As shown in Scheme 2, after the C145 is activated by a proton transfer to H41, thus forming the ion pair complex E (+/-) :I, the covalent complex is formed by the nucleophilic attack of the sulfur atom of C145 to the Cb atom of the B3 inhibitor. Then, the reaction is completed by the transfer of the proton from the protonated H41 to either the Ca atom, to render the E-I final covalent adduct, or to the carbonyl oxygen atom then ending in E-I . Exploration of both mechanisms by M06-2X/6-31+G(d,p)/MM FEP calculations revealed that the formation of the former (i.e. the direct addition mechanism) is both thermodynamically and kinetically favored with respect to the formation of E-I ' (see Figure in Supporting information). Thus, while the reaction that renders the E-I product is strongly exergonic (-16.2 kcal•mol -1 ), the energy of E-I ' product appears to be 15.2 kcal•mol -1 higher than the initial reactants state, E:I. These differences in the reaction energies are also associated, as mentioned, with significant differences in activation energies; 13.7 and 21.0 kcal•mol -1 to form E-I and E-I ' , respectively.