Oxygen K-edge Research Articles

Nucleobase Lesions and Strand Breaks in Dry DNA Thin Film Selectively Induced by Monochromatic Soft X-rays

To verify the possibility of "selective damage induction" in DNA, the yields of base lesions as well as strand breaks have been measured in dry plasmid DNA films irradiated with highly monochromatized soft X-rays in the energy region of 270-760 eV, which includes the carbon, nitrogen, and oxygen K-edges. The yields of both pyrimidine and purine base lesions, observed as Nth-sensitive and Fpg-sensitive sites, respectively, are strikingly high at the oxygen K-edge (560 eV) but extremely low at an energy just below the nitrogen K-edge (380 eV) as compared with the yields observed at other photon energies. The yields at 560 eV are enhanced 9.6-fold and 27-fold for Nth-sensitive and Fpg-sensitive sites, respectively, compared with those at 380 eV. The yield of prompt single strand breaks is also enhanced at the oxygen K-ionization energy, but only 2-fold, as compared with that at 380 eV. Our results strongly suggest that (1) the K-shell ionization of oxygen in both the nucleobases as well as in other parts of DNA and in the hydrating water molecules bound to DNA, but not the K-shell ionization of nitrogen in the nucleobases, most likely contributes to the induction of nucleobase lesions and that (2) migration of electrons and holes is involved differentially in the production of each type of DNA lesion. These results could potentially lead to new methods for "partially selective induction" of specific types of DNA damage through tuning the energy of soft X-rays.

Inner-shell excitation and fragmentation of small acetaldehyde clusters at the oxygen K-edge

Inner-shell excitation spectra and fragmentation of acetaldehyde (AA) clusters have been studied in the oxygen K-edge region under cluster beam conditions. We identified intense production of a series of protonated clusters (AA) n H +, in the time-of-flight spectra of the AA clusters. Cluster-specific excitation spectra could be generated without contribution of free molecules by monitoring partial-ion-yield spectra of the fragments originating from the clusters. Comparison of the cluster-specific band with the molecular band revealed that the first resonance O1s→ π* CO band of small AA clusters shifts to a high energy by ∼0.15 eV relative to the free molecule. The O1s→ π* CO band of small clusters was compared well with the theoretical prediction derived for the most stable dimer configuration. The band-shift of the O1s→ π* CO was interpreted as being due to the augmentation of HOMO–LUMO energy gap upon complexation where a hydrogen bonding interaction could be identified.

Hydrogen bonding in acetone clusters probed by near-edge x-ray absorption fine structure spectroscopy in the carbon and oxygen K-edge regions

Hydrogen bonding in acetone clusters was investigated using near-edge x-ray absorption fine structure (NEXAFS) spectroscopy and density functional theory calculations in the carbon and oxygen K-edge regions. The partial-ion-yield (PIY) curves of the cluster ions were measured as the NEXAFS spectra of acetone clusters. In the carbon K-edge region, the first resonance peak, which was assigned to the C(CO) 1s-->pi( *)(C=O) resonance transition, showed no substantial change in the PIY curves of the acetone clusters, while the C(CH3) 1s-->3ppi(CH(3)) excitation feature was found to be strongly suppressed. The selective suppression of the C(CH3) 1s-->3ppi(CH(3)) resonance transition can be explained by the change in the character of the 3ppi(CH(3)) orbital due to the C=O...H-C type of hydrogen-bonding interaction. On the other hand, the NEXAFS spectra of the acetone molecule and clusters were almost identical in the oxygen K-edge region, except for a small shift in the pi( *)(C=O) resonance of 0.13 eV, because the character of the pi( *)(C=O) orbital remained, regardless of the C=O...H-C hydrogen bonding interaction.

Structure and dynamics in liquid water from x-ray absorption spectroscopy

Oxygen K-edge x-ray absorption spectra of water are discussed. The spectra of gas-phase water, liquid water and ice illustrate the sensitivity of oxygen K-edge x-ray absorption spectroscopy to hydrogen bonding in water. Transmission mode spectra of amorphous and crystalline ice are compared to x-ray Raman spectra of ice. The good agreement consolidates the experimental spectrum of crystalline ice and represents an incentive for theoretical calculations of the oxygen K-edge absorption spectrum of crystalline ice. Time-resolved infrared-pump and x-ray absorption probe results are finally discussed in the light of this structural interpretation.

