Vol 62, No 6 (2017)
- Year: 2017
- Articles: 28
- URL: https://journals.rcsi.science/1063-7745/issue/view/12016
Review
Methods of chemical and phase composition analysis of gallstones
Abstract
This review presents the instrumental methods used for chemical and phase composition investigation of gallstones. A great body of data has been collected in the literature on the presence of elements and their concentrations, obtained by fluorescence microscopy, X-ray fluorescence spectroscopy, neutron activation analysis, proton (particle) induced X-ray emission, atomic absorption spectroscopy, high-resolution gamma-ray spectrometry, electron paramagnetic resonance. Structural methods—powder X-ray diffraction, infrared spectroscopy, Raman spectroscopy—provide information about organic and inorganic phases in gallstones. Stone morphology was studied at the macrolevel with optical microscopy. Results obtained by analytical scanning and transmission electron microscopy with X-ray energy dispersive spectrometry are discussed. The chemical composition and structure of gallstones determine the strategy of removing stone from the body and treatment of patients: surgery or dissolution in the body. Therefore one chapter of the review describes the potential of dissolution methods. Early diagnosis and appropriate treatment of the disease depend on the development of clinical methods for in vivo investigation, which gave grounds to present the main characteristics and potential of ultrasonography (ultrasound scanning), magnetic resonance imaging, and X-ray computed tomography.
Diffraction and Scattering of Ionizing Radiations
Development of methods for ultrasonic scanning of X-ray wavelength
Abstract
The method for X-ray wavelength tuning using an adaptive element (a quartz monolithic resonator modulated by a standing longitudinal low-frequency ultrasonic wave) has been proposed and implemented. This method is characterized by high tuning accuracy and possibility of scanning X-ray beam parameters with a time resolution of up to 3 μs.
Small-angle X-ray scattering study of the influence of solvent replacement (from H2O to D2O) on the initial crystallization stage of tetragonal lysozyme
Abstract
The composition of lysozyme solutions in D2O under conditions favorable for the formation of tetragonal crystals has been investigated at different protein concentrations by small-angle X-ray scattering using the synchrotron radiation. In addition to lysozyme monomers, dimeric and octameric species are found in the crystallization solutions; the octamer content increases with an increase in the protein concentration. A comparison of the data with those obtained under similar conditions but with H2O used as a solvent has shown that the replacement of light water with heavy one leads to increase of octamer volume fraction in solution.
Structure of Inorganic Compounds
Crystal structure of the solid solution NH4Al0.62Cr0.38(SO4)2 · 12H2O
Abstract
The solid solution NH4Al0.62Cr0.38(SO4)2 · 12H2O was studied by X-ray diffraction. The crystal structure was determined in a series of the maximal subgroups Pa3̄ > R3̄ > P1̄ > P1. Reflections forbidden in sp. gr. Pa3̄ are indicative of symmetry lower than cubic. In the centrosymmetric models under consideration, all sulfate groups are oppositely oriented with respect to each other. In non-centrosymmetric sp. gr. P1, four of the eight sulfate groups have the same orientation, whereas the other four groups are oriented in an opposite direction.
Structure of Organic Compounds
X-ray diffraction analysis of 4- and 4′-substituted CnH2n + 1O–C6H3(OH)–CH=N–C6H4–CmH2m + 1 (n/m = 2/1 and 3/4) salicylideneanilines
Abstract
X-ray diffraction study of two crystalline modifications of С2Н5O–C6H3(OН)–СН=N–C6H4–CH3 (1a, sp. gr. Р21/n, and 1b, sp. gr. С2/c) and С3H7O–C6H3(OН)–СН=N–C6H4–C4H9 (2, sp. gr. Р212121) has been performed. The 1a crystal structure contains two independent molecules. The molecules are conformationally nonrigid with respect to the mutual rotation of benzene rings; the dihedral angles between their planes are 29.19° and 26.00° in the independent molecules of 1a, 18.72° in the molecule of 1b, and 50.35° in the molecule of 2. The crystal packing of the compounds is discussed.
