Kurchatov Synchrotron Radiation Source Research Articles

Preliminary X-ray Diffraction Analysis of Purine Nucleoside Phosphorylase from the Haloalkaliphilic Bacterium Halomonas chromatireducens

Crystals of the enzyme purine nucleoside phosphorylase from the extremophilic bacterium Halomonas Chromatireducens AGD 8-3, suitable for X-ray diffraction, were grown by the vapor-diffusion method. The X-ray diffraction data were collected from these crystals at the Belok beamline of the Kurchatov synchrotron radiation source (National Research Centre “Kurchatov Institute”) at 100 K to 1.80 Å resolution. The X-ray diffraction data were processed in the space groups P1, P2, P21, and P622. The structure was solved by the molecular replacement method taking into account the twinning in the space groups P21 and P1 with one and two hexamers of the enzyme per asymmetric unit, respectively.

Developing an Interferometric Method for Measuring the Transverse Dimensions of a Particle Beam in Cyclic Accelerators

This work is devoted to the development of a method for measuring beam sizes in cyclic charged particle accelerators using an interferometer based on the Young scheme with a double-slit diaphragm. We have carried out an experimental verification of the original spectral method for scanning the interference pattern. The results of measurements of the spectrum of low-frequency oscillations of the beam of the storage ring of the Kurchatov Synchrotron Radiation Source (KSRS) obtained by means of the Optical Observation Station (OOS) of the storage ring are presented.

Upgrade of the BioMUR beamline at the Kurchatov synchrotron radiation source for serial small-angle X-ray scattering experiments in solutions

Technical and methodological work was carried out to improve the quality of the experiments at the small-angle X-ray scattering (SAXS) beamline ”BioMUR” at the Kurchatov synchrotron radiation source, commissioned in 2018. Scatterless slits (JJ X-ray company, Denmark) were installed and tested, and the beam adjustment scheme of the “BioMUR” modified accordingly. Now outdated and not very effective mylar windows were replaced by mica vacuum windows providing significantly lower parasitic scattering. SAXS experiments on the solutions of weakly scattering lysozyme and bovine serum albumin proteins confirmed the significant improvement in the signal-to-noise ratio achieved due to the upgrade of the “BioMUR”.

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.

Исследование пигментов и связующих красочных слоев росписей храма X–XIII вв. на плато Эски-Кермен

In 2018–2019, the excavations of an aisleless church dated from the tenth to thirteenth centuries and located in quarter II on the territory of a provincial Byzantine town atop of the plateau of Eski-Kermen discovered fragments of wall-plaster with polychrome painting. There are several shades of green, two shades of red, white (beige), yellow (ochre), and grey-brown colours. This paper presents the results of studies of the colour layer, determines pigments and cohesive colour components, and uncovers the features of the painting technique applied to the walls of the church. Four groups of samples were selected for the study featuring: 1 – white, 2 – yellow, 3 – red, and 4 – green colours. The elemental composition of the colour layer was studied by scanning electron microscopy combined with energy-dispersive X-ray microanalysis (SEM/EDX). The phase constitution of the samples was investigated by X-ray powder diffraction (XRD) method with the use of diffractometers operated in a transmission mode at the Kurchatov synchrotron radiation source. The chemical composition of colour layers was studied by infrared spectroscopy, and the study of cohesive colour materials was carried out by gas chromatography with mass spectrometry (GC/MS). The elemental composition and phase constitution of the white colour indicated the use of lime whitewash. Yellow ochre (goethite) was used as yellow colour. Red colour features the presence of hematite typical for the group of pigments united under the name of red soils. However, the discovery of 1% goethite typical for yellow ochres in the phase constitution of one sample allows the possibility that burnt yellow ochre was used as a red pigment. The green colour was green soil (glauconite and celadonite). It should be noted that none of the examined samples of red pigment contained traces of vermilion, which occurred in ancient paintings in the Crimea and was typical for Byzantine wall-paintings. In all the samples of pigments contained a significant degree of calcite (36-98%), possibly due to the presence of particles of undercolour in the measured samples of wall paintings, or diluting the pigment with lime water for the making of wall-painting featuring fresco technique. The use of the latter technique is also indicated by the presence of white lime colour. The traces of cohesive component in the form of fish glue and protein products from chicken eggs found in the red and green paint samples also suggests the use of the dry painting technique. Therefore, there are reasons to suppose that the painting of the quarter church of Eski-Kermen used two techniques, fresco and dry plaster paintings.

