The use of free energy perturbation empirical valence bond (FEP/EVB) molecular dynamics technique for microscopic modeling of atom exchange reactions is examined. In particular, the analytical Morse and anti-Morse potentials for unpaired electron interactions are incorporated in the framework of molecular mechanics force field. Peroxidation of phenol is studied as a test case. The corresponding free energy profiles of hydrogen atom transfer are calculated by the FEP/EVB method in gas phase and chloroform. The reaction potential energy profile is also determined using DFT calculations. The FEP/EVB simulations correctly predict linear approach of reactants, tight structure of the transition state, and lower activation barrier in gas phase compared to solution.