Hiding in Plain Sight: Unmasking the Diffuse Spectral Signatures of the Protonated N‑Terminus in Isolated Dipeptides Cooled in a Cryogenic Ion Trap

Survey vibrational predissociation spectra of several representative protonated peptides and model compounds reveal very diffuse absorptions near 2500 cm^–1 that are traced to pentagonal cyclic ionic hydrogen bonds (C₅ interactions) involving the excess charge centers. This broadening occurs despite the fact that the ions are cooled close to their vibrational zero-point levels and their spectra are obtained by predissociation of weakly bound adducts (H₂, N₂, CO₂) prepared in a cryogenic ion trap. The C₅ band assignments are based on H/D isotopic substitution, chemical derivatization, solvation behavior, and calculated spectra. We evaluate the extent to which this broadening is caused by anharmonic coupling in the isolated molecules by including cubic coupling terms in the normal mode expansion of the potential energy surface. This analysis indicates that the harmonic H-bonded stretching vibration is mixed with dark background states over much of the energy range covered by the observed features. The difficulty with identifying these features in earlier studies of dipeptides is traced to both the breadth and the fact they are calculated to be intrinsically weaker than cases involving linear variations of the N···H⁺···O motif