Geometrical characterization of pyrimidine base molecules adsorbed on Cu() surfaces: XPS and NEXAFS studies

Quantitative determination of the local structure of thymine on Cu(110) using scanned-energy mode photoelectron diffraction

“…For the initial room temperature deposited layer Fig. 3 agrees well with the previously-reported O 1s and N 1s SXPS [8] although there are differences in absolute binding energies of ~0.5 eV. This is probably attributable to differences in calibration methods; in our case the absolute energy calibrations was based on the Cu 3s peaks taken to have a photoelectron binding energy of 122.45 eV [16,17].…”

“…4 shows the O K-edge NEXAFS spectra recorded at grazing incidence, and at normal incidence in each of the two principle azimuths, from thymine adsorbed on Cu(110) at room temperature, and in a single azimuthal plane from a deposition at ~530 K. The photon energy calibration used in preparing these spectra is based on a very weak O Kedge feature in the incident flux attributable to O contamination in the optics. This feature was assigned an energy of 531 eV; while this calibration method is far from exact, the resulting room temperature preparation data are in excellent agreement with those of Furukawa et al [8]. Notice that the incident beam is horizontal (with a horizontal plane of polarisation), so as the angle of incidence is varied by rotating the sample about a vertical axis, the azimuth of the incidence plane is also the azimuth of the polarisation vector of the incident radiation.…”

“…These peaks are assigned, as in the earlier study of Furukawa et al [8], orientation is adopted by the species on the surface following deposition at a temperature above that at which TPD implies that (further) dehydrogenation occurs. The fact that the π* C=O resonance is a doublet is attributed to the inequivalence of the two C=O carbonyls within the adsorbed molecule, despite the fact that the more local probe of SXPS indicates that the two O atoms are almost equivalent.…”

“…Temperature-programmed desorption (TPD) spectra show that if the molecule is adsorbed at room temperature and heated, H 2 is desorbed at a temperature around 463 K, indicating that a partial dehydrogenation occurs in this temperature range, while complete dissociation occurs around 638 K [9,11]. Soft X-ray photoelectron spectroscopy (SXPS) of the species formed by room temperature adsorption [8] indicates that the two O atoms in the molecule are essentially equivalent, but that the two N atoms differ, probably due to deprotonation of one of these NH species. RAIRS data from the species formed at room temperature and at high (558 K) temperature, and also by annealing a surface dosed at room temperature to higher temperatures, clearly show significant differences, but the interpretation of these spectra in terms of models of the surface bonding is controversial.…”

X-ray induced damage in DNA monitored by X-ray photoelectron spectroscopy

“…The C 1s spectra and also N 1s, O 1s, and P 2p do not show any changes for DNA kept in ultrahigh vacuum conditions after 6 h. Previous studies reported 1s core electron binding energies for selected elements of different species, i.e., C 1s spectra were recorded for condensed phase of all nucleobases, 13,15 N 1s for thymine 15,16 and guanine, 15 and O 1s for cytosine 16 and thymine. 15,16 In the present work, high resolution C 1s spectra of DNA nucleobases are shown in Fig. 2 and exhibit a complicated structure due to contributions from different molecular species containing carbon atoms.…”