inorganic compounds
Penikisite, BaMg2Al2(PO4)3(OH)3, isostructural with bjarebyite
aDepartment of Geosciences, University of Arizona, 1040 E. 4th Street, Tucson, Arizona 85721-0077, USA
*Correspondence e-mail: bowman90@email.arizona.edu
The bjarebyite group of minerals, characterized by the general formula BaX2Y2(PO4)3(OH)3, with X = Mg, Fe2+ or Mn2+, and Y = Al or Fe3+, includes five members: bjarebyite BaMn2+2Al2(PO4)3(OH)3, johntomaite BaFe2+2Fe3+2(PO4)3(OH)3, kulanite BaFe2+2Al2(PO4)3(OH)3, penikisite BaMg2Al2(PO4)3(OH)3, and perloffite BaMn2+2Fe3+2(PO4)3(OH)3. Thus far, the crystal structures of all minerals in the group, but penikisite, have been determined. The present study reports the first of penikisite (barium dimagnesium dialuminium triphosphate trihydroxide) using single-crystal X-ray diffraction data of a crystal from the type locality, Mayo Mining District, Yukon Territory, Canada. Penikisite is isotypic with other members of the bjarebyite group with P21/m, rather than triclinic (P1 or P-1), as previously suggested. Its structure consists of edge-shared [AlO3(OH)3] octahedral dimers linking via corners to form chains along [010]. These chains are decorated with PO4 tetrahedra (one of which has m) and connected along [100] via edge-shared [MgO5(OH)] octahedral dimers and eleven-coordinated Ba2+ ions (site symmetry m), forming a complex three-dimensional network. O—H⋯O hydrogen bonding provides additional linkage between chains. Microprobe analysis of the crystal used for data collection indicated that Mn substitutes for Mg at the 1.5% (apfu) level.
Related literature
For penikisite, see: Mandarino et al. (1977). For other mineral members in the bjarebyite group, see: Moore & Araki (1974); Cooper & Hawthorne (1994); Kolitsch et al. (2000); Elliott & Willis (2011). For the definition of polyhedral distortion, see: Robinson et al. (1971).
Experimental
Crystal data
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Refinement
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Data collection: APEX2 (Bruker, 2004); cell 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).
Supporting information
10.1107/S1600536812051793/hb7009sup1.cif
contains datablocks I, New_Global_Publ_Block. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812051793/hb7009Isup2.hkl
The penikisite crystal used in this study is from the type locality, 16 miles north of the Hess River, Mayo Mining District, Yukon Territory, Canada and is in the collection of the RRUFF project (http://rruff.info/R060160), donated by Mark Mauthner. Its chemistry was determined with a CAMECA SX50 electron microprobe (8 analysis points), yielding the empirical chemical formula, calculated on the basis of 13.5 O atoms, Ba1.00(Mg1.97Mn0.03)Σ=2Al2.00(P1.00O4)3(OH)3 (OH was estimated by charge balance and difference).
The H atoms were located from difference Fourier syntheses and their positions refined freely with a fixed isotropic displacement (Uiso = 0.03). The highest residual peak in the difference Fourier maps was located at (0.4023, 0.2932, 0.2033), 0.71 Å from Ba, and the deepest hole at (0.5192, 1/4, 0.3234), 0.63 Å from Ba.
