Conventional X-ray Powder Diffraction Data Research Articles

Synthesis and structural characterization of 3-[1-[4-(2-methylpropyl)phenyl]ethyl]-6-(4-fluorophenyl)-1,2,4-triazolo[3,4-b]-1,3,4-thiadiazole

3-[1-[4-(2-Methylpropyl)phenyl]ethyl]-6-(4-fluorophenyl)-1,2,4-triazolo[3,4-b]-1,3,4-thiadiazole (C21H21FN4S) has been synthesized as a member of a series of triazolothiadiazoles having NSAIDs moieties with cytotoxic activity. The crystal structure of this new compound has been solved and refined using conventional laboratory X-ray powder diffraction data and optimized using density functional techniques. The final structure solution was achieved by Rietveld refinement using soft restraints on all non-H atom bond lengths and angles. This compound crystallizes in $P\bar{1}\;$ space group, with the unit cell parameters a = 5.5880(4) Å, b = 9.3074(7) Å, c = 19.497(4) Å, α = 99.311(10)°, β = 91.925(9)°, γ = 98.199(6)°, and V = 988.8(2) Å3. To complement and verify the structure solution of the compound, the density functional theory (DFT) calculations were performed by using the local density approximation and the generalized gradient approximation for exchange-correlation energy. In order to see the effect of the van der Waals interactions on the electronic structure, the relevant structure was also optimized with B3LYP-D2, PBE-D2, and optB88-vdW functionals. The refined crystal structure was confirmed by the DFT calculations. The best agreement with the experimental structure was achieved by optB88-vdW functional.

Local structure and oxide-ion conduction mechanism in apatite-type lanthanum silicates

The local structure of apatite-type lanthanum silicates of general formula La9.33+x(SiO4)6O2+3x/2 has been investigated by combining the atomic pair distribution function (PDF) method, conventional X-ray and neutron powder diffraction (NPD) data and density functional theory (DFT) calculations. DFT was used to build structure models with stable positions of excess oxide ions within the conduction channel. Two stable interstitial positions were obtained in accordance with literature, the first one located at the very periphery of the conduction channel, neighbouring the SiO4 tetrahedral units, and the second one closer to the channel axis. The corresponding PDFs and average structures were then calculated and tested against experimental PDFs obtained by X-ray total scattering and NPD Rietveld refinements results gathered from literature. It was shown that of the two stable interstitial positions obtained with DFT only the second one located within the channel is consistent with experimental data. This result consolidates one of the two main conduction mechanisms along the c-axis reported in the literature, namely the one involving cooperative movement of O4 and Oi ions.

Kinetics of Formation and Crystal Structure Determination of Sr4Al6O12SO4

The sulphoaluminate of strontium, Sr4Al6O12SO4, was synthesized by solid state reaction from mixture of SrCO3, Al2O3 and SrSO4 (3:3:1 molar ratio) as pellets. The kinetics of formation has been studied in the range of temperature between 850oC and 1100oC using quantitative X-ray powder diffraction data (XRD) analysis. Likewise, at room temperature, the crystal structure was determined from conventional X-ray powder diffraction data using direct methods and it was refined by the Rietveld method. The kinetics mechanisms that showed the best fit, were identified as geometrical contraction at grain boundary (R1.1) and nucleation and growing by energy law (P1.1). The activation energy values obtained were 145.47KJmol-1 (R1.1) and 151.35KJmol-1 (P1.1), respectively. The resulting crystal structure was orthorhombic type (a: 13.32802A, b: 13.34430A and c: 9.38704A). The observed adjustment parameters were RB: 0.0985, Rwp: 0.137, Rp: 0.0925 and Chi2: 1.94.

Structure Re-determination of LASSBio-294 – a cardioactive compound of the N-acylhydrazone class – using X-ray powder diffraction data

