Carbon K-shell Research Articles

Inner shell excitation and dissociation of condensed formamide

Carbon and nitrogen K-shell excitation and dissociation of condensed formamide at 96 K were studied by near edge X-ray absorption fine structure (NEXAFS) recorded by total electron yield (TEY), total ion yield (TIY) and photon-stimulated desorption (PSD) yield of H + measurements. It was found that electronic transitions from the C 1s or the N 1s to the σ ∗ (CH and/or NH) enhanced ion yields of H + from the CH and/or NH functional groups. This selective dissociation indicates that the corresponding unoccupied molecular orbital has an antibonding character of the CH and/or NH. To investigate the molecular orientation of condensed formamide, incidence-angle-dependent TEY-NEXAFS spectra were measured. The CNO plane of the adsorbed formamide molecule is determined to be tilted away from the surface by an averaged angle of about 42°.

Re-analysis of the K-shell spectrum of benzene

Abstract The carbon K-shell spectrum of gaseous benzene has been recorded by inner-shell electron energy loss spectroscopy (ISEELS) under electric-dipole conditions (2 keV, small angle) with a resolution of 0.17 eV. Ab initio configuration interaction calculations performed in the frame of the equivalent core model have helped in the assignment of the experimental spectrum. They emphasize the importance of the multi-configurational approach and the role of the Rydberg orbitals in the assignment of some features. The band located at 289.09 eV is assigned to Rydberg excitations and a 3π* transition mixed with doubly excited configurations, and not to an anti-bonding (C–H) transition as suggested previously. Because of a large 3s/3d character of the (C–H)* orbital, the corresponding peak appears above the ionization threshold. The 293.8 eV band contains in-plane resonances and very likely also several doubly excited states with a 3π* contribution.

Transmission Electron Diffraction at 200 eV and Damage Thresholds below the Carbon K Edge.

Transmission electron diffraction patterns from ultra-thin aromatic and aliphatic organic films at beam energies of 200 eV-1 keV have been recorded in a custom low energy electron transmission (LEET) chamber. A significant reduction of the molecular damage cross-section, measured by fading of diffraction spots, was found for thin films of the aromatic perylene when the beam energy was reduced from 400 to 200 eV. The corresponding measurements for the aliphatic tetracontane showed a smaller "threshold energy" and the differences are discussed. Electron beam damage from other aromatic materials has also been studied at low energy. Comparison of the carbon K shell ionization cross-section and the measured damage cross-sections show that carbon K-shell ionization is strongly correlated with the damage observed in aromatics at beam energies higher than 284 eV. Calculation of the minimum number of unit cells needed for imaging a single molecule, and comparison of calculated elastic with measured damage cross-sections both indicate new possibilities for imaging biomolecules with low energy electrons.

Transmission Electron Diffraction at 200 eV and Damage Thresholds below the Carbon K Edge

Abstract Transmission electron diffraction patterns from ultra-thin aromatic and aliphatic organic films at beam energies of 200 eV–1 keV have been recorded in a custom low energy electron transmission (LEET) chamber. A significant reduction of the molecular damage cross-section, measured by fading of diffraction spots, was found for thin films of the aromatic perylene when the beam energy was reduced from 400 to 200 eV. The corresponding measurements for the aliphatic tetracontane showed a smaller “threshold energy” and the differences are discussed. Electron beam damage from other aromatic materials has also been studied at low energy. Comparison of the carbon K shell ionization cross-section and the measured damage cross-sections show that carbon K-shell ionization is strongly correlated with the damage observed in aromatics at beam energies higher than 284 eV. Calculation of the minimum number of unit cells needed for imaging a single molecule, and comparison of calculated elastic with measured damage cross-sections both indicate new possibilities for imaging biomolecules with low energy electrons.

