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PubMed2006

Structure of Ce2RhIn8: an example of complementary use of high-resolution neutron powder diffraction and reciprocal-space mapping to study complex materials.

The room-temperature crystal structure of the heavy fermion antiferromagnet Ce2RhIn8, dicerium rhodium octaindide, has been studied by a combination of high-resolution synchrotron X-ray reciprocal-space mapping of single crystals and high-resolution time-of-flight neutron powder diffraction. The structure is disordered, exhibiting a complex interplay of non-periodic, partially correlated planar defects, coexistence and segregation of polytypic phases (induced by periodic planar ;defects'), mosaicity (i.e. domain misalignment) and non-uniform strain. These effects evolve as a function of temperature in a complicated way, but they remain down to low temperatures. The room-temperature diffraction data are best represented by a complex mixture of two polytypic phases, which are affected by non-periodic, partially correlated planar defects, differ slightly in their tetragonal structures, and exhibit different mosaicities and strain values. Therefore, Ce2RhIn8 approaches the paracrystalline state, rather than the classic crystalline state and thus several of the concepts of conventional single-crystal crystallography are inapplicable. The structural results are discussed in the context of the role of disorder in the heavy-fermion state and in the interplay between superconductivity and magnetism.

Journal Article↗
PubMed2004

Structures of Fe(II) spin-crossover complexes from synchrotron powder-diffraction data.

Crystal structure determination and analysis have been carried out for the two spin-crossover compounds [Fe(teeX)(6)](BF(4))(2) (teeX is haloethyltetrazole; X = I: teei; X = Br: teeb), in both their high-spin (near 300 K) and their low-spin states (T = 90 K), using high-resolution powder-diffraction data collected at the ESRF (Grenoble, France) and SPring8 (Japan) synchrotron radiation facilities. The structures of teei have been solved using various direct-space structure determination techniques (grid search, genetic algorithm and parallel tempering) and refined with the Rietveld method using geometrical restraints. In the case of teeb, a structural model was found but a full refinement was not successful because of the presence of a significant amount of an amorphous component. Analysis of the structures (space group P2(1)/c, Z = 2) and diffraction data, and the absence of phase transitions, show the overall structural similarity of these compounds and lead to the conclusion that the gradual spin-crossovers are likely to be accompanied by small structural changes only.

Journal Article↗
PubMed1997

Time-resolved X-ray powder diffraction using a large-area CCD-based detector and Rietveld refinement: solid-state polymerization of S2N2 to (SN)x.

A kinetic study of the solid-state polymerization of disulfur dinitride (S2N2) to polysulfur nitride [(SN)x] has been performed, combining monochromatic high-energy (lambda = 0.3263 A) synchrotron radiation X-ray powder diffraction, a large-area (ø = 220 mm) CCD-based X-ray image-intensifier detector and Rietveld refinement. Recently developed techniques for detector calibration and reduction of two-dimensional images to one-dimensional diffraction patterns have been employed for data processing/analysis. Good fits were obtained after Rietveld refinement [Rp = 8.4%, wRp = 9.4%, sin(theta(max))/lambda = 0.585 A(-1)] of diffraction patterns of S2N2 from images with 2 s exposure time. The solid-state polymerization of S2N2 to (SN)x, was followed at a maximum rate of two diffraction images per minute. Scale factors and cell parameters for S2N2 and beta-(SN), as functions of time were readily obtained after Rietveld refinement of the diffraction patterns obtained from each individual image throughout the polymerization. The polymerization was preceded by a lattice distortion of S2N2, and at 50% conversion the a axis had decreased by about 1% and the c axis had increased about 1%. The polymerization yielded not only the expected polymer beta-(SN)x, but also a small amount of a compound that could be another phase of (SN)x.

Journal Article↗
PubMed2001

Metal imidazolato complexes: synthesis, characterization, and X-ray powder diffraction studies of group 10 coordination polymers.

Binary metal imidazolates of the group 10 metals have been prepared and typically found amorphous. However, the intermediacy of a number of (poly)crystalline species during their formation has been evidenced; their selective preparation and characterization, by chemical, spectroscopic, and thermal methods and their structure solution by the ab initio X-ray powder diffraction technique lead to the discovery of new interesting structural features, such as those of polymeric Ni(Him)(2)(im)(CH(3)COO) (Him = imidazole) and of the hydrogen-bonded polymers of general Pd(x)Pt(1-x)(Him)(2)(im)(2) formula (x = 0, 0.5, 1). The latter are built upon 2D frameworks of (pseudo)square meshes, which, in the pure Pd derivative, form an entangled structure based upon interpenetrating 2D layers, coupled in pairs. The different structures are discussed in terms of different conformations of the new "im-H-im" ligand, which acts as monoanionic exobidentate fragment, similar to im, pyrazolate (pz), "pz-H-pz", and pyrimidin-2-olate.

