Hakite from Příbram, Czech Republic: compositional variability, crystal structure and the role in Se mineralization

2016 ◽  
Vol 80 (6) ◽  
pp. 1115-1128 ◽  
Author(s):  
P. Škácha ◽  
J. Sejkora ◽  
L. Palatinus ◽  
E. Makovicky ◽  
J. Plášil ◽  
...  
Keyword(s):  
Czech Republic ◽  
Diffraction Data ◽  
Empirical Formula ◽  
Structure Refinement ◽  
Sensu Stricto ◽  
Electron Diffraction Data ◽  
X Ray Diffraction ◽  
Transmission Electron ◽  
Precession Electron Diffraction ◽  
Dominant Member

AbstractHakite, ideally Cu10Hg2Sb4Se13, is a Se-dominant member of the tetrahedrite group occurring at only a few localities in the World. A new occurrence of this mineral in the Příbram uranium and base-metal ore district, Central Bohemia, Czech Republic, is reported in this paper. Hakite was found to be locally abundant and was identified in several samples with Se mineralization. Three chemically distinct types of hakite were distinguished based on electron microprobe study, Hg-rich hakite (hakitesensu stricto), Zn-rich hakite and Cd-rich hakite. Hg-hakite dominates among the samples studied. Its average empirical formula based on 29 apfu (n= 54) is (Cu5.61Ag0.39)∑6.00Cu4.00(Hg1.61Zn0.20Cu0.19Cd0.15Fe0.04)∑2.19(Sb3.85As0.28)∑4.13(Se11.55S1.14)∑12.69. Less common is the Zn-hakite, (Cu5.80Ag0.20)∑6.00Cu4.00(Zn1.33Hg0.42Cd0.22Cu0.18Fe0.01)∑2.16(Sb3.85As0.26)∑4.11(Se10.92S1.81)∑12.73(n= 22), and rare Cd-hakite has an empirical formula (n= 7) of (Cu5.84Ag0.16)∑6.00Cu4.00(Cd1.27Zn0.60Cu0.10Hg0.07Fe0.02)∑2.06(Sb4.00As0.19)∑4.19(Se12.14S0.61)∑12.75. The refined unit cell of Hg-hakite from Příbram, obtained from powder X-ray diffraction data, isa= 10.8783(3) Å withV= 1287.3(1) Å3(Z= 4, for the cubic space groupI4̄3m). Structure refinement from the precession electron diffraction data collected on the transmission electron microscope (R= 24.4% for 424 observed reflections), confirmed that hakite is isostructural with tetrahedrite. The evolution of hydrothermal fluids, from which Se mineralization formed, suggests a distinct enrichment in sulfur and depletion in selenium over the time span of crystallization.

Al analogue of chayesite from a lamproite of Cancarix, SE Spain, and its crystal structure

2020 ◽  
Vol 196 (3) ◽  
pp. 193-198
Author(s):  
Natalia V. Zubkova ◽  
Nikita V. Chukanov ◽  
Christof Schäfer ◽  
Konstantin V. Van ◽  
Igor V. Pekov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Diffraction Data ◽  
Empirical Formula ◽  
Structure Refinement ◽  
Crystal Chemical ◽  
Chemical Formula ◽  
Crystal Chemical Formula ◽  
X Ray Diffraction ◽  
Se Spain ◽  
X Ray

Al analogue of chayesite (with Al > Fe3+) was found in a lamproite from Cancarix, SE Spain. The mineral forms green thick-tabular crystals up to 0.4 mm across in cavities. The empirical formula derived from EMP measurements and calculated on the basis of 17 Mg + Fe + Al + Si apfu is (K0.75 Na0.20 Ca0.11)Mg3.04 Fe0.99 Al1.18 Si11.80 O30. The crystal structure was determined from single crystal X-ray diffraction data ( R = 2.38%). The mineral is hexagonal, space group P 6/ mcc, a = 10.09199(12), c = 14.35079(19) Å, V = 1265.78(3) Å3, Z = 2. Fe is predominantly divalent. Al is mainly distributed between the octahedral A site and the tetrahedral T 2 site. The crystal chemical formula derived from the structure refinement is C (K0.73 Na0.16 Ca0.11)B (Na0.02)4 A(Mg0.42 Al0.29 Fe0.29)2 T 2(Mg0.71 Fe0.16 Al0.13)3 T 1(Si0.985 Al0.015)12 O30.

