supplementary materials


HTML versionpdf versioncif file3d viewstructure factorssupplementary materialsCIF check reportsimilar papers Open access

Acta Cryst. (2013). E69, i4-i5    [ doi:10.1107/S1600536812051793 ]

Penikisite, BaMg2Al2(PO4)3(OH)3, isostructural with bjarebyite

M. G. Bowman, R. T. Downs and H. Yang

Abstract top

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 structure determination 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 space group 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 site symmetry 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.

Comment top

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).

Related literature top

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 top

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).

Refinement top

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.

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: 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).

Figures top
[Figure 1] Fig. 1. Crystal structure of penikisite in polyhedral representation. Large and small spheres represent Ba and H atoms, respectively.
[Figure 2] 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.
Barium dimagnesium dialuminium triphosphate trihydroxide top
Crystal data top
Al4H6Mg3.94Mn0.06O30P6·2(Ba)F(000) = 549
Mr = 576.77nearly cube
Monoclinic, P121/m1Dx = 3.688 Mg m−3
Hall symbol: -P 2ybMo Kα radiation, λ = 0.71073 Å
a = 8.9577 (4) ÅCell parameters from 6030 reflections
b = 12.0150 (5) Åθ = 2.9–32.6°
c = 4.9079 (2) ŵ = 4.72 mm−1
β = 100.505 (2)°T = 293 K
V = 519.37 (4) Å3Cube, green
Z = 20.09 × 0.09 × 0.08 mm
Data collection top
Bruker APEXII CCD
diffractometer		1970 independent reflections
Radiation source: fine-focus sealed tube1925 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.020
φ and ω scanθmax = 32.6°, θmin = 2.9°
Absorption correction: multi-scan
(SADABS; Sheldrick 2005)		h = −13→12
Tmin = 0.676, Tmax = 0.704k = −15→18
7681 measured reflectionsl = −7→7
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.015All 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 reflectionsΔρmax = 0.72 e Å−3
119 parametersΔρmin = −0.80 e Å−3
1 restraintExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0021 (5)
Crystal data top
Al4H6Mg3.94Mn0.06O30P6·2(Ba)V = 519.37 (4) Å3
Mr = 576.77Z = 2
Monoclinic, P121/m1Mo Kα radiation
a = 8.9577 (4) ŵ = 4.72 mm−1
b = 12.0150 (5) ÅT = 293 K
c = 4.9079 (2) Å0.09 × 0.09 × 0.08 mm
β = 100.505 (2)°
Data collection top
Bruker APEXII CCD
diffractometer		1970 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick 2005)		1925 reflections with I > 2σ(I)
