In this research, we investigate the effect of structural variation of Nafion 117 on the nanophase-segregation and transport properties using molecular modeling approach. In this study we replace the sulfate group of nafion117 with three different phosphate groups, and characterize its effect on nanophase-segregated structure and transport of water/protons at 80^oC with various water contents. The three groups that will be tested are: simply changing the sulfur to phosphorus in the Nafion117 tail group, changing the entire tail group to a polyvinyl phosphate, and changing the tail group to a difluoromethandiphosphonic acid. This will be done by simulating the new molecular structures using molecular dynamic simulations at 80^oC under isobaric conditions using LAMMPS. Dreiding force field will be partially modified to handle perfluorocarbon compounds, water, and hydronium. The equations of motion will be integrated using Verlet algorithm with a 1-fs time step, and the PPPM method to evaluate the electrostatic interactions. After an equilibration cycle, each system will then be simulated for an extra 2 ns to sample structures for statistical treatment. By simulating the proton conductivity of these molecules we seek to understand the relationship among underlying polar groups, nanophase-segregated structure, and transport which would serve in designing new polymer electrolyte membranes.