Unambiguous vibrational band assignments have been made to 4'-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI), a model compound of the green fluorescent protein (GFP) chromophore, with the use of isotopic labeling at positions C1, C3, N4, C5, and the bridging Calpha. Vibrational spectra were collected using Raman and IR spectroscopy and ab initio normal mode calculations were performed using density functional theory (DFT) and a 6-31G** basis set. Although several reports of calculations and measurements on GFP model compounds have recently appeared, we are able to definitively assign normal modes for the first time because of the use of isotopic labeling. Specifically, in the region between 1750 and 1550 cm(-1), we have identified marker bands both in Raman and IR spectra for cationic, neutral, and anionic forms of the chromophore. The Raman bands at 1744 (cation), 1697 (neutral), and 1665 cm(-1) (anion) are assigned to nu(C=O) arising from the imidazolinone carbonyl group, whereas the bands at 1647 (cation), 1642 (neutral), and 1631 cm(-1) (anion) are assigned to nu(C=C) for the exocyclic C=C double bond. In addition, a band at 1567 (neutral) and 1556 cm(-1) (anion) is assigned to a normal mode delocalized over the imidazolinone ring and exocyclic double bond. Importantly, a band at 1582 cm(-1) in cationic HBDI also involves a contribution from N-H bending of the protonated imidazolinone N4-H and consequently is very sensitive to deuteration. Because the Raman spectra of neutral and anionic HBDI in H2O and D2O are virtually identical, the sensitivity of the 1582 cm(-1) band in cationic HBDI to deuteration provides a means of identifying protonation of the imidazolinone ring in green fluorescent protein. These assignments are discussed with reference to the Raman spectra of GFPs obtained in an earlier study (Bell, A. F.; He, X.; Wachter, R. M.; Tonge, P. J. Biochemistry 2000, 39, 4423-4431) and are crucial for interpreting the vibrational spectra of GFPs.