Redetermination of ruizite, Ca2Mn(3+) 2[Si4O11(OH)2](OH)2·2H2O.
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ABSTRACT:
SUBMITTER: Fendrich KV
PROVIDER: S-EPMC4992915 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The crystal structure of metarossite, ideally CaV2O6·2H2O [chemical name: calcium divanadium(V) hexa-oxide dihydrate], was first determined using precession photographs, with fixed isotropic displacement parameters and without locating the positions of the H atoms, leading to a reliability factor R = 0.11 [Kelsey & Barnes (1960 ?). Can. Mineral.6, 448-466]. This communication reports a structure redetermination of this mineral on the basis of single-crystal X-ray diffraction data of a natural sample from the Blue Cap mine, San Juan County, Utah, USA (R1 = 0.036). Our study not only confirms the structural topology reported in the previous study, but also makes possible the refinement of all non-H atoms with anisotropic displacement parameters and all H atoms located. The metarossite structure is characterized by chains of edge-sharing [CaO8] polyhedra parallel to [100] that are themselves connected by chains of alternating [VO5] trigonal bipyramids parallel to [010]. The two H2O mol-ecules are bonded to Ca. Analysis of the displacement parameters show that the [VO5] chains librate around [010]. In addition, we measured the Raman spectrum of metarossite and compared it with IR and Raman data previously reported. Moreover, heating of metarossite led to a loss of water, which results in a transformation to the brannerite-type structure, CaV2O6, implying a possible dehydration pathway for the compounds M2+V2O6·xH2O, with M = Cu, Cd, Mg or Mn, and x = 2 or 4.
| S-EPMC5120707 | biostudies-other
Project description:The crystal structure of conichalcite [calcium copper(II) arsenate(V) hydroxide], with ideal formula CaCu(AsO(4))(OH), was redetermined from a natural twinned specimen found in the Maria Catalina mine (Chile). In contrast to the previous refinement from photographic data [Qurashi & Barnes (1963 ?). Can. Mineral. 7, 561-577], all atoms were refined with anisotropic displacement parameters and with the H atom located. Conichalcite belongs to the adelite mineral group. The Jahn-Teller-distorted [CuO(6)] octa-hedra share edges, forming chains running parallel to [010]. These chains are cross-linked by eight-coordinate Ca atoms and by sharing vertices with isolated AsO(4) tetra-hedra. Of five calcium arsenate minerals in the adelite group, the [MO(6)] (M = Cu, Zn, Co, Ni and Mg) octa-hedron in conichalcite is the most distorted, and the donor-acceptor O-H?O distance is the shortest.
| S-EPMC2960568 | biostudies-literature
Project description:The crystal structure of katayamalite, ideally KLi3Ca7Ti2(SiO3)12(OH)2 (potassium trilithium hepta-calcium dititanium dodeca-silicate di-hydroxide), was previously reported in triclinic symmetry (C-1), with isotropic displacement parameters for all atoms and without the H-atom position [Kato & Murakami (1985 ?). Mineral. J. 12, 206-217]. The present study redetermines the katayamalite structure with monoclinic symmetry (space group C2/c) based on single-crystal X-ray diffraction data from a sample from the type locality, Iwagi Island, Ehime Prefecture, Japan, with anisotropic displacement parameters for all non-H atoms, and with the H atoms located by difference Fourier analysis. The structure of katayamalite contains a set of six-membered silicate rings inter-connected by sheets of Ca atoms on one side and by an ordered mixture of Li, Ti and K atoms on the other side, forming layers which are stacked normal to (001). From the eight different metal sites, three are located on special positions, viz. one K and one Li atom on twofold rotation axes and one Ca atom on an inversion center. The Raman spectrum of kataymalite shows a band at 3678?cm(-1), similar to that observed for hydroxyl-amphiboles, indicating no or very weak hydrogen bonding.
