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Acta Crystallogr Sect E Struct Rep Online. 2010 May 1; 66(Pt 5): o1189–o1190.
Published online 2010 April 28. doi:  10.1107/S1600536810014583
PMCID: PMC2979045

2-Amino-4-meth­oxy-6-methyl­pyrimidin-1-ium picrate

Abstract

In the title salt, C6H10N3O+·C6H2N3O7 , the dihedral angle between the mean planes of the benzene and pyridine rings is 3.1 (1)°. In the cation, the meth­oxy group is almost coplanar with the pyridine ring [C—O—C—N = −0.6 (2)°]. The p-nitro [C—C—N—O = −1.17 (19)°] and one o-nitro [C—C—N—O = 1.83 (19)°] group in the anion are essentially coplanar with the benzene ring. The other disordered o-nitro group containing the major occupancy [0.868 (6)] O atom is twisted −29.0 (2)° from the mean plane of the benzene ring. A bifurcated N—H(...)(O.O) hydrogen bond and weak C—H(...)O intermolecular inter­action between the cation and anion produce a network of infinite O—H(...)O—H(...)O—H chains along the c axis in the [101] plane which helps to establish crystal packing. Comparison to a DFT computational calculation indicates that significant conformational changes occur in the free state.

Related literature

For the synthesis of imidazo[1,2-a]pyrimidines, see: Katritzky et al. (2003 [triangle]). For related structures, see: Ferguson et al. (1984 [triangle]); Glidewell et al. (2003 [triangle]); Narayana et al. (2008 [triangle]); Scheinbeim & Schempp, (1976 [triangle]); Schlueter et al. (2006 [triangle]); Subashini et al. (2006 [triangle]). For density functional theory, see: Hehre et al. (1986 [triangle]); Schmidt & Polik (2007 [triangle]).

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Object name is e-66-o1189-scheme1.jpg

Experimental

Crystal data

  • C6H10N3O+·C6H2N3O7
  • M r = 368.28
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o1189-efi1.jpg
  • a = 8.9442 (3) Å
  • b = 6.2793 (3) Å
  • c = 27.0354 (8) Å
  • β = 94.471 (3)°
  • V = 1513.78 (10) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.14 mm−1
  • T = 200 K
  • 0.52 × 0.46 × 0.35 mm

Data collection

  • Oxford Diffraction Gemini diffractometer
  • Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007 [triangle]) T min = 0.986, T max = 1.000
  • 15870 measured reflections
  • 6133 independent reflections
  • 3107 reflections with I > 2σ(I)
  • R int = 0.031

Refinement

  • R[F 2 > 2σ(F 2)] = 0.054
  • wR(F 2) = 0.160
  • S = 0.94
  • 6133 reflections
  • 256 parameters
  • 24 restraints
  • H-atom parameters constrained
  • Δρmax = 0.43 e Å−3
  • Δρmin = −0.29 e Å−3

Data collection: CrysAlis PRO (Oxford Diffraction, 2007 [triangle]); cell refinement: CrysAlis RED (Oxford Diffraction, 2007 [triangle]); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97) (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810014583/bt5240sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810014583/bt5240Isup2.hkl

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

Acknowledgments

KPK thanks the UGC, New Delhi, for the sanction of a Faculty Improvement Programme. RJB acknowledges the NSF MRI program (grant No. CHE-0619278) for funds to purchase an X-ray diffractometer.

supplementary crystallographic information

Comment

The synthesis of imidazo[1,2-a]pyrimidines has been widely investigated and is one of the most common strategies in the use of 2-aminopyrimidine as the starting material (Katritzky et al., 2003). Recently, the hydrogen-bonding patterns in 2-amino-4,6-dimethylpyrimidinium picrate has been reported (Subashini et al., 2006). In continuation of our work on picrates of biologically important molecules, we have prepared a new picrate of 2-amino-4-methoxy-6-methylpyrimidine, [C6H10N3 O]+, [C6H2N3O7]- and its crystal structure is reported.

