Oksana Plekan

Tautomerism in cytosine and uracil: an experimental and theoretical core level spectroscopic study

The O, N, and C 1s core level photoemission spectra of the nucleobases cytosine and uracil have been measured in the vapor phase, and the results have been interpreted via theoretical calculations. Our calculations accurately predict the relative binding energies of the core level features observed in the experimental photoemission results and provide a full assignment. In agreement with previous work, a single tautomer of uracil is populated at 405 K, giving rise to relatively simple spectra. At 450 K, three tautomers of cytosine, one of which may consist of two rotamers, are identified, and their populations are determined. This resolves inconsistencies between recent laser studies of this molecule in which the rare imino-oxo tautomer was not observed and older microwave spectra in which it was reported.

Electronic structure of aromatic amino acids studied by soft x-ray spectroscopy

The electronic structure of phenylalanine, tyrosine, tryptophan, and 3-methylindole in the gas phase was investigated by x-ray photoemission spectroscopy (XPS) and near edge x-ray absorption fine structure (NEXAFS) spectroscopy at the C, N, and O K-edges. The XPS spectra have been calculated for the four principal conformers of each amino acid, and the spectra weighted by the Boltzmann population ratios calculated from published free energies. Instead of the single peaks expected from the stoichiometry of the compounds, the N 1s core level spectra of phenylalanine and tryptophan show features indicating that more than one conformer is present. The calculations reproduce the experimental features. The C and O 1s spectra do not show evident effects due to conformational isomerism. The calculations predict that such effects are small for carbon, and for oxygen it appears that only broadening occurs. The carbon K-edge NEXAFS spectra of these aromatic amino acids are similar to the published data of the corresponding molecules in the solid state, but show more structure due to the higher resolution in the present study. The N K-edge spectra of tryptophan and 3-methylindole differ from phenylalanine and tyrosine, as the first two both contain a nitrogen atom located in a pyrrole ring. The nitrogen K-edge NEXAFS spectra of aromatic amino acids do not show any measurable effects due to conformational isomerism, in contrast to the photoemission results. Calculations support this result and show that variations of the vertical excitation energies of different conformers are small, and cannot be resolved in the present experiment. The O NEXAFS spectra of these three aromatic compounds are very similar to other, simpler amino acids, which have been studied previously.

Core Level Study of Alanine and Threonine

Core level X-ray photoemission spectra (XPS) and near edge X-ray absorption fine structure (NEXAFS) spectra of alanine and threonine in the gas phase have been measured at the carbon, nitrogen, and oxygen K edges and interpreted in the light of theoretical calculations. For the computations, a set of approximations is made which allows sufficiently accurate calculations of several conformers to be performed in reasonable computing time. The accuracy has been checked by comparing results obtained for proline to our previous, higher level calculations. The photoemission spectra at the carbon and oxygen edges are assigned and compared. The nitrogen 1s photoemission peaks show anomalous broadening which we relate to the populations and types of conformers. The carbon K-edge NEXAFS spectra of alanine and threonine are compared with our previous data on glycine and resonances assigned accordingly. The nitrogen K-edge NEXAFS spectra of alanine and threonine do not show measurable effects due to the population of conformers, in contrast to the photoemission results. At the oxygen K edge, the spectra of these amino acids are similar with two prominent peaks assigned to transitions of O 1s electrons from the oxo and hydroxyl groups to vacant pi* and sigma* orbitals and additional intensity for threonine due to the second OH group. Conformer effects are observable in photoemission but appear to be more difficult to resolve in photoabsorption. We explain this by energetic shifts of opposite sign for the core hole states and unoccupied orbitals, which causes partial cancelation in NEXAFS but not in photoemission.

Tautomerism in Cytosine and Uracil: A Theoretical and Experimental X-ray Absorption and Resonant Auger Study

The core level photoabsorption spectra of the nucleobases cytosine and uracil in the gas phase have been measured and the results interpreted with theoretical calculations using an ab initio Green’s function approach. A single tautomer of uracil is populated, in agreement with previous work, while three tautomers of cytosine are clearly identified, whose identity and relative populations at the temperature of the experiment were reported previously. The second-order ADC approach to polarization propagator was employed in calculations of X-ray photoabsorption energies and intensities. The theoretical spectra have been constructed as Boltzmann-factor-weighted sums of individual tautomer spectra. These theoretical spectra are in good agreement with the experimental photoabsorption results at the oxygen, nitrogen, and carbon edges. In addition we report resonant Auger spectra of the valence band of cytosine, which support previous assignments of the character of the valence band states.

Coherent control with a short-wavelength free-electron laser

Researchers demonstrate correlation of two colours (63.0 and 31.5 nm wavelengths) in a free-electron laser and control photoelectron angular distribution by adjusting phase with 3 attosecond resolution.

