As the global demand for energy continues to rise, proton exchange membrane (PEM) fuel cells have received considerable interest as clean, efficient energy conversion devices. PEM fuel cells offer high power density, fast startup time, and are light weight which make them promising candidates for stationary, portable, and automotive use.1 An ideal PEM must exhibit high proton conductivity but low electrical conductivity, sustained mechanical durability over several operating cycles, and high thermal and chemical stability. Currently, perfluorosulfonic acid (PFSA) ionomers are the most widely used PEMs.PFSA membranes consist of a hydrophobic poly(tetrafluoroethylene) (PTFE) backbone with hydrophilic sulfonic acid-terminated perfluoroether pendant side chains. Proton conduction in PFSA membranes relies heavily on the adsorption of water. Hydration results in the formation of hydrophilic domains where proton dissociation of the sulfonic acid groups occurs facilitating long-range proton transport. The high proton conductivity in currently available PFSA membranes, however, is only observed at high levels of hydration leading to adverse water cross-over due to electro-osmotic drag and permeation and limits the operating temperature to below the boiling point of water which demands the use of expensive platinum-based catalysts.2 This has led to immense effort to develop membranes with high proton conductivity at lower hydration allowing for higher temperature operation.The hydrophilic domains containing the water molecules, protons, and acidic groups are only a few nanometers in diameter.3 The structural and dynamical properties of water and protons under confinement differ distinctly from the bulk. These properties are also influenced by the sulfonic acid group density, the level of hydration, and the nature of the confined environment.3 Furthermore, proton transport in these materials is highly dependent on the structure and dynamics of hydrogen bonds, which are considerably impacted by nanoscale confinement. As such, an understanding of how the confined environment affects the nature of confined water is needed. Due to the small scale of the confined dimensions and the complexity of the membrane, model systems are often used to study nanoconfinement effects.Carbon nanotubes (CNTs) provide simple, well-structured model systems to investigate nanoscale confinement while also allowing for systematic alteration of relevant parameters. Previous ab initio molecular dynamics (AIMD) simulations have been performed to investigate the influence of nanoconfinement, the nature of the confined surface, and sulfonic acid group density on proton dissociation and transport in simplified model PFSA systems of bare and fluorinated CNTs of various diameters functionalized with −CF2SO3H groups at low hydration levels.4-7 The present work extends upon this using AIMD to study the effect of nanoconfinement on: (1) water molecules at different densities, (2) water molecules with an excess proton, and (3) aqueous triflic acid at hydration levels of λ = 1-3 (λ ≡ n H2O/n SO3H). CNTs with chirality (14,0) and (17,0), having diameters of 11.0 and 13.3 Å, were chosen to explore the effect of the confinement dimension on structural and dynamical properties, and the nanotube walls were either left bare or fluorinated to determine the influence of the surface hydrophobicity. Periodic boundary conditions were imposed with 4 Å of vacuum added to the perpendicular directions to avoid interactions with other images in the supercell, and up to 30 ps trajectories were obtained in the microcanonical ensemble. Examples of the systems are shown in Figures 1-3. The simulations reveal for each system that fluorinating the CNT walls results in considerably different molecular arrangements and hydrogen bonding than in the bare CNTs and also influences the nature of the proton(s).