Many N-acylhydrazone derivatives synthetized in LASSBio® cannot be prepared as single crystals of sufficient size and/or quality for structure determination to be carried out using single crystal X-ray diffraction techniques. This article highlights the opportunity for determining crystal structures of this class of compounds directly from powder diffraction data. For this task, the crystal structure of LASSBio-294 was re-determined by means of conventional X-ray powder diffraction data and so, compared with the crystal structure already determined for single crystal data. LASSBio-294 is a cardioactive compound of the N-acylhydrazone class, which can become part of the therapeutic interventions designed to decrease exertional fatigue, and, consequently, improve the quality of life of patients suffering from chronic heart failure. Its final crystal structure was refined by means of the Rietveld method (Rietveld, 1967; 1969). This drug crystallizes in a monoclinic (P21/c) space group, with unit cell parameters a = 11.3413(3) Å, b = 12.3573(4) Å, c = 9.0158(3) Å, β = 89.821(2)°, V = 1263.55(7) Å3, Z = 4, Ź = 1 and ρcalc = 1.4419(1) g cm−3. The goodness-of-fit indicator and R-factors were, respectively: χ2 = 1.203, RBragg = 0.696%, Rwp = 5.59%, Rexp = 4.65% and Rp = 4.18%. The molecules in LASSBio-294 are H-bonded along the c-axis involving the atoms N(3)–H(8)···O(4).

The structure of cubic MOF [{Ca(H2O)6}{CaGd(oxydiacetate)3}2].4H2O. A comparison between structural models obtained from Rietveld refinement of conventional and synchrotron X-ray powder diffraction data and standard refinement of single-crystal X-ray diffraction data

The structure of the metal–organic framework (MOF) compound [{Ca(H2O)6}{CaGd(oxydiacetate)3}2]·4H2O was determined by single-crystal X-ray diffraction and refined using conventional single-crystal X-ray diffraction data. In addition, the structure was refined using powder diffraction data collected from two sources, a conventional X-ray diffractometer in Bragg–Brentano geometry and a 12-detector high resolution synchrotron-based diffractometer in transmission geometry. Data from the latter were processed in three different ways to account for crystalline decay or radiation damage. One dataset was obtained by averaging the multiple detector patterns, another dataset was obtained by cutting the non-overlapping portions of each detector to consider only the first few minutes of data collection and a dose-corrected dataset was obtained by fitting the independent peaks in every dataset and extrapolating the intensity and peak position to the initial time of data collection or to zero-absorbed dose. The compared structural models obtained show that special processing of powder diffraction data produced a much accurate model, close to the single-crystal-based model for this particular compound with heavy atoms in high symmetry positions that do not contribute to a significant number of diffraction intensities.

Synthesis, Calorimetric and X ray diffraction studies of the solid Solution [Rb0.92(NH4)0.08]2TeCl4Br2

The structure of [Rb0.92(NH4)0.08]2TeCl4Br2 has been determined from conventional X-ray powder diffraction data, by Rietveld method, in P4/mnc tetragonal space group (a = 7.315 (2) Å, c = 10.354(4) Å, Z = 2). The refinement of the structure led to final factor χ2 = 4.20%. The structure is considered as isolated octahedred TeCl4Br22−. These anions show a 4° rotation around the fourfold axis against the cubic arrangement of the K2PtCl6 type structure. The monovalent cations (Rb+/NH4+) are located between the octahedra ensuring the stability of the structure by ionic and hydrogen bonding contacts: Rb.…Cl/Br and N-H…Cl/Br. At low temperature a second order transition phase was detected at 213K by DSC.

Ab initio structure determination of 3,4-diaminopyridin-1-ium dihydrogen phosphate

The structure of 3,4-diaminopyridin-1-ium dihydrogen phosphate, [C5H3(NH)(NH2)2]+ (H2PO4)−, is solved from conventional X-ray powder diffraction data in direct space (monoclinic unit cell with a = 16.0725(9) Å, b = 7.7301(3) Å, c = 14.6189(9) Å, β = 96.869(1)°, V = 1803.2(2) Å3, Z = 8, and space group I2/c), and optimized by energy minimization in the solid state. In the crystal structure of the title compound, dihydrogenphosphate tetrahedra are linked by strong hydrogen O-H…O bonds forming chains running parallel to the b-axis. Antiparallelly π–π stacked DAP cations form molecular columns in the spaces between the chains. Although the dominant interaction of the molecules with their surroundings is electrostatic, their bonding are further enhanced by N-H…O and C-H…O hydrogen bonds.

Structure Determination of Monohydrated Trifolin (Kaempferol 3-O-β-D-Galactopyranoside) from Laboratory Powder Diffraction Data

The crystal structure of monohydrated trifolin (kaempferol 3-O-β-D-galactopyranoside) (an important biologically active compound, which was isolated from the aerial part of Consolida oliveriana) has been determined from conventional laboratory X-ray powder diffraction data. Variable counting time technique was used during measurement and crystal structure was solved by means of Monte Carlo algorithm. The final structure was achieved by Rietveld refinement using both constraints and restraints on interatomic bond lengths and angles.

