IRMPD Spectroscopy of a Protonated, Phosphorylated Dipeptide

Abstract

The protonated, phosphorylated dipeptide [GpY+H](+) is characterized by mid-infrared multiple-photon dissociation (IRMPD) spectroscopy and quantum-chemical calculations. The ions are generated in an external electrospray source and analyzed in a Fourier transform ion cyclotron resonance mass spectrometer, and their fragmentation is induced by resonant absorption of multiple photons emitted by a tunable free-electron laser. The IRMPD spectra are recorded in the 900-1730 cm(-1) range and compared to the absorption spectra computed for the lowest energy structures. A detailed calibration of computational levels, including B3LYP-D and coupled cluster, is carried out to obtain reliable relative energies of the low-energy conformers. It turns out that a single structure can be invoked to assign the IRMPD spectrum. Protonation at the N terminus leads to the formation of a strong ionic hydrogen bond with the phosphate P=O group in all low-energy structures. This leads to a P=O stretching frequency for [GpY+H](+) that is closer to that of [pS+H](+) than to that of [pY+H](+) and thus demonstrates the sensitivity of this mode to the phosphate environment. The COP phosphate ester stretching mode is confirmed to be an intrinsic diagnostic for identification of which type of amino acid is phosphorylated.

The sodium cation-bound dimer of theophylline: IRMPD spectroscopy of a highly symmetric electrostatically bound species

“…It is well established that hybrid DFT methods such as B3LYP generally outperform local or gradient-corrected DFT, and MP2 for the prediction of fundamental frequencies and their associated infrared intensities [7,13,56,[59][60][61][62][63][64][65][66]. Fundamental frequencies calculated by the MP2 method are significantly more costly and sometimes less accurate than those produced by B3LYP, thus, all geometry optimizations and calculated frequencies reported here have been obtained using the B3LYP method.…”

Insights into the fragmentation pathways of gas-phase protonated sulfoserine

“…IRMPD spectroscopy thus serves as a direct structural probe of gas-phase ions and can be used for structural elucidation of said ions, especially when combined with theoretical infrared (IR) frequency calculations and/or comparison to experimental spectra of synthetic standards. This technique has proven successful in many areas, including the study of PTMs [18][19][20][21] and of the fragmentation chemistry of peptides [22][23][24][25] and remains promising for many additional future applications.…”

Effect of Mid-infrared Free-Electron Laser Irradiation on Refolding of Amyloid-Like Fibrils of Lysozyme into Native Form

“…A mid-infrared free-electron laser (mid-IR FEL) can excite the specific bonds within mid-IR region, including amide bands, accounting for its use in multi-photon dissociation reactions [4, 27] and ablation of biological tissues and various proteins [1, 5, 28, 30, 31]. Investigators in Vanderbilt University have performed mid-IR FEL-induced ablation of cornea tissue, observing secondary structural changes and peptide fragmentation of collagen [29, 36].…”