Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters
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Open Access
- 17 September 2009
- journal article
- research article
- Published by American Chemical Society (ACS) in The Journal of Physical Chemistry B
- Vol. 113 (40) , 13279-13290
- https://doi.org/10.1021/jp902584c
Abstract
The dynamic and energetic properties of the alkali and halide ions were calculated using molecular dynamics (MD) and free energy simulations with various different water and ion force fields including our recently developed water-model-specific ion parameters. The properties calculated were activity coefficients, diffusion coefficients, residence times of atomic pairs, association constants, and solubility. Through calculation of these properties, we can assess the validity and range of applicability of the simple pair potential models and better understand their limitations. Due to extreme computational demands, the activity coefficients were only calculated for a subset of the models. The results qualitatively agree with experiment. Calculated diffusion coefficients and residence times between cation−anion, water−cation, and water−anion showed differences depending on the choice of water and ion force field used. The calculated solubilities of the alkali−halide salts were generally lower than the true solubility of the salts. However, for both the TIP4PEW and SPC/E water-model-specific ion parameters, solubility was reasonably well-reproduced. Finally, the correlations among the various properties led to the following conclusions: (1) The reliability of the ion force fields is significantly affected by the specific choice of water model. (2) Ion−ion interactions are very important to accurately simulate the properties, especially solubility. (3) The SPC/E and TIP4PEW water-model-specific ion force fields are preferred for simulation in high salt environments compared to the other ion force fields.Keywords
This publication has 51 references indexed in Scilit:
- Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular SimulationsThe Journal of Physical Chemistry B, 2008
- Molecular Basis of the Apparent Near Ideality of Urea SolutionsBiophysical Journal, 2007
- Structural Roles of Monovalent Cations in the HDV RibozymeStructure, 2007
- The Effects of Metal Ions on the Structure and Stability of the DNA Gyrase B ProteinJournal of Molecular Biology, 2005
- Anion Binding to Nucleic AcidsStructure, 2004
- Anion concentration modulates the conformation and stability of the molten globule of cytochrome cJBIC Journal of Biological Inorganic Chemistry, 2003
- AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of moleculesComputer Physics Communications, 1995
- A Comparison of Alternative Approaches to Free Energy CalculationsThe Journal of Physical Chemistry, 1994
- Comparison of simple potential functions for simulating liquid waterThe Journal of Chemical Physics, 1983
- Some Topics in the Theory of FluidsThe Journal of Chemical Physics, 1963