Local analysis of the edge dislocation core in BaTiO3 thin film by STEM‐EELS

The a <100> edge dislocation core formed in an epitaxial BaTiO(3) (BTO) thin film grown on a substrate was investigated by scanning transmission electron microscopy combined with electron energy-loss spectroscopy. Elemental analysis using core-loss spectrum indicates that the atomic ratios of O/Ti and Ba/Ti are decreased at the dislocation core. The near-edge fine structure of the oxygen K-edge recorded from the dislocation core differs slightly from that of relaxed BTO region, which suggests that Ba-O bonding is decreased at the dislocation core. The structure of the dislocation core is discussed using a high-angle annular dark-field image and the electron energy-loss spectroscopy results.

Photoemission and Photoabsorption Spectroscopy of Glycyl-Glycine in the Gas Phase

The high-resolution outer and inner valence band (VB) spectra, as well as core level X-ray photoemission (XPS) and near edge X-ray absorption fine structure (NEXAFS) spectra at the carbon, nitrogen, and oxygen K-edges of glycyl-glycine in the gas phase have been measured, and the results interpreted by means of ab initio calculations. By comparison with our previous glycine spectra, the features characteristic of the peptide bond in the carbon, nitrogen, and oxygen XPS and NEXAFS spectra of glycyl-glycine have been identified and assigned. The K-edge NEXAFS spectra at all edges were found to be in reasonable agreement with published electron energy loss spectra, but showed more prominent structure due to the higher resolution. Effects on the nitrogen K-edge NEXAFS spectrum of glycyl-glycine due to intramolecular hydrogen bonding were observed. The N(NH(2)) 1s --> pi*(CN) resonance shifts to 0.6 eV lower energy, due to internal hydrogen bonding between the NH(2) and NH groups.

EPR study of radiation damage to DNA irradiated with synchrotron soft X-rays around nitrogen and oxygen K-edge

In order to obtain detailed insights into the physicochemical mechanism of DNA damage induction, “ in situ” measurement of electron paramagnetic resonance (EPR) signal from DNA constituent nucleobases, guanine and adenine, has been performed in a vacuum using monochromatic synchrotron soft X-rays. We found that short-lived unpaired electron species arise only during irradiation to the evaporated thin film on a surface. The EPR spectrum of the short-lived species significantly depends on the photon energy irradiated, and the spin concentration obtained from the EPR spectra shows a similar fine structure to the X-ray photoabsorption spectra (X-ray absorption near edge structure; XANES). For the adenine sample, the spin concentration alters strikingly by water absorption on the sample surface. Trapping of photo- or Auger electrons into a newly generated potential in the nucleobases as the consequence of photoelectric effect is suggested as mechanisms of the induction of the short-lived species.

Morphology and Electronic Structure of the Oxide Shell on the Surface of Iron Nanoparticles

