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In this paper, we study the relationship between nanoparticles’ structure/composition and the chemical nature of the molecules to be identified in surface enhanced Raman scattering (SERS) spectroscopy. Three types of nanoparticles (NPs) were synthesized, including Ag, Au, and silver coated by gold (Ag@Au), in order to study the resulting enhancement effects. When a rhodamine 6G dye molecule was used to assemble the NPs, it was found that Ag NPs exhibited the highest enhancement activity. However, when a thiol containing 3-amino-1,2,4-triazole-5-thiol molecule was used to assemble the NPs, it was found that the Ag@Au NPs exhibited high Raman activity as well as the Ag NPs. The results give insight into how the chemical properties of the molecules to be analyzed play an important role in the SERS detection. An additional parameter of the analysis reveals the relative stability of the three types of NP probes synthesized with regard to oxidation in the presence of different mediating molecules and varying salt concentrations. The results are of interest in designing and employing NP probes to detect biological molecules using colorimetric and SERS based approaches.