Ion transport through perfluorosulfonic acid ionomers such as Nafion(R) is controlled by both the microstructure of the polymer and the charge and water distribution in the hydrated polymer. We present here the results of theoretical calculations on the side chain of Nafion(R), establishing microscopic information for the modeling of water and proton transport in the membrane. Optimized geometries for the trifluoromethane sulfonic acid fragment (CF3SO3H), the di-trifluoromethane ether fragment (CF3OCF3), and the side chain (CF3-OCF2CF(CF3)OCF2CF2SO3H) were determined by means of both ab initio Hartree Fock theory with second order Moller-Plesset electron correlation corrections, and density functional theory with Becke's three parameter hybrid method. Several rotational potential energy surfaces were calculated to assess chain flexibility and proton accessibility. A probe water molecule was added to each of the fragments to characterize hydrophilic sites. These calculations confirmed that the sulfonic acid group is hydrophilic and the ethers are hydrophobic. Molecular dynamics simulations were then performed on the side chain to check the conditions required to stretch the pendant chain. Thermal averages of several structural parameters assessing the flexibility and stretch of the chain were computed from selected conformations produced in the simulation and these results indicate that although the sulfonate group is free to rotate, the chain stretches little. The construction of a potential energy surface for rotation about the second ether group suggests that the side chain exists in a folded or curled up conformation. A physical continuum dielectric solvent model was used to obtain free energies of electrostatic interaction of the fragments and the full chain with the solvent.