Dynamics simulations were performed to study soft landing of SiNCS + and (CH3)2SiNCS+ ions on a self-assembled monolayer of perfluorinated alkanethiols on gold (F-SAM). Using classical trajectories, the short-time collision dynamics (picosecond scale) were investigated to analyze trapping probabilities for these silyl ions. Thermal desorption of trapped ions was simulated by using "boxed molecular dynamics" (BXD). The simulations predict substantial ion trapping in the collisions of these ions with the F-SAM, especially when the projectile's incident direction is normal to the surface. Desorption of the SiNCS+ ion occurs significantly faster than desorption of the methylated ion, which may explain why soft landing was experimentally observed for the latter ion only [Miller, S. A.; Luo, H.; Pachuta, S. J.; Cooks, R. G. Science 1997, 275, 1447-1450; Luo, H.; Miller, S. A.; Cooks, R. G.; Pachuta, S. J. Int. J. Mass. Spectrom. Ion Processes 1998, 174, 193-217]. The free energy profiles for desorption of these ions show minima at 15 Å above the gold slab, indicating that the silyl ion has a preference to reside on top of the monolayer. Deep penetration of the ion into the monolayer is prevented by a large free energy barrier. However, according to DFT calculations, if this process occurred, the SiNCS+ ion could strongly bind to the Au(111) surface that supports the perfluorinated alkanethiol chains.