Coronadit z dolu Řimbaba v Bohutíně u Příbrami (Česká republika)

2021 ◽  
Vol 29 (2) ◽  
pp. 281-284
Author(s):  
Petr Pauliš ◽  
Luboš Vrtiška ◽  
Zdeněk Dolníček ◽  
Radana Malíková ◽  
Ondřej Pour
Keyword(s):  
Czech Republic ◽  
Diffraction Data ◽  
Empirical Formula ◽  
Unit Cell ◽  
Chemical Analyses ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Along with the abundant pyromorphite, relatively frequent coronadite was found in the Řimbaba mine in Bohutín near Příbram (Czech Republic). Coronadite forms up to 5 mm thick black matt and greasy coatings and cavity fillings. The unit cell parameters of coronadite, refined from the powder X-ray diffraction data, are a 9.943(17), b 2.876(8), c 9.820(11) Å, β 90.4(5)° and V 280.8(9) Å3 (space group I2/m). Chemical analyses correspond to the empirical formula Pb1.53Sb0.07Zn0.02(Mn4+5.62Mn3+2.06)O16.

scholarly journals Accurate structure refinement from 3D electron diffraction data

2014 ◽  
Vol 70 (a1) ◽  
pp. C374-C374
Author(s):  
Lukáš Palatinus ◽  
Cinthia Corrêa ◽  
Gwladys Mouillard ◽  
Philippe Boullay ◽  
Damien Jacob
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Structure Refinement ◽  
Three Dimensional ◽  
Diffraction Theory ◽  
Electron Diffraction Data ◽  
Dynamical Structure ◽  
Present Contribution ◽  
Figures Of Merit ◽  
Precession Electron Diffraction

Structure determination from electron diffraction data has seen an enormous progress over the past few years. At present, complex structures with hundreds of atoms in the unit cell can be solved from electron diffraction using the concept of electron diffraction tomography (EDT), possibly combined with precession electron diffraction (PED) [1]. Unfortunately, the initial model is typically optimized using the kinematical approximation to calculate model diffracted intensities. This approximation is quite inaccurate for electron diffraction and leads to high figures of merit and inaccurate results with unrealistically low standard uncertainties. The obvious remedy to the problem is the use of dynamical diffraction theory to calculate the model intensities in structure refinement. This technique has been known and used before, but it has not become very popular, because good fits could be obtained only for sufficiently perfect and sufficiently thin crystals. It has been shown recently on several zone-axis patterns [2] that the quality of the refinement can be improved by using precession electron diffraction. In the present contribution we demonstrate that the same approach can be successfully used to refine crystal structures against non-oriented patterns acquired by EDT combined with PED (PEDT in short). Because the PEDT technique provides three-dimensional diffraction information, it can be used for a complete structure refinement. Several test examples demonstrate that the dynamical structure refinement yields better figures of merit and more accurate results than the refinement using kinematical approximation.

Structure refinement from precession electron diffraction data

2013 ◽  
Vol 69 (2) ◽  
pp. 171-188 ◽  
Author(s):  
Lukáš Palatinus ◽  
Damien Jacob ◽  
Priscille Cuvillier ◽  
Mariana Klementová ◽  
Wharton Sinkler ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Structure Refinement ◽  
Electron Diffraction Data ◽  
Precession Electron Diffraction

scholarly journals Structure refinement against precession electron diffraction data

2012 ◽  
Vol 68 (a1) ◽  
pp. s60-s60
Author(s):  
L. Palatinus ◽  
M. Klementova ◽  
D. Jacob ◽  
P. Cuvillier ◽  
W. Sinkler ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Structure Refinement ◽  
Electron Diffraction Data ◽  
Precession Electron Diffraction

scholarly journals Refinements on electron diffraction data of β-glycine in MoPro: a quest for an improved structure model

2021 ◽  
Vol 54 (4) ◽  
Author(s):  
Kunal Kumar Jha ◽  
Barbara Gruza ◽  
Michał Leszek Chodkiewicz ◽  
Christian Jelsch ◽  
Paulina Maria Dominiak
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Structure Refinement ◽  
Electron Diffraction Data ◽  
Bethe Equation ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atom Model ◽  
X Ray Scattering

