Condensed organic molecules have distinct mechanical and electronic properties that differ from their metallic and organometallic counterparts. In the field of organic electronics, organic materials are an attractive alternative to inorganic materials due to their lower cost and inherent flexibility. In addition, organic molecules can be readily integrated into biological systems to perform functions on the molecular and cellular level. In this work, we explore three condensed organic systems using computational modeling methods. First, we investigate the formation of a heterojunction formed by two organic semiconductors: C60 growth on pentacene. This system is driven by an interest in flexible electronics, effective charge transport characteristics, and organic solar cells. Using coarse-grained molecular dynamics and kinetic monte carlo simulations, we elucidate the growth mechanics and surface morphology as a function of temperature. Second, we investigate the solution-phase structure of sulfonated oligothioetheramides (oligoTEAs), which will allow us to probe the interface between chemical sequence and macro-molecular structure. By understanding the atomic and molecular configuration space, we can predict macromolecular binding and target recognition in biological contexts. Here, we were able to validate and illuminate the mechanics behind oligomer collapse using aqueous phase molecular dynamics. Finally, we characterize the mechanical and chemical properties of an organic woven material, COF-505, which couples the flexibility of organic molecules with the strength of covalent or- ganic frameworks. Using molecular dynamics and a suite of optimization methods, we parameterize a force field describing this material. Subsequently, we characterize gas diffusion through COF-505 as a function of thermal and mechanical stress. While this new material has yet to be deployed in an applied setting, we expect this new hybrid material to have applications related to gas adsorption and carbon capture.