scholarly journals About the Role of Fluorine-Bearing Apatite in the Formation of Oxalate Kidney Stones

Crystals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 486
Author(s):  
Anatolii V. Korneev ◽  
Olga V. Frank-Kamenetskaya ◽  
Alina R. Izatulina
Keyword(s):  
Kidney Stones ◽  
Microprobe Analysis ◽  
Fluorine Content ◽  
Unit Cell ◽  
Simultaneous Increase ◽  
Cell Parameters ◽  
Ph Values ◽  
Mineral Phases ◽  
Calcium Oxalates

Using electron microprobe analysis, 17 kidney stones containing apatite were studied. According to the results of the research, it was found that the apatite of all the oxalate kidney stones contained fluorine, while in the apatite of the phosphate kidney stones, fluorine was present in trace amounts or absent. Direct correlation between the amount of oxalate mineral phases and the fluorine content was observed. Ionic substitutions in the apatite of kidney stones have a multidirectional effect on the unit cell parameters. The fluorine content increases with the increase of a unit cell parameter, which is probably associated with a simultaneous increase in the amount of H2O in the structure of apatite. The results of thermodynamic modeling show that fluorapatite is stable at lower pH values than hydroxylapatite, and therefore can be a precursor of calcium oxalates crystallization.

scholarly journals Crystal Chemistry and High-Temperature Behaviour of Ammonium Phases NH4MgCl3·6H2O and (NH4)2Fe3+Cl5·H2O from the Burned Dumps of the Chelyabinsk Coal Basin

Minerals ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 486 ◽  
Author(s):  
Andrey A. Zolotarev ◽  
Elena S. Zhitova ◽  
Maria G. Krzhizhanovskaya ◽  
Mikhail A. Rassomakhin ◽  
Vladimir V. Shilovskikh ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Temperature ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Coal Basin ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Mineral Phases

The technogenic mineral phases NH4MgCl3·6H2O and (NH4)2Fe3+Cl5·H2O from the burned dumps of the Chelyabinsk coal basin have been investigated by single-crystal X-ray diffraction, scanning electron microscopy and high-temperature powder X-ray diffraction. The NH4MgCl3·6H2O phase is monoclinic, space group C2/c, unit cell parameters a = 9.3091(9), b = 9.5353(7), c = 13.2941(12) Å, β = 90.089(8)° and V = 1180.05(18) Å3. The crystal structure of NH4MgCl3·6H2O was refined to R1 = 0.078 (wR2 = 0.185) on the basis of 1678 unique reflections. The (NH4)2Fe3+Cl5·H2O phase is orthorhombic, space group Pnma, unit cell parameters a = 13.725(2), b = 9.9365(16), c = 7.0370(11) Å and V = 959.7(3) Å3. The crystal structure of (NH4)2Fe3+Cl5·H2O was refined to R1 = 0.023 (wR2 = 0.066) on the basis of 2256 unique reflections. NH4MgCl3·6H2O is stable up to 90 °C and then transforms to the less hydrated phase isotypic to β-Rb(MnCl3)(H2O)2 (i.e., NH4MgCl3·2H2O), the latter phase being stable up to 150 °C. (NH4)2Fe3+Cl5·H2O is stable up to 120 °C and then transforms to an X-ray amorphous phase. Hydrogen bonds provide an important linkage between the main structural units and play the key role in determining structural stability and physical properties of the studied phases. The mineral phases NH4MgCl3·6H2O and (NH4)2Fe3+Cl5·H2O are isostructural with natural minerals novograblenovite and kremersite, respectively.

Embreyite: structure determination, chemical formula and comparative crystal chemistry

2018 ◽  
Vol 82 (2) ◽  
pp. 275-290 ◽  
Author(s):  
Vadim M. Kovrugin ◽  
Oleg I. Siidra ◽  
Igor V. Pekov ◽  
Nikita V. Chukanov ◽  
Dmitry A. Khanin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Microprobe Analysis ◽  
Direct Methods ◽  
Structural Similarity ◽  
Structural Type ◽  
Unit Cell ◽  
Single Crystal Xrd ◽  
Cell Parameters ◽  
Distorted Octahedra

