Crystal structure of the uranyl arsenate mineral hugelite, Pb2(UO2)3O2(AsO4)2(H2O)5, revisited: a correct unit cell, twinning and hydrogen bonding.
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ABSTRACT:
SUBMITTER: Plasil J
PROVIDER: S-EPMC8182802 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The title compound, NaCa(AsO(4)), was synthesized using a hydro-thermal method at 633-643?K. It has a dense structure composed of alternating layers of distorted [CaO(6)] octa-hedra and layers of [AsO(4)] tetra-hedra and distorted [NaO(6)] octa-hedra, stacked along the a axis. The As, Ca and two O atoms lie on the mirror plane at y = 1/4 (i.e. 4c), while the Na atom lies on an inversion centre (1/2, 1/2, 0) (i.e. 4b). Each distorted [CaO(6)] octa-hedron shares four equatorial common O vertices with four neighboring octa-hedra, forming a layer parallel to (100), whereas each distorted [NaO(6)] octa-hedron shares two opposite edges with two neighboring ones, forming a chain running along [010]. Each isolated [AsO(4)] tetra-hedron shares two edges with two different [NaO(6)] octa-hedra in one [NaO(6)] chain and a vertex with another chain. Simultaneously the above [AsO(4)] tetra-hedron located in a four-membered [CaO(6)] ring shares one edge of its base facet with one [CaO(6)] octa-hedron and three corners with three other [CaO(6)] octa-hedra of one [CaO(6)] layer, and the remaining apex is shared with another [CaO(6)] layer. [NaO(6)] octa-hedra and [CaO(6)] octa-hedra are linked to each other by sharing edges and vertices.
| S-EPMC3238576 | biostudies-literature
Project description:A new mixed hexaphyrin, pyrihexaphyrin (0.1.0.0.1.0) (1), was prepared via an acid catalyzed cyclization between 5,5'-(pyridine-2,6-diyl)bis(pyrrole-2-carbaldehyde) (2) and terpyrrole (3). This expanded porphyrin undergoes a ring contraction upon metallation with uranyl silylamide [UO2[N(SiMe3)2]2] under anaerobic conditions followed by purification over basic aluminum oxide exposed to air. The uranyl-contracted pyrihexaphyrin (0.0.0.0.1.0) complex (4) produced as a result contains a unique structural architecture and possesses a formally 22 π-electron globally aromatic periphery, as inferred from NMR spectroscopy, single crystal X-ray diffraction, and computational analyses. Support for the proposed contraction mechanism came from experimental data and DFT calculations. Proton NMR and mass spectroscopic analysis provided the first insight into expanded porphyrin-mediated activation of the uranyl dication (UO2 2+).
| S-EPMC6552508 | biostudies-literature
Project description:The title compound, sodium calcium trimagnesium tris-(arsenate), an alluaudite-like arsenate, was prepared by solid-state reaction at high temperature. The structure is built up from edge-sharing MgO(6) octa-hedra in chains associated with the AsO(4) arsenate groups. The three-dimensional network leads to two different tunnels occupied statistically by Na(+) and Ca(2+). One As and one Mg atom lie on twofold rotation axes; one Na and one Ca are disordered over two sites with occupancies of 0.7 and 0.3 and these sites lie on a twofold rotation axis and an inversion centre, respectively.
| S-EPMC2961449 | biostudies-literature
Project description:In the title compound, tris-odium dicobalt arsenate diarsenate, Na?Co?AsO?As?O?, the two Co atoms, one of the two As and three of the seven O atoms lie on special positions, with site symmetries 2 and m for the Co, m for the As, and 2 and twice m for the O atoms. The two Na atoms are disordered over two general and special positions [occupancies 0.72?(3):0.28?(3) and 0.940?(6):0.060?(6), respectively]. The main structural feature is the association of the CoO? octa-hedra in the ab plane, forming Co?O?? units, which are corner- and edge-connected via AsO? and As?O? arsenate groups, giving rise to a complex polyhedral connectivity with small tunnels, such as those running along the b- and c-axis directions, in which the Na? ions reside. The structural model is validated by both bond-valence-sum and charge-distribution methods, and the distortion of the coordination polyhedra is analyzed by means of the effective coordination number.