Data collection: APEX2 (Bruker, 2004); cell
SAINT (Bruker, 2004); data reduction: SAINT (Bruker, 2004); 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).Fig. 1. Crystal structure of penikisite in polyhedral representation. Large and small spheres represent Ba and H atoms, respectively. | |
Fig. 2. The crystal structure of penikisite, showing atoms, except for H, with displacement ellipsoids at the 99% probability level. Gray, pink, green, yellow, and red ellipsoids represent Ba, Mg, Al, P, and O atoms, respectively. H atoms are given as turquoise spheres with an arbitrary radius. |
Al4H6Mg3.94Mn0.06O30P6·2(Ba) | F(000) = 549 |
Mr = 576.77 | nearly cube |
Monoclinic, P121/m1 | Dx = 3.688 Mg m−3 |
Hall symbol: -P 2yb | Mo Kα radiation, λ = 0.71073 Å |
a = 8.9577 (4) Å | Cell parameters from 6030 reflections |
b = 12.0150 (5) Å | θ = 2.9–32.6° |
c = 4.9079 (2) Å | µ = 4.72 mm−1 |
β = 100.505 (2)° | T = 293 K |
V = 519.37 (4) Å3 | Cube, green |
Z = 2 | 0.09 × 0.09 × 0.08 mm |
Bruker APEXII CCD diffractometer | 1970 independent reflections |
Radiation source: fine-focus sealed tube | 1925 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.020 |
ϕ and ω scan | θmax = 32.6°, θmin = 2.9° |
Absorption correction: multi-scan (SADABS; Sheldrick 2005) | h = −13→12 |
Tmin = 0.676, Tmax = 0.704 | k = −15→18 |
7681 measured reflections | l = −7→7 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.015 | All H-atom parameters refined |
wR(F2) = 0.039 | w = 1/[σ2(Fo2) + (0.020P)2 + 0.2753P] where P = (Fo2 + 2Fc2)/3 |
S = 1.14 | (Δ/σ)max = 0.001 |
1970 reflections | Δρmax = 0.72 e Å−3 |
119 parameters | Δρmin = −0.80 e Å−3 |
1 restraint | Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0021 (5) |
Al4H6Mg3.94Mn0.06O30P6·2(Ba) | V = 519.37 (4) Å3 |
Mr = 576.77 | Z = 2 |
Monoclinic, P121/m1 | Mo Kα radiation |
a = 8.9577 (4) Å | µ = 4.72 mm−1 |
b = 12.0150 (5) Å | T = 293 K |
c = 4.9079 (2) Å | 0.09 × 0.09 × 0.08 mm |
β = 100.505 (2)° |
Bruker APEXII CCD diffractometer | 1970 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick 2005) | 1925 reflections with I > 2σ(I) |
Tmin = 0.676, Tmax = 0.704 | Rint = 0.020 |
7681 measured reflections |
R[F2 > 2σ(F2)] = 0.015 | 1 restraint |
wR(F2) = 0.039 | All H-atom parameters refined |
S = 1.14 | Δρmax = 0.72 e Å−3 |
1970 reflections | Δρmin = −0.80 e Å−3 |
119 parameters |
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) | |
Ba | 0.547869 (12) | 0.7500 | 0.74171 (2) | 0.00734 (5) | |
Mg | 0.29439 (5) | −0.11139 (4) | 0.20677 (10) | 0.00705 (9) | 0.9850 (1) |
Mn | 0.29439 (5) | −0.11139 (4) | 0.20677 (10) | 0.00705 (9) | 0.0150 (1) |
Al | 0.09176 (4) | 0.40084 (3) | 0.12947 (8) | 0.00401 (8) | |