Chelate complexes of lead(II) with nitrilotris(methylenephosphonic) acid [Pb{μ5-NH(CH2PO3H)3}] and Na4[Pb2(H2O)2{μ3-N(CH2PO3)3H2}2] · 10H2O: Synthesis, structure, and asymmetry of lone 6s pair
Abstract
Two complexes of Pb(II) with nitrilotris(methylenephosphonic) acid are synthesized and their crystal structures are determined. Nitrilotris(methylenephosphonato)lead(II) [Pb{μ5-NH(CH2PO3H)3}] is a coordination 3D polymer; space group Pī, Z = 2. The coordination polyhedron of Pb is a distorted pentagonal bipyramid with the N atom at one of the equatorial positions. Tetrasodium bis[aquanitrilotris(methylenephosphonatoplumbate( II)] decahydrate Na4[Pb2(H2O)2{μ3-N(CH2PO3)3H2}2] · 10H2O crystallizes in space group Pī, Z = 2. The degree of asymmetry of the coordination polyhedra of lead atoms characterizing the localization of the lone 6s electron pair is estimated.
N-[4-(3-Methyl-3-phenyl-cyclobutyl)-thiazol-2-yl]-N′-pyridin-2-ylmethylene-chloro-acetic acid hydrazide: Synthesis and configurational assignment based on X-ray, 1H, and 13C NMR and theoretical calculations
Abstract
In this study, quantum chemical calculations based on the density functional theory have been carried out to examine the effects of N-[4-(3-methyl-3-phenyl-cyclobutyl)-thiazol-2-yl]-N′-pyridin-2-ylmethylene- chloro-acetic acid hydrazide. The calculated values are compared with the experimental data available for these molecules as a mean of validation of our proposed chemistry model. Aided by normal coordinate analysis and potential energy distributions, a confident vibrational assignment of all fundamentals is proposed herein. Additional support is given by 1H and 13C NMR spectra recorded with the sample dissolved in CDCl3 and by predicted chemical shifts at the B3LYP/6-31G(d)/6-311G+(d) levels obtained using the gauge-invariant atomic orbital method. The calculated HOMO and LUMO energies also confirm that the charge transfer occurs within the molecule. Thiazole-based compounds are potential storehouse for exploiting CH···O and CH···N hydrogen bonding interactions for molecular self-assembly.
Synthesis and structural characterization of a Cu(I) complex with 4-(1H-imidazol-1-yl)phenyl)methanone ligands
Abstract
A copper complex with V-shaped ligands, [(L1)Cu2Cl2]n (1), (L1 = 4-(1H-imidazol-1-yl)phenyl) methanone) has been synthesized and characterized by IR spectroscopy, elemental analyses and singlecrystal X-ray diffraction. The crystal of 1 is monoclinic, sp. gr. C2/c with the unit cell parameters a = 17.9496(13), b = 15.3440(13), c = 7.2983(7) Å, and β = 112.875(6)°, Z = 4, R1 = 0.0681, and wR2 = 0.1736 (I > 2 σ). The solid state structure of 1 consists of 2D metal aromatic chloride layers, which are propagating along the bc plane to form a 3D network through hydrogen bonds.
Crystal structure and optoelectronic properties of antiaromatic compound 3,4,9,10-tetrahydrodicyclopenta[cd,lm]perylene
Abstract
An antiaromatic compound 3,4,9,10-tetrahydrodicyclopenta[cd,lm] perylene, was synthesized by a coupling reaction. Its crystal structure was determined by X-ray diffraction. Crystal structures shows that the antiaromatic compounds are aggregated to J-aggregation materials. It further results ultrafast charge separation at organic interface and electron transfer in the aggregation materials. UV-vis spectrum shows that title compound has a broad UV-vis light absorbance at the wavelength range from 250 to 470 nm and a 2.67 eV energy gap value between the highest occupied and the lowest unoccupied molecular orbital energy levels.
Synthesis, spectral characterization, and single crystal structure studies of biologically relevant bis-indoline heterocyclic scaffold
Abstract
The new biologically relevant compound, 5,5″-methoxy-1′-methyl-1H,1″H-[3,3′:3′,3″-terindol]-2′(1′H)-one was synthesized, in 89% yield, by the one-pot reaction between 5-methoxyindole and 1-methylisatin in the presence of a low-cost and environmentally benign commercially available sulfamic acid as an organocatalyst and have been characterized by elemental analyses, IR spectra, and single crystal X-ray analysis. The crystals are orthorhombic, sp. gr. Pbca, Z = 8. The structure is stabilized by N–H···O and C–H···O interactions.
