Laboratory Powder Diffraction Data Research Articles

Hydrogen bonding patterns and C-H...π interactions in the structure of the antiparkinsonian drug (R)-rasagiline mesylate determined using laboratory and synchrotron X-ray powder diffraction data.

The structure of (R)-rasagiline mesylate [(R)-RasH+·Mes-], an active pharmaceutical ingredient used to treat Parkinson's disease, is presented. The structure was determined from laboratory and synchrotron powder diffraction data, refined using the Rietveld method, and validated and optimized using dispersion-corrected DFT calculations. The unit-cell parameters obtained in both experiments are in good agreement and the refinement with both datasets converged to good agreement factors. The final parameters obtained from laboratory data were a = 5.4905 (8), b = 6.536 (2), c = 38.953 (3) Å, V = 1398.0 (4) Å3 and from synchrotron powder data were a = 5.487530 (10) Å, b = 6.528939 (12) Å, c = 38.94313 (9) Å, V = 1395.245 (5) Å3 with Z = 4 and space group P212121. Preferred orientation was properly accounted for using the synchrotron radiation data, leading to a March-Dollase parameter of 1.140 (1) instead of the 0.642 (1) value obtained from laboratory data. In the structure, (R)-RasH+ moieties form layers parallel to the ab plane connected by mesylate ions through N-H...O and C-H...O hydrogen bonds. These layers stack along the c axis and are further connected by C-H...π interactions. Hirshfeld surface analysis and fingerprint plot calculations indicate that the main interactions are: H...H (50.9%), H...C/C...H (27.1%) and H...O/O...H (21.1%).

A new polymorphic form of Na2SeO3·5H2O: structure determination from X-ray laboratory powder diffraction

A new polymorphic form of sodium selenite pentahydrate is reported in this contribution. We determined its crystal structure from laboratory powder diffraction data recorded at room temperature. It crystallizes in the monoclinic system P21/n with Z = 4. The lattice parameters are a = 15.01473(16) Å, b = 7.03125(7) Å, c = 8.13336(10) Å, β = 98.4458(10)°, and V = 849.345(16) Å3. The crystal structure exhibits a layered structure with isolated 1D chains running along the b-axis.

Crystal structure of 5-(3-methoxyphenyl)indoline-2,3-dione

The crystal structure of 5-(3-methoxyphenyl)indoline-2,3-dione (C15H11NO3) was solved and refined using laboratory powder diffraction data and optimized using density functional techniques. The title compound crystallizes in space group Pbca with a = 11.1772(3) Å, b = 7.92536(13) Å, c = 27.0121(7) Å, and V = 2392.82(10) Å3. The asymmetric unit contains one molecule. Isatin molecules are joined into almost flat chains along the a direction by N–H⋯O bonds. The chains are linked into layers by π-stacking interactions. Finally, the third dimension of the crystal is formed by weaker C–H⋯π and C–H⋯O contacts.

Structural Insights into Layered Tetrahalocuprates(II) Based on Small Unsaturated and Cyclic Primary Ammonium Cations.

Layered hybrid halometallates represent a promising class of multifunctional materials, yet with many open challenges regarding the interaction between building blocks. In this work, we present a synthetic and analytical methodology for the efficient synthesis and structural analysis of a series of novel tetrahalocuprate(II) hybrids based on small alkylammonium cations. Observed robustness in geometrical motifs provided a platform for crystal structure determination, even from the complex laboratory powder diffraction data. The slight differences in inorganic layer geometry and severe differences in organic bilayer packing are quantified using well-established descriptors for these materials, and dependences of geometric parameters on anion and cation choice are accounted for. Temperature dependence of structural parameters for one of the tetrachlorocuprate hybrids that was chosen as a model unveils a possible geometrical origin of thermochromism in these materials.

Crystal structure of donepezil hydrochloride form III, C24H29NO3⋅HCl

The crystal structure of donepezil hydrochloride, form III, has been solved with FOX using laboratory powder diffraction data previously submitted to and published in the Powder Diffraction File. Rietveld refinement with GSAS yielded monoclinic lattice parameters of a = 14.3662(9) Å, b = 11.8384(6) Å, c = 13.5572(7) Å, and β = 107.7560(26)° (C24H30ClNO3, Z = 4, space group P21/c). The Rietveld-refined structure was compared to a density functional theory (DFT)-optimized structure, and the structures exhibit excellent agreement. Layers of donepezil molecules parallel to the (101) planes are maintained by columns of chloride anions along the b-axis, where each chloride anion hydrogen bonds to three donepezil molecules each.