An Experimental and Theoretical Core-Level Study of Tautomerism in Guanine

The core level photoemission and near edge X-ray photoabsorption spectra of guanine in the gas phase have been measured and the results interpreted with the aid of high level ab initio calculations. Tautomers are clearly identified spectroscopically, and their relative free energies and Boltzmann populations at the temperature of the experiment (600 K) have been calculated and compared with the experimental results and with previous calculations. We obtain good agreement between experiment and the Boltzmann weighted theoretical photoemission spectra, which allows a quantitative determination of the ratio of oxo to hydroxy tautomer populations. For the photoabsorption spectra, good agreement is found for the C 1s and O 1s spectra but only fair agreement for the N 1s edge.

Adsorption of Histidine and Histidine-Containing Peptides on Au(111)

The adsorption of histidine (His) and three His-derived peptides on Au(111) has been studied by soft X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure spectroscopy (NEXAFS) at the nitrogen and oxygen K edges. The peptides were glycyl-histidine (Gly-His), glycyl-histidine-glycine (Gly-His-Gly), and glycyl-glycyl-histidine (Gly-Gly-His) and were adsorbed at saturated coverage on the Au(111) surface from aqueous solution. Coverages of 1 and 0.5 monolayers (ML) of His were adsorbed by evaporation in vacuum and compared with 1 ML deposited from solution. There were no significant chemical differences between the monolayers deposited in vacuum or from solution. The Au 4f core level shift indicates that a chemisorption rather than a physisorption bond is formed. In both deposited phases, His bonds to the gold surface in anionic form via the imino nitrogen atom of the imidazole ring and the oxygen atoms of the carboxylate group. N and O K-edge NEXAFS indicate that the ring and carboxylate triangle of adsorbed His are tilted at approximately 35 degrees and approximately 27 degrees, respectively, with respect to the Au(111) surface. The peptides bond to the gold surface in a mode similar to the single His molecule, via the imino and carboxylate groups, while the peptide group is at a steep angle to the surface. However, the peptides adsorb with a higher atomic density, consistent with the peptide groups being above the surface. There are also differences between Gly-His-Gly and Gly-Gly-His, implying that the sequence within the peptide has a significant influence on the bonding geometry.

Valence photoionization and photofragmentation of aromatic amino acids

The valence photoelectron spectra of the aromatic amino acids phenylalanine, tyrosine, tryptophan and 3-methylindole in the gas phase have been investigated by soft X-ray radiation. The photoemission spectra of the outer valence regions are similar to previously reported He I spectra, although relative peak intensities are different due to the different photon energy. The spectral range has been extended to the inner valence region and new information has been obtained. The photofragmentation mass spectra of the aromatic amino acids were measured after ionization by noble gas resonance radiation at energies from 8.4 to 21.2 eV. The main peak in the mass spectra of phenylalanine corresponds to loss of the aromatic functional group, while for tyrosine and tryptophan it is due to the loss of the carboxylic and amino groups. Lower photon energies lead to ‘softer’ ionization, with reduced fragmentation and increased parent ion signal.

A modular end-station for atomic, molecular, and cluster science at the low density matter beamline of FERMI@Elettra

The low density matter end-station at the new seeded free electron laser FERMI@Elettra is a versatile instrument for the study of atoms, molecules and clusters by means of electron and ion spectroscopies. Beams of atoms, molecules and helium droplets as well as clusters of atoms, molecules and metals can be produced by three different pulsed valves. The atomic and molecular beams may be seeded, and the clusters and droplets may be pure, or doped with other atoms and molecules. The electrons and ions produced by the ionization and fragmentation of the samples by the intense light of FERMI can be analysed by the available spectrometers, to give mass spectra and energy as well as angular distributions of charged particles. The design of the detector allows simultaneous detection of electrons and ions using velocity map imaging and time-of-flight techniques respectively. The instruments have a high energy/mass resolution and large solid-angle collection efficiency. We describe the current status of the apparatus and illustrate the potential for future experiments.

Electronic state resolved PEPICO spectroscopy of pyrimidine

Photoionization techniques, such as photoelectron spectroscopy (PES) and photoionization mass spectrometry (PIMS), are well-established and powerful methods for studying the spectroscopy of isolated bio-organic molecules and their fate under vacuum ultraviolet (VUV) irradiation. Measuring the energy selected electron leaving a molecular ion in coincidence with other particles, such as ions, can provide even deeper insights into the mechanisms of the interaction of molecules with ionizing radiation. We have thus implemented the electronic state resolved photoelectron photoIon coincidence (ER-PEPICO) technique in our laboratory. Here, we report our newly constructed apparatus, and its application for characterizing fragmentation processes occurring in pyrimidine. Ionization of the two highest molecular orbitals (MOs) of the valence band does not lead to fragmentation of the resulting ion. The third band observed in photoemission is due to the ionization of two MOs, and leads mainly to the formation of the parent ion. The next three electronic states are not resolved experimentally and appear as a single band; their ionization leads to fragments of mass to charge ratio m/e= 53 (C3H3N+), while ionization of deeper lying MOs leads mostly to m/e= 26 (C2H2+). We compare our data with previous non-coincidence photoionization results and describe the problems encountered and their solutions.