CONSPECTUS: The vital importance of energy to society continues to demand a relentless pursuit of energy responsive materials that can bridge fundamental chemical structures at the molecular level and achieve improved functionality and performance. This demand can potentially be realized by harnessing the power of self-assembly, a spontaneous process where molecules or much larger entities form ordered aggregates as a consequence of predominately noncovalent (weak) interactions. Self-assembly is the key to bottom-up design of molecular devices, because the nearly atomic-level control is very difficult to realize in a top-down, for example, lithographic, approach. However, while function in simple systems such as single crystals can often be evaluated a priori, predicting the function of the great variety of self-assembled molecular architectures is complicated by the lack of understanding and control over nanoscale interactions, mesoscale architectures, and macroscale order. To establish a foundation toward delivering practical solutions, it is critical to develop an understanding of the chemical and physical mechanisms responsible for the self-assembly of molecular and hybrid materials on various support substrates. Typical molecular self-assembly involves noncovalent intermolecular and substrate-molecule interactions. These interactions remain poorly understood, due to the combination of many-body interactions compounded by local or collective influences from the substrate atomic lattice and electronic structure. Progress toward unraveling the underlying physicochemical processes that control the structure and macroscopic physical, chemical, mechanical, electrical, and transport properties of materials increasingly requires tight integration of theory, modeling, and simulation with precision synthesis, advanced experimental characterization, and device measurements. Theory, modeling, and simulation can accelerate the process of materials understanding and design by providing atomic level understanding of the underlying physicochemical phenomena (illuminating connections between experiments). It can also provide the ability to explore new materials and conditions before they are realized in the laboratory. With tight integration and feedback with experiment, it becomes feasible to identify promising materials or processes for targeted energy applications. In this Account, we highlight recent advances and success in using an integrated approach based on electronic structure simulations and scanning probe microscopy techniques to study and design functional materials formed from the self-assembly of molecules into supramolecular or polymeric architectures on substrates.