Laboratory Powder Diffraction Data Research Articles

Structural characterization of anhydrous and bishydrated calcium hexafluorosilicate by powder diffraction methods

The synthesis and X-ray powder diffraction data for the long-known CaSiF6 and CaSiF6·2H2O species are reported. Their crystal structures have been determined from laboratory powder diffraction data by simulated annealing and full-profile Rietveld refinement methods. CaSiF6·2H2O was found to crystallize in the monoclinic P21/n space group with unit-cell parameters: a = 10.48107(9), b = 9.18272(7), c = 5.72973(5) Å, β = 98.9560(6)°, V = 544.733(8) Å3, and Z = 4. The crystal structure of CaSiF6·2H2O, eventually found to be isomorphous with SrSiF6·2H2O (but not with the Mg analogue—a hexahydrate phase), contains centrosymmetric [Ca(μ-H2O)2Ca]4+ dimers, interconnected by hexafluorosilicate anions, in a dense 3D framework. The crystal structure is completed by a further water molecule, terminally bound to the Ca2+ ion, which, consequently, attains a F5O3 octacoordination. Thermodiffractometric measurements allowed the determination of the linear and volumetric thermal expansion coefficients of CaSiF6·2H2O, which showed a minor contraction, along a, on heating. CaSiF6 is trigonal, space group R-3, a = 5.3497(3), c = 13.5831(11) Å, V = 336.66(5) Å3, and Z = 3, and isomorphous with several other species of MIIAIVF6 or MIAVF6 formulation, among which several silicates, germanates, and stannates.

Powder diffraction and solid state DFT study of thetrans-bis(5-methylsalicylato)-bis(N,N-diethylnicotinamide)-diaquacopper(II) complex structure

The title compound, [Cu(5-Mesal) 2 (denia) 2 (H 2 O) 2 ] (5-Mesal = 5-methylsalicylato, denia = N , N -diethylnicotinamide) crystallizes in the triclinic unit cell. Crystal structure was solved from the laboratory powder diffraction data. Each copper(II) atom is situated on an inversion centre and is coordinated by two O atoms from two 5-Mesal ligands [Cu—O 2.00(3) Å], two N atoms from two denia ligands [Cu—N 2.05(2) Å], and two water molecules [Cu—Ow 2.80(3) Å] in a highly distorted octahedral geometry. In the crystal structure, intermolecular O—H … O hydrogen bonds link the molecules into chains extended in direction [1 –1 0]. The optimization in solid state with DFT/plane-waves approach revealed the large value of Cu—Ow bond length [2.793 Å].

SANJUANITE: AB INITIO CRYSTAL-STRUCTURE SOLUTION FROM LABORATORY POWDER-DIFFRACTION DATA, COMPLEMENTED BY FTIR SPECTROSCOPY AND DT-TG ANALYSES

Sanjuanite, Al 2 (PO 4 )(SO 4 )(OH)·9H 2 O, is a microcrystalline fibrous mineral found in Pennsylvanian slates belonging to the Los Jejenes Formation at the Pocito Department, San Juan Province, Argentina. Sanjuanite is monoclinic, space group P 2 1 / n , with unit-cell dimensions a 13.9163(5), b 17.2422(5), c 6.1125(3) A, β 98.255(4)°, V 1450.7(5) A 3 and Z = 4. Its crystal structure has been solved and refined from laboratory powder-diffraction data (Bragg–Brentano geometry, Cu K α 1,2 radiation, scintillation detector). Integrated intensities extending to a resolution of 1.15 A were introduced in XLENS and processed with the S–FFT algorithm. Except for one O atom, the other atoms appeared in the Fourier map of the best direct-methods solution. Subsequent restrained Rietveld refinement converged to a χ 2 value of 2.47. The structure of sanjuanite is composed of infinite aluminophosphate chains running parallel to c and located at (x, y) = (0,0) and (½,½). Isolated (SO 4 ) 2− groups and H 2 O molecules connect the groups of chains. Hydrogen bonding plays a key role in the stabilization of the structure. The group formed by pairs of double chains of alternating (PO 4 ) and (AlO 6 ) present in sanjuanite bears no close resemblance to any known mineral structure. The FTIR spectrum and DTA–TGA curves of sanjuanite are provided. Chemically related species include kribergite and hotsonite, whose structures remain unknown. The formation of sanjuanite is probably related to the oxidation of sulfides (mostly pyrite and marcasite) under arid conditions, which produces sulfuric acid that releases Al from silicates in pelitic rocks. The source of P remains unknown.

