scholarly journals Crystal structure determination of a lifelong biopersistent asbestos fibre using single-crystal synchrotron X-ray micro-diffraction

IUCrJ ◽  
2021 ◽  
Vol 8 (1) ◽  
pp. 76-86
Author(s):  
Carlotta Giacobbe ◽  
Dario Di Giuseppe ◽  
Alessandro Zoboli ◽  
Magdalena Lassinantti Gualtieri ◽  
Paola Bonasoni ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Atomic Structure ◽  
Structure Refinement ◽  
Latency Period ◽  
Parietal Pleura ◽  
Asbestos Fibre ◽  
X Ray ◽  
Amphibole Asbestos ◽  
Iron Pool

The six natural silicates known as asbestos may induce fatal lung diseases via inhalation, with a latency period of decades. The five amphibole asbestos species are assumed to be biopersistent in the lungs, and for this reason they are considered much more toxic than serpentine asbestos (chrysotile). Here, we refined the atomic structure of an amosite amphibole asbestos fibre that had remained in a human lung for ∼40 years, in order to verify the stability in vivo. The subject was originally exposed to a blend of chrysotile, amosite and crocidolite, which remained in his parietal pleura for ∼40 years. We found a few relicts of chrysotile fibres that were amorphous and magnesium depleted. Amphibole fibres that were recovered were undamaged and suitable for synchrotron X-ray micro-diffraction experiments. Our crystal structure refinement from a recovered amosite fibre demonstrates that the original atomic distribution in the crystal is intact and, consequently, that the atomic structure of amphibole asbestos fibres remains stable in the lungs for a lifetime; during which time they can cause chronic inflammation and other adverse effects that are responsible for carcinogenesis. The amosite fibres are not iron depleted proving that the iron pool for the formation of the asbestos bodies is biological (haemoglobin/plasma derived) and that it does not come from the asbestos fibres themselves.

Effects of dietary alteration of bicarbonate and magnesium on rat bone

1986 ◽  
Vol 250 (2) ◽  
pp. F302-F307 ◽  
Author(s):  
J. M. Burnell ◽  
C. Liu ◽  
A. G. Miller ◽  
E. Teubner
Keyword(s):  
Crystal Structure ◽  
Bone Formation ◽  
X Ray Diffraction ◽  
X Ray ◽  
Growing Rats ◽  
Final Composition ◽  
Rat Bone

To study the effects of bicarbonate and magnesium on bone, mild acidosis and/or hypermagnesemia were produced in growing rats by feeding ammonium chloride and/or magnesium sulfate. Bone composition, quantitative histomorphometry, and mineral x-ray diffraction (XRD) characteristics were measured after 6 wk of treatment. The results demonstrated that both acidosis (decreased HCO3) and hypermagnesemia inhibited periosteal bone formation, and, when combined, results were summative; and the previously observed in vitro role of HCO3- and Mg2+ as inhibitors of crystal growth were confirmed in vivo. XRD measurements demonstrated that decreased plasma HCO3 resulted in larger crystals and increased Mg resulted in smaller crystals. However, the combined XRD effects of acidosis and hypermagnesemia resembled acidosis alone. It is postulated that the final composition and crystal structure of bone are strongly influenced by HCO3- and Mg2+, and the effects are mediated by the combined influence on both osteoblastic bone formation and the growth of hydroxyapatite.

Crystal structure of potassium tetraperoxomolybdate (VI) K2[Mo(O2)4]

2005 ◽  
Vol 20 (3) ◽  
pp. 203-206 ◽  
Author(s):  
M. Grzywa ◽  
M. Różycka ◽  
W. Łasocha
Keyword(s):  
Crystal Structure ◽  
Low Temperature ◽  
Diffraction Pattern ◽  
Powder Diffraction ◽  
Rietveld Method ◽  
Structure Refinement ◽  
Crystal Structure Refinement ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters

Potassium tetraperoxomolybdate (VI) K2[Mo(O2)4] was prepared, and its X-ray powder diffraction pattern was recorded at low temperature (258 K). The unit cell parameters were refined to a=10.7891(2) Å, α=64.925(3)°, space group R−3c (167), Z=6. The compound is isostructural with potassium tetraperoxotungstate (VI) K2[W(O2)4] (Stomberg, 1988). The sample of K2[Mo(O2)4] was characterized by analytical investigations, and the results of crystal structure refinement by Rietveld method are presented; final RP and RWP are 9.79% and 12.37%, respectively.

