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Abstract
Molecular dynamics (MD) and ab initio molecular dynamics (AIMD) simulations provide a powerful framework for investigating the molecular-scale mechanisms that govern structure, dynamics, and reactivity in heterogeneous environments. This dissertation explores two central themes: proton transport in aqueous and interfacial systems, and the structure and dynamics of ionic liquids, by combining state-of-the-art simulation methodologies with free-energy sampling and polarizable force field development. The first part of this work focuses on proton solvation and transport in different environments. Using enhanced sampling methods, the transfer of hydrophobic solutes across water-oil interfaces was examined in the presence of different electrolytes. Remarkably, hydronium cations were found to stabilize hydrophobic solutes in aqueous phases and at interfaces, counteracting the expected salting-out effect of conventional ions. Additionally, the interfacial structure and dynamics of hydrated protons were investigated at water-air and water-oil interfaces. These studies revealed that interfacial environments promote Zundel-like proton structures and modulate proton-hopping kinetics, leading to an anti-correlation between discrete hopping and vehicular diffusion. Further AIMD simulations of aqueous sulfuric acid solutions uncovered the formation of metastable shared-proton contact ion pairs, stabilized by unusual hydrogen bonding, induction interactions, and solvation effects. Finally, by integrating AIMD simulations with ultrafast optical Kerr-effect experiments, the mechanisms of proton transport in sulfuric acid solutions were resolved. Proton hopping was identified as the dominant contributor to ionic conductivity, with excellent agreement between simulated diffusion constants and experimental measurements. The second part of this dissertation examines ionic liquids (ILs), with a focus on polarization effects. At the air-liquid interface of a room temperature ionic liquid, simulations showed that nonpolarizable models significantly overestimate structural order and underestimate dynamics, while scaled-charge models provide only limited improvement. By contrast, polarizable force fields accurately captured interfacial properties, underscoring the importance of explicit electronic polarization. To extend this approach, new Drude-based polarizable force fields were developed for amino acid ionic liquids (AAILs), a class of promising green solvents. These models accurately represented polarization and hydrogen bonding, revealing slow, heterogeneous dynamics distinct from those of conventional ILs and exposing the limitations of scaled-charge approximations. A supplementary video illustrates proton rattling events, highlighting the dynamic nature of proton sharing between bisulfate anions. Together, these studies advance the molecular-level understanding of proton transport and ionic-liquid behavior in heterogeneous environments. By bridging AIMD, polarizable force fields, and experimental validation, this dissertation establishes a transferable framework for probing interfacial processes and designing functional electrolytes.