P1 | 0.15736 (6) | 0.7500 | 0.68481 (10) | 0.00467 (9) | |
P2 | 0.33413 (4) | 0.44282 (3) | 0.70566 (7) | 0.00495 (7) | |
O1 | 0.27909 (16) | 0.7500 | 0.9471 (3) | 0.0072 (2) | |
O2 | 0.23251 (16) | 0.7500 | 0.4303 (3) | 0.0068 (2) | |
O3 | 0.05983 (11) | 0.64525 (9) | 0.6850 (2) | 0.00791 (18) | |
O4 | 0.36649 (12) | 0.55738 (9) | 0.6050 (2) | 0.00846 (18) | |
O5 | 0.25965 (11) | 0.45434 (9) | 0.9697 (2) | 0.00811 (18) | |
O6 | 0.22678 (12) | 0.38012 (9) | 0.4741 (2) | 0.00917 (18) | |
O7 | 0.47653 (12) | 0.37189 (9) | 0.7901 (2) | 0.00821 (18) | |
OH8 | 0.12478 (17) | 0.2500 | 0.0077 (3) | 0.0083 (3) | |
OH9 | 0.06100 (12) | 0.55814 (9) | 0.1891 (2) | 0.00679 (17) | |
H1 | 0.137 (4) | 0.2500 | −0.147 (8) | 0.030* | |
H2 | 0.046 (3) | 0.585 (2) | 0.325 (5) | 0.030* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Ba | 0.00667 (6) | 0.00826 (7) | 0.00724 (6) | 0.000 | 0.00171 (4) | 0.000 |
Mg | 0.0069 (2) | 0.0070 (2) | 0.00715 (19) | 0.00042 (16) | 0.00119 (16) | −0.00064 (16) |
Mn | 0.0069 (2) | 0.0070 (2) | 0.00715 (19) | 0.00042 (16) | 0.00119 (16) | −0.00064 (16) |
Al | 0.00373 (17) | 0.00395 (17) | 0.00440 (16) | −0.00027 (13) | 0.00091 (13) | 0.00002 (13) |
P1 | 0.00489 (19) | 0.0050 (2) | 0.00428 (18) | 0.000 | 0.00138 (15) | 0.000 |
P2 | 0.00499 (14) | 0.00536 (15) | 0.00459 (14) | 0.00024 (11) | 0.00113 (11) | 0.00027 (10) |
O1 | 0.0072 (6) | 0.0085 (6) | 0.0055 (6) | 0.000 | 0.0001 (5) | 0.000 |
O2 | 0.0088 (6) | 0.0061 (6) | 0.0062 (6) | 0.000 | 0.0036 (5) | 0.000 |
O3 | 0.0082 (4) | 0.0069 (4) | 0.0095 (4) | −0.0029 (3) | 0.0040 (3) | −0.0015 (3) |
O4 | 0.0101 (4) | 0.0070 (4) | 0.0083 (4) | −0.0001 (3) | 0.0018 (3) | 0.0023 (3) |
O5 | 0.0084 (4) | 0.0102 (5) | 0.0067 (4) | −0.0008 (4) | 0.0037 (3) | −0.0006 (3) |
O6 | 0.0093 (4) | 0.0100 (5) | 0.0073 (4) | −0.0002 (4) | −0.0008 (3) | −0.0015 (3) |
O7 | 0.0058 (4) | 0.0087 (5) | 0.0102 (4) | 0.0021 (3) | 0.0018 (3) | 0.0020 (3) |
OH8 | 0.0110 (6) | 0.0071 (6) | 0.0071 (6) | 0.000 | 0.0027 (5) | 0.000 |
OH9 | 0.0078 (4) | 0.0076 (4) | 0.0049 (4) | −0.0001 (3) | 0.0012 (3) | −0.0016 (3) |
Ba—O7i | 2.7669 (10) | Mg—O5x | 2.2090 (12) |
Ba—O7ii | 2.7669 (10) | Al—O3xi | 1.8523 (11) |
Ba—O1 | 2.7744 (14) | Al—O6 | 1.9080 (11) |
Ba—O4 | 2.8370 (11) | Al—O5xii | 1.9287 (10) |
Ba—O4iii | 2.8370 (11) | Al—OH9 | 1.9397 (11) |
Ba—O6iv | 2.9019 (11) | Al—OH9xiii | 1.9440 (11) |
Ba—O6v | 2.9019 (10) | Al—OH8 | 1.9477 (7) |
Ba—O2 | 2.9566 (15) | P1—O2 | 1.5232 (14) |
Ba—OH8v | 2.9658 (15) | P1—O1 | 1.5278 (15) |
Ba—O7v | 2.9661 (10) | P1—O3 | 1.5321 (10) |
Ba—O7iv | 2.9661 (10) | P1—O3iii | 1.5321 (10) |
Mg—O4vi | 2.0490 (11) | P2—O4 | 1.5083 (11) |
Mg—O7vii | 2.0591 (11) | P2—O7 | 1.5272 (11) |
Mg—O1viii | 2.0864 (10) | P2—O6 | 1.5443 (11) |