Journal Article↗
PubMed2002

gamma-Sodium gallate: a Rietveld refinement using X-ray powder diffraction.

Tetrahedrally coordinated oxides usually present polymorphism, but for NaGaO(2), only the beta polymorph has been reported. In this work, the synthesis and structural characterization of gamma-sodium gallate, gamma-NaGaO(2), are presented. The crystal structure belongs to the orthorhombic system, space group Pbca (No. 61), and has been characterized by a Rietveld refinement of the X-ray powder diffraction pattern. The structure is similar to those exhibited by the gamma phases of many tetrahedral oxides.

Journal Article↗
PubMed2001

Metabolic pathways of dithiocarbamates from laboratory powder diffraction data.

In order to correlate the reactivity and molecular structures of dithiocarbamates, the crystal structures of 6-dimethylamino-5-nitropyrimidin-4-yl N,N-diethyldithiocarbamate, C11H17N5O2S2, (Ia), and 6-methylamino-5-nitropyrimidin-4-yl N,N-diethyldithiocarbamate, C10H15N5O2S2, (Ib), and of the product of thermolysis of (Ib), namely 4-diethylamino-6-methylamino-5-nitropyrimidinium chloride monohydrate, C9H16N5(O2)(+).Cl(-).H2O, (II), have been determined from X-ray laboratory powder diffraction data. Conformational preferences in (Ia) and (Ib) were studied on the density functional theory (DFT) level. Deviation of the reaction centre of the molecule from planarity and breakage of the secondary S...O contact cause switching between two alternative pathways of thermolysis.

Anti-Infective Agents↗
PubMed2000

Cardiolipin, alpha-D-glucopyranosyl, and L-lysylcardiolipin from gram-positive bacteria: FAB MS, monofilm and X-ray powder diffraction studies.

Cardiolipin preparations from Streptococcus B, Listeria welshimeri, Staphylococcus aureus, and a glucosyl and lysyl derivative of cardiolipin were analysed for fatty acid composition and fatty acid combinations. Three different fatty acid patterns are described and up to 17 molecular species were identified in Streptococcus B lipids by high resolution FAB MS. The physicochemical properties of these lipids were characterised in the sodium salt form by monofilm experiments and X-ray powder diffraction. All lipids formed stable monofilms. The minimal space requirement of unsubstituted cardiolipin was dictated by the fatty acid pattern. Substitution with L-lysine led to a decrease of the molecular area, substitution with D-glucopyranosyl to an increase. On self assembly at 100% relative humidity, all preparations adopted lamellar structures. They showed a high degree of order, in spite of the heterogeneous fatty acid compositions and numerous fatty acid combinations. The repeat distances in lamellar fluid phase varied between 4.99 and 5. 52 nm, the bilayer thickness between 3.70 and 4.46 nm. Surprising were the low values of sorbed water per molecule of the glucosyl and lysyl derivatives which were 58 and 60%, compared with those of the respective cardiolipin. When Na(+) was replaced as counterion by Ba(2+), the bilayer structure was retained, but the lipids were in the lamellar gel phase and the fatty acids were tilted between 32 and 53 degrees away from the bilayer normal. Wide angle X-ray diffraction studies and electron density profiles are also reported. Particular properties of glucosyl cardiolipin are discussed.

Cardiolipins↗
PubMed2006

Complex zeolite structure solved by combining powder diffraction and electron microscopy.

Many industrially important materials, ranging from ceramics to catalysts to pharmaceuticals, are polycrystalline and cannot be grown as single crystals. This means that non-conventional methods of structure analysis must be applied to obtain the structural information that is fundamental to the understanding of the properties of these materials. Electron microscopy might appear to be a natural approach, but only relatively simple structures have been solved by this route. Powder diffraction is another obvious option, but the overlap of reflections with similar diffraction angles causes an ambiguity in the relative intensities of those reflections. Various ways of overcoming or circumventing this problem have been developed, and several of these involve incorporating chemical information into the structure determination process. For complex zeolite structures, the FOCUS algorithm has proved to be effective. Because it operates in both real and reciprocal space, phase information obtained from high-resolution transmission electron microscopy images can be incorporated directly into this algorithm in a simple way. Here we show that by doing so, the complexity limit can be extended much further. The power of this approach has been demonstrated with the solution of the structure of the zeolite TNU-9 (|H9.3|[Al9.3Si182.7O384]; ref. 10) with 24 topologically distinct (Si,Al) atoms and 52 such O atoms. For comparison, ITQ-22 (ref. 11), the most complex zeolite known to date, has 16 topologically distinct (Si,Ge) atoms.

