Molecular dynamics simulations are used to probe the response of a sel
f-assembled monolayer of hexadecanethiol chemisorbed on a gold(111) su
rface to compression with a flat surface and a surface with atomic-sca
le roughness in the form of surface asperities. The film responds elas
tically with only a uniform change in tilt angle upon compression to l
ow loads with the flat surface. In contrast, our results show that the
asperities are able to get closer to the substrate relative to the fl
at surface at comparable loads without completely disrupting the film
and that at higher loads the monolayer film disorders by creating a la
rge number of gauche defects in order to accommodate the asperity. The
findings presented in this work support conclusions based on recent s
canning tunneling microscopy studies on self-assembled monolayers that
imaging occurs at surface asperities which penetrate the film.