Ionic molecular dynamics simulations

Straatsma, T.P, Berendsen, H.J.C. Free energy of ionic hydration Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations. J. Chem. Phys. 89 (1988) 5876-5886. 

The concentration of salt in physiological systems is on the order of 150 mM, which corresponds to approximately 350 water molecules for each cation-anion pair. Eor this reason, investigations of salt effects in biological systems using detailed atomic models and molecular dynamic simulations become rapidly prohibitive, and mean-field treatments based on continuum electrostatics are advantageous. Such approximations, which were pioneered by Debye and Huckel [11], are valid at moderately low ionic concentration when core-core interactions between the mobile ions can be neglected. Briefly, the spatial density throughout the solvent is assumed to depend only on the local electrostatic poten-... 

Chang TM, Peterson KA, Dang LX (1995) Molecular-dynamics simulations of liquid, interface, and ionic solvation of polarizable carbon-tetrachloride. J Chem Phys 103(17) 7502-7513... 

This volume of Modem Aspects covers a wide spread of topics presented in an authoritative, informative and instructive manner by some internationally renowned specialists. Professors Politzer and Dr. Murray provide a comprehensive description of the various theoretical treatments of solute-solvent interactions, including ion-solvent interactions. Both continuum and discrete molecular models for the solvent molecules are discussed, including Monte Carlo and molecular dynamics simulations. The advantages and drawbacks of the resulting models and computational approaches are discussed and the impressive progress made in predicting the properties of molecular and ionic solutions is surveyed. 

Molecular dynamic simulations representing benzene in [MMIM]C1 and [MMIMJPFg established a correlation of the (high) solubility of benzene in ionic liquids with the strong electrostatic field around the aromatic molecule associated with the 7i-electrons. The high polarizability of benzene also contributes to the high solubility 94). 

Kubicki J.D. and Lasaga A.G. (1988) Molecular dynamics simulations of Si02 melt and glass ionic and covalent models. Am. Mineral. 73, 941-955. 

Del Popolo, M.G., Lynden-Bell, R.M., and Kohanoff, J., Ab initio molecular dynamics simulation of a room temperature ionic liquid, /. Phys. Chem. B, 109, 5895-5902, 2005. 

Bhargava, B.L., and Balasubramanian, S., Intermolecular structure and dynamics in an ionic liquid A Car-Parrinello molecular dynamics simulation study of 1,3-dimethylimidazolium chloride, Chem. Phys. Lett., 417, 486-491, 2006. 

In view of the studies [75] of aqueous NaCl solutions by using molecular-dynamics simulation, one may suggest that our models are applicable61 only at low salt concentrations Cm, for which the Kirkwood correlation factor g could be calculated from Eq. (414d), where the ionic contribution Ae on(0) is not involved. 

Since Poisson-Boltzmann theory neglects all ion-ion correlations (see Sect. 2.2) one is tempted to assume that their incorporation into the theoretical treatment would resolve the discrepancy. However, the comparison displayed in Fig. 8 shows clearly that these correlational effects can only be made responsible for a part of the deviations. Since the two different approaches, using a correlation-corrected density functional theory and Molecular Dynamics simulations, agree very well with each other, it becomes obvious that the discrepancy between them and the experiment is not due to the neglect of ionic correlations. 

We showed previously that a simple model for the ion-hydration interactions, which separates the ion-hydration forces in a long-range term due to the behavior of water as a continuous dielectric (the screened image force) and a short-range term due to the discreetness of the water molecules (SM/SB), can explain almost quantitatively a number of phenomena related to the electrolyte interfaces.6 In this article, we examined the limitations of the model in predicting the distributions of ions near the air/water interface, by comparison with molecular dynamics simulations. It is clear that the real ion-hydration forces are more complicated than the simple model employed here however, the interfacia] phenomena (including specific ionic effects) can be understood, at least qualitatively, in terms of this simple approach. 

Another illustration of the power of molecular dynamics simulation can be drawn from the sphere of enzyme catalysis. Many enzyme-catalyzed reactions proceed at a rate that depends on the diffusion-limited association of the substrate with the active site. Sharp et al. [28] have carried out Brownian dynamics simulations of the association of superoxide anions with superoxide dismutase (SOD). The active center in SOD is a positively charged copper atom. The distribution of charge over the enzyme is not uniform, and so an electric field is produced. Using their model, Sharp et al. [28] have shown that the electric field enhances the association of the substrate with the enzyme by a factor of 30 or more. Their calculations also predict correctly the response of the association rate to changes in ionic strength and amino... 

Guardia E, Marti J, Garcia-Tarres L et al (2005) A molecular dynamics simulation study of hydrogen bonding in aqueous ionic solutions. J Mol Liq 117 63-67... 

Simulations of charged systems are very important. Common examples are plasmas, ionic solutions, dipole system and electronic systems. Because all pairs are included in the sum of eq. (2), the computer time only depends on the number of atoms and the number of time steps. For this reason my results should be applicable to all similar systems. I will discuss here only results for molecular dynamics simulations. The situation for Monte Carlo is completely parallel, although the actual coding is different since atoms are moved singly rather than all together. 

Based on the position of an ion in the Hoftneister series, it is possible to foretell the relative effectiveness of anions or cations in an enormous number of systems. The rank of an ion was related to its kosmotropicity, surface tension increments, and salting in and salting out of salt solutions (see below) [25]. A quantitative physical chemistry description of this phenomenon is not far off. Molecular dynamics simulations that considered ionic polarizability were found to be valuable tools for elucidating salt effects [26,27]. 

Finally, there is the theoretical method of approaching ionic solvation including the molecular dynamics simulations. These have become increasingly used because they are cheap and quick. However, MD methods use two-body interaction equations and the parameters used here need experimental data to act as a guide for the determination of parameters that fit. 

The iast part of our treatment of the central aspects of the chapter concerned molecular dynamics. We showed the power of molecular dynamics simulations in ionic solutions and what excellent agreement can be obtained between, say, the distribution function of water molecules around an ion calculated from molecular dynamics simulation and that measured by neutron diffraction. 

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