N—H...O and C—H...F hydrogen bonds in the incommensurately modulated crystal structure of adamantan-1-ammonium 4-fluorobenzoate

At low temperatures the organic salt adamantan-1-ammonium 4-fluorobenzoate, C10H18N+·C7H4FO2−, possesses an incommensurately modulated crystal structure. The effect of the modulation on the atomic arrangement and intermolecular interactions is studied by analysing single-crystal X-ray diffraction data within the (3 + 1)-dimensional superspace approach and superspace groupP21/n(α0γ)00. The modulation strongly affects the position of the atoms as well as their atomic displacement parameters. Nevertheless, the molecular cations and anions are built by rigid moieties, which vary their orientation with respect to each other as a function of the phase of the modulationt. Cations and anions are connected into slabs by dense N—H...O and C—H...F hydrogen-bonded networks, which are characterized by being rather rigid and which show only a little variation as a function of the phase of the modulationt.

Download Full-text

Crystal Structure of Moganite and Its Anisotropic Atomic Displacement Parameters Determined by Synchrotron X-ray Diffraction and X-ray/Neutron Pair Distribution Function Analyses

Minerals ◽

10.3390/min11030272 ◽

2021 ◽

Vol 11 (3) ◽

pp. 272

Author(s):

Seungyeol Lee ◽

Huifang Xu ◽

Hongwu Xu ◽

Joerg Neuefeind

Keyword(s):

Crystal Structure ◽

Distribution Function ◽

Single Crystal ◽

Pair Distribution Function ◽

Atomic Displacement ◽

Single Crystal Xrd ◽

X Ray Diffraction ◽

X Ray ◽

Neutron Pair ◽

Atomic Displacement Parameters

The crystal structure of moganite from the Mogán formation on Gran Canaria has been re-investigated using high-resolution synchrotron X-ray diffraction (XRD) and X-ray/neutron pair distribution function (PDF) analyses. Our study for the first time reports the anisotropic atomic displacement parameters (ADPs) of a natural moganite. Rietveld analysis of synchrotron XRD data determined the crystal structure of moganite with the space group I2/a. The refined unit-cell parameters are a = 8.7363(8), b = 4.8688(5), c = 10.7203(9) Å, and β = 90.212(4)°. The ADPs of Si and O in moganite were obtained from X-ray and neutron PDF analyses. The shapes and orientations of the anisotropic ellipsoids determined from X-ray and neutron measurements are similar. The anisotropic ellipsoids for O extend along planes perpendicular to the Si-Si axis of corner-sharing SiO4 tetrahedra, suggesting precession-like movement. Neutron PDF result confirms the occurrence of OH over some of the tetrahedral sites. We postulate that moganite nanomineral is stable with respect to quartz in hypersaline water. The ADPs of moganite show a similar trend as those of quartz determined by single-crystal XRD. In short, the combined methods can provide high-quality structural parameters of moganite nanomineral, including its ADPs and extra OH position at the surface. This approach can be used as an alternative means for solving the structures of crystals that are not large enough for single-crystal XRD measurements, such as fine-grained and nanocrystalline minerals formed in various geological environments.

Download Full-text

Synthesis, crystal structure and molecular conformation of (±)-1-oxoferruginol and (±)-shonanol

Zeitschrift für Kristallographie - Crystalline Materials ◽

10.1524/zkri.219.10.659.50814 ◽

2004 ◽

Vol 219 (10) ◽

Author(s):

