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

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 +, Mg 2+, Ca 2+, Sr 2+, and Ba 2+ 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 Mg 2+. As a result, 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 biologically important anionic groups.

Authors:
 [1];  [2]
  1. The Centre of Higher Technologies, Tashkent, (Uzbekistan). Dept. of Physics
  2. Max Planck Institute of Biophysics, Frankfurt (Germany). Dept. of Theoretical Biophysics
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1498069
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 148; Journal Issue: 7; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Mamatkulov, Shavkat, and Schwierz, Nadine. Force fields for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties. United States: N. p., 2018. Web. doi:10.1063/1.5017694.
Mamatkulov, Shavkat, & Schwierz, Nadine. Force fields for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties. United States. doi:10.1063/1.5017694.
Mamatkulov, Shavkat, and Schwierz, Nadine. Wed . "Force fields for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties". United States. doi:10.1063/1.5017694. https://www.osti.gov/servlets/purl/1498069.
@article{osti_1498069,
title = {Force fields for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties},
author = {Mamatkulov, Shavkat and Schwierz, Nadine},
abstractNote = {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+. As a result, 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 biologically important anionic groups.},
doi = {10.1063/1.5017694},
journal = {Journal of Chemical Physics},
issn = {0021-9606},
number = 7,
volume = 148,
place = {United States},
year = {2018},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
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