Tmin = 0.676, Tmax = 0.704Rint = 0.020
7681 measured reflectionsθmax = 32.6°
Refinement top
R[F2 > 2σ(F2)] = 0.015All H-atom parameters refined
wR(F2) = 0.039Δρmax = 0.72 e Å−3
S = 1.14Δρmin = −0.80 e Å−3
1970 reflectionsAbsolute structure: ?
119 parametersFlack parameter: ?
1 restraintRogers parameter: ?
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
Ba0.547869 (12)0.75000.74171 (2)0.00734 (5)
Mg0.29439 (5)−0.11139 (4)0.20677 (10)0.00705 (9)0.9850 (1)
Mn0.29439 (5)−0.11139 (4)0.20677 (10)0.00705 (9)0.0150 (1)
Al0.09176 (4)0.40084 (3)0.12947 (8)0.00401 (8)
P10.15736 (6)0.75000.68481 (10)0.00467 (9)
P20.33413 (4)0.44282 (3)0.70566 (7)0.00495 (7)
O10.27909 (16)0.75000.9471 (3)0.0072 (2)
O20.23251 (16)0.75000.4303 (3)0.0068 (2)
O30.05983 (11)0.64525 (9)0.6850 (2)0.00791 (18)
O40.36649 (12)0.55738 (9)0.6050 (2)0.00846 (18)
O50.25965 (11)0.45434 (9)0.9697 (2)0.00811 (18)
O60.22678 (12)0.38012 (9)0.4741 (2)0.00917 (18)
O70.47653 (12)0.37189 (9)0.7901 (2)0.00821 (18)
OH80.12478 (17)0.25000.0077 (3)0.0083 (3)
OH90.06100 (12)0.55814 (9)0.1891 (2)0.00679 (17)
H10.137 (4)0.2500−0.147 (8)0.030*
H20.046 (3)0.585 (2)0.325 (5)0.030*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Ba0.00667 (6)0.00826 (7)0.00724 (6)0.0000.00171 (4)0.000
Mg0.0069 (2)0.0070 (2)0.00715 (19)0.00042 (16)0.00119 (16)−0.00064 (16)
Mn0.0069 (2)0.0070 (2)0.00715 (19)0.00042 (16)0.00119 (16)−0.00064 (16)
Al0.00373 (17)0.00395 (17)0.00440 (16)−0.00027 (13)0.00091 (13)0.00002 (13)
P10.00489 (19)0.0050 (2)0.00428 (18)0.0000.00138 (15)0.000
P20.00499 (14)0.00536 (15)0.00459 (14)0.00024 (11)0.00113 (11)0.00027 (10)
O10.0072 (6)0.0085 (6)0.0055 (6)0.0000.0001 (5)0.000
O20.0088 (6)0.0061 (6)0.0062 (6)0.0000.0036 (5)0.000
O30.0082 (4)0.0069 (4)0.0095 (4)−0.0029 (3)0.0040 (3)−0.0015 (3)
O40.0101 (4)0.0070 (4)0.0083 (4)−0.0001 (3)0.0018 (3)0.0023 (3)
O50.0084 (4)0.0102 (5)0.0067 (4)−0.0008 (4)0.0037 (3)−0.0006 (3)
O60.0093 (4)0.0100 (5)0.0073 (4)−0.0002 (4)−0.0008 (3)−0.0015 (3)
O70.0058 (4)0.0087 (5)0.0102 (4)0.0021 (3)0.0018 (3)0.0020 (3)
OH80.0110 (6)0.0071 (6)0.0071 (6)0.0000.0027 (5)0.000
OH90.0078 (4)0.0076 (4)0.0049 (4)−0.0001 (3)0.0012 (3)−0.0016 (3)
Geometric parameters (Å, º) top
Ba—O7i2.7669 (10)Mg—O5x2.2090 (12)
Ba—O7ii2.7669 (10)Al—O3xi1.8523 (11)
Ba—O12.7744 (14)Al—O61.9080 (11)
Ba—O42.8370 (11)Al—O5xii1.9287 (10)
Ba—O4iii2.8370 (11)Al—OH91.9397 (11)
Ba—O6iv2.9019 (11)Al—OH9xiii1.9440 (11)
Ba—O6v2.9019 (10)Al—OH81.9477 (7)
Ba—O22.9566 (15)P1—O21.5232 (14)
Ba—OH8v2.9658 (15)P1—O11.5278 (15)
Ba—O7v2.9661 (10)P1—O31.5321 (10)
Ba—O7iv2.9661 (10)P1—O3iii1.5321 (10)
Mg—O4vi2.0490 (11)P2—O41.5083 (11)
Mg—O7vii2.0591 (11)P2—O71.5272 (11)
