This paper presents classical dynamics simulations of Si(CD3)+3 scattering from a hexanethiolate self-assembled monolayer on Au(111) and from a clean Au(111) surface. Simulations are performed with a united atom model using purely repulsive scattering potentials. These simulations predict the partitioning of the incident ion kinetic energy into the scattered ion kinetic energy and the internal modes of both the surface and the ion. For the organic surface, the simulations predict energy transfer to surface, ion internal, and ion kinetic energies of 0.78, 0.11, and 0.12 of the collision energy. The corresponding transfer efficiencies of 0.12, 0.21, and 0.65 were calculated for the Au(111) surface. These computational results compare well with the experimental results on the same systems which are reported in the preceding paper. The simulations predict near specular scattering for both surfaces. They also demonstrate that the ion penetrates only the topmost two to three layers of Me atoms of the organic surface and that it spends up to 250 fs in contact with the surface. Finally, these calculations determine the dependence of energy transfer on the incident ion angle.