Swastik Mondal ◽

Monika Mukherjee ◽

Arnab Roy ◽

Debabrata Mukherjee

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Diffraction Data ◽

Molecular Conformation ◽

Membered Ring ◽

Methyl Groups ◽

Single Bond ◽

X Ray Diffraction ◽

X Ray ◽

Chemical Structures

Abstract(±)-1-oxoferruginol and (±)-shonanol, two potential intermediates in the synthesis of tricyclic diterpenoid ferruginol, have been prepared and crystal structures of the compounds have been investigated using single-crystal X-ray diffraction data. The methyl groups of the isopropyl moiety in (±)-shonanol are disordered over two positions with occupation factors 0.65(1) and 0.35(1), respectively. Although the chemical structures of two compounds are very similar, a C—C single bond in the terminal six-membered ring of (±)-1-oxoferruginol is replaced by a C=C bond in (±)-shonanol, the quantitative isostructurality index calculations indicate that the structures are not isostructural. Intermolecular O—H…O hydrogen bonds between pairs of molecules in the compounds related by center of inversion lead to characteristic dimers forming R

Download Full-text

The whole range of hydrogen bonds in one crystal structure: neutron diffraction and charge-density studies of N,N-dimethylbiguanidinium bis(hydrogensquarate)

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768111043138 ◽

2011 ◽

Vol 67 (6) ◽

pp. 552-559 ◽

Cited By ~ 26

Author(s):

Mihaela-Diana Şerb ◽

Ruimin Wang ◽

Martin Meven ◽

Ulli Englert

Keyword(s):

Crystal Structure ◽

Hydrogen Bond ◽

High Resolution ◽

Hydrogen Bonds ◽

Neutron Diffraction ◽

Electron Density ◽

Organic Salt ◽

X Ray Diffraction ◽

Covalent Character ◽

X Ray

N,N-Dimethylbiguanidinium bis(hydrogensquarate) features an impressive range of hydrogen bonds within the same crystal structure: neighbouring anions aggregate to a dianionic pair through two strong O—H...O interactions; one of these can be classified among the shortest hydrogen bonds ever studied. Cations and anions in this organic salt further interact via conventional N—H...O and nonclassical C—H...O contacts to an extended structure. As all these interactions occur in the same sample, the title compound is particularly suitable to monitor even subtle trends in hydrogen bonds. Neutron and high-resolution X-ray diffraction experiments have enabled us to determine the electron density precisely and to address its properties with an emphasis on the nature of the X—H...O interactions. Sensitive criteria such as the Laplacian of the electron density and energy densities in the bond-critical points reveal the incipient covalent character of the shortest O—H...O bond. These findings are in agreement with the precise geometry from neutron diffraction: the shortest hydrogen bond is also significantly more symmetric than the longer interactions.

Download Full-text

Synthesis, structural characterization, and hydrogen bonds of Co9(OH)14[SO4]2

Zeitschrift für Naturforschung B ◽

10.1515/znb-2017-0046 ◽

2017 ◽

Vol 72 (7) ◽

pp. 505-510

Author(s):

Hamdi Ben Yahia ◽

Masahiro Shikano ◽

Ilias Belharouak

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Single Crystal ◽

Structural Characterization ◽

Diffraction Data ◽

Atmospheric Oxygen ◽

Molar Ratio ◽

X Ray Diffraction ◽

X Ray ◽

Triclinic System

AbstractThe new compound Co9(OH)14[SO4]2 was synthesized using a hydrothermal method from LiF, Na2SO3, and Co(CH3COO)2·4H2O in a molar ratio of 1:1:1 in the presence of atmospheric oxygen. Its crystal structure was determined from single crystal X-ray diffraction data. Co9(OH)14[SO4]2 crystallizes in the triclinic system, space group P1̅ with a=7.693(2) Å, b=8.318(2) Å, c=8.351(2) Å, α=82.375(5)°, β=77.832(4)°, γ=68.395(4)°, V=484.8(2) Å3, and Z=2. Its structure is composed of cobalt-containing sheets interconnected by SO4 tetrahedra. Bent and symmetrically trifurcated hydrogen bonds have been observed. Furthermore, structural similarities with hydrozincite and brucite minerals have been noticed.

