Dynamics of Ar atom collisions with a perfluorinated alkanethiol self-assembled monolayer (F-SAM) surface on gold were investigated by classical trajectory simulations and atomic beam scattering techniques. Both explicit-atom (EA) and united-atom (UA) models were used to represent the F-SAM surface; in the UA model, the CF3 and CF2 units are represented as single pseudoatoms. Additionally the nonbonded interactions in both models are different. The simulations show the three limiting mechanisms expected for collisions of rare gas atoms (or small molecules) with SAMs, that is, direct scattering, physisorption, and penetration. Surface penetration results in a translational energy distribution, P(E-f), that can be approximately fit to the Boltzmann for thermal desorption, suggesting that surface accommodation is attained to a large extent. Fluorination of the alkanethiol monolayer leads to less energy transfer in Ar collisions. This results from a denser and stiffer surface structure in comparison with that of the alkanethiol SAM, which introduces constraints for conformational changes which play a significant role in the energy-transfer process. The trajectory simulations predict P(E-f) distributions in quite good agreement with those observed in the experiments. The results obtained with the EA and UA models are in reasonably good agreement, although there are some differences.