The title compound,(I), C12H12N6O8, crystallizes as a salt with one C6H10N3 O+, C6H2N3O7- , cation-anion pair in the asymmetric unit (Fig. 1). The dihedral angle between the mean planes of the benzene and pyridine rings is 3.10°. In the cation the methoxy group is almost coplanar with the pyridine ring [C6B-O1B-C5B-N3B torsion angle = -0.63 (19)°]. Bond distances and angles in both the cation and anion are in normal ranges (Allen, 2002). The p [torsion angle C3A-C4A-N4A-O41A = 1.17 (18)°] and one o [torsion angle C1A-C2A-N2A-O21A = 1.83 (19)°] nitro group in the anion are nearly coplanar with the benzene ring. The other disordered o nitro group containing the predomoinate oxygen atom (occupancy = 0.868 (6)) is twisted -29.0 (2)\5 from the mean plane of the benzene ring. Bifurcated intramolecular donor, N1B, [O1A [N1B—H1BB···O21A. & N1B—H1BB···O1A] and acceptor, O1A, [N1B—H1BB···O1A & N2B—H2BA···O1A] hydrogen bonds and a weak C3B—H3BB···O62A(0.868 (6)) hydrogen bond interaction (Table 2) between the cation and anion produces a network of infinite O—H···O—H···O—H chains along the c axis in the [101] plane which helps to establish crystal packing (Fig. 2).

A density functional theory (DFT) geometry optimization molecular orbital calculation (Schmidt & Polik, 2007) was performed on the independent cation-anion pair (C6H10N3 O+, C6H2N3O7- ) within the asymmetric unit with the B3LYP 6-31-G(d) basis set (Hehre et al., 1986). Starting geometries were taken from X-ray refinement data. The dihedral angle between the mean planes of the benzene and pyridine rings increases to 28.10°. In the anion, the mean planes of the two o-nitro groups become twisted by 23.14° and 24.20°, respectively, from the mean plane of the benzene ring. The mean plane of the p-nitro group remains planar to the benzene ring. The mean plane of the methoxy group in the cation also remains planar to the pyridine ring. These observations suggest that the bifurcated N—H···(O,O) donor and acceptor hydrogen bonds and weak C—H···O intermolecular interactions play a significant role in crystal stability.

Experimental

4-Methoxy-6-methylpyrimidin-2-amine (1.39 g, 0.01 mol) was dissolved in 25 ml of ethanol. Picric acid (2.29 g, 0.01 mol) was dissolved in 15 ml of water. Both the solutions were mixed and to this, 5 ml of 5M HCl was added and stirred for few minutes. The formed complex was filtered and dried. Good quality crystals were grown from ethanol solution by slow evaporation (m. p.: 399 K). Composition: Found (Calculated): C: 39.09 (39.14); H: 3.24 (3.28); N: 22.77% (22.82%).

Refinement

All of the H atoms were placed in their calculated positions and then refined using the riding model with C—H = 0.95-0.98 Å, N—H = 0.88 Å, and with Uiso(H) = 1.18-1.52Ueq(C,N).

Figures

Fig. 1.
Molecular structure of the C6H10N3 O+, C6H2N3O7- cation-anion pair showing the atom labeling scheme and 50% probability displacement ellipsoids. Only the predominate component of the disordered nitro group is displayed. Dashed lines indicate hydrogen ...
Fig. 2.
Packing diagram of the title compound, viewed down the b axis. Dashed lines indicate hydrogen bonds.