Crystal structure of 3-[(3,4-dinitro-1H-pyrazol-1-yl)-NNO-azoxy]-4-nitro-1,2,5-oxadiazole

The crystal structure of a novel high-energy density material 3-[(3,4-dinitro-1H-pyrazol-1-yl)-NNO-azoxy]-4-nitro-1,2,5-oxadiazole C5HN9O8 was determined and refined using laboratory powder diffraction data. The diffraction data and database analysis were insufficient to distinguish two candidate structures from the solution step. Density functional theory with periodic boundary conditions optimizations were used to choose the correct one. 3-[(3,4-Dinitro1H-pyrazol-1-yl)-NNO-azoxy]-4-nitro-1,2,5-oxadiazole crystallizes in space group Pbca with a = 8.3104(2) Å, b = 14.2198(5) Å, c = 19.4264(7) Å, V = 2295.66(14) Å3. The molecular conformation contains a weak intramolecular hydrogen bond C–H⋯O–N, and the structure is dominated by weak O⋯π and O⋯O contacts.

Crystal structure of 3,3′-(E)-diazene-1,2-diylbis{4-[(3,4-dinitro-1H-pyrazol-1-yl)-NNO-azoxy]-1,2,5-oxadiazole}

The crystal structure of a novel high-energy density material 3,3′-(E)diazene-1,2-diylbis{4-[(3,4-dinitro-1H-pyrazol-1-yl)-NNO-azoxy]-1,2,5-oxadiazole} (C10H2N18O12) was determined and refined using laboratory powder diffraction data. The title compound crystallizes in space group P21/c with a = 9.5089(3) Å, b = 11.6331(4) Å, c = 10.6270(3) Å, β = 116.2370(12), V = 1054.43(6) Å3. The asymmetric unit contains half of the molecule. The molecular conformation contains a weak intramolecular hydrogen bond C–H⋯O–N, both nitro groups are disordered, and the structure is dominated by weak O⋯π and O⋯O contacts.

Temperature- and moisture-dependent studies on alunogen and the crystal structure of meta-alunogen determined from laboratory powder diffraction data

Starting from a synthetic sample with composition Al2(SO4)3·16.6H2O, the high-temperature- and moisture-dependent behavior of alunogen has been unraveled by TGA measurements, in situ powder X-ray diffraction as well as by gravimetric moisture sorption/desorption studies. Heating experiments using the different techniques show that alunogen undergoes a first dehydration process already starting at temperatures slightly above 40 °C. The crystalline product of the temperature-induced dehydration corresponds to the synthetic equivalent of meta-alunogen and has the following chemical composition: Al2(SO4)3·13.8H2O or Al2(SO4)3(H2O)12·1.8H2O. At 90 °C a further reaction can be monitored resulting in the formation of an X-ray amorphous material. The sequence of “amorphous humps” in the patterns persists up to 250 °C, where a re-crystallization process is indicated by a sudden appearance of a larger number of sharp Bragg peaks. Phase analysis confirmed this compound to be anhydrous Al2(SO4)3. Furthermore, meta-alunogen can be also obtained from alunogen at room temperature when stored at relative humidities (RH) lower than 20 %. The transformation is reversible, however, water sorption of meta-alunogen to alunogen and the corresponding desorption reaction show considerable hysteresis. For RH values above 80 %, deliquescence of the material was observed. Structural investigations on meta-alunogen were performed using a sample that has been stored at dry conditions (0 % RH) over phosphorus pentoxide. Powder diffraction data were acquired on an in-house high-resolution diffractometer in transmission mode using a sealed glass capillary as sample holder. Indexing resulted in a triclinic unit cell with the following lattice parameters: a = 14.353(6) Å, b = 12.490(6) Å, c = 6.092(3) Å, α = 92.656(1)°, β = 96.654(1)°, γ = 100.831(1)°, V = 1062.8(8) Å3 and Z = 2. These data correct earlier findings suggesting an orthorhombic cell. Ab-initio structure solution in space group Poverline{1}, using simulated annealing, provided a chemically meaningful structure model. The asymmetric unit of meta-alunogen contains three symmetry independent SO4-tetrahedra and two Al(H2O)6 octahedra. The polyhedra are isolated, however, linkage between them is provided by Coulomb interactions and hydrogen bonding. In addition to the water molecules which directly belong to the coordination environment of the aluminum cations there are two additional zeolitic water sites (Ow1 and Ow2). If both positions are fully occupied meta-alunogen corresponds to a 14-hydrate. Structural similarities and differences between the previously unknown structure of meta-alunogen and alunogen are discussed in detail. Since hydrous aluminum sulfates have been postulated to occur in Martian soils, our results may help identifying meta-alunogen by X-ray diffraction not only on the surface of the Earth but also using the Curiosity Rover’s ChemMin instrument.

