Electronic structure calculations were performed to understand highly decoupled conductivities recently reported in protic ionic liquids (Pits). To develop a molecular-level understanding of the mechanisms of proton conductivity in PILs, minimum-energy structures of trimethylamine, imidazole, lidocaine, and creatinine (CRT) with the addition of one to three phosphoric acid (PA) molecules were determined at the B3LYP/6-311G** level of theory with the inclusion of an implicit solvation model (SMD with epsilon = 61). The proton affinity of the bases and zero-point energy corrected binding energies were computed at a similar level of theory. Proton dissociation from PA occurs in all systems, resulting in the formation of ion pairs due to the relatively strong basicity of the bases (proton acceptors) and the effect of the high dielectric constant solvent in stabilizing the charge separation. The second and third PA molecules preferentially form "ring-like" hydrogen bonds with one another instead of forming hydrogen bonds at the donor and acceptor sites of the bases. Potential energy scans reveal that the bases with stronger proton affinity exert greater influence on the energetics of proton transfer between the individual PA molecules. However, the effects are minimal when shifted into a single-well from a double-well potential. Barrierless proton transfer was observed to occur in the CRT system with several PA molecules present, implying that the CRT may be a promising PA-based PIL.