QEXAFS method implementation using adaptive X-ray optical elements

A modification of the of high-speed high-resolution X-ray absorption spectroscopy (Quick Extended X-ray Absorption Fine Structure, QEXAFS) method based on an adaptive bending element of X-ray optics is described. This technique was implemented at the Langmuir station of the Kurchatov Synchrotron Radiation Source (KISI-Kurchatov). The absorption spectrum of a model sample, bromine in a sodium bromide compound, was recorded. A recording speed up to 5 seconds per spectrum was achieved in the continuously recording regime. The method is applicable for obtaining information about both the structure and dynamics of a wide range of objects, ordered and disordered, in any aggregate state.

Polarization and Interference Effects in the Resonant Diffraction of Synchrotron Radiation

The features of the technique of resonant synchrotron-radiation (SR) diffraction are considered. The energy, angular, polarization, and temperature dependences of Bragg reflections at incident radiation energies that are close to the absorption edges of material atoms are studied using this technique. These dependences contain information about the electronic, magnetic, and structural features of the objects under study. The contribution of several scattering channels to the formation of the diffraction spectrum leads to the appearance of interference effects making it possible to obtain information about the scattered radiation phase. Results of some studies of resonant SR diffraction performed at the Kurchatov SR source are presented.

The small-angle X-ray scattering beamline BioMUR at the Kurchatov synchrotron radiation source

Abstract A small-angle X-ray scattering beamline BioMUR has been constructed and is now in operation at the Kurchatov synchrotron radiation source (Moscow Russian Federation). Using X-ray optic elements and equipment of the former beamlines DICSY (Kurchatov source) and X33 (EMBL c/o DESY) Hamburg, Germany, BioMUR has been commissioned to deliver an optimized configuration that provides a significant improvement in the quality of small-angle scattering patterns at the Kurchatov synchrotron radiation source. It allows one to study a wide spectrum of samples at different conditions using the automated control software.

Study of Kinetics of Solid Phase Transition in Tetracosane С24Н50 by High-Resolution Synchrotron X-Ray Powder Diffraction

Using the small-angle synchrotron X-ray diffraction method at the research facility “BELOK” of the Kurchatov synchrotron radiation source at the NRC Kurchatov Institute, it was shown that the first-order solid phase transition in tetracosane C24H50 passes according to a heterogeneous mechanism in a narrow temperature range ΔT ~ 1 K in accordance with the theory of diffuse phase transitions.

Development of a Microfluidic Chip for Protein Crystallization by the Microbatch Method

A composite microfluidic chip (MFC), which comprises a technological system for protein crystal growth followed by X-ray crystallography, was developed. Crystallization tests were performed using chicken egg-white lysozyme, aminotransferase from Methanococcus vannielii, and esterase PMGL2 from the permafrost metagenomic library. Materials (borosilicate glass and poly(methyl methacrylate)) for MFC fabrication were compared. The use of poly(methyl methacrylate) was shown to allow comparative in situ X-ray crystallography of protein crystals directly in the chip. Investigations and experiments were carried out at the BELOK beamline at the Kurchatov synchrotron radiation source (National Research Centre “Kurchatov Institute”).

