An Investigation of Protonation Sites and Conformations of Protonated Amino Acids by IRMPD Spectroscopy

Abstract

The protonation sites and structures of a series of protonated amino acids (Gly, Ala, Pro, Phe, Lys and Ser) are investigated by means of infrared multiple-photon dissociation (IRMPD) spectroscopy and electronic-structure calculations. The IRMPD spectra of the protonated species are recorded using the combination of a free-electron laser (FEL) and an electrospray-ion-trap mass spectrometer. The structures of different possible isomers of these protonated species are optimized at the B3LYP/6-311+G(d, p) level of theory and the IR spectra calculated using the same computational method. For every amino acid studied herein, the current results indicate that a proton is bound to the alpha-amino nitrogen, except for lysine, in which the protonation site is the amino nitrogen in the side chain. According to the calculated and experimental IRMPD results, the structures of the protonated amino acids may be assigned unambiguously. For Gly, Ala, and Pro, in each of the most stable isomers the protonated amino group forms an intramolecular hydrogen bond with the adjacent carbonyl oxygen. In the case of Gly, the isomer containing a proton bound to the carbonyl oxygen is theoretically possible. However, it does not exist under the experimental conditions because it has a significantly higher energy (i.e. 26.6 kcal mol(-1)) relative to the most stable isomer. For Ser and Phe, the protonated amino group forms two intramolecular hydrogen bonds with both the adjacent carbonyl oxygen and the side-chain group in each of the most stable isomers. In protonated lysine, the protonated amino group in the side chain forms two hydrogen bonds with the alpha-amino nitrogen and the carbonyl oxygen, which is a cyclic structure. Interestingly, for protonated lysine the zwitterionic structure is a local minimum energy isomer, but the experimental spectrum indicates that it does not exist under the experimental conditions. This is consistent with the fact that the zwitterionic isomer is 9.2 kcal mol(-1) higher in free energy at 298 K than the most stable isomer. The carbonyl stretching vibration in the range of 1760-1800 cm(-1) is especially sensitive to the structural change. In addition, IRMPD mechanisms for the protonated amino acids are also investigated.

Consecutive Fragmentation Mechanisms of Protonated Ferulic Acid Probed by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations

“…Relative Gibbs free energies (298 K) are reported in kJ mol −1 Electronic structure calculations have been performed using the Gaussian 09 software package [32]. All geometry optimizations and associated frequency calculations have been performed at the B3LYP/6-311+G(d,p) level of theory, which has been shown to be a reliable protocol, with a good compromise between accuracy and cost, for smaller systems such as those described here [13,14,16,24,[33][34][35][36]. All harmonic frequencies obtained at this level of theory were scaled by 0.9679 [37] in order to compensate for errors arising from the use of a harmonic oscillator approximation in calculating the frequencies, as well as long range electron correlation effects.…”

Characterizing the Intramolecular H-bond and Secondary Structure in Methylated GlyGlyH+ with H2 Predissociation Spectroscopy

“…An important overall goal of such studies is to expand the sequence coverage available in proteomic analyses by rationalizing the fragmentation pathways [e.g., observed in collision-induced dissociation (CID)] in a structural context [3][4][5][6][7]. Vibrational spectroscopy is emerging as a powerful means with which to elucidate such structures by revealing peptide conformations and protonation sites through theoretical analysis of the observed band patterns [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27]. This spectroscopic data is most often available through the integration of tunable infrared laser photodissociation with mass spectrometry and, in most cases, spectra of the mass-selected ions are obtained under ambient temperature conditions using infrared multiple photon dissociation (IRMPD) [28][29][30][31][32][33].…”

Chirality effects in gas-phase spectroscopy and photophysics of molecular and ionic complexes: contribution of low and room temperature studies

“…It is possible to compare the efficiency of ejection of the chiral reference R* and the analyte A from the complex, for the two enantiomers A R and A S in the so-called Kinetic Method or its variant [16,29,35]. Recently, Ion Mobility [36,37] or Electron-Capture Dissociation have also been applied to chiral recognition [38].…”

“…The homochiral and heterochiral complex will be called hereafter SS-Cam-AlaH + and SR-Cam-AlaH + , respectively. The two components of the complex exist in one conformer only and protonation is expected to occur on the most basic site, the α amino nitrogen of alanine [36,107,253]. One therefore expects a strongly NH + …O hydrogen-bonded complex to be formed, for which conformational mobility is limited to flexibility around the intermolecular hydrogen bond.…”