Copper and manganese modified zeolites play key roles in selective oxidation catalytic reactions. Combining Density Functional Perturbation Theory (DFPT) implemented in VASP, and infrared spectroscopy experiments, we have studied and elucidated the incorporation of Cu 2+ and Mn 2+ in the framework of SiBEA zeolite. Six isomers are investigated for both models CuSiBEA and MnSiBEA. The energy stability study identified the most stable isomer in each case, which correspond to M-O2 bent moieties in the vicinity of hydroxyl groups. The isomers are then characterized by experimental and theoretical IR spectra. Both experimental and calculated IR spectra are in good agreement highlighting the presence of active sites (Cu-OH and Mn-OH) in the obtained models. The accurate molecular description of the nature of the active sites presented in this work will be important for understanding the catalysis going on and for developing novel catalytic processes.