In this thesis, theoretical ab initio treatments of two-body molecular collision reactions are studied, having in common that the interaction region including all coupling mechanisms driving the reaction amounts to a molecular description. The main goal is to gain an understanding in the underlying coupling mechanisms involved in these reactions.The thesis is divided into three projects. In project one, mutual neutralization in collisions of Na⁺ + I⁻, C⁺ + Cl⁻ and H⁺+H⁻ are studied, with an emphasis on the inclusion of spin-orbit and/or rotational couplings which are most often neglected for in mutual neutralization. Scattering quantities are computed ab initio and compared to approximative models and experimental results. In project two, the problem of asymptotic non-adiabatic couplings is studied. Specifically, the inclusion of higher order terms in the reprojection method is shown to give a much faster convergence of the relevant scattering cross section. The method is here applied to mutual neutralization in H⁺+H⁻collisions and inelastic scattering in Li+Na and H+H collisions. In project three, a generalized pseudo Jahn-Teller model is introduced an applied to electronic resonant states of H₃. Model parameters are extracted using electron scattering calculations resultingin a non-Hermitian Hamiltonian describing the system. The topology of the resulting complex adiabatic potential energy surfaces, including complex conical intersections and non-Hermitian degeneracies, are furthermore studied and classified.