Motivated by the development of a microelectromechanical (MEMS) corrosion sensor which utilises a thin polydimethylsiloxane (PDMS) membrane as a permeable medium, molecular dynamics (MD) simulation is used to study the diffusion of CH4, N2 and O2 penetrates in uncrosslinked PDMS. Both PDMS and penetrates are modelled within the MD framework using a hybrid coarse-grained interatomic potential; the accuracy of this model and its ability to capture structural aspects of PDMS, including bulk densities and radius of gyration, is evaluated. Diffusion constants and activation energies are computed after reaching steady state using simulation models with ‘long’ and ‘short’ PDMS chains (above and below the entanglement molecular weight of PDMS, respectively). Diffusion coefficients computed using short-chain models are higher than those with long-chain models, due to the presence of molecular entanglements in the long-chain PDMS systems. A linear correlation is found between the natural logarithm of the diffusion constant and the activation energy for diffusion in agreement with experimentally determined phenomenological relationships.