Ionic ligands dramatically influences various ground and excited state properties of CdSe quantum dots (QDs). Ligands therefore, can be used to tailor CdSe QDs properties for application ranging from biolabeling, solar energy harvesting to display technology. Atomic level investigation was performed via Density Functional Theory (DFT) calculations, these calculations provide insight to the effects of hydride (H-) and Phenyldithiocarbamates (PTC) on CdSe QDs. When simulating the effect of H- treatment on CdSe QDs, the photoluminescence (PL) increase because H- reacts with surface ions to form H2Se and Cd2+–H- bonds. These interaction are beneficial when creating a display however, the interaction between PTC and CdSe QDs could lead to poor solar cells. When PTC ligands are exchanged with native ligands PTC decomposes. DFT calculations provide evidence that these products of the decomposition can also exchange with native ligands “polluting” the surface. This pollutants could decrease the efficient of the solar cell by causing defect states preventing the separation of the electron and hole pair. Atomic level DFT calculations has shown the necessity to understand the interaction between ionic ligands and CdSe QDs for their ground and excited state properties.