We describe molecular orbital theory and ab initio molecular dynamics studies of acid/base equilibria of clusters AH : (H₂O)_n ⇔A⁻ : H⁺(H₂O)_n in low hydration regime (n = 1–4), where AH is a model of perfluorinated sulfonic acids, RSO₃H (R = CF₃CF₂), encountered in polymer electrolyte membranes for fuel cells. Free energy calculations on the neutral and ion pair structures for n = 3 indicate that the two configurations are close in energy and are accessible in the fluctuation dynamics of proton transport. For n = 1, 2 the only relevant configuration is the neutral form. This was verified through ab initio metadynamics simulations. These findings suggest that bases are directly involved in the proton transport at low, n = 3, hydration level, but not at lower hydration levels, n ≤ 2. In addition, the gas phase proton affinity of the model sulfonic acid H was found to be comparable to the proton affinity of water. The free energy profile for proton exchange between a protonated acid–water cluster configuration and a neutral acid–hydronium ion cluster configuration showed that such configurations are nearly isoenergetic. Thus, protonated acids can also play a role in proton transport under low hydration conditions and under high concentration of protons.