Classical chemical dynamics simulations were performed to compare the efficiency of energy transfer in collisions of Ar with 300 K CH3- and OH-terminated alkyl thiol self-assembled monolayer surfaces (i.e., H-SAM and HO-SAM) and compare with previous experiments (Anal. Chim. Acta 2003, 496, 249). The experiments show that energy is transferred less efficiently to the HO-SAM. The H-SAM has a periodic, ordered surface structure, whereas the surface of the HO-SAM has a disordered, "glassy" structure as a result of "clustering" of the terminal OH groups. The Ar atom has a much stronger physisorption interaction with the HO-SAM, arising from the strong Ar⋯O van der Waals interaction. Though the simulations show that physisorption is more important for Ar atoms colliding with the HO-SAM, energy transfer is less efficient to this surface. The latter results from a significant difference in the energy transfer for direct collisions with the two surfaces. More energy is deposited in the H-SAM for direct collisions. This difference appears to arise from enhanced efficiency to excite interchain intermolecular modes for the H-SAM as compared to the HO-SAM. The OH-group clustering enhances surface rigidity and decreases the efficiency of exciting intermolecular modes in direct collisions of Ar atoms with the HO-SAM. Overall, the energy transfer efficiencies determined from the simulations are in excellent agreement with experiment. The simulations suggest that the so-called trapping desorption (TD) component of the experimental translational energy distribution, for Ar + H-SAM scattering, actually consists of both physisorption and direct trajectories.