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PubMed2006

High-spin- and low-spin-state structures of [Fe(chloroethyltetrazole)6](ClO4)2 from synchrotron powder diffraction data.

The spin-crossover complex [Fe(teec)(6)](ClO(4))(2) (teec = chloroethyltetrazole) exhibits a 50 % incomplete spin crossover in the temperature range 300-30 K. Time-resolved synchrotron powder diffraction experiments have been carried out to elucidate its structural behavior. We report crystal structure models of this material at 300 K (high spin) and 90 K (low spin), as solved from synchrotron powder diffraction data by using Genetic Algorithm and Parallel Tempering techniques and refined with Rietveld refinement. During short synchrotron powder diffraction experiments (five minutes duration) two distinguishable lattices were observed the quantities of which vary with temperature. The implication of this phenomenon, that is interpreted as a structural phase transition associated with the high-to-low spin crossover, and the structural characteristics of the high-spin and low-spin models are discussed in relation to other compounds showing a similar type of spin-crossover behavior.

Journal Article↗
PubMed2004

The impact of powder diffraction on the structural characterization of organic crystalline materials.

The bulk properties of organic crystalline materials depend on their molecular and crystal structures but, as many of these materials cannot be prepared in a suitable form for conventional single-crystal diffraction studies, structural characterization and rationalization of these properties must be obtained from powder diffraction data. The recent development of direct-space structure solution methods has enabled the study of a wide range of organic materials using powder diffraction data, many of structural complexity only made tractable by these advances in methodology. These direct-space methods are based on a number of global optimization techniques including Monte Carlo, simulated annealing, genetic algorithm and differential evolution approaches. In this article, the implementation and relative efficiency and reliability of these methods are discussed, and their impact on the structural study of organic materials is illustrated by examples of polymorphic systems, pharmaceutical, pigment and polypeptide structures and compounds used in the study of intermolecular networks.

Algorithms↗
PubMed2005

Applications of X-ray powder diffraction in materials chemistry.

X-ray powder diffraction is a standard technique in materials chemistry, yet it is often still used in the laboratory as a "one-hit" technique, e.g. for fingerprinting and following the progress of reactions. It is important, however, that the wealth of information available from powder data is not overlooked. While it is only possible here to scratch the surface of possibilities, a range of examples from our research is used to emphasize some of the more accessible techniques and to highlight successes as well as potential problems. The first example is the study of solid solution formation in the oxide systems Ba(3-3x)La(2x)V2O8 and Sr(4-x)Ba(x)Mn3O10 and in the silicate-hydroxyapatite bioceramic, Ca10(PO4)6-x(SiO4)x(OH)2-x. Database mining is also explored, using three phases within the pseudobinary phase diagram Li3SbO4-CuO as examples. All three phases presented different challenges: the structure of Li3SbO4 had been previously reported in higher symmetry than was actually the case, Li3Cu2SbO6 was found to be isostructural with Li2TiO3 but the cation ordering had to be rationalized, and Li3CuSbO5 was believed to be triclinic, presenting challenges in indexing the powder pattern. Quantitative phase analysis is briefly discussed, with the emphasis both on success (determination of amorphous phase content in a novel cadmium arsenate phase) and on possible failure (compositional analysis in bone mineral); the reasons for the problems in the latter are also explored. Finally, the use of an area detector system has been shown to be of value in the study of orientational effects (or lack of them) in non- and partially-ordered biomaterials, including p-HEMA, annulus fibrosis of lumbar discs, and keratin in the horn of cow's hooves.

Animals↗
PubMed2005

X-ray powder diffraction beamline at D10B of LNLS: application to the Ba2FeReO6 double perovskite.

A new beamline, fully dedicated to X-ray powder diffraction (XPD) measurements, has been installed after the exit port B of the bending magnet D10 at the Brazilian Synchrotron Light Laboratory (LNLS) and commissioned. The technical characteristics of the beamline are described and some performance indicators are listed, such as the incoming photon flux and the angular/energy resolutions obtainable under typical experimental conditions. The results of a Rietveld refinement for a standard sample of Y2O3 using high-resolution data are shown. The refined parameters match those found in the literature, within experimental error. High-resolution XPD measurements on Ba2FeReO6 demonstrate a slight departure from the ideal cubic double-perovskite structure at low temperatures, not detected by previous powder diffraction experiments. The onset of the structural transition coincides with the ferrimagnetic ordering temperature, Tc approximately equal to 315 K. Subtle structural features, such as those reported here for Ba2FeReO6, as well as the determination and/or refinement of complex crystal structures in polycrystalline samples are ideal candidate problems to be investigated on this beamline.

Brazil↗
PubMed2003

X-ray powder diffraction patterns for certain fluoroquinolone antibiotic drugs.