An iron (Fe) nanoparticle exposed to air at room temperature will be instantly covered by an oxide shell that is typically approximately 3 nm thick. The nature of this native oxide shell, in combination with the underlying Fe(0) core, determines the physical and chemical behavior of the core-shell nanoparticle. One of the challenges of characterizing core-shell nanoparticles is determining the structure of the oxide shell, that is, whether it is FeO, Fe(3)O(4), gamma-Fe(2)O(3), alpha-Fe(2)O(3), or something else. The results of prior characterization efforts, which have mostly used X-ray diffraction and spectroscopy, electron diffraction, and transmission electron microscopic imaging, have been framed in terms of one of the known Fe-oxide structures, although it is not necessarily true that the thin layer of Fe oxide is a known Fe oxide. In this Article, we probe the structure of the oxide shell on Fe nanoparticles using electron energy loss spectroscopy (EELS) at the oxygen (O) K-edge with a spatial resolution of several nanometers (i.e., less than that of an individual particle). We studied two types of representative particles: small particles that are fully oxidized (no Fe(0) core) and larger core-shell particles that possess an Fe core. We found that O K-edge spectra collected for the oxide shell in nanoparticles show distinct differences from those of known Fe oxides. Typically, the prepeak of the spectra collected on both the core-shell and the fully oxidized particles is weaker than that collected on standard Fe(3)O(4). Given the fact that the origin of this prepeak corresponds to the transition of the O 1s electron to the unoccupied state of O 2p hybridized with Fe 3d, a weak pre-edge peak indicates a combination of the following four factors: a higher degree of occupancy of the Fe 3d orbital; a longer Fe-O bond length; a decreased covalency of the Fe-O bond; and a measure of cation vacancies. These results suggest that the coordination configuration in the oxide shell on Fe nanoparticles is defective as compared to that of their bulk counterparts. Implications of these defective structural characteristics on the properties of core-shell structured iron nanoparticles are discussed.

Time-resolved X-ray absorption spectroscopy of infrared-laser-induced temperature jumps in liquid water

A time-resolved X-ray absorption study of the structural dynamics of liquid water on a picosecond timescale is presented. We apply femtosecond midinfrared pulses to resonantly excite the intramolecular O–H stretching band of liquid water and monitor the transient response in the oxygen K-edge absorption spectrum with picosecond X-ray pulses. In this way, structural changes in the hydrogen bond network of liquid water upon an ultrafast temperature jump of approximately 20 K are investigated. The changes of the X-ray absorption as induced by such a temperature jump are about 3.2%. This demonstrates that our method serves as a sensitive probe of transient structural changes in liquid water and that combined infrared-laser–synchrotron experiments with substantially shorter X-ray pulses, such as generated with a femtosecond slicing scheme, are possible.

Physical properties of amorphous solid interstellar material from X-ray absorption spectroscopy of Scorpius X-1

High-quality, high-resolution X-ray spectra were obtained of Sco X-1 with the Reflection Grating Spectrometer (RGS) onboard the XMM-Newton satellite. The spectrum around the oxygen K-edge is searched for signatures indicative for EXAFS. Analysis shows a clear indication of EXAFS with photo-electron scattering distances in the absorbing medium in a range that applies to many solids. When scattering of the photo-electron on Oxygen atoms is assumed, the oxygen-to-oxygen atom distances found are 2.75 A. This fits with distances as found in amorphous water ice, although water ice is thought to be an unlikely constituent of the diffuse interstellar clouds that form the absorbing medium towards Sco X-1.

Optical emission of biaxial ZnO–ZnS nanoribbon heterostructures

The electronic structure and optical properties of biaxial ZnO-ZnS heterostructure nanoribbons (NRs) have been investigated using x-ray absorption near-edge structures (XANES) and x-ray excited optical luminescence (XEOL). The XANES were recorded in total electron yield and wavelength-selected photoluminescence yield across the K- and L(3,2)-edges of zinc and sulfur and the K-edge of oxygen. The XEOL from the NRs exhibit a very weak band-gap emission at 392 nm and two intense defect emissions at 491 and 531 nm. The synchrotron x-ray pulse ( approximately 100 ps, 153 ns repetition rate) was used to track the optical decay dynamics from ZnO-ZnS NR, which can be described by two lifetimes (7.6 and 55 ns). Comparison with similar measurements for ZnO and ZnS nanowires reveals that the luminescence from ZnO-ZnS NRs was dominated by the ZnO component of the NR as the ZnS component contributes little. The implication of this observation is discussed.

A sample cell to study hydrate formation with x-ray scattering

We present a new sample cell for measuring nonresonant inelastic x-ray scattering spectra of a tetrahydrofuran (THF)-water liquid mixture and THF hydrate. The hydrate is formed inside the cell after nucleation seeds have been offered by a special magnetic stirring mechanism. Hydrate formation was verified by wide angle x-ray scattering and nonresonant x-ray Raman scattering spectra at the oxygen K-edge. A broad range of scattering angles can be studied with this cell which is necessary for momentum transfer dependent inelastic x-ray scattering. This cell is ideal to examine other liquid hydrate formers or other liquid samples, which have to be mixed in situ during the measurements.

