Monochromatized Synchrotron Radiation Research Articles

X-ray induced luminescence spectroscopy for DNA damaging intermediates aided by a monochromatic synchrotron radiation

Purpose To identify the bonding sites of initial radiation interaction with DNA and to trace the following chemical reaction sequences on the pathway of damage induction, we carry out a spectroscopy XIL (X-ray induced luminescence) using soft X-ray synchrotron radiation. This is a nondestructive analysis of the excited intermediate species produced in a molecular mechanism on the damage induction pathway. Materials and Methods We introduce aqueous samples of UMP (uridine-5’-monophosphate) in the vacuum by the use of a liquid micro-jet technique. The luminescence in the region of UV-VIS (from visible to ultraviolet) radiation induced after the absorption of monochromatic soft X-ray by aqueous UMP is measured with sweeping the soft X-ray energy in the region of 370–560 eV. Results The enhanced XIL intensities for aqueous UMP in the region of soft X-ray of 410–530 eV (in “water window” region) are obtained. The enhancement of XIL intensities in the UV-VIS region, relative to the water control, is explained by the excitation and ionization of a K-shell electron of nitrogen atoms in the uracil moiety. The enhanced XIL intensities do not match the structure of XANES (X-ray absorption near-edge structure) of the aqueous UMP. This suggests that the XIL intensities reflect the quantum yields of luminescence, or the quantum yields for conversion by UMP of an absorbed X-ray into UV-VIS radiation. In this paper, spectra of luminescence are shown to be resolved by combining low pass filters. The filtered luminescence spectra are obtained at the center of gravity (λc) of the band pass wavelength regions at λc = 270nm, 295 nm, 340 nm, 385 nm, 450 nm, and 525 nm., which show a trend similar to the fluorescence of nucleobases induced by ultraviolet radiation. Conclusion It is concluded that the origin of the observed XIL is the hydrated uracil moiety in aqueous UMP, decomposition of which is suppressed by the migration of excess charge and internal energy after the double ionization due to Auger decay.

Photoionization of methanol: a molecular source for the prebiotic chemistry

Methanol is one of the most abundant and ubiquitous molecules in the space. Its chemistry is fundamental to understand the molecular growing from prebiotic molecules, ions and radicals. In this work the reaction of labelled methanol CD3OH•+ radical cation, produced with different internal energies by monochromatic synchrotron radiation, with neutral CD3OH was studied. The dynamics of the main reaction channels were investigated by theoretical calculations. The results show how these processes can be considered suitable pathways for the formation of fundamental species as CH3O(H)H+, CH3O•, •CH2OH, CH2O which are potential precursors to prebiotic molecules.

Restoring size of detonation nanodiamonds from small-angle x-ray scattering of polychromatic synchrotron radiation beam

Over the past two decades, LIH SB RAS and BINP SB RAS have jointly conducted experiments on time-resolved (TR) small-angle x-ray scattering (SAXS) with detonating high explosives. The purpose of these experiments is to restore the dynamics of carbon species condensation to diamond nanoparticles by analyzing series of SAXS patterns behind the detonation front measured in real time with fast detectors. This knowledge is crucial for the development of reliable detonation models. In this paper, we compare SAXS patterns of identical nanodiamond samples measured at the TR-SAXS extreme state of matter end-station (BINP SB RAS) in the static mode under realistic conditions simulating fast real-time measurements with polychromatic SR beam and traditional SAXS BioMUR beamline at the Kurchatov Synchrotron Radiation Source (NRC “Kurchatov Institute”) with monochromatic synchrotron radiation (SR) beam. These experiments confirm that the size of scattering inhomogeneities determined in dynamic experiments with single bunch exposure with polychromatic SR beam is correct.

