Klajite, MnCu4(AsO4)2(AsO3OH)2(H2O)10, from Jáchymov (Czech Republic): the second world occurrence

2014 ◽  
Vol 78 (1) ◽  
pp. 119-129 ◽  
Author(s):  
J. Plášil ◽  
A. V. Kasatkin ◽  
R. Škoda ◽  
P. Škácha
Keyword(s):  
Czech Republic ◽  
Current Data ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Data Set ◽  
X Ray ◽  
Ideal Stoichiometry ◽  
Second World ◽  
Bond Valence Analysis

AbstractKlajite, MnCu4(AsO4)2(AsO3OH)2(H2O)10, the Mn-Cu-bearing member of the lindackerite group, was found in Jáchymov, Czech Republic, as the second world occurrence. It is associated with ondrušite and other arsenate minerals growing on the quartz gangue with disseminated primary sulfides, namely tennantite and chalcopyrite. Electron-microprobe data showed klajite aggregates to be chemically inhomogeneous at larger scales, varying from Mn-Ca-rich to Cu-rich domains. The chemical composition of the the Mn-rich parts of aggregates can be expressed by the empirical formula (Mn0.46Ca0.22Cu0.07Mg0.02)∑0.77(Cu3.82Mg0.14Ca0.03Zn0.01)∑4.00(As1.94Si0.06)∑2.00O8[AsO2.73(OH)1.27]2(H2O)10 (mean of seven representative spots; calculated on the basis of As + Si + P = 4 a.p.f.u. (atoms per formula unit) and 10 H2O from ideal stoichiometry), showing a slight cationic deficiency at the key Me-site. According to single-crystal X-ray diffraction, klajite from Jáchymov is triclinic, P , with a = 6.4298(8), b = 7.9716(8), c = 10.707(2) Å, α = 85.737(12)°, β = 80.994(13)°, γ = 84.982(10)°, and V = 538.85(14) Å3, Z = 1. The crystal structure was refined to R1 = 0.0628 for 1034 unique observed reflections (with Iobs > 3σ(I)), confirming that klajite (Mn-Cu member) and ondrušite (Ca-Cu member) are isostructural. The current data-set allowed determination of the positions of several hydrogen atoms. Discussion on hydrogen bonding networks in the structure of klajite as well as detailed bond-valence analysis are provided.

Determination of depth profiles from X-ray diffraction data

1993 ◽  
Vol 8 (2) ◽  
pp. 122-126 ◽  
Author(s):  
Paul Predecki
Keyword(s):  
Diffraction Data ◽  
Direct Method ◽  
Sample Surface ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Depth Profiles ◽  
A Direct Method

A direct method is described for determining depth profiles (z-profiles) of diffraction data from experimentally determined τ-profiles, where z is the depth beneath the sample surface and τ is the 1/e penetration depth of the X-ray beam. With certain assumptions, the relation between these two profile functions can be expressed in the form of a Laplace transform. The criteria for fitting experimental τ-data to functions which can be utilized by the method are described. The method was applied to two τ-data sets taken from the literature: (1) of residual strain in an A1 thin film and (2) of residual stress in a surface ground A12O3/5vol% TiC composite. For each data set, it was found that the z-profiles obtained were of two types: oscillatory and nonoscillatory. The nonoscillatory profiles appeared to be qualitatively consistent for a given data set. The oscillatory profiles were considered to be not physically realistic. For the data sets considered, the nonoscillatory z-profiles were found to lie consistently above the corresponding τ-profiles, and to approach the τ-profiles at large z, as expected from the relation between the two.

scholarly journals Absolute configuration of naturally occurring glabridin

2013 ◽  
Vol 69 (11) ◽  
pp. 1212-1216 ◽  
Author(s):  
Charlotte Simmler ◽  
Frank R. Fronczek ◽  
Guido F. Pauli ◽  
Bernard D. Santarsiero
Keyword(s):  
Absolute Configuration ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Naturally Occurring ◽  
Nmr Data ◽  
Stereochemical Analysis ◽  
Medium Pressure Liquid Chromatography ◽  
Species Specific