X-ray powder diffraction (XRD) data for six pure fluoroquinolone antibiotic drugs, ciprofloxacin, norfloxacin, enrofloxacin, ofloxacin, pefloxacin and sparfloxacin have been obtained using a powder diffractometer. The drugs were scanned from a Bragg angle (2theta) of 10 degrees to 70 degrees. The obtained data were tabulated in terms of the lattice spacing (A) and relative line intensities (I/I(I)). This new information may be useful for the identification of these drugs.

Anti-Infective Agents↗
PubMed2003

In situ monitoring of wet granulation using online X-ray powder diffraction.

PURPOSE: Polymorphic transformations during the wet granulation of a metastable polymorph of flufenamic acid were monitored in situ using online X-ray powder diffraction. The resulting data were used in testing a proposed process induced transformation rate model, which allows the extent and occurrence of polymorphic transformations during wet granulation to be controlled by adjusting the granulation time. METHODS: A small-scale, top mixing granulator was designed for compatibility with novel X-ray powder diffraction equipment (available from X-Ray Optical Systems of East Greenbush, NY). RESULTS: The unique polycapillary optic and X-ray source allowed the transformation of the metastable to the stable polymorph to be followed during the granulation. Following a diffraction peak each for the metastable and stable forms demonstrated that polymorphic transformations during the wetting phase of granulation follow the trends predicted by the model. CONCLUSIONS: The advanced online monitoring may allow real-time control of the process by the adjustment of process parameters, such as granulation time, and clearly qualifies as a PAT (process analytical technology).

Flufenamic Acid↗
PubMed2000

Ab initio structure determination and Rietveld refinement of a high-temperature phase of zirconium hydrogen phosphate and a new polymorph of zirconium pyrophosphate from in situ temperature-resolved powder diffraction data.

The collected in situ temperature-resolved synchrotron powder data revealed that the transformation of the recently reported three-dimensional tau-Zr(HPO4)2 to cubic ZrP2O7 goes through two intermediate phases. The first intermediate phase, rho-Zr(HPO4)2, is formed in a reversible phase transition at 598 K, which involves both rearrangement and disordering of the hydrogen phosphate groups of tau-Zr(HPO4)2. At 688 K condensation of the hydrogen phosphate groups leads to the formation of the second intermediate, a new polymorph of zirconium pyrophosphate (beta-ZrP2O7). Heating above 973 K results in the gradual transformation of beta-ZrP2O7 to cubic zirconium pyrophosphate (alpha-ZrP2O7). The crystal structures of the two intermediate phases were solved from the in situ powder diffraction data using direct methods and refined using the Rietveld method. Both phases are orthorhombic, space group Pnnm and Z = 2. The lattice parameters for the two phases are: p-Zr(HPO4)2: a = 8.1935 (2), b = 7.7090 (2), c = 5.4080 (1) A; beta-ZrP2O7: a = 8.3127 (5), b = 6.6389 (4), c = 5.3407 (3) A. The formation mechanism for the new zirconium pyrophosphate polymorph, beta-ZrP2O7, is discussed in relation to structurally restricted soft chemistry.

Diphosphates↗
PubMed2006

Accurate structure factors and experimental charge densities from synchrotron X-ray powder diffraction data at SPring-8.

Accurate structure factors of silicon and diamond have been experimentally determined from powder diffraction data measured at the third-generation synchrotron-radiation source SPring-8, BL02B2. The accuracy of the obtained structure factors has been evaluated by comparing with structure factors in the literature measured by the Pendellösung method and with some from theoretical calculations. The results indicate that the structure factors from powder data are accurate enough to discuss the experimental charge-density distributions of these materials. The number of structure factors of silicon determined in the present study is 104, which is three times more than that of previous Pendellösung data. The experimental charge densities have been obtained by the maximum-entropy method from the present structure factors. The charge densities at bond mid-points for silicon and diamond show good agreement with different kinds of theoretical calculations. The present study proved that the powder diffraction at SPring-8 is a promising method for determination of experimental charge density for a wider range of materials.

Data Interpretation, Statistical↗
PubMed2005

Structure determination of homoleptic AuI, AgI, and CuI aryl/alkylethynyl coordination polymers by X-ray powder diffraction.

This article describes the structure determination of five homoleptic d(10) metal-aryl/alkylacetylides [RC triple bond CM] (M=Cu, R=tBu 1, nPr 2, Ph 3; R=Ph, M=Ag 4; Au 5) by using X-ray single-crystal and powder diffraction. Complex 1.C6H6 reveals an unusual Cu20 catenane cluster structure that has various types of tBuC triple bond C-->Cu coordination modes. By using this single-crystal structure as a starting model for subsequent Rietveld refinement of X-ray powder diffraction data, the structure of the powder synthesized from CuI and tBuC triple bond CH was found to have the same structure as 1. Complex 2 has an extended sheet structure consisting of discrete zig-zag Cu4 subunits connected through bridging nPrC triple bond C groups. Complex 3 forms an infinite chain structure with extended Cu-Cu ladders (Cu-Cu=2.49(4)-2.83(2) A). The silver(I) congener 4 is iso-structural to 3 (average Ag-Ag distance 3.11 A), whereas the gold(I) analogue 5 forms a Au...Au honeycomb network with PhC triple bond C pillars (Au-Au=2.98(1)-3.26(1) A). Solid-state properties including photoluminescence, nu(C triple bond C) stretching frequencies and thermal stability of these polymeric systems are discussed in the context of the determined structures.

