Nitzan Mayorkas

Raman spectral signatures as conformational probes of gas phase flexible molecules

A novel application of ionization-loss stimulated Raman spectroscopy (ILSRS) for monitoring the spectral features of four conformers of a gas phase flexible molecule is reported. The Raman spectral signatures of four conformers of 2-phenylethylamine are well matched by the results of density functional theory calculations, showing bands uniquely identifying the structures. The measurement of spectral signatures by ILSRS in an extended spectral range, with a conventional laser source, is instrumental in facilitating the unraveling of intra- and intermolecular interactions that are significant in biological structure and activity.

Vibrational and vibronic spectra of tryptamine conformers

Conformation-specific ionization-detected stimulated Raman spectra, including both Raman loss and Raman gain lines, along with visible-visible-ultraviolet hole-burning spectra of tryptamine (TRA) conformers have been measured simultaneously, with the aim of obtaining new data for identifying them. The slightly different orientations of the ethylamine side chain relative to the indole lead to unique spectral signatures, pointing to the presence of seven TRA conformers in the molecular beam. Comparison of ionization-loss stimulated Raman spectra to computationally scaled harmonic Raman spectra, especially in the alkyl C-H and amine N-H stretch regions together with the retrieved information on the stabilities of the TRA conformers assisted their characterization and structural identification. The prospects and limitations of using these spectroscopic methods as potential conformational probes of flexible molecules are discussed.

Heavy water hydration of mannose: the anomeric effect in solvation, laid bare

The presence and consequences of the anomeric effect have been explored and directly exposed, through an investigation of the vibrational spectroscopy of the doubly and triply hydrated α and β anomers of phenylD-mannopyranoside, (PhMan) isolated under molecular beam conditions in the gas phase. The experiments have been aided by the simple trick of substituting D2O for H2O, which has the advantage of isotopically isolating the carbohydrate (OH) bands from the water (OD) bands. Recording the double resonance, IR-UV ion dip spectra of the hydrated complexes, α- and β-PhMan·(D2O)2,3 in a series of ‘proof of principle’ experiments, revealed that these heavy water molecules engage the key endocyclic oxygen atom, O5, allowing the anomeric effect to be probed through a combination of vibrational spectroscopy and quantum chemical calculations. Importantly, in the dihydrates, both anomers adopt the same conformation and the two water molecules occupy the same template. One of them acts as a remarkably sensitive reporter, able to sense and expose subtle stereoelectronic changes through the resulting changes in its hydrogen-bonded interaction with the substrate.

Simultaneous Ionization-Detected Stimulated Raman and Visible-Visible-Ultraviolet Hole-Burning Spectra of Two Tryptamine Conformers.

A key first step toward probing structures and interactions of individual conformers of isolated flexible molecules is uncovering their characteristic spectral signatures. Here, conformation-specific ionization-detected stimulated Raman (IDSR) and visible-visible-ultraviolet hole-burning spectra were measured simultaneously to determine the unique signatures of the two most stable conformers of tryptamine in the gas phase. These signatures together with the comparison of the IDSR spectra to the computationally predicted Raman spectra assisted in their characterization and structural identification. This new approach offers high selectivity and is foreseen to be an improved diagnostic tool for dissection of conformers of flexible molecules.

Ionization-loss stimulated Raman spectroscopy for conformational probing of flexible molecules

The approach of studying structural and dynamical properties of flexible molecules is of substantial interest, as it allows decoding the shapes and intrinsic properties of isolated molecular constituents, which have an influence on the selectivity and functionality in biological processes. Combining quantum computation methods with double resonance or infrared hole burning techniques, mainly covering hydride stretch vibrations, recently led to great progress in understanding the structure of a variety of biological building blocks. Measurements of spectra in the lower frequency range, with relatively compact and convenient laser sources, still pose major challenges. For this reason, the method of ionization-loss stimulated Raman spectroscopy (ILSRS) has been developed and applied for monitoring the spectral features of the 2-phenylethanol prototype. The bands observed in the Raman spectra of its two conformers uniquely identify their structures and are in accord with anharmonic results obtained by density functional theory calculations. These findings point to future opportunities for ILSRS as a powerful conformational probe and set new standards for detailed interrogation of structure and intra- and inter-molecular interactions.

Photofragment ionization-loss stimulated Raman spectroscopy of a hydrated neurotransmitter: 2-phenylethylamine–water

Different types of spectral signatures and their interpretation provide valuable information on intra- and inter-molecular interactions that lead to unique shapes of molecules and clusters. Here, ionization-loss stimulated Raman (ILSR) spectra of the 2-phenylethylamine–water (PEA–H2O) cluster were obtained by monitoring the spectral signatures of PEA and of CH2NH2–H2O (a hydrated portion of the PEA tail) fragment ions. The ILSR spectra of both fragments were found to be similar, indicating that they are actually reminiscent of the PEA–H2O cluster signature. Comparison of the photofragment spectra to anharmonic calculated Raman spectra of the different conformers of the PEA–H2O clusters, suggests a structure with PEA similar to that of the most stable gauche conformer, with H2O hydrogen bonded to the nitrogen lone pair.

A new method for determining absorption cross sections out of initially excited vibrational states

A first experimental demonstration, combining the methods of vibrationally mediated photodissociation (VMP) and ionization-loss stimulated Raman spectroscopy (ILSRS) for measuring cross sections for dissociation of vibrationally excited levels is reported. The action spectrum obtained in the VMP of methylamine exhibits enhancement of the H photofragment yield as a result of initial vibrational excitation and the ILSRS monitors the fraction of molecules being excited. The partial cross sections for H production out of the sampled vibrational states and the extent of mode selectivity were thus determined.

Revealing the hot bands in the regions of the N-H and C-H stretch fundamentals of pyrrole.

Photoacoustic Raman spectra of gaseous pyrrole in the 3504-3535 and 3068-3152 cm(-1) energetic windows were measured, to obtain new information about the hot bands in the vicinity of the N-H(ν1) and C-H(ν2) stretch fundamentals, respectively. The observed vibrational patterns are characterized by sharp Q-branches, where the strong bands reflect the fundamentals and the weaker ones, as established from their temperature dependence, are hot bands. From the simulation of the observed spectra, the band origins and nondiagonal anharmonicities were determined. Comparison of the latter values to the anharmonicities, x(ij) (i = 1, 2 and j = 16, 15, 14, 12, 11) obtained from anharmonic calculations at the B3LYP/6-311++G(d,p), B3LYP/cc-pVQZ and MP2/cc-pVTZ levels, aided the tentative assignment of the hot bands. The retrieved parameters add new data to the extensive set of already known vibrational constants of pyrrole.