The title compound {systematic name: 4-[(3R)-8,8-dimethyl-3,4-dihydro-2H-pyrano[2,3-f]chromen-3-yl]benzene-1,3-diol, commonly named glabridin}, C20H20O4, is a species-specific biomarker from the rootsGlycyrrhiza glabraL. (European licorice, Fabaceae). In the present study, this prenylated isoflavan has been purified from an enriched CHCl3fraction of the extract of the root, using three steps of medium-pressure liquid chromatography (MPLC) by employing HW-40F, Sephadex LH-20 and LiChroCN as adsorbents. Pure glabridin was crystallized from an MeOH–H2O mixture (95:5 v/v) to yield colorless crystals containing one molecule per asymmetric unit (Z′ = 1) in the space groupP212121. Although the crystal structure has been reported before, the determination of the absolute configuration remained uncertain. Stereochemical analysis, including circular dichroism, NMR data and an X-ray diffraction data set with Bijvoet differences, confirms that glabridin, purified from its natural source, is found only in a C3Rconfiguration. These results can therefore be used as a reference for the assignment of the configuration and enantiopurity of any isolated or synthetic glabridin sample.

NEUTRON DIFFRACTION DETERMINATION OF THE HYDROGEN POSITIONS IN NATROLITE

1964 ◽  
Vol 42 (2) ◽  
pp. 229-240 ◽  
Author(s):  
B. H. Torrie ◽  
I. D. Brown ◽  
H. E. Petch
Keyword(s):  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Oxygen Atom ◽  
Water Molecule ◽  
Neutron Diffraction Data ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Diffraction Determination

Neutron diffraction data obtained with single crystals of natrolite, Na2Al2Si3O10.2H20, have been analyzed using Fourier difference synthesis arid least squares methods. The details of the aluminosilicate framework were found to be in agreement with the results of earlier X-ray diffraction studies. The oxygen atom of the water molecule is linked by bent hydrogen bonds to two oxygen atoms in the framework, making an O—O—O angle of 134°. Lying almost in the O—O—O plane, the hydrogen atoms are located at distances of 0.94 ± 0.03 and 0.98 ± 0.02 Å from the oxygen of the water molecule and make with it an H—O—H angle of 108°. Natrolite thus provides an excellent example of the ability of the water molecule to resist the influence of the environment in opening the H—O—H angle.

scholarly journals Hydrogen disorder in kaatialaite Fe[AsO2(OH)2]5H2O from Jáchymov, Czech Republic: determination from low-temperature 3D electron diffraction

IUCrJ ◽  
2021 ◽  
Vol 8 (1) ◽  
pp. 116-123
Author(s):  
Gwladys Steciuk ◽  
Juraj Majzlan ◽  
Jakub Plášil
Keyword(s):  
Hydrogen Bonding ◽  
Czech Republic ◽  
Electron Diffraction ◽  
Low Temperature ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Heavy Atoms ◽  
Recent Developments ◽  
3D Electron

Kaatialaite mineral Fe[AsO2(OH)2]5H2O from Jáchymov, Czech Republic forms white aggregates of needle-shaped crystals with micrometric size. Its structure at ambient temperature has already been reported but hydrogen atoms could not be identified from single-crystal X-ray diffraction. An analysis using 3D electron diffraction at low temperature brings to light the hydrogen positions and the existence of hydrogen disorder. At 100 K, kaatialaite is described in a monoclinic unit cell of a = 15.46, b = 19.996, c = 4.808 Å, β = 91.64° and V = 1485.64 Å3 with space group P21/n. The hydrogen sites were revealed after refinements both considering the dynamical effects and ignoring them. The possibility to access most of the hydrogen positions, including partially occupied ones among heavy atoms, from the kinematical refinement is due to the recent developments in the analysis of 3D electron data. The hydrogen bonding observed in kaatialaite provides examples of H2O configurations that have not been observed before in the structures of oxysalts with the presence of unusual inverse transformer H2O groups.

