A new aromatic thiolate protected gold nanomolecule Au-99(SPh)(42) has been synthesized by reacting the highly stable Au-144(SCH2CH2Ph)(60) with thiophenol, HSPh. The ubiquitous Au-144(SR)(60) is known for its high stability even at elevated temperature and in the presence of excess thiol. This report demonstrates for the first time the reactivity of the Au-144(SCH2CH2Ph)(60) with thiophenol to form a different 99-Au atom species. The resulting Au-99(SPh)(42) compound, however, is unreactive and highly stable in the presence of excess aromatic thiol. The molecular formula of the title compound is determined by high resolution electrospray mass spectrometry (ESI-MS) and confirmed by the preparation of the 99-atom nanomolecule using two ligands, namely, Au-99(SPh)(42) and Au-99(SPh-OMe)(42). This mass spectrometry study is an unprecedented advance in nanoparticle reaction monitoring, in studying the 144-atom to 99-atom size evolution at such high m/z (similar to 12k) and resolution. The optical and electrochemical properties of Au-99(SPh)(42) are reported. Other substituents on the phenyl group, HS-Ph-X, where X = -F, -CH3, -OCH3, also show the Au-144 to Au-99 core size conversion, suggesting minimal electronic effects for these substituents. Control experiments were conducted by reacting Au-144(SCH2CH2Ph)(60) with HS-(CH2)n-Ph (where n = 1 and 2), bulky ligands like adamantanethiol and cyclohexanethiol. It was observed that conversion of Au-144 to Au-99 occurs only when the phenyl group is directly attached to the thiol, suggesting that the formation of a 99-atom species is largely influenced by aromaticity of the ligand and less so on the bulkiness of the ligand.