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Articles

Effects of ion–water Lennard-Jones potentials on the hydration dynamics around a monovalent atomic ion in molecular dynamics simulations

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Pages 83-91 | Received 17 Jul 2019, Accepted 26 Sep 2019, Published online: 11 Oct 2019

References

  • Laage D, Elsaesser T, Hynes JT. Water dynamics in the hydration shells of biomolecules. Chem Rev. 2017 Mar;117:10694–10725. doi: 10.1021/acs.chemrev.6b00765
  • Åqvist J. Ion-water interaction potentials derived from free energy perturbation simulations. J Phys Chem. 1990 Oct;94:8021–8024. doi: 10.1021/j100384a009
  • Joung IS, Cheatham TE. Determination of Alkali and Halide monovalent Ion parameters for use in explicitly solvated biomolecular simulations. J Phys Chem B. 2008 Jul;112:9020–9041. doi: 10.1021/jp8001614
  • Guàrdia E, Martí J, García-Tarrés L, et al. A molecular dynamics simulation study of hydrogen bonding in aqueous ionic solutions. J Mol Liq. 2005 Mar;117:63–67. doi: 10.1016/j.molliq.2004.08.004
  • Gereben O, Pusztai L. On the accurate calculation of the dielectric constant from molecular dynamics simulations: the case of SPC/E and SWM4-DP water. Chem Phys Lett. 2011 Apr;507:80–83. doi: 10.1016/j.cplett.2011.02.064
  • Berendsen HJC, Postma JPM, van Gunsteren WF, et al. Interaction models for water in relation to protein hydration. Intermolecular Forces. Dordrecht: Springer; 1981. p. 331–342.
  • Berendsen HJC, Grigera JR, Straatsma TP. The missing term in effective pair potentials. J Phys Chem. 1987 Nov;91:6269–6271. doi: 10.1021/j100308a038
  • Jorgensen WL, Chandrasekhar J, Madura JD, et al. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79:926–935. doi: 10.1063/1.445869
  • Mahoney MW, Jorgensen WL. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J Chem Phys. 2000 May;112:8910–8922. doi: 10.1063/1.481505
  • Rick SW. A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums. J Chem Phys. 2004 Apr;120:6085–6093. doi: 10.1063/1.1652434
  • Abascal J, Vega C. A general purpose model for the condensed phases of water: TIP4P/2005. J Chem Phys. 2005;123:234505. doi: 10.1063/1.2121687
  • Piana S, Donchev AG, Robustelli P, et al. Water dispersion interactions strongly influence simulated structural properties of disordered protein states. J Phys Chem B. 2015 Apr;119:5113–5123. doi: 10.1021/jp508971m
  • Wu Y, Tepper HL, Voth GA. Flexible simple point-charge water model with improved liquid-state properties. J Chem Phys. 2006 Jan;124:024503. doi: 10.1063/1.2136877
  • González MA, Abascal JLF. A flexible model for water based on TIP4P/2005. J Chem Phys. 2011 Dec;135:224516. doi: 10.1063/1.3663219
  • Caldwell JW, Kollman PA. Structure and properties of neat liquids using nonadditive molecular dynamics: water, Methanol, and N-Methylacetamide. J Phys Chem. 2002 May;99:6208–6219. doi: 10.1021/j100016a067
  • Jensen KP, Jorgensen WL. Halide, Ammonium, and Alkali Metal Ion parameters for modeling aqueous solutions. J Chem Theory Comput. 2006 Nov;2:1499–1509. doi: 10.1021/ct600252r
  • Joung IS, Cheatham TE III. Molecular dynamics simulations of the dynamic and energetic properties of Alkali and Halide ions using water-model-specific Ion parameters. J Phys Chem B. 2009 Oct;113:13279–13290. doi: 10.1021/jp902584c
  • Kim JS, Wu Z, Morrow AR, et al. Self-diffusion and viscosity in electrolyte solutions. J Phys Chem B. 2012 Sep;116:12007–12013. doi: 10.1021/jp306847t
  • Ding Y, Hassanali AA, Parrinello M. Anomalous water diffusion in salt solutions. Proc Natl Acad Sci. 2014 Mar;111:3310–3315. doi: 10.1073/pnas.1400675111
  • Kurisaki I, Takahashi T. Assessment of dynamic properties of water around a monovalent ion: A classical molecular dynamics simulation study. Comput Theor Chem. 2011 Jun;966:26–30. doi: 10.1016/j.comptc.2011.02.004
  • Rappe AK, Casewit CJ, Colwell KS, et al. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J Am Chem Soc. 1992 Dec;114:10024–10035. doi: 10.1021/ja00051a040
  • Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys. 1977 Mar;23:327–341. doi: 10.1016/0021-9991(77)90098-5
  • Essmann U, Perera L, Berkowitz ML, et al. A smooth particle mesh Ewald method. J Chem Phys. 1995 Nov;103:8577–8593. doi: 10.1063/1.470117
  • Case DA, Cheatham TE, Darden T, et al. The Amber biomolecular simulation programs. J Comput Chem. 2005 Dec;26:1668–1688. doi: 10.1002/jcc.20290
  • McCall DW, Douglass DC. The effect of ions on the self-diffusion of water. I. Concentration dependence. J Phys Chem. 1965 Jun;69:2001–2011. doi: 10.1021/j100890a034
  • Kaatze U. The dielectric properties of water in its different states of interaction. J Solution Chem. 1997 Nov;26:1049–1112. doi: 10.1007/BF02768829
  • Marcus Y. Ionic radii in aqueous solutions. Chem Rev. 1988 Dec;88:1475–1498. doi: 10.1021/cr00090a003
  • Li P, Song LF, Kenneth M, et al. Systematic parameterization of monovalent ions employing the nonbonded model. J Chem Theory Comput. 2015 Mar;11:1645–1657. doi: 10.1021/ct500918t

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