Diffusion of two small penetrant molecules, O-2 and N-2, in the bulk amorphous polyimide of 3,3’,4,4’-benzophenonetetracarboxylic dianhydride and 2,2-dimethyl-1,3-(4-aminophenoxy)propane is studied with molecular dynamics simulations. This polyimide is abbreviated as PI-2. The temperature of the simulation is chosen to be slightly below the experimental glass transition temperature of PI-2 (230 degrees C, or 503 K). The ratio of the diffusion coefficients of O-2 and N-2 in PI-2 from the simulation compares favorably with experimental results of the same ratio in structurally similar glassy polyimides. Detailed analysis is performed for the diffusion of O-2 in PI-2. Throughout the molecular dynamics trajectory, O-2 for most of the time is trapped in certain locations (voids) of the polymer matrix. The residence time is on the order of 100 ps. Occasionally, an O-2 goes into a fast motion and translates rapidly to a neighboring void. Some voids are visited by different O-2 at different times, indicating that although the thermal fluctuations of the polymer matrix play an important part in the diffusion process, conformational relaxation of the polymer chains may not be important for estimating the diffusion coefficient. The chemical and geometric environment of O-2 is studied via the pair correlation functions of the diffusant molecules and the atoms in the polymer. For some of the atoms in PI-2, the peaks in the pair correlation functions do not correspond exactly to the sum of the van der Waals radii of the atom in the diffusant molecule and the atom in the polymer chain. This finding indicates that the local packing of the amorphous polymer tends to shield some of the atoms from close contact with the diffusant molecules in the diffusion process. The atomic groupings in PI-2 that have the greatest exposure to O-2 are identified.