023).

https://doi.org/10.1007/s00894-023-05514-7

M. Liu, S. Wang. Mcdock: A monte carlo simulation approach to the molecular docking problem. J. Comput. Aid. Mol. Des. 13 (5), 435 (1999).

K. Coutinho, H.C. Georg, T.L. Fonseca, V. Ludwig, S. Canuto. An efficient statistically converged average configuration for solvent effects. Chem. Phys. Lett. 437 (1), 148 (2007).

https://doi.org/10.1016/j.cplett.2007.02.012

A.A. Adeniyi, M.E. S. Soliman. Implementing qm in docking calculations: Is it a waste of computational time? Drug. Discov. Today 22 (8), 1216 (2017).

https://doi.org/10.1016/j.drudis.2017.06.012

A.I. Samtsevich, L.A. Bulavin, L.F. Sukhodub, T.Y. Nikolaienko. Interaction of dna nucleotide bases with anticancer drug thiotepa: Molecular docking and quantummechanical analysis. Ukr. Biochem. J. 86 (2), 50 (2014).

https://doi.org/10.15407/ubj86.02.050

G.M. Morris, M. Lim-Wilby. Molecular docking. In: Molecular Modeling of Proteins, Methods Molecular Biology. Edited by A. Kukol (Humana Press, 2008).

https://doi.org/10.1007/978-1-59745-177-2_19

M. Huix-Rotllant, N. Ferre. Analytic energy, gradient, and hessian of electrostatic embedding QM/MM based on electrostatic potential-fitted atomic charges scaling linearly with the MM subsystem size. J. Chem. Theory Comput. 17 (1), 538 (2021).

https://doi.org/10.1021/acs.jctc.0c01075

J.F. Gonthier, S.N. Steinmann, M.D. Wodrich, C. Corminboeuf. Quantification of "fuzzy" chemical concepts: A computational perspective. Chem. Soc. Rev. 41 (13), 4671 (2012).

https://doi.org/10.1039/c2cs35037h

S. Riniker. Fixed-charge atomistic force fields for molecular dynamics simulations in the condensed phase: An overview. J. Chem. Inf. Model. 58 (3), 565 (2018).

https://doi.org/10.1021/acs.jcim.8b00042

C. Oostenbrink, A. Villa, A.E. Mark, W.F. Van Gunsteren. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 25 (13), 1656 (2004).

https://doi.org/10.1002/jcc.20090

G. Cavallo, P. Metrangolo, R. Milani, T. Pilati, A. Priimagi, G. Resnati, G. Terraneo. The halogen bond. Chem. Rev. 116 (4), 2478 (2016).

https://doi.org/10.1021/acs.chemrev.5b00484

M.R. Scholfield, C.M.V. Zanden, M. Carter, P.S. Ho. Halogen bonding (X-bonding): A biological perspective. Protein Sci. 22 (2), 139 (2013).

https://doi.org/10.1002/pro.2201

P. Politzer, J.S. Murray, M.C. Concha. σ-hole bonding between like atoms; a fallacy of atomic charges. J. Mol. Model. 14 (8), 659 (2008).

https://doi.org/10.1007/s00894-008-0280-5

T.Y. Nikolaienko, L.A. Bulavin. Localized orbitals for optimal decomposition of molecular properties. Int. J. Quantum Chem. 119 (3), e25798 (2019).

https://doi.org/10.1002/qua.25798

T.Y. Nikolaienko. The maximum occupancy condition for the localized property-optimized orbitals. Phys. Chem. Chem. Phys. 21 (9), 5285 (2019).

https://doi.org/10.1039/C8CP07276K

E.R. Davidson. Reduced Density Matrices in Quantum Chemistry (Academic Press, 1976) [ISBN: 9780122058509].

A.J. Thakkar, A.C. Tanner, V.H. Smith. Inter-relationships between various representations of one-matrices and related densities: A road map and an example. In: Density Matrices and Density Functionals. Edited by R. Erdahl, V.H. Smith (Springer Netherlands, 1987).

https://doi.org/10.1007/978-94-009-3855-7_17

I. Mayer. Bond Orders and Energy Components: Extracting Chemical Information from Molecular Wave Functions (CRC Press, Taylor & Francis, 2017) [ISBN: 9781420090116].

L.D. Landau, E.M. Lifshitz. The Classical Theory of Fields (Pergamon Press, 1975) [ISBN: 9780080181769].

E.R. Davidson, A.E. Clark. A viewpoint on population analyses. Int. J. Quantum Chem. 122 (8) (2022).

https://doi.org/10.1002/qua.26860

J.S. Murray, P. Politzer. The electrostatic potential: An overview. WIRES Comput. Mol. Sci. 1 (2), 153 (2011).

https://doi.org/10.1002/wcms.19

A. Alenaizan, L.A. Burns, C.D. Sherrill. Python implementation of the restrained electrostatic potential charge model. Int. J. Quantum Chem. 120 (2), e26035 (2020).

https://doi.org/10.1002/qua.26035

T. Nikolaienko, L. Bulavin, D. Hovorun. Effective atomic charges of canonical 2-deoxyribonucleotides and their conformational dependences. Uk.r J. Phys. 57 (10), 1024.

T.Y. Nikolaienko, L.A. Bulavin, D.M. Hovorun. Can we treat ab initio atomic charges and bond orders as conformation-independent electronic structure descriptors? RSC Adv. 6 (78), 74785 (2016).

https://doi.org/10.1039/C6RA17055B

L. Goerigk, A. Hansen, C. Bauer, S. Ehrlich, A. Najibi, S. Grimme. A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions. Phys. Chem. Chem. Phys. 19 (48), 32184 (2017).

https://doi.org/10.1039/C7CP04913G

R.M. Parrish, L.A. Burns, D.G.A. Smith, A.C. Simmonett, A.E. DePrince, E.G. Hohenstein, U. Bozkaya, A.Y. Sokolov, R. Di Remigio, R.M. Richard, J.F. Gonthier, A.M. James, H.R. McAlexander, A. Kumar, M. Saitow, et al. Psi4 1.1: An open-source electronic structure program emphasizing automation, advanced libraries, and interoperability. J. Chem. Theory Comput. 13 (7), 3185 (2017).

https://doi.org/10.1021/acs.jctc.7b00174

T. Lu, F. Chen. Multiwfn: A multifunctional wavefunction analyzer. J. Comput. Chem. 33 (5), 580 (2012).

https://doi.org/10.1002/jcc.22885

Downloads

Published

2023-11-29

How to Cite

Nikolaienko, T., & Bulavin, L. (2023). Approximating Electrostatic Potential of Molecules with Point Charges Mimicking the Electron Pairs. Ukrainian Journal of Physics, 68(10), 673. https://doi.org/10.15407/ujpe68.10.673

Issue

Section

Physics of liquids and liquid systems, biophysics and medical physics

Most read articles by the same author(s)

1 2 3 4 5 > >>