The advancement in 3D electron diffraction (3D ED) techniques that lead to a revolution in molecular structure determination using nano-sized crystals is now achieving atomic resolution. The structures can be obtained from 3D ED data with tools similar to those used for X-ray structure determination. In this context, the MoPro software, originally designed for structure and charge density refinements using X-ray diffraction data, has been adapted. Structure refinement on 3D ED data was achieved via implementation of electron scattering factors available in the literature and by application of the Mott–Bethe equation to X-ray scattering factors computed from the multipolar atom model. The multipolar model was parametrized using the transferable pseudoatom databanks ELMAM2 and UBDB. Applying the independent atom model (IAM), i.e. spherical neutral atom refinement, to 3D ED data on β-glycine in MoPro resulted in structure and refinement statistics comparable to those obtained from other well known software. Use of the transferred aspherical atom model (TAAM) led to improvement of the refinement statistics and a better fit of the model to the 3D ED data as compared with the spherical atom refinement. The anisotropic displacement parameters of non-H atoms appear underestimated by typically 0.003 Å2 for the non-H atoms in IAM refinement compared with TAAM. Thus, MoPro is shown to be an effective tool for crystal structure refinement on 3D ED data and allows use of a spherical or a multipolar atom model. Electron density databases can be readily transferred with no further modification needed when the Mott–Bethe equation is applied.

The crystal chemistry of the uranyl carbonate mineral grimselite, (K, Na)3Na[(UO2)(CO3)3](H2O), from Jáchymov, Czech Republic

2012 ◽  
Vol 76 (3) ◽  
pp. 443-453 ◽  
Author(s):  
J. Plášil ◽  
K. Fejfarová ◽  
R. Skála ◽  
R. Škoda ◽  
N. Meisser ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Czech Republic ◽  
Structure Refinement ◽  
Unit Cell ◽  
Carbonate Mineral ◽  
X Ray Diffraction ◽  
The Czech Republic ◽  
Cell Parameters ◽  
Uranyl Carbonate ◽  
Diffraction Peaks

AbstractTwo crystals of the uranyl carbonate mineral grimselite, ideally K3Na[(UO2)(CO3)3](H2O), from Jáchymov in the Czech Republic were studied by single-crystal X-ray diffraction and electron-probe microanalysis. One crystal has considerably more Na than the ideal chemical composition due to substitution of Na into KO8 polyhedra; the composition of the other crystal is nearer to ideal, and similar to synthetic grimselite. The presence of Na atoms in KO8 polyhedra, which are located in channels in the crystal structure, reduces their volume, and as a result the unit-cell volume also decreases. Structure refinement shows that the formula for the sample with the anomalously high Na content is (K2.43Na0.57)Σ3.00Na[(UO2)(CO3)3](H2O). The unit-cell parameters, refined in space group P2c, are a = 9.2507(1), c = 8.1788(1) Å, V = 606.14(3) Å3 and Z = 2. The crystal structure was refined to R1 = 0.0082 and wR1 = 0.0185 with a GOF = 1.33, based on 626 observed diffraction peaks [Iobs>3σ(I)].

Hrabákite, Ni9PbSbS8, a new member of the hauchecornite group from Příbram, Czech Republic

2021 ◽  
pp. 1-8
Author(s):  
Jiří Sejkora ◽  
Pavel Škácha ◽  
Jakub Plášil ◽  
Zdeněk Dolníček ◽  
Jana Ulmanová
Keyword(s):  
Czech Republic ◽  
Diffraction Data ◽  
New Mineral ◽  
X Ray Diffraction ◽  
Calculated Density ◽  
X Ray ◽  
Reflected Light ◽  
Mohs Hardness ◽  
Cation Sites ◽  
The Ideal