The crystal structure of trandolapril, C24H34N2O5: an example of the utility of raw data deposition in the powder diffraction file

The crystal structure of trandolapril has been solved by parallel tempering using the FOX software package with laboratory powder diffraction data submitted to and published in the Powder Diffraction File. Rietveld refinement was performed with the software package GSAS yielding orthorhombic lattice parameters of a = 19.7685(4), b = 15.0697(4), and c = 7.6704(2) Å (C24H34N2O5, Z = 4, space group P212121). The Rietveld refinement results were compared with density functional theory (DFT) calculations performed with CRYSTAL14. While the structures are similar, discrepancies are observed in the configuration of the octahydroindole ring between the Rietveld and DFT structures, suggesting the refined and calculated molecules are diastereomers.

Temperature- and moisture-dependent powder X-ray diffraction studies of kanemite (NaSi2O4(OH)·3H2O)

AbstractThe high-temperature- and moisture-dependent behaviour of synthetic kanemite (NaSi2O4(OH)·3H2O orSKS-10) has been studied byin situpowder X-ray diffraction. Heating experiments in the range between ambient temperatures and 250°C confirm earlier investigations that the dehydration of kanemite occurs in two steps. According to our results the two different reactions start at ∼30 and 75°C. The dehydration products have the following compositions: NaSi2O4(OH)·H2O (monohydrate) and NaSi2O4(OH), respectively. The crystal structures of both phases have been solved at ambient conditionsab initiofrom laboratory powder diffraction data using samples that have been carefully dehydrated at 60 and 150°C, respectively, and refined subsequently by the Rietveld method. Basic crystallographic data are as follows: NaSi2O4(OH)·H2O: orthorhombic, space groupPna21,a= 7.2019(1),b= 15.3252(2),c= 4.8869(1) Å,V= 539.37(1) Å3,Z= 4; NaSi2O4(OH): monoclinic, space groupP21,a= 6.3873(1),b= 4.8876(1),c= 7.1936(1) Å, β = 93.36(1)°,V= 224.19(1) Å3,Z= 2. Both compounds belong to the group of single-layer silicates based on Si2O4(OH) sheets. The sodium cations are located between the tetrahedral sheets and are surrounded by oxygen atoms from silicate anions and/or water molecules. Depending on the dehydration step the coordination numbers of the alkali ions vary between six (kanemite) and five (NaSi2O4(OH)). Kanemite and its two dehydration products show structural similarities which are discussed in detail. Moisture-dependent diffraction studies at ambient temperatures indicate that kanemite is stable between 10% and at least 90% relative humidity. Below the lower threshold a transformation to the monohydrate phase was observed. Dehydration and rehydration as a function of humidity is reversible. However, this process is combined with a significant loss of crystallinity of the samples.

Structures of 2 new sulfates, Na2M(SO4)2(M=Co, Ni), with rare SO42-coordination

In this study the structures of two new sulfates, Na2M(SO4)2(M=Co, Ni), were determined via both single crystal diffraction and neutron and laboratory X-ray diffraction data. The structural analysis was initiated with single crystal diffraction of the cobalt analogue and while this elucidated the cation positions the oxygen positions were still elusive. Therefore, combined Rietveld refinements of laboratory and neutron powder diffraction data was performed employing both hard constraints and soft restraints. The 5 K neutron data of both compounds are isostructural with the room temperature data as shown by Rietveld refinements. Refinements show that the transition metal ions are in a pseudo octahedral coordination that is better represented by a trigonal bipyramid, where one of the ligands is an edge of a SO42-tetrahedra. This rare coordination of sulfate tetrahedra was corroborated by spectroscopic techniques: UV-vis, Raman, and infrared. Additionally these compounds adopt large unit cells within the space group C2/c: Na2Co(SO4)2vol=4137.17(1)Å3and Na2Ni(SO4)2vol=4080.17(5) Å3.

