organic compounds
E)-1-methyl-2-[2-(2-methoxphenyl)ethenyl]-4-nitro-1H-imidazole
of (aLaboratoire des Produits Naturels d'Origine Végétale et de Synthèse Organique, PHYSYNOR, Université Constantine 1, 25000 Constantine, Algeria, bUnité de Recherche de Chimie de l'Environnement et Moléculaire Structurale (CHEMS), Université Constantine 1, 25000 , Algeria, and cDépartement Sciences de la Matière, Faculté des Sciences Exactes et Sciences de la Nature et de la Vie, Université Oum El Bouaghi, Algeria
*Correspondence e-mail: bouacida_sofiane@yahoo.fr
In the 13H13N3O3, the 2-(2-methoxphenyl)ethenyl unit is connected to the methyl-nitroimidazole 1-methyl-4-nitro-1H-imidazole moiety. The molecule is quasi-planar and the planes of the two rings form a dihedral angle of 0.92 (11)°. The crystal packing can be described as layers parallel to the (011) plane, stabilized by intermolecular C—H⋯O hydrogen bonding, resulting in the formation of an infinite three-dimensional network linking these layers. Strong π–π stacking interactions are observed, viz. benzene–benzene, imidazole–imidazole and benzene–imidazole rings, with centroid–centroid distances of 3.528 (2), 3.457 (2) and 3.544 (2) Å, respectively. Intensity statistics indicated by non-merohedry, with refined weighs of the twin components of 0.3687:0.6313.
of the title compound, CCCDC reference: 1015965
1. Related literature
For the synthesis and applications of this important class of compounds, see: Hori et al. (1997); Bourdin-Trunz et al. (2011). For our previous work on imidazole derivatives, see: Alliouche et al. (2014); Zama et al. (2013); Bahnous et al. (2012).
2. Experimental
2.1. Crystal data
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2.3. Refinement
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Data collection: APEX2 (Bruker, 2006); cell SAINT (Bruker, 2006); data reduction: SAINT; program(s) used to solve structure: SIR2002 (Burla et al., 2005); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and DIAMOND (Brandenburg & Berndt, 2001); software used to prepare material for publication: WinGX (Farrugia, 2012).
Supporting information
CCDC reference: 1015965
10.1107/S1600536814017206/hg5400sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536814017206/hg5400Isup2.hkl
The title compound was obtained as a yellow-green solid in 83% of yield by heating a solution of (E)-1-methyl-2-[(2-methoxphenyl)-1-ethenyl]-5-nitroimidazole in nitrobenzene at 160°C during 24 h in the presence of catalytic