The sorption properties of polymers and the mobility of penetrants are the main factors which determine the trans-membrane processes. Other factors concern the membrane material structure and chemical nature. In this paper, we consider the case of polymers with similar structure units, namely a polymer and its pre-polymer (polybenzoxazinoneimide and imide-containing polyamic acid). The available experimental data show a great difference in the pervaporation process using these two polymeric membranes. Some explanation of this difference can be found at the atomic-level study. A comparative analysis of the diffusion of water and isopropanol molecules was carried out using the density functional theory and molecular dynamics simulations.