Carbon K-shell Research Articles

Stain-free mapping of polymer-blend morphologies via application of high-voltage STEM-EELS hyperspectral imaging to low-loss spectra

Polymer blends composed of multiple types of polymers are used for various industrial applications; therefore, their morphologies must be understood to predict and improve their physical properties. Herein, we propose a spectral imaging method based on scanning transmission electron microscopy (STEM) and electron energy-loss spectroscopy to map polymer morphologies with nanometric resolution as an alternative to the conventional electron staining technique. In particular, the low-loss spectra of the 5–30 eV energy-loss region were measured to minimize electron irradiation damage rather than the core-loss spectra, such as carbon K-shell absorption spectra, which require significantly longer recording times. Medium-voltage (200 kV) and high-voltage (1000 kV) STEM was used at various temperatures to compare the degrees of electron-beam damage resulting from various electron energies and sample temperatures. A multivariate curve resolution technique was used to isolate the constituent spectra and visualize their distributions by distinguishing the characteristic peaks derived from various chemical species. High-voltage STEM was more useful than medium-voltage STEM for analyzing thicker samples while suppressing ionization damage.

X-Ray Spectroscopy of Interstellar Carbon: Evidence for Scattering by Carbon-bearing Material in the Spectrum of 1ES 1553+113

Molecules and particles make up ∼40%–70% of carbon in the interstellar medium, yet the exact chemical structure of these constituents remains unknown. We present carbon K-shell absorption spectroscopy of the Galactic interstellar medium obtained with the Low Energy Transmission Grating Spectrometer on board the Chandra Observatory that directly addresses this question. We probe several lines of sight, using bright active galactic nuclei as backlighters. We make our measurements differentially with respect to the bright source Mrk 421, in order to take the significant carbon K absorption in the instrument into account. In the spectrum of the blazar 1ES 1553+113 we find evidence for a novel feature: strong extinction on the low-energy side of the neutral C 1s−2p resonance, which is indicative of scattering by graphite particles. We find evidence for characteristic particle radii of order 0.1–0.15 μm. If this explanation for the feature is correct, limits on the mass of the available carbon along the line of sight may imply that the grains are partially aligned, and the X-rays from the source may have intrinsic polarization.

Adsorption configurations of furan molecule on Si(100)-2×1 surface by X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectra

The electronic and geometric structures of several possible configurations of furan(CHO) molecule chemisorbed on Si(100)-2×1 surface have been studied by X-ray spectroscopy, which is important for the design of semiconductor materials with unique properties. The Carbon K-shell (C-1s) X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra of several predicted adsorbed configurations have been simulated and calculated using density functional theory and cluster model. Our results show that the XPS and NEXAFS spectra of several possible adsorbed configurations were structurally dependent. Compared with XPS, NEXAFS spectra showed stronger structure dependence on the system; therefore, it can be well used to distinguish the configurations of furan molecule chemisorbed on Si(100)-2×1 surface. In order to explore the relationship between the spectra and structures of furan's adsorption configurations precisely, the spectral contributions of non-equivalent carbon atoms in different structural environments were also calculated.

Monte Carlo Simulation of Double-Strand Break Induction and Conversion after Ultrasoft X-rays Irradiation.

This paper estimates the yields of DNA double-strand breaks (DSBs) induced by ultrasoft X-rays and uses the DSB yields and the repair outcomes to evaluate the relative biological effectiveness (RBE) of ultrasoft X-rays. We simulated the yields of DSB induction and predicted them in the presence and absence of oxygen, using a Monte Carlo damage simulation (MCDS) software, to calculate the RBE. Monte Carlo excision repair (MCER) simulations were also performed to calculate the repair outcomes (correct repairs, mutations, and DSB conversions). Compared to 60Co γ-rays, the RBE values for ultrasoft X-rays (titanium K-shell, aluminum K-shell, copper L-shell, and carbon K-shell) for DSB induction were respectively 1.3, 1.9, 2.3, and 2.6 under aerobic conditions and 1.3, 2.1, 2.5, and 2.9 under a hypoxic condition (2% O2). The RBE values for enzymatic DSBs were 1.6, 2.1, 2.3, and 2.4, respectively, indicating that the enzymatic DSB yields are comparable to the yields of DSB induction. The synergistic effects of DSB induction and enzymatic DSB formation further facilitate cell killing and the advantage in cancer treatment.

