The gas-phase structures of protonated histidine (His) and the side-chain model, protonated 4-phenyl imidazole (PhIm), are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by the free electron laser FELIX. To identify the structures present in the experimental studies, the measured IRMPD spectra are compared to spectra calculated at a B3LYP/6-311+G(d,p) level of theory. Relative energies of various conformers are provided by single point energy calculations carried out at the B3LYP, B3P86, and MP2(full) levels using the 6-311+G(2d,2p) basis set. On the basis of these experiments and calculations, the IRMPD action spectrum for H+(His) is characterized by a mixture of [N-pi,N-alpha] and [N-pi,CO] conformers, with the former dominating. These conformers have the protonated nitrogen atom of imidazole adjacent to the side-chain (N-pi) hydrogen bonding to the backbone amino nitrogen (N-alpha) and to the backbone carbonyl oxygen, respectively. Comparison of the present results to recent IRMPD studies of protonated histamine, the radical His(center dot+) cation, H+(HisArg), H-2(2+)(HisArg), and M+(His), where M+ = Li+, Na+, K+, Rb+, and Cs+, allows evaluation of the vibrational motions associated with the observed bands. (c) 2012 Elsevier B.V. All rights reserved.