In situ growth of SrFe12O19

SrFe12O19 is a highly anisotropic ferrimagnetic compound with relatively high remanence and high coercivity, which is used in permanent magnets. Permanent magnets are everywhere in our daily life and they are responsible for the interconversion between motion and electricity in electrical components ranging from headphones to wind turbines. Three key parameters, important for making permanent magnets, are an anisotropic structure, size of the nanocrystallites and the microstructure. In situ X-ray powder diffraction has been used to follow the growth kinetics of SrFe12O19 under hydrothermal conditions. Synthesis of SrFe12O19 (Sr-Hexaferrite) nanocrystals by hydrothermal methods have the advantage of allowing exhaustive control of the reaction parameters. We have studied the growth and kinetics of SrFe12O19 by carring out time resolved synchrotron experiments at MAX-lab, Sweden. The experiments were carried out at elevated pressure (250 bar) and in temperatures ranging from 250 to 400 oC. The diffraction data allow us to follow the evolution of the crystallite size as function of temperature, time and composition. By controlling the composition of the precursor we can tailor the size of the nanocrystallites. The obtained data have shown that the synthesis takes place through a conversion of tiny hexagonal shaped FeOOH nanocrystallites into the SrFe12O19. Several ex situ studies under comparable conditions have been carried out to compare the magnetic properties and the obtained nanocrystallites have been investigated using high resolution laboratory powder diffraction data.

The influence of hydrogen bonding on the planar arrangement of melamine in crystal structures of its solvates, cocrystals and salts

The hydrogen bonding patterns of melamine as well as mono- and diprotonated melamine have been analysed in five crystal structures of a solvate, a cocrystal and three organic and inorganic salts, namely, melamine DMSO solvate ([mel]·DMSO (1)), melamine theobromine cocrystal ([mel]·[TBR]3 (2)), dimelaminium ethylenediaminetetraacetate ([mel-H]2[EDTA-H2]·2H2O (3)), anhydrous dimelaminium sulfate ([mel-H]2[SO4] (4)), and anhydrous melaminium dinitrate ([mel-H2][NO3]2 (5)). Melamine is a versatile molecular building block (tecton) in cocrystals, solvates and salts. Depending on the degree of protonation and/or other molecules or ions present in the structure, parallels could be drawn to determine whether melamine is arranged in a cross-linked manner, in undulating sheets or in the form of perfectly planar sheets in the structure. Graph set analysis was used to compare the geometry of hydrogen bond interactions of the new structures with those of other structures published in the literature. Solvent drop-assisted solid state reactions (kneading) were performed for “green” synthesis of the compounds. The organic salt 3 has high thermal stability as shown by variable-temperature X-ray powder diffraction, which is presumably related to its extensive hydrogen bond network. Rietveld refinements were carried out on laboratory powder diffraction data to confirm the structures of the compounds obtained from single-crystal data.

Coordinative versatility of a Schiff base containing thiophene: Synthesis, characterization and biological activity of zinc(II) and silver(I) complexes

The synthesis, spectroscopic characterization and crystal description based on powder diffraction data, and antimycobacterial assays of silver(I) and zinc(II) complexes with Schiff base N,N′-bis(thiophen-2-ylmethylene)ethane-1,2-diamine ThioEn, are here reported. The [Ag(ThioEn)]NO3, AgThioEn, [Ag(ThioEn)2]NO3, Ag(ThioEn)2 and [ZnCl2(ThioEn)], ZnThioEn complexes were obtained by reaction of the ThioEn with silver(I) nitrate or zinc(II) chloride in methanolic solution. ThioEn was previously obtained by reacting ethylenediamine (En) with 2-thiophenecarboxaldehyde (Thio). The complexes were characterized by elemental (C, H and N) and thermal (TG-DTA) analyses and 13C and 1H NMR and FT-IR spectroscopic measurements. The three crystal structures were determined and refined from laboratory powder diffraction data only. The AgThioEn complex has a polymeric structure where the ligand acts as bridge between Ag(I) ions, while Ag(ThioEn)2 and ZnThioEn are monomers complexes with ThioEn acting as chelating ligand. Both silver(I) complexes showed to be effective against Mycobacterium tuberculosis.

Structure determination of three polymorphs of xylazine from laboratory powder diffraction data

The crystal structures of three xylazine hydrochloride [N-(2,6-dimethylphenyl)-5,6-dihydro-4H-1,3-thiaz-2-amine hydrochloride] polymorphs A, Z and X have been solved from powder diffraction data and refined using Rietveld refinement. Data were obtained with Cu Kα radiation. All polymorphs were found to have structures with Z' = 1 and Z = 4. All the structures determined contained strong hydrogen bonds between the amino groups and chloride anions. The crystal structures of forms A and X featured π-π stacking interactions.