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 Recommended X-ray single-crystal structure refinement and Rietveld refinement procedure for tremolite

2021 ◽  
Vol 77 (4) ◽  
Author(s):  
Paolo Ballirano ◽  
Beatrice Celata ◽  
Alessandro Pacella ◽  
Ferdinando Bosi
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Rietveld Refinement ◽  
Structure Refinement ◽  
Point Of View ◽  
Single Crystal Structure ◽  
Crystal Structure Refinement ◽  
Statistical Point ◽  
X Ray ◽  
Refinement Procedure

A detailed description of the structure of the amphibole-supergroup minerals is very challenging owing to their complex chemical composition that renders the process of cation partition extremely difficult, particularly because of the occurrence of multivalent elements. Since amphiboles naturally occur under a fibrous morphology and have largely been used to produce asbestos, there is a growing demand for detailed and accurate structural data in order to study the relationships between structure, composition and toxicity. The present study proposes a recommended refinement procedure for both X-ray single-crystal structure refinement (SREF) and Rietveld analysis for tremolite, selected as a test case. The corresponding structural results are compared to estimate the `degree of confidence' of the Rietveld refinement with regard to SREF. In particular, it is shown that the interpretation of the electron density of the tremolite structure by SREF is model dependent. By assuming that the site-scattering values from SREF should be as close as possible to those from electron microprobe analysis, as a crucial constraint for the correct description of the final crystal-chemical model, it is found that it is best satisfied by using partially ionized scattering curves (SCs) for O and Si, and neutral SCs (neutral oxygen curves or NOCs) for other atoms. This combination leads to the best fit to the diffraction data. Moreover, it is found that Rietveld refinement using NOCs produces the best structural results, in excellent agreement with SREF. It is worth noting that, due to the complexity of the diffraction pattern and the fairly large number of freely refinable parameters, refinements with different combinations of SCs produce results almost indistinguishable from a statistical point of view, albeit showing significant differences from a structural point of view.

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.

scholarly journals Crystal structure of a pyridoxal 5′-phosphate-dependent aspartate racemase derived from the bivalve mollusc Scapharca broughtonii

2017 ◽  
Vol 73 (12) ◽  
pp. 651-656 ◽  
Author(s):  
Taichi Mizobuchi ◽  
Risako Nonaka ◽  
Motoki Yoshimura ◽  
Katsumasa Abe ◽  
Shouji Takahashi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Active Site ◽  
Metal Binding ◽  
Bivalve Mollusc ◽  
Active Site Residues ◽  
X Ray ◽  
Aspartate Racemase ◽  
Scapharca Broughtonii

Aspartate racemase (AspR) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that is responsible for D-aspartate biosynthesis in vivo. To the best of our knowledge, this is the first study to report an X-ray crystal structure of a PLP-dependent AspR, which was resolved at 1.90 Å resolution. The AspR derived from the bivalve mollusc Scapharca broughtonii (SbAspR) is a type II PLP-dependent enzyme that is similar to serine racemase (SR) in that SbAspR catalyzes both racemization and dehydration. Structural comparison of SbAspR and SR shows a similar arrangement of the active-site residues and nucleotide-binding site, but a different orientation of the metal-binding site. Superposition of the structures of SbAspR and of rat SR bound to the inhibitor malonate reveals that Arg140 recognizes the β-carboxyl group of the substrate aspartate in SbAspR. It is hypothesized that the aromatic proline interaction between the domains, which favours the closed form of SbAspR, influences the arrangement of Arg140 at the active site.

Microporous crystal structure of labuntsovite-Fe and high-pressure behavior up to 23 GPa

2018 ◽  
Vol 74 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Sergey M. Aksenov ◽  
Elena A. Bykova ◽  
Ramiza K. Rastsvetaeva ◽  
Nikita V. Chukanov ◽  
Irina P. Makarova ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
Single Crystal ◽  
Cross Section ◽  
Structure Refinement ◽  
Alkaline Complex ◽  
X Ray ◽  
Cell Parameters ◽  
Diamond Anvil ◽  
The Stability

Labuntsovite-Fe, an Fe-dominant member of the labuntsovite subgroup, was first discovered in the Khibiny alkaline massif on Mt Kukisvumchorr [Khomyakov et al. (2001). Zap. Vseross. Mineral. Oba, 130, 36–45]. However, no data are published about the crystal structure of this mineral. Labuntsovite-Fe from a peralkaline pegmatite located on Mt Nyorkpakhk, in the Khibiny alkaline complex, Kola Peninsula, Russia, has been investigated by means of electron microprobe analyses, single-crystal X-ray structure refinement, and IR and Raman spectroscopies. Monoclinic unit-cell parameters of labuntsovite-Fe are: a = 14.2584 (4), b = 13.7541 (6), c = 7.7770 (2) Å, β = 116.893 (3)°; V = 1360.22 (9) Å3; space group C2/m. The structure was refined to final R 1 = 0.0467, wR 2 = 0.0715 for 3202 reflections [I > 3σ(I)]. The refined crystal chemical formula is (Z = 2): Na2K2Ba0.7[(Fe0.5Ti0.1Mg0.05)(H2O)1.3]{[Ti2(Ti1.9Nb0.1)(O,OH)4][Si4O12]2}·4H2O. The high-pressure in situ single-crystal X-ray diffraction study of the labuntsovite-Fe has been carried out in a diamond anvil cell. The labuntsovite-type structure is stable up to 23 GPa and phase transitions are not observed. Calculations using the BM3 equation of state resulted in the bulk modulus K = 72 (2) GPa, K′0 = 3.7 (2) and V 0 = 1363 (2) Å3. Compressing of the heteropolyhedral zeolite-like framework leads to the deformation of main structural units. Octahedral rods show the gradual increase of distortion and the wave-like character of rods becomes more distinct. Rod deformations result in the distortion of the silicon–oxygen ring which is not equal in different directions. Structural channels are characterized by a different ellipticity–pressure relationship: the cross-section of the largest channel I and channel II demonstrates the stability of the geometrical characteristics which practically do not depend on pressure: ∊channel I ≃ 0.85 (4) (cross-section is rather regular) and ∊channel II ≃ 0.52 (2) within the whole pressure range. However, channel III is characterized by the increasing of ellipticity with pressure (∊ = 0.40 → 0.10).

