Organic materials with a judicious choice of functionalization have emerged as attractive candidates for use as active layers in new electronic technologies. This includes applications such as flexible displays, wearable electronics, and storage devices for gas separation and the capture of solutes such as chemical warfare agents. However, their use in the electronics industry is somewhat limited due to their tendency to pack into multiple, structurally distinct forms (a phenomenon known as polymorphism). For applications in energy storage technologies, due to the versatility of synthesis of organic framework materials, there remains an ongoing need to both elucidate and optimize the principles that govern performance with respect to size- and chemical- selectivity towards organic solutes. To address these challenges, we conducted detailed computational studies to develop a better understanding of the relationship between nanoscale structure and macroscale properties. Understanding polymorphism in organic semiconductors (OS) is critically important since any slight variation in π orbital overlap can lead to drastic differences in the charge carrier mobility. But finding polymorphs is a challenging task, because they are prone to structural reversibility, and have traditionally involved an iterative sampling with the possible structural space driven by those structures that lead to the lowest energy polymorphs (Y. Diao et al., J. Am. Chem. Soc. 136, 17046–17057, 2014). We have addressed this issue here by incorporating Bayesian Optimization into Molecular Dynamics (MD) simulations to predict polymorphs. Our test case was a high-performing organic semiconductor, bis(trimethylsilyl) [1]benzothieno[3,2-b]-benzothiophene (diTMS-BTBT). Our novel approach uncovered the relationship between minimizing the total energy as a function of a chosen design parameter and allowed us to identify the optimal structures by running time-consuming, expensive simulations for only a fraction (~15-20 percent) of the entire set of possible candidates (consisting of over 500 structures). Next, we expanded our investigation to use density functional theory to elucidate the molecular-scale mechanism behind the polymorphic transition in two related organic semiconductors, ditert-butyl [1]benzothieno[3,2-b]-benzothiophene (ditBu-BTBT) and diTMS-BTBT. By comparing their packing environment, we established a molecular "design rule" for selectively accessing both the so-called "nucleation and growth'' and "cooperative'' transition pathways in organic crystals. Finally, we characterized the structural and physical properties of two exemplars of organic woven materials, COF-506 and HKUST-1 MOF functionalized with large (10 nm-dia.) Palladium nanoparticles. Using MD, we explored the propensity of both these materials to be suitable for small-molecule gas diffusion within their densely interwoven matrix of structural entities. Our multiscale computational studies improve our current understanding of structure-property relationships in organic systems, providing key insight into the accelerated development of next-generation electronic materials.