Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Synthesis of the Tetragonal Phase of Zintl's NaTl and Its Structure Determination from Powder Diffraction Data.

ABSTRACT: A tetragonal distortion of the long-time known NaTl structure at 298 K was observed in different experimental setups, including Zintl's original procedure of reducing Tl(I)-iodide by sodium liquid ammonia solutions. The powder diffraction pattern obtained by the high temperature synthesis using classical solid-state techniques allowed a model-independent unambiguous structure solution and refinement of tetragonal distorted NaTl (Rp = 0.0179, wRp = 0.0246, R = 0.0477, wR = 0.0527, GooF = 1.24).

SUBMITTER: Tiefenthaler S

PROVIDER: S-EPMC6515420 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Synthesis of the Tetragonal Phase of Zintl's NaTl and Its Structure Determination from Powder Diffraction Data.

Tiefenthaler Susanne S Korber Nikolaus N Gärtner Stefanie S

Materials (Basel, Switzerland) 20190425 8

A tetragonal distortion of the long-time known NaTl structure at 298 K was observed in different experimental setups, including Zintl's original procedure of reducing Tl(I)-iodide by sodium liquid ammonia solutions. The powder diffraction pattern obtained by the high temperature synthesis using classical solid-state techniques allowed a model-independent unambiguous structure solution and refinement of tetragonal distorted NaTl (Rp = 0.0179, wRp = 0.0246, R = 0.0477, wR = 0.0527, GooF = 1.24). ...[more]

PMID: 31027267

Similar Datasets

Crystal structure of Pigment Red 254 from X-ray powder diffraction data.

Project description:The crystal structure of Pigment Red 254 [P.R. 254, C18H10Cl2N2O2; systematic name: 3,6-bis-(4-chloro-phen-yl)-2,5-di-hydro-pyrrolo-[3,4-c]pyrrole-1,4-dione] was solved from laboratory X-ray powder diffraction data using the simulated annealing method followed by Rietveld refinement because the very low solubility of the pigment in all solvents impedes the growth of single crystals suitable for X-ray analysis. The mol-ecule lies across an inversion center. The dihedral angle between the benzene ring and the pyrrole ring in the unique part of the mol-ecule is 11.1 (2)°. In the crystal, mol-ecules are linked via N-H⋯O hydrogen bonds, forming chains along [110] incorporating R22(8) rings.

| S-EPMC5382609 | biostudies-literature

Crystal structure of 2,5-di-hydroxy-terephthalic acid from powder diffraction data.

Project description:The crystal structure of anhydrous 2,5-dhy-droxy-terephthalic acid, C8H6O6, was solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The published structure of 2,5-di-hydroxy-terephthalic acid dihydrate was also optimized. The carb-oxy-lic acid groups form strong hydrogen bonds, which form centrosymmetric rings with graph set R 2 2(8). These hydrogen bonds link the mol-ecules into chains along [011]. There is an intra-molecular O-H⋯O hydrogen bond between the hydroxyl group and the carbonyl group of the carb-oxy-lic acid. The hydrogen bonding in the dihydrate is very different. Although the intra-molecular hy-droxy/carb-oxy-lic acid hydrogen bond is present, the water mol-ecule acts as an acceptor to the carb-oxy-lic acid and a donor to two other oxygen atoms. The carb-oxy-lic acid groups do not inter-act with each other directly.

| S-EPMC9535832 | biostudies-literature

Pimobendan B from powder diffraction data.

Project description:The title mol-ecule, C19H18N4O2 {systematic name: (RS)-6-[2-(4-meth-oxy-phen-yl)-1H-benzimidazol-5-yl]-5-methyl-4,5-di-hydro-pyridazin-3(2H)-one}, adopts an extended conformation. The dihedral angles between the central benzimidazole ring sytem and the pendant meth-oxy-phenyl and pyridazinone residues are 1.41?(18) and 9.7?(3)°, respectively. In the crystal, N-H?N hydrogen bonds link the imadazole groups into [001] chains, and pairs of N-H?O hydrogen bonds link the pyridazinone groups into dimers. Together, these generate a two-dimensional supra-molecular structure parallel to (010). The layers are linked by C-H?? inter-actions.

| S-EPMC3919548 | biostudies-literature

Alaptide from synchrotron powder diffraction data.

Project description:THE TITLE COMPOUND [SYSTEMATIC NAME: (8S)-8-methyl-6,9-diaza-spiro-[4.5]decane-7,10-dione], C(9)H(14)N(2)O(2), consists of two connected rings, viz. a piperazine-2,5-dione (DKP) ring and a five-membered ring. The DKP ring adopts a slight boat conformation and the bonded methyl group is in an equatorial position. The five-membered ring is in an envelope conformation. In the crystal structure, inter-molecular N-H?O hydrogen bonds link mol-ecules into chains running parallel to the c axis.

| S-EPMC2983785 | biostudies-literature

Structure Determination of Biogenic Crystals Directly from 3D Electron Diffraction Data.

