A series of gold nanoparticles stabilized by the adsorption of heterocyclic mercaptan derivatives, including 2-mercaptopyridine (2MPy), 2-mercaptopyrimidine (2MPm) and 4-mercaptopyridine (4MPy), were synthesized and characterized by TEM, FTIR, UV-vis, and XPS. The adsorption of 2MPy molecules led to the most stable and uniform nanoparticles. In contrast, the 4MPy-coated nanoparticles showed a strong tendency to form 3D aggregates, which is attributed to cross linking between sulfur groups on neighboring particles. FTIR and UV-vis spectroscopy were employed to study the chemical conformation of the heterocyclic molecules on the gold surface. Significant differences between the IR spectra of the functionalized nanoparticles and the free mercaptan molecules were observed. Interpretations of these IR spectra were achieved with the aid of ab initio calculations. We found that the "thione form" is predominant when the molecules are either in a polycrystalline state or in methanol solution; however, they are stabilized in the "thiol-like form" when adsorbed on the particles. The XPS spectra of the 2MPy nanoparticles showed narrow peaks with the expected peak position. In contrast, the peaks in the spectra of the 2MPm- and 4MPy-passivated nanoparticles were strongly shifted. Oxidization of the sulfur group was detected in the 4MPy-modified nanoparticles, indicating that some molecules were adsorbed onto the gold surface via their nitrogen groups.