Acetylene↗
PubMed2004

Shadowing and absorption corrections of high-pressure powder diffraction data: toward accurate electron-density determinations.

The shadowing of the primary beam and of reflections from a powder crystal sample enclosed in a diamond-anvil high-pressure cell (DAC) is described for unrestricted data-collection procedures. The corrections account for the shadowing of the data measured with point- or area-detector diffractometers and can be applied for any containers of environment devices enclosing a powdered sample. The general procedure for correcting the powder diffraction data can be applied for analysing and optimizing diffractometric procedures of data collection and provides facilities for collecting high-pressure powder diffraction data with the DAC positioned optimally and rotated to counteract the preferred-orientation and particle-size effects, and to increase the resolution of data. The quadrature effects of numerical integration for the accuracy of computed corrections have been analysed.

Journal Article↗
PubMed2004

Binding of N-acetylglucosamine oligosaccharides to hen egg-white lysozyme: a powder diffraction study.

The binding of N-acetylglucosamine oligosaccharides (NAGn, n = 2-6) to hen egg-white lysozyme (HEWL; EC 3.2.1.17) was investigated by X-ray powder diffraction at room temperature. Each NAGn examined was found to bind to lysozyme in rapid-precipitation preparations in 1.0 M NaCl pH 6.0 buffer. The location of each NAGn was easily found from difference Fourier maps generated from structure factors extracted during preliminary Rietveld refinements. Full NAGn-protein structures were subjected to combined Rietveld and stereochemical restraint refinements (Rwp = 2.28-2.59%; Rp = 1.81-2.04%; RF2 = 3.91-5.80%) and revealed binding modes for NAGn that depended on the length of the NAG oligosaccharide. The NAG2 ligand was found in the BC sites in the cleft of HEWL, NAG3 was found to bind in both the ABC and BCD sites in the ratio 35:65 and NAG4 and NAG5 bound to the ABCD and ABCDE sites, respectively, while NAG6 only bound to sites ABCDE, leaving the F site empty with the remaining saccharide ring located in a solvent region adjacent to the A site. All protein powder diffraction patterns in this study consisted of extremely sharp Bragg peaks consistent with approximately 1 microm crystallites that were devoid of line-broadening defects. Details of the stereochemical restraints used in these refinements and their impact on structural validation are also discussed.

Acetylglucosamine↗
PubMed2006

Adsorption structures of water in NaX studied by DRIFT spectroscopy and neutron powder diffraction.

Diffuse reflectance infrared Fourier transform spectroscopic (DRIFTS) measurements (4000-1500 cm(-1)) and the results of neutron powder diffraction have been combined to study the structure of adsorption complexes of water in a NaX zeolite at different water loadings (25, 48, 72, and 120 water molecules per unit cell, respectively). Sharp bands corresponding to non-hydrogen-bonded OH groups of water molecules and broad associate bands due to hydrogen-bonded molecules are observed in the DRIFT spectra. We observe a remarkable downshift of the high-frequency associate band in a narrow temperature interval when the water amount decreases from 120 to 72 molecules per unit cell, which could signify some kind of "phase transition" for the water inside the zeolite cavities. Neutron powder diffraction results show that water molecules are predominantly localized in or near the 12-ring windows. Water molecules with hydrogen-bonded and non-hydrogen-bonded OH groups were found, in agreement with the observation of sharp and broad bands in the DRIFT spectra. We find strong evidence for the formation of cyclic hexamers of water molecules localized in the 12-ring windows, which are further stabilized by hydrogen bonds to framework oxygen atoms.

Adsorption↗
PubMed2005

Application notes on the use of softer X-rays for anomalous powder diffraction.

An in-vacuum diffractometer has been modified to collect powder diffraction data from a sample of promazine hydrochloride. Strong anomalous contrast has been observed at, or close to, the sulphur edge. Based on the data collected, a bespoke diffractometer has been designed that, together with minor changes to the geometry of the experiment, will enable the routine collection of powder data at absorption edges below 5.5 keV.

Equipment Design↗
PubMed2001

Structure determination of two intercalated compounds VOPO4.(CH2)4O and VOPO4.OH-(CH2)2-O-(CH2)2-OH; synchrotron powder diffraction and molecular modelling.

