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Anomalous scattering for small-molecule crystallography.

Anomalous dispersion techniques in small-molecule crystallography have been used in recent years with the advent of intense tunable X-radiation from synchrotron X-ray sources. By tuning the wavelength of the radiation close to the absorption edges of specific elements, it is possible to identify and distinguish between atoms which are close together in atomic number, even when two or more such atoms occupy a single site. Anomalous dispersion techniques can also be used to distinguish between valence states of different sites of an element by the valence contrast method or to determine the coordination geometry of an atom. In some cases, when the coordination of an atom is asymmetric, the absorption-edge position may depend on the orientation of the crystal. Finally, anomalous dispersion techniques can be used for ab initio structure solution from powder diffraction data. The properties of microporous materials often depend on the incorporation of metal atoms into the framework. Two or more metal atoms close together in atomic number may be incorporated, sometimes occupying a single site. In one study the site of an Ni atom in the aluminophosphate NiAPO was determined by anomalous dispersion techniques and data from the NSLS. Also, the location of the isomorphously substituted cobalt over two crystallographically different zinc sites was determined in the zincophosphate CoZnPO-CZP, in a five-wavelength study using data from ELETTRA.

Journal Article↗

XAFS study on a pressure-induced superconductor Cs3C60 under high pressure.

Cs K-edge XAFS of Cs3C60 which is a pressure-induced superconductor were measured at 21 and 34 kbar by using a diamond anvil cell (DAC) in order to obtain the structural information under high pressure, and to clarify the origin of the pressure-induced superconductivity. The distances and the mean square displacements between the Cs and C atoms are consistent with those determined by X-ray powder diffraction. Consequently, the high-pressure XAFS can give the reliable structural-information on a fullerene superconductor under high pressure. We also show the procedure of the analysis of high-pressure XAFS with DAC in detail.

Journal Article↗

Lattice parameters and structural phase transition of lanthanum titanate perovskite, La0.68(Ti0.95,Al0.05)O3.

Lattice parameters and the structural phase transition of La(0.68)(Ti(0.95),Al(0.05))O(3) have been investigated in situ in the temperature range 301-689 K by the synchrotron radiation powder diffraction (SR-PD) technique. High-angular-resolution SR-PD is confirmed to be a powerful technique for determining precise lattice parameters around a phase-transition temperature. The title compound exhibits a reversible phase transition between orthorhombic and tetragonal phases at 622.3 +/- 0.6 K. The following results were obtained: (i) the lattice parameters increased continuously with temperature, while the b/a ratio decreased continuously with temperature and became unity at the orthorhombic-tetragonal transition point; (ii) no hysteresis was observed between the lattice-parameter values measured on heating and on cooling. Results (i) and (ii) indicate that the orthorhombic-tetragonal phase transition is continuous and reversible. The b/a ratio is found to exhibit a more continuous temperature evolution than does the order parameter for a typical second-order phase transition based on Landau theory.

Journal Article↗

In situ observation of phase transformation in an Fe-Zn system at high temperatures using an image plate.

A unique system has been developed for in situ observation of phase transformation at high temperatures. Changes in powder-diffraction patterns from a heated specimen can be measured continuously by scanning an image plate located behind a slit. A heating system has been designed for a sheet specimen ( approximately 5 x 6 mm) using Joule heating, and it can heat the specimen up to 1100 K at a rate of up to 160 K s(-1), where effects of thermal expansion are minimized by a mechanism releasing stress. This system was applied to Zn-coated ( approximately 8 micro m in thickness) steel. At temperatures higher than the melting point of Zn, different types of Fe-Zn intermetallics formed sequentially through rapid interdiffusion. Changes in phase and crystallographic structure were monitored with a time resolution of less than a few seconds. It has been found that an addition of a small amount of an element, such as P, into Fe changes the incubation time before the alloying reaction starts. This system has been shown to have the potential for application to in situ observation of other reactions at high temperatures.

Journal Article↗

Ranitidine bismuth citrate: a novel anti-ulcer agent with different physico-chemical characteristics and improved biological activity to a bismuth citrate-ranitidine admixture.

