Carbon K-shell Ionization Research Articles

Ab Initio Molecular Dynamics Simulations to Interpret the Molecular Fragmentation Induced in Deoxyribose by Synchrotron Soft X-Rays

It has been suggested that core ionization in DNA atoms could induce complex, irreparable damage. Synchrotron soft X-rays have been used to probe the damage induced by such events in thin films of DNA components. In a complementary approach, we investigate the fragmentation dynamics following a carbon or oxygen K-shell ionization in 2-deoxy-D-ribose (DR), a major component in the DNA chain. Core ionization of the sugars hydration layer is also studied. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics (MD) simulations. The ultrafast dissociation dynamics of the core ionized molecule, prior Auger decay, is modeled for about 10 fs. We show that the core-ionization of oxygen atoms within DR or its hydration layer may induce proton transfers towards nearby molecules, before Auger decay. In a second step, we model an Auger effect occurring either at the beginning or at the end of the core–hole dynamics. Two electrons are removed from the deepest valence molecular orbitals localized on the initially core-ionized oxygen atom (O*), and this electronic state is propagated by means of Ehrenfest MD. We show an ultrafast dissociation of the DR2+ molecule C-O* bonds, which, in most cases, seems independent of the time at which Auger decay occurs.

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.

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.

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.

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.

Observation of the Anisotropy of the Inelastic Scattering of Fast Electrons Accompanied by the K-shell Ionization of a Carbon Nanotube

The angular distribution of inelastically scattered electrons following the carbon K-shell ionization of a carbon nanotube (CNT) has been studied by using an energy-filtered transmission electron microscope. The energy-filtered scattering patterns of the CNT, whose cylindrical axis is oriented in the perpendicular direction with respect to the incident-electron beam, show anisotropic angular distributions caused by the p symmetry in the pi* and sigma* unoccupied states into which a K electron jumps, and the cylindrical shape of the CNT. Corresponding inelastic scattering cross sections, differential in solid angle, have been calculated within the first Born approximation by considering that each carbon atom has three, mutually orthogonal, unoccupied p orbitals, which are oriented in directions perpendicular or parallel to the tube surface. The observed angular patterns agree well with theoretical results, which are linear combinations of the differential cross sections accompanied by the transitions to pi* and sigma* states. A series of the fittings of the experimental patterns at successive values of energy loss provides magnitudes of the pi* and sigma* components, which can be called partial electron energy-loss spectra accompanied by the transitions to the pi* and sigma* states.

Observation of the anisotropy of the inelastic scattering of fast electrons accompanied by the K-shell ionization of a carbon nanotube

The angular distribution of inelastically scattered electrons following the carbon K-shell ionization of a carbon nanotube (CNT) has been studied by using an energy-filtered transmission electron microscope. The energy-filtered scattering patterns of the CNT, whose cylindrical axis is oriented in the perpendicular direction with respect to the incident-electron beam, show anisotropic angular distributions caused by the p symmetry in the pi* and sigma* unoccupied states into which a K electron jumps, and the cylindrical shape of the CNT. Corresponding inelastic scattering cross sections, differential in solid angle, have been calculated within the first Born approximation by considering that each carbon atom has three, mutually orthogonal, unoccupied p orbitals, which are oriented in directions perpendicular or parallel to the tube surface. The observed angular patterns agree well with theoretical results, which are linear combinations of the differential cross sections accompanied by the transitions to pi* and sigma* states. A series of the fittings of the experimental patterns at successive values of energy loss provides magnitudes of the pi* and sigma* components, which can be called partial electron energy-loss spectra accompanied by the transitions to the pi* and sigma* states.

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.

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.

