The polysiloxanes are known to have unusually high permeabilities, and have therefore been much investigated with regard to their possible use as gasseparation membranes. In particular, their permeabilities are much higher than those of n-alkanes such as polyethylene (PE), a polymer which has already been extensively investigated using molecular dynamics simulations. In order to gain insight into the molecular origin of this high permeability, such simulations have been carried out on hypothetical model systems in which the structure of the polyethylene chain [-CH2-CH2-]x is converted step-wise into that of the most important polysiloxane, poly(dimethylsiloxane) (PDMS) [-Si(CH3)2-O-]x. The structural modifications thus investigated include (i) increase in the C-C bond length, (ii) change of the system's density from the density of PE to the density of PDMS, (iii) change of bond angles of PE to the alternate bond angles of PDMS, (iv) replacement of the torsional potential of PE by the torsional potential of PDMS, (v) change of masses of CH2 units along the chain to alternate masses of Si(CH3)2 and 0 units, (vi) change of Lennard-Jones parameters of CH2 groups for the appropriate parameters of Si and 0 units. At each of the six steps the self-diffusion coefficients of polymer segments and penetrant molecules (CO2) were calculated, allowing for the assessment of the influence of the structure of the polymer on the diffusion of the penetrant.