Abstract The new mineral hrabákite (IMA2020-034) was found in siderite–sphalerite gangue with minor dolomite–ankerite at the dump of shaft No. 9, one of the mines in the abandoned Příbram uranium and base-metal district, central Bohemia, Czech Republic. Hrabákite is associated with Pb-rich tučekite, Hg-rich silver, stephanite, nickeline, millerite, gersdorffite, sphalerite and galena. The new mineral occurs as rare prismatic crystals up to 120 μm in size and allotriomorphic grains. Hrabákite is grey with a brownish tint. Mohs hardness is ca. 5–6; the calculated density is 6.37 g.cm–3. In reflected light, hrabákite is grey with a brown hue. Bireflectance is weak and pleochroism was not observed. Anisotropy under crossed polars is very weak (brownish tints) to absent. Internal reflections were not observed. Reflectance values of hrabákite in air (Rmin–Rmax, %) are: 39.6–42.5 at 470 nm, 45.0–47.5 at 546 nm, 46.9–49.2 at 589 nm and 48.9–51.2 at 650 nm). The empirical formula for hrabákite, based on electron-microprobe analyses (n = 11), is (Ni8.91Co0.09Fe0.03)9.03(Pb0.94Hg0.04)0.98(Sb0.91As0.08)0.99S7.99. The ideal formula is Ni9PbSbS8, which requires Ni 47.44, Pb 18.60, Sb 10.93 and S 23.03, total of 100.00 wt.%. Hrabákite is tetragonal, P4/mmm, a = 7.3085(4), c = 5.3969(3) Å, with V = 288.27(3) Å3 and Z = 1. The strongest reflections of the calculated powder X-ray diffraction pattern [d, Å (I)(hkl)] are: 3.6543(57)(200); 3.2685(68)(210); 2.7957(100)(211); 2.3920(87)(112); 2.3112(78)(310); 1.8663(74)(222); and 1.8083(71)(302). According to the single-crystal X-ray diffraction data (Rint = 0.0218), the unit cell of hrabákite is undoubtedly similar to the cell reported for tučekite. The structure contains four metal cation sites, two Sb (Sb1 dominated by Pb2+) and two Ni (with minor Co2+ content) sites. The close similarity in metrics between hrabákite and tučekite is due to similar bond lengths of Pb–S and Sb–S pairs. Hrabákite is named after Josef Hrabák, the former professor of the Příbram Mining College.

scholarly journals Redetermination of Sr2PdO3 from single-crystal X-ray data

2019 ◽  
Vol 75 (1) ◽  
pp. 30-32
Author(s):  
Gohil S. Thakur ◽  
Hans Reuter ◽  
Claudia Felser ◽  
Martin Jansen
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Diffraction Data ◽  
Structure Refinement ◽  
Structure Type ◽  
X Ray Diffraction ◽  
High Quality ◽  
X Ray ◽  
Cell Parameters ◽  
Anisotropic Displacement Parameters

The crystal structure redetermination of Sr2PdO3 (distrontium palladium trioxide) was carried out using high-quality single-crystal X-ray data. The Sr2PdO3 structure has been described previously in at least three reports [Wasel-Nielen & Hoppe (1970). Z. Anorg. Allg. Chem. 375, 209–213; Muller & Roy (1971). Adv. Chem. Ser. 98, 28–38; Nagata et al. (2002). J. Alloys Compd. 346, 50–56], all based on powder X-ray diffraction data. The current structure refinement of Sr2PdO3, as compared to previous powder data refinements, leads to more precise cell parameters and fractional coordinates, together with anisotropic displacement parameters for all sites. The compound is confirmed to have the orthorhombic Sr2CuO3 structure type (space group Immm) as reported previously. The structure consists of infinite chains of corner-sharing PdO4 plaquettes interspersed by SrII atoms. A brief comparison of Sr2PdO3 with the related K2NiF4 structure type is given.

scholarly journals Crystal structure refinement of magnesium zinc divanadate, MgZnV2O7, from powder X-ray diffraction data

2021 ◽  
Vol 77 (6) ◽  
pp. 588-591
Author(s):  
Stephanie J. Hong ◽  
Jun Li ◽  
Mas A. Subramanian
Keyword(s):  
Crystal Structure ◽  
Diffraction Data ◽  
Structure Refinement ◽  
Atomic Ratio ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Trigonal Bipyramidal ◽  
Wyckoff Position ◽  
Distorted Trigonal Bipyramidal

The crystal structure of magnesium zinc divanadate, MgZnV2O7, was determined and refined from laboratory X-ray powder diffraction data. The title compound was synthesized by a solid-state reaction at 1023 K in air. The crystal structure is isotypic with Mn0.6Zn1.4V2O7 (C2/m; Z = 6) and is related to the crystal structure of thortveitite. The asymmetric unit contains two metal sites with statistically distributed magnesium and zinc atoms with the atomic ratio close to 1:1. One (Mg/Zn) metal site (M1) is located on Wyckoff position 8j and the other (M2) on 4h. Three V sites (all on 4i), and eight O (three 8j, four 4i, and one 2b) sites complete the asymmetric unit. The structure is an alternate stacking of V2O7 layers and (Mg/Zn) atom layers along [20\overline{1}]. It is distinct from other related structures in that each V2O7 layer consists of two groups: a V2O7 dimer and a V4O14 tetramer. Mixed-occupied M1 and M2 are coordinated by oxygen atoms in distorted trigonal bipyramidal and octahedral sites, respectively.

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