Molecular dynamics crystal structures

Since the EFG is a very sensitive function of the molecular and crystal structure, the resonance frequencies and band shapes are specific to each compound, and NQR data can be used for determining unambiguous sample identification, local electronic structure, atomic arrangement, order/disorder phenomena, and crystal phase transformations. In addition, molecular dynamics in the solid state can be studied. Furthermore, since NQR data are sensitive to changes in temperature and pressure, there is the possibility of obtaining strain information. 

The complex dynamic and structural properties reveal the influence of SPEU on the molecular dynamics and structure of PHBV, by forming in-termolecular hydrogen bonds and setting up of energy and steric barriers to PHBV crystallization. In terms of design of new biomedical composites, results presented have a scientific and practical interest to describe their behavior at water-temperature exposure. 

Parrinello M and Rahman A 1980 Crystal structure and pair potentials a molecular dynamics study Phys. Rev.L 45 1196-9... 

To enable an atomic interpretation of the AFM experiments, we have developed a molecular dynamics technique to simulate these experiments [49], Prom such force simulations rupture models at atomic resolution were derived and checked by comparisons of the computed rupture forces with the experimental ones. In order to facilitate such checks, the simulations have been set up to resemble the AFM experiment in as many details as possible (Fig. 4, bottom) the protein-ligand complex was simulated in atomic detail starting from the crystal structure, water solvent was included within the simulation system to account for solvation effects, the protein was held in place by keeping its center of mass fixed (so that internal motions were not hindered), the cantilever was simulated by use of a harmonic spring potential and, finally, the simulated cantilever was connected to the particular atom of the ligand, to which in the AFM experiment the linker molecule was connected. 

Abstract. This paper presents results from quantum molecular dynamics Simula tions applied to catalytic reactions, focusing on ethylene polymerization by metallocene catalysts. The entire reaction path could be monitored, showing the full molecular dynamics of the reaction. Detailed information on, e.g., the importance of the so-called agostic interaction could be obtained. Also presented are results of static simulations of the Car-Parrinello type, applied to orthorhombic crystalline polyethylene. These simulations for the first time led to a first principles value for the ultimate Young s modulus of a synthetic polymer with demonstrated basis set convergence, taking into account the full three-dimensional structure of the crystal. 

In principle, we could find the minimum-energy crystal lattice from electronic structure calculations, determine the appropriate A-body interaction potential in the presence of lattice defects, and use molecular dynamics methods to calculate ab initio dynamic macroscale material properties. Some of the problems associated with this approach are considered by Wallace [1]. Because of these problems it is useful to establish a bridge between the micro-... 

Another special case of weak heterogeneity is found in the systems with stepped surfaces [97,142-145], shown schematically in Fig. 3. Assuming that each terrace has the lattice structure of the exposed crystal plane, the potential field experienced by the adsorbate atom changes periodically across the terrace but exhibits nonuniformities close to the terrace edges [146,147]. Thus, we have here another example of geometrically induced energetical heterogeneity. Adsorption on stepped surfaces has been studied experimentally [95,97,148] as well as with the help of both Monte Carlo [92-94,98,99,149-152] and molecular dynamics [153,154] computer simulation methods. 

Whenever the polymer crystal assumes a loosely packed hexagonal structure at high pressure, the ECC structure is found to be realized. Hikosaka [165] then proposed the sliding diffusion of a polymer chain as dominant transport process. Molecular dynamics simulations will be helpful for the understanding of this shding diffusion. Folding phenomena of chains are also studied intensively by Monte Carlo methods and generalizations [166,167]. 

M. Parrinello and A. Rahman, Crystal structure and pair potentials A molecular-dynamics... 

This article reviews progress in the field of atomistic simulation of liquid crystal systems. The first part of the article provides an introduction to molecular force fields and the main simulation methods commonly used for liquid crystal systems molecular mechanics, Monte Carlo and molecular dynamics. The usefulness of these three techniques is highlighted and some of the problems associated with the use of these methods for modelling liquid crystals are discussed. The main section of the article reviews some of the recent science that has arisen out of the use of these modelling techniques. The importance of the nematic mean field and its influence on molecular structure is discussed. The preferred ordering of liquid crystal molecules at surfaces is examined, along with the results from simulation studies of bilayers and bulk liquid crystal phases. The article also discusses some of the limitations of current work and points to likely developments over the next few years. 

It is worth noting that much of the development work for the MM force fields has centred on low energy structures of molecules. Consequently, some of the force constants are less applicable to higher energy molecular structures that can occur in molecular dynamics simulations of liquid crystals. 

The rapid rise in computer speed over recent years has led to atom-based simulations of liquid crystals becoming an important new area of research. Molecular mechanics and Monte Carlo studies of isolated liquid crystal molecules are now routine. However, care must be taken to model properly the influence of a nematic mean field if information about molecular structure in a mesophase is required. The current state-of-the-art consists of studies of (in the order of) 100 molecules in the bulk, in contact with a surface, or in a bilayer in contact with a solvent. Current simulation times can extend to around 10 ns and are sufficient to observe the growth of mesophases from an isotropic liquid. The results from a number of studies look very promising, and a wealth of structural and dynamic data now exists for bulk phases, monolayers and bilayers. Continued development of force fields for liquid crystals will be particularly important in the next few years, and particular emphasis must be placed on the development of all-atom force fields that are able to reproduce liquid phase densities for small molecules. Without these it will be difficult to obtain accurate phase transition temperatures. It will also be necessary to extend atomistic models to several thousand molecules to remove major system size effects which are present in all current work. This will be greatly facilitated by modern parallel simulation methods that allow molecular dynamics simulations to be carried out in parallel on multi-processor systems [115]. 

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