We report a study on the reactions of protonated cysteine (CysH(+)) and tryptophan (TrpH(+)) with the lowest electronically excited state of molecular oxygen (O-2, a(1)Delta(g)), including the measurement of the effects of collision energy (E-col) on reaction cross sections over the center-of-mass E-col range of 0.05 to 1.0 eV. Electronic structure calculations were used to examine properties of complexes, transition states and products that might be important along the reaction coordinate. For CysH(+) + O-1(2)., the product channel corresponds to C-alpha-C-beta bond rupture of a hydroperoxide intermediate CysOOH(+) accompanied by intramolecular H atom transfer, and subsequent dissociation to H2NCHCO2H+, CH3SH and ground triplet state O-2. The reaction is driven by the electronic excitation energy of O-1(2), the so-called dissociative excitation energy transfer. Quasi-classical direct dynamics trajectory simulations were calculated for CysH(+) + O-1(2) at E-col = 0.2 and 0.3 eV, using the B3LYP/6-21G method. Most trajectories formed intermediate complexes with significant lifetime, implying the importance of complex formation at the early stage of the reaction. Dissociative excitation energy transfer was also observed in the reaction of TrpH(+) with O-1(2), leading to dissociation of a TrpOOH(+) intermediate. In contrast to CysOOH(+), TrpOOH(+) dissociates into a glycine molecule and charged indole side chain in addition to ground-state O-2 because this product charge state is energetically favorable. The reactions of CysH(+) + O-1(2) and TrpH(+) + O-1(2) present similar E-col dependence, i.e., strongly suppressed by collision energy and becoming negligible at E-col > 0.5 eV. This is consistent with a complex-mediated mechanism where a long-lived complex is critical for converting the electronic energy of O-1(2) to the form of internal energy needed to drive complex dissociation.