ABSTRACTEmbreyite from the Berezovskoe, Urals, Russia, was studied by the means of powder X-ray diffraction (XRD), single-crystal XRD, infrared spectroscopy and microprobe analysis. The empirical formula of embreyite obtained on the basis of microprobe analysis is Pb1.29Cu0.07Cr0.52P0.43O4(without taking into account the presence of H2O). An examination of single-crystal XRD frames of the tested crystals cut from embreyite intergrowths revealed split reflection spots of weak intensities, even after a long exposure time. The crystal structure of embreyite (monoclinic,C2/m,a= 9.802(16),b= 5.603(9),c= 7.649(12) Å, β = 114.85(3)oandV= 381.2(11) Å3) has been solved by direct methods and refined toR1= 0.050 for 318 unique observed reflections. The powder XRD patterns of the holotype embreyite and the fresh material studied are close in bothdvalues and the intensities match the pattern calculated from the structural single-crystal XRD data. The unit-cell parameters were re-calculated for the holotype sample using a new cell setting and correspondinghklindices. The crystal structure of embreyite is based on layers formed by corner-sharing mixed chromate-phosphate tetrahedra and PbO6distorted octahedra. The interlayer space is filled by disordered Pb2+and Cu2+cations. Generally, the crystal structure of embreyite can be referred to the structural type of palmierite. {Pb[(Cr,P)O4]2]} layers in embreyite are similar in topology to those in yavapaiite-type compounds. The general formula of embreyite can be represented as (Pbx$M_y^{2 +} $□1–x–y)2{Pb[(Cr,P)O4]2}(H2O)n, whereM2+= Cu and Zn and 0.5 ≤x+y≤ 1, or, in the simplified form: (Pb,Cu,□)2{Pb[(Cr,P)O4]2}(H2O)n. The simplified formula of embreyite is similar in stoichiometry to vauquelinite and may explain the existence of the solid-solution series. The determination of the crystal structure of embreyite may also help to resolve the crystal chemical nature of cassedanneite. The XRD pattern of cassedanneite contains a distinct reflection withd= 13.9 Å, forbidden for the embreyite unit cell. This feature may indicate the doubling of thecunit-cell parameter of cassedanneite in comparison with embreyite. We assume that cassedanneite has structural similarity to embreyite with, presumably, a disordered distribution of Cr and V.

scholarly journals Purification, crystallization and preliminary crystallographic analysis of DR0248, an MNT–HEPN fused protein fromDeinococcus radiodurans

2015 ◽  
Vol 71 (1) ◽  
pp. 49-53
Author(s):  
Gaelle Pesce ◽  
Simone Pellegrino ◽  
Sean McSweeney ◽  
AnaMaria Goncalves ◽  
Daniele de Sanctis
Keyword(s):  
Deinococcus Radiodurans ◽  
Crystallographic Analysis ◽  
Unit Cell ◽  
Nucleotide Binding Domain ◽  
Unit Cell Parameters ◽  
Dodecyldimethylamine Oxide ◽  
Space Group ◽  
Cell Parameters ◽  
Nucleotidyl Transferase

DR0248 is a protein identified in theDeinococcus radiodurans(DR) genome that is predicted to encompass two domains: an N-terminal minimal nucleotidyl transferase domain (MNT) and a C-terminal higher eukaryotes and prokaryotes nucleotide-binding domain (HEPN). These two domains, usually encoded in two ORFs, have been suggested to play the role of a toxin–antitoxin (TA) system in prokaryotes. Recombinant DR0248 was overexpressed and purified fromEscherichia coliand diffraction-quality crystals were obtained in the presence of the detergent molecules dodecyldimethylamine oxide (DDAO) and octaethylene glycol monododecyl ether (C12E8), which were used as crystallization additives. Crystals grown with DDAO diffracted to a resolution of 2.24 Å and belonged to space groupC2221, with unit-cell parametersa= 98.4,b= 129.9,c= 59.2 Å. Crystals grown with C12E8 diffracted to a resolution of 1.83 Å and belonged to space groupP212121, with unit-cell parametersa= 51.6,b= 87.2,c= 108.2 Å. The structure was solved by multiwavelength anomalous dispersion from zinc bound to the protein using a single crystal obtained in the presence of DDAO.

scholarly journals New data on gersdorffite and associated minerals from the Peloritani Mountains (Sicily, Italy)