Local Charge Disproportion in a High-Performance Perovskite

The temperature-dependent local charge disproportion in the (Ba0.5Sr0.5)(Co0.8Fe0.2)O3−δ perovskite-type oxide (denoted as BSCF) was monitored by in situ electron energy-loss spectroscopy applying monochromized electrons in a transmission electron microscope. At elevated temperatures, oxygen is removed from the crystal lattice in these perovskite-type oxides that is due to a reduction of the transition metal sites. To determine the site-specific valence in the BSCF perovskite, we measured the cobalt and iron L-edges and the oxygen K-edge on increasing the temperature from 298 to 1223 K. It was found that the loss of oxygen at elevated temperatures is mainly due to a reduction of the cobalt site compared to the iron site. The understanding of the site specific redox behavior in this material is important in explaining its long-term instability at intermediate temperatures, which has not been elucidated priory this study.

Analysis of silica-supported vanadia by X-ray absorption spectroscopy: Combined theoretical and experimental studies

In this study we combine density-functional theory (DFT) calculations on oxygen core excitations in vanadia-silica model clusters with in situ X-ray absorption fine structure (NEXAFS) measurements near the oxygen K-edge of vanadia model catalysts supported by silica SBA-15 in order to analyze structural details of the vanadia species. The silica support is found to contribute to the NEXAFS spectrum in an energy range well above that of the vanadium oxide units allowing a clear separation between the corresponding contributions. Further, differently coordinated oxygen which is characteristic for particular vanadia species, monomeric or non-monomeric, can be identified in the theoretical spectra consistent with the oxygen K-edge NEXAFS measurements. The comparison of the theoretical and experimental NEXAFS spectra provides clear evidence that under in situ conditions different molecular vanadia species, in particular non-monomeric V x O y , exist at the catalyst surface and the exclusive presence of monomeric vanadia groups can be ruled out. The present analysis goes beyond earlier work applying vibrational spectroscopy to the present systems where, as a result of extended vibrational coupling, a separation between vanadia, silica, and interface contributions was less successful.

Probing the hydrogen-bond network of water via time-resolved soft X-ray spectroscopy

We report time-resolved studies of hydrogen bonding in liquid H(2)O, in response to direct excitation of the O-H stretch mode at 3 mum, probed via soft X-ray absorption spectroscopy at the oxygen K-edge. This approach employs a newly developed nanofluidic cell for transient soft X-ray spectroscopy in the liquid phase. Distinct changes in the near-edge spectral region (XANES) are observed, and are indicative of a transient temperature rise of 10 K following transient laser excitation and rapid thermalization of vibrational energy. The rapid heating occurs at constant volume and the associated increase in internal pressure, estimated to be 8 MPa, is manifested by distinct spectral changes that differ from those induced by temperature alone. We conclude that the near-edge spectral shape of the oxygen K-edge is a sensitive probe of internal pressure, opening new possibilities for testing the validity of water models and providing new insight into the nature of hydrogen bonding in water.

Correlating NEXAFS characterization of Co–W and Ni–W bimetallic carbide catalysts with reactivity for dry reforming of methane

Abstract The effect of temperature on the structure and performance of Co–W–C and Ni–W–C catalysts for dry reforming of methane (DRM) has been investigated using both reactors and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. For Co–W–C, the DRM reactivity is greatly improved after being exposed to methane at 850 °C. For Ni–W–C, however, the catalytic performance before such exposure is good, although no obvious difference has been found in the catalytic performance before and after exposure to methane at 850 °C. In this work, NEXAFS has been applied to characterize the fresh and spent catalysts, both before and after exposure to the reactants at 850 °C, for both Co–W–C and Ni–W–C. Three NEXAFS regions have been investigated for each catalyst: the carbon K-edge, the oxygen K-edge and the L-edge of either cobalt or nickel. NEXAFS results provide insights into the possible origins for the different performance of those two different carbides. To exhibit reasonable reactivity for DRM, Ni–W oxide and Co–W oxide are required to be reduced, and the active stable catalysts must contain large amounts of carbon so that WC and either Ni or Co are seen in the bulk. NEXAFS results indicate that Ni–W–C can be reduced to a greater extent and at a lower temperature than Co–W–C. In addition, NEXAFS measurements reveal the formation of graphitic carbon at or near the surface region. This species can play a critical role in the reactivity and stability of the catalysts for DRM.

