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

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.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](P-O) = 0.002 Å
• Disorder in main residue
• R factor = 0.015
• wR factor = 0.039
• Data-to-parameter ratio = 16.6

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT420_ALERT_2_B D-H Without Acceptor       OH8    -   H1     ...          ?

Alert level C
PLAT068_ALERT_1_C Reported F000 Differs from Calcd (or Missing)...          ?
PLAT077_ALERT_4_C Unitcell contains non-integer number of atoms ..          ?
PLAT480_ALERT_4_C Long H...A H-Bond Reported H1     ..  O6      ..       2.66 Ang.
PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) .....          1

Alert level G
FORMU01_ALERT_1_G  There is a discrepancy between the atom counts in the
            _chemical_formula_sum and _chemical_formula_moiety. This is
            usually due to the moiety formula being in the wrong format.
            Atom count from _chemical_formula_sum:   H3 Al2 Ba1 Mg1.97 Mn.03 O15
            Atom count from _chemical_formula_moiety:H6 Al4 Ba2 Mg3.94 Mn.06 O30
PLAT004_ALERT_5_G Info: Polymeric Structure Found with Dimension .          2
PLAT005_ALERT_5_G No _iucr_refine_instructions_details  in the CIF          ?
PLAT045_ALERT_1_G Calculated and Reported Z Differ by ............       0.50 Ratio
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported   _diffrn_ambient_temperature        293 K
PLAT232_ALERT_2_G Hirshfeld Test Diff (M-X)  Al     --  OH9     ..        7.5 su
PLAT232_ALERT_2_G Hirshfeld Test Diff (M-X)  Al     --  OH9_i   ..        6.3 su
PLAT301_ALERT_3_G Note: Main Residue  Disorder ...................          8 Perc.
PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels ..........          2
PLAT793_ALERT_4_G The Model has Chirality at P1      (Verify) ....          R
PLAT793_ALERT_4_G The Model has Chirality at P2      (Verify) ....          S
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          1

   0 ALERT level A = Most likely a serious problem - resolve or explain
   1 ALERT level B = A potentially serious problem, consider carefully
   4 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  13 ALERT level G = General information/check it is not something unexpected

   5 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   3 ALERT type 2 Indicator that the structure model may be wrong or deficient
   3 ALERT type 3 Indicator that the structure quality may be low
   5 ALERT type 4 Improvement, methodology, query or suggestion
   2 ALERT type 5 Informative message, check

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S1. Comment

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

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).

S2. Experimental

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, Ba_1.00(Mg_1.97Mn_0.03)_Σ=2Al_2.00(P_1.00O₄)₃(OH)₃ (OH was estimated by charge balance and difference).

S3. Refinement

The H atoms were located from difference Fourier syntheses and their positions refined freely with a fixed isotropic displacement (U_iso = 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

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

	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.

Barium dimagnesium dialuminium triphosphate trihydroxide

Crystal data

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) Å^3	Cube, green
Z = 2	0.09 × 0.09 × 0.08 mm

Data collection

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

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.015	All H-atom parameters refined
wR(F^2) = 0.039	w = 1/[σ^2(Fo^2) + (0.020P)^2 + 0.2753P] where P = (Fo^2 + 2Fc^2)/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+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0021 (5)

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 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 (Ų)

	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*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

Geometric parameters (Å, º)

Ba—O7^i	2.7669 (10)	Mg—O5^x	2.2090 (12)
Ba—O7^ii	2.7669 (10)	Al—O3^xi	1.8523 (11)
Ba—O1	2.7744 (14)	Al—O6	1.9080 (11)
Ba—O4	2.8370 (11)	Al—O5^xii	1.9287 (10)
Ba—O4^iii	2.8370 (11)	Al—OH9	1.9397 (11)
Ba—O6^iv	2.9019 (11)	Al—OH9^xiii	1.9440 (11)
Ba—O6^v	2.9019 (10)	Al—OH8	1.9477 (7)
Ba—O2	2.9566 (15)	P1—O2	1.5232 (14)
Ba—OH8^v	2.9658 (15)	P1—O1	1.5278 (15)
Ba—O7^v	2.9661 (10)	P1—O3	1.5321 (10)
Ba—O7^iv	2.9661 (10)	P1—O3^iii	1.5321 (10)
Mg—O4^vi	2.0490 (11)	P2—O4	1.5083 (11)
Mg—O7^vii	2.0591 (11)	P2—O7	1.5272 (11)
Mg—O1^viii	2.0864 (10)	P2—O6	1.5443 (11)
Mg—O2^ix	2.1227 (10)	P2—O5	1.5680 (10)
Mg—OH9^vi	2.1729 (11)
O4^vi—Mg—O7^vii	83.31 (4)	O3^xi—Al—OH9^xiii	89.97 (5)
O4^vi—Mg—O1^viii	144.07 (5)	O6—Al—OH9^xiii	170.24 (5)
O7^vii—Mg—O1^viii	83.17 (5)	O5^xii—Al—OH9^xiii	94.31 (5)
O4^vi—Mg—O2^ix	79.75 (5)	OH9—Al—OH9^xiii	77.04 (5)
O7^vii—Mg—O2^ix	105.87 (5)	O3^xi—Al—OH8	92.21 (5)
O1^viii—Mg—O2^ix	72.26 (5)	O6—Al—OH8	92.49 (6)
O4^vi—Mg—OH9^vi	94.50 (4)	O5^xii—Al—OH8	90.69 (5)
O7^vii—Mg—OH9^vi	168.32 (5)	OH9—Al—OH8	170.59 (5)
O1^viii—Mg—OH9^vi	104.78 (5)	OH9^xiii—Al—OH8	96.50 (6)
O2^ix—Mg—OH9^vi	84.93 (5)	O2—P1—O1	109.67 (8)
O4^vi—Mg—O5^x	102.80 (5)	O2—P1—O3	109.74 (5)
O7^vii—Mg—O5^x	97.57 (4)	O1—P1—O3	108.60 (5)
O1^viii—Mg—O5^x	111.89 (4)	O2—P1—O3^iii	109.74 (5)
O2^ix—Mg—O5^x	156.55 (5)	O1—P1—O3^iii	108.60 (5)
OH9^vi—Mg—O5^x	71.65 (4)	O3—P1—O3^iii	110.46 (8)
O3^xi—Al—O6	85.88 (5)	O4—P2—O7	113.41 (6)
O3^xi—Al—O5^xii	174.52 (5)	O4—P2—O6	109.59 (6)
O6—Al—O5^xii	89.36 (5)	O7—P2—O6	107.74 (6)
O3^xi—Al—OH9	94.60 (5)	O4—P2—O5	109.04 (6)
O6—Al—OH9	94.47 (5)	O7—P2—O5	106.57 (6)
O5^xii—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.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
OH8—H1···O6^xii	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.