| S-EPMC3772399 | biostudies-literature
Project description:The crystal structure of brackebuschite, ideally Pb2Mn(3+)(VO4)2(OH) [dilead(II) manganese(III) vanadate(V) hydroxide], was redetermined based on single-crystal X-ray diffraction data of a natural sample from the type locality Sierra de Cordoba, Argentina. Improving on previous results, anisotropic displacement parameters for all non-H atoms were refined and the H atom located, obtaining a significant improvement of accuracy and an unambiguous hydrogen-bonding scheme. Brackebuschite belongs to the brackebuschite group of minerals with general formula A 2 M(T1O4)(T2O4)(OH, H2O), with A = Pb(2+), Ba, Ca, Sr; M = Cu(2+), Zn, Fe(2+), Fe(3+), Mn(3+), Al; T1 = As(5+), P, V(5+); and T2 = As(5+), P, V(5+), S(6+). The crystal structure of brackebuschite is based on a cubic closest-packed array of O and Pb atoms with infinite chains of edge-sharing [Mn(3+)O6] octa-hedra located about inversion centres and decorated by two unique VO4 tetra-hedra (each located on a special position 2e, site symmetry m). One type of VO4 tetra-hedra is linked with the (1) ∞[MnO4/2O2/1] chain by one common vertex, alternating with H atoms along the chain, while the other type of VO4 tetra-hedra link two adjacent octa-hedra by sharing two vertices with them and thereby participating in the formation of a three-membered Mn2V ring between the central atoms. The (1) ∞[Mn(3+)(VO4)2OH] chains run parallel to [010] and are held together by two types of irregular [PbO x ] polyhedra (x = 8, 11), both located on special position 2e (site symmetry m). The magnitude of the libration component of the O atoms of the (1) ∞[Mn(3+)(VO4)2OH] chain increases linearly with the distance from the centerline of the chain, indicating a significant twisting to and fro of the chain along [010]. The hy-droxy group bridges one Pb(2+) cation with two Mn(3+) cations and forms an almost linear hydrogen bond with a vanadate group of a neighbouring chain. The O⋯O distance of this inter-action determined from the structure refinement agrees well with Raman spectroscopic data.
| S-EPMC4778839 | biostudies-literature
Project description:The crystal structure of kovdorskite, ideally Mg(2)PO(4)(OH)·3H(2)O (dimagnesium phosphate hydroxide trihydrate), was reported previously with isotropic displacement paramaters only and without H-atom positions [Ovchinnikov et al. (1980 ?). Dokl. Akad. Nauk SSSR.255, 351-354]. In this study, the kovdorskite structure is redetermined based on single-crystal X-ray diffraction data from a sample from the type locality, the Kovdor massif, Kola Peninsula, Russia, with anisotropic displacement parameters for all non-H atoms, with all H-atom located and with higher precision. Moreover, inconsistencies of the previously published structural data with respect to reported and calculated X-ray powder patterns are also discussed. The structure of kovdorskite contains a set of four edge-sharing MgO(6) octa-hedra inter-connected by PO(4) tetra-hedra and O-H?O hydrogen bonds, forming columns and channels parallel to [001]. The hydrogen-bonding system in kovdorskite is formed through the water mol-ecules, with the OH(-) ions contributing little, if any, to the system, as indicated by the long H?A distances (>2.50?Å) to the nearest O atoms. The hydrogen-bond lengths determined from the structure refinement agree well with Raman spectroscopic data.
| S-EPMC3274836 | biostudies-other
Project description:The crystal structure of despujolsite [tricalcium manganese bis-(sulfate) hexahydroxide tri-hydrate], the Ca/Mn member of the fleischerite group, ideally Ca(3)Mn(4+)(SO(4))(2)(OH)(6)·3H(2)O, was previously determined based on X-ray diffraction intensity data from photographs, without H-atom positions located [Gaudefroy et al. (1968 ▶). Bull. Soc. Fr. Minéral. Crystallogr.91, 43-50]. The current study redetermines the structure of despujolsite from a natural specimen, with all H atoms located and with higher precision. The structure of despujolsite is characterized by layers of CaO(8) polyhedra (m.. symmetry) inter-connected by Mn(OH)(6) octa-hedra (32. symmetry) and SO(4) tetra-hedra (3.. symmetry) along [001]. The average Ca-O, Mn-O and S-O bond lengths are 2.489, 1.915, and 1.472 Å, respectively. There are two distinct hydrogen bonds that stabilize the structural set-up. This work represents the first description of hydrogen bonds in the fleischerite group of minerals.
