Presented here is a first principles based molecular modeling investigation of the possible role of the side chain in effecting proton transfer in the short-side-chain perfluorosulfonic acid fuel cell membrane under minimal hydration conditions. Extensive searches for the global minimum energy structures of fragments of the polymer having two pendant side chains of distinct separation (with chemical formula: CF(3)CF(O(CF(2))(2)SO(3)H)(CF(2))(n)CF(O(CF(2))(2)SO(3)H)CF(3), where n = 5, 7, and 9) with and without explicit water molecules have shown that the side chain separation influences both the extent and nature of the hydrogen bonding between the terminal sulfonic acid groups and the number of water molecules required to transfer the proton to the water molecules of the first hydration shell. Specifically, we have found that fully optimized structures at the B3LYP/6-311G** level revealed that the number of water molecules needed to connect the sulfonic acid groups scaled as a function of the number of fluoromethylene groups in the backbone, with one, two, and three water molecules required to connect the sulfonic acid groups in fragments with n = 5, 7, and 9, respectively. With the addition of explicit water molecules to each of the polymeric fragments, we found that the minimum number of water molecules required to effect proton transfer also increases as the number of separating tetrafluoroethylene units in the backbone is increased. Furthermore, calculation of water binding energies on CP-corrected potential energy surfaces showed that the water molecules bound more strongly after proton dissociation had occurred from the terminal sulfonic acid groups independent of the degree of separation of the side chains. Our calculations provide a baseline for molecular results that can be used to assess the impact of changes of polymer chemistry on proton conduction, including the side chain length and acidic functional group.