| S-EPMC3393142 | biostudies-other
Project description:The reaction of UO2 (OAc)2 ⋅ 2H2 O with the biologically inspired ligand 2-salicylidene glucosamine (H2 L1 ) results in the formation of the anionic trinuclear uranyl complex [(UO2 )3 (μ3 -O)(L1 )3 ]2- (12- ), which was isolated in good yield as its Cs-salt, [Cs]2 1. Recrystallization of [Cs]2 1 in the presence of 18-crown-6 led to formation of a neutral ion pair of type [M(18-crown-6)]2 1, which was also obtained for the alkali metal ions Rb+ and K+ (M=Cs, Rb, K). The related ligand, 2-(2-hydroxy-1-naphthylidene) glucosamine (H2 L2 ) in a similar procedure with Cs+ gave the corresponding complex [Cs(18-crown-6)]2 [(UO2 )3 (μ3 -O)(L2 )3 ([Cs(18-crown-6)]2 2). From X-ray investigations, the [(UO2 )3 O(Ln )3 ]2- anion (n=1, 2) in each complex is a discrete trinuclear uranyl species that coordinates to the alkali metal ion via three uranyl oxygen atoms. The coordination behavior of H2 L1 and H2 L2 towards UO2 2+ was investigated by NMR, UV/Vis spectroscopy and mass spectrometry, revealing the in situ formation of the 12- and 22- dianions in solution.
| S-EPMC8252515 | biostudies-literature
Project description:Most of the highly radioactive spent nuclear fuel (SNF) around the world is destined for final disposal in deep-mined geological repositories. At the end of the fuel's useful life in a reactor, about 96% of the SNF is still UO2. Thus, the behaviour of UO2 in SNF must be understood and evaluated under the weathering conditions of geologic disposal, which extend to periods of hundreds of thousands of years. There is ample evidence from nature that many uranium deposits have experienced conditions for which the formation of coffinite, USiO4, has been favoured over uraninite, UO2+x, during subsequent alteration events. Thus, coffinite is an important alteration product of the UO2 in SNF. Here, we present the first evidence of the formation of coffinite on the surface of UO2 at the time scale of laboratory experiments in a solution saturated with respect to amorphous silica at pH = 9, room temperature and under anoxic conditions.
| S-EPMC7376029 | biostudies-literature
Project description:Concentration- and time-dependent genomic changes in the mouse urinary bladder following exposure to arsenate in drinking water for up to twelve weeks. Inorganic arsenic (Asi) is a known human bladder carcinogen. The objective of this study was to examine the concentration dependence of the genomic response to Asi in the urinary bladders of mice. C57BL/6J mice were exposed for 1 or 12 weeks to arsenate in drinking water at concentrations of 0.5, 2, 10, and 50 mg As/L. Urinary bladders were analyzed using gene expression microarrays. A consistent reversal was observed in the direction of gene expression change: from predominantly decreased expression at 1 week to predominantly increased expression at 12 weeks. These results are consistent with evidence from in vitro studies of an acute adaptive response that is suppressed on longer exposure due to down-regulation of Fos. Pathways with the highest enrichment in gene expression changes were associated with epithelial-to-mesenchymal transition, inflammation, and proliferation. Benchmark dose (BMD) analysis determined that the lowest median BMD values for pathways were above 5 mg As/L, despite the fact that pathway enrichment was observed at the 0.5 mg As/L exposure concentration. This disparity may result from the non-monotonic nature of the concentration-responses for the expression changes of a number of genes, as evidenced by the much fewer gene expression changes at 2 mg As/L compared to lower or higher concentrations. Pathway categories with concentration-related gene expression changes included cellular morphogenesis, inflammation, apoptosis/survival, cell cycle control, and DNA damage response. The results of this study provide evidence of a concentration-dependent transition in the mode of action for the subchronic effects of Asi in mouse bladder cells in the vicinity of 2 mg Asi/L.