| S-EPMC3200628 | biostudies-literature
Project description:In contrast to the previous refinement from photographic data [Ferrari et al. (1955 ?). Gazz. Chim. Ital.84, 169-174], the present redetermination of the title compound, caesium hexa-aqua-magnesium arsenate(V), revealed the Cs atom to be on Wyckoff position 4d instead of Wyckoff position 4b of space group F3m. The structure can be derived from the halite structure. The centres of the complex [Mg(OH(2))(6)] octa-hedra and the AsO(4) tetra-hedra (both with 3m symmetry) are on the respective Na and Cl positions. The building units are connected to each other by O-H?O hydrogen bonds. The Cs(+) cations (3m symmetry) are located in the voids of this arrangement and exhibit a regular cubocta-hedral 12-coordination to the O atoms of the water mol-ecules. The O atom bonded to As has 2mm site symmetry (Wyckoff position 24f) and the water-mol-ecule O atom has m site symmetry (Wyckoff position 48h).
| S-EPMC2967843 | biostudies-other
Project description:The crystal structure of Ce[B(5)O(8)(OH)(H(2)O)]NO(3)·2H(2)O, cerium(III) aqua-hydroxidoocta-oxidopenta-borate nitrate dihydrate, has been redetermined from single-crystal X-ray diffraction data. In contrast to the previous determination [Li et al. (2003 ?). Chem. Mater.15, 2253-2260], the present study reveals the location of all H atoms, slightly different fundamental building blocks (FBBs) of the polyborate anions, more reasonable displacement ellipsoids for all non-H atoms, as well as a model without disorder of the nitrate anion. The crystal structure is built from corrugated polyborate layers parallel to (010). These layers, consisting of [B(5)O(8)(OH)(H(2)O)](2-) anions as FBBs, stack along [010] and are linked by Ce(3+) ions, which exhibit a distorted CeO(10) coordination sphere. The layers are additionally stabilized via O-H?O hydrogen bonds between water mol-ecules and nitrate anions, located at the inter-layer space. The [BO(3)(H(2)O)]-group shows a [3 + 1] coordination and is considerably distorted from a tetra-hedral configuration. Bond-valence-sum calculation shows that the valence sum of boron is only 2.63 valence units (v.u.) when the contribution of the water mol-ecule (0.49?v.u.) is neglected.
| S-EPMC3344287 | biostudies-literature
Project description:The crystal structure of eveite, ideally Mn(2)(AsO(4))(OH) [dimanganese(II) arsenate(V) hydroxide], was refined from a single crystal selected from a co-type sample from Långban, Filipstad, Varmland, Sweden. Eveite, dimorphic with sarkinite, is structurally analogous with the important rock-forming mineral andalusite, Al(2)OSiO(4), and belongs to the libethenite group. Its structure consists of chains of edge-sharing distorted [MnO(4)(OH)(2)] octa-hedra (..2 symmetry) extending parallel to [001]. These chains are cross-linked by isolated AsO(4) tetra-hedra (..m symmetry) through corner-sharing, forming channels in which dimers of edge-sharing [MnO(4)(OH)] trigonal bipyramids (..m symmetry) are located. In contrast to the previous refinement from Weissenberg photographic data [Moore & Smyth (1968 ?). Am. Mineral.53, 1841-1845], all non-H atoms were refined with anisotropic displacement param-eters and the H atom was located. The distance of the donor and acceptor O atoms involved in hydrogen bonding is in agreement with Raman spectroscopic data. Examination of the Raman spectra for arsenate minerals in the libethenite group reveals that the position of the peak originating from the O-H stretching vibration shifts to lower wavenumbers from eveite, to adamite, zincolivenite, and olivenite.
| S-EPMC3238575 | biostudies-literature
Project description:The structure of the hexa-gonal modification of caesium hexa-aqua-magnesium phosphate has been redetermined from single-crystal X-ray data. The previous refinement from photographic data [Ferrari, Calvaca & Nardelli (1955 ?). Gazz. Chim. Ital.85, 1232-1238] was basically confirmed, but with all H atoms located and with all non H-atoms refined with anisotropic displacement parameters. The structure can be derived from the NiAs structure type: the PO(4) tetra-hedra (3m. symmetry) are on the Ni positions and the complex [Mg(OH(2))(6)] octa-hedra (3m. symmetry) are on the As positions. The building units are connected to each other by hydrogen bonds. The Cs(+) cations (3m. symmetry) are located in the voids of this arrangement and exhibit a distorted cubocta-hedral 12-coordination by the O atoms of the water mol-ecules.
| S-EPMC2961905 | biostudies-other