Molecular dynamic simulation solid-state studies

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. 

Ab initio molecular-dynamics simulations, introduced by Car and Par-rinello [112], have the ambition to model biological systems in laboratoryrelevant conditions, i.e., either in solution or in solid phase (see, e.g., [113-115]). Recently, Carloni et al. [116] applied this method to a study of the first hydrolysis step of cisplatin. They were able to reproduce satisfactorily the free energy of activation and provided a model for the transition state. Their preliminary results, which include a model of the transition state for the chelation step of the reaction between the diaqua form of cisplatin, cA-[Pt(NH3)2(H20)2]2+, and d(GpG), seem to indicate that ab initio modeling of substitution reactions on heavy-metal centers may become possible in the near future. The main drawback of Car-Parrinello calculations - their considerable computer-time cost - can be expected to abate in the next years... 

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... 

HMX (1,3,5, 7-tetranitro-l, 3,5,7-tetraazacyclooctane) is widely used as an ingredient in various explosives and propellants. A molecular solid at standard state, it has four known pol5miorphs, one of which, the 8 phase is comprised of six molecules per unit cell, as depicted in Fig. 10. We study the chemical decomposition of the dense fluid of this phase by conducting a high-density and temperature (p = 1.9 g/cm, T = 3500 K) quantum mechanical based molecular dynamics simulation. [50] To our knowledge, this is the first reported ab initio based/molecular dynamics study of an explosive material at extreme conditions for extended reaction times of up to 55 picoseconds, thus allowing the formation of stable product molecules. 

Several techniques have been used to investigate dynamic properties of urea inclusion compounds, including solid-state NMR, incoherent quasielastic neutron scattering ESR, molecular dynamics simulation, Raman, infrared, dielectric loss, and x-ray diffraction. In addition to investigations of the dynamics of the guest molecules, the dynamic properties of the urea molecules have also been studied. 

This review of extensive molecular dynamics simulations of systems with relatively large numbers of atoms illustrates how it is now possible to begin the study of cooperative molecular motion involving interactions between skeletal vibrations and conformational isomers. Supercomputers have accomplished the extreme slow-motion display necessary to analyze simultaneous, cooperative changes. One can extrapolate that one more order of magnitude in atoms, and the extension of the analyzed time into the nanosecond range, can resolve many of the basic problems of the defect solid state of linear, flexible macromolecules. 

The relevant literature on lactose dissolution in water has been reviewed in a paper which describes a mathematical model for this process/ Short time scale molecular dynamics simulations of sucrose in water and DMSO indicated that the conformations in both solvents are similar to that accepted in the crystalline state/ Solid-liquid equilibria for aqueous sucrose have been studied by use of an UNIQUAC model/ A comparison of GROMOS force field and Ha force field in molecular dynamics simulations of glucose crystals indicated superior performance by the latter method/ Predicted crystal structures of P-D-glucose, P-D-galactose, P-D-allose, a-D-glucose, a-D-galactose, and a-D-talose matched or nearly matched the X-ray-derived data in four cases/ ... 

In this chapter we will review the recent developments in simulating and modelling proton transport. We will put a special emphasis on studies employing classical and quantum molecular-dynamics simulations, but also include basic studies that have focussed on model systems using accurate quantum-chemical methods. Proton-transport and dilfusion phenomena in liquids - such as water, inorganic acids, or organic liquids - will be discussed as well as in biomolecules, solid-state materials, and at the solid-liquid interface. Many of these materials are used in proton-transporting fuel-cell membranes, so that membrane materials will be the focus of the last section. 

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