This dissertation examines the effects of phase transfers with thiol ligands on the optical properties of quantum dots (QDs) in water by investigating two systems: i) dihydrolipoic acid (DHLA)-capped PbS QDs and ii) thiolated DNA-capped core/shell CdSe/CdS QDs. QDs are bright, monodisperse, and tunable hydrophobic nanoparticles with high photoluminescence (PL)...