Key to the future of renewable energy, the largely unexplored set of organic polymers needed for new technologies such as organic cathode batteries and alkaline exchange membrane fuel cells (AEMFCs) demands new approaches to understand and improve critical properties. These materials are in unique, solvated environments---under applied voltages or in corrosive, alkaline settings---which make them susceptible to dissolution and device disruption. This thesis describes novel applications and techniques using Joint Density Functional Theory (JDFT) to understand and inform the design of these new organic materials. In the emerging field of AEMFCs, we begin by considering their chemical stability against attack by the hydroxide ions (OH$^-$) that they are designed to transport. We carry out a detailed \emph{ab initio} transition-state theory analysis to determine the absolute reaction rate for this AEM degradation process, finding excellent agreement with experiment. We find that, for these unique organic materials in these complex solvated systems, accuracy of the determined lifetime of this class of organic polymers requires selection of robust electronic and fluid models as well as characterization of the impact of hydrophobic regions formed by interstrand interactions. After reviewing the underlying techniques, we then introduce a novel method for computing redox potentials in organic battery materials by extending the Delta-SCF approach of quantum chemistry to solvated systems. After calibrating our results to an appropriate electrochemical potential scale, we accurately predict the redox values for a set of small test molecules, some characteristic larger molecules, and then phenothiazine-based polymer fragments. We demonstrate that these materials undergo significant restructuring during cycling that cannot be ignored and that capturing the complete solvation details is necessary to characterize organic materials once polymerized. Finally, we produce new results for the phenothiazine-based polymer PT-DMPD, finding excellent agreement with the first two redox potentials and uncover a mystery regarding the third redox peak. In addition, by examining the location of the electron holes introduced during redox events, we provide insight into possible degradation mechanisms for this system. Finally, two other key features of interest in designing new AEM materials, beyond their chemical stability, are mechanical stability and OH$^-$ transport. These properties, however, depend on the overall membrane structures that form on longer length-scales. To address this, we develop a novel, fully three-dimension approach to compute large-scale polymer structure based on a combination of the Cahn-Hilliard equation with microscopic \emph{ab initio} calculations interaction energetics between polymer units. Moreover, we develop methods to use the resulting structure information to predict experimental observables including transmission electron microscopy (TEM) and small angle X-ray scattering (SAXS) as well as properties of direct import to membrane performance, including mechanical stability and ion conductivity. This new approach has significant promise in aiding the development of new polymer systems. As a tractable and robust bridge between experimental techniques and theoretical methods to develop organic materials for renewable energy, these new analyses provide needed avenues for informed design.