Mg—O1viii2.0864 (10)P2—O61.5443 (11)
Mg—O2ix2.1227 (10)P2—O51.5680 (10)
Mg—OH9vi2.1729 (11)
O4vi—Mg—O7vii83.31 (4)O3xi—Al—OH9xiii89.97 (5)
O4vi—Mg—O1viii144.07 (5)O6—Al—OH9xiii170.24 (5)
O7vii—Mg—O1viii83.17 (5)O5xii—Al—OH9xiii94.31 (5)
O4vi—Mg—O2ix79.75 (5)OH9—Al—OH9xiii77.04 (5)
O7vii—Mg—O2ix105.87 (5)O3xi—Al—OH892.21 (5)
O1viii—Mg—O2ix72.26 (5)O6—Al—OH892.49 (6)
O4vi—Mg—OH9vi94.50 (4)O5xii—Al—OH890.69 (5)
O7vii—Mg—OH9vi168.32 (5)OH9—Al—OH8170.59 (5)
O1viii—Mg—OH9vi104.78 (5)OH9xiii—Al—OH896.50 (6)
O2ix—Mg—OH9vi84.93 (5)O2—P1—O1109.67 (8)
O4vi—Mg—O5x102.80 (5)O2—P1—O3109.74 (5)
O7vii—Mg—O5x97.57 (4)O1—P1—O3108.60 (5)
O1viii—Mg—O5x111.89 (4)O2—P1—O3iii109.74 (5)
O2ix—Mg—O5x156.55 (5)O1—P1—O3iii108.60 (5)
OH9vi—Mg—O5x71.65 (4)O3—P1—O3iii110.46 (8)
O3xi—Al—O685.88 (5)O4—P2—O7113.41 (6)
O3xi—Al—O5xii174.52 (5)O4—P2—O6109.59 (6)
O6—Al—O5xii89.36 (5)O7—P2—O6107.74 (6)
O3xi—Al—OH994.60 (5)O4—P2—O5109.04 (6)
O6—Al—OH994.47 (5)O7—P2—O5106.57 (6)
O5xii—Al—OH983.07 (5)O6—P2—O5110.45 (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.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
OH8—H1···O6xii0.79 (4)2.66 (3)3.3180 (16)142 (1)
OH9—H2···O30.78 (3)1.89 (3)2.6512 (13)166 (3)
Symmetry code: (xii) x, y, z−1.
Selected bond lengths (Å) top
Mg—O7i2.0591 (11)Al—OH81.9477 (7)
Mg—O1ii2.0864 (10)P1—O21.5232 (14)
Mg—O2iii2.1227 (10)P1—O11.5278 (15)
Mg—OH9iv2.1729 (11)P1—O31.5321 (10)
Mg—O5v2.2090 (12)P1—O3ix1.5321 (10)
Al—O3vi1.8523 (11)P2—O41.5083 (11)
Al—O61.9080 (11)P2—O71.5272 (11)
Al—O5vii1.9287 (10)P2—O61.5443 (11)
Al—OH91.9397 (11)P2—O51.5680 (10)
Al—OH9viii1.9440 (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.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
OH8—H1···O6vii0.79 (4)2.66 (3)3.3180 (16)141.9 (12)
OH9—H2···O30.78 (3)1.89 (3)2.6512 (13)166 (3)
Symmetry code: (vii) x, y, z−1.
Acknowledgements top

The authors gratefully acknowledge support of this study by the Science Foundation Arizona.

references
References top

Bruker (2004). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.

Cooper, M. & Hawthorne, F. C. (1994). Can. Mineral. 32, 15–19.

Downs, R. T. & Hall-Wallace, M. (2003). Am. Mineral. 88, 247–250.

Elliott, P. & Willis, A. C. (2011). Mineral. Mag. 75, 317–325.

Kolitsch, U., Pring, A. & Tiekink, E. R. T. (2000). Mineral. Petrol. 70, 1–14.

Mandarino, J. A., Sturman, B. D. & Corlett, M. I. (1977). Can. Mineral. 15, 393–395.

Moore, P. B. & Araki, T. (1974). Am. Mineral. 59, 567–572.

Robinson, K., Gibbs, G. V. & Ribbe, P. H. (1971). Science, 172, 567–570.

Sheldrick, G. M. (2005). SADABS. University of Göttingen, Germany.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.