Molecular dynamics (MD) simulations were performed to investigate the influence of molecular structure on the ability of n-alkanethiolate self-assembled monolayers (SAMs) on gold and copper to act as barrier films against through-film oxygen transport as relevant to the uses of these films in corrosion inhibition. Specific explorations focused on the effects of the packing density of the adsorbates, their chain length, and the size of the diffusing species. The MD simulations showed that the resistances offered by these monolayers against transport of small molecules strongly depend on the penetrant size and that the free volume alignment within these films has a large impact on the diffusivities of oxygen through them. The MD simulations revealed that the barrier for transport through these films increase by similar to 0.3 to 0.6 kJ/mol for increases in their thickness of only roughly an angstrom. MD simulations show the existence of a middle section in these SAMs for n >= 12 that was more crystalline and dense than the rest of the monolayer. The barrier resistances offered by these films toward oxygen transport, as calculated by the MD simulations, were a function of the crystallinity, density, and thickness of the middle section of the SAMs.