The molecular model is one of the most appealing to explain the peculiar optical properties of Carbon nanodots (CNDs) and was proven to be successful for the bottom up synthesis, where a few molecules were recognized. Among the others, citrazinic acid is relevant for the synthesis of citric acid-based CNDs. Here we report a combined experimental and computational approach to discuss the formation of different protonated and deprotonated species of citrazinic acid and their contribution to vibrational and magnetic spectra. By computing the free energy formation in water solution, we selected the most favoured species and we retrieved their presence in the experimental surface enhanced Raman spectra. As well, the chemical shifts are discussed in terms of tautomers and rotamers of most favoured species. The expected formation of protonated and de-protonated citrazinic acid ions under extreme pH conditions was proven by evaluating specific interactions with H2SO4 and NaOH molecules. The reported results confirm that the presence of citrazinic acid and its ionic forms should be considered in the interpretation of the spectroscopic features of CNDs.