Crystal Structure Determination from Laboratory X-ray Powder Diffraction Data

Structure determination from laboratory powder diffraction data can be considered routine today as emphasized by the significant increase in the number of published structures, both organic and/or inorganic compounds solved in this way. In the past about 10 years, many significant developments in instrumentation, such as computer technology and powder diffraction methodology, allow determination of crystal structures, the size and complexity of which are only limited by data quality and computing power. New detector technologies (mostly strip detectors), faster PCs and powerful methods of structure solution (especially the direct space and the charge flipping methods) contributed most to an ever increasing success rate. Also monochromater for incident beam (like CuKα1 or MoKα1) is not always required for structure determination.

Crystal structure of the mineral strontiodresserite from laboratory powder diffraction data

The crystal structure of the mineral strontiodresserite, (Sr,Ca)Al2(CO3)2(OH)4⋅H2O, from the Francon Quarry, Montreal, Quebec, Canada, has been solved from laboratory powder diffraction data using a combination of charge-flipping and simulated annealing methods. The structure is orthorhombic in space group Pnma with a=16.0990(7), b=5.6133(3), and c=9.1804(4) Å (Z=4) and the framework of the mineral is isostructural with that of dundasite. The strontium has a coordination number of 9 and the carbonate anions form a bridge between the SrO9 polyhedra and AlO6 octahedra. The water molecule lies in a channel that runs parallel to the b axis. An ordered network of hydrogen atoms could be uniquely determined from crystal-chemical principles in the channels of strontiodresserite. Ab initio density functional theory (DFT) energy minimization of the whole structure gave results in full agreement with X-ray refinement results for nonhydrogen atoms. The stability of this model (as well as that of the corresponding model of dundasite) in the proposed Pnma space group was tested by DFT optimization in space group P1 of random small distortions of this structure. This test confirms that both minerals are isostructural, including their hydrogen-bond networks.

Crystal structure solution of the mineral sanjuanite from laboratory powder diffraction data

Crystal structure solution of the mineral sanjuanite from laboratory powder diffraction data

Ezetimibe anhydrate, determined from laboratory powder diffraction data

Ezetimibe {systematic name: (3R,4S)-1-(4-fluorophenyl)-3-[(3S)-3-(4-fluorophenyl)-3-hydroxypropyl]-4-(4-hydroxyphenyl)azetidin-2-one}, C(24)H(21)F(2)NO(3), is used to lower cholesterol levels by inhibiting cholesterol resorption in the human intestine. The crystal structure of ezetimibe anhydrate was solved from laboratory powder diffraction data by means of real-space methods using the program DASH [David et al. (2006). J. Appl. Cryst. 39, 910-915]. Subsequent Rietveld refinement with TOPAS Academic [Coelho (2007). TOPAS Academic User Manual. Version 4.1. Coelho Software, Brisbane, Australia] led to a final R(wp) value of 8.19% at 1.75 A resolution. The compound crystallizes in the space group P2(1)2(1)2(1) with one molecule in the asymmetric unit. The molecules are closely packed and two intermolecular hydrogen bonds form an extended hydrogen-bond architecture.

