Bioconjugated CdSe quantum dots are promising reagents for bioimaging applications. Experimentally, the binding of a short peptide has been found to redshift the optical absorption of nanoclusters [J. Tsay et al., J. Phys. Chem. B 109, 1669 (2005)]. This study examines this issue by performing density functional theory (DFT) and time-dependent-DFT calculations to study the ground state and low-lying excited states of (CdSe)(6)[SCH(3)](-), a transition metal complex built by binding methanethiolate to a CdSe molecular cluster. Natural bond orbital results show that the redshift is caused by ligand-inorganic cluster orbital interaction. The highest occupied molecular orbital (HOMO) of (CdSe)(6) is dominated by selenium 4p orbitals; in contrast, the HOMO of (CdSe)(6)[SCH(3)](-) is dominated by sulfur 3p orbitals. This difference shows that [SCH(3)](-) binding effectively introduces filled sulfur orbitals above the selenium 4p orbitals of (CdSe)(6). The resulting smaller HOMO-LUMO gap of (CdSe)(6)[SCH(3)](-) indeed leads to redshifts in its excitation energies compared to (CdSe)(6). In contrast, binding of multiple NH(3) destabilizes cadmium 5p orbitals, which contribute significantly to the lowest unoccupied molecular orbital (LUMO) of (CdSe)(6), while leaving the selenium 4p orbitals near the HOMO relatively unaffected. This has the effect of widening the HOMO-LUMO gap of (CdSe)(6)6NH(3) compared to (CdSe)(6). As expected, the excitation energies of the passivated (CdSe)(6)6NH(3) are also blueshifted compared to (CdSe)(6). As far as NH(3) is a faithful representation of a surfactant, the results clearly illustrate the differences between the electronic effects of an alkylthiolate versus those of surfactant molecules. Surface passivation of (CdSe)(6)[SCH(3)](-) is then simulated by coating it with multiple NH(3) molecules. The results suggest that the [SCH(3)](-) adsorption induces a redshift in the excitation energies in a surfactant environment.