Transition metal doping of semiconductor nanomaterials, particularly magnetic dopant ions, is of great interest for the synthesis of diluted magnetic semiconductors (DMS) with spintronic-based applications. The incorporation of magnetic ions into quantum dots (QDs) would be particularly useful since the quantum confinement of these materials is theorized to enhance magneto-optical related properties. One major challenge in this field is the segregation of dopant ions towards the outer regions of the QD due to the exclusion of dopants during the nucleation process, thereby inhibiting the magneto-optical properties. In this dissertation, we address the dopant segregation challenge by exploring the underlying mechanisms which control doping along with QD nucleation and growth. To examine the nucleation process, we focus on the synthesis and doping of magic-sized clusters (MSC), which are suggested to be non-classical nucleation intermediates. We begin by studying doped Cd/S/SPh based molecular clusters for two reasons: 1) we are able to explore the mechanisms which control doping within a well-defined system which is analogous to larger nanocrystals and 2) we can utilize these doped clusters as single source precursors (SSP) with the goal of understanding what happens to the dopant ions during cluster conversion and subsequent nanocrystal nucleation. The use of pre-doped clusters as seeds for the synthesis of doped MSCs demonstrates the possibility of dopant retention during nucleation and allows us to gain mechanistic insight to the conversion process. Additionally, identifying the dopant speciation within the MSC allows us to discern structural information. We investigate this cluster conversion process further by complementary characterization methods to gain more insight into MSC formation. Lastly, we investigate the role MSCs play within the non-classical nucleation process to understand how MSCs evolve, either by dissolution or an aggregative mechanism, to form larger nanostructures. From this, we can determine the effectiveness of doping MSCs as a means to dope larger nanostructures. This work addresses the possibilities for control over dopant location within QDs by gaining insight into the growth mechanism from the conversion of pre-doped SSPs.