BACKGROUND: Ranitidine bismuth citrate (RBC) is a new chemical entity for the treatment of peptic ulcer disease. RESULTS: RBC is freely soluble in water (more than 600 mg/mL at pH 4.6), whereas an equimolar admixture of its component molecules, bismuth citrate and ranitidine, formed an almost totally insoluble suspension. Even at very low pH values (around 2.0), the solubility of bismuth in ranitidine bismuth citrate was at least two-fold better than in the admixture. Comparison of several physico-chemical characteristics indicated that RBC possessed significantly different melting point properties, X-ray powder diffraction patterns, infra-red spectra and 13C-NMR solid-state spectra to the admixture. Ranitidine bismuth citrate inhibited human pepsin isoenzymes 1, 2, 3 and 5 but the admixture was inactive. RBC showed approximately two-fold greater anti-Helicobacter pylori activity in vitro than the admixture (geometric mean minimum inhibitory concentrations of 12.5 and 25.7 mg/L, respectively) and was more rapidly bactericidal. In a mouse model of gastric H. pylori colonization, 200 mg/kg of bismuth, given as RBC, eradicated the organism from all mice while only 10% of infections were eradicated by equivalent levels of bismuth in admixture form. CONCLUSION: It is believed that the significantly greater solubility of RBC, especially at lower pH values, is highly relevant to its better antipepsin and anti-H. pylori action compared to the insoluble admixture of bismuth citrate and ranitidine.

Animals↗

Interfacial reactions and silicate formation in highly dispersed Lu2O3-SiO2 system.

Solid state interface reactions in highly dispersed Lu2O3-SiO2 binary oxide system were studied at 600-1100 degrees C with X-ray powder diffraction (XRD), high-resolution transmission electron microscopy (HRTEM) and Fourier Transform Infrared spectroscopy (FTIR). The results show that at 600-900 degrees C an amorphous, nanometer thick Lu-O-Si layer covering SiO2 particles exists in the system. At higher temperatures the breakage of the layer into amorphous islands occurs and crystalline silicates with various structures are formed. In particular, Lu4[Si3O10][SiO4] silicate, analogue of B-type Dy-Tm disilicates, forms at 1000 degrees C.

Journal Article↗

Study of a rat model for calcium oxalate crystal formation without severe renal damage in selected conditions.

BACKGROUND: Although nephrotoxic in high doses, ethylene glycol (EG) has been used with ammonium chloride (NH(4)Cl) or vitamin D(3) to study calcium oxalate stone formation in rat models. In the present study we used EG alone or with NH(4)Cl to study hyperoxaluria, crystaluria, and crystal attachment to renal epithelial cells in rats with minimal renal damage. METHODS: Six-week-old male Sprague-Dawley (SD) rats were given food and special drinking water. In experiment 1 the drinking water contained 1.0% NH(4)Cl plus four different concentrations of EG (0.8%, 0.4%, 0.2%, 0.1%). In experiment 2 the drinking water contained EG alone (0.8%, 0.4%, 0.2%, 0.1%). Urine was collected for 24 h before the rats were sacrificed. In experiment 1 the rats were sacrificed 5-13 days after starting the special water. In experiment 2 the rats were sacrificed 7-21 days after starting the special water. Bladder urine was also obtained. Blood and urine were tested for calcium, phosphorus, and creatinine. In addition, urine was tested for pH, oxalate and N-acetyl-beta-D glucosaminidase (NAG). Kidney sections were stained with hematoxylin-eosin, von Kossa and Pizzolato stain. Crystal morphology was determined using polarizing microscopy, and composition was determined using high-resolution X-ray powder diffraction. RESULTS: Experiment 1: Aggravation of renal function, an increase in urinary oxalate and NAG excretion, and crystals observed in the kidneys all correlated with EG concentration and length of drinking time. In bladder urine, calcium oxalate monohydrate (COM) crystals exceeded calcium oxalate dihydrate (COD) crystals. Experiment 2: Renal function remained unchanged. Oxalate excretion increased and NAG increased slightly. Crystals occurred only in the papillary tip region. Crystals in bladder urine were mostly COD. CONCLUSION: In the current rat model, calcium oxalate crystaluria could be induced without severe renal damage in selected cases. Either and/or both COM and COD might form and interact with kidney epithelium. We propose different experimental conditions to study the various phases of calcium oxalate stone formation in young male SD rats.

Acetylglucosaminidase↗

Mechanism of drug dissolution rate enhancement from beta-cyclodextrin-drug systems.

The influence of beta-cyclodextrin on the physicochemical properties of bendrofluazide, chlorothiazide, hydrochlorothiazide and hydroflumethiazide was investigated using solubility, X-ray powder diffraction, differential scanning calorimetry (DSC) and intrinsic dissolution rate methods. The solubility of each drug was enhanced in the presence of beta-cyclodextrin, the effect being greatest with bendrofluazide. X-ray diffraction data on equimolar freeze dried systems indicated the formation of solid state inclusion complex only in the case of bendrofluazide. The relative increase in initial dissolution rate of drug from freeze dried systems varied from sixty fold for bendrofluazide to three fold for hydroflumethiazide. The observed dissolution rates were intermediate between those predicted by the classical two component soluble complex model and a carrier controlled model. It was concluded that the enhanced drug dissolution rates, which are above those predicted by the soluble complex model, are due to an extension of carrier phase dissolution control to higher drug weight fractions than predicted by the soluble complex model and that this was a consequence of the disparate solubilities of the carrier and drug.

