Calculations of the geometries and energies of the alkaline mordenites (MOR) CsxNa1–xMOR (where x = 0, 0.25, 0.5, 0.75, and 1) with and without toluene are reported. Differential scanning calorimetry (DSC) experiments are also shown. First, a structural stabilization of a pure silica zeolite was performed. Then four structures with different positions of the sodium atoms of the MOR with a molar ratio Si/Al = 5 were evaluated. The most stable structure was used to sequentially exchange sodium for cesium. In all cases, atoms are free to move to reach a local minimum of total energy. Toluene is initially located in three different geometries and the energy optimization calculation relocates it properly. Adsorption situations were observed when the electrons from the toluene aromatic ring interact with the sodium or cesium present within the main channel. DSC measurements were made with different amounts of toluene incorporated in MOR without cesium and in another with 7% of cesium. This technique indicated that the incorporation of Cs improved the adsorption capacity of the zeolite. The overall theoretical results are in good agreement with experimental evidence and constitute a reliable basis to advance in the study of new functionalized materials.