Sander Jaeqx

Ir spectroscopy of isolated neutral and protonated adenine and 9-methyladenine

IR spectroscopy is employed to study isolated adenine and its derivative 9-methyladenine in both their neutral and protonated forms. The IR spectra of neutral adenine and 9-methyladenine are measured in a molecular beam expansion via IR-UV ion-dip spectroscopy in the 525 to 1750 cm(-1) region. For adenine, UV excitation selects the 9H tautomer to give a conformer-selective IR spectrum. For 9-methyladenine, only one tautomer exists because of the methyl substitution at the N(9) position. The experimental spectra agree closely with spectra computed for these tautomers at the B3LYP/6-311++G(df,pd) level of theory. These spectra complement previous tautomer-specific IR spectra in the hydrogen stretching range. The 9H-adenine spectrum obtained is compared to a previously recorded FTIR spectrum of adenine at 280 °C, which shows close agreement, although the 7H tautomer cannot be excluded from contributing. Protonated adenine and 9-methyladenine are generated by electrospray ionization and studied via IR multiple-photon dissociation (IRMPD) spectroscopy. Comparison of the experimental spectra with computed spectra allows identification of the protonation site, which suggests that the 1-9 tautomer is the dominant contributor to the spectra.

Gas-Phase Peptide Structures Unraveled by Far-IR Spectroscopy: Combining IR-UV Ion-Dip Experiments with Born–Oppenheimer Molecular Dynamics Simulations†

Vibrational spectroscopy provides an important probe of the three-dimensional structures of peptides. With increasing size, these IR spectra become very complex and to extract structural information, comparison with theoretical spectra is essential. Harmonic DFT calculations have become a common workhorse for predicting vibrational frequencies of small neutral and ionized gaseous peptides. Although the far-IR region (<500 cm(-1)) may contain a wealth of structural information, as recognized in condensed phase studies, DFT often performs poorly in predicting the far-IR spectra of peptides. Here, Born-Oppenheimer molecular dynamics (BOMD) is applied to predict the far-IR signatures of two γ-turn peptides. Combining experiments and simulations, far-IR spectra can provide structural information on gas-phase peptides superior to that extracted from mid-IR and amide A features.

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.

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

Two C(9)H(7) 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 m/z = 228 and 230. A surprisingly high selectivity has been found: The species with m/z = 230 is identified to be para-terphenyl, whereas m/z = 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.

Gas-phase salt bridge interactions between glutamic acid and arginine

The gas-phase side chain-side chain (SC-SC) interaction and possible proton transfer between glutamic acid (Glu) and arginine (Arg) residues are studied under low-temperature conditions in an overall neutral peptide. Conformation-specific IR spectra, obtained with the free electron laser FELIX, in combination with density functional theory (DFT) calculations, provide insight into the occurrence of intramolecular proton transfer and detailed information on the conformational preferences of the peptides Z-Glu-Alan-Arg-NHMe (n = 0,1,3). Low-energy structures are obtained using molecular dynamics simulations via the simulated annealing approach, resulting in three types of SC-SC interactions, in particular two types of pair-wise interactions and one bifurcated interaction. These low-energy structures are optimized and frequency calculations are performed using the B3LYP functional, for structural analysis, and the M05-2x functional, for relative energies, employing the 6-311+G(d,p) basis set. Comparison of experimental and computed spectra suggests that only a single conformation was present for each of the three peptides. Despite the increasing spacing between the Glu and Arg residues, the peptides have several types of interactions in common, in particular specific SC-SC and dispersion interactions between the Arg side chain and the phenyl ring of the Z-cap. Comparison with previous experiments on Ac-Glu-Ala-Phe-Ala-Arg-NHMe as well as molecular dynamics simulations further suggest that the pairwise interaction observed here is indeed energetically most favorable for short peptide sequences.

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.

Far-infrared spectra of the tryptamine A conformer by IR-UV ion gain spectroscopy

We present far infrared spectra of the conformer A of tryptamine in the 200 to 500 cm-1 wavenumber range along with resonant photoionization spectra of the far-infrared excited conformer A of tryptamine. We show that single-far-infrared photon excited tryptamine has highly structured resonance enhanced multi-photon ionization spectra, revealing the mode composition of the S1-state. Upon multiple-far-infrared photon absorption, the resonance enhanced multi-photon ionization spectrum broadens allowing ion gain spectroscopy to be performed. In the ion gain spectrum we detect the fundamental far-infrared modes but also combination and overtone bands with high efficiency. The implications to dip spectroscopy using a free electron laser compared to more conventional light sources are discussed.