Agardite-(Y), Cu(2+) 6Y(AsO4)3(OH)6·3H2O.

Agardite-(Y), with a refined formula of Cu(2+) 5.70(Y0.69Ca0.31)[(As0.83P0.17)O4]3(OH)6·3H2O [ideally Cu(2+) 6Y(AsO4)3(OH)6·3H2O, hexa-copper(II) yttrium tris-(arsenate) hexa-hydroxide trihydrate], belongs to the mixite mineral group which is characterized by the general formula Cu(2+) 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 tetra-hedra (site symmetry m..). Hy-droxyl 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 hexa-gonal rings comprised of CuO5 and AsO4 polyhedra in a 2:1 ratio, and contain free mol-ecules of lattice water.

Related literature

For background to the mixite mineral group, see: Dietrich et al. (1969 ▶); Hess (1983 ▶); Aruga & Nakai (1985 ▶); Mereiter & Preisinger (1986 ▶); Olmi et al. (1988 ▶); Miletich et al. (1997 ▶); Kunov et al. (2002 ▶); Frost et al. (2005 ▶); Sejkora et al. (2005 ▶); Plášil et al. (2009 ▶). For research on the sorption of toxic chemicals by minerals, see: Leone et al. (2013 ▶). For information on mineral nomenclature, see: Hatert & Burke (2008 ▶).

Experimental

Crystal data

Cu5.70(Y0.69Ca0.31)[(As0.83P0.17)O4]3(OH)6·3H2O

M = 985.85

Hexagonal,

a = 13.5059 (5) Å

c = 5.8903 (2) Å

V = 930.50 (6) Å3

Z = 2

Mo Kα radiation

μ = 13.13 mm−1

T = 293 K

0.10 × 0.02 × 0.02 mm

Data collection

Bruker APEXII CCD diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 2004 ▶) T min = 0.353, T max = 0.779

20461 measured reflections

786 independent reflections

674 reflections with I > 2σ(I)

R int = 0.048

Refinement

R[F 2 > 2σ(F 2)] = 0.032

wR(F 2) = 0.086

S = 1.14

786 reflections

60 parameters

1 restraint

H-atom parameters not refined

Δρmax = 2.34 e Å−3

Δρmin = −0.79 e Å−3

Data collection: APEX2 (Bruker, 2004 ▶); cell refinement: SAINT (Bruker, 2004 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: XtalDraw (Downs & Hall-Wallace, 2003 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶).

Crystal structure: contains datablock(s) I. DOI: 10.1107/S1600536813023477/wm2763sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813023477/wm2763Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Cu5.70(Y0.69Ca0.31)[(As0.83P0.17)O4]3(OH)6·3H2O	Dx = 3.519 Mg m−3
Mr = 985.85	Mo Kα radiation, λ = 0.71073 Å
Hexagonal, P63/m	Cell parameters from 786 reflections
Hall symbol: -P 6c	θ = 2.3–27.6°
a = 13.5059 (5) Å	µ = 13.13 mm−1
c = 5.8903 (2) Å	T = 293 K
V = 930.50 (6) Å3	Acicular needle, green
Z = 2	0.10 × 0.02 × 0.02 mm
F(000) = 936

Bruker APEXII CCD diffractometer	786 independent reflections
Radiation source: fine-focus sealed tube	674 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.048
φ and ω scan	θmax = 27.6°, θmin = 3.0°
Absorption correction: multi-scan (SADABS; Bruker, 2004)	h = −17→17
Tmin = 0.353, Tmax = 0.779	k = −17→17
20461 measured reflections	l = −6→7

Refinement on F2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.032	H-atom parameters not refined
wR(F2) = 0.086	w = 1/[σ2(Fo2) + (0.0413P)2 + 5.6747P] where P = (Fo2 + 2Fc2)/3
S = 1.14	(Δ/σ)max = 0.020
786 reflections	Δρmax = 2.34 e Å−3
60 parameters	Δρmin = −0.79 e Å−3
1 restraint

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 F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

	x	y	z	Uiso*/Ueq	Occ. (<1)
Y	0.6667	0.3333	0.2500	0.0084 (5)	0.69 (2)
Ca	0.6667	0.3333	0.2500	0.0084 (5)	0.31 (2)
Cu	0.41303 (5)	0.31598 (5)	0.50234 (10)	0.0113 (2)	0.950 (9)
As	0.49505 (6)	0.15100 (6)	0.7500	0.0087 (3)	0.828 (15)
P	0.49505 (6)	0.15100 (6)	0.7500	0.0087 (3)	0.172 (15)
O1	0.5739 (3)	0.1820 (3)	0.5182 (6)	0.0161 (9)
O2	0.3919 (5)	0.4007 (4)	0.2500	0.0180 (12)
O3	0.4124 (5)	0.2123 (5)	0.7500	0.0180 (12)
OH4	0.3688 (5)	0.3768 (5)	0.7500	0.0174 (12)
OH5	0.4421 (5)	0.2456 (5)	0.2500	0.0233 (14)
OW1	0.134 (3)	0.170 (3)	0.2500	0.221 (15)*	0.7676 (7)
OW2	0.0000	0.0000	0.5000	1.4 (4)*	0.697 (2)

