A Hamiltonian is described in which some degrees of freedom are represented by normal modes and the remainder retain their complete couplings and anharmonicities. The classical equations of motion for this Hamiltonian may be efficiently integrated in Cartesian coordinates. This Hamiltonian is used to study the mode specificity of energy transfer in Ne-atom collisions with alkanethiolate chains and a monolayer of il-hexyl thiolate chains self-assembled on Au{111}. The intermolecular and intramolecular degrees of freedom for these chain and self-assembled monolayer (SAM) systems are represented by normal modes. Collinear collisions with n-hexyl and n-octadecyl thiolate chains show that only one mode is excited at low collision energies. Mode specificity is also observed in Ne-atom collisions with the SAM. As expected from the adiabatic/ impulsive model of T --> V energy transfer, higher frequency modes of the chains and monolayer are excited as the Ne-atom translational energy is increased. A comparison, between this normal mode model and an anharmonic surface model, suggests it is efficient energy transfer to highly anharmonic modes of the surface which give rise to the Boltzmann component in the translational energy distribution of the scattered Ne atoms.