2021 ◽  
Vol 33 (6) ◽  
pp. 717-726
Author(s):  
Daniela Mauro ◽  
Cristian Biagioni ◽  
Federica Zaccarini
Keyword(s):  
Crystal Structure ◽  
Microprobe Analysis ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Quartz Veins ◽  
Group I

Abstract. Gersdorffite, ideally NiAsS, and associated minerals from Contrada Zillì (Peloritani Mountains, Sicily, Italy) have been characterized through electron microprobe analysis and X-ray diffraction. Primary minerals, hosted in quartz veins, are represented by gersdorffite, tetrahedrite-(Fe), and chalcopyrite with minor pyrite and galena. Rare aikinite inclusions were observed in tetrahedrite-(Fe) and chalcopyrite. Gersdorffite occurs as euhedral to subhedral crystals, up to 1 mm in size, with (Sb,Bi)-enriched cores and (Fe,As)-enriched rims. Its chemical composition is (Ni0.79−0.95Fe0.18−0.04Co0.04−0.01)(As0.90−1.03Sb0.10−0.00Bi0.02−0.00)S0.98−0.92. It crystallizes in the space group P213, with unit-cell parameters a=5.6968(7) Å, V=184.88(7) Å3, and Z=4, and its crystal structure was refined down to R1= 0.035. Associated tetrahedrite-(Fe) has chemical formula (Cu5.79Ag0.07)Σ5.86(Cu3.96Fe1.59Zn0.45)Σ6.00(Sb3.95As0.17Bi0.03)Σ4.15S13.06, with unit-cell parameters a= 10.3815(10) Å, V=1118.9(3) Å3, and space group I-43m. Its crystal structure was refined to R1=0.027. Textural and crystallographic data suggest a polyphasic crystallization of gersdorffite under low-temperature conditions.

Structure of Pb-rich chabournéite from Jas Roux, France

2015 ◽  
Vol 71 (1) ◽  
pp. 81-88 ◽  
Author(s):  
Cristian Biagioni ◽  
Yves Moëlo ◽  
Georges Favreau ◽  
Vincent Bourgoin ◽  
Jean-Claude Boulliard
Keyword(s):  
Crystal Structure ◽  
Microprobe Analysis ◽  
Electron Microprobe Analysis ◽  
Structural Formula ◽  
Unit Cell ◽  
Single Crystal Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Cation Sites ◽  
Pyramidal Groups

The crystal structure of a specimen of `Pb-rich' chabournéite from Jas Roux, Hautes-Alpes, France, with the chemical formula obtained by electron microprobe analysis of Ag0.04 (1)Tl2.15 (2)Pb0.64 (1)Sb5.12 (1)As5.05 (1)S17.32 (5), has been solved by X-ray single-crystal diffraction on the basis of 36 550 observed reflections (withFo> 4σFo) with a finalR1= 0.074. Pb-rich chabournéite is triclinicP1, with unit-cell parametersa= 8.5197 (4),b= 42.461 (2),c= 16.293 (8) Å, α = 83.351 (2), β = 90.958 (2), γ = 84.275 (2)°,V= 5823 (3) Å3. Its structural formula is close to [Tl2(Pb0.8Tl0.1Sb1.1)](Sb4.1As4.9)S17, withZ= 8. Its crystal structure is formed by the alternation of two pairs of slabs along thebaxis, deriving from the SnS and PbS archetypes, respectively. 104 independent cation sites and 136 S sites occur in the unit cell. Slab interfaces show the alternation, alongc, of Tl sites, ninefold coordinated, with Pb, Sb or mixed/split (Pb,Sb) and (Pb,Tl) sites. Within the slabs, 72 independentM3+sites (M3+= As, Sb) occur. ConsideringM3+—S bond distances shorter than 2.70 Å,MS3triangular pyramidal groups are condensed according to variousMmSnchain fragments (`polymers'). The solution of the crystal structure of chabournéite allows its comparison with the closely related homeotypes protochabournéite and dalnegroite.