Inner-Shell Damage Thresholds Below 1kv in Cu-Phthalocyanine

Abstract In 1970, Breedlove and Trammel predicted that, because of radiation damage, the direct imaging of individual organic molecules by electron or X-ray microscopy was not possible. This follows from an analysis, above IkeV, of the beam energy dependence of the ratio of inelastic scattering cross sections (some of which causes damage) to elastic cross sections (used to form the image). To minimize damage, we have therefore constructed a transmission electron microscope with nanometer resolution, which operates at 7 - 300 eV, below the threshold for most inelastic processes. Recently we have obtained our first images of TMV with this instrument. Isaacson first suggested that the K-shell ionization of carbon may be the most important damage process. Although less probable than valence excitation, it dumps more energy into the system, and the decay products are highly damaging. A subsequent study of electron beam damage in several π- bonded hydrocarbon crystals down to about 200 eV showed that a damage threshold does exist at about IkeV incident energy which can be explained by the carbon K-shell ionization. (Multiple scattering increases the energy threshold from 285eV).

Lethal Effect of Carbon K-Shell Photoionizations in Chinese Hamster V79 Cell Nuclei: Experimental Method and Theoretical Analysis

To test a possible specific effect of carbon K-shell ionizations in DNA, survival curves for Chinese hamster V79 cells were measured for X irradiations at energies below and above the carbon K-shell ionization threshold. Specific values of the X-ray energies (250 and 340 eV) were chosen to ensure isoattenuation of the two kinds of radiation within the cell. An enhancement of lethality by a factor of about 2 was found for X rays at 340 eV compared to below the threshold at 250 eV. This may be attributed to the production of highly efficient carbon K-shell ionizations located on DNA. A model of X-ray lethality (Goodhead et al., Radiat. Prot. Dosim. 52, 217-223, 1994) was extended to allow for a possible lethal effect from clusters of reactive species induced by K-shell photoionizations (K-shell clusters). Within this model, the increase in lethality above the carbon K-shell threshold may be explained by a value of 2% for the lethal efficiency of K-shell clusters overlapping the DNA. An extrapolation to the lethal effect of more complex ion-induced K-shell ionizations indicates that K-shell ionization may be a major process in the biological effectiveness of heavy ions.

Competition between decay and dissociation of core-excited carbonyl sulfide studied by x-ray scattering

We show the first evidence of dissociation during resonant inelastic soft X-ray scattering. Carbon and oxygen K-shell and sulfur L-shell resonant and non-resonant X-ray emission spectra were measured using monochromatic synchrotron radiation for excitation and ionization. After sulfur, L2,3 -> {\pi}*, {\sigma}* excitation, atomic lines are observed in the emission spectra as a consequence of competition between de-excitation and dissociation. In contrast the carbon and oxygen spectra show weaker line shape variations and no atomic lines. The spectra are compared to results from ab initio calculations and the discussion of the dissociation paths is based on calculated potential energy surfaces and atomic transition energies.

The core excitation of pyridine and pyridazine: An electron spectroscopy and ab initio study

The carbon and nitrogen K-shell excitation spectra of gaseous pyridine and pyridazine were recorded using the electron-energy loss spectroscopy under electric-dipole conditions (2 keV, small angle) with a resolution of 0.2 eV. Ab initio Configuration interaction calculations in the frame of the equivalent core model were performed in order to help in the assignment of the spectral features. The spectra are dominated by the transitions to the 1π* and σ* type orbitals. The C1s spectra of both molecules are close to that of benzene: The intensity of Rydberg transitions are enhanced by an important valence σC–H* character; the 1s→3π* transition is mixed with double excitations and give rise to several states, some of them lying above the ionization thresholds. Finally, the N1s spectra of both molecules are similar to the s-triazine one.

Investigation of acetylene adsorbed on Cu(100) by multiple-scattering cluster method

The carbon K-shell near-edge X-ray absorption fine structure (NEXAFS) spectra of acetylene adsorbed on Cu(100) have been analyzed by the multiple-scattering cluster method. It is identified that the features appearing in the NEXAFS spectra are corresponding to the π∗ and σ∗ resonances as well as the interaction between CH and CC σ∗. Furthermore, it is shown that the Cu(100) substrate acts on the acetylene molecule strongly, which leads to a new feature between the π∗ and σ∗ resonances. It has been found that the molecular plane of C 2H 2 is perpendicular to the surface, but the molecules no longer keep in a line, the hydrogen atoms ascend which make the HCC bond angle around 150°. By a comparison between theory and experiment [1], we found the CC bond length about 1.30 Å and the CC pair adsorbed in a two-fold aligned bridge site.

