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

Abstract

Infrared multiple-photon dissociation (IRMPD) spectroscopy has been used to examine the gas-phase conformations of a series of short protonated polyproline ions (Pro3–Pro6), their CID/IRMPD fragmentation pathways, and the associated fragment identities. Consistent with previous findings, and in combination with density functional theory (DFT) and MM/MD methods, a series of conformers for the protonated parent ions having their first peptide bond in the cis conformation has been identified. This conformation maximizes the solvation of the protonated N-terminus and stabilizes these compact globular-type conformations. This is in contrast to the PPI and PPII polyproline-type helices reported for larger polyproline peptides in solution. As well, this conformation leads to a unique fragmentation pattern upon collisional or multiple-photon activation. We report observation of the uncommon, but thermodynamically favored, diketopiperazine-type b2+ fragment ion. Formation of b2+ ions along the diketopiperazine pathway is in line with a cis configuration of the first amide linkage in the protonated parent ion. Additionally, the parent ion conformations, fragmentation pathways, and proton affinities of the resulting fragments have been related to the observed proline-effect in CID mass spectra.