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Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations
Open accessAbstract
The thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations is analyzed. The hydration of the ions Na+ , K+ , Ca++ , F−, Cl−, and Br− is used as the process to illustrate the potential utility of the method. A neon–water system is used as a reference system. The parameters that influence the performance and accuracy of the thermodynamic integration, in which the potential interaction parameters are gradually and continuously changed, are studied. These parameters include the total simulation time, the magnitude of the time step for the numerical integration of the equations of motion, the system size, and the cutoff radii for the intermolecular interactions. Fast convergence is found for the Gibbs free energy difference between Ne and Na+ with respect to total simulation time. The time step and system size are relatively unimportant. The use of cutoff radii, for the ion–water but especially unfortunately also the water–water intermolecular interactions, seriously influences the results obtained. A simple correction for the use of cutoff radii cannot be made. Results are compared to experimental values.
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Citations
Cites
Thermodynamics of Ion Hydration as a Measure of Effective Dielectric Properties of Water
Noyes, R. M. (1962) · Journal of the American Chemical Society · doi:10.1021/ja00863a002 · Cited by 456
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van Gunsteren, W. F., Bakowies, D., Baron, R., Chandrasekhar, I., Christen, M., Daura, X., Gee, P., Geerke, D. P., Glättli, A., Hünenberger, P. H., et al. (2006) · Angewandte Chemie International Edition · doi:10.1002/anie.200502655 · Cited by 561
Halide, Ammonium, and Alkali Metal Ion Parameters for Modeling Aqueous Solutions
Jensen, K. P., & Jorgensen, W. L. (2006) · Journal of Chemical Theory and Computation · doi:10.1021/ct600252r · Cited by 451
Zinc binding in proteins and solution: A simple but accurate nonbonded representation
Stote, R. H., & Karplus, M. (1995) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340230104 · Cited by 354
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Hess, B., Holm, C., & van der Vegt, N. (2006) · The Journal of Chemical Physics · doi:10.1063/1.2185105 · Cited by 147
Metadata
- Authors
- Straatsma, T. P., & Berendsen, H. J. C.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 1988-11-01
- Volume
- 89
- Issue
- 9
- Pages
- 5876-5886
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W2079318633
- Cited by
- 521
- References
- 1
- FWCI
- 5.80
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Straatsma, T. P., & Berendsen, H. J. C. (1988). Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations. The Journal of Chemical Physics. https://doi.org/10.1063/1.455539
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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