Infrared multiphoton dissociation spectroscopy of protonated N-acetyl-alanine and alanyl-histidine

Using Fourier transform ion cyclotron resonance mass-spectrometry (FT-ICR-MS) in combination with infrared multiphoton dissociation (IRMPD) spectroscopy, at the free electron laser (FEL) facility CLIO in Orsay (France), we obtain the IR spectra, in the 900-1900 cm−1 range, of two model protonated dipeptides: N-acetyl-alanine (AcNH-Ala) and alanyl-histidine (Ala-His). By comparison with simulated spectra, calculated at the B3LYP/6-31++G** level for many low-lying possible conformers of these two species, we are able to assign the position of the protonation site, on the acetyl oxygen for AcNH-Ala and on the side-chain imidazole nitrogen for Ala-His, and to obtain some more information on the low-lying equilibrium structures of these two species in the gas phase.