Molecular dynamics simulation of n-nonadecane in urea inclusion compound. I. Comparison with quasielastic neutron scattering experiment

The diffusive dynamics of n-nonadecane molecules in urea inclusion compound at 180 K are examined using molecular dynamics simulations. Incoherent quasielastic neutron scattering profiles are calculated from the simulation trajectories and compared with experiment. The effect on the calculated scattering functions of varying the model system in the simulation is examined. Interactions between alkane chains within the channels are found to strongly influence their rotational and translational dynamics and associated scattering spectra. The diffusive alkane dynamics is well described in terms of the molecules moving as rigid bodies. Analytical models of restricted translational and rotational rigid-molecule diffusion of the alkanes are fitted to the simulation-derived scattering functions in the time and energy domains. The effects of the experimental instrumental energy resolution function on the scattering functions and on the dynamical parameters obtained by fitting to the analytical models are examined. The calculations indicate that whereas the translational dynamics are converged on the time scales accessible to the experiment and the simulation, rotational motions exist that are too slow to be detected experimentally.