Molecular semiconductors are promising candidates for active components of organic electronic devices as they have tunable optoelectronic properties and can be incorporated into lightweight, large-area, flexible devices. Numerous challenges to commercial implementation of molecular semiconductors exist, stemming from structural heterogeneities in polycrystalline thin films that influence charge transport. The microstructure of thin film active layers depends on both chemical structure and processing conditions. Thus, it is important to develop understanding of the complex relationships that govern these systems.This thesis explores chemistry-structure-function relationships across multiple length scales in molecular semiconductor systems. We developed relationships between chemical structure and optoelectronic properties through design of coronene derivatives for visibly transparent organic photovoltaics (OPVs). We screened potential molecules using computed energetic properties, from which we selected and synthesized three coronene derivatives for use in the active layers of visibly transparent OPVs. This project demonstrated how integrated computational and experimental efforts can accelerate materials design.We also characterized the solid-state packing of molecular semiconductors to elucidate relationships between structure and device function. We explored the role of halogenated coronene derivatives on the stability of OPVs and found halogenated coronenes, which are amorphous as-deposited, crystallized during aging. The crystallization produced gaps between device layers, hindering charge extraction and degrading OPV performance.We also examined the impact of atomistic substitution in the side groups of two functionalized pentacenes, controlling side group size but increasing electron density, which increased the structural phase space accessed. This work established that solid-state packing of functionalized acenes depends on both side group size and electron density. Finally, we explored the impact of grain boundaries on the kinetics of polymorphic transformations in a naphthalene tetracarboxylic diimide. We determined grain boundaries lower the activation energy by initiating polymorphic transformations. This work demonstrated the importance of grain boundaries, which are common in organic systems,for both their impact on charge transport and as initiators of polymorphic transformations.Collectively, this thesis highlights the importance of developing robust chemistry-structure-function relationships that can guide material development. We demonstrate methodologies and illuminate concepts that will enable future improvement to the performance and stability of organic electronics.