Mg—O2ix | 2.1227 (10) | P2—O5 | 1.5680 (10) |
Mg—OH9vi | 2.1729 (11) | ||
O4vi—Mg—O7vii | 83.31 (4) | O3xi—Al—OH9xiii | 89.97 (5) |
O4vi—Mg—O1viii | 144.07 (5) | O6—Al—OH9xiii | 170.24 (5) |
O7vii—Mg—O1viii | 83.17 (5) | O5xii—Al—OH9xiii | 94.31 (5) |
O4vi—Mg—O2ix | 79.75 (5) | OH9—Al—OH9xiii | 77.04 (5) |
O7vii—Mg—O2ix | 105.87 (5) | O3xi—Al—OH8 | 92.21 (5) |
O1viii—Mg—O2ix | 72.26 (5) | O6—Al—OH8 | 92.49 (6) |
O4vi—Mg—OH9vi | 94.50 (4) | O5xii—Al—OH8 | 90.69 (5) |
O7vii—Mg—OH9vi | 168.32 (5) | OH9—Al—OH8 | 170.59 (5) |
O1viii—Mg—OH9vi | 104.78 (5) | OH9xiii—Al—OH8 | 96.50 (6) |
O2ix—Mg—OH9vi | 84.93 (5) | O2—P1—O1 | 109.67 (8) |
O4vi—Mg—O5x | 102.80 (5) | O2—P1—O3 | 109.74 (5) |
O7vii—Mg—O5x | 97.57 (4) | O1—P1—O3 | 108.60 (5) |
O1viii—Mg—O5x | 111.89 (4) | O2—P1—O3iii | 109.74 (5) |
O2ix—Mg—O5x | 156.55 (5) | O1—P1—O3iii | 108.60 (5) |
OH9vi—Mg—O5x | 71.65 (4) | O3—P1—O3iii | 110.46 (8) |
O3xi—Al—O6 | 85.88 (5) | O4—P2—O7 | 113.41 (6) |
O3xi—Al—O5xii | 174.52 (5) | O4—P2—O6 | 109.59 (6) |
O6—Al—O5xii | 89.36 (5) | O7—P2—O6 | 107.74 (6) |
O3xi—Al—OH9 | 94.60 (5) | O4—P2—O5 | 109.04 (6) |
O6—Al—OH9 | 94.47 (5) | O7—P2—O5 | 106.57 (6) |
O5xii—Al—OH9 | 83.07 (5) | O6—P2—O5 | 110.45 (6) |
Symmetry codes: (i) −x+1, y+1/2, −z+2; (ii) −x+1, −y+1, −z+2; (iii) x, −y+3/2, z; (iv) −x+1, y+1/2, −z+1; (v) −x+1, −y+1, −z+1; (vi) x, −y+1/2, z; (vii) −x+1, y−1/2, −z+1; (viii) x, y−1, z−1; (ix) x, y−1, z; (x) x, −y+1/2, z−1; (xi) −x, −y+1, −z+1; (xii) x, y, z−1; (xiii) −x, −y+1, −z. |
D—H···A | D—H | H···A | D···A | D—H···A |
OH8—H1···O6xii | 0.79 (4) | 2.66 (3) | 3.3180 (16) | 142 (1) |
OH9—H2···O3 | 0.78 (3) | 1.89 (3) | 2.6512 (13) | 166 (3) |
Symmetry code: (xii) x, y, z−1. |
Experimental details
Crystal data | |
Chemical formula | Al4H6Mg3.94Mn0.06O30P6·2(Ba) |
Mr | 576.77 |
Crystal system, space group | Monoclinic, P121/m1 |
Temperature (K) | 293 |
a, b, c (Å) | 8.9577 (4), 12.0150 (5), 4.9079 (2) |
β (°) | 100.505 (2) |
V (Å3) | 519.37 (4) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 4.72 |
Crystal size (mm) | 0.09 × 0.09 × 0.08 |
Data collection | |
Diffractometer | Bruker APEXII CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick 2005) |
Tmin, Tmax | 0.676, 0.704 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7681, 1970, 1925 |
Rint | 0.020 |
(sin θ/λ)max (Å−1) | 0.757 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.015, 0.039, 1.14 |
No. of reflections | 1970 |
No. of parameters | 119 |
No. of restraints | 1 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.72, −0.80 |
Computer programs: APEX2 (Bruker, 2004), SAINT (Bruker, 2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), XtalDraw (Downs & Hall-Wallace, 2003), publCIF (Westrip, 2010).
