We have performed the first systematic density functional theory study of the coordination of three biomedically significant ligands, acetylcysteine, dihydrolipoic acid, and dopamine, to a small quantum dot (QD), Zn6S6. An exhaustive search for the global minima structures of the ligands and of the ligand–QD species identified several isomers of each compound close in energy to the global minimum structures. The isomeric variety is explained by the presence of several functional groups in the ligands and thus by numerous possibilities of their coordination to the QD. The global minimum structures of the three ligand–QD complexes were further studied with a larger basis set and implicit water effects. The three complexes were shown to be stable, with the anionic ligand species coordinated to the QD being generally more stable than the neutral compounds. The QD distortions because of the coordination with the anionic ligands were much more pronounced than those with the neutral ligands. Charge transfer from both the neutral and anionic ligands to the QD upon the ligand coordination was detected.