2011-09-15 | GSE32102 | GEO
Project description:H-bonding between protein surface polar/charged groups and water is one of the key factors of protein hydration. Here, we introduce an Accessible Surface Area (ASA) model for computationally efficient estimation of a free energy of water-protein H-bonding at any given protein conformation. The free energy of water-protein H-bonds is estimated using empirical formulas describing probabilities of hydrogen bond formation that were derived from molecular dynamics simulations of water molecules at the surface of a small protein, Crambin, from the Abyssinian cabbage (Crambe abyssinica) seed. The results suggest that atomic solvation parameters (ASP) widely used in continuum hydration models might be dependent on ASA for polar/charged atoms under consideration. The predictions of the model are found to be in qualitative agreement with the available experimental data on model compounds. This model combines the computational speed of ASA potential, with the high resolution of more sophisticated solvation methods.
| S-EPMC2279814 | biostudies-literature
Project description:Concentration- and time-dependent genomic changes in the mouse urinary bladder following exposure to arsenate in drinking water for up to twelve weeks. Inorganic arsenic (Asi) is a known human bladder carcinogen. The objective of this study was to examine the concentration dependence of the genomic response to Asi in the urinary bladders of mice. C57BL/6J mice were exposed for 1 or 12 weeks to arsenate in drinking water at concentrations of 0.5, 2, 10, and 50 mg As/L. Urinary bladders were analyzed using gene expression microarrays. A consistent reversal was observed in the direction of gene expression change: from predominantly decreased expression at 1 week to predominantly increased expression at 12 weeks. These results are consistent with evidence from in vitro studies of an acute adaptive response that is suppressed on longer exposure due to down-regulation of Fos. Pathways with the highest enrichment in gene expression changes were associated with epithelial-to-mesenchymal transition, inflammation, and proliferation. Benchmark dose (BMD) analysis determined that the lowest median BMD values for pathways were above 5 mg As/L, despite the fact that pathway enrichment was observed at the 0.5 mg As/L exposure concentration. This disparity may result from the non-monotonic nature of the concentration-responses for the expression changes of a number of genes, as evidenced by the much fewer gene expression changes at 2 mg As/L compared to lower or higher concentrations. Pathway categories with concentration-related gene expression changes included cellular morphogenesis, inflammation, apoptosis/survival, cell cycle control, and DNA damage response. The results of this study provide evidence of a concentration-dependent transition in the mode of action for the subchronic effects of Asi in mouse bladder cells in the vicinity of 2 mg Asi/L. Female C57Bl/J mice will be exposed to COLD Arsenate in drinking water. One week interium sac on 7/18/06. 100 samples including liver, lung, kidney and bladder. Bladder will be analyzed with microarrays, 24 samples. Twelve week terminal sac on 10/05/06. 75 total samples including lung, kidney, and bladder. Bladdler will be analyzed by microarray, 25 samples. Drinking water containing As will be prepared weekly with monitoring to determine amount used by mice. Following tissues will be available for genomic study: Bladder, liver, lung, and kidney.
2011-09-14 | E-GEOD-32102 | biostudies-arrayexpress
Project description:Single crystals of Zn2(HTeO3)(AsO4), dizinc(II) hydroxidodioxidotellurate(IV) oxidoarsenate(V), were obtained as one of the by-products in a hydro-thermal reaction between Zn(NO3)2·6H2O, TeO2, H3AsO4 and NH3 in molar ratios of 2:1:2:10 at 483 K for seven days. The asymmetric unit of Zn2(HTeO3)(AsO4) contains one Te (site symmetry m), one As (m), one Zn (1), five O (three m, two 1) and one H (m) site. The ZnII atom exhibits a coordination number of 5 and is coordinated by four oxygen atoms and a hydroxide group, forming a distorted trigonal bipyramid. The hydroxide ion is positioned at a significantly larger distance on one of the axial positions of the bipyramid. The [ZnO4OH] polyhedra are connected to each other by corner-sharing to form ∞ 2[ZnO3/2(OH)1/2O1/1] layers extending parallel to (001). The TeIV atom is coordinated by three oxygen atoms and a hydroxide group in a one-sided manner in the shape of a bis-phenoid, revealing stereochemical activity of its 5s 2 electron lone pair. The AsV atom is coordinated by four oxygen atoms to form the tetra-hedral oxidoarsenate(V) anion. By corner-sharing, [TeO3OH] and [AsO4] groups link adjacent ∞ 2[ZnO3/2(OH)1/2O1/1] layers along [001] into a three-dimensional framework structure.
| S-EPMC8100263 | biostudies-literature