The crystal structure of barikaite

2013 ◽  
Vol 77 (8) ◽  
pp. 3093-3104 ◽  
Author(s):  
E. Makovicky ◽  
D. Topa
Keyword(s):  
Lone Electron Pair ◽  
Microprobe Analysis ◽  
Electron Microprobe Analysis ◽  
Unit Cell ◽  
Double Layers ◽  
Group Setting ◽  
Cell Parameters ◽  
Lattice Setting ◽  
Cation Sites ◽  
Trigonal Prismatic

AbstractElectron microprobe analysis of barikaite (Topa et al., 2013) indicates the chemical formula Ag2.90Tl0.04Pb9.31As11.26Sb8.12S40.37. Barikaite is monoclinic, with a 8.533(1) Å, b 8.075(1) Å, c 24.828(2) Å, and β 99.077(1)°; unit-cell volume 1689.2 Å3 and the space-group setting is P21/n. This compares well with the unit-cell parameters of rathite Pb10Tl0.9As17.9Sb1.3Ag2S40 from the Lengenbach deposit with the same lattice setting. Barikaite is a member of sartorite homologous series (N = 4). The unit cell of barikaite contains eight cation sites and ten anion sites. Four of the cation sites have mixed occupancies – the split sites As2–Sb2, As3–Sb3, Ag5–As5 and the site Me6 with three cations involved. Two of the lead sites, Pb1 and Pb2, display tricapped trigonal prismatic coordinations and alternate along the 8.53 Å a direction. They form zig-zag walls parallel to (001). There are three distinct [100] columns of alternating cations, As1–(As, Sb)2, Sb4–(As, Sb)3 and (As, Ag)5–(Pb, Sb)6 which together form trapezoidally configured single (013) layers. These layers aggregate into tightly-bonded double layers, separated by lone electron pair micelles. In barikaite, the predominantly As-occupied and Sb-occupied sites are distributed in a chess-board-like scheme.

Unit-cell parameters for scapolite solid solutions and a discontinuity at Me75, ideally NaCa3[Al5Si7O24](CO3)

2013 ◽  
Vol 28 (4) ◽  
pp. 269-275
Author(s):  
Sytle M. Antao
Keyword(s):  
Solid Solution ◽  
Unit Cell Volume ◽  
Microprobe Analysis ◽  
Electron Microprobe Analysis ◽  
Unit Cell ◽  
Formula Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters

Twenty-seven scapolite samples from various localities and with compositions between Me6–93 were obtained using electron microprobe analysis (EMPA). Their unit-cell parameters were obtained using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and Rietveld structure refinements using space group P42/n. The EMPA data show the well-known discontinuity at Me75. In addition, the unit-cell parameters, especially c, show a discontinuity at Me75 (=five Al atoms per formula unit, apfu), ideally NaCa3[Al5Si7O24](CO3), where the scapolite solid solution is divided into two (Me% = [Ca/(Ca + Na + K)] × 100). A maximum c parameter value occurs at Me37.5 (=four Al apfu ideally), where complete Al–Si, Na–Ca, and Cl–CO3 order occurs. The unit-cell volume, V, varies smoothly with Me% and Al apfu across the series.

scholarly journals Solid solution formation in the metatorbernite–metazeunerite system (Cu(UO 2 ) 2 (PO 4 ) 2− x (AsO 4 ) x . n H 2 O) and their stability under conditions of variable temperature

2019 ◽  
Vol 377 (2147) ◽  
pp. 20180242 ◽  
Author(s):  
Joanna Kulaszewska ◽  
Sandra Dann ◽  
Peter Warwick ◽  
Caroline Kirk
Keyword(s):  
Solid Solution ◽  
Low Temperatures ◽  
Variable Temperature ◽  
Unit Cell ◽  
Tetragonal Symmetry ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Mineral Phases

Mineral phases which can be thought of as members of a metatorbernite–metazeunerite solid solution (Cu(UO 2 ) 2 (PO 4 ) 2− x (AsO 4 ) x .8H 2 O have been identified in radioactive samples from spoil heaps at the uranium mine site in South Terras, Cornwall (grid reference SW935523) . A complete solid solution (0 <  x  < 2) was synthesized by precipitation from solution using uranium (VI) nitrate and copper (II) chloride and phosphoric acid/arsenic acid in the appropriate molar proportions. Refined unit cell parameters determined by Pawley fitting of powder X-ray diffraction data showed a linear variation in the a unit cell parameter according to Vegard's Law, allowing the composition of the natural mineral phases found at South Terras to be determined from measurement of their unit cell parameters. High-resolution variable-temperature synchrotron powder X-ray diffraction studies were carried out at the Diamond Light Source on three members of this solid solution ( x  = 0, 1, 2) and showed different structural behaviour as a function of composition and temperature. Metatorbenite ( x  = 0) retains its tetragonal symmetry at low temperatures and dehydrates to an amorphous phase at 473 K, whereas metazeunrite ( x  = 2) transforms to an orthorhombic phase at low temperatures, regains its tetragonal symmetry on heating to 323 K and undergoes a further transition to an, as yet, unidentified phase at 473 K. This article is part of the theme issue ‘Fifty years of synchrotron science: achievements and opportunities’.