Ab initiostructure determination of bethanechol chloride

The structure of bethanechol chloride C7H17ClN2O2is solved from conventional X-ray powder diffraction data in direct space [monoclinic unit cell witha=8.8749(3) Å,b=16.4118(7) Å,c=7.1373(3) Å,β=93.803(1)°,V=1037.29(7) Å3,Z=4, and space groupP21/n]. The existence of a second orthorhombic closely related form is discussed.

The Application of the Fundamental Parameters Approach as Implemented in TOPAS to Divergent Beam Powder Diffraction Data

The fundamental parameters approach (FPA) as implemented in TOPAS is investigated for analyses of conventional X-ray powder diffraction (XRPD) data. The FPA involves the convolution of a series of models, each one constituting an individual contribution to the geometric portion of the instrument profile function (IPF). Parameters within each model are refined by least squares to yield a presumably accurate description of the experiment. If one wishes to interrogate the functionality of said models, a diffractometer wherein the uncertainties in optical character are minimized is required. To this end, a diffractometer was built at NIST which featured conventional divergent beam optics in conjunction with a well aligned, stiff, and accurate goniometer assembly. Initial results indicated that the detector arm was flexing; this problem has been addressed with the fabrication and installation of a new arm and counterweight assembly. Data collected from NIST Standard Reference Material (SRM) 660a, lanthanum hexaboride, are analyzed using the FPA method to yield conclusions on the validity of the models with respect to shape and position of the diffraction profiles.

Synthesis and crystal structure of PdSnTe

Abstract The compound with composition PdSnTe was prepared by heating of stoichiometric amount of Pd, Sn and Te in silica glass tube at 400 °C. Its crystal structure was refined by Rietveld method using conventional X-ray powder diffraction data. PdSnTe shows orthorhombic symmetry, space group Pbca with unit cell parameters a = 6.5687(2), b = 6.6028(2), c = 12.8849(4) A, V = 558.8(1) A3 and Z = 8. The title compound can be viewed as a ternary-ordered variant of α-NiAs2-type structure, it is isostructural with PtSiTe. Temperature dependence of electrical conductivity and Hall coefficient are presented, it suggests semimetallic or strongly degenerated semiconductor behaviour of the prepared compound.

Crystal structure determination of CoGeTe from powder diffraction data

The crystal structure of cobalt germanium telluride CoGeTe has been determined by direct methods using integrate intensities of conventional X-ray powder diffraction data and subsequently refined with the Rietveld method. The title compound was prepared by heating of stoichiometric amount of Co, Ge and Te in silica glass tube at 670 °C. CoGeTe adopts orthorhombic symmetry, space group Pbca with unit cell parameters a = 6.1892(4) Å, b = 6.2285(4) Å, c = 11.1240(6) Å, V = 428.8(1) Å 3 and Z = 8. Its crystal structure is formed by [CoGe 3Te 3] octahedra sharing both edges and corners. CoGeTe represents a ternary ordered variant of α-NiAs 2 type structure. An important feature present in CoGeTe is an occurrence of short Co–Co distance across the shared edge of [CoGe 3Te 3] octahedra. Differential thermal analysis (DTA) has revealed that CoGeTe melts incongruently at about 725 °C; CoGeTe decomposes into GeTe, CoGe and CoTe 2. Temperature dependence of the electrical conductivity and value of Seebeck coefficient at 300 K are also reported.

Molecular versus crystal symmetry in tri-substituted triazine, benzene and isocyanurate derivatives

The crystal structures of triethyl-1,3,5-triazine-2,4,6-tricarboxylate (I), triethyl-1,3,5-benzenetricarboxylate (II) and tris-2-hydroxyethyl isocyanurate (III) have been determined from conventional laboratory X-ray powder diffraction data using the differential evolution structure solution technique. The determination of these structures presented an unexpectedly wide variation in levels of difficulty, with only the determination of (III) being without complication. In the case of (I) structure solution resulted in a Rietveld refinement profile that was not ideal, but was subsequently rationalized by single-crystal diffraction as resulting from disorder. Refinement of structure (II) showed significant variation in side-chain conformation from the initial powder structure solution. Further investigation showed that the structure solution optimization had indeed been successful, and that preferred orientation had a dramatic effect on the structure-solution R-factor search surface. Despite the presence of identical side chains in (I) and (II), only the triazine-based system retains threefold molecular symmetry in the crystal structure. The lack of use of the heterocyclic N atom as a hydrogen-bond acceptor in this structure results in the formation of a similar non-centrosymmetric network to the benzene-based structure, but with overall three-dimensional centrosymmetry. The hydrogen-bonded layer structure of (III) is similar to that of other isocyanurate-based structures of this type.

