A theoretical study on average structures of molecules using direct ab initio MD method

Abstract

To elucidate the stability and the structure of a molecule, it is important to take account of the flexibility of the molecule. An equilibrium structure is a local minimum structure at the bottom of the potential energy surface; it differs from an average structure which is related to an observed dynamic structure in real systems. For different molecules which have similar structures, equilibrium structures may be similar, but average structures and the flexibility of molecules may differ. Here, octane and 1,2-diethoxyethane, either of which has a linear structure with 8 heavy atoms, are taken as the objective molecules. Equilibrium structures are calculated in the framework of ab initio MO method, and average structures and the flexibility of molecules are calculated using direct ab initio MD method. There are a lot of conformers of octane and 1,2-dithoxyethane in a small range of energy with low barrier heights. Based on the MD trajectories, we find that the average structures and the flexibility of both molecules are different, although the equilibrium structures are similar.