Molecular dynamics simulation of n-nonadecane in urea inclusion compound. II. Rotational distribution and elastic incoherent structure factor

Abstract

The rotational distribution of n-nonadecane molecules around the channel axis in urea inclusion compound at 180 K is examined using molecular dynamics simulation and compared with data derived from incoherent neutron scattering experiment. The potential surface for rotation and translation of a single guest n-nonadecane molecule in a urea channel contains helical valleys. However, it is found that the incommensurate packing of the n-alkane molecules in the inclusion compound prevents their executing helical motion. The calculated rotational potential of mean force exhibits a barrier of ∼0.3 kcal/mol for transitions of the molecules between equivalent sixfold minima. The motion of the urea host molecules is coupled to that of the guest molecules which undergo jump rotational diffusion when the urea substructure is fixed in the simulation and continuous diffusion when the urea molecules are allowed to move. The elastic incoherent structure factor (EISF), which is determined by the rotational distribution of the alkane chains, is computed from the simulations and compared with experiment. When derived using the same approximations, the experimental and simulation-derived EISFs are in agreement. However, the EISF has not converged to its long-time limit in the experiment. A converged EISF is obtained from the simulation by applying appropriate averaging. The origins of the differences between the converged and experimental EISFs are discussed.