Dynamic simulation of orientational disorder in organic crystals: methyl groups, trifluoromethyl groups and whole molecules

Abstract

Large amplitude librations of atomic groups or of entire molecules in their crystals are simulated using optimized intermolecular potentials and crystal structures deposited in the Cambridge Structural Database. The analysis proceeds by a simple static model in which reorientations take place in a fixed environment, or by Monte Carlo (MC) simulation of equilibria dotted by rotational defects, or eventually by full Molecular Dynamics (MD). The simplest approach provides a valuable qualitative preview, but MC and MD are becoming easily accessible to the general solid-state chemist thanks to the facilities of the newly developed Milano Chemistry Molecular Simulation (MiCMoS) platform. Their combined results offer a wealth of information on the behaviour of phenyl–methyl and phenyl–trifluoromethyl groups, almost invariably affected by rotational flipping, whose nature and consequences are discussed with respect to disorder modelling in the refinement of X-ray structures. Whole-body reorientation takes place in flat molecules, benzene being the well-known prototype, but also in a very large molecule like coronene. Molecular dynamics of rotations in the cyclohexa-1,4-diene crystal offer a spectacular picture of the energetic profiles with jumping times. The dynamic oscillations described here are seldom considered in the formulation of crystal `bonds' or of `synthon' stability.