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

Abstract

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 (C 5 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 (H 2 , N 2 , CO 2 ) prepared in a cryogenic ion trap. The C 5 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.

Gas-phase conformations of small polyprolines and their fragment ions by IRMPD spectroscopy

“…The calculated spectrum in the 2900-3700 cm À1 region contains CÀ ÀH stretches below 3000 cm À1 and NÀ ÀH stretches between 3100 and 3300 cm À1 . These bands are, however, unobserved experimentally because of the relatively low pulse energy from the OPO below $3000 cm À1 and the likely high degree of anharmonicity associated with the strongly hydrogen-bonded amine NÀ ÀH stretches [51][52][53]. The unbound carboxyl COÀ ÀH stretch at $3590 cm À1 corresponds very well to the experimentally measured band in this region.…”

The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations

“…105, the broad band at around 2500 cm −1 is a signature of the N· · · H+ · · · O bond in the protonated N-terminus in isolated dipeptides. Similar results were obtained for protonated polyalanine peptides.…”

Snapshots of Proton Accommodation at a Microscopic Water Surface: Understanding the Vibrational Spectral Signatures of the Charge Defect in Cryogenically Cooled H+(H2O)n=2–28 Clusters

“…At the low temperatures relevant for the present experiments, the dominant quantum effect is zero-point motion, which is known to couple soft modes to strongly H-bonded stretches. 99,100 We believe that this is a major factor responsible for the large widths of the features associated with the hydronium OH stretch vibrations in the cold clusters. Important future directions will involve a more quantitative explanation for the spectral breadth as well as determination of the temperature dependence of the spectral patterns.…”