Chiral photoelectron angular distributions from ionization of achiral atomic and molecular species

We show that the combination of two achiral components - atomic or molecular target plus a circularly polarized photon - can yield chirally structured photoelectron angular distributions. For photoionization of CO, the angular distribution of carbon K-shell photoelectrons is chiral when the molecular axis is neither perpendicular nor (anti-)parallel to the light propagation axis. In photo-double-ionization of He, the distribution of one electron is chiral, if the other electron is oriented like the molecular axis in the former case and if the electrons are distinguishable by their energy. In both scenarios, the circularly polarized photon defines a plane with a sense of rotation and an additional axis is defined by the CO molecule or one electron. This is sufficient to establish an unambiguous coordinate frame of well-defined handedness. To produce a chirally structured electron angular distribution, such a coordinate frame is necessary, but not sufficient. We show that additional electron-electron interaction or scattering processes are needed to create the chiral angular distribution.

Geometric and electronic structures of pyrazine molecule chemisorbed on Si(100) surface by XPS and NEXAFS spectroscopy

The geometric and electronic structures of several possible adsorption configurations of the pyrazine (C4H4N2) molecule covalently attached to Si(100) surface, which is of vital importance in fabricating functional nano-devices, have been investigated using X-ray spectroscopies. The Carbon K-shell (1s) X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy of predicted adsorbed structures have been simulated by density functional theory with cluster model calculations. Both XPS and NEXAFS spectra demonstrate the structural dependence on different adsorption configurations. In contrast to the XPS spectra, it is found that the NEXAFS spectra exhibiting conspicuous dependence on the structures of all the studied pyrazine/Si(100) systems can be well utilized for structural identification. In addition, according to the classification of carbon atoms, the spectral components of carbon atoms in different chemical environments have been investigated in the NEXAFS spectra as well.

Molecular inner-shell photoabsorption/photoionization cross sections at core-valence-separated coupled cluster level: Theory and examples.

Oxygen, nitrogen, and carbon K-shell photoabsorption and photoionization cross sections have been calculated within core-valence-separated coupled cluster (CC) linear response theory for a number of molecular systems, namely, water, ammonia, ethylene, carbon dioxide, acetaldehyde, furan, and pyrrole. The cross sections below and above the K-edge core ionization thresholds were obtained, on the same footing, from L2 basis set calculations of the discrete electronic pseudospectrum yielded by an asymmetric-Lanczos-based formulation of CC linear response theory at the CC singles and doubles (CCSD) and CC singles and approximate doubles (CC2) levels. An analytic continuation procedure for both discrete and continuum cross sections as well as a Stieltjes imaging procedure for the photoionization cross section were applied and the results critically compared.

Landscape of s-triazine molecule on Si(100) by a theoretical x-ray photoelectron spectroscopy and x-ray absorption near-edge structure spectra study**Project supported by the National Natural Science Foundation of China (Grant Nos. 11874242, 11804196, and 11804197).

The chemisorbed structure for an aromatic molecule on a silicon surface plays an important part in promoting the development of organic semiconductor material science. The carbon K-shell x-ray photoelectron spectroscopy (XPS) and the x-ray absorption near-edge structure (XANES) spectra of the interfacial structure of an s-triazine molecule adsorbed on Si(100) surface have been performed by the first principles, and the landscape of the s-triazine molecule on Si(100) surface has been described in detail. Both the XPS and XANES spectra have shown their dependence on different structures for the pristine s-triazine molecule and its several possible adsorbed configurations. By comparison with the XPS spectra, the XANES spectra display the strongest structural dependency of all of the studied systems and thus could be well applied to identify the chemisorbed s-triazine derivatives. The exploration of spectral components originated from non-equivalent carbons in disparate local environments has also been implemented for both the XPS and XANES spectra of s-triazine adsorbed configurations.

Ultrafast isomerization in acetylene dication after carbon K-shell ionization

Ultrafast proton migration and isomerization are key processes for acetylene and its ions. However, the mechanism for ultrafast isomerization of acetylene [HCCH]2+ to vinylidene [H2CC]2+ dication remains nebulous. Theoretical studies show a large potential barrier ( > 2 eV) for isomerization on low-lying dicationic states, implying picosecond or longer isomerization timescales. However, a recent experiment at a femtosecond X-ray free-electron laser suggests sub-100 fs isomerization. Here we address this contradiction with a complete theoretical study of the dynamics of acetylene dication produced by Auger decay after X-ray photoionization of the carbon atom K shell. We find no sub-100 fs isomerization, while reproducing the salient features of the time-resolved Coulomb imaging experiment. This work resolves the seeming contradiction between experiment and theory and also calls for careful interpretation of structural information from the widely applied Coulomb momentum imaging method.

