For all the systems studied below, electrostatics were calculated using Ewald sPME. The range separation value, β, was chosen in each system so that the contributions to the real-space potential arising from charges outside the chosen cutoff radius are less than a threshold value of 10 -8 kcal•mol -1 . The 5th-order B-splines and tinfoil boundary conditions were used for all systems. An SCF convergence threshold of 10 -5 Hartree was used for all the QM/MM calculations. An additional correction of the velocities has been applied at each integration step of each MD simulation to enforce the translational and rotational invariance of the center of mass of the system. Both self-consistent versions of DFTB have been employed in combination with appropriate sets of parameters, including the MIO set for organic molecules, the OB2 set for organic and biological molecules, and the halorg set for halogens for DFTB2, and the 3OB set for organic and biological systems for DFTB3. To take the system from the initial to the final thermodynamic state we performed umbrella sampling, a biased molecular dynamics, to sample all the configurations along the reaction coordinate. The free energy profiles were reconstructed from Umbrella Sampling by applying the Weighted Histogram Analysis method (WHAM) algorithm through the code provided by Grossfield . The details for the umbrella sampling calculations and the QM/MM MD are described in the supporting information.