We have prepared gold nanoparticles covered with N-isobutyryl-l-cysteine and N-isobutyryl-d-cysteine, respectively. These particles with a mean particle size smaller than 2 nm are highly soluble in water and are amenable to chiroptical techniques such as vibrational circular dichroism (VCD) and circular dichroism (CD) spectroscopy. Density functional theory shows that the VCD spectra are sensitive toward the conformation of the adsorbed thiol. Based on the comparison between the experimental VCD spectrum and the calculated VCD spectra for different conformers, a preferential conformation of the thiol adsorbed on the gold particles can be proposed. In this conformation the carboxylate group interacts with the gold particle in addition to the sulfur. The particles could furthermore be separated according to their charge and size into well-defined compounds. The optical absorption spectra revealed a well-quantized electronic structure and a systematic red-shift of the absorption onset with increasing gold core size, which was manifested in a color change with particle size. Some compounds showed basically identical absorption spectra as analogous gold particles protected with l-glutathione. This shows that these particles have identical core sizes (10−12, 15 and 18 gold atoms, respectively) and indicates that the number and arrangement of the adsorbed thiol are the same, independent of the two thiols, which have largely different sizes. Some separated compounds show strong optical activity with opposite sign when covered with the d- and l-enantiomer, respectively, of N-isobutyryl-cysteine. The origin of the optical activity in the metal-based transitions is discussed. The observations are consistent with a mechanism based on a chiral footprint on the metal core imparted by the adsorbed thiol.