We present an experimental and theoretical investigation of the vibrational spectra of cytosine and protonated cytosine. In addition, we study spectra of cytosine and protonated cytosine with the mass of N1-H hydrogen changed to the mass of the methyl group. In this way the spectra of the heterocyclic part of cytidine are simulated. Spectral interpretation is based on the double harmonic approximation and scaled quantum mechanical (SQM) methodology. The scale factors of the ab initio HF/6-31G* and density functional Becke3-LYP/6-31G* force fields are adjusted using the frequencies and intensities measured for crystalline samples of anhydrous cytosine, cytosine monohydrate, and cytosine hydrochloride of known crystal structures. The same sets of scale factors are used for interpretation of vibrational spectra of both the neutral and protonated cytosine. These scale factors are also recommended for the spectral calculations of other nucleic acid bases and oligonucleotides. The consistency in transferring scale factors among different molecules is improved by using ring stretching scale factors that are linearly decreasing with the magnitude of the respective force constant. The original IR and Raman spectra of neutral and acidic aqueous solutions of cytosine are compared to the spectra of crystalline samples and to the calculated spectra. It is shown that frequency deviations caused by molecular environment and deviations between calculated spectra and spectra of aqueous solutions are of the same magnitude. Larger uncertainties that remain for wagging and torsional vibrations of the cytosine amino group, due to its largely anharmonic character, are significantly decreased upon cytosine protonation, which makes the cytosine amino group planar and more stiff in its out-of-plane degrees of freedom. The relative stabilities of tautomers of protonated cytosine in the gas phase and in a polar solvent are investigated at the ab initio level of theory with methods involving Hartree-Fock, MP2, MP4, and polarizable continuum approximations. In addition, discrete description of aqueous solvation was employed by using an empirical Langevine dipole model. According to these calculations, O2-protonated (enol) cytosine should slightly prevail in the gas phase, whereas in aqueous solution the N3-protonated form of cytosine is 3 +/- 1 kcal/mol more stable than the enol tautomer. The energetic grounds, as well as our analysis of the vibrational spectra, support the recent finding of Purrello et al. (J. Am. Chem. Sec. 1993, 115, 760) that the enol form of protonated cytosine, in the form of cytidine monophosphate, is present in small amounts in acidic aqueous solution.