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ii Proton transfer (PT) in fuel cell membranes consists of proton hopping along the hydrogen bond network (structural diffusion, occurs in the time scale of picoseconds) and the diffusion of the proton carrier between hops (vehicular diffusion, occurs in the time scale of nanoseconds). In this study, multi-scale modeling using quantum mechanics (QM), classical molecular dynamics (MD), and Atom-centered Density Matrix Propagation (ADMP) ab initio molecular dynamics (AIMD) using ONIOM hybrid calculations have been employed to investigate PT and the structure of the hydrogen bond network in phosphoric acid (PA)-doped polybenzimidazole membranes. QM calculations at the B3LYP/6-31++G(d,p) level of theory were performed to calculate gas-phase proton affinity, interaction energy, and energy barriers for different PT pathways between benzimidazole, PA, water molecules, and their corresponding ions. Results of energy barriers indicate a general trend that PT is prone to occur between the same molecules or between a molecule and its corresponding ion. Classical MD simulations using the Condensed-phase Optimized Molecular Potentials fo