Two polymorphs of 2-ethyl-3-hydroxy-6-methylpyridinium hydrogenN-acetyl-L-glutamate from powder diffraction data

The title salt, C8H12NO(+)·C7H10NO5(-), crystallizes in two polymorphic modifications, viz. monoclinic (M) and orthorhombic (O). The crystal structures of both polymorphic modifications have been established from laboratory powder diffraction data. The crystal packing motifs in the two polymorphs are different, but the conformations of the anions are generally similar. In M, the anions are linked by pairs of hydrogen bonds of the N-H···O and O-H···O types into chains along the b-axis direction, and neighbouring molecules within the chain are related by the 21 screw axis. The cations link these chains via O-H···O and N-H···O hydrogen bonds into layers parallel to (001). In O, the anions are linked by O-H···O hydrogen bonds into helices along [001], and neighbouring molecules within the helix are related by the 21 screw axis. The neighbouring helical turns are linked by N-H···O hydrogen bonds. The cations link the helices via O-H···O and N-H···O hydrogen bonds, thus forming a three-dimensional network.

Arrangement of Rh3+ions infac-triamminetrichloridorhodium from powder data and infac-triamminetrinitratorhodium crystals twinned by merohedry

The rhodium complexes [RhCl3(NH3)3], (I), and [Rh(NO3)3(NH3)3], (II), are built from octahedral RhX3(NH3)3 units; in (I) they are isolated units, while in (II) the units are stacked in columns with partially filled sites for the Rh atoms. The octahedra of monoclinic crystals of (I) are linked by N-H···Cl hydrogen bonds and the Rh(3+) ions are located on the mirror planes. In the trigonal crystals of (II), the discontinuous `columns' along the threefold axis are linked by N-H···O hydrogen bonds. The structure of (I) has been solved using laboratory powder diffraction data, the structure of (II) has been solved by single-crystal methods using data from a merohedrally twinned sample. Both compounds possess low solubility in water.

Use of TALP with laboratory powder diffraction data from 2D detectors

The viability of the direct-space strategy TALP (Vallcorbaet al., 2012b) to solve crystal structures of molecular compounds from laboratory powder diffraction data is shown. The procedure exploits the accurate metric refined from a ‘Bragg-Brentano’ powder pattern to extract later the intensity data from a second ‘texture-free’ powder pattern with the DAJUST software (Vallcorbaet al., 2012a). The experimental setup for collecting this second pattern consists of a circularly collimated X-ray beam and a 2D detector. The sample is placed between two thin Mylar®foils, which reduces or even eliminates preferred orientation. With the combination of the DAJUST and TALP software a preliminary but rigorous structural study of organic compounds can be carried out at the laboratory level. In addition, the time-consuming filling of capillaries with diameters thinner than 0.3mm is avoided.

Two polymorphs of afobazole from powder diffraction data

Afobazole {systematic name: 2-[2-(morpholin-4-yl)ethylsulfanyl]-1H-benzimidazole} is a new anxiolytic drug and Actins, Auzins & Petkune [(2012). Eur. Patent EP10163962] described four polymorphic modifications. In the present study, the crystal structures of two monoclinic polymorphs, 5-ethoxy-2-[2-(morpholin-4-ium-4-yl)ethylsulfanyl]-1H-benzimidazol-3-ium dichloride, C15H23N3O2S(2+)·2Cl(-), (II) and (IV), have been established from laboratory powder diffraction data. The crystal packing and conformation of the dications in (II) and (IV) are different. In (II), there are channels in the [001] direction, which offer atmospheric water molecules an easy way of penetrating into the crystal structure, thus explaining the higher hygroscopicity of (II) compared with (IV).

Structure of the inclusion complex of β-cyclodextrin with lipoic acid from laboratory powder diffraction data

The crystal structure of the inclusion complex of β-cyclodextrin with lipoic acid was determined from laboratory powder diffraction data. Thermogravimetric data was used to estimate the number of water molecules in the crystal structure. Lipoic acid is included in β-cyclodextrin through its primary face with the five-membered ring reaching the center plane of the cyclodextrin cavity and its fatty acid chain adopting a bent conformation. Lipoic acid and β-cyclodextrin form a channel-like packing which is stabilized by guest-host hydrogen bonding and close contacts, host-host intermolecular interactions and hydrogen bonding involving the water molecules.