Structural investigation of the nickel 3-methylglutarate from powder diffraction demonstrating adaptability of the inorganic skeleton of MIL-77

Ni20[(C6H8O4)20(H2O)8]∙33H2O, a new nickel(II) 3-methylglutarate, was prepared hydrothermally (180 °C, 48 h, autogenous pressure) from a 1:1.5:2:180 mixture of nickel (II) sulphate hexahydrate, 3-methylglutaric acid, sodium hydroxide, and water. It crystallizes in the cubic system (space group P4332, Z=1) with a=16.8488(5) Å and V=4783.1(4) Å3. Its structure was solved from conventional X-ray powder diffraction data. It presents a three-dimensional network of edge-sharing nickel octahedra, lined by deprotonated organic anions. This remarkable oxide network with corrugated 20-membered rings is constructed from homochiral helices. The rings intersect each other to generate large crossing channels full of water along [111].

Crystal structure of hexagonal SrAl 2O 4 at 1073 K

The crystal structure of SrAl 2O 4 at 1073 K was determined from conventional X-ray powder diffraction data using direct methods, and it was further refined by the Rietveld method. The structure was hexagonal (space group P6 3, Z = 6 ) with a=0.89260(3) nm, c=0.84985(2) nm and V=0.58639(3) nm 3. Final reliability indices were R wp=7.87%, R p=5.87% and R B =4.19%. The [AlO 4] tetrahedra are linked to form trigonally distorted rings and they are joined in layers. These layers are stacked with a two-layer repeat and connected by the tetrahedral apices. All of the Sr atoms occupy the centers of the rings when viewed along the c-axis. The structure is described as a stuffed derivative of tridymite.

Crystal structure, phase transition and anisotropic thermal expansion of barium zirconium diorthophosphate, BaZr(PO 4) 2

The crystal structure of BaZr(PO 4) 2 at 298 K was determined from conventional X-ray powder diffraction data using direct methods, and it was further refined by the Rietveld method. The structure was monoclinic (space group C2/ m, Z = 2 ) with a = 0.85629 ( 3 ) nm , b = 0.53082 ( 2 ) nm , c = 0.78956 ( 2 ) nm , β = 93.086 ( 1 ) ° and V = 0.35836 ( 2 ) nm 3 . Final reliability indices were R wp = 8.21 % , R p = 5.64 % and R B = 2.92 % . The atom arrangement is similar to that of yavapaiite (KFe(SO 4) 2), however, these crystal structures differ distinctly in the coordination numbers of barium and potassium atoms; the former is tenfold coordinated, whereas the latter is sixfold coordinated. The powder specimens were also examined by high-temperature XRD and DTA to reveal the occurrence of a phase transition from monoclinic to orthorhombic at 732 K during heating. Upon cooling the reverse transition occurred at 710 K. The monoclinic crystal expanded almost one-dimensionally along [503] during the heating process. The orthorhombic phase also showed a tendency to expand one-dimensionally along the c-axis above 732 K.

Single Crystal and Powder Diffraction Characterization of Three Polymorphic Forms of Acitretin

