Local ordering and dynamics of plastic crystals

Resumen

Many materials of scientific interest show a disordered phase, with their molecules presenting positional disorder, orientational disorder or both. Processes of interest to life also occur in these kind of phases as it is the case of liquid water present in many biochemical problems of interest such as protein folding. The study of these disordered phases is inherently difficult due to their lack of periodicity as in ordered crystals. In this work, molecular dynamics simulations (MD) are used to study two disordered phases: the liquid and the plastic crystal. The configurations obtained by MD are analyzed using different methodologies to obtain insights into the local ordering of the molecules and into their dynamics. The local ordering of the systems is studied using the Euler angles method considering the molecules as rigid bodies. Probability distributions describing the positional and orientational molecular ordering are obtained. These probability distributions are analysed using information theory concepts that provide a deeper understanding of the results. Two systems of interest are studied: hexachloroethane and water. The structure of the liquid and plastic crystal phases of hexacloroethane are investigated and the results from MD and the local ordering analyses are compared to previous works using simulations and neutron diffraction experiments. A Bayesian approach is used in order to obtain the intra-molecular structure of the molecule from the neutron diffraction experimental data, a set of parameters in better agreement with the plastic phase is obtained compared to previous electron diffraction experiments. Liquid water at room conditions is studied on the short range order, presenting a contribution to the ongoing topic of its local structure. The ordering of water at distances beyond the first hydration shell is also studied using the information theory approach. Findings of this work support recent experimental and simulation data showing the existance of long range correlations in water. Finally, plastic crystals phases of water found at high pressures by MD are studied and compared to a high pressure liquid and the ice vii form by comparing their local ordering and dynamics. The methodologies used in this work provide a powerful technique to analyse disordered phases and the results obtained will contribute to the understanding on the structure of such phases.