Octahedral As in M + arsenates – architecture and seven new members

2007 ◽  
Vol 63 (2) ◽  
pp. 205-215 ◽  
Author(s):  
Karolina Schwendtner ◽  
Uwe Kolitsch
Keyword(s):  
Hydrogen Bonds ◽  
Diffraction Data ◽  
Inorganic Compounds ◽  
Length Distribution ◽  
The Novel ◽  
X Ray Diffraction ◽  
New Members ◽  
X Ray ◽  
Average Bond ◽  
Bond Length Distribution

Arsenates with arsenic in octahedral coordination are very rare. The present paper provides an overview of all known M + arsenates(V) containing octahedrally coordinated arsenic (M + = Li, Na, K, Rb, Cs, Ag) and the crystal structures (determined from single-crystal X-ray diffraction data) of the following seven new hydrothermally synthesized members belonging to six different structure types, four of which are novel: LiH2As3O9, LiH3As2O7, NaHAs2O6-type KHAs2O6, KH3As4O12 and isotypic RbH3As4O12, CsAs3O8 and NaH2As3O9-type AgH2As3O9. The main building unit of these compounds is usually an As4O14 cluster of two edge-sharing AsO6 octahedra sharing two apical corners each with two AsO4 tetrahedra. The different connectivity between these clusters defines the different structure types. The novel CsAs3O8 structure, based on a derivative of the As4O14 cluster, is the most condensed of all these M + arsenates, with an O/As ratio of only 2.67 compared with values of 2.75–3.5 for the remaining members. This is achieved through polymerization of the cluster derivatives to infinite chains of edge-sharing AsO6 octahedra. The [4]As/[6]As ratio drops to only 0.5. All but two of the protonated title compounds show protonated AsO6 octahedra. Hydrogen bonds range from very strong to weak. An analysis of bond-length distribution and average bond lengths in AsO6 octahedra in inorganic compounds leads to an overall mean As—O distance for all known AsO6 octahedra (with R factors < 0.072) of 1.830 (2) Å.

Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis

2022 ◽  
Vol 78 (2) ◽  
Author(s):  
Sehrish Akram ◽  
Arshad Mehmood ◽  
Sajida Noureen ◽  
Maqsood Ahmed
Keyword(s):  
Hydrogen Bonds ◽  
Glutamic Acid ◽  
Single Crystal ◽  
Diffraction Data ◽  
Density Functional ◽  
Quantitative Estimation ◽  
Topological Analysis ◽  
Pyroglutamic Acid ◽  
X Ray Diffraction ◽  
X Ray

Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.

On the effect of Ga and In substitutions in the Ca11Bi10and Yb11Bi10bismuthides crystallizing in the tetragonal Ho11Ge10structure type

2018 ◽  
Vol 74 (3) ◽  
pp. 269-273 ◽  
Author(s):  
Alexander Ovchinnikov ◽  
Svilen Bobev
Keyword(s):  
Bond Length ◽  
Length Distribution ◽  
Structural Response ◽  
Structure Type ◽  
First Principle ◽  
X Ray Diffraction ◽  
Interatomic Distances ◽  
X Ray ◽  
Type Bond ◽  
Bond Length Distribution

The Ga- and In-substituted bismuthides Ca11GaxBi10–x, Ca11InxBi10–x, Yb11GaxBi10–x, and Yb11InxBi10–x(x< 2) can be readily synthesized employing molten Ga or In metals as fluxes. They crystallize in the tetragonal space groupI4/mmmand adopt the Ho11Ge10structure type (Pearson codetI84; Wyckoff sequencen2m j h2e2d). The structural response to the substitution of Bi with smaller and electron-poorer In or Ga has been studied by single-crystal X-ray diffraction methods for the case of Ca11InxBi10–x[x= 1.73 (2); octabismuth undecacalcium diindium]. The refinements show that the In atoms substitute Bi only at the 8hsite. The refined interatomic distances show an unconventional – for this structure type – bond-length distribution within the anionic sublattice. The latter can be viewed as consisting of isolated Bi3−anions and [In4Bi820−] clusters for the idealized Ca11In2Bi8model. Formal electron counting and first-principle calculations show that the peculiar bonding in this compound drives the system toward an electron-precise state, thereby stabilizing the observed bond-length pattern.

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

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

scholarly journals Synthesis of the first nickel borate nitrate K7Ni[B18O24(OH)9](NO3)6· (H3BO3)

2019 ◽  
Vol 74 (10) ◽  
pp. 757-764
Author(s):  
Michael Zoller ◽  
Klaus Wurst ◽  
Hubert Huppertz
Keyword(s):  
Stainless Steel ◽  
Nitric Acid ◽  
Hydrothermal Synthesis ◽  
Boric Acid ◽  
Diffraction Data ◽  
The Novel ◽  
X Ray Diffraction ◽  
X Ray ◽  
Complex Nickel ◽  
Nitrate Anions

AbstractThe novel potassium nickel borate nitrate K7Ni[B18O24(OH)9](NO3)6 ·(H3BO3) was obtained from a simple hydrothermal synthesis in a stainless-steel autoclave at T = 513 K starting with nickel dichloride hexahydrate, and boric and nitric acid with the pH adjusted to 8 by KOH. Single-crystal X-ray diffraction data provided the basis for the structure analysis and refinement. The compound crystallizes in the trigonal space group R3̅ (no. 148) with the lattice parameters a = 1222.29(8) and c = 5478.4(4) pm. Generally, K7Ni[B18O24(OH)9](NO3)6 ·(H3BO3) is comprised of nitrate layers and complex nickel borate layers surrounded by boric acid, nitrate anions, and potassium cations.

