Adsorption and dynamics of acetonitrile molecules in mordenite zeolite have been studied by a combination of molecular dynamics and electronegativity equalization methods. Computation results predict adsorption of the molecules in both the main channels and the side pockets of the structure. Adsorption in the side pockets is favored but is hampered by a sterical hindrance and an energy barrier between main channels and side pockets. Increase of the temperature as well as of the adsorbate loading lead to an increase of the occupation of the side pockets. Analysis of the molecular dipole and atomic charges distributions reveal that confinement in the side pockets enhances the polarization of acetonitrile. Charge redistribution together with a high residence time of the molecules in the side pockets explain the easier protonation by hydroxyl groups in the side pockets, in agreement with experimental data.