Mg—O7i | 2.0591 (11) | Al—OH8 | 1.9477 (7) |
Mg—O1ii | 2.0864 (10) | P1—O2 | 1.5232 (14) |
Mg—O2iii | 2.1227 (10) | P1—O1 | 1.5278 (15) |
Mg—OH9iv | 2.1729 (11) | P1—O3 | 1.5321 (10) |
Mg—O5v | 2.2090 (12) | P1—O3ix | 1.5321 (10) |
Al—O3vi | 1.8523 (11) | P2—O4 | 1.5083 (11) |
Al—O6 | 1.9080 (11) | P2—O7 | 1.5272 (11) |
Al—O5vii | 1.9287 (10) | P2—O6 | 1.5443 (11) |
Al—OH9 | 1.9397 (11) | P2—O5 | 1.5680 (10) |
Al—OH9viii | 1.9440 (11) |
Symmetry codes: (i) −x+1, y−1/2, −z+1; (ii) x, y−1, z−1; (iii) x, y−1, z; (iv) x, −y+1/2, z; (v) x, −y+1/2, z−1; (vi) −x, −y+1, −z+1; (vii) x, y, z−1; (viii) −x, −y+1, −z; (ix) x, −y+3/2, z. |
D—H···A | D—H | H···A | D···A | D—H···A |
OH8—H1···O6vii | 0.79 (4) | 2.66 (3) | 3.3180 (16) | 141.9 (12) |
OH9—H2···O3 | 0.78 (3) | 1.89 (3) | 2.6512 (13) | 166 (3) |
Symmetry code: (vii) x, y, z−1. |
Acknowledgements
The authors gratefully acknowledge support of this study by the Science Foundation Arizona.
References
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The bjarebyite group of minerals is characterized by the general chemical formula BaX2Y2(PO4)3(OH)3, where X=Mn2+, Fe2+ or Mg and Y=Al or Fe3+, and includes five members: bjarebyite BaMn2+2Al2(PO4)3(OH)3, johntomaite BaFe2+2Fe3+2(PO4)3(OH)3, kulanite BaFe2+2Al2(PO4)3(OH)3, penikisite BaMg2Al2(PO4)3(OH)3, and perloffite BaMn2+2Fe3+2(PO4)3(OH)3. Except for penikisite, the crystal structures of all other minerals in the group have been determined (Moore and Araki, 1974; Cooper and Hawthorne, 1994; Kolitsch et al., 2000; Elliot & Willis, 2011), which all possess space group P21/m. Penikisite was first described by Mandarino et al. (1977) as triclinic with space group P1 or P1 (albeit strongly pseudomonoclinic), based on the observation of asymmetric optical dispersion. Since then, no detailed crystallographic study on penikisite has been reported. In our efforts to understand the hydrogen bonding environments in minerals, we conducted a structure determination of penikisite from the type locality by means of single-crystal X-ray diffraction.
Penikisite is isotypic with other members of the bjarebyite group, with space group P21/m. Its structure consists of edge-shared [AlO3(OH)3] octahedral dimers connected via corners to form chains along [010]. These chains are decorated with PO4 tetrahedra and linked along [100] via edge-shared MgO5(OH) octahedral dimers and eleven-coordinated Ba atoms to form a complex three-dimensional network (Figs. 1 and 2). The hydrogen bonding provides additional linkage between chains.
Similar to other minerals in the bjarebyite group, the YO5(OH) octahedra in penikisite are noticeably distorted, as measured by the octahedral angle variance (OAV) and quadratic elongation (OQE) (Robinson et al., 1971), which are 188 and 1.057, respectively. In contrast, the OAV and OQE values are 32 and 1.010 for the XO3(OH)3 octahedra in penikisite. From penikisite to the Fe-analogue kulanite (Cooper and Hawthorne, 1994), and to the Mn-analogue bjarebyite (Moore and Araki, 1974), the average X-O distance increases from 2.117 to 2.146, and to 2.162 Å, respectively, in accordance with the increase in the ionic radius in this site.
There are two hydrogen bonds in penikisite, one between OH8 and O6 [3.318 (2) Å] and the other between OH9 and O3 [2.651 (1) Å], agreeing well with the results obtained by Elliott & Willis (2011) from perloffite. However, Cooper and Hawthorne (1994) proposed a disorder model for H1 in kulanite. The H atoms were not located in the structure of bjarebyite (Moore and Araki, 1974) or johntomaite (Kolitsch et al., 2000).