Molecular dynamics simulation study of cyclohexane guest molecules in the cyclohexane/thiourea inclusion compound Original Research Article

Molecular dynamics simulations of the cyclohexane/thiourea inclusion compound within the high temperature rhombohedral phase (at 173 and 273 K) are presented. The simulated systems consist of 96/288 cyclohexane/thiourea molecules, corresponding to 12 contiguous host thiourea channels of approximately 50 Å length. The atomic trajectories were obtained over 600 ps assuming rigid molecules. The orientational distribution of cyclohexane guest molecules is described through the polar angles between the guest molecular C3m symmetry axis and the thiourea host reference frame. From the molecular dynamics simulations we obtain the three-dimensional orientational distribution functions P(θ,ϕ). It is shown that the cyclohexane guest molecules reorient about the C3c and the C2 symmetry axes of the crystallographic 32 site. The incoherent intermediate scattering functions have been computed from molecular dynamics trajectories, allowing the development of theoretical models that could be used to interpret the dynamics of cyclohexane guest molecules from experiments.