Crystal data

C6H10N3O+·C6H2N3O7F(000) = 760
Mr = 368.28Dx = 1.616 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3951 reflections
a = 8.9442 (3) Åθ = 4.6–34.8°
b = 6.2793 (3) ŵ = 0.14 mm1
c = 27.0354 (8) ÅT = 200 K
β = 94.471 (3)°Prism, yellow
V = 1513.78 (10) Å30.52 × 0.46 × 0.35 mm
Z = 4

Data collection

Oxford Diffraction Gemini diffractometer6133 independent reflections
Radiation source: fine-focus sealed tube3107 reflections with I > 2σ(I)
graphiteRint = 0.031
Detector resolution: 10.5081 pixels mm-1θmax = 34.9°, θmin = 4.6°
[var phi] and ω scansh = −11→14
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007)k = −9→9
Tmin = 0.986, Tmax = 1.000l = −42→43
15870 measured reflections

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.054Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.160H-atom parameters constrained
S = 0.94w = 1/[σ2(Fo2) + (0.0847P)2] where P = (Fo2 + 2Fc2)/3
6133 reflections(Δ/σ)max < 0.001
256 parametersΔρmax = 0.43 e Å3
24 restraintsΔρmin = −0.29 e Å3

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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)

xyzUiso*/UeqOcc. (<1)
O1A0.55766 (10)0.25342 (17)0.27447 (3)0.0282 (2)
O21A0.30234 (11)0.2803 (2)0.21683 (4)0.0407 (3)
O22A0.31232 (12)0.2676 (2)0.13799 (4)0.0545 (4)
O41A0.75641 (11)0.24825 (17)0.05802 (3)0.0317 (2)
O42A0.97162 (12)0.2438 (2)0.09966 (4)0.0505 (4)
O61A1.00309 (15)0.1699 (4)0.27556 (5)0.0322 (5)0.868 (6)
O62A0.83577 (17)0.3370 (5)0.31386 (5)0.0433 (6)0.868 (6)
O61B1.0068 (10)0.311 (3)0.2751 (3)0.040 (3)0.132 (6)
O62B0.8309 (11)0.195 (3)0.3157 (3)0.038 (3)0.132 (6)
O1B0.28372 (11)0.24739 (17)0.49248 (3)0.0326 (2)
N2A0.37356 (11)0.26925 (19)0.18027 (4)0.0241 (2)
N4A0.83482 (12)0.24677 (19)0.09742 (4)0.0251 (2)
N6A0.87761 (11)0.25092 (18)0.27698 (4)0.0222 (2)
N1B0.30287 (11)0.25263 (17)0.32338 (3)0.0193 (2)
H1BA0.20440.24900.31910.023*
H1BB0.35680.25550.29750.023*
N2B0.52320 (11)0.25912 (18)0.37421 (3)0.0194 (2)
H2BA0.57410.26300.34770.023*
N3B0.28659 (11)0.24940 (18)0.40787 (3)0.0209 (2)
C1A0.61812 (12)0.2561 (2)0.23423 (4)0.0173 (2)
C2A0.53717 (12)0.2594 (2)0.18562 (4)0.0175 (2)
C3A0.60696 (13)0.2561 (2)0.14188 (4)0.0183 (2)
H3AA0.54900.25880.11090.022*
C4A0.76183 (13)0.2487 (2)0.14336 (4)0.0184 (2)
C5A0.85022 (12)0.2451 (2)0.18818 (4)0.0186 (2)
H5AA0.95650.23890.18880.022*
C6A0.77977 (12)0.2506 (2)0.23132 (4)0.0173 (2)