Comparison of the double-photoionization processes in triphenylene and corannulene with coronene

We have studied the production of doubly charged molecular ions by a single photon for the aromatic molecules triphenylene (C18H12) and corannulene (C20H10) using monochromatized synchrotron radiation from 18 eV to 270 eV. We compare our results with previously published data for partially deuterated benzene (C6H3D3), pyrene (C16H10), and coronene (C24H12). The question that we address in this paper is how the different but similar molecular structures of coronene, corannulene, and triphenylene affect the photon-energy dependence of the ratio of doubly to singly charged parent ions. A theoretical analysis of the main features in terms of independent molecular subsystems will be discussed.

Photon-excitation photon-emission maps (PhexPhem maps) with rovibronic resolution as a data base for theory and astrophysics part I: method and first results for H2

Dispersed fluorescence of wavelengths between 75 and 180 nm has been recorded after excitation of room temperature by narrow bandwidth monochromatized synchrotron radiation. Spectra have been taken in the exciting-photon energy range between 11 and 18 eV for discrete energy steps of 2.5 meV at a bandwidth of about 10 meV. The exciting-photon energy bandwidth has been narrow enough to induce transitions between individual rovibronic states. The resolution in the dispersed fluorescence detection was partly sufficient to resolve fluorescent transitions between individual rovibronic states. The recorded intensities are presented as two-dimensional photon-excitation photon-emission (PhexPhem) maps. They give a complete overview of experimental dispersed VUV/ FUV fluorescence spectra of H2 for these excitation energies, covering excitation from to all known singly excited states. The presented proof of principle experiments show a way to generate spectroscopic reference data for theory benchmarking and the interpretation of astrophysical observations.

Quantitative analysis of the physical properties of CsI, GAGG, LuAG, CWO, YAG, BGO, and GOS scintillators using 10-, 20- and 34-keV monochromated synchrotron radiation

The light yield, spatial resolution, and image quality of inorganic scintillators (CsI:Tl (CsI), Gd3Al2Ga3O12: Ce (GAGG), Lu3Al5O12: Ce (LuAG), CdWO4 (CWO), Y3Al5O12: Ce (YAG), Bi4Ge3O12 (BGO), and Gd2O2S: Tb (GOS)) were investigated using monochromated synchrotron radiation. For quantitative analysis, the same imaging system composed of a relay lens system and a camera was used for all scintillators. The light yield of GOS was highest, followed in order by CsI, GAGG, CWO, YAG, LuAG, and BGO. The spatial resolution of micro X-ray radiographic images using GAGG and LuAG was highest, followed by using CsI, CWO, and YAG. The image qualities were almost the same, except for GOS. These results indicate that CsI is suitable for micro X-ray radiography and computed tomography with a low X-ray flux source, and GAGG and LuAG are suitable with a high X-ray flux source.

Millisecond time-resolved serial oscillation crystallography of a blue-light photoreceptor at a synchrotron.

The recent development of serial crystallography has popularized time-resolved crystallography as a technique to determine the structure of protein-reaction intermediate states. However, most approaches rely on the availability of thousands to millions of microcrystals. A method is reported here, using monochromatic synchrotron radiation, for the room-temperature collection, processing and merging of X-ray oscillation diffraction data from <100 samples in order to observe the build up of a photoreaction intermediate species. Using this method, we monitored with a time resolution of 63 ms how the population of a blue-light photoreceptor domain in a crystal progressively photoconverts from the dark to the light state. The series of resulting snapshots allows us to visualize in detail the gradual rearrangement of both the protein and chromophore during this process.

Mechanistic insights of Sn-based non-chemically-amplified resists under EUV irradiation