Bendroflumethiazide↗

Metronidazole-induced myocardial depression: chemical and pharmacological studies on the role of calcium in-vitro.

The interaction of metronidazole with calcium to form a water-soluble complex has been studied by titration with ethylenediaminetetraacetate (EDTA), direct current and pulse polarographic reduction steps of the nitro-group at pH 5 and 7, and by ultraviolet absorption. Stoichiometric calculations, X-ray powder diffraction pattern of the synthesized metronidazole-calcium complex, and molecular ion peak at m/z 381 in the mass spectrum of this product, showed that a 2:1 complex is formed. The interaction of metronidazole with calcium on myocardial contractile performance of guinea-pig electrically-driven isolated left atria in physiological solution was also examined. Metronidazole induced a sustained, concentration-dependent depression of the tension that was reversed by changing the bathing fluid to physiological solution, and/or by adding excess calcium ion. The drug-induced negative inotropic response was antagonized competitively by increasing calcium ion in the bath, whereas noradrenaline antagonized metronidazole-induced negative inotropic responses non-competitively. Addition of the metronidazole-calcium complex to the bath did not affect normal myocardial contractile performance. The results show that metronidazole produces a direct negative inotropic effect on isolated atrial muscles by interfering with Ca2+, and by preventing Ca2+ function in the events leading to contractile activity of atrial muscles.

Animals↗

Effects of grinding and humidification on the transformation of conglomerate to racemic compound in optically active drugs.

The effects of grinding and humidification on the transformation of conglomerate to racemic compound have been investigated by X-ray powder diffraction (XPD), differential scanning calorimetry (DSC) and infrared (IR) spectroscopy for leucine, norleucine, valine, serine, tartaric acid and malic acid. Racemic physical mixtures were prepared by physical mixing of equimolar quantities of D and I. crystals using a mortar and pestle. Ground mixtures were obtained by grinding the physical mixtures with a vibrational mill. Humidification was performed by storing the physical mixtures and the ground mixtures in a desiccator containing saturated aqueous salt solutions at 40 degrees C. When physical mixtures of malic acid, tartaric acid and serine were ground, the XPD peaks of the racemic compounds were observed. The XPD patterns of humidified physical mixtures of these compounds also showed the formation of the racemic compounds. This indicated that grinding or humidification of malic acid, tartaric acid and serine induced the transformation of conglomerate to racemic compound crystals. When, on the other hand, the physical mixtures of valine, leucine and norleucine were ground, peaks of racemic compounds were not detected in the XPD pattern. After humidification of the ground mixtures of valine, leucine and norleucine, however, the XPD peaks of racemic compounds were observed. DSC and IR studies revealed consistent results. We concluded that grinding or humidification of malic acid, tartaric acid and serine could induce the transformation of a conglomerate to racemic compound. In contrast, humidifying after grinding was needed to bring about the transformation in leucine, norleucine and valine.

Calorimetry, Differential Scanning↗

Structure of haloform intercalated C60 and its influence on superconductive properties.

CHCl3 and CHBr3 intercalated C60 have attracted particular interest after a superconductivity transition temperature (Tc) of up to 117 K was discovered. We have determined the structure using synchrotron x-ray powder-diffraction and found that the expansion of the lattice mainly takes place in one dimension (triclinic b axis), leaving planes of C60 molecules on an approximately hexagonal, slightly expanded lattice. We have performed tight-binding band structure calculations for the surface layer. In spite of the slight expansion of the layers, for the range of dopings where a large Tc has been observed, the density of states at the Fermi energy is smaller for C60.2CHCl3 and C60.2CHBr3 than for C60. This suggests that the lattice expansion alone cannot explain the increase of Tc.

Journal Article↗

Formation of a one-dimensional array of oxygen in a microporous metal-organic solid.

We report the direct observation of dioxygen molecules physisorbed in the nanochannels of a microporous copper coordination polymer by the MEM (maximum entropy method)/Rietveld method, using in situ high-resolution synchrotron x-ray powder diffraction measurements. The obtained MEM electron density revealed that van der Waals dimers of physisorbed O2 locate in the middle of nanochannels and form a one-dimensional ladder structure aligned to the host channel structure. The observed O-O stretching Raman band and magnetic susceptibilities are characteristic of the confined O2 molecules in one-dimensional nanochannels of CPL-1 (coordination polymer 1 with pillared layer structure).

Journal Article↗

Uric acid dihydrate: crystallography and identification.

Unit-cell dimensions and optical data for uric acid and uric acid dihydrate show that there are structural resemblances, but that either can be readily distinguished by x-ray methods or by optical techniques. Density separation may be unsatisfactory because the dihydrate can lose water rather easily. Powder diffraction data are given.

