The flexibility of the side chain and effects of conformational changes in the backbone on hydration and proton transfer in the short-side-chain (SSC) perfluorosulfonic acid fuel cell membrane have been investigated through first principles based molecular modelling studies. Potential energy profiles determined at the B3LYP/6-31G(d,p) level in the two pendant side chain fragments: CF(3)CF(-O(CF(2))(2)SO(3)H)-(CF(2))(7)-CF(-O(CF(2))(2)SO(3)H)CF(3) indicate that the largest CF(2)-CF(2) rotational barrier along the backbone is nearly 28.9 kJ mol(-1) higher than the minimum energy staggered trans conformation. Furthermore, the calculations reveal that the stiffest portion of the side chain is near to its attachment site on the backbone, with CF-O and O-CF(2) barriers of 38.1 and 28.0 kJ mol(-1), respectively. The most flexible portion of the side chain is the carbon-sulfur bond, with a barrier of only 8.8 kJ mol(-1). Extensive searches for minimum energy structures (at the B3LYP/6-311G(d,p) level) of the same polymeric fragment with 4-7 explicit water molecules reveal that the perfluorocarbon backbone may adopt either an elongated geometry, with all carbons in a trans configuration, or a folded conformation as a result of the hydrogen bonding of the terminal sulfonic acids with the water. These electronic structure calculations show that the fragments displaying the latter 'kinked' backbone possessed stronger binding of the water to the sulfonic acid groups, and also undergo proton dissociation with fewer water molecules. The calculations point to the importance of the flexibility in both the backbone and side chains of PFSA membranes to effectively transport protons under low humidity conditions.