Journal Article↗
PubMed2006

A comparison of glycans and polyglycans using solid-state NMR and X-ray powder diffraction.

Individual polyglycans and their corresponding monomers have been studied separately for several decades. Attention has focused primarily on the modifications of these polyglycans instead of the simple relationship between the polyglycans themselves and their corresponding monomers. Two polyglycans, chitin and chitosan, were examined along with their respective monomeric units, N-acetyl-D-glucosamine (GlcNAc) and (+)D-glucosamine (GlcN) using solid-state proton decoupling Magic Angle Turning (MAT) techniques and X-Ray Powder Diffraction (XRPD). A down-field shift in isotropic (13)C chemical shifts was observed for both polymers in Cross Polarization/Magic Angle Spinning (CP/MAS) spectra. An explanation of misleading peak assignments in previous NMR studies for these polyglycans was determined by comparing sideband patterns of the polymers with their corresponding monomers generated in a 2D FIve pi REplicated Magic Angle Turning (FIREMAT) experiment processed by Technique for Importing Greater Evolution Resolution (TIGER). Structural changes in the crystalline framework were supported by XRPD diffraction data.

Acetylglucosamine↗
PubMed2001

Full phase analysis of portland clinker by penetrating synchrotron powder diffraction.

Fabrication of portland cements commonly depends on X-ray fluorescence (XRF), which measures the elemental compositions. XRF is used to adjust the raw material proportions and to control the process conditions. However, to predict the mechanical strength of the resulting concrete, it is essential to know the phase composition which is, so far, indirectly inferred by the Bogue method. Here, we report a phase analysis of an industrial portland clinker containing six crystalline phases, Ca3SiO5, Ca2SiO4, Ca4Al2Fe2O10, Ca3Al2O6, NaK3(SO4)2, and CaO, by Rietveld refinement of synchrotron X-ray powder diffraction data (lambda = 0.442377 A). Even the minor component, CaO 0.45(2)%, was readily analyzed. We have also carried out a phase study of the same clinker with laboratory X-rays to characterize the changes in the detection limit and errors. Furthermore, by adding a suitable crystalline standard to the same clinker, we have determined the overall amorphous phase content. The procedure established for this state-of-the-art phase analysis shows the high precision that can be achieved by using penetrating X-rays, which is of interest not only in cement chemistry but in other industrially important multiphase systems such as slags, superalloys, or catalysts.

Journal Article↗
PubMed2007

Neutron powder diffraction with (nat)Sm: crystal structures and magnetism of a binary samarium deuteride and a ternary samarium magnesium deuteride.

Binary SmH(3) (trigonal, a=656.7(3), c=680.1(3) pm, P$\bar 3$c1, Z=6), ternary SmMg2H7 (tetragonal, a=626.47(6), c=937.2(2) pm, P4(1)2(1)2, Z=4) and the corresponding deuterides SmD3 (a=653.9(1)m, c=676.7(2) pm) and SmMg2D7 (a=624.10(1), c=934.81(2) pm) have been prepared by hydrogenation (deuteration) of elemental samarium and the Laves phase SmMg2, respectively, and investigated by X-ray and neutron powder diffraction and SQUID and vibration magnetometry. The problem of the enormous neutron absorption of the natural isotopic mixture (natSm) is circumvented by carefully choosing the neutron wavelength (approximately 50 pm) and the use of double-walled cylindrical sample holders and a high-intensity neutron diffractometer (D4c at ILL). SmD3 crystallises with a tysonite-type structure and has three independently ordered deuterium atom sites with trigonal-planar, trigonal-pyramidal and tetrahedral metal environments and Sm--D bond lengths in the range 220(1)-258(1) pm (average: 235 pm). SmMg2D7 is a new deuteride that crystallises with an LaMg2D7-type structure. It displays four fully occupied deuterium sites having triangular and tetrahedral metal environments and Sm--D bond lengths in the range 227.6(5)-246.8(8) pm (average: 239 pm). These are the first samarium-deuterium bond lengths to be reported. Both deuterides are paramagnetic down to 2 K (SmD3: mueff=0.63(1) muB, thetap approximately -4 K; SmMg2D7: mueff=0.57(2) muB, thetap approximately -4 K). Their crystal structures and chemical and physical properties suggest mainly ionic bonding according to the limiting ionic formulae Sm3+(H-)3 and Sm3+(Mg2+)2(H-)7.