scholarly journals Ardennite-bearing mineral association related to sulfide-free ores with chalcophile metals at Nežilovo, Pelagonian Massif, North Macedonia

2021 ◽  
Vol 33 (4) ◽  
pp. 433-445
Author(s):  
Marko Bermanec ◽  
Nikita V. Chukanov ◽  
Ivan Boev ◽  
Božidar Darko Šturman ◽  
Vladimir Zebec ◽  
...  
Keyword(s):  
Single Crystal ◽  
Microprobe Analysis ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Mineral Association ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Formation Conditions ◽  
Pelagonian Massif

Abstract. Among numerous minerals determined at Nežilovo, Pelagonian Massif, North Macedonia, ardennite-(As) has been discovered in two different associations and studied by means of optical microscopy, electron microprobe analysis (EMPA), and single-crystal and powder X-ray diffraction methods. The refractive indices of ardennite-(As) from Nežilovo are α=1.537(2), β=1.579(1) and γ=1.741(1), where γ corresponds to the c direction. The optical axial angle is 2Vx=49(1)∘. EMPA of the investigated samples yields the following empirical formulae: [Mn3.272+Ca0.73]Σ4.00[Al4.18Mg1.24Fe0.29Mn0.193+Zn0.10]Σ6.00(Si4.73Al0.27)Σ5.00(As0.96Si0.03V0.01)Σ1.00O22 [OH5.36(H2O)0.64]Σ6.00 for ardennite-(As) and (K0.95Na0.04Ba0.02)Σ1.01(Al1.44Fe0.303+Mg0.20Mn0.03Ti0.02 Zn0.01)Σ2.00(Si3.21Al0.79O10) (OH1.97O0.03)Σ2.00 for the associated red mica. The unit cell parameters of ardennite-(As) determined by X-ray powder diffraction are a=8.757(2) Å, b=5.836(2) Å, c=18.578(2) Å and V=941.97 Å3. The unit cell parameters of ardennite-(As) were also determined by single-crystal X-ray diffraction and are a=8.760(1) Å, b=5.838(1) Å, c=18.582(2) Å and V=950.30 Å3. Regularities of isomorphism in ardennite-related minerals are discussed. The presence of ardennite-(As) in association with 2M1 and 3T phengite polytypes provides evidence for three separate stages of formation. Conditions at which ardennite-(As) crystallized have been estimated based on compositional features of associated micas.

The orientation of sickle hemoglobin fibers within fascicles

1988 ◽  
Vol 46 ◽  
pp. 400-401
Author(s):  
Christopher A. Miller ◽  
Bridget Carragher ◽  
William A. McDade ◽  
Robert Josephs
Keyword(s):  
Sickle Cell ◽  
Sickle Cell Anemia ◽  
Relative Orientation ◽  
Unit Cell ◽  
Red Cell ◽  
High Ph ◽  
Sickle Hemoglobin ◽  
Polar Crystal ◽  
Helical Configuration

Highly ordered bundles of deoxyhemoglobin S (HbS) fibers, termed fascicles, are intermediates in the high pH crystallization pathway of HbS. These fibers consist of 7 Wishner-Love double strands in a helical configuration. Since each double strand has a polarity, the odd number of double strands in the fiber imparts a net polarity to the structure. HbS crystals have a unit cell containing two double strands, one of each polarity, resulting in a net polarity of zero. Therefore a rearrangement of the double strands must occur to form a non-polar crystal from the polar fibers. To determine the role of fascicles as an intermediate in the crystallization pathway it is important to understand the relative orientation of fibers within fascicles. Furthermore, an understanding of fascicle structure may have implications for the design of potential sickling inhibitors, since it is bundles of fibers which cause the red cell distortion responsible for the vaso-occlusive complications characteristic of sickle cell anemia.

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