MacNaughton Jb

The attachment of amino fragment to purine: inner-shell structures and spectra

The impact of the amino fragment (-NH(2)) attachment on the inner-shell structures and spectra of unsubstituted purine and the purine ring of adenine are studied. Density functional theory calculations, using the LB94/TZ2P//B3LYP/TZVP model, reveal significant site-dependent electronic structural changes in the inner shell of the species. A condensed Fukui function indicates that all of the N and C sites, except for N((1)) and C((5)), demonstrate significant electrophilic reactivity (f(-) > 0.5 in |e|) in the unsubstituted purine. Once the amino fragment binds to the C((6)) position of purine to form adenine, the electrophilic reactivity of these N and C sites is greatly reduced. As expected, the C((6)) position experiences substantial changes in energy and charge transfer, owing to the formation of the C-NH(2) bond in adenine. The present study reveals that the N1s spectra of adenine inherit the N1s spectra of the unsubstituted purine, whereas the C1s spectra experience significant changes although purine and adenine have geometrically similar carbon frames. The findings also indicate that the attachment of the NH(2) fragment to purine exhibits deeply rooted influences to the inner-shell structures of DNA/RNA bases. The present study suggests that some fragment-based methods may not be applicable to spectral analyses in the inner shell.

Comparative theoretical and experimental study of the radiation-induced decomposition of glycine.

The radiation-induced decomposition of glycine is studied using a combination of near-edge X-ray absorption fine structure (NEXAFS) measurements and DFT calculations. The measured spectra show strong dose- or time-dependent effects consistent with a complex, multistep decomposition. Principal component analysis was used to determine the number of distinct molecules that were needed to explain the observed changes in the measured spectra, and the emerging absorption features are assigned to various product molecules through comparison with simulated spectra of several model compounds. It is clear from the experiment that the major effect of soft X-ray irradiation is the fragmentation of the molecule, primarily at the carbonyl sites. Peptide formation is shown to occur under irradiation; a condensation reaction initiated by the removal of a carbonyl oxygen is the proposed mechanism. This study utilizes a novel approach to the study of radiation damage that can occur during measurements and suggests that it may be possible to use simulated model spectra to correct for these effects in measured spectra.

Resonant inelastic soft x-ray scattering and electronic structure of LiBC

The electronic structure of LiBC has been studied using soft x-ray fluorescence measurements. Resonant inelastic x-ray scattering (RIXS) spectra were measured with the excitation energy tuned to the boron and carbon K-edges. RIXS spectra show dispersive features, which were assigned to the calculated energy bands using the site-selective quantitative band mapping method based on the concept of k-momentum conservation. It is concluded that while the electronic structure calculations are in general agreement with experimental spectra, carbon and boron K-emission bands show some deviation due to an incomplete hybridization of the C 2p–B 2p states.

σ and π-band dispersion of graphite from polarized resonant inelastic X-ray scattering measurements

Resonant inelastic X-ray scattering of highly oriented pyrolytic graphite (HOPG) is observed above the C 1s threshold at different polarization angles. It is shown that combining the polarization and excitation energy dependence of X-ray emission spectra makes it possible to perform quantitative band mapping selective to the chemical bonding (σ and π).

Optical XAFS of ZnO Nanowires at the Zn K‐Edge and Related Phenomena

We report x‐ray excited optical luminescence (XEOL) from one‐dimensional nanostructures of ZnO excited with photon energies across the Zn K‐edge. The optical luminescence shows an UV and a green emission band characteristic of near band edge and defect emission, respectively. The optical channels were used in turn to monitor the Zn K‐edge XAFS to high k values. The densities of states of oxygen character in the valence band were also studied with x‐ray emission spectroscopy (XES). The Zn K‐edge decay dynamics was examined with time‐resolved x‐ray excited optical luminescence.