Force fields for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties

The Journal of Chemical Physics
Shavkat I Mamatkulov, Nadine Schwierz

Abstract

Metal cations are essential in many vital processes. In order to capture the role of different cations in all-atom molecular dynamics simulations of biological processes, an accurate parametrization is crucial. Here, we develop force field parameters for the metal cations Li+, Na+, K+, Cs+, Mg2+, Ca2+, Sr2+, and Ba2+ in combination with the TIP3P water model that is frequently used in biomolecular simulations. In progressing toward improved force fields, the approach presented here is an extension of previous efforts and allows us to simultaneously reproduce thermodynamic and kinetic properties of aqueous solutions. We systematically derive the parameters of the 12-6 Lennard-Jones potential which accurately reproduces the experimental solvation free energy, the activity derivative, and the characteristics of water exchange from the first hydration shell of the metal cations. In order to reproduce all experimental properties, a modification of the Lorentz-Berthelot combination rule is required for Mg2+. Using a balanced set of solution properties, the optimized force field parameters aim to capture the fine differences between distinct metal cations including specific ion binding affinities and the kinetics of cation binding to ...Continue Reading

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Citations

Jul 29, 2020·Nature Chemical Biology·Jakob GebelVolker Dötsch
Jan 17, 2020·The Journal of Chemical Physics·Max F DöpkeRemco Hartkamp
Jun 15, 2020·The Journal of Chemical Physics·Nadine Schwierz
Oct 18, 2020·Proceedings of the National Academy of Sciences of the United States of America·Mateusz SikoraAchilleas S Frangakis
Nov 19, 2020·Physical Chemistry Chemical Physics : PCCP·Kiana Gholamjani MoghaddamShirin Faraji
Jun 4, 2021·Journal of Chemical Information and Modeling·Jiarong PengHaiyang Zhang
Jul 23, 2021·The Journal of Physical Chemistry. B·Philip LocheDouwe Jan Bonthuis
Jul 28, 2021·Journal of Chemical Information and Modeling·Yongguang ZhangHaiyang Zhang
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Dec 17, 2020·The Journal of Physical Chemistry. B·Christopher P BaryiamesCarlos R Baiz
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Aug 30, 2021·Proteins·Silvia GervasoniAdrian J Mulholland
Dec 4, 2021·The Journal of Physical Chemistry. B·Yejie QiuHaiyang Zhang

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