Since the industrial revolution, anthropogenic greenhouse gas emissions, namely from hydrocarbon combustion, have been rising steadily, leading to increasing global temperature and potentially catastrophic climate implications. International recognition of emissions driven temperature rise has led to mitigation frameworks, most prominently the Paris Agreement within the United Nations Framework Convention on Climate Change (UNFCCC) that aims to limit warming to well below 2˚C above pre-industrial levels. However, global energy demand has never been higher, with projections of increased energy demand over the coming decades. To reconcile these two diverging trajectories, an unprecedented transition to low-carbon energy systems is required. Imperatively, this requires contributions across all scales of the energy innovation system, from fundamental research to pilot-scale application to commercial deployment to government policy supports. This dissertation spans much of the course of this innovation system, providing snapshots of research along the way from atomic level insight to policy level recommendations. Beginning at the smallest scale, Density Functional Theory coupled with the Nudged Elastic Band method provides resolution on the atomic interactions at play in reactive systems. Benchmarking the performance of this approach across families of reactions provides a foundation for how to extend this methodology to complex problems. Then, these principles are verified on the thiol-Michael addition, a popular reaction in organic chemistry. After delineating the thiol-Michael addition’s reaction kinetics, a previously undiscovered reaction step is defined to support the cyclic nature of the reaction. Subsequent verification of this step with experimentally observed kinetics shows the predictive potential of this approach. With a solid foundation in place, this approach is applied at the fundamental level of the energy innovation system. Meticulous delineation of a posited reaction for the synthesis of lead sulfide quantum dots provides insight into controlled and scalable production of these materials for next-generation solar photovoltaics. At an applied level, Molecular Dynamics is employed to investigate the behaviour of next-generation materials for optimization of performance. Rising adoption of electric vehicles has led to increased demand of lithium for batteries and necessitates specialized extraction methods from low-concentration sources. Through simulation of the supercritical carbon dioxide extraction of lithium from geothermal brine, a binding free energy metric is related to the extraction efficiency and selectivity over sodium. Then, these metrics are juxtaposed with extractant structure to describe the chemical behaviour behind enhanced performance. Similarly, increasing energy demand has necessitated innovative approaches to improved energy efficiency. Simulation of the assembly of phase change material capsules - important for energy storage applications - reveals the dynamical behaviour of phase change material synthesis and the relationship between molecular structure and material performance. Moving now to a large scale, evaluation of process level economic and environmental performance connects these next-generation materials to more tangible metrics for evaluating commercial and emissions reduction potential. In particular, carbon capture, utilization, and storage processes offer promising pathways for net-zero production of fuels, chemicals, and other renewable products. Evaluation of an integrated electrocatalytic and biocatalytic carbon dioxide utilization process relates technological improvements to resulting economics, providing a roadmap to achieve profitable bioplastic production, along with policy mechanisms that could support this transformation. The impact of these policy mechanisms is related back to market diffusion and ultimate emissions mitigation potential of low carbon technology using a case study of a CO2-to-diesel process within Canada’s market and policy environment. This is in addition to public acceptance and commitment. These relationships underscore the importance of strategic policy on meeting the Paris Agreement target. Despite advancements across scales of the energy innovation system, a coordinated effort from all stakeholders is critical to the ultimate success, or failure, of this global energy transition. My work embraces this coordinated approach, demonstrating advancements across scales that, together, drive forward the innovation of low-carbon energy systems.