Formulating high sensitivity and resolution in Extreme Ultraviolet (EUV) resists is a serious concern regarding the adaptation of EUV lithography. The incorporation of a high optical density Sn compound in MAPDST-co-ADSM (4-(methacryloyloxy)phenyl) dimethylsulfoniumtrifluoromethane sulfonate-co-acetyldibutylstannyl methacrylate, a non-CAR photoresist, exhibits lithography resolution for sub-15 nm node when patterned under e-beam and Helium ion irradiation. The synthesized resists were irradiated at 103.5 eV (~92 eV) using monochromatic synchrotron radiation. After EUV irradiation and oxidation, the resists were investigated using XPS, NEXAFS and by theoretical calculations (FEFF9 modeling program). It was observed significant changes in the labile CF3SO3– moiety, but interestingly its total dissociation or desorption was not observed after long exposure times. Bonds rearrangements of formation of SnO2 and new S–C/C–F functionalities after irradiation were detected. Those complex processes suggested the existence of important sinks for the high photon energy absorbed, which in turn increased the lithography resolution. The present results highlight the importance of the incorporation of a heavy metal covalently linked to the main polymer structure. The enhanced resolution observed in the MAPDST-co-ADSM resist formulation using standard processing conditions, establishes its potential candidature as a EUVL resist for rapid prototyping of semiconductor devices.

Spectral µCT with an energy resolving and interpolating pixel detector.

A main challenge in x-ray µCT with laboratory radiation derives from the broad spectral content, which in contrast to monochromatic synchrotron radiation gives rise to reconstruction artifacts and impedes quantitative reconstruction. Due to the low spectral brightness of these sources, monochromatization is unfavorable and parallel recording of a broad bandpath is practically indispensable. While conventional CT sums up all spectral components into a single detector value, spectral CT discriminates the data in several spectral bins. Here we show that a new generation of charge integrating and interpolating pixel detectors is ideally suited to implement spectral CT with a resolution in the range of 10 µm. We find that the information contained in several photon energy bins largely facilitates automated classification of materials, as demonstrated for of a mouse cochlea. Bones, soft tissues, background and metal implant materials are discriminated automatically. Importantly, this includes taking a better account of phase contrast effects, based on tailoring reconstruction parameters to specific energy bins.

Hydration of Nucleobase as Probed by Electron Emission of Uridine-5′-Mono-Phosphate (UMP) in Aqueous Solution Induced by Nitrogen K-Shell Ionization

To identify the precise early radiation processes of DNA lesions, we measure electron kinetic energy spectra emitted from uridine-5′ monophosphate (UMP) in aqueous solution for the photoionization of the N 1s orbital electron and for the following Auger effect using a monochromatic soft X-ray synchrotron radiation at energies above the nitrogen K-shell ionization threshold. The change of photoelectron spectra for UMP in aqueous solutions at different proton concentrations (pH = 7.5 and 11.3) is ascribed to the chemical shift of the N3 nitrogen atom in uracil moiety of canonical and deprotonated forms. The lowest double ionization potentials for aqueous UMP at different pH obtained from the Auger electron spectra following the N 1s photoionization values show the electrostatic aqueous interaction of uracil moiety of canonical (neutral) and deprotonated (negatively charged) forms with hydrated water molecules.

X-ray computed tomography investigation of dilation of mineral-filled PVC under monotonic loading

The deformation-induced dilation of mineral-filled polyvinyl chloride (PVC) is investigated by means of polychromatic X-ray absorption tomography (XCT). Axisymmetric notched tensile specimens are strained to prescribed elongations using a tensile test apparatus and subsequently scanned by XCT after relaxation. During straining, surface deformations are quantified by digital image correlation (DIC) and contour tracking. The influence of stress triaxiality and strain rate on dilation is investigated by using tensile specimens with three different notch radii, all strained to three deformation levels at two different nominal strain rates. Pronounced reduction of density, corresponding to an increase of volume, is observed for all specimens in the XCT scans, but markedly different relative density distributions are measured for the three geometries. The accuracy of the polychromatic XCT density estimates is evaluated against data obtained with monochromatic synchrotron radiation computed tomography (sr-XCT), and a comparison to surface deformation-based dilation estimates is presented.

