Model perfluorosulfonic acid systems were constructed by functionalizing the inner walls of carbon nanotubes with fluorosulfonic acid groups. These systems were studied using ab initio molecular dynamics to investigate the nature of the interactions between water and the sulfonic acid groups and the dynamics of the water and hydrated protons as a function of water content. Specifically, the influence of the separation distance of the sulfonic acid groups on the dissociation of the proton, the formation of Zundel or Eigen ions, and proton transport and diffusion. The systems were created by decorating (14,0), (16,0) and (17,0) zig-zag carbon nanotubes with two or three -CF2SO3H groups. Water molecules were then added to hydrate the systems to values of 1-3 H2O/SO3H, resulting in a total of nine distinct simulation cells. The geometry of the cells was optimized and then heated to 300K via repeated velocity rescaling. Once equilibrated, trajectories were obtained in a microcanonical ensemble for up to 20 ps.