Download Full-text

Revision of the crystal structure of ulrichite, CaCu2+(UO2)(PO4)2·4H2O

Mineralogical Magazine ◽

10.1180/0026461016560003 ◽

2001 ◽

Vol 65 (6) ◽

pp. 717-724 ◽

Cited By ~ 14

Author(s):

U. Kolitsch ◽

G. Giester

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Diffraction Data ◽

X Ray Diffraction ◽

Coordination Polyhedra ◽

Space Group ◽

X Ray ◽

Bond Angles ◽

Area Detector

AbstractThe crystal structure of ulrichite, CaCu2+(UO2)(PO4)2·4H2O (space group P21/c, a = 12.784(3), b = 6.996(1), c = 13.007(3)Å, β = 91.92(1)°, V = 1162.7(4)Å3, Z = 4) was redetermined using X-ray diffraction data measured from a twinned crystal with Mo-Kα radiation and a CCD area detector (2510 unique reflections with Fo > 4σ(Fo), R1 = 8.8%). Ulrichite crystallizes in space group P21/c rather than C2/m reported previously. The newly determined atomic positions give reasonable coordination polyhedra. One unique Ca atom is irregularly coordinated by eight O atoms (<Ca–O> = 2.46 Å). One unique U atom shows a {2+5} coordination with characteristic bond angles and lengths (1.806(11)Å, 1.842(12)Å and five bonds between 2.252(15) and 2.441(11)Å). Furthermore, the structure contains groups in which strongly elongated CuO6 ‘octahedra’ (also describable as CuO4 squares) are corner-linked to two PO4 tetrahedra via two opposite, equatorial O atoms. Edge- and corner-sharing UO7, CaO8 and PO4 polyhedra form heteropolyhedral sheets parallel to (001) that are linked to adjacent sheets via the CuO6 ‘octahedra’ and hydrogen bonds.

Download Full-text

Powder X-ray diffraction of varenicline hydrogen tartrate Form B (Chantix®), (C13H14N3)(HC4H4O6)

Powder Diffraction ◽

10.1017/s088571562100035x ◽

2021 ◽

pp. 1-3

Author(s):

James A. Kaduk ◽

Amy M. Gindhart ◽

Thomas N. Blanton

Keyword(s):

Crystal Structure ◽

Hydrogen Bonds ◽

Powder Diffraction ◽

Diffraction Data ◽

Density Functional ◽

Powder Diffraction Data ◽

X Ray Diffraction ◽

Powder Diffraction File ◽

Space Group ◽

X Ray

The crystal structure of varenicline hydrogen tartrate Form B (Chantix®) has been refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Varenicline hydrogen tartrate Form B crystallizes in space group P212121 (#19) with a = 7.07616(2), b = 7.78357(2), c = 29.86149(7) Å, V = 1644.706(6) Å3, and Z = 4. The hydrogen bonds were identified and quantified. Hydrogen bonds link the cations and anions in zig-zag chains along the b-axis. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

Download Full-text

Redetermination of the crystal structure of R 5Si4 (R = Pr, Nd) from single-crystal X-ray diffraction data

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989020002789 ◽

2020 ◽

Vol 76 (4) ◽

pp. 510-513

Author(s):

Kaori Yokota ◽

Ryuta Watanuki ◽

Miki Nakashima ◽

Masatomo Uehara ◽

Jun Gouchi ◽

...

Keyword(s):

