Solid state molecular dynamics

RJ. Webb, M.D. Lowery, Y. Shiomi, M. Swai, RJ. Witlebort and DA4. Hendikksoii, lnorg.Chem., 1992, 31,5211 [solid state molecular dynamics]. 

The conformational preference of 1,3,5-trithiane-l-oxide has been determined in solution and in the solid state . and dynamic NMR studies indicated that the S=0 bond is equatorial (182) in solution, as did molecular mechanics calculations. Surprisingly, the axial conformation (183) is preferred in the crystalline state. 

To examine the solid as it approaches equilibrium (atom energies of 0.025 eV) requires molecular dynamic simulations. Molecular dynamic (MD) simulations follow the spatial and temporal evolution of atoms in a cascade as the atoms regain thermal equilibrium in about 10 ps. By use of MD, one can follow the physical and chemical effects that influence the final cascade state. Molecular dynamics have been used to study a variety of cascade phenomena. These include defect evolution, recombination dynamics, liquid-like core effects, and final defect states. MD programs have also been used to model sputtering processes. 

According to LPM, a libration of 15° about the pseudo twofold axis (II) is enough to average the local molecular conformation, because it corresponds to a >3 <-> C2 Civ C2 >3 isomerization as highlighted by the marked asymmetry of reaction path II, however, the intermolecular environment cannot be averaged. More importantly, as shown by very recent XRD studies on the effect of temperature on the solid state molecular structure of Fe3(CO)i2, ° such large libration still persists at 160 and even at 100 K thus, it cannot be the dynamic process that is frozen out at 180... 

In this chapter we shall consider four important problems in molecular n iudelling. First, v discuss the problem of calculating free energies. We then consider continuum solve models, which enable the effects of the solvent to be incorporated into a calculation witho requiring the solvent molecules to be represented explicitly. Third, we shall consider the simi lation of chemical reactions, including the important technique of ab initio molecular dynamic Finally, we consider how to study the nature of defects in solid-state materials. 

In Chapter 2, a brief discussion of statistical mechanics was presented. Statistical mechanics provides, in theory, a means for determining physical properties that are associated with not one molecule at one geometry, but rather, a macroscopic sample of the bulk liquid, solid, and so on. This is the net result of the properties of many molecules in many conformations, energy states, and the like. In practice, the difficult part of this process is not the statistical mechanics, but obtaining all the information about possible energy levels, conformations, and so on. Molecular dynamics (MD) and Monte Carlo (MC) simulations are two methods for obtaining this information... 

Molecular mechanics methods have been used particularly for simulating surface-liquid interactions. Molecular mechanics calculations are called effective potential function calculations in the solid-state literature. Monte Carlo methods are useful for determining what orientation the solvent will take near a surface. Molecular dynamics can be used to model surface reactions and adsorption if the force held is parameterized correctly. 

Models for description of liquids should provide us with an understanding of the dynamic behavior of the molecules, and thus of the routes of chemical reactions in the liquids. While it is often relatively easy to describe the molecular structure and dynamics of the gaseous or the solid state, this is not true for the liquid state. Molecules in liquids can perform vibrations, rotations, and translations. A successful model often used for the description of molecular rotational processes in liquids is the rotational diffusion model, in which it is assumed that the molecules rotate by small angular steps about the molecular rotation axes. One quantity to describe the rotational speed of molecules is the reorientational correlation time T, which is a measure for the average time elapsed when a molecule has rotated through an angle of the order of 1 radian, or approximately 60°. It is indirectly proportional to the velocity of rotational motion. 

The analogy drawn between -stacked solids and duplex DNA has provided a useful starting point for experiments to probe and understand DNA-medi-ated CT. As with the -stacked solids, the DNA base pair array can provide an effective medium for long range CT. Mechanistically, however, the differences between DNA and these solid state materials may be even more important to consider. Duplex DNA, as a molecular -stacked structure, undergoes dynamical motion in solution. The time-dependent and sequence-dependent structures that arise serve to modulate and gate CT. Indeed in probing DNA CT as a function of sequence and sequence-dependent structure, we may better understand mechanistically how CT proceeds and how DNA CT may be utilized. 

A unique characteristic of polyesters is their ability to undergo additional condensation reactions during processing or when in the solid state. These reactions redistribute the molecular weight of the polymer until a dynamic equilibrium is established. Water, when present at high temperatures in polyester melts, can depolymerize polyesters via a hydrolysis reaction. For this reason, manufacturers must carefully dry the polymer before processing. 

---