C1B0.36982 (12)0.2538 (2)0.36869 (4)0.0169 (2)
C2B0.59876 (14)0.2586 (2)0.42009 (4)0.0243 (3)
C3B0.76596 (15)0.2631 (3)0.42302 (5)0.0375 (4)
H3BA0.80520.26420.45790.056*
H3BB0.79960.39140.40650.056*
H3BC0.80300.13660.40660.056*
C4B0.51754 (14)0.2534 (3)0.46052 (5)0.0300 (3)
H4BA0.56520.25210.49320.036*
C5B0.35982 (14)0.2501 (2)0.45220 (4)0.0235 (3)
C6B0.12228 (16)0.2460 (3)0.48535 (5)0.0344 (3)
H6BA0.07990.24540.51770.052*
H6BB0.08910.11840.46670.052*
H6BC0.08800.37320.46680.052*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O1A0.0188 (4)0.0497 (7)0.0167 (4)0.0001 (4)0.0047 (3)0.0008 (4)
O21A0.0198 (4)0.0763 (9)0.0263 (5)0.0020 (5)0.0042 (4)−0.0057 (5)
O22A0.0213 (5)0.1159 (13)0.0248 (5)−0.0006 (6)−0.0071 (4)0.0054 (6)
O41A0.0354 (5)0.0456 (6)0.0138 (4)−0.0003 (5)−0.0010 (3)0.0000 (4)
O42A0.0219 (5)0.1061 (12)0.0246 (5)0.0017 (6)0.0091 (4)0.0009 (6)
O61A0.0179 (6)0.0502 (13)0.0273 (6)0.0077 (7)−0.0054 (4)−0.0034 (7)
O62A0.0343 (7)0.0769 (18)0.0180 (6)0.0094 (9)−0.0035 (5)−0.0166 (8)
O61B0.021 (4)0.077 (9)0.023 (4)−0.006 (5)−0.005 (3)0.002 (5)
O62B0.023 (4)0.069 (8)0.022 (4)−0.009 (5)0.001 (3)0.008 (4)
O1B0.0272 (5)0.0534 (7)0.0183 (4)−0.0004 (5)0.0076 (3)0.0000 (4)
N2A0.0153 (4)0.0341 (7)0.0226 (5)−0.0017 (5)−0.0001 (4)0.0013 (5)
N4A0.0252 (5)0.0352 (6)0.0153 (4)−0.0001 (5)0.0031 (4)0.0001 (5)
N6A0.0180 (4)0.0324 (6)0.0157 (4)−0.0022 (5)−0.0016 (3)0.0014 (5)
N1B0.0148 (4)0.0265 (5)0.0163 (4)0.0003 (5)−0.0002 (3)−0.0010 (4)
N2B0.0152 (4)0.0278 (6)0.0152 (4)−0.0004 (5)0.0001 (3)0.0002 (4)
N3B0.0180 (4)0.0273 (6)0.0177 (4)0.0012 (5)0.0025 (3)0.0001 (4)
C1A0.0162 (5)0.0202 (6)0.0155 (4)0.0003 (5)0.0019 (4)−0.0006 (5)
C2A0.0143 (4)0.0208 (6)0.0171 (5)−0.0007 (5)−0.0005 (4)−0.0006 (5)
C3A0.0196 (5)0.0191 (6)0.0158 (4)−0.0012 (5)−0.0011 (4)0.0003 (5)
C4A0.0196 (5)0.0229 (6)0.0129 (4)0.0003 (5)0.0031 (4)0.0006 (5)
C5A0.0159 (5)0.0229 (6)0.0168 (5)−0.0005 (5)0.0007 (4)0.0007 (5)
C6A0.0163 (5)0.0218 (6)0.0134 (4)0.0010 (5)−0.0014 (3)0.0004 (5)
C1B0.0154 (5)0.0172 (5)0.0181 (5)0.0001 (5)0.0008 (4)−0.0002 (5)
C2B0.0170 (5)0.0354 (7)0.0200 (5)−0.0001 (6)−0.0023 (4)0.0009 (5)
C3B0.0174 (5)0.0706 (12)0.0235 (6)−0.0024 (7)−0.0037 (4)0.0003 (7)
C4B0.0225 (6)0.0505 (9)0.0164 (5)−0.0006 (7)−0.0022 (4)−0.0003 (6)
C5B0.0227 (5)0.0320 (7)0.0162 (5)−0.0005 (6)0.0039 (4)0.0009 (5)
C6B0.0252 (6)0.0494 (9)0.0302 (6)−0.0014 (7)0.0124 (5)−0.0013 (7)