Synthesen, Kristallstrukturen und magnetische Eigenschaften von [Li(12-Krone-4)2][Li(12-Krone-4)(OH2)]2[Nb6Cl18], [Li(15-Krone-5)2(OH2)]3[Nb6Cl18] und [(18-Krone-6)2(O2H5)]3[Nb6Cl18] / Syntheses, Crystal Structures and Magnetic Behaviour of [Li(12-Krone-4)2][Li(12-Krone-4)(OH2)]2[Nb6Cl18], [Li(15-Krone-5)2(OH2)]3[Nb6Cl18] and [(18-Krone-6)2(O2H5)]3[Nb6Cl18]

2001 ◽  
Vol 56 (10) ◽  
pp. 1025-1034 ◽  
Author(s):  
Markus Ströbele ◽  
H.-Jtirgen Meyer
Keyword(s):  
Crystal Structure ◽  
Water Molecule ◽  
Crown Ethers ◽  
Magnetic Measurements ◽  
Structure Refinement ◽  
Magnetic Behaviour ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Paramagnetic Behaviour

The title compounds were prepared through reactions of Li2Nb6Cl16 with the corresponding crown ethers in acetone. All three compounds were obtained as dark brown crystals. Their structures were solved with the means of single-crystal X-ray diffraction.[Li(12-crown-4)2][Li(12-crown-4)(OH2)]2[Nb6Cl18]: space group P21/n, Z =2, a = 1320.4(1), b = 1879.1(1), c = 1321.7(1) pm, ß = 92.515(6)°, R1 = 0.0297 (I>2σ(I)). The crystal structure contains Li+ sandwiched by two 12-crown-4-ethers plus Li+ coordinated by one 12-crown-4- ether and one water molecule.[Li(15-crown-5)2(OH2)]3[Nb6Cl18]: space group R3̅, Z = 3, a = b = 2081.7(1), c = 1991.7(1) pm, R1 = 0.0395 (I > 2σ(I)). In the crystal structure Li+ and one water molecule are sandwiched by two 15-crown-5-ethers.[(18-crown-6)2(O2H5)]3[Nb6Cl18]: space group P1̅, Z = 1 ,a = 1405.1(1), b = 1461.1(2), c = 1492.2(2) pm; α = 98.80(1)°, ß = 98.15(1)°, γ = 97.41(1)°, R1 = 0.0538 (I > 2σ(I)). H5O2+ was found in the structure refinement sandwiched between two 18-crown-6-ethers.All compounds reported contain [Nb6Cl18] clusters with Nb-Nb distances between 299 and 301 pm. The paramagnetic behaviour expected for [Nb6Cl18]3- in all three compounds was confirmed by magnetic measurements.

Ideal and Real Structure of Ti5O4(PO4)4: X-ray and HRTEM Investigations

1998 ◽  
Vol 54 (6) ◽  
pp. 722-731 ◽  
Author(s):  
F. Reinauer ◽  
R. Glaum
Keyword(s):  
Crystal Structure ◽  
Electron Microscopy ◽  
Structure Refinement ◽  
Ideal Structure ◽  
Crystal Data ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Transmission Electron ◽  
The Ideal

The crystal structure of pentatitanium tetraoxide tetrakis(phosphate), Ti5O4(PO4)4, has been determined and refined from X-ray diffraction single-crystal data [P212121 (No. 19), Z = 4, a = 12.8417 (12), b = 14.4195 (13), c = 7.4622 (9) Å (from Guinier photographs); conventional residual R 1 = 0.042 for 2556 Fo > 4σ(Fo ), R 1 = 0.057 for all 3276 independent reflections; 282 parameters; 29 atoms in the asymmetric unit of the ideal structure]. The structure is closely related to those of β-Fe2O(PO4)-type phosphates and synthetic lipscombite, Fe3(PO4)4(OH). While these consist of infinite chains of face-sharing MO6 octahedra, in pentatitanium tetraoxide tetrakis(phosphate) only five-eighths of the octahedral voids are occupied according to □3Ti5O4(PO4)4. Four of the five independent Ti4+O6 show high radial distortion [1.72 ≤ d(Ti−O) ≤ 2.39 Å] and a typical 1 + 4 + 1 distance distribution. The fifth Ti4+O6 is an almost regular octahedron [1.91 ≤ d(Ti−O) ≤ 1.98 Å]. Partial disorder of Ti4+ over the available octahedral voids is revealed by the X-ray structure refinement. High-resolution transmission electron microscopy (HRTEM) investigations confirm this result.

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