Structure of Macromolecular Compounds
Small-angle X-Ray analysis of macromolecular structure: the structure of protein NS2 (NEP) in solution
Abstract
A complex structural analysis of nuclear export protein NS2 (NEP) of influenza virus A has been performed using bioinformatics predictive methods and small-angle X-ray scattering data. The behavior of NEP molecules in a solution (their aggregation, oligomerization, and dissociation, depending on the buffer composition) has been investigated. It was shown that stable associates are formed even in a conventional aqueous salt solution at physiological рН value. For the first time we have managed to get NEP dimers in solution, to analyze their structure, and to compare the models obtained using the method of the molecular tectonics with the spatial protein structure predicted by us using the bioinformatics methods. The results of the study provide a new insight into the structural features of nuclear export protein NS2 (NEP) of the influenza virus A, which is very important for viral infection development.
Application of virtual screening and molecular dynamics for the analysis of selectivity of inhibitors of HU proteins targeted to the DNA-recognition site
Abstract
DNA-Binding HU proteins are essential for the maintenance of genomic DNA supercoiling and compaction in prokaryotic cells and are promising pharmacological targets for the design of new antibacterial agents. The virtual screening for low-molecular-weight compounds capable of specifically interacting with the DNA-recognition loop of the HU protein from the mycoplasma Spiroplasma melliferum was performed. The ability of the initially selected ligands to form stable complexes with the protein target was assessed by molecular dynamics simulation. One compound, which forms an unstable complex, was eliminated by means of a combination of computational methods, resulting in a decrease in the number of compounds that will pass to the experimental test phase. This approach can be used to solve a wide range of problems related to the search for and validation of low-molecular-weight inhibitors specific for a particular protein target.
Purification, isolation, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 from Drosophila melanogaster
Abstract
The spatial organization of the genome is controlled by a special class of architectural proteins, including proteins containing BTB domains that are able to dimerize or multimerize. The centrosomal protein 190 is one of such architectural proteins. The purification, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 are reported. The crystallization conditions were found by the vapor-diffusion technique. The crystals diffracted to 1.5 Å resolution and belonged to sp. gr. P3221. The structure was solved by the molecular replacement method. The structure refinement is currently underway.
Preliminary small-angle X-ray scattering and X-ray diffraction studies of the BTB domain of lola protein from Drosophila melanogaster
Abstract
The Drosophila genome has several dozens of transcription factors (TTK group) containing ВТВ domains assembled into octamers. The LOLA protein belongs to this family. The purification, crystallization, and preliminary X-ray diffraction and small-angle X-ray scattering (SAXS) studies of the BTB domain of this protein are reported. The crystallization conditions were found by the vapor-diffusion technique. A very low diffraction resolution (8.7 Å resolution) of the crystals was insufficient for the determination of the threedimensional structure of the BTB domain. The SAXS study demonstrated that the BTB domain of the LOLA protein exists as an octamer in solution.
Global conformational changes induced by the removal of the carboxyl group of D456 in the cleavage scaffold of nickase BspD6I: Structural and electrostatic analysis
Abstract
The three-dimensional structure of the D456A mutant of the nicking endonuclease Nt.BspD6I was determined. According to the concept of the cleavage scaffold, the replacement of D456 by A456, which resulted in complete (100%) loss of nickase activity, was shown to be a trigger of structural changes in the cleavage-scaffold region. Besides, the displacement of Е482 and the rotation of Н449 toward the N-terminal domain initiate conformational changes in the D1 recognition subdomain of the N-terminal domain with the result that the centers of mass of the С- and N-terminal domains are brought into close proximity to each other. Electrostatic calculations showed that changes in the free energy and electrostatic interactions for the mutant nickase are distributed predominantly in the N-terminal domain and that these changes are not attenuated in a radial fashion away from the mutation site but have a distinct direction.
A luminescent 2D → 3D Cd complex via π-π* interaction based on bis(4-(1H-imidazol-1-yl)phenyl)amine and 1,3-dicarboxybenzene acid
Abstract
A new coordination polymer, {[Cd(BIPA)(1,3-bdc)](DMF)}n, based on bis(4-(1H-imidazol-1- yl)phenyl)amine (BIPA) and 1,3-dicarboxybenzene (1,3-H2bdc) was synthesized and showing 2D → 3D structure via π-π* interaction of BIPA molecules in the nearby networks in the complex. Investigation of photophysical properties showed that the complex exhibits a strong emission in the range of 350–425 nm (λmax = 375 nm upon excitation at 327 nm).
