| Proton solvation and transport (PS&T) in the condensed phase is one of the most fundamental and important processes, occurring in numerous chemical reactions, biological functions, and material applications. The molecular modeling of this essential phenomenon is particularly challenging due to the delocalized characteristics of the excess proton charge. This thesis is devoted to further develop the multistate empirical valence bond (MS-EVB) model, and to expand its applications to the biologically important ion channels (e.g., aquaporin channels, influenza A virus M2 channel), the acidic aqueous solutions of nonpolar neopentane hydrocarbon, as well as the imidazole-based proton exchange membrane fuel cells. By means of computer simulations using the MS-EVB model, the proton transport behavior has been extensively investigated in the abovementioned systems, and the corresponding calculated structural, energetic and dynamical properties are all in good agreement with experimental results. Furthermore, our studies have provided new insights into the proton solvation structures, proton transport mechanisms, and proton-triggered phenomena in a wide spectrum of environments, and these insights may facilitate a more systematic anti-flu drug design as well as a more efficient construction of anhydrous proton-conducting membranes. Finally, an efficient force-matching approach for MS-EVB has been developed, and was shown to substantially reduce the computational cost of nonbonded interactions by an order of magnitude in comparison to the original MS-EVB model. |