Project description:Highly reflective assemblies of purine, pteridine, and flavin crystals are used in the coloration and visual systems of many different animals. However, structure determination of biogenic crystals by single-crystal XRD is challenging due to the submicrometer size and beam sensitivity of the crystals, and powder XRD is inhibited due to the small volumes of powders, crystalline impurity phases, and significant preferred orientation. Consequently, the crystal structures of many biogenic materials remain unknown. Herein, we demonstrate that the 3D electron diffraction (3D ED) technique provides a powerful alternative approach, reporting the successful structure determination of biogenic guanine crystals (from spider integument, fish scales, and scallop eyes) from 3D ED data confirmed by analysis of powder XRD data. The results show that all biogenic guanine crystals studied are the previously known β-polymorph. This study highlights the considerable potential of 3D ED for elucidating the structures of biogenic molecular crystals in the nanometer-to-micrometer size range. This opens up an important opportunity in the development of organic biomineralization, for which structural knowledge is critical for understanding the optical functions of biogenic materials and their possible applications as sustainable, biocompatible optical materials.

| S-EPMC10853906 | biostudies-literature

Methyl-ergometrine maleate from synchrotron powder diffraction data.

Project description:The title compound {systematic name: 9,10-didehydro-N-[1-(hydroxy-meth-yl)prop-yl]-d-lysergamide maleate}, C(20)H(26)N(3)O(2) (+)·C(4)H(3)O(4) (-), contains a large rigid ergolene group. This group consists of an indole plane connected to a six-membered carbon ring adopting an envelope conformation and N-methyl-tetra-hydro-pyridine where the methyl group is in an equatorial position. In the crystal, inter-molecular N-H?O, O-H?N and O-H?O hydrogen bonds form an extensive three-dimensional hydrogen-bonding network, which holds the cations and anions together.

| S-EPMC2972137 | biostudies-literature

Exploiting powder X-ray diffraction for direct structure determination in structural biology: the P2X4 receptor trafficking motif YEQGL.

Project description:We report the crystal structure of the 5-residue peptide acetyl-YEQGL-amide, determined directly from powder X-ray diffraction data recorded on a conventional laboratory X-ray powder diffractometer. The YEQGL motif has a known biological role, as a trafficking motif in the C-terminus of mammalian P2X4 receptors. Comparison of the crystal structure of acetyl-YEQGL-amide determined here and that of a complex formed with the μ2 subunit of the clathrin adaptor protein complex AP2 reported previously, reveals differences in conformational properties, although there are nevertheless similarities concerning aspects of the hydrogen-bonding arrangement and the hydrophobic environment of the leucine sidechain. Our results demonstrate the potential for exploiting modern powder X-ray diffraction methodology to achieve complete structure determination of materials of biological interest that do not crystallize as single crystals of suitable size and quality for single-crystal X-ray diffraction.

| S-EPMC3121957 | biostudies-literature

Crystal structure of trirubidium citrate from laboratory X-ray powder diffraction data and DFT comparison.

Project description:The crystal structure of trirubidium citrate, 3Rb+·C6H5O73-, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The two independent Rb+ cations are seven- and eight-coordinate, with bond-valence sums of 0.99 and 0.92 valence units. The coordination polyhedra share edges and corners to form a three-dimensional framework. The only hydrogen bond is an intra-molecular one between the hy-droxy group and the central carboxyl-ate, with graph set S(5). The hydro-phobic methyl-ene groups lie in pockets in the framework.

| S-EPMC5290576 | biostudies-literature

Phasing electron diffraction data by molecular replacement: strategy for structure determination and refinement.

Project description:Electron crystallography is arguably the only electron cryomicroscopy (cryo EM) technique able to deliver atomic resolution data (better then 3 Å) for membrane proteins embedded in a membrane. The progress in hardware improvements and sample preparation for diffraction analysis resulted in a number of recent examples where increasingly higher resolutions were achieved. Other chapters in this book detail the improvements in hardware and delve into the intricate art of sample preparation for microscopy and electron diffraction data collection and processing. In this chapter, we describe in detail the protocols for molecular replacement for electron diffraction studies. The use of a search model for phasing electron diffraction data essentially eliminates the need of acquiring image data rendering it immune to aberrations from drift and charging effects that effectively lower the attainable resolution.

| S-EPMC3851287 | biostudies-literature

Crystal structure of calcium perchlorate anhydrate, Ca(ClO4)2, from laboratory powder X-ray diffraction data.

Project description:The crystal structure of calcium perchlorate anhydrate was determined from laboratory X-ray powder diffraction data. The title compound was obtained by heating hydrated calcium perchlorate [Ca(ClO4)2·xH2O] at 623?K in air for 12?h. It crystallizes in the ortho-rhom-bic space group Pbca and is isotypic with Ca(AlD4)2. The asymmetric unit contains one Ca, two Cl and eight O sites, all on general sites (Wyckoff position 8c). The crystal structure consists of isolated ClO4- tetra-hedra and Ca2+ cations. The Ca2+ cation is coordinated by eight O atoms of eight symmetry-related ClO4- tetra-hedra within a distorted square-anti-prismatic environment.

| S-EPMC5946979 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data