Physical Properties of Crystals
Anomalies of properties in a series of K2CoxNi1−x(SO4)2 · 6H2O mixed crystals
Abstract
The microhardness and thermal stability of K2CoxNi1–x(SO4)2 · 6H2O mixed crystals have been investigated. Microhardness peaks and dehydration onset temperatures are found in the composition range x = 0.05–0.23. The observed anomalies of properties are related to the anomalous changes in the structural parameters of the crystals in this composition range with an increase in the cobalt content. It is shown that structural imperfection of the crystals depends on the sectorial inhomogeneity and reaches a maximum at x = 0.43–0.54.
Surface and Thin Films
Ga2O3–In2O3 thin films on sapphire substrates: Synthesis and ultraviolet photoconductivity
Abstract
The structure and electrical and optical properties of β-Ga2O3–In2O3 thin films on sapphire substrates with different orientations have been investigated. The samples have been prepared by annealing of gallium–indium metallic films on sapphire substrates in air at different gallium-to-indium ratios in the initial mixture. The photoconductivity of these structures in the solar-blind ultraviolet spectral region has been examined.
Epitaxial low-temperature growth of In0.5Ga0.5As films on GaAs(100) and GaAs(111)A substrates using a metamorphic buffer
Abstract
A complex investigation of epitaxial In0.5Ga0.5As films grown on GaAs substrates with crystallographic orientations of (100) and (111)A in the standard high- and low-temperature modes has been performed. The parameters of the GaAs substrate and In0.5Ga0.5As film were matched using the technology of step-graded metamorphic buffer. The electrical and structural characteristics of the grown samples have been studied by the van der Pauw method, atomic force microscopy, scanning electron microscopy, and transmission/ scanning electron microscopy. The surface morphology is found to correlate with the sample growth temperature and doping with silicon. It is revealed that doping of low-temperature In0.5Ga0.5As layers with silicon significantly reduces both the surface roughness and highly improves the structural quality. Pores 50–100 nm in size are found in the low-temperature samples.
Study of magnetic metal periodic structures by X-Ray and electron microscopy methods
Abstract
Complex studies of magnetic periodic metallic systems based on Dy/Gd layers have been carried out by X-ray diffraction, resonance X-ray reflectometry, transmission electronic microscopy, and energydispersve microanalysis. The application of these methods and joint analysis of their results provide an effective approach to study of the structure and determination of the parameters of individual layers and interfaces and their structural quality with a high degree of reliability.
Nanomaterials and Crystals
Study of the structural features of ε-Co nanoparticles synthesized by cobalt carbonyl decomposition in the presence of surfactant
Abstract
Cobalt nanoparticles (3–7 nm in size) obtained by cobalt carbonyl decomposition in 1,2-dichlorobenzene in the presence of surfactants (trioctylphosphine oxide and oleic acid) have been studied by a complex of structural methods: small-angle X-ray scattering, electron diffraction, and transmission electron microscopy. The nanoparticles synthesized are found to consist of the cubic ε-Со phase; their crystal structure is described within the sp. gr. P4132, a = 6.097 Å. Using small-angle X-ray scattering, the size and shape of nanoparticles have been determined directly in the liquid dispersion. Most of the particles have a spherical shape; their average size is ≈3.5 ± 0.5 nm, which agrees with the electron microscopy data. Possible factors causing the ε-phase formation during synthesis of metallic Co nanoparticles are discussed.
Optical analysis of nanoparticle packing after drying in microdroplets
Abstract
The optical spectra of nanostructured patterns with different degrees of order, obtained by dehydration self-assembly of nanoparticles in solution microdroplets placed on a planar substrate, have been analyzed. The reflectance spectrum of the best-ordered pattern contains a characteristic peak, the position of which is determined by the average lattice period in the layer. It is shown that the height of this peak depends on the degree of order of the pattern structure. Patterns with different degrees of order have been simulated using a software for modeling the self-assembly process, which takes into account the properties of particles, substrate, and solvent, as well as the contact line dynamics during solvent evaporation. A peak occurs in the reflectance spectrum due to the resonance Rayleigh scattering in the ordered layer. The described technique for optical diagnostics can be used to analyze the degree of particle order in a pattern.
Comparative analysis of the structural and morphological features of biogenic and synthesized goethite nanoparticles
Abstract
A comparative analysis of the relationship between the morphological forms and magnetic properties of natural goethite particles from the crust of weathering of the Far East and Vietnam basalts and pure, chemically synthesized goethite particles was performed using Mössbauer spectroscopy, X-ray diffraction analysis, and scanning electron microscopy. It is shown how the shape of biogenic goethite particles affects their magnetic properties, which significantly differ from the magnetic properties of chemically synthesized samples.
