11 research outputs found
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 C<sub>9</sub>H<sub>7</sub> 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<sup>–1</sup> 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
Can far-IR action spectroscopy combined with BOMD simulations be conformation selective?
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<sup>+</sup> 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
Contains fulltext :
117014.pdf (publisher's version ) (Closed access
Phenylpropargyl radicals and their dimerization products: An ir/uv double resonance study
Contains fulltext :
103616.pdf (publisher's version ) (Closed access