Molecular photo cross sections with the LCGTO–Xα method using Stieltjes imaging

A method for calculating and symmetry analyzing total molecular photoionization cross sections is presented. The technique is based on the LCGTO–Xα method and employs Stieltjes imaging. It allows applications to molecular systems comparable in size to those treated so far with the continuum multiple-scattering Xα method, but avoids the pitfalls of the muffin-tin approximation to the electronic potential. Photo cross sections for valence ionization of CO are found in good agreement with experiment and with previous calculations. From a final state symmetry analysis for the 1π level, the absence of kσ* shape resonance which appears in the 4σ and the 5σ ionization channels is attributed to small transition moments. This is in contrast to a previous treatment where this difference has been rationalized as caused by a channel dependent final state potential. The photoionization cross sections for the four highest valence orbitals of benzene were calculated in better agreement with experiment than found in a previous Xα–SW treatment. The improvement is especially significant for the 1e1g(π) highest occupied molecular orbital where at least part of the experimentally observed structures are attributed to shape resonances. Some of the observed resonance features in the valence orbital photo cross sections of benzene were identified with resonances found in carbon K-shell ionization.

Electron beam ionization damage processes in p-terphenyl

Abstract Ionization damage leading to atomic displacements has been studied in crystals of p-terphenyl using low-energy electron beams. Significant damage is observed only for beam energies in excess of ∼ 1·5 keV. This can be explained on the basis that carbon K-shell ionization is the dominant process. The effective damage threshold is, however, raised well above the K-shell binding energy by competition with the valence excitation loss process.

Inner shell electron energy loss studies of HCN and C 2N 2

Small angle inelastic scattering of electrons with several kilovolts impact energy has been used to study carbon and nitrogen K-shell excitation and ionization of HCN and C 2N 2. The observed energy loss structures are assigned to promotions of K-shell electrons to valence and Rydberg orbitals. High resolution spectra (<100 meV fwhm) of the most intense inner shell transitions in HCN are reported. Excitation and ionization energies of the radicals HN 2 and HCO are derived from the HCN inner shell spectra using the equivalent core analogy.

K-shell excitation of HCN by electron energy loss spectroscopy

Small angle inelastic scattering of fast electrons has been used to study carbon and nitrogen K-shell excitation and ionization of HCN. The K→π* transitions in HCN have been investigated with high resolution.

The impact parameter dependence of carbon K-shell ionization by proton and helium impact

The impact parameter dependence of carbon K-shell ionization by 100 KeV amu proton or helium impact has been measured by a coincidence technique. The results are compared with theories which take the adiabatic relaxation of the K-electron due to the Coulomb field of the projectile into account.

Inelastic Interactions of Electrons with Polystyrene: Calculations of Mean Free Paths, Stopping Powers, and CSDA Ranges

A theoretical description of the inelastic interactions of electrons with solid polystyrene is presented. The response of the valence electrons to energy and momentum transfers is determined by a model insulator theory; carbon K-shell ionization cross sections are derived from atomic, generalized oscillator strengths. Contributions to the inverse mean free path and stopping power due to these two excitation processes are derived and tabulated for incident electrons with energies from 10 eV to 10 keV. Electron ranges in the continuous-slowing-down approximation are calculated and tabulated for electrons with energies from 15 eV to 10 keV.

Carbon, nitrogen, neon and argon K-shell ionization by proton and helium-ion impact: X-ray emission cross sections and fluorescence yields

K-shell X-ray emission cross sections are determined for gas targets (methane, nitrogen, neon, argon) ionized by H+, He+ and He2+ impact (energies from 100 to 2400 keV). The fluorescence yield for carbon, nitrogen and neon is calculated using known Auger cross sections; the absolute uncertainty is 20-30%, the relative values are determined within 5-10%. The impact-energy dependences of the fluorescence yields and of the detection efficiencies are measured. Both increase with decreasing impact energy. Values of the ionization cross sections are compared with BEA and PWBA calculations. The latter, corrected for binding, polarization and Coulomb deflection effects, are in reasonable agreement with experiment, especially for the projectile ratios (ratios of cross sections for He+ compared with H+ impact).