Molecular Motion by Refinement of TLS Matrices from High Resolution Laboratory Powder Diffraction Data: Implementation in the Program TOPAS and Application to Crystalline Naphthalene

Molecular motion by refinement of TLS matrices from high resolution laboratory powder diffraction data: implementation in the program TOPAS and application to crystalline naphthalene

Structural and thermal characterization of zolpidem hemitartrate hemihydrate (form E) and its decomposition products by laboratory x-ray powder diffraction

The crystal structure of zolpidem hemitartrate hemihydrate (I, Form E) has been solved from high-resolution laboratory powder diffraction data. It crystallizes in the orthorhombic P212121 space group with a = 22.4664(6) Å, b = 26.0420(7) Å, and c = 7.4391(1) Å. Protonation of zolpidem molecules could not be unambiguously determined. Thermal stability of Form E has been investigated by TG–DTA and in situ by temperature resolved X-ray powder diffraction. Water loss occurs between 50°C ≤ t ≤ 100°C while structure decomposition commences at approximately 120°C yielding zolpidem tartrate (II) and pure zolpidem base (III) in approximately equimolar amounts. Crystal structures of II and III have been solved simultaneously from a single powder pattern of thermally decomposed I. Zolpidem tartrate crystallizes in the orthorhombic P212121 space group with a = 19.9278(8) Å, b = 15.1345(8) Å, and c = 7.6246(2) Å (at 140°C). Zolpidem base crystallizes in the orthorhombic Pcab space group with a = 9.9296(4) Å, b = 18.4412(9) Å, and c = 18.6807(9) Å (at 140°C). In the reported crystal structures zolpidem molecules form stacks through π–π interaction or dipole–dipole interactions while tartrate moieties, if present, form hydrogen bonded chains. Water molecule in I forms a hydrogen bond to the imidazole nitrogen atom of the zolpidem molecule. Free space in the crystal structure of I could allow for the additional water molecules and thus a variable water content. © 2009 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 99:871–878, 2010

K3TaF8from laboratory X-ray powder data

The crystal structure of tripotassium octa­fluorido­tantalate, K3TaF8, determined from laboratory powder diffraction data by the simulated annealing method and refined by total energy minimization in the solid state, is built from discrete potassium cations, fluoride anions and monocapped trigonal–prismatic [TaF7]2− ions. All six atoms in the asymmetric unit are in special positions of the P63mc space group: the Ta and one F atom in the 2b (3m) sites, the K and two F atoms in the 6c (m) sites, and one F atom in the 2a (3m) site. The structure consists of face-sharing K6 octa­hedra with a fluoride anion at the center of each octa­hedron, forming chains of composition [FK3]2+ running along [001] with isolated [TaF7]2− trigonal prisms in between. The structure of the title compound is different from the reported structure of Na3TaF8 and represents a new structure type.

Crystal structure determination of N,N′-1,4-phenylene-bis(3-oxobutanamide) from laboratory powder diffraction data

Abstract The compound N,N′-1,4-phenylene-bis(3-oxobutanamide) is an industrial intermediate used in the synthesis of azo pigments. Crystallisation experiments only led to the dihydrate form; drying the dihydrate at 120 °C leads to an anhydrous form, but suitable single crystals of the anhydrous form could not be grown. Therefore, its crystal structure was determined from laboratory powder diffraction data. The structure was solved by real-space methods using the program DASH and refined by the Rietveld method using the program TOPAS. The anhydrous form crystallises in P21/c, Z = 2 with lattice parameters a = 16.9749(5) Å, b = 4.8648(1) Å, c = 8.5372(2) Å, β = 93.396(2)°. The crystal structure of the dihydrate was determined by single-crystal structure analysis. The dihydrate crystallises in P – 1, Z = 1 with a = 5.0116(1) Å, b = 5.2199(2) Å, c = 14.7803(5) Å, α = 88.396(1)°, β = 80.250(1)°, γ = 81.439(1)°. In both crystal structures the molecule, which has a centre of symmetry, is situated on an inversion centre. For the anhydrous form dispersion-corrected DFT calculations were used to confirm the structure.