The crystal structures of two intercalated compounds have been determined using a combination of synchrotron powder diffraction and molecular mechanics simulations: (1) vanadyl phosphate intercalated with tetrahydrofuran, VOPO(4).(CH(2))(4)O, and (2) vanadyl phosphate intercalated with diethylene glycol, VOPO(4).HO(CH(2))(2)O(CH(2))(2)OH. Both intercalates preserve the tetragonal space group P4/n, as found in the host structure VOPO(4).2H(2)O. (1): a = 6.208, c = 8.930 A, Z = 2, D(x) = 2.51 g cm(-3); (2): a = 6.223, c = 11.417 A, Z = 2, D(x) = 2.66 g cm(-3). Both intercalates exhibit the same type of orientational disorder in the arrangement of guest molecules, as observed in the same host compound intercalated with water. These two intercalates also exhibit, rather surprisingly, perfect ordering in layer stacking without the displacement disorder, characteristic of many intercalated layered structures. Thanks to this regularity in the arrangement of guests and layers, synchrotron powder diffraction could be used in the present structure determination. The present results also enabled the analysis of the effect of geometrical parameters characterizing the mutual host-guest complementarity and the effect of host-guest and guest-guest interaction on the crystal packing of intercalates.

Journal Article↗
PubMed2006

Molecular structure of a D-homoandrostanyl steroid derivative: single crystal and powder diffraction analyses.

The knowledge of the structure of a molecular crystal is frequently a prerequisite for the understanding of its solid state properties. Even though single-crystal diffractometry is the method of choice when it comes to crystal structure determination, methods using powder diffraction data become more and more competitive. There has been much recent interest in the development of a new generation of "direct-space" approaches that are particularly suited for molecular crystals. The crystallographic structure of a steroid derivative molecule (17,17-di-n-propyl-17a-aza-D-homo-5alpha-androstan-3beta-ol) was obtained in two independent ways: from a single crystal by laboratory X-rays and from a polycrystalline powder by high-resolution synchrotron powder diffraction. The molecule crystallizes in the orthorhombic space group P2(1)2(1)2(1) (a = 6.5346, b = 17.6006 and c = 19.6978 A). Hydrogen bonds form infinite chains of molecules parallel to the c axis.

Androstanols↗
PubMed2000

Structure determination from conventional powder diffraction data: application to hydrates, hydrochloride salts, and metastable polymorphs.

Recent advances in crystallographic computing have made it possible to solve by powder diffraction methods structures that have not been possible to solve by single-crystal methods. Although there is vast improvement in the quality of data obtained from high-intensity synchrotron radiation, we found that surprisingly reliable results can be obtained from conventional laboratory sources. In this article we examine the application of Monte Carlo/simulated annealing methods for the determination of structures ranging in complexity from 9 to 15 degrees of freedom. We re-determine the structures of papaverine hydrochloride and erythromycin A dihydrate by the powder diffraction method and compare the structures to those determined by single-crystal diffraction methods. The structure of a metastable polymorphic form of acetohexamide, form B, is solved and examined spectroscopically. Its structure has not previously been solved by single-crystal techniques because of the small size of its crystals.

Acetohexamide↗
PubMed2006

Single-crystal X-ray and neutron powder diffraction investigation of the phase transition in tetrachlorobenzene.

The polymorphic phase transition of 1,2,4,5-tetrachlorobenzene (TCB) has been investigated using neutron powder diffraction and single-crystal X-ray diffraction. The diffraction experiments show a reversible phase change that occurs as a function of temperature with no apparent loss of sample quality on transition between the two phases. Neutron powder diffraction gives detailed information on the molecular structural changes and lattice parameters from 2 K to room temperature. The structure of the low-temperature form has been elucidated for the first time using single-crystal X-ray diffraction. Comparison of the alpha and beta structures show that they are both based on the same sheet motif, with the differences between the two being very subtle, except in terms of crystal symmetry. Detailed analysis of the structures revealed the changes required for inter-conversion. A computational polymorph search showed that these two sheet structures are more thermodynamically stable than alternative herringbone-type structures.

Journal Article↗
PubMed2005

Very large swelling in hybrid frameworks: a combined computational and powder diffraction study.

Using a combination of simulations and powder diffraction, we report here the study of the very large swelling of a three-dimensional nanoporous iron(III) carboxylate (MIL-88) which exhibits almost a reversible doubling (approximately 85%) of its cell volume while fully retaining its open-framework topology. The crystal structure of the open form of MIL-88 has been successfully refined and indicates that atomic displacements larger than 4 angstroms are observed when water or various alcohols are adsorbed in the porous structure, revealing an unusually flexible crystallized framework. X-ray thermodiffractometry shows that only a displacive transition occurs during the swelling phenomenon, ruling out any bond breaking.

Journal Article↗