Fourier transform infrared difference spectra are reported for the CO adduct of human hemoglobin versus deoxyHb, in H2O and D2O. In addition to the well-known CO stretching and S-H(D) stretching bands, the difference spectra reveal numerous bands in the 1200-1700 cm(-1) region, a number of which are assigned. Several amide modes are identified via their frequencies and D2O sensitivities. Bands arising from histidine protonation have also been found via comparison of the difference spectra at different pH(D) values, with the aid of aqueous histidine spectra. Of particular interest is the observation of a negative band at 1697 cm(-1), which is assigned to the C=O stretch of carboxylic acid. This carboxylic acid is tentatively identified as the side chain of Asp beta 99, because it is missing in the difference spectrum of Hb Kempsey, a mutant in which Asp beta 99 is replaced by Asn. Asp beta 99 forms a critical contact with Tyr alpha 42 across the alpha(1) beta(2) interface in deoxyHb, which is broken upon ligation. Protonation of Asp beta 99 in deoxyHb is consistent with UV resonance Raman evidence that Tyr alpha 42 is the acceptor rather than the donor of the quaternary H-bond.