Atomistic molecular dynamics simulations were performed to study hydrated Nafion systems large enough (approximately 2 million atoms, approximately 30 nm box length) to directly observe several hydrophilic domains at the molecular level. These systems consisted of six of the most significant and relevant morphological models of Nafion to-date: (1) the cluster-channel model, (2) the parallel cylinder model, (3) the local order model, (4) the lamellar model, (5) the rod network model, and (6) a "random" model that does not directly assume any particular geometry, distribution, or morphology. Each system was initially built to closely approximate the proposed hydrophilic cluster structure in a given model. Molecular dynamics simulations were then used to observe resulting changes from and behavior of the assumed initial configurations. These simulations revealed fast intercluster "bridge" formation and network percolation in all models. Sulfonate groups were found inside these bridges and played a significant role in percolation. Sulfonates also strongly aggregated around and inside clusters. Cluster surfaces were analyzed to study the hydrophilic-hydrophobic interface. Interfacial area and cluster volume significantly increased during the simulations, and radial distribution functions and structure factors were also calculated. All nonrandom models clearly exhibited the characteristic experimental scattering peak, underscoring the insensitivity of this measurement to hydrophilic domain structure and highlighting the need for future work to clearly distinguish morphological models of Nafion.

An electronically polarizable model, based on the AMBER nonpolarizable model, has been developed for the ionic liquid (IL) 1-ethyl-3-methyl-imidazolium nitrate (EMIM(+)/NO(3)(-)). Molecular dynamics simulation studies were then performed with both the polarizable and nonpolarizable models. These studies suggest EMIM(+) cations have a strong tendency to pack with their neighboring imidazolium rings nearly parallel to each other, bridged by hydrogen bonds to NO(3)(-) anions. Polarization has two key effects, (1) additional charge-dipole and dipole-dipole interactions enhance short-range electrostatic interactions and (2) screening reduces long-range electrostatic interactions. As a result, the polarizable model exhibited enhanced hydrogen bonding compared to the nonpolarizable model, while the latter retained more ordered long-range spatial correlations than the former. Though EMIM(+) has a very short nonpolar ethyl tail group, spatial heterogeneity, previously observed with long-chain ILs, was observed in this system and has been quantified using the heterogeneity order parameter. The polarizable model was slightly more heterogeneous than the nonpolarizable model. The enhanced spatial heterogeneity of the polarizable model is again attributed to the stronger short-range electrostatic interactions, which "push" the nonpolar tails away from the polar heads, leading to more aggregation and a strongly altered ionic packing pattern around NO(3)(-) as observed by a different anion-anion center-of-mass partial radial distribution function g(--) (r). Interestingly, both models seemed to "remember" the crystal structure even at temperatures significantly higher (approximately 90 K higher) than the melting point (311 K). Along with the results on the dynamical properties reported in the accompanying paper, the current study demonstrates that electronic polarizability is significant in ionic liquid systems.