Previous studies have shown that the permeation through these silica-based membranes is based on a mechanism that involves the hopping of gas species between solubility sites. A molecular modeling approach, namely density functional theory, is used to calculate activation energies of permeation for various gases (He, H2, Ne, CO, CO2, CH4) through silica-based membranes. Permeation through these membranes is modeled as passage of the permeating species through 6-membered siloxane rings, which act as critical openings between the solubility sites. Within DFT, the Becke3lyp with accurate basis sets (6-311G (2d, p), LANL2DZ) is applied to optimize these ring structures and the permeating species. The activation energies are estimated as the interaction energy of the permeating species approaching and passing through H12Si5O6X cyclosiloxane based rings. These siloxane rings contain aluminum, boron, silicon, titanium, yttrium and zirconium, which can be introduced into the structure to potentially improve the permeation properties of the silica membranes. The optimized siloxane based rings have a buckled conformation due to the asymmetry created by the inorganic oxides. The calculated activation energies of the buckled silica-yttria and silica-zirconia rings (20–40 kJ mol-1) are found to be similar to those reported for planar silica rings (10–30 kJ mol-1). The calculated activation energies for the buckled silica-alumina, silica-boria, silica-titania rings (60–100 kJ mol-1) are found to be higher than those reported for planar silica rings and suggest a much denser structure for these membranes.