Single Crystal ◽

Diffraction Data ◽

Three Dimensional ◽

Atomic Displacement ◽

Crystal Data ◽

X Ray Diffraction ◽

Acta Cryst ◽

X Ray ◽

Atomic Displacement Parameters ◽

First Time

The crystal structures of praseodymium silicide (5/4), Pr5Si4, and neodymium silicide (5/4), Nd5Si4, were redetermined using high-quality single-crystal X-ray diffraction data. The previous structure reports of Pr5Si4 were only based on powder X-ray diffraction data [Smith et al. (1967). Acta Cryst. 22 940–943; Yang et al. (2002b). J. Alloys Compd. 339, 189–194; Yang et al., (2003). J. Alloys Compd. 263, 146–153]. On the other hand, the structure of Nd5Si4 has been determined from powder data [neutron; Cadogan et al., (2002). J. Phys. Condens. Matter, 14, 7191–7200] and X-ray [Smith et al. (1967). Acta Cryst. 22 940–943; Yang et al. (2002b). J. Alloys Compd. 339, 189–194; Yang et al., (2003). J. Alloys Compd. 263, 146–153] and single-crystal data with isotropic atomic displacement parameters [Roger et al., (2006). J. Alloys Compd. 415, 73–84]. In addition, the anisotropic atomic displacement parameters for all atomic sites have been determined for the first time. These compounds are confirmed to have the tetragonal Zr5Si4-type structure (space group: P41212), as reported previously (Smith et al., 1967). The structure is built up by distorted body-centered cubes consisting of Pr(Nd) atoms, which are linked to each other by edge-sharing to form a three-dimensional framework. This framework delimits zigzag channels in which the silicon dimers are situated.

Download Full-text

High-pressure synthesis and crystal structure of the mixed-cation borate Ga4In4B15O33(OH)3

Zeitschrift für Naturforschung B ◽

10.1515/znb-2019-0014 ◽

2019 ◽

Vol 74 (4) ◽

pp. 357-363

Author(s):

Daniela Vitzthum ◽

Hubert Huppertz

Keyword(s):

Crystal Structure ◽

High Pressure ◽

High Temperature ◽

Diffraction Data ◽

X Ray Diffraction ◽

Synthesis And Crystal Structure ◽

X Ray ◽

Mixed Cation ◽

High Pressure High Temperature ◽

Pressure Synthesis

AbstractThe mixed cation triel borate Ga4In4B15O33(OH)3 was synthesized in a Walker-type multianvil apparatus at high-pressure/high-temperature conditions of 12.5 GPa and 1300°C. Although the product could not be reproduced in further experiments, its crystal structure could be reliably determined via single-crystal X-ray diffraction data. Ga4In4B15O33(OH)3 crystallizes in the tetragonal space group I41/a (origin choice 2) with the lattice parameters a = 11.382(2), c = 15.244(2) Å, and V = 1974.9(4) Å3. The structure of the quaternary triel borate consists of a complex network of BO4 tetrahedra, edge-sharing InO6 octahedra in dinuclear units, and very dense edge-sharing GaO6 octahedra in tetranuclear units.

Download Full-text

Single-crystal investigation of Ce5AgxGe4−x (x = 0.1−1.08) with Sm5Ge4 type

Zeitschrift für Naturforschung B ◽

10.1515/znb-2020-0091 ◽

2020 ◽

Vol 75 (8) ◽

pp. 765-768

Author(s):

Bohdana Belan ◽

Dorota Kowalska ◽

Mariya Dzevenko ◽

Mykola Manyako ◽

Roman Gladyshevskii

Keyword(s):

Crystal Structure ◽

Single Crystal ◽

Diffraction Data ◽

Binary Compound ◽

Lattice Parameters ◽

X Ray Diffraction ◽

Space Group ◽

X Ray

AbstractThe crystal structure of the phase Ce5AgxGe4−x (x = 0.1−1.08) has been determined using single-crystal X-ray diffraction data for Ce5Ag0.1Ge3.9. This phase is isotypic with Sm5Ge4: space group Pnma (No. 62), Pearson code oP36, Z = 4, a = 7.9632(2), b = 15.2693(5), c = 8.0803(2) Å; R1 = 0.0261, wR2 = 0.0460, 1428 F2 values and 48 variables. The two crystallographic positions 8d and 4c show Ge/Ag mixing, leading to a slight increase in the lattice parameters as compared to those of the pure binary compound Ce5Ge4.

Download Full-text