Nanocrystalline solids have become the subject of intense study due to their unique optical properties and their capacity to form self-assembled superlattices making them suitable for use in a variety of applications such as solar cells, light-emitting devices, etc. In this thesis, we have used atomically and molecularly explicit Molecular Dynamics simulations to create a fundamental understanding of these systems. We have shown that size of the nanocrystal and the grafting density of ligands can affect the morphology of the ligand corona. We have studied the links between processing conditions and the resultant symmetry of the superlattice, whether face-centered cubic (fcc) or body-centered cubic (bcc) structures. Our results for the free energies of the system provide definitive proof of a clear dependence of preferred superlattice symmetry on the ratio of ligand length to nanocrystal size. We also provide a fundamental understanding regarding the effect of microstructural details on the electronic structure and charge transfer properties in nanocrystal superlattices. Specifically, we have shown that the charge transfer rate between nanocrystals depends on the shape and ratio of the areas of the different facets on the nanocrystal core. The impact of this kind of study is the provision of key insights into molecularscale information about the relative roles of surface-bound ligands and nanoparticle cores that are very difficult to determine experimentally. This insight, we hope, can be leveraged to ably guide future experimental studies.