Crystallography↗

A Benzene-Thermal Synthetic Route to Nanocrystalline GaN

A thermal reaction of Li3N and GaCl3 in which benzene was used as the solvent under pressure has been carried out for the preparation of 30-nanometer particles of gallium nitride (GaN) at 280°C. This temperature is much lower than that of traditional methods, and the yield of GaN reached 80%. The x-ray powder diffraction pattern indicated that sample was mainly hexagonal-phase GaN with a small fraction of rocksalt-phase GaN, which has a lattice constant a = 4.100 angstroms. This rocksalt structure, which had been observed previously only under high pressure (at least 37 gigapascals) was observed directly with high-resolution electron microscopy.

Journal Article↗

A reduction-pyrolysis-catalysis synthesis of diamond

Diamond powder was synthesized through a metallic reduction-pyrolysis-catalysis route with the reaction of carbon tetrachloride and sodium at 700 degreesC, in which the sodium was used as reductant and flux. This temperature is much lower than that of traditional methods. The x-ray powder diffraction patterns showed three strong peaks of diamond. The Raman spectrum showed a sharp peak at 1332 inverse centimeters, which is characteristic of diamond. Although the yield was only 2 percent, this method is a simple means of forming diamond.

Journal Article↗

Reduction of uranium(VI) phosphate during growth of the thermophilic bacterium Thermoterrabacterium ferrireducens.

The thermophilic, gram-positive bacterium Thermoterrabacterium ferrireducens coupled organotrophic growth to the reduction of sparingly soluble U(VI) phosphate. X-ray powder diffraction and X-ray absorption spectroscopy analysis identified the electron acceptor in a defined medium as U(VI) phosphate [uramphite; (NH4)(UO2)(PO4) . 3H2O], while the U(IV)-containing precipitate formed during bacterial growth was identified as ningyoite [CaU(PO4)2 . H2O]. This is the first report of microbial reduction of a largely insoluble U(VI) compound.

Microscopy, Electron, Scanning↗

Molecular modelling of the three-dimensional structure and conformational flexibility of bacterial lipopolysaccharide.

Molecular modelling techniques have been applied to calculate the three-dimensional architecture and the conformational flexibility of a complete bacterial S-form lipopolysaccharide (LPS) consisting of a hexaacyl lipid A identical to Escherichia coli lipid A, a complete Salmonella typhimurium core oligosaccharide portion, and four repeating units of the Salmonella serogroup B O-specific chain. X-ray powder diffraction experiments on dried samples of LPS were carried out to obtain information on the dimensions of the various LPS partial structures. Up to the Ra-LPS structure, the calculated model dimensions were in good agreement with experimental data and were 2.4 nm for lipid A, 2.8 nm for Re-LPS, 3.5 nm for Rd-LPS, and 4.4 nm for Ra-LPS. The maximum length of a stretched S-form LPS model bearing four repeating units was evaluated to be 9.6 nm; however, energetically favored LPS conformations showed the O-specific chain bent with respect to the Ra-LPS portion and significantly smaller dimensions (about 5.0 to 5.5 nm). According to the calculations, the Ra-LPS moiety has an approximately cylindrical shape and is conformationally well defined, in contrast to the O-specific chain, which was found to be the most flexible portion within the molecule.

Carbohydrate Conformation↗

Submicroscopic crystals in osteoarthritic synovial fluids.

OBJECTIVES: To investigate the hypothesis that synovial fluid (SF) from patients with osteoarthritis (OA) may contain calcium phosphate crystals that are either too small, or too few in number to be identified by conventional light microscopy techniques. METHODS: Twelve SF from 11 patients with established knee OA, five SF from patients with rheumatoid arthritis (RA), and two control samples of SF from patients with pseudogout were subjected to an enzyme/hypochlorite extraction procedure. The patients with OA and RA had no radiographic evidence of chondrocalcinosis, or SF crystals on polarised light microscopy. Extracted material was examined and analysed by analytical electron microscopy (AEM) and x ray powder diffraction (XRD). RESULTS: Mineral was found in 11 of 12 OA samples, ranging from 2-120 micrograms/ml SF. Analytical electron microscopy revealed calcium pyrophosphate dihydrate (CPPD) crystals in five (confirmed by XRD in three) and basic calcium phosphates (BCP) in eight (five on XRD). Two samples with confirmed CPPD contained some rods with a mean length below 100 nm. The majority of BCP clusters were also less than 100 nm in diameter. BCP was detected in 1/5 RA samples. Control samples contained CPPD crystals of the expected size range of 0.42-17.9 microns. CONCLUSIONS: The data indicate that many OA SF may contain CPPD or BCP crystals which are too small or too few in number to be identified by conventional techniques. Crystal deposition is not an 'on-off' phenomenon in OA.

Aged↗