Carbon K-shell near-edge structure calculations for graphite using the multiple-scattering approach

The near-edge absorption fine structure of carbon in graphite has been calculated using the multiple-scattering approach. The effects of both a neutral carbon absorber and taking into account the effect of the core hole by using a nitrogen (Z + 1) absorber atom are considered. The best agreement with experiment was obtained for the case of the nitrogen absorber and a cluster of 145 atoms, with the calculated near-edge structure (NES) containing the main features observed experimentally. A splitting near the onset of the -peak, similar to that seen experimentally, was found to occur in the calculated NES for one of the two inequivalent carbon atoms in the graphite structure. This splitting was not observed in the calculated NES for a single sheet of graphite, supporting the proposition that it only occurs in well ordered graphite. This result supports the proposition that the splitting originates from a sharp -peak and a dipole-allowed bandlike contribution associated to the branch of the free-electron-like interlayer states.

Statistical description of shake satellites in Auger spectra. Oxygen and carbon Auger spectra of the CO molecule

A technique of transition arrays is employed to calculate the shape of the shake-satellite spectra in the oxygen and carbon K-shell Auger spectra of the CO molecule. Good agreement of the overall spectral shapes with the experiment is obtained. The oxygen KV-VVV shake-satellite spectrum also compares well with that calculated earlier within more rigorous line by line scheme.

Theoretical X-ray emission spectra for the fluoromethane molecules following carbon K-shell ionization

Carbon K X-ray emission transition energies and probabilities have been calculated for the fluoromethane series of molecules CH 4− x F x , where x is 0–4, subsequent to carbon K-shell photoionization. Four methods were used to calculate the transition probabilities: the ground state frozen orbital method, the core-hole frozen orbital method, the transition state method, and the fully relaxed orbital method. The results were compared between each method and with the experimental values. It was established that the fully relaxed method is the preferred method, and is a tractable method for molecules of this size.

Multiple-scattering approaches to carbon K-shell near-edge X-ray absorption fine structure of graphite

The multiple-scattering cluster method was first employed to calculate the theoretical near-edge X-ray absorption fine structure (NEXAFS) spectrum of graphite. Studies on the polarization dependence on the incident vector E classify spectral features into pi and sigma resonances. Characterization of the carbon K-shell NEXAFS spectra of the species modelled by both a single layer and a multilayer has been performed. It reveals that a pi * resonance originally located at around 989 eV splits with the accumulation of the number of atoms included in the cluster. Multilayer calculation has little influence on the NEXAFS spectrum. Our calculation coincides with the experimental results fairly well. In addition, it has been found to be in good agreement with the final density of states derived from band-structure calculations.

X-ray Linear Dichroism Microscopy

Chemical-specific x-ray linear dichroism was observed in an x-ray microscope as evidenced by changes in relative contrast upon azimuthal rotation of the sample. As a demonstration, thin sections of a partially ordered polymer fiber were examined with a transmission x-ray microscope near the carbon K-shell absorption edge to provide chemical-specific imaging at 50-nanometer spatial resolution. The observed dichroism and change in contrast upon rotation arise from the polarization dependence of the near-edge x-ray absorption cross section and can be used to image the orientation of specific chemical bonds.

Multiple Scattering Cluster Approach to Oxygen and Carbon K-shell NEXAFS Spectra of HCOO-Cu(110)

We have calculated the oxygen and carbon K-shell near-edge X-ray absorption fine structure (NEXAFS) spectra of formate (HCOO) adsorbed on Cu(110) surface in terms of the multiple-scattering cluster method. The calculation shows that the molecular bond-length LC-O=1.26±0.01Å,the adsorption distance of oxygen LO-Cu=1.99±0.04Å. We have found the C-H resonance existing in the carbon K-shell NEXAFS spectra. The origin of the C-H resonance has been discussed.