Experimental determination of line energies, line widths and relative transition probabilities of the Gadolinium L x-ray emission spectrum

In this work the most intense x-ray lines of the L-emission spectrum of gadolinium with respect to line energies, natural line widths, and relative transition probabilities were investigated using monochromatized synchrotron radiation. The measurements were realized in the PTB laboratory at BESSY II by means of an in-house built von Hamos spectrometer based on up to two full-cylinder HAPG mosaic crystals. The von Hamos spectrometer is calibrated by means of elastically scattered photons from the employed synchrotron radiation beamline leading to a well-defined energy scale and an experimentally determined spectrometer response. A selective excitation of the gadolinium L subshells was carried out to ensure a robust deconvolution of neighboring emission lines of different L subshells. The experimental results are discussed in the context of existing data from common databases and published values since significant deviations, especially for the L and L emission lines, are observed. We further substantiate and discuss two satellite lines at the low-energy side of the L and L emission lines arising from the N4,5 subshell.

Selection of CVD Diamond Crystals for X-ray Monochromator Applications Using X-ray Diffraction Imaging

A set of 20 single crystal diamond plates synthesized using chemical vapor deposition (CVD) was studied using X-ray diffraction imaging to determine their applicability as side-bounce (single-reflection) Laue monochromators for synchrotron radiation. The crystal plates were of optical grade (as provided by the supplier) with (001) nominal surface orientation. High dislocation density was found for all samples. Distortions in the crystal lattice were quantified for low-index Laue reflections of interests using rocking curve topography. Maps of effective radius of curvature in the scattering plane were calculated using spline interpolation of the rocking curve peak position across the studied plates. For several selected plates, nearly flat regions with large effective radius of curvature were found ( R 0 ≳ 30 − 70 m, some regions as large as 1 × 4 mm 2 ). The average width of the rocking curve for these regions was found to be about 150 μ rad (r.m.s.). These observations suggest that the selected CVD diamond plates could be used as intermediate-bandwidth monochromators refocusing the radiation source to a specific location downstream with close to 1:1 distance ratio.

Vibrational effects in the photo-ion yield spectrum of the SiH2+ molecular ion following 2p inner-shell excitation

We report on complementary theoretical and laboratory investigations of the 2p ion yield cross sections for the molecular-ion series SiHn+ (n = 1, 2, 3), in the 95-108 eV photon energy range, below the L-shell threshold. The experiments used an electron cyclotron resonance (ECR) plasma molecular-ion source coupled with monochromatised synchrotron radiation in a merged-beam configuration. The experimental spectra are compared with total photoabsorption cross-sectional profiles calculated using an ab initio configuration interaction method inclusive of spin-orbit coupling and the vibrational dynamics. The experimental results show vibrationally resolved resonances for SiH2+ in the 98-102 eV range. The calculations indicate twenty four core-excited states below the energy of 102 eV, of which only four contribute significantly to the observed spectrum. These states correspond to the excitation of an atomic-like 2p electron to the SiH2+ (5a1) valence orbital.

Evaluation of dislocations under the electrodes of GaN pn diodes by X-ray topography

We have successfully obtained the clear images of the dislocation mapping even under the electrodes of the GaN vertical pn diodes by reflection X-ray topography using monochromatic synchrotron radiation (SPring-8, BL16B2 & BL20B2). This is a powerful analysis because of the non-destructive and rapid tool unlike the etch-pit method and TEM (transmission electron microscopy). This allows us to directly study the relationship between the dislocation and the leakage current. Applying this method to vertical pn diodes on Na-flux GaN substrates, we found that leakage current per dislocation is of the order of 10 pA. This analysis has a potential to reveal the killer dislocation structure.

Emission spectra of atomic and molecular nitrogen from photolysis of ammonia in solid neon

Dilute samples of NH3 and ND3 in solid neon near 4 K were irradiated at 200 or 173 or 143 nm with light from a synchrotron. We recorded emission spectra of atomic N, involving states 4So, 2Po and 2Do, and of molecular N2, involving states X 1Σg+, A 3Σu+, B 3Πg and C 3Πu in systems with vibrational progressions in the lower states. The emission spectra covered the near-ultraviolet, visible and near-infrared regions from 200 to 1100 nm; the far-ultraviolet absorption spectrum for the precursor NH3 in solid neon was also measured. Recorded for samples in darkness after irradiation at 143 nm during warming from ∼5 K to ∼8 K, thermoluminescent spectra consisted mostly of lines emitted by molecular N2. The analysis of these spectra, and their temporal development, provides information about the nature of dissociative and trapping processes in solid neon under cryogenic conditions involving monochromatic synchrotron radiation.