The crystal and molecular structure of a 1:1 complex of 5-bromouridine and dimethylsulphoxide

1968 ◽  
Vol 302 (1469) ◽  
pp. 225-236 ◽  
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bonds ◽  
Oxygen Atom ◽  
Diffraction Data ◽  
Crystal And Molecular Structure ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Anisotropic Temperature

A complex consisting of one molecule of 5-bromouridine ( BUR ) and one molecule of di­methylsulphoxide ( DMSO ) has been prepared in the form of monoclinic crystals. The unit cell parameters are as follows, a = 13⋅65 ± 0⋅01, b = 4.820 ± 0⋅005, c = 12⋅09 ± 0⋅01 Å, β = 91⋅8 ± 0.1°, space group P 2 1 . X-ray diffraction data ( ⋋ = 1⋅5418 Å) for 1389 independent reflexions were collected and the structure was determined from Patterson syntheses which gave the coordinates of the bromine and sulphur atoms. Fourier syntheses followed by least-squares refinement (including anisotropic temperature parameters) reduced the agreement index R to 0⋅067. The bond lengths and angles for each molecule are given, and it is shown that hydrogen bonds are formed between the oxygen atom of the DMSO molecule and the 03' and 05' of the BUR molecules. A comparison is made between the conformation of the BUR molecule in this complex and that of the same molecule in two other structures.

scholarly journals New superprotonic crystals with dynamically disordered hydrogen bonds: cation replacements as the alternative to temperature increase

2017 ◽  
Vol 73 (6) ◽  
pp. 1105-1113 ◽  
Author(s):  
Elena V. Selezneva ◽  
Irina P. Makarova ◽  
Inna A. Malyshkina ◽  
Nadezhda D. Gavrilova ◽  
Vadim V. Grebenev ◽  
...  
Keyword(s):  
High Temperature ◽  
Dielectric Properties ◽  
Hydrogen Bonds ◽  
Single Crystals ◽  
Diffraction Data ◽  
Room Temperature ◽  
Ambient Conditions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Superprotonic Phase

Investigations of new single crystals grown in the K3H(SO4)2–(NH4)3H(SO4)2–H2O system from solutions with different K:NH4 concentration ratios have been carried out. Based on the X-ray diffraction data, the atomic structure of the crystals was determined at room temperature taking H atoms into account. It has been determined that [K0.43(NH4)0.57]3H(SO4)2 crystals are trigonal at ambient conditions such as the superprotonic phase of (NH4)3H(SO4)2 at high temperature. A distribution of the K and N atoms in the crystal was modelled on the basis of the refined occupancies of K/N positions. Studies of dielectric properties over the temperature range 223–353 K revealed high values of conductivity of the crystals comparable with the conductivity of known superprotonic compounds at high temperatures, and an anomaly corresponding to a transition to the phase with low conductivity upon cooling.

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

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.

scholarly journals Use of the Bruker AXS SMART BREEZE™ System for Macromolecular X-ray Data Collection

2016 ◽  
Vol 13 (4) ◽  
Author(s):  
Christiana Standle ◽  
Blake Overson ◽  
Cody Black ◽  
Guizella Rocabado ◽  
Bruce Howard
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Undergraduate Research ◽  
Inorganic Compounds ◽  
Copper Anode ◽  
X Ray Diffraction ◽  
Small Unit ◽  
X Ray ◽  
Unit Cells ◽  
Protein Enzyme

The Bruker AXS SMART BREEZE™ system is a single-crystal X-ray diffractometer designed to collect data from crystals of small organic or inorganic compounds. It is typically equipped with a Molybdenum-anode sealed tube to facilitate data collection from small unit cells. We recently acquired this system, but chose to have it installed with a copper-anode sealed tube with the hope of using it to collect data from larger unit cells such as those found in crystals of proteins or other macromolecules. This is the first and only BREEZE™ system installed by Bruker AXS with a copper-anode to date. Here we show that this system is capable of efficiently collecting quality X-ray diffraction data from crystals of the enzymes lysozyme and xylanase. This capability to collect diffraction data from both macromolecular and small-molecule crystals greatly expands the scope of undergraduate research projects that can be addressed using this instrument. KEYWORDS: X-ray; Diffraction; Crystallography; Diffractometer; Protein; Enzyme; Crystal; Structure

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

2001 ◽  
Vol 65 (6) ◽  
pp. 717-724 ◽  
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.

Opening and Narrowing of the Water H—O—H Angle by Hydrogen-Bonding Effects: Re-inspection of Neutron Diffraction Data

1998 ◽  
Vol 54 (4) ◽  
pp. 464-470 ◽  
Author(s):  
T. Steiner
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Secondary Effects ◽  
X Ray Diffraction ◽  
X Ray ◽  
Sample Average

For 71 water molecules donating two Ow—H...O hydrogen bonds, the correlation of the covalent H—O—H angle and the O...Ow...O angle is inspected from 49 well refined organic and organometallic neutron diffraction crystal structures. Compared to sample average, the water angle is opened for large and narrowed for small O...Ow...O angles. Notably, the H—O—H angle is widened compared with the gas phase value even for small O...Ow...O. Related behavior is observed for chloride anion acceptors. The correlation exhibits a considerable scatter which should not be interpreted as experimental inaccuracies, but as secondary effects. Possible secondary effects are multi-center hydrogen bonding and effects of coordination to the water O atom. In a comparative test, low-temperature X-ray diffraction data were shown to be completely unsuitable for this type of analysis. The dependence of the C—O—H angle on the C—O...O angle in hydrogen bonds donated by hydroxyl groups in carbohydrates is also shown.

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