Effect of Al and Y incorporation on the structure of HfO2

We have investigated the structural changes in HfO2 thin films upon Y and Al incorporation. The crystallinity of the films is examined by transmission electron diffraction. The local coordination symmetries of the Hf atoms in the films are revealed by the profile of the oxygen K-edge measured in the electron energy loss spectroscopy (EELS). The EEL spectra are then simulated using real-space multiple-scattering method. We found a good agreement between the simulated and the experimental EELS result of the pure HfO2. The Y incorporation indeed stabilized HfO2 to a cubic structure. Nevertheless, it also contributed to possible lattice distortion and/or creation of complex defect states other than O vacancies, causing discrepancies between the experimental and the simulated results. As a comparison, the local symmetry of Hf is largely degraded upon the incorporation of Al, which not only amorphorized HfO2, but also introduced significantly amount of O vacancies in the film.

X-ray Absorption Spectroscopy of the Nucleotide Bases at the Carbon, Nitrogen, and Oxygen K-Edges

Near-edge X-ray absorption fine structure spectra of three pyrimidine (viz., cytosine, uracil, and thymine) and two purine (viz., adenine and guanine) nucleobases, which are the key constituents of DNA and RNA, were measured at the C, N, and O K-edges using the self-absorption-free partial electron yield mode. The nucleobase samples were prepared as highly pure native polycrystalline powder films. The spectra are analyzed in terms of the electronic structure of the nucleobases. Subtle chemical effects related to the molecular structures of these heterocyclic compounds with extended pi-electron systems are considered and discussed.

X-ray Raman scattering for structural investigation of silica/silicate minerals

We have performed X-ray Raman scattering (XRS) measurements on the oxygen K and silicon L absorption edges of four silica minerals: α-quartz, α-cristobalite, coesite, and stishovite. We have also calculated the partial electron densities of states (DOSs) and compared these with the XRS spectra. This study demonstrates that the short-range structure around the atom of interest strongly influences the XRS spectral features. Importantly, the oxygen K-edge XRS spectra are found to reflect the p-orbital DOS while the silicon L-edge spectra reflect the s- and d-orbital DOSs, even when a product of a momentum transfer and a mean radius of a electron orbit (1s for oxygen and 2p for silicon), Qr, is close to or larger than unity. Building on this, calculations of the partial DOSs for other silica phases are presented, including ultra-high-pressure phases, which provide a good reference for further XRS study of silica and silicate minerals. XRS measurements should be performed on not only either of oxygen or silicon but also on many kinds of constituent elements to reveal the structural change of glasses/melts of silicates under extreme conditions.

Inelastic x-ray scattering of dense solid oxygen: evidence for intermolecular bonding.

The detailing of the intermolecular interactions in dense solid oxygen is essential for an understanding of the rich polymorphism and remarkable properties of this element at high pressure. Synchrotron inelastic x-ray scattering measurements of oxygen K-edge excitations to 38 GPa reveal changes in electronic structure and bonding on compression of the molecular solid. The measurements show that O(2) molecules interact predominantly through the half-filled 1pi(g)* orbital <10 GPa. Enhanced intermolecular interactions develop because of increasing overlap of the 1pi(g)* orbital in the low-pressure phases, leading to electron delocalization and ultimately intermolecular bonding between O(2) molecules at the transition to the epsilon-phase. The epsilon-phase, which consists of (O(2))(4) clusters, displays the bonding characteristics of a closed-shell system. Increasing interactions between (O(2))(4) clusters develop upon compression of the epsilon-phase, and provide a potential mechanism for intercluster bonding in still higher-pressure phases.