Redetermination of the solvent-free crystal structure of l-proline.
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ABSTRACT:
SUBMITTER: Koenig JJ
PROVIDER: S-EPMC6072995 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The crystal structure of mercury(I) sulfate (or mercurous sulfate), Hg2SO4, was re-determined based on modern CCD data. In comparison with the previous determination from Weissenberg film data [Dorm (1969 ?). Acta Chem. Scand. 23, 1607-1615], all atoms were refined with anisotropic displacement parameters, leading to higher precision in terms of bond lengths and angles [e.g. Hg-Hg = 2.5031?(7) compared to 2.500?(3)Å]. The structure consists of alternating rows along [001] of Hg2 (2+) dumbbells (generated by inversion symmetry) and SO4 (2-) tetra-hedra (symmetry 2). The dumbbells are linked via short O-Hg-Hg-O bonds to the sulfate tetra-hedra into chains extending parallel to [20-1]. More remote O-Hg-Hg-O bonds connect these chains into a three-dimensional framework.
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Project description:The crystal structure of the title compound, Tb2Ni7, was redetermined from single-crystal X-ray diffraction data. In comparison with previous studies based on powder X-ray diffraction data [Lemaire et al. (1967). C. R. Acad. Sci. Ser. B, 265, 1280-1282; Lemaire & Paccard (1969). Bull. Soc. Fr. Mineral. Cristallogr. 92, 9-16; Buschow & van der Goot (1970). J. Less-Common Met. 22, 419-428], the present redetermination affords refined coordinates and anisotropic displacement parameters for all atoms. A partial occupation for one Tb atom results in the non-stoichiometric composition Tb1.962?(4)Ni7. The title compound adopts the Ce2Ni7 structure type and can also be derived from the CaCu5 structure type as an inter-growth structure. The asymmetric unit contains two Tb sites (both site symmetries 3m.) and five Ni sites (.m., mm2, 3m., 3m., -3m.). The two different coordination polyhedra of Tb are a Frank-Kasper polyhedron formed by four Tb and 12 Ni atoms and a pseudo Frank-Kasper polyhedron formed by two Tb and 18 Ni atoms. The four different coordination polyhedra of Ni are Frank-Kasper icosa-hedra formed by five Tb and seven Ni atoms, four Tb and eight Ni atoms, three Tb and nine Ni atoms, and six Tb and six Ni atoms, respectively.
| S-EPMC4158487 | biostudies-literature
Project description:The crystal structure of the room-temperature modification of K[Hg(SCN)3], potassium tri-thio-cyanato-mercurate(II), was redetermined based on modern CCD data. In comparison with the previous report [Zhdanov & Sanadze (1952 ?). Zh. Fiz. Khim. 26, 469-478], reliability factors, standard deviations of lattice parameters and atomic coordinates, as well as anisotropic displacement parameters, were revealed for all atoms. The higher precision and accuracy of the model is, for example, reflected by the Hg-S bond lengths of 2.3954?(11), 2.4481?(8) and 2.7653?(6)?Å in comparison with values of 2.24, 2.43 and 2.77?Å. All atoms in the crystal structure are located on mirror planes. The Hg(2+) cation is surrounded by four S atoms in a seesaw shape [S-Hg-S angles range from 94.65?(2) to 154.06?(3)°]. The HgS4 polyhedra share a common S atom, building up chains extending parallel to [010]. All S atoms of the resulting (1) ?[HgS2/1S2/2] chains are also part of SCN(-) anions that link these chains with the K(+) cations into a three-dimensional network. The K-N bond lengths of the distorted KN7 polyhedra lie between 2.926?(2) and 3.051?(3)?Å.
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Project description:The crystal structure of the title compound, cadmium sulfate monohydrate or poly[(?2-aqua)(?4-sulfato)-cadmium], was redetermined based on modern CMOS (complementary metal oxide silicon) data. In comparison with the previous study [Bregeault & Herpin (1970 ?). Bull. Soc. Fr. Mineral. Cristallogr. 93, 37-42], all non-H atoms were refined with anisotropic displacement parameters and the hydrogen-bonding pattern unambiguously established due to location of the hydrogen atoms. In addition, a significant improvement in terms of precision and accuracy was achieved. In the crystal, the Cd(2+) cation is coordinated by four O atoms of four sulfate anions and two O atoms of water mol-ecules, forming a distorted octa-hedral trans-[CdO6] polyhedron. Each sulfate anion bridges four Cd(2+) cations and each water mol-ecule bridges two Cd(2+) cations, leading to the formation of a three-dimensional framework, with Cd?Cd separations in the range 4.0757?(2)-6.4462?(3)?Å. O-H?O hydrogen-bonding inter-actions of medium strength between the coordinating water mol-ecules and sulfate anions consolidate the crystal packing.
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Project description:Single crystals of NbF4, niobium(IV) tetra-fluoride, were synthesized by disproportionation of Nb2F5 at 1273?K in a sealed niobium tube, extracted and studied by single-crystal X-ray diffraction. Previous reports on the crystal structure of NbF4 were based on X-ray powder diffraction data and the observed isotypicity to SnF4 [Gortsema & Didchenko (1965 ?). Inorg. Chem. 4, 182-186; Schäfer et al. (1965 ?). J. Less Common Met. 9, 95-104]. The data obtained from a single-crystal X-ray diffraction study meant the atomic coordinates could now be refined as well as their anisotropic displacement parameters, leading to a significant improvement of the structural model of NbF4. In the structure, the Nb atom is octahedron-like surrounded by six F atoms of which four are bridging to other NbF6 octa-hedra, leading to a layer structure extending parallel to the ab plane.