Geometric parameters (Å, °)

O1A—C1A1.2523 (13)N3B—C5B1.3204 (15)
O21A—N2A1.2190 (13)N3B—C1B1.3416 (14)
O22A—N2A1.2284 (14)C1A—C2A1.4503 (15)
O41A—N4A1.2287 (13)C1A—C6A1.4545 (16)
O42A—N4A1.2205 (14)C2A—C3A1.3797 (15)
O61A—N6A1.2357 (17)C3A—C4A1.3834 (16)
O62A—N6A1.2182 (17)C3A—H3AA0.9500
O61B—N6A1.221 (10)C4A—C5A1.3944 (15)
O62B—N6A1.210 (9)C5A—C6A1.3685 (15)
O1B—C5B1.3283 (14)C5A—H5AA0.9500
O1B—C6B1.4418 (17)C2B—C4B1.3593 (17)
N2A—C2A1.4605 (14)C2B—C3B1.4916 (18)
N4A—C4A1.4477 (14)C3B—H3BA0.9800
N6A—C6A1.4565 (14)C3B—H3BB0.9800
N1B—C1B1.3210 (14)C3B—H3BC0.9800
N1B—H1BA0.8800C4B—C5B1.4112 (18)
N1B—H1BB0.8800C4B—H4BA0.9500
N2B—C2B1.3654 (15)C6B—H6BA0.9800
N2B—C1B1.3687 (14)C6B—H6BB0.9800
N2B—H2BA0.8800C6B—H6BC0.9800
C5B—O1B—C6B117.54 (10)C3A—C4A—C5A121.63 (10)
O21A—N2A—O22A122.12 (11)C3A—C4A—N4A119.53 (10)
O21A—N2A—C2A120.33 (10)C5A—C4A—N4A118.84 (10)
O22A—N2A—C2A117.55 (10)C6A—C5A—C4A118.20 (10)
O42A—N4A—O41A123.06 (10)C6A—C5A—H5AA120.9
O42A—N4A—C4A118.35 (10)C4A—C5A—H5AA120.9
O41A—N4A—C4A118.59 (10)C5A—C6A—C1A124.91 (10)
O62B—N6A—O62A43.1 (8)C5A—C6A—N6A115.86 (10)
O62B—N6A—O61B121.1 (6)C1A—C6A—N6A119.22 (9)
O62A—N6A—O61B104.4 (6)N1B—C1B—N3B119.52 (10)
O62B—N6A—O61A106.5 (6)N1B—C1B—N2B118.64 (9)
O62A—N6A—O61A123.08 (13)N3B—C1B—N2B121.84 (10)
O61B—N6A—O61A42.4 (9)C4B—C2B—N2B118.22 (11)
O62B—N6A—C6A120.6 (5)C4B—C2B—C3B123.65 (11)
O62A—N6A—C6A119.45 (12)N2B—C2B—C3B118.13 (11)
O61B—N6A—C6A118.3 (4)C2B—C3B—H3BA109.5
O61A—N6A—C6A117.40 (10)C2B—C3B—H3BB109.5
C1B—N1B—H1BA120.0H3BA—C3B—H3BB109.5
C1B—N1B—H1BB120.0C2B—C3B—H3BC109.5
H1BA—N1B—H1BB120.0H3BA—C3B—H3BC109.5
C2B—N2B—C1B121.33 (9)H3BB—C3B—H3BC109.5
C2B—N2B—H2BA119.3C2B—C4B—C5B117.54 (11)
C1B—N2B—H2BA119.3C2B—C4B—H4BA121.2
C5B—N3B—C1B116.75 (10)C5B—C4B—H4BA121.2
O1A—C1A—C2A124.65 (10)N3B—C5B—O1B119.64 (11)
O1A—C1A—C6A123.03 (10)N3B—C5B—C4B124.31 (10)
C2A—C1A—C6A112.30 (9)O1B—C5B—C4B116.05 (11)
