Agardite-(Y), Cu2+ 6Y(AsO4)3(OH)6·3H2O

Agardite-(Y), with a refined formula of Cu2+ 5.70(Y0.69Ca0.31)[(As0.83P0.17)O4]3(OH)6·3H2O [ideally Cu2+ 6Y(AsO4)3(OH)6·3H2O, hexacopper(II) yttrium tris(arsenate) hexahydroxide trihydrate], belongs to the mixite mineral group which is characterized by the general formula Cu2+ 6 A(TO4)3(OH)6·3H2O, where nine-coordinated cations in the A-site include rare earth elements along with Al, Ca, Pb, or Bi, and the T-site contains P or As. This study presents the first structure determination of agardite-(Y). It is based on the single-crystal X-ray diffraction of a natural sample from Jote West mine, Pampa Larga Mining District, Copiapo, Chile. The general structural feature of agardite-(Y) is characterized by infinite chains of edge-sharing CuO5 square pyramids (site symmetry 1) extending down the c axis, connected in the ab plane by edge-sharing YO9 polyhedra (site symmetry -6..) and corner-sharing AsO4 tetrahedra (site symmetry m..). Hydroxyl groups occupy each corner of the CuO5-square pyramids not shared by a neighboring As or Y atom. Each YO9 polyhedron is surrounded by three tubular channels. The walls of the channels, parallel to the c axis, are six-membered hexagonal rings comprised of CuO5 and AsO4 polyhedra in a 2:1 ratio, and contain free molecules of lattice water.

Agardite-(Y) was first described from the oxidation zone of the Bou-Skour copper deposit in Jebel Sahro, Morocco (Dietrich et al., 1969). It has since been found in many other localities, including Germany, England, Spain, France, U.S. (Dietrich et al., 1969), Italy (Olmi et al., 1988), Czech Republic (Plášil et al., 2009 and Bulgaria (Kunov et al., 2002). In these studies, unit-cell parameters were presented, but no details of the crystal structure. Amid identification of minerals for the RRUFF project (http://rruff.info/R070649), we detected sprays of relatively large, well-crystalized, acicular agardite-(Y) from the Jote West mine, Pampa Larga Mining District, Copiapo, Chile (Fig. 1). Thereby, this study represents the first crystal structure determination of agardite-(Y), by means of single-crystal X-ray diffraction.
The structure of agardite-(Y) consists of infinite chains of edge-sharing CuO 5 square-pyramids (site symmetry 1) extending down the c-axis, connected in the ab-plane by edge-sharing, YO 9 -polyhedra (site symmetry 6..) and cornersharing AsO 4 -tetrahedra (site symmetry m..) (Fig. 2). Hydroxyl groups (OH4 & OH5) occupy each corner of the CuO 5polyhedra not shared by a neighboring As or Y atom. Based on bond valance calculations, OH4 (bond valance sum = 1.07 valence units (v.u.)) donates a hydrogen bond to O1 (bond valance sum = 1.93 v.u.), at the apex of the CuO 5 -polyhedron, while also accepting a hydrogen bond from OH5 (bond valance sum = 1.26 v.u.). Each YO 9 -polyhedron is surrounded by three tubular channels (Fig. 3). The walls of the channels, parallel to the c-axis, are 6-membered, hexagonal rings comprised of CuO 5 -and AsO 4 -polyhedra in a ratio of 2:1, respectively, and contain free molecules of lattice water. The water positions form a ring inside the channel, similar to the 2.7 Å radius ring reported by Hess (1983) in agardite- (Ce) supplementary materials sup-2 Acta Cryst. (2013). E69, i61-i62 and the five water sites reported by Miletich et al. (1997). In our model of agardite-(Y), we defined two distinct water sites, OW1 and OW2, although there are many statistically possible locations. OW1 is positioned as a 2.93 Å radius ring inside the channel and OW2 is situated at the center of the channel. This sample's Raman spectrum (Fig. 4) shows a broad H 2 O band, centered at 3400 cm -1 , and protruding from it are two small bands signifying two OH modes.
Previous studies have utilized thermogravimetric analysis to examine the nature of both the lattice water and the Hydroxyl groups in synthetic mixite-group minerals Frost et al., 2005). In both studies, ~3 lattice (channel) H 2 O molecules were driven off when samples were heated to 373 K, and dehydroxylation was observed when temperatures reached 523 K. Mixite structural decomposition occurs upon the loss of the hydroxyl groups, which is made evident by the inability to rehydrate samples heated above the 523 K level . Previously, the lattice water was thought to also contribute to the stability of the mixite-group crystal structure; however, Miletich et al. (1997) showed a very low value of activation energy for dehydration in mixite, indicating that the water molecules are not bonded to any cation. Our findings support the hypothesis that such water molecules are not involved in bonding; Cu-OW bond lengths are >3.5 Å and bond valance calculations show Cu (valence sum = 2.11 v.u.) and As (valence sum = 5.19 v.u.) to be fully bonded. Therefore, it appears that lattice water is not essential to the stability of the agardite-(Y) crystal structure.

Experimental
The agardite-(Y) specimen used in this study was from the Jote West mine,

Refinement
Due to similar X-ray scattering power, all REE were treated as Y. Y and Ca were allowed to share the A-site and their abundances were refined under consideration of full occupancy. Additionally, As and P were allowed to share the T-site and their abundances were also constrained under consideration of full occupancy. The occupancy of the Cu site was refined freely, revealing a slight underoccupation of 0.950 (9). Various models were attempted in refining the lattice water positions, including split-site models. However, the refinement adopted here is the only one that converged. The exceptionally large isotropic displacement parameters for OW1 and OW2 are expected because these site represent essentially free molecules in a large channel. The total number of O atoms for the two water sites was constrained to 6. H atoms could not be assigned reliably and were excluded from refinement. The highest residual peak in the difference Fourier maps was located at (0, 0, 0.5), 0.00 Å from OW2, and the deepest hole at (0.4927, 0.8006, 0.3668), 0.91 Å from As.

Figure 2
The crystal structure of agardite-(Y). Yellow square-pyramids, gray tetrahedra and blue polyhedra represent CuO 5 , AsO 4 and YO 9 units, respectively. Cyan spheres, with arbitrary radius, represent the O atoms of lattice water molecules.  The crystal structure of agardite-(Y) represented with displacement ellipsoids at the 99% probability level. Yellow, gray, blue and red ellipsoids represent Cu, As, Y and O, respectively. O atoms of lattice water molecules, shown as cyan spheres, are represented with an arbitrary radius.

Figure 4
Raman spectrum of agardite-(Y). The broad water vibration band is centered at 3400 cm -1 , and the two small bands protruding from the water band signifying two OH modes. where P = (F o 2 + 2F c 2 )/3 (Δ/σ) max = 0.020 Δρ max = 2.34 e Å −3 Δρ min = −0.79 e Å −3 Special details Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > σ(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger. Geometric parameters (Å, º)