The Born-Oppenheimer approximation, which allows a decoupling of electronic and nuclear motion, underlies the investigation of molecular dynamics. In some cases this decoupling is not possible, so that nuclear motion can induce changes in electronic state. It is then necessary to account for collision-induced transitions between multiple potential energy surfaces. This is an inherently quantum phenomena. In this dissertation we present a new way to visualize these non-adiabatic transitions in chemical reactions of open-shell atoms. Toward this end, we have developed new algorithms and developed a MATLAB-based software suite for simulating non-adiabatic reactions. We have also determined new molecular potential energy surfaces and their couplings required to simulate the reactive dynamics.