Abstract Modeling zeolites structure including strongly interaction extra-framework species by using DFT is still a difficult task now a day. To face this problem, we have introduced here a simulated annealing (SA) method to obtain global minimum energies. This approximation has been applied to describing the structure of free common zeolites. Basically, the SA idea is to perform a molecular dynamics (MD) by increasing the temperature steps by steps to overcome local energy minima, after that, by subsequent energy optimization it is possible to move to a different local minimum. This procedure was done up to the temperatures of 300 and 400 K. MD, as well as, geometry optimization were carried out in a periodic framework and dispersion corrected Density Functional Theory (DFT) calculations using VASP. The results show that it seems to be very important to accomplish SA calculation in order to obtain an adequate global minimum, reducing the energy of the system up to 0.072 e V T O 2 . The impact on computing interaction energies with adsorbed molecules is high, with large implications in predicting adsorption, separation, ion-exchange and catalytic properties. Our results are in good agreement with known experimental and theoretical literature.