The theoretical investigation of the scattering of copper phthalocyanine molecules in the surface field taking account of the vibration-rotational interaction was performed by molecular dynamics method, its propagator modification of the second order of accuracy. A software complex was developed to simulate the interaction of gas molecule assembly with a solid surface at a given temperature and gas volume density. Comparative analysis of molecule scattering was performed for the continuous and crystal silicon substrate models. The following elementary processes were investigated: 1) the scattering of a molecule on Si surface; 2) the collision of two molecules in gas phase; 3) the collision of two molecules one of which is bound on the Si surface.