Density functional theory (B3LYP) calculations combined with the 6-31++G(d,p) basis set have been carried out on protonated carbonyl bases RHC=O (R = F, CH3, NH2) and R2C=O (R = F, H, CH3). The substituent effects on the equilibrium structures and vibrational frequencies of protonated bases are discussed. Protonation results in spectacular changes of the CF and CH bond lengths and the frequencies and intensities of the nu(CF) and nu(CH) stretching vibrations. These features are discussed in terms of the lone pair effect. Correlations between the nu(OH) and nu(CK) stretching frequencies and the corresponding OH and CH distances are presented. The relative changes of distances and angles are on the average 10 times higher for protonation than for hydrogen bond formation. The hydrogen bond energies are linearly correlated to the proton affinities of the corresponding sites and positive departures from the linearity are observed for closed dimers where the distance between the hydrogen atom of the substituent and the (C) atom of water is lower than 2.5 Angstrom. Cooperativities evaluated from infrared frequency shifts are different and seem to be more sensitive to the angular properties. (C) 2000 Elsevier Science B.V. All rights reserved.