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Project description:Single crystals of poly[?4-tartrato-?(6) O (1),O (3):O (1'):O (2),O (4):O (4')-lead], [Pb(C4H4O6)] n , were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002 ?). Acta Cryst. C58, m596-m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb(2+) cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb(2+) cations. The resulting three-dimensional framework is stabilized by O-H?O hydrogen bonds between the OH groups of one tartrate anion and the carboxyl-ate O atoms of adjacent anions.
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Project description:The crystal structure of the title compound, C7H5BrO2, was originally studied using photographic data at room temperature with Cu K? radiation [Ferguson & Sim (1962 ?). Acta Cryst. 15, 346-350]. The present study was undertaken at 120?K with a CCD diffractometer using Cu K? radiation, and resulted in improved geometrical parameters. In the mol-ecule, the carb-oxy group is inclined to the benzene ring by 18.7?(2)° and there is a close intra-molecular Br?O contact of 3.009?(3)?Å. In the crystal, mol-ecules are linked by pairs of O-H?O hydrogen bonds, forming inversion dimers with the classical R 2 (2)(8) ring motif for carb-oxy-lic acids. Neighbouring dimers are linked by weak C-H?O hydrogen bonds, forming tapes propagating in [1-10]. Adjacent tapes inter-act by slipped parallel ?-? inter-actions [inter-centroid distance = 3.991?(2), inter-planar distance = 3.509?(2)?Å, slippage = 1.900?Å] to form columns approximately along the b-axis direction. Neighbouring columns inter-act dispersively, forming a three-dimensional framework structure.
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Project description:The crystal structure of the β-polymorph of ZnMoO4 was re-determined on the basis of single-crystal X-ray diffraction data. In comparison with previous powder X-ray diffraction studies [Katikaneani & Arunachalam (2005 ▸). Eur. J. Inorg. Chem. pp. 3080-3087; Cavalcante et al. (2013 ▸). Polyhedron, 54, 13-25], all atoms were refined with anisotropic displacement parameters, leading to a higher precision with respect to bond lengths and angles. β-ZnMoO4 adopts the wolframite structure type and is composed of distorted ZnO6 and MoO6 octa-hedra, both with point group symmetry 2. The distortion of the octa-hedra is reflected by variation of bond lengths and angles from 2.002 (3)-2.274 (4) Å, 80.63 (11)-108.8 (2)° for equatorial and 158.4 (2)- 162.81 (14)° for axial angles (ZnO6), and of 1.769 (3)-2.171 (3) Å, 73.39 (16)-104.7 (2), 150.8 (2)-164.89 (15)° (MoO6), respectively. In the crystal structure, the same type of MO6 octa-hedra share edges to built up zigzag chains extending parallel to [001]. The two types of chains are condensed by common vertices into a framework structure. The crystal structure can alternatively be described as derived from a distorted hexa-gonally closed packed arrangement of the O atoms, with Zn and Mo in half of the octa-hedral voids.
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Project description:The crystal structure of the serine protease subtilisin Carlsberg in anhydrous acetonitrile was determined at 2.3 A resolution. It was found to be essentially identical to the three-dimensional structure of the enzyme in water; the differences observed were smaller than those between two independently determined structures in aqueous solution. The hydrogen bond system of the catalytic triad is intact in acetonitrile. The majority (99 of 119) of enzyme-bound, structural water molecules have such a great affinity to subtilisin that they are not displaced even in anhydrous acetonitrile. Of the 12 enzyme-bound acetonitrile molecules, 4 displace water molecules and 8 bind where no water had been observed before. One-third of all subtilisin-bound acetonitrile molecules reside in the active center, occupying the same region (P1, P2, and P3 binding sites) as the specific protein inhibitor eglin c.
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Project description:The structure of zymonic acid (systematic name: 4-hy-droxy-2-methyl-5-oxo-2,5-di-hydro-furan-2-carb-oxy-lic acid), C6H6O5, which had previously eluded crystallographic determination, is presented here for the first time. It forms by intra-molecular condensation of parapyruvic acid, which is the product of aldol condensation of pyruvic acid. A redetermination of the crystal structure of pyruvic acid (systematic name: 2-oxo-propanoic acid), C3H4O3, at low temperature (90 K) and with increased precision, is also presented [for the previous structure, see: Harata et al. (1977 ▸). Acta Cryst. B33, 210-212]. In zymonic acid, the hy-droxy-lactone ring is close to planar (r.m.s. deviation = 0.0108 Å) and the dihedral angle between the ring and the plane formed by the bonds of the methyl and carb-oxy-lic acid carbon atoms to the ring is 88.68 (7)°. The torsion angle of the carb-oxy-lic acid group relative to the ring is 12.04 (16)°. The pyruvic acid mol-ecule is almost planar, having a dihedral angle between the carb-oxy-lic acid and methyl-ketone groups of 3.95 (6)°. Inter-molecular inter-actions in both crystal structures are dominated by hydrogen bonding. The common R 2 2(8) hydrogen-bonding motif links carb-oxy-lic acid groups on adjacent mol-ecules in both structures. In zymonic acid, this results in dimers about a crystallographic twofold of space group C2/c, which forces the carb-oxy-lic acid group to be disordered exactly 50:50, which scrambles the carbonyl and hydroxyl groups and gives an apparent equalization of the C-O bond lengths [1.2568 (16) and 1.2602 (16) Å]. The other hydrogen bonds in zymonic acid (O-H⋯O and weak C-H⋯O), link mol-ecules across a 21-screw axis, and generate an R 2 2(9) motif. These hydrogen-bonding inter-actions propagate to form extended pleated sheets in the ab plane. Stacking of these zigzag sheets along c involves only van der Waals contacts. In pyruvic acid, inversion-related mol-ecules are linked into R 2 2(8) dimers, with van der Waals inter-actions between dimers as the only other inter-molecular contacts.
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