First-principles calculations of X-ray absorption spectra for warm dense methane

X-ray absorption spectrum is a powerful tool for atomic structure detection on materials under extreme conditions. Here, we perform first-principles molecular dynamics and X-ray absorption spectrum calculations for warm dense methane under thermodynamical conditions along a Hugoniot curve. From the molecular dynamics trajectories, the detailed atomic structures are examined for each condition. The carbon K-shell X-ray absorption spectrum is calculated, and its change with temperature and pressure is discussed. The methane systems under extreme conditions may contain radicals CHx (x = 1,2,3), molecules CH4, and carbon chains CmHn (m,n >1). These various products show quite different contributions to the total X-ray spectrum due to the different atomic and electronic structures. The change of the total X-ray spectrum along the Hugoniot curve is then attributed to the change of the products induced by the temperature and pressure. Some clear signatures on the X-ray absorption spectrum under different thermodynamical conditions are proposed, which provide useful information for future X-ray experiments.

A mechanistic study of gold nanoparticle radiosensitisation using targeted microbeam irradiation

Gold nanoparticles (GNPs) have been demonstrated as effective radiosensitizing agents in a range of preclinical models using broad field sources of various energies. This study aimed to distinguish between these mechanisms by applying subcellular targeting using a soft X-ray microbeam in combination with GNPs. DNA damage and repair kinetics were determined following nuclear and cytoplasmic irradiation using a soft X-ray (carbon K-shell, 278 eV) microbeam in MDA-MB-231 breast cancer and AG01522 fibroblast cells with and without GNPs. To investigate the mechanism of the GNP induced radiosensitization, GNP-induced mitochondrial depolarisation was quantified by TMRE staining, and levels of DNA damage were compared in cells with depolarised and functional mitochondria. Differential effects were observed following radiation exposure between the two cell lines. These findings were validated 24 hours after removal of GNPs by flow cytometry analysis of mitochondrial depolarisation. This study provides further evidence that GNP radiosensitisation is mediated by mitochondrial function and it is the first report applying a soft X-ray microbeam to study the radiobiological effects of GNPs to enable the separation of physical and biological effects.

Theoretical identification of seven C80 fullerene isomers by XPS and NEXAFS spectroscopy.

The carbon K-shell (1s) X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy of the seven isolated-pentagon-rule (IPR) isomers of fullerene C80 have been calculated by means of density functional theory (DFT) theoretically. We have demonstrated the relationship between molecular structures and related X-ray spectroscopies. The dependence of the XPS spectra on the structures of the seven C80 molecules is imperfect, while the NEXAFS spectra show strong dependence on the seven fullerene molecules, so the NEXAFS spectra can be employed to identify all of the studied isomers. The spectral components of different local environments have been explored in detail.

X-ray scattering measurements on imploding CH spheres at the National Ignition Facility.

We have performed spectrally resolved x-ray scattering measurements on highly compressed polystyrene at pressures of several tens of TPa (100Mbar) created by spherically convergent shocks at the National Ignition Facility. Scattering data of line radiation at 9.0 keV were recorded from the dense plasma shortly after shock coalescence. Accounting for spatial gradients, opacity effects, and source broadening, we demonstrate the sensitivity of the elastic scattering component to carbon K-shell ionization while at the same time constraining the temperature of the dense plasma. For six times compressed polystyrene, we find an average temperature of 86 eV and carbon ionization state of 4.9, indicating that widely used ionization models need revision in order to be suitable for the extreme states of matter tested in our experiment.

Molecular frame photoelectron angular distributions for core ionization of ethane, carbon tetrafluoride and 1,1-difluoroethylene

Molecular frame photoelectron angular distributions (MFPADs) are measured in electron–ion momentum imaging experiments and compared with complex Kohn variational calculations for carbon K-shell ionization of carbon tetrafluoride (CF4), ethane (C2H6) and 1,1-difluoroethylene (C2H2F2). While in ethane the polarization averaged MFPADs show a tendency at low energies for the photoelectron to be emitted in the directions of the bonds, the opposite effect is seen in CF4. A combination of these behaviors is seen in difluoroethylene where ionization from the two carbons can be distinguished experimentally because of their different K-shell ionization potentials. Excellent agreement is found between experiment and simple static-exchange or coupled two-channel theoretical calculations. However, simple electrostatics do not provide an adequate explanation of the suggestively simple angular distributions at low electron ejection energies.

Ultrafast isomerization initiated by X-ray core ionization.

Rapid proton migration is a key process in hydrocarbon photochemistry. Charge migration and subsequent proton motion can mitigate radiation damage when heavier atoms absorb X-rays. If rapid enough, this can improve the fidelity of diffract-before-destroy measurements of biomolecular structure at X-ray-free electron lasers. Here we study X-ray-initiated isomerization of acetylene, a model for proton dynamics in hydrocarbons. Our time-resolved measurements capture the transient motion of protons following X-ray ionization of carbon K-shell electrons. We Coulomb-explode the molecule with a second precisely delayed X-ray pulse and then record all the fragment momenta. These snapshots at different delays are combined into a 'molecular movie' of the evolving molecule, which shows substantial proton redistribution within the first 12 fs. We conclude that significant proton motion occurs on a timescale comparable to the Auger relaxation that refills the K-shell vacancy.

