High explosives represent a class of materials known as energetic materials, in which providing an external stimulus of impact, heat, and electric shock can result in rapid exothermic reactions. Hence, there has always been a considerable research focus into the development, production, optimization, and control of these materials, aiming to increase explosive capabilities while also decreasing overall sensitivity to ignition.The study of impact induced chemical initiation of explosives is an inherent multiscale problem that requires time and length scales not accessible by a single experiment or calculation. The works presented here provide a theoretical effort to contribute to bottom-up modeling of the physics and chemistry phenomena in reacting high explosives using molecular dynamics simulations. Focus will be placed how energy localizes in the molecular crystal TATB, an insensitive high explosive.The first energy localization topic covered is an intra-molecular localization and distribution of the kinetic energy. Molecular dynamics is inherently classical, which partition energy equally between all modes. However, most molecular explosives should follow a quantum description, where energy is partitioned between modes following the Bose-Einstein distributions. A semi-classical approximation called the ‘quantum thermal bath’ is applied here to study classical vs. quantum effects for both shock and thermal initiation of chemistry. These results show, not only the importance of the changes to specific heat, which is expected, but the influence of the zero-point energy on reactivity.The idea of energy localization is then expanded to the microstructural level, focusing on hotspots, which are areas of extreme temperature following interactions between a shockwave and the microstructure. To date, hotspots have been characterized and described by the localization of their temperature fields only. This work develops a description of the potential energy field in the hotspot, which is markedly different from the temperature field and cannot be predicted from it, as has been previously assumed. This latent potential energy, that is non-thermal, manifests from intra-molecular strain in which individual molecules in the hotspot become highly distorted. This strain energy is shown to be driven by plastic flow during the formation of the hotspot.Lastly, the influence of the latent PE in hotspots on chemical reactivity is assessed. Reactive molecular dynamics calculations of shock induced pore collapse creates a hotspot in which deformed molecules can be separately assessed from undeformed ones. Deformed molecules are shown to react faster, follow different ensemble statistics, and undergo different first step reaction pathways. To better study these deformation under equilibrium, the Many-Bodied Steered MD method is developed in which multiple deformation modes are explored. It is shown that different deformation paths in the same molecule leads to different mechanochemical accelerations of kinetics and a different alteration of first step reaction pathways.