Molecular dynamics simulations polarization effects

The semi-empirical bond polarization model is a powerful tool for the calculation of, 3C chemical shift tensors. For most molecules the errors of this model are in the same order of magnitude as the errors of ab initio methods, under the condition that the surrounding of the carbon is not too much deformed by small bond angles. A great advantage of the model is that bond polarization calculations are very fast. The chemical shift tensors of small molecules can be estimated in fractions of a second. There is also virtually no limit for the size of the molecule. Systems with a few thousand atoms can be calculated with a standard PC within a few minutes. Possible applications are repetitive calculations during molecular dynamics simulations for the interpretation of dynamic effects on 13C chemical shift distribution. 

It was recently shown via molecular dynamics simulations14 that, in the close vicinity of a surface, water molecules exhibit an anomalous dielectric response, in which the local polarization is not proportional to the local electric field. The recent findings are also in agreement with earlier molecular dynamics simulations, which showed that the polarization of water oscillates in the vicinity of a dipolar surface,11,14 leading therefore to a nonmonotonic hydration force.15 Previous models for oscillatory hydration forces, based either on volume-excluded effects,18,19 or on a nonlocal dielectric constant,f4 predicted many oscillations with a periodicity of 2 A, which is inconsistent with these molecular dynamics simulations,11,18,14 in which the polarization exhibits only a few oscillations in the vicinity of the surface, with a larger periodicity. 

In this chapter we will mostly focus on the application of molecular dynamics simulation technique to understand solvation process in polymers. The organization of this chapter is as follow. In the first few sections the thermodynamics and statistical mechanics of solvation are introduced. In this regards, Flory s theory of polymer solutions has been compared with the classical solution methods for interpretation of experimental data. Very dilute solution of gases in polymers and the methods of calculation of chemical potentials, and hence calculation of Henry s law constants and sorption isotherms of gases in polymers are discussed in Section 11.6.1. The solution of polymers in solvents, solvent effect on equilibrium and dynamics of polymer-size change in solutions, and the solvation structures are described, with the main emphasis on molecular dynamics simulation method to obtain understanding of solvation of nonpolar polymers in nonpolar solvents and that of polar polymers in polar solvents, in Section 11.6.2. Finally, the dynamics of solvation with a short review of the experimental, theoretical, and simulation methods are explained in Section 11.7. 

Tinte et al.54 have carried out molecular dynamic simulations of first-principles based effective Hamiltonian for PSN under pressure and of PMN at ambient pressure that clearly exhibit a relaxor state in the paraelectric phase. Analysis of the short-to-medium range polar order allows them to locate Burns temperature Tb. Burns temperature is identified as the temperature below which dynamic nanoscale polar clusters form. Below TB, the relaxor state characterized by enhanced short-to-medium range polar order (PNR) pinned to nanoscale chemically ordered regions. The calculated temperature-pressure phase diagram of PSN demonstrates that the stability of the relaxor state depends on a delicate balance between the energetics that stabilize normal ferroelectricity and the average strength of quenched "random" local fields. 

Specific polarization effects, beyond those modelled by a continuum dielectric model and the movement of certain atoms, are neglected in MIF calculations. Many-body effects are also neglected by use of a pair-wise additive energy function. Polarizable force fields are, however, becoming more common in the molecular mechanics force fields used for molecular dynamics simulations, and MIFs could be developed to account for polarizability via changes in charge magnitude or the induction of dipoles upon movement of the probe. 

Statistical thermodynamics is also changing in recent years. Newly developed RISM (Reference Interactions Site Model) theory has no restriction on the shape of solute species, in contrast to old theories in which spherical species are usually assumed. Ab initio calculations are being combined with molecular dynamic simulations. This combination becomes possible because of the improvement of high-speed computers. The polarization effect and multibody problem will be... 

Recendy, validity of the two assumptions regarding the free energy proflie, parabolic and solute independence of the force constants, has been examined by several authors. These assumptions have been predicted from the continuum dielecuic models and commonly adopted in many of the early works. Kakitani et alJ discussed the nonlinearity of solvation related to ET in polar solvents, and Carter and Hynes performed molecular dynamics simulations of the charge separation (CS) and the charge recombination (CR) reactions to observe such non-linear effects. More recently, Ando et alf discussed these problems and they observed no such non-linear effects. Due to the non-linear nature of the hypemetted chain (HNC) closure to solve the RISM equation, our method can shed light on the non-linearity of the free energy profiles. In section III, we apply our method, which is outlined briefly in section II, to the CS reaction which was previously studied by Carter and Hynes, and discuss the problems mentioned above based on the obtained free energy profiles. 

Acetanilide, and some of its isotopomers, have been studied by INS spectroscopy [56-58]. The dispersion curves of the fully deuterated material have been measured by coherent INS [59]. A comprehensive analysis of acetanilide in the solid state was carried out with molecular dynamics simulations [57]. This includes all the lattice modes, as shown in Fig. 10.27 The simulations suggested that the barrier to the methyl torsion was enhanced when the peptide group is hydrogen-bonded and that this was a through-bond polarization effect. The methyl torsion was... 

The characteristics of water in the neighborhood of mixed-functional solutes containing both polar and nonpolar groups will be reviewed and illustrated by the detailed results obtained from a molecular dynamics simulation of a dilute aqueous solution of an alanine dlpeptlde. Both the solvent effect on the dlpeptlde and that of the dlpeptlde on the solvent will be described. 

The shell model has its origin in the Born theory of lattice dynamics, used in studies of the phonon dispersion curves in crystals.70,71 Although the Born theory includes the effects of polarization at each lattice site, it does not account for the short-range interactions between sites and, most importantly, neglects the effects of this interaction potential on the polarization behavior. The shell model, however, incorporates these short-range interactions.72,73 The earliest applications of the shell model, as with the Born model, were to analytical studies of phonon dispersion relations in solids.74 These early applications have been well reviewed elsewhere.71,75-77 In general, lattice dynamics applications of the shell model do not attempt to account for the dynamics of the nuclei and typically use analytical techniques to describe the statistical mechanics of the shells. Although the shell model continues to be used in this fashion,78 lattice dynamics applications are beyond the scope of this chapter. In recent decades, the shell model has come into widespread use as a model Hamiltonian for use in molecular dynamics simulations it is these applications of the shell model that are of interest to us here. 

Many of the systems previously discussed, for example, the S l, and ion pair reactions, involve some type of charge separation, creation, or transfer. This movement of charge has a substantial effect on the polar solvent in which the reaction takes place. These effects are strongly related to those seen in the solvation dynamics studied by several groups through molecular dynamics simulations. The field of solvation dynamics, in its theoretical, computational... 

---