Surface ligands of semiconductor quantum dots (QDs) critically influence their properties and functionalities. It is of strong interest to understand the structural characteristics of surface ligands and how they interact with the QDs. Three quantum dot (QD) systems (CdSe, ZnSe, and ZnS) with primary aliphatic amine capping ligands were characterized primarily by FT-IR spectroscopy as well as NMR, UV-vis, and fluorescence spectroscopy, and by transmission electron microscopy (TEM). Representative primary amines ranging from 8 to 16 carbons were examined in the vapor phase, KBr pellet, and neat and were compared to the QD samples. The strongest hydrogen-bonding effects of the adsorbed ligands were observed in CdSe QDs with the weakest observed in ZnS QDs. There was an observed splitting of the N-H scissoring mode from 1610 cm(-1) in the neat sample to 1544 and 1635 cm(-1) when bound to CdSe QDs, which had the largest splitting of this type. The splitting is attributed to amine ligands bound to either Cd or Se surface sites, respectively. The effect of exposure of the QDs dispersed in nonpolar medium to methanol as a crashing agent was also examined. In the CdSe system, the Cd-bound scissoring mode disappeared, possibly due to methanol replacing surface cadmium sites. The opposite was observed for ZnSe QDs, in which the Se-bound scissoring mode disappeared. It was concluded that surface coverage and ligand bonding partners could be characterized by FT-IR and that selective removal of surface ligands could be achieved through introduction of competitive binding interactions at the surface.