Structures from Powders: Polynuclear Hg(II) Complexes Containing the Flexible Bisimidazolylmethane Ligand

Several polynuclear Hg(II) complexes containing the flexible ditopic bisimidazolylmethane ligand (C(7)H(8)N(4), bim) have been prepared by reaction of equimolar quantities of mercury salts (acetate, cyanide, thiocyanate, chloride, and iodide) in EtOH or acetonitrile solution. Their crystal and molecular structures were retrieved from laboratory powder diffraction data, and their thermal properties were fully characterized, including the determination of the thermal expansion coefficients and the related strain tensor using thermodiffractometric methods. [Hg(bim)(CH(3)COO)(2)](2) consists of cyclic dimers with chelating acetates, while the [Hg(bim)X(2)](n) species (X = Cl, CN, SCN, and I) are one-dimensional polymers, with dangling X groups. A further complex of nominal Hg(2)(bim)Cl(2) formulation was also prepared, but the complexity and nonideality of its powder diffraction traces prevented the determination of its main structural features.

Structures of six industrial benzimidazolone pigments from laboratory powder diffraction data

The crystal structures of six industrially produced benzimidazolone pigments [Pigment Orange 36 (beta phase), Pigment Orange 62, Pigment Yellow 151, Pigment Yellow 154 (alpha phase), Pigment Yellow 181 (beta phase) and Pigment Yellow 194] were determined from laboratory X-ray powder diffraction data by means of real-space methods using the programs DASH and MRIA, respectively. Subsequent Rietveld refinements were carried out with TOPAS. The crystal phases correspond to those produced industrially. Additionally, the crystal structures of the non-commercial compound 'BIRZIL' (a chloro derivative of Pigment Yellow 194) and of a dimethylsulfoxide solvate of Pigment Yellow 154 were determined by single-crystal structure analyses. All eight crystal structures are different; the six industrial pigments even exhibit five different hydrogen-bond topologies. Apparently, the good application properties of the benzimidazolone pigments are not the result of one specific hydrogen-bonding pattern, but are the result of a combination of efficient molecular packing and strong intermolecular hydrogen bonds.

The Crystal Structure of [Mg2(H2O)6(HCO3)3]+Cl–, Containing a Magnesium-based Hetero-polycation

The crystal structure of di-magnesium hexahydrate trihydrogencarbonate chloride, [Mg2(H2O)6- (HCO3)3]+Cl−, has been determined from high-resolution laboratory powder diffraction data (lattice parameters at r. t.: a = 8.22215(2), c = 39.5044(2) Å, V = 2312.85(2) Å3, space group R3̄̄c, Z = 6). The crystal structure of [Mg2(H2O)6(HCO3)3]+Cl− is built up of alternating sheets of Cl− anions and complex [Mg2(H2O)6(HCO3)3]+ cations consisting of two Mg(OH2)3O3 octahedra interconnected by three disordered hydrogen carbonate groups. The packing can be described as a cubic close packing of [Mg2(H2O)6(HCO3)3]+ cations with the Cl− anions filling all octahedral voids. In the temperature range from r. t. up to decomposition, which takes place in the range 398 K < T < 413 K, no structural phase transition occurs.

Structures of mono-unsaturated triacylglycerols. V. The β′1-2, β′-3 and β2-3 polymorphs of 1,3-dilauroyl-2-oleoylglycerol (LaOLa) from synchrotron and laboratory powder diffraction data

The crystal structures of the beta'(1)-2, the beta'-3 and the beta(2)-3 polymorphs of 1,3-dilauroyl-2-oleoylglycerol have been solved from powder diffraction data. The packing of the beta(2)-3 polymorph is similar to that of other cis mono-unsaturated triacylglycerols. Both the beta' polymorphs are crystallized in a novel type of packing in which one of the saturated lauroyl chains is packed side-by-side with part of the unsaturated oleoyl chain.