Crystal Growth
Growth of faces of K2CoxNi1 – x(SO4)2 · 6H2O mixed crystals
Abstract
Data on the morphology and normal growth rate of the (110) and (001) faces, velocities of step motion, and slopes of dislocation hillocks on the (001) face of K2CoxNi1–x(SO4)2 · 6H2O crystals at different supersaturations of solutions with a Co/Ni ratio equal to 1: 1 or 1: 2 have been obtained using a Michelson interferometer. The morphology of the (110) faces is found to be the same for solutions of both compositions. Powerful dislocation sources with large Burgers vectors dominate on the (001) face. The morphology of the (001) surface is rougher than that of (110), especially in a 1: 2 solution at high supersaturation. The (110) faces grow more slowly as compared with (001). The kinetic coefficients of steps on the (001) face are identical in the 1: 1 and 1: 2 solutions. The influence of the kinetic and morphological characteristics of (001) faces on the single-crystal quality is analyzed.
Interferometric study of the growth kinetics of K2Co(SO4)2 · 6H2O and K2Ni(SO4)2 · 6H2O crystals
Abstract
The growth kinetics of the (001) and (110) faces of K2Co(SO4)2 · 6H2O and K2Ni(SO4)2 · 6H2O crystals in the kinetic mode has been in situ investigated for the first time by laser interferometry. The method used makes it possible to measure the slope p of the growing vicinal hillock and the normal growth rate R. The average step velocity ν = R/p as a function of supersaturation σ has been calculated based on these data. The kinetic coefficients of steps are determined. Some conclusions on the optimal growth conditions for crystals are drawn.
Relationship between the nucleation and precrystallization liquid phase during homogeneous crystallization of metals
Abstract
A comparative estimation of the size parameters of clusters of precrystallization liquid phase (PLP) of metals and critical crystalline nuclei has revealed the sizes of critical crystalline nuclei to be smaller than those of PLP clusters. Based on the results of estimation of the radii of critical crystalline nucleus by the methods of classical theory and molecular dynamics, it has been found for the first time that the radius of critical crystalline nucleus is about 0.2–0.4 of the PLP cluster radius. This fact confirmed the hypothesis of Ubellode et al. about the formation of a transition layer with a partially ordered structure between the solid and liquid phases. A scheme of the nucleation and growth of a crystalline nucleus under conditions of transition layer formation is proposed.
Apparatus
Neutron time-of-flight reflectometer GRAINS with horizontal sample plane at the IBR-2 reactor: Possibilities and prospects
Abstract
A new time-of-flight neutron reflectometer GRAINS with a horizontal sample plane (vertical scattering plane) has recently been put into operation at the pulsed reactor IBR-2 (JINR, Dubna). The scattering geometry applied makes it possible to carry out complex studies of nanostructured interfaces in solid and liquid states by measuring the specular reflectivity and the intensity of diffuse scattering of thermal neutrons from open surfaces and hidden interlayer boundaries, including solid-liquid interfaces, over a wide momentum transfer range. The classical analysis of specular reflectivity allows one to determine the scattering length density profile in the object under study in a direction perpendicular to the interface for a thickness of ~100 nm with a resolution of 1 nm. The analysis of off-specular (diffuse) neutron scattering makes it possible to characterize lateral correlations on surfaces and interlayer boundaries. The paper summarizes the first experience in the operation of the GRAINS reflectometer. The instrument characteristics are presented together with the possibilities for experiments with solid and liquid samples illustrated with simple systems. Further steps for the development of the reflectometer are discussed.
Crystallographic Software
Description of the atomic disorder (local order) in crystals by the mixed-symmetry method
Abstract
An approach to the description of local atomic disorder (short-range order) in single crystals by the mixed-symmetry method based on Bragg scattering data is proposed, and the corresponding software is developed. In defect-containing crystals, each atom in the unit cell can be described by its own symmetry space group. The expression for the calculated structural factor includes summation over different sets of symmetry operations for different atoms. To facilitate the search for new symmetry elements, an “atomic disorder expert” was developed, which estimates the significance of tested models. It is shown that the symmetry lowering for some atoms correlates with the existence of phase transitions (in langasite family crystals) and the anisotropy of physical properties (in rare-earth dodecaborides RB12).