Future energy production and storage in the chemical and refinery industries, stationary power generation, and transportation sectors will employ a diverse suite of technologies, including renewables, such as biomass, untapped energy resources, and processes with improved energy efficiency. Heterogeneous nanocatalysts will play an ever-increasing role in these technologies. Increased precision in molecular architecture over multiple length scales and/or tailored multi-functionality will often be needed in these materials. Advances in computational-based discovery of such nanomaterials are described through examples that predict the molecular architecture of emergent catalytic materials and reveal mechanisms of colloidal metal nanoparticle growth.