Structures from powders: Diflorasone diacetate

Diflorasone diacetate, a steroid anti-inflammatory drug (marketed as Diacort ® or Florone ® by Pfizer) and used in the treatment of skin disorders, can be prepared as anhydrous form, DD1 (as deposited in the US pharmacopoeia), or as a monohydrated phase, DDW. Heating the DDW form above 90 °C, a mixture of DD1 and of a new anhydrous polymorph, DD2 is obtained. Further heating of this mixture, or of pure DD1, up to 230 °C (only a few degrees before melting!), generates an elusive anhydrous DD3 polymorph. Their crystal structures, determined uniquely from laboratory powder diffraction data, show the isomorphous character of the DDW and DD1 forms, while the DD2 and DD3 polymorphs crystallize with markedly different unit cells. Crystals of the DD1, DD2 and DDW forms are orthorhombic, P2 12 12 1, a = 29.386(1) Å; b = 10.4310(9) Å, c = 8.1422(7) Å, V = 2495.8(3) Å 3 for DD1; a = 15.2639(10) Å; b = 11.7506(7) Å, c = 13.8931(11) Å, V = 2491.9(3) Å 3 for DD2; a = 30.311(2) Å; b = 10.6150(9) Å, c = 7.9337(7) Å, V = 2552.7(4) Å 3 for DDW; while the lattice parameters for the monoclinic P2 1 DD3 species are a = 11.5276(10) Å; b = 13.8135(11) Å, c = 7.8973(7) Å, β = 103.053(6)°, V = 1225.0(2) Å 3. These compounds have also been fully characterized by thermo analytical methods, as well by 13C, 19F, and 1H NMR spectroscopy.

Combined powder diffraction and solid-state DFT study of [Cu (2,6-dimethoxynicotinate)2(μ-ronicol)2] n complex

Abstract Crystal structure of the title compound was solved from the laboratory powder diffraction data in the P21/c space group. Because Rietveld refinement yielded inaccurate geometry of the structural moieties the structure was finally refined by means of geometry optimization using DFT/plane waves approach in the solid state. The asymmetric unit of [Cu{2,6-(MeO)2nic}2(μ-ron)2] n consists of the copper(II) atom located on an inversion centre, one 2,6-dimethoxynicotinate anion and one ronicol molecule which acts as a bridging ligand coordinated via oxygen atom of the hydroxymethyl group as well as the nitrogen atom of the pyridine ring – μ-ron = bridging 3-pyridylmethanol. Each copper (II) complex unit is connected to the other four units through the ronicol ligands forming 2D sheets running parallel to the bc plane. The structure is stabilized by a strong intramolecular hydrogen bond O—H…O and supported by weak C—H…O hydrogen bonds.

A comparative study of crystal structure of a Cu(II) dicyanamide compound determined independently from X-ray powder- and single-crystal analyses

Abstract The dicyanamido diethelenetriamine copper (II) compound, C8H13CuN9 (I), has been synthesized, and structurally characterized independently using X-ray powder- and single-crystal diffraction data. The direct methods program package EXPO-2004 has been used for structure solution from laboratory powder diffraction data. Intermolecular N—H···N hydrogen bonds in (I) generate R2 2(16) rings, which are fused forming molecular columns propagating along the [100] direction. Further linking of parallel columns through N—H···N hydrogen bonds results into a three-dimensional supramolecular network.

The crystal structure of Pigment Yellow 181 from laboratory powder diffraction data

The crystal structure of the β polymorph of Pigment Yellow 181 was solved from laboratory X-ray powder diffraction data and Rietveld refined. In the crystal structure, the molecules are essentially planar, with extensive hydrogen bonding between the molecules.

Structure determination of Mg3(OH)5Cl·4H2O (F5 phase) from laboratory powder diffraction data and its impact on the analysis of problematic magnesia floors

The crystal structure with the idealized formula Mg(3)(OH)(5)Cl.4H(2)O, the so-called F5 phase according to 5Mg(OH)(2).MgCl(2).8H(2)O in the system MgCl(2)-MgO-H(2)O, has been solved ab initio from high-quality laboratory powder diffraction data at room temperature. The F5 phase is structurally related to 3Mg(OH)(2).MgCl(2).8H(2)O (F3 form). The F5 phase consists of infinite triple chains with one Mg(OH)(6) and two Mg(OH)(4)(OH(2))(2) octahedra as building units intercalated by chlorides, which are partly substituted by disordered hydroxides in the real structure. The F5 phase is of technological importance as the most important binder phase in Sorel cements. Knowledge of the crystal structure enables the full quantitative phase analysis of magnesia cements for the first time, which turns out to be very helpful in the search for possible causes of broken or bleached magnesia floors. Two real-life examples are given.