Journal Article↗
PubMed2004

A novel cadmium aminophosphonate: X-ray powder diffraction structure, solid-state IR and NMR spectroscopic determination of the fine structure of the organic moieties.

A new divalent cadmium phosphonate, Cd2Cl2(H2O)4(H2L), has been synthesized from the ethylenediamine-N,N'-bis(methylenephosphonic acid) (H4L). The obtained microcrystalline compound has been characterized by solid-state IR spectra and 13C, 31P, and 113Cd CP MAS NMR. The static 13P NMR spectra have been also recorded to give the delta11, delta22, and delta33 chemical shift parameters for both compounds. The spectral data, collected for Cd2Cl2(H2O)4(H2L), are in an agreement with its X-ray powder diffraction structure solved with the cell dimensions a = 16.6105(10), b = 7.1572(4), and c = 6.8171(4) A and beta = 98.327(4) degrees. The octahedral coordination sphere of the cadmium atoms consists of two phosphonate oxygen atoms, two water oxygen atoms, and the two chlorine atoms. Cadmium atoms are bridged by the chlorine atoms forming four-membered rings. The phosphorus atoms exhibit a tetrahedral coordination with two oxygen atoms bonded to the cadmium atoms with P-O distances of 1.503(10) and 1.504(10) A. The third oxygen atom, showing a longer P-O distance (1.546(9) A), is not bonded to the metal center, nor is it bonded to a proton. The combined IR and NMR proton-phosphorus cross-polarization kinetic data together with the X-ray data confirm that the cadmium phosphonate has the zwitterionic structure (NH2(+)CH2P(O2Cd2)O-) similar to the initial aminophosphonic acid H4L.

Journal Article↗
PubMed2003

Quantification of crystalline forms in active pharmaceutical ingredient and tablets by X-ray powder diffraction.

A Merck development compound was known to exist in several polymorphic forms, hydrates and solvates. The polymorphic forms were characterized and the most thermodynamically stable form at room temperature was identified and taken into development. During routine stability analysis it became apparent that the crystalline form of the compound was converting from one form to another in tablets that were stored at 40 degrees C/75% relative humidity in open containers. This form conversion did not occur when the active pharmaceutical ingredient (API) alone was stored under these conditions. This paper describes the development and application of an X-ray powder diffraction method for the determination of the relative content of the two crystalline forms in API and within the final formulation. Results of monitoring the crystalline form conversion are reported and a possible mechanism of conversion is postulated.

Crystallization↗
PubMed1979

Fate of nickel subsulfide during carcinogenesis studied by autoradiography and X-ray powder diffraction.

Sarcomas in mice were induced by i.m. and s.c. administration of 63Ni- and 35S-labeled nickel subsulfide (Ni3S2), and the fate of the Ni3S2 was studied in tumors and normal tissues during carcinogenesis. Whole-body autoradiography showed a gradual loss of solubilized 63Ni and 35S radioactivity from the site of injection. There was also a loss of nonsolubilized dust particles which appeared to be phagocytized by reticuloendothelial cells in the liver, spleen, and regional lymph nodes. Microautoradiography showed that the totally dominating radioactivity within both the 63Ni3S2- and the Ni3(35)S2-induced tumors was associated with dust particles. There was no specific or excessive localization of solubilized radioactivity in the tumors or in metastases (when present). Two patterns of localization of dust particles within the tumors were observed: one with particles concentrated in a central part of the tumor and one with the particles present in the periphery of the tumor. X-ray powder diffraction of the insoluble crystalline material in the tumors indicated that a conversion of the alpha Ni3S2 to alpha Ni7S6 and beta NiS had occurred.

Animals↗
PubMed2006

Synthesis, solid-state NMR, and X-ray powder diffraction characterization of group 12 coordination polymers, including the first example of a C-mercuriated pyrazole.

Cadmium and mercury acetates have been reacted with pyrazole (Hpz) and 3,5-dimethylpyrazole (Hdmpz), affording distinct mixed-ligand species, selectively prepared upon slightly modifying the reaction conditions. Two polymorphs of [{Cd(mu-ac)2(Hpz)2}n], as well as the [{Cd(mu-ac)2(Hdmpz)2}n] species (Hac = acetic acid), were obtained by solution chemistry, while the two-dimensional [{Cd3(mu3-ac)4(mu-pz)2(Hpz)2}n] and [{Cd(mu-ac)(mu-pz)}n] polymers were prepared upon controlled thermal treatment of one of the [{Cd(mu-ac)2(Hpz)2}n] forms. Two mercury derivatives, [{Hg3(mu-ac)3(mu-pz)3}n] and [{Hg(ac)(mu-dmpz)}n], were also prepared, the latter containing one-dimensional chains of Hg(II) ions bridged by C-mercuriated Hdmpz ligands. All their crystal structures (but one) were determined by powder diffraction methods using conventional X-ray laboratory equipment, supported by 13C CPMAS NMR measurements. The latter method helped in assigning a C-metalated nature to an amorphous material of [Hg(ac)(pz)] formula, obtained by employing EtOH as a solvent. A few other Hdmpz-containing cadmium acetates were also prepared, but their polyphasic nature, evidenced by diffraction methods, hampered their complete structural characterization.