X-ray reflectivity with a twist: Quantitative time-resolved X-ray reflectivity using monochromatic synchrotron radiation

We have developed an improved method of time-resolved x-ray reflectivity (XRR) using monochromatic synchrotron radiation. Our method utilizes a polycapillary x-ray optic to create a range of incident angles and an area detector to collect specular reflections. By rotating the sample normal out of the plane of the incident fan, we can separate the surface diffuse scatter from the reflectivity signal, greatly improving the quality of the XRR spectra compared to previous implementations. We demonstrate the time-resolved capabilities of this system, with the temporal resolution as low as 10 ms, by measuring XRR during the annealing of Al/Ni nano-scale multilayers, and use this information to extract the activation energy for interdiffusion in this system.

Influence of energy bandwidth of pink beam on small angle X-ray scattering

Compared with the traditional monochromatic synchrotron radiation beam, a pink beam is a quasi-monochromatic beam which can be obtained by screening a harmonic of the undulator. The energy bandwidth ( $$\Delta E{/}E$$ ) of a pink beam is about $$10^{-2}$$ . Despite the intensity gain from the quasi-monochromatic beam, the decrease in the energy resolution will lead the collected data to be smeared. To study the influence of the energy bandwidth on the small angle X-ray scattering (SAXS) by experiments and verify the feasibility of SAXS with a pink beam. Firstly, the influence of different energy bandwidths on SAXS has been studied by simulation and experiment. Then, TEM tests have been performed and compared with the experimental results. It has been shown that the scattering curves deviate slightly from the traditional monochromatic ones. This deviation does not influence the data processing for the maximum deviation of the results is just less than 2%. In return, the gain in the intensity (one to two orders of magnitude) makes the pink beam very important for the time-resolved SAXS. Further, the results of TEM and SAXS have shown an excellent agreement. This work proves that the pink beam could be used for SAXS directly without a desmearing procedure. Benefiting from the increase in the beam intensity, the exposure time can be greatly shortened, thus enhancing the utilization efficiency of the synchrotron radiation.

Experimental and theoretical determination of the L-fluorescence yields of bismuth

The knowledge of atomic fundamental parameters such as the mass attenuation coefficients or fluorescence yields with low uncertainties, is of decisive importance in elemental quantification involving x-ray fluorescence analysis techniques. For example, several databases giving the mass attenuation coefficients are accessible and frequently used within a large community of users. These compilations are most often in good agreement for photon energies in the hard x-ray ranges. However, they significantly differ for low photon energies and around the absorption edges of the elements. Some review articles present compilations of measured fluorescence yields values found in the literature. However reliable measurements are not so many illustrating the inherent difficulties. Mass attenuation coefficients of bismuth were determined experimentally in the photon energy range from 100 eV to 30 keV by using monochromatized synchrotron radiation at SOLEIL (France). The fluorescence yields of the three L-subshells of bismuth were also determined using a reflection geometry setup. The application of high-accuracy experimental techniques resulted in low uncertainty mass attenuation coefficients and L-subshell fluorescence yields that are directly compared to existing databases and with updated relativistic configuration mixing Dirac–Fock calculations including QED corrections.

Direct observation of stacking fault shrinkage in 4H-SiC at high temperatures by in-situ X-ray topography using monochromatic synchrotron radiation

An in-situ X-ray topography system using monochromatic synchrotron radiation for the observation of the stacking faults in 4H-SiC during a high-temperature annealing process was developed. We demonstrated that the stacking faults in nitrogen-doped 4H-SiC not only expand but also shrink at high temperatures. Furthermore, it was confirmed that the types of the core structure of partial dislocations enclosing the stacking fault can be determined at high temperatures.