Experimental Study of Two-Beam X-Ray Diffractometry Using Synchrotron Radiation

A new scheme of two-beam X-ray diffractometry on the “X-Ray Crystallography and Physical Materials Science” (XCPM) beamline at the Kurchatov Synchrotron Radiation Source (KSRS) has been experimentally investigated. The scheme includes a standard double-crystal monochromator and a narrow slit installed in front of the sample. Measurements have been performed for the Si 111 and 311 reflections in the monochromator and the Si 111 and 220 reflections in the sample crystal. It is shown that this scheme allows one to obtain a near-proper diffraction reflection curve even in the case of symmetric diffraction if the Bragg angle for the monochromator exceeds the Bragg angle for the crystal sample by a factor of 2 or more. The experimental results coincide well with the theory.

The Composition of Paints of the Paintings on Stone Cist Slabs from Karakol (Altai)

Among the important antiquities of Altai Bronze Age, Karakol burial site (dated to the beginning of the 2nd mill. BCE) can be selected. The images are overlapped; the ones synchronous to the burial ritual were performed in a complex technique, including painting, pecking, engraving, and abrasion. Studies at the National Research Centre “Kurchatov Institute” (NRC KI), including scanning electron microscopy combined with X-ray microanalysis and powder X-ray diffraction on the Belok station (Kurchatov synchrotron radiation source (KSRS)), revealed that red (ochres of different hues) and black (soot) pigments were used to to produce paint at the Karakol site. An analysis of the red paints showed their composition to be homogeneous within one burial but differ from burial to burial. An analysis of the colored line on slab 1 (Karakol, burial 3, mound 2) made it possible to establish its natural origin and reasonably reject the hypothesis that it was painted.

Microfluidic Cell for Studying the Precrystallization Stage Structure of Protein Solutions by Small-Angle X-Ray Scattering

A microfluidic cell has been developed for studying the structure of protein solutions using small-angle X-ray scattering. The use of prefabricated elements, which provide a small sample volume, allows one to adjust the microfluidic cell parameters to specific problems. Tests of lysozyme solutions were performed on a laboratory diffractometer AMUR-K (Institute of Crystallography, Russian Academy of Sciences), BM29 beamline (ESRF, Grenoble), and “DICSY” beamline of the Kurchatov synchrotron radiation source (National Research Centre “Kurchatov Institute”). Experiments showed that, when a 60-μm-thick quartz glass of special purity grade is applied as an X-ray-transparent window, the intrinsic level of cell background scattering in the range of measured angles is lower than that for quartz capillaries, due to which the measurement accuracy can be increased.

Magnetic Dichroism in the Reflectivity of Linearly Polarized Synchrotron Radiation from a Ti(10 nm)/Gd0.23Co0.77(250 nm)/Ti(10 nm) Sample

The dichroic effect (“rotated” polarization) in the reflectivity from a magnetically ordered sample is experimentally studied at the station PHASE of the Kurchatov Synchrotron Radiation Source. The experiments are performed for the Gd0.23Co0.77 film, which has a compensation temperature Tcomp ≈ 433 K, using linearly polarized radiation of the photon energy of 7930 eV (L2 absorption edge of gadolinium) at room temperature. The developed theory of reflectivity accounted for the magnetic contributions to the scattering amplitude predicts the appearance of a peak for the orthogonal (to the incident polarization) polarization of the reflected radiation near the critical angle of the total external reflection. The experiment reveals the significant difficulties because of the incomplete σ polarization of the synchrotron beam, the beam instability, and so on. Therefore, a rotated-polarization peak has been detected near the critical angle but at the limits of the measurement accuracy. In principle, our experimental technique could be an alternative to circular polarization experiments, which are widely used at synchrotrons to study magnetic ordering. However, as we have shown, it makes high demands of the radiation source parameters.