Cadmium↗
PubMed2005

Moisture-triggered 1,3,5-triazine-based Cu(II) molecular switch: a combined X-ray single-crystal and powder diffraction study.

A solvothermal synthetic procedure has been exploited to prepare the new [Cu(3)L(NO(3))(6)](n) coordination polymer (1) by reaction of the polydentate N,N'-{2,4-di-[(di-pyridin-2-yl)amine]-1,3,5-triazine}ethylenediamine ligand (opytrizediam L) with copper(II) nitrate. 1 has been structurally characterized by means of the conventional X-ray single-crystal diffraction technique. It crystallizes in the monoclinic C2/c space group with a = 16.830(3), b = 20.701(4), c = 18.170(4) Angstroms, beta = 113.26(3) degrees, V = 5816(2) Angstroms(3), Z = 4. 1 consists of trinuclear Cu(3)L(NO(3))(5) units connected by means of a nitrato-O,O' bridge. The resulting chains are involved in weak interchain head-to-tail pi-pi stacking interactions. In the presence of moisture, 1 is readily converted into the hydrated [Cu(3)L(NO(3))(5)](NO(3)).H(2)O form (2). This second phase, monoclinic P2(1)/c, consists of isolated [Cu(3)L(NO(3))(5)](+) and (NO(3))(-) ions which accommodate water molecules in the crystal lattice. These subtle chemical and structural modifications accompanying the moisture-triggered 1-to-2 transformation have been demonstrated through a X-ray powder diffraction study. A thermodiffractometric analysis has evidenced that this solid-to-solid transformation is fully reversible, i.e., thermally induced dehydration of 2 restores 1. The analysis of the temperature dependence of the magnetic susceptibility for 2 has revealed very weak ferromagnetic interactions, consistent with the large Cu...Cu separation (ca. 7.5 Angstroms) in the trinuclear units.

Journal Article↗
PubMed2001

Structure of compounds E(SnMe3)4 (E = Si, Ge) as seen by high-resolution X-ray powder diffraction and solid-state NMR.

The compounds tetrakis(trimethylstannyl)germane, Ge(SnMe3)4 (1), and tetrakis(trimethylstannyl)silane, Si(SnMe3)4 (2), have crystal structures with the quasispherical molecules in a closed-packed stacking. At room temperature both structures have the space group P1 (Z = 2) with a = 9.94457 (5), b = 14.52927 (8), c = 9.16021 (5) A, alpha = 90.53390 (30), beta = 111.73080 (30), gamma = 90.0049 (4) degrees, and V = 1229.414 (12) A3 for (1) and a = 9.92009 (7), b = 14.51029 (11), c = 9.13585 (7) A, alpha = 90.4769 (4), beta = 111.6724 (4), gamma = 89.9877 (6) degrees, and V = 1222.037 (16) A3 for (2). The molecules are found to be ordered as a result of steric interactions between neighboring molecules, as shown by analyzing the distances between the atoms. Upon heating, both compounds undergo a first-order phase transition at temperatures T(c) = 348 +/- 5 K, as characterized by a relative jump of the lattice parameter of approximately 16%. At 353 K, both structures have the space group P1 (Z = 4), with a = 14.2037 (2) A, and V = 2865.52 (7) A3 for (1) and a = 14.1346 (2) A, and V = 2823.90 (7) A3 for (2). Rietveld refinements were performed for the low-temperature phases measured at T = 295 K [R(wp) = 0.0844 for (1), R(wp) = 0.0940 for (2)] and for the high-temperature phases measured at T = 353 K [R(wp) = 0.0891 for (1), R(wp) = 0.0542 for (2)]. The combination of high-resolution X-ray powder diffraction measurements and variable-temperature magic-angle-spinning 13C, 29Si and 119Sn NMR experiments demonstrates low crystallographic and molecular (C1) symmetries for the low-temperature phases of (1) and (2) at temperatures T < 348 +/- 5 K and high crystallographic symmetry due to rotational disorder for the high-temperature phases at temperatures T > 348 +/- 5 K.

Journal Article↗