C3A—C2A—C1A123.31 (10)O1B—C6B—H6BA109.5
C3A—C2A—N2A115.63 (10)O1B—C6B—H6BB109.5
C1A—C2A—N2A121.06 (9)H6BA—C6B—H6BB109.5
C2A—C3A—C4A119.64 (10)O1B—C6B—H6BC109.5
C2A—C3A—H3AA120.2H6BA—C6B—H6BC109.5
C4A—C3A—H3AA120.2H6BB—C6B—H6BC109.5
O1A—C1A—C2A—C3A−178.06 (12)C2A—C1A—C6A—N6A178.84 (11)
C6A—C1A—C2A—C3A0.43 (19)O62B—N6A—C6A—C5A−158.8 (10)
O1A—C1A—C2A—N2A2.7 (2)O62A—N6A—C6A—C5A151.0 (2)
C6A—C1A—C2A—N2A−178.78 (11)O61B—N6A—C6A—C5A22.2 (11)
O21A—N2A—C2A—C3A−177.43 (13)O61A—N6A—C6A—C5A−26.1 (2)
O22A—N2A—C2A—C3A2.02 (18)O62B—N6A—C6A—C1A21.3 (10)
O21A—N2A—C2A—C1A1.83 (19)O62A—N6A—C6A—C1A−29.0 (2)
O22A—N2A—C2A—C1A−178.72 (13)O61B—N6A—C6A—C1A−157.8 (11)
C1A—C2A—C3A—C4A0.2 (2)O61A—N6A—C6A—C1A153.92 (16)
N2A—C2A—C3A—C4A179.42 (12)C5B—N3B—C1B—N1B179.78 (12)
C2A—C3A—C4A—C5A−0.2 (2)C5B—N3B—C1B—N2B−0.12 (19)
C2A—C3A—C4A—N4A−179.57 (12)C2B—N2B—C1B—N1B−179.40 (12)
O42A—N4A—C4A—C3A178.82 (13)C2B—N2B—C1B—N3B0.5 (2)
O41A—N4A—C4A—C3A−1.17 (19)C1B—N2B—C2B—C4B−0.2 (2)
O42A—N4A—C4A—C5A−0.59 (19)C1B—N2B—C2B—C3B179.57 (13)
O41A—N4A—C4A—C5A179.42 (13)N2B—C2B—C4B—C5B−0.3 (2)
C3A—C4A—C5A—C6A−0.5 (2)C3B—C2B—C4B—C5B179.86 (15)
N4A—C4A—C5A—C6A178.91 (12)C1B—N3B—C5B—O1B179.54 (12)
C4A—C5A—C6A—C1A1.2 (2)C1B—N3B—C5B—C4B−0.5 (2)
C4A—C5A—C6A—N6A−178.78 (12)C6B—O1B—C5B—N3B−0.6 (2)
O1A—C1A—C6A—C5A177.37 (13)C6B—O1B—C5B—C4B179.43 (14)
C2A—C1A—C6A—C5A−1.14 (19)C2B—C4B—C5B—N3B0.8 (2)
O1A—C1A—C6A—N6A−2.6 (2)C2B—C4B—C5B—O1B−179.30 (14)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1B—H1BA···O61Bi0.882.092.883 (10)150
N1B—H1BA···O61Ai0.882.132.9309 (17)151
N1B—H1BB···O1A0.881.952.7223 (13)146
N1B—H1BB···O21A0.882.202.8855 (14)134
N2B—H2BA···O1A0.881.972.7380 (12)145
N2B—H2BA···O62B0.882.553.303 (10)144
N2B—H2BA···O62A0.882.623.381 (2)145

Symmetry codes: (i) x−1, y, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BT5240).

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