The Small-Angle Neutron Scattering Data Analysis of the Phospholipid Transport Nanosystem Structure

The small-angle neutron scattering technique (SANS) is employed for investigation of structure of the phospholipid transport nanosystem (PTNS) elaborated in the V.N.Orekhovich Institute of Biomedical Chemistry (Moscow, Russia). The SANS spectra have been measured at the YuMO small-angle spectrometer of IBR-2 reactor (Joint Institute of Nuclear Research, Dubna, Russia). Basic characteristics of polydispersed population of PTNS unilamellar vesicles (average radius of vesicles, polydispersity, thickness of membrane, etc.) have been determined in three cases of the PTNS concentrations in D2O: 5%, 10%, and 25%. Numerical analysis is based on the separated form factors method (SFF). The results are discussed in comparison with the results of analysis of the small-angle X-ray scattering spectra collected at the Kurchatov Synchrotron Radiation Source of the National Research Center “Kurchatov Institute” (Moscow, Russia).

High-Throughput Small-Molecule Crystallography at the ‘Belok’ Beamline of the Kurchatov Synchrotron Radiation Source: Transition Metal Complexes with Azomethine Ligands as a Case Study

This paper concisely describes capabilities of the ‘Belok’ beamline at the Kurchatov synchrotron radiation source, related to high-throughput small-molecule X-ray crystallography. As case examples, a series of four novel transition metal complexes with azomethine ligands were selected. The complexes demonstrate somewhat unexpected changes in the coordination geometry and nuclearity in response to the introduction of substituents in the ligand’s periphery.

New frontiers in water purification: highly stable amphopolycarboxyglycinate-stabilized Ag–AgCl nanocomposite and its newly discovered potential

A simple synthetic procedure for high-stable dispersions of porous composite Ag/AgCl nanoparticles stabilized with amphoteric surfactant sodium tallow amphopolycarboxyglycinate has been proposed for the first time. The prepared samples were characterized by UV–vis spectroscopy, x-ray powder diffraction (XRD), x-ray photoelectron spectroscopy, small area electron diffraction (SAED), scanning electron microscopy (SEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), and electron probe micro-analysis. In addition, measurements (carried out at the Kurchatov synchrotron radiation source stations) of the Ag K-edge extended x-ray absorption fine structure (EXAFS) and x-ray absorption near edge structure (XANES) spectra and XRD of the prepared nanoparticles have been performed. The obtained results suggest that small-sized Ag clusters are homogeneously distributed in the mass of the AgCl nanoparticle (~80 nm) formed during the synthesis. The Ag/AgCl dispersion demonstrates photocatalytic activity (with respect to methyl orange) and high bactericidal activity against E. coli. This activity is superior to the activity of both Ag and AgCl nanoparticles stabilized by the same surfactant. Thus, porous composite Ag/AgCl nanoparticles can be used as a multifunctional agent that is able to remove both pollutants and bacterium from water.

Debye-scherrer diffraction in the backscattering geometry at the kurchatov synchrotron radiation source: Part 2. Equipment, pilot experiments, and data processing

Equipment is constructed, a technique is developed, and experimental results on Debye-Scherrer diffraction in the backscattering geometry are obtained. A special program for diffraction ring processing is developed. The prospects for use of this technique for materials science purposes are discussed.

Debye-Scherrer diffraction in the backscattering geometry at the Kurchatov Synchrotron Radiation source. Part 1. Characterization of the method

A technique for Debye-Scherrer diffraction in the backscattering geometry is developed at the Kurchatov Synchrotron Radiation source. It is shown that the sensitivity of the method to a relative change in the lattice constant is higher by two orders of magnitude than that in the forward-scattering geometry. The requirements for experimental apparatus are discussed.

Upgraded X-ray topography and microtomography beamline at the Kurchatov synchrotron radiation source

An upgraded X-ray Topography and Microtomography (XRT-MT) station is described, the parameters of the optical schemes and detectors are given, and the experimental possibilities of the station are analyzed. Examples of tomographic reconstructions are reported which demonstrate spatial resolutions of 2.5 and 10 μm at fields of view of 2.5 and 10 mm, respectively.