Photoionization and photofragmentation of multiply charged Lu3N@C80 ions

SynopsisRelative cross sections for photoionization and photofragmentation of endohedral fullerene Lu3N@C80q+ (q=1,2,3) ions have been measured employing the new photon-ion spectrometer PIPE at PETRA III. Prominent structures related to the carbon K-shell ionization threshold were observed in the energy range 280 to 330 eV.

Spatiotemporal isolation of attosecond soft X-ray pulses in the water window.

Attosecond pulses at photon energies that cover the principal absorption edges of the building blocks of materials are a prerequisite for time-resolved probing of the triggering events leading to electronic dynamics such as exciton formation and annihilation. We demonstrate experimentally the isolation of individual attosecond pulses at the carbon K-shell edge (284 eV) in the soft X-ray water window with pulse duration below 400 as and with a bandwidth supporting a 30-as pulse duration. Our approach is based on spatiotemporal isolation of long-wavelength-driven harmonics and validates a straightforward and scalable approach for robust and reproducible attosecond pulse isolation.

Multi-fragment vector correlation imaging. A search for hidden dynamical symmetries in many-particle molecular fragmentation processes

State-of-the-art multi-fragment imaging techniques like the COLTRIMS reaction microscope unveil the complete momentum pattern in low-energy atomic and molecular many-particle fragmentation processes much like the bubble chamber in high-energy particle physics. The excellent momentum resolution far below 1 m e a 0 E h/ħ (1 a.u.) and the high multi-fragment detection efficiency of the COLTRIMS technique reveal the dynamic correlation of bound many-particle systems as they are fragmented into the continuum. For the fragmentation process of carbon monoxide following carbon K-shell ionization using 306 eV photons (right and left circularly polarized) hν + CO → ephoto + O+ + C+ + eK-Auger, the vector correlations between all fragments were measured in coincidence for each event. According to the common view of this process, the photoelectron and Auger electron emission probe different aspects of the time-dependent fragmentation process, i.e. the ‘time evolution’ of fragmentation. Based on measured vectors and vector combinations (e.g. vector products) of (1) the absorbed photon, (2) the emitted photoelectron and (3) ions, the Auger electron emission can be investigated with respect to the axes and planes defined by these vector combinations for each event in order to explore dynamical symmetries in multi-particle systems.

Advantages of intermediate X-ray energies in Zernike phase contrast X-ray microscopy

Understanding the hierarchical organizations of molecules and organelles within the interior of large eukaryotic cells is a challenge of fundamental interest in cell biology. Light microscopy is a powerful tool for observations of the dynamics of live cells, its resolution attainable is limited and insufficient. While electron microscopy can produce images with astonishing resolution and clarity of ultra-thin (<1μm thick) sections of biological specimens, many questions involve the three-dimensional organization of a cell or the interconnectivity of cells. X-ray microscopy offers superior imaging resolution compared to light microscopy, and unique capability of nondestructive three-dimensional imaging of hydrated unstained biological cells, complementary to existing light and electron microscopy.Until now, X-ray microscopes operating in the “water window” energy range between carbon and oxygen k-shell absorption edges have produced outstanding 3D images of cryo-preserved cells. The relatively low X-ray energy (<540eV) of the water window imposes two important limitations: limited penetration (<10μm) not suitable for imaging larger cells or tissues, and small depth of focus (DoF) for high resolution 3D imaging (e.g., ~1μm DoF for 20nm resolution). An X-ray microscope operating at intermediate energy around 2.5keV using Zernike phase contrast can overcome the above limitations and reduces radiation dose to the specimen. Using a hydrated model cell with an average chemical composition reported in literature, we calculated the image contrast and the radiation dose for absorption and Zernike phase contrast, respectively. The results show that an X-ray microscope operating at ~2.5keV using Zernike phase contrast offers substantial advantages in terms of specimen size, radiation dose and depth-of-focus.

The K-shell spectra of tetrahydrofuran studied by electron energy loss spectroscopy and abinitio calculations

Ab initio calculations have been carried out in order to assign the bands observed in the carbon and oxygen K-shell spectra of gaseous tetrahydrofuran (THF), measured using inner-shell electron energy loss spectroscopy (ISEELS). The good agreement between the theoretical and the measured spectra allows us to re-assign precisely most of the peaks. The ionisation energies are calculated for the first time and found to be consistent with a quantum defect analysis of the core excitation energies. The calculated spectra for the C2v, C2 and Cs geometries of the molecule show very small differences. Thus, K-shell spectroscopy cannot be used to solve the controversy on the geometry of THF.