Correlation between the carbon K-shell X-ray emission rates in molecules and their π bond order

For the first time, a clear correlation is shown between carbon K-shell X-ray emission rates from molecules that contain carbon (C) atoms and their π bond orders. This correlation is based on the present calculation for C 2H 2, C 2H 4, and C 2H 6 and previous calculations of Larkins for CO, CO 2, HCN, and CH 3OH. Because the π bond order has an inverse linear relationship with the bond length, the C K-shell X-ray emission rate correlates with the bond length as well. Some rationale for the findings based on electronegativity and charge distribution, is given, The correlation manifests itself in a chemical effect on the C K-shell X-ray emission rate.

Vibrationally resolved threshold photoemission of N 2 and CO at the N and C K-edges

Zero-kinetic-energy photoelectron spectroscopy was used to measure the Franck—Condon factors for the carbon and nitrogen K-shell ionized states in N 2 and CO. Corresponding features in the two spectra showed nearly identical energy spacings, both below and above the ionization threshold, as predicted by the equivalent-core model. The equilibrium bond length, R e, for the CO C-1s −1 state was determined to be 1.077±0.005 Å, and R e for the N 2 N-1s −1 state was found to be 1.077±0.010 Å, changes of −0.051 Å for CO and −0.020 Å for N 2 from their ground-state equilibrium bond lengths. The two-electron states corresponding to 1s −1 val −1π* were examined in the binding energy region predicted by Green function calculations. Two-electron states absent in the X-ray photoemission spectrum are present in both molecules and show evidence of vibrational structure.

Transmission electron microscopy and electron energy loss spectroscopy of C 60 fullerite

The crystal structure and the electronic structure of crystalline C 60 grown from a benzene solution have been studied by transmission electron microscopy and energy loss spectroscopy. Electron diffraction patterns and high-resolution images reveal an hcp structure ( a = 1.01±0.01 nm, c = 1.65±0.02 nm) with stacking disorders. Electron energy loss spectra in a low-loss region revealed not only two collective excitations at 6.5 and 26 eV but also several single-electron excitations. From carbon K-shell excitation, spectral information on unoccupied π ∗ and σ ∗ bands has been obtained.

Multiple-scattering analysis of the structure of ethylene adsorbed on the Cu(100) surface.

The carbon K-shell near-edge x-ray-absorption fine-structure (NEXAFS) spectra of gas-phase ethylene molecules and ethylene adsorbed on the Cu(100) surface have been calculated by the multiple-scattering cluster method. The calculated result shows the existence of the C-H scattering resonance in carbon K-shell NEXAFS spectra of the adsorbed ethylene molecules. By a comparison between the theoretical results and the experimental spectra, we have found that the C-C bond midpoint occupies a fourfold hollow site 1.3 \AA{} above the Cu surface with the C-C axis being parallel to the [001] or [010] direction. The bond lengths of C-C and Cu-C are equal to 1.46\ifmmode\pm\else\textpm\fi{}0.04 and 1.90\ifmmode\pm\else\textpm\fi{}0.03 \AA{}, respectively, and the H-C-H bond angle equals 130\ifmmode\pm\else\textpm\fi{}5\ifmmode^\circ\else\textdegree\fi{}. These results are in agreement with those of Fourier-transform analysis of the surface extended x-ray-absorption fine structure.

Unfilled orbitals of C60 and C70 from carbon K-shell X-ray absorption fine structure

The K-shell near-edge X-ray absorption fine structure spectra of solid C60 and C70 have been recorded with high spectral resolution. The spectra exhibit sharp resonances associated with transitions to unfilled π* molecular orbitals and, at higher energy, broader resonances associated with σ*-like orbitals. The observed energy splitting of the π* resonances can be accounted for by published extended Hückel calculations. Our data clearly reveal that the fullerence films resemble molecular solids with considerably stronger intra-molecular than inter-molecular interactions.