Acitretin [all-trans-9-(4-methoxy-2,3,6-trimethylphenyl)-3,7-dimethyl-2,4,6,8-nonatetraenoic acid or 3-methoxy-2-methyl-17-nor-1,2,3,4-tetradehydroretinoic acid], a widely marketed oral synthetic retinoid, introduced for clinical use as effective therapy against psoriasis, was found to crystallize in three polymorphic modifications (hereafter, I, II, and III), the crystal structures of which have been determined by single-crystal diffractometry (form I) or X-ray powder diffraction methods (form II and III) from conventional laboratory data only. In these latter cases, real space techniques (simulated annealing and whole-profile pattern matching) have been employed. Polymorph I crystallizes in space group P21, Z=8, with unit cell parameters a=7.894(1), b=58.454(6), c=8.161(1) Å, β=102.04(1)°, and V=3682.9(8) Å3. Polymorph II crystallizes in space group P21/n, Z=4, with unit cell parameters a=13.999(2), b=10.714(1), c=12.465(2) Å, β=98.76(5)°, and V=1847.9(3) Å3. Polymorph III crystallizes in space group P21/c, Z=4, with unit cell parameters a=3.0751(4), b=4.0487(4), c=14.956(2) Å, β=100.41(7)°, and V=1831.3(4) Å3. Polymorph I, found to be identical with that deposited in the European Pharmacopeia, shows four crystallographically independent Acitretin molecules, arranged in pairs through conventional hydrogen-bonded carboxylic dimers; also in form II, carboxylic dimers are observed, located on crystallographic inversion centres, while in form III, a catameric arrangement of the carboxylic residues, winding up about the rather short monoclinic axis, generates one-dimensional chains of hydrogen-bonded Acitretin molecules. Thermal analysis showed that form I can be quantitatively transformed into form II by moderate heating near 200°C, under vacuum. These results show that ab initio structural studies from conventional laboratory X-ray powder diffraction (XRPD) data are fully providing the opportunity to investigate the structural aspects of moderately complex substances also in the absence of single crystals, disclosing the crystal chemistry of a few polymorphs of pharmaceutically relevant species. © 2005 Wiley-Liss, Inc. and the American Pharmacists Association

Crystal structure and phase transitions of strontium zirconium diorthophosphate, SrZr(PO4)2

The crystal structure of SrZr(PO4)2 at 298K was determined from conventional X-ray powder diffraction data using direct methods, and it was further refined by the Rietveld method. The structure was triclinic (space group P1̄, Z=2) with a=0.77508(4)nm, b=0.78887(5)nm, c=0.51251(3)nm, α=95.754(3)°, β=90.228(2)°, γ=92.474(2)°, and V=0.31149(3)nm3. Final reliability indices were Rwp=8.51%, Rp=6.07%, and RB=2.46%. The powder specimens were also examined by high-temperature XRD and differential thermal analysis to reveal the occurrence of phase transitions from triclinic to monoclinic at 405K, then to hexagonal (or trigonal) at 1196K during heating. Upon cooling, the reverse change of the latter transition occurred at 1175K. The subsequent monoclinic-to-triclinic transition was martensitic and incomplete during further cooling to 298K. The monoclinic phase is most probably isostructural with yavapaiite. The present paper has described, for the first time, the higher- and lower-temperature polymorphs of the yavapaiite-type structure.

Crystal structure of new Li + ion conducting perovskites: Li 2 xCa 0.5− xTaO 3 and Li 0.2[Ca 1− ySr y] 0.4TaO 3

Two new solid solutions—Li 2 x Ca 0.5− x TaO 3 (0.05⩽ x⩽0.25) and Li 0.2[Ca 1− y Sr y ] 0.4TaO 3 (0< y⩽0.15)—based on the A defective ABO 3 perovskite structural type, are synthesized. The crystal structures of these Li + ion conducting compounds are solved from synchrotron radiation and conventional X-ray powder diffraction data. The unit cells exhibit a classical orthorhombic distortion of the cubic perovskite model (space group Pnma No. 62) with parameters close to 2 a p , 2 a p, 2 a p ( a p, primitive cubic cell parameter). The distortion of the cubic aristotype arises from the three tilts system a + b − b − of the TaO 6 octahedra. For the same lithium content ( x=0.10), the Sr 2+ substitution to Ca 2+ is found to enhance the electrical conductivity by quasi-one order of magnitude (at 200 °C, bulk dc conductivity values are close to 2.3×10 −6 and 1.1×10 −5 S cm −1 for Li 0.2Ca 0.4TaO 3 and Li 0.2[Ca 0.9Sr 0.1] 0.4TaO 3, respectively).

Ab initio structure determination of new compound Ba3(BO3)(PO4)

The crystal structure of new compound Ba3BPO7 was determined by ab initio method from high-resolution conventional X-ray powder diffraction data. The Rietveld refinement converged to Rp=5.92%, Rwp=8.87%, Rexp=5.00% with the following details: Hexagonal, space group P63mc, a=5.4898 (1)Å, c=14.7551(1)Å, Z=2. The basic unit of the structure is the [BaO10]–[BO3]–[PO4] polar polyhedra-chain composed of Ba1–B–P–O cluster. These chains, running along c-axis, stack in a HCP mode to build the whole structure with triangular prism channels. The channels are parallel to c-axis too, in which Ba2 and Ba3 are located.