MD simulation of the dynamics of chlorocyclohexane guest molecules in the thiourea inclusion compound

We present the results of molecular dynamics simulations of the chlorocyclohexane/thiourea inclusion compound within the high temperature rhombohedral and low temperature monoclinic phases of the composite crystal. By defining a molecular reference frame by means of two vectors (n) over right arrow and (p) over right arrow, we have been able to analyze separately the reorientations of the guest molecules as a whole in the laboratory reference frame and the reorientations of the guest molecules about an intramolecular reference axis. In the rhombohedral phase, we found that the chlorocyclohexane guest molecules reorient as a whole over six favored sites around the C-3 and the C-2 symmetry axes of the crystallographic site (D-3 point group). In the low temperature phase, the symmetry elements of phase I are lost and the guest molecules sit in general positions with a dynamic disorder among two orientations. Orientational distribution functions and space-time correlation functions (intermediate incoherent neutron scattering laws) for the dynamics of (n) over right arrow and (p) over right arrow have been analyzed in both structural phases. These results are discussed in relation to incoherent quasi-elastic neutron scattering (QENS) experiments and compared to those previously obtained for the cyclohexane/thiourea inclusion compound. Marked differences between both systems have been found for the reorientations of guest molecules. These simulations will be exploited to interpret QENS experiments in view of elucidating the phase transition mechanisms in these compounds. (C) 2003 Elsevier Science B.V. All rights reserved.