Mapping gas phase dipeptide motions in the far-infrared and terahertz domain

International audienceVibrational signatures of Ac-Phe-AA-NH2 dipeptides are recorded and analysed in the far IR/THz spectral domain (100-800 cm-1, 3-24 THz), with the 'AA' amino acid chosen within the series 'AA' = Gly, Ala, Pro, Cys, Ser, Val. Phe stands for phenylalanine. IR-UV ion dip experiments are conducted on the free electron laser FELIX and combined with DFT-based molecular dynamics simulations for the calculation of the dynamical anharmonic vibrational spectra. The excellent agreements between the experimental and theoretical spectra of the Ac-Phe-AA-NH2 series allow us to make detailed and unambiguous mapping of the vibrational motions into three main domains: 700-800 cm-1 for C-H waggings, 400-700 cm-1 for N-H waggings, with a one-to-one signature per amide N-H backbone group, 0-400 cm-1 for delocalized and large amplitude collective motions over the dipeptide backbone, with backbone torsional motions arising <100 cm-1

Phenylpropargyl Radicals and Their Dimerization Products: An IR/UV Double Resonance Study

Two C₉H₇ isomers, 1-phenylpropargyl and 3-phenylpropargyl, have been studied by IR/UV double resonance spectroscopy in a free jet. The species are possible intermediates in the formation of soot and polycyclic aromatic hydrocarbons (PAH). The radicals are generated by flash pyrolysis from the corresponding bromides and ionized at 255–297 nm in a one-color, two-photon process. Mid-infrared radiation between 500 and 1800 cm^–1 is provided by a free electron laser (FEL). It is shown that the two radicals can be distinguished by their infrared spectra. In addition, we studied the dimerization products originating from the phenylpropargyl self-reaction. We utilize the fact that the pyrolysis tube can be considered to be a flow reactor permitting us to investigate the chemistry in such a thermal reactor. Dimerization of phenylpropargyl produces predominately species with <i>m</i>/<i>z</i> = 228 and 230. A surprisingly high selectivity has been found: The species with <i>m</i>/<i>z</i> = 230 is identified to be <i>para</i>-terphenyl, whereas <i>m</i>/<i>z</i> = 228 can be assigned to 1-phenylethynyl-naphthalene. The results allow to derive a mechanism for the dimerization of phenylpropargyl and suggest hitherto unexplored pathways to the formation of soot and PAH

Conformational Study of Z‑Glu-OH and Z‑Arg-OH: Dispersion Interactions versus Conventional Hydrogen Bonding

The gas-phase conformational preferences of the model dipeptides Z-Glu-OH and Z-Arg-OH have been studied in the low-temperature environment of a supersonic jet. IR-UV ion-dip spectra obtained using the free electron laser FELIX provide conformation-specific IR spectra, which in combination with density functional theory (DFT) allow us to determine the conformational structures of the peptides. Molecular dynamics modeling using simulated annealing generates a variety of low-energy structures, for which geometry optimization and frequency calculations are then performed using the B3LYP functional with the 6-311+G­(d,p) basis set. By comparing experimental and theoretical IR spectra, three conformations for Z-Glu-OH and two for Z-Arg-OH have been identified. For three of the five structures, the dispersion interaction provides an important contribution to the stabilization, emphasizing the importance of these forces in small peptides. Therefore, dispersion-corrected DFT functionals (M05-2X and B97D) have also been employed in our theoretical analysis. Second-order Møller–Plesset perturbation theory (MP2) has been used as benchmark for the relative energies of the different conformational structures. Finally, we address the ongoing debate on the gas-phase structure of arginine by elucidating whether isolated arginine is canonical, tautomeric, or zwitterionic

Unraveling the Benzocaine–Receptor Interaction at Molecular Level Using Mass-Resolved Spectroscopy

The benzocaine–toluene cluster has been used as a model system to mimic the interaction between the local anesthetic benzocaine and the phenylalanine residue in Na⁺ channels. The cluster was generated in a supersonic expansion of benzocaine and toluene in helium. Using a combination of mass-resolved laser-based experimental techniques and computational methods, the complex was fully characterized, finding four conformational isomers in which the molecules are bound through N–H···π and π···π weak hydrogen bonds. The structures of the detected isomers closely resemble those predicted for benzocaine in the inner pore of the ion channels, giving experimental support to previously reported molecular chemistry models

Gas-phase salt bridge interactions between glutamic acid and arginine

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Phenylpropargyl radicals and their dimerization products: An ir/uv double resonance study

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