The permeation properties of hybrid inorganic-organic membrane with a silica crystalline framework are studied using quasi-non-equilibrium molecular dynamics. In particular the authors consider the single gas permeation of carbon dioxide and methane using the silica framework with phenyl groups inserted. The authors compare two types of membrane models, namely (a) single-pore with phenyl groups inserted (PSPM), and (b) single-pore without phenyl groups inserted (SPM) are developed. The pore diameter in the SPM model affects the performance of gas permeation. For the PSPM models the diameter significantly affects the selectivity; the optimum diameter is found to be 0.4 nm. This leads to a carbon dioxide permeance of 2.87 X 10(-4) moi m(-2) s(-1) Pa, methane permeance of 1.66 x 10(-5) mol m(-2) s(-1) Pa-1 and a selectivity of 17.3. Finally based on the pore size two permeation mechanisms are analyzed from the atomic level and the effect of the number of phenyl groups (phenyl group pairs) in one type of membrane model is discussed. (C) 2011 Elsevier B.V. All rights reserved.