Approximating Electrostatic Potential of Molecules with Point Charges Mimicking the Electron Pairs
DOI:
https://doi.org/10.15407/ujpe68.10.673Keywords:
electrostatic interaction energy, electron charge density, molecular electrostatic potential, atomic chargesAbstract
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).
Downloads
Published
How to Cite
Issue
Section
License
Copyright Agreement
License to Publish the Paper
Kyiv, Ukraine
The corresponding author and the co-authors (hereon referred to as the Author(s)) of the paper being submitted to the Ukrainian Journal of Physics (hereon referred to as the Paper) from one side and the Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine, represented by its Director (hereon referred to as the Publisher) from the other side have come to the following Agreement:
1. Subject of the Agreement.
The Author(s) grant(s) the Publisher the free non-exclusive right to use the Paper (of scientific, technical, or any other content) according to the terms and conditions defined by this Agreement.
2. The ways of using the Paper.
2.1. The Author(s) grant(s) the Publisher the right to use the Paper as follows.
2.1.1. To publish the Paper in the Ukrainian Journal of Physics (hereon referred to as the Journal) in original language and translated into English (the copy of the Paper approved by the Author(s) and the Publisher and accepted for publication is a constitutive part of this License Agreement).
2.1.2. To edit, adapt, and correct the Paper by approval of the Author(s).
2.1.3. To translate the Paper in the case when the Paper is written in a language different from that adopted in the Journal.
2.2. If the Author(s) has(ve) an intent to use the Paper in any other way, e.g., to publish the translated version of the Paper (except for the case defined by Section 2.1.3 of this Agreement), to post the full Paper or any its part on the web, to publish the Paper in any other editions, to include the Paper or any its part in other collections, anthologies, encyclopaedias, etc., the Author(s) should get a written permission from the Publisher.
3. License territory.
The Author(s) grant(s) the Publisher the right to use the Paper as regulated by sections 2.1.1–2.1.3 of this Agreement on the territory of Ukraine and to distribute the Paper as indispensable part of the Journal on the territory of Ukraine and other countries by means of subscription, sales, and free transfer to a third party.
4. Duration.
4.1. This Agreement is valid starting from the date of signature and acts for the entire period of the existence of the Journal.
5. Loyalty.
5.1. The Author(s) warrant(s) the Publisher that:
– he/she is the true author (co-author) of the Paper;
– copyright on the Paper was not transferred to any other party;
– the Paper has never been published before and will not be published in any other media before it is published by the Publisher (see also section 2.2);
– the Author(s) do(es) not violate any intellectual property right of other parties. If the Paper includes some materials of other parties, except for citations whose length is regulated by the scientific, informational, or critical character of the Paper, the use of such materials is in compliance with the regulations of the international law and the law of Ukraine.
6. Requisites and signatures of the Parties.
Publisher: Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine.
Address: Ukraine, Kyiv, Metrolohichna Str. 14-b.
Author: Electronic signature on behalf and with endorsement of all co-authors.