	U11	U22	U33	U12	U13	U23
Y	0.0102 (5)	0.0102 (5)	0.0048 (7)	0.0051 (3)	0.000	0.000
Ca	0.0102 (5)	0.0102 (5)	0.0048 (7)	0.0051 (3)	0.000	0.000
Cu	0.0183 (4)	0.0153 (4)	0.0042 (4)	0.0113 (3)	0.0006 (2)	0.0003 (2)
As	0.0116 (4)	0.0086 (4)	0.0055 (4)	0.0048 (3)	0.000	0.000
P	0.0116 (4)	0.0086 (4)	0.0055 (4)	0.0048 (3)	0.000	0.000
O1	0.0184 (18)	0.0214 (19)	0.0109 (17)	0.0118 (16)	0.0039 (14)	0.0024 (14)
O2	0.029 (3)	0.025 (3)	0.009 (2)	0.020 (3)	0.000	0.000
O3	0.025 (3)	0.020 (3)	0.012 (3)	0.013 (2)	0.000	0.000
OH4	0.027 (3)	0.023 (3)	0.009 (2)	0.017 (2)	0.000	0.000
OH5	0.042 (4)	0.026 (3)	0.011 (3)	0.023 (3)	0.000	0.000

Y—O1i	2.384 (3)	Cu—OH5	1.908 (3)
Y—O1ii	2.384 (3)	Cu—OH4	1.911 (3)
Y—O1iii	2.384 (3)	Cu—O2	1.982 (3)
Y—O1	2.384 (3)	Cu—O3	2.019 (4)
Y—O1iv	2.384 (3)	Cu—O1iv	2.290 (4)
Y—O1v	2.384 (3)	As—O1vi	1.652 (3)
Y—OH5ii	2.647 (6)	As—O1	1.652 (3)
Y—OH5iv	2.647 (6)	As—O3	1.690 (5)
Y—OH5	2.647 (6)	As—O2vii	1.692 (5)
O1i—Y—O1ii	136.02 (6)	O1v—Y—OH5iv	67.84 (12)
O1i—Y—O1iii	80.86 (13)	OH5ii—Y—OH5iv	120.000 (1)
O1ii—Y—O1iii	83.01 (17)	O1i—Y—OH5	67.84 (12)
O1i—Y—O1	83.01 (17)	O1ii—Y—OH5	138.49 (8)
O1ii—Y—O1	80.86 (13)	O1iii—Y—OH5	138.49 (8)
O1iii—Y—O1	136.02 (6)	O1—Y—OH5	67.84 (12)
O1i—Y—O1iv	136.02 (6)	O1iv—Y—OH5	68.19 (12)
O1ii—Y—O1iv	80.86 (13)	O1v—Y—OH5	68.19 (12)
O1iii—Y—O1iv	136.02 (6)	OH5ii—Y—OH5	120.0
O1—Y—O1iv	80.86 (13)	OH5iv—Y—OH5	120.0
O1i—Y—O1v	80.86 (13)	OH5—Cu—OH4	174.6 (3)
O1ii—Y—O1v	136.02 (6)	OH5—Cu—O2	80.14 (17)
O1iii—Y—O1v	80.86 (13)	OH4—Cu—O2	99.09 (17)
O1—Y—O1v	136.02 (6)	OH5—Cu—O3	98.49 (17)
O1iv—Y—O1v	83.01 (17)	OH4—Cu—O3	81.53 (16)
O1i—Y—OH5ii	68.19 (12)	O2—Cu—O3	172.1 (2)
O1ii—Y—OH5ii	67.84 (12)	OH5—Cu—O1iv	84.2 (2)
O1iii—Y—OH5ii	67.84 (12)	OH4—Cu—O1iv	101.26 (19)
O1—Y—OH5ii	68.19 (12)	O2—Cu—O1iv	96.13 (18)
O1iv—Y—OH5ii	138.49 (8)	O3—Cu—O1iv	91.46 (18)
O1v—Y—OH5ii	138.49 (8)	O1vi—As—O1	111.5 (3)
O1i—Y—OH5iv	138.49 (8)	O1vi—As—O3	112.08 (15)
O1ii—Y—OH5iv	68.19 (12)	O1—As—O3	112.08 (15)
O1iii—Y—OH5iv	68.19 (12)	O1vi—As—O2vii	108.17 (16)
O1—Y—OH5iv	138.49 (8)	O1—As—O2vii	108.17 (16)
O1iv—Y—OH5iv	67.84 (12)	O3—As—O2vii	104.4 (3)