Perutz and Kendrew: The Heroic Era of Structural Molecular Biology

2020 ◽  
pp. 90-109
Author(s):  
John Meurig Thomas
Keyword(s):  
Amino Acid ◽  
Human Populations ◽  
Amino Acid Residues ◽  
Experimental Equipment ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
New Approach ◽  
X Ray ◽  
Diffraction Patterns

When Perutz and Kendrew embarked on their determination of the structures of haemoglobin and myoglobin, most scientists felt that they would never succeed. These molecules contain approximately thousands of non-hydrogen atoms, whereas those molecules that had yielded to X-ray analysis previously contained fewer than a hundred non-hydrogen atoms. For real progress to be made in solving the structures of the giant proteins, a fundamentally new approach had to be evolved, which inter alia required massive computer power to handle the data contained in hundreds of thousands of X-ray diffraction patterns, and new experimental equipment like ultra-stable X-ray sources were required to record the diffraction data. The first successes were registered by Kendrew, who was able to reveal, in unprecedented detail, the atomically resolved structure of myoglobin with its haem group (containing a central iron atom) and all the details of the amino acid residues that constituted the backbone chain of the protein. Likewise, haemoglobin revealed its secrets. This also led to the discovery of sickle-cell anaemia, the first ever recorded molecular disease. It also shed new light on the pathology of anomalous haemoglobins in human populations.

Sem and X-Ray Analysis of Renal and Biliary Calculi

1976 ◽  
Vol 34 ◽  
pp. 306-307
Author(s):  
R. J. Narconis ◽  
G. L. Johnson
Keyword(s):  
Chemical Constituents ◽  
Natural State ◽  
X Ray Diffraction ◽  
Chemical Methods ◽  
X Ray ◽  
Additional Dimension ◽  
Biliary Calculi ◽  
Calculus Formation ◽  
Scanning Electron

Analysis of the constituents of renal and biliary calculi may be of help in the management of patients with calculous disease. Several methods of analysis are available for identifying these constituents. Most common are chemical methods, optical crystallography, x-ray diffraction, and infrared spectroscopy. The application of a SEM with x-ray analysis capabilities should be considered as an additional alternative.A scanning electron microscope equipped with an x-ray “mapping” attachment offers an additional dimension in its ability to locate elemental constituents geographically, and thus, provide a clue in determination of possible metabolic etiology in calculus formation. The ability of this method to give an undisturbed view of adjacent layers of elements in their natural state is of advantage in determining the sequence of formation of subsequent layers of chemical constituents.

New Coordination Compounds of Fe(III) with Organic Ligands

2009 ◽  
Vol 59 (12) ◽  
Author(s):  
Mihaela Flondor ◽  
Ioan Rosca ◽  
Doina Sibiescu ◽  
Mihaela-Aurelia Vizitiu ◽  
Daniel-Mircea Sutiman ◽  
...  
Keyword(s):  
Chemical Analysis ◽  
Complex Compounds ◽  
Organic Ligands ◽  
X Ray Diffraction ◽  
X Ray ◽  
Elemental Chemical Analysis ◽  
Structural Formulae ◽  
Paramagnetic Properties

In this paper the synthesis and the study of some complex compounds of Fe(III) with ligands derived from: 2-(4-chloro-phenylsulfanyl)-1-(2-hydroxy-3,5-diiodo-phenyl)-ethanone (HL1), 1-(3,5-dibromo-2-hydroxy-phenyl)-2-phenylsulfanyl-ethanone(HL2), and 2-(4-chloro-phenylsulfanyl)-1-(3,5-dibromo-2-hydroxy-phenyl)-ethanone (HL3) is presented. The characterization of these complexes is based on method as: the elemental chemical analysis, IR and ESR spectroscopy, M�ssbauer, the thermogravimetric analysis and X-ray diffraction. Study of the IR and chemical analysis has evidenced that the precipitates form are a complexes and the combination ratio of M:L is 1:2. The central atoms of Fe(III) presented paramagnetic properties and a octaedric hybridization. Starting from this precipitation reactions, a method for the gravimetric determination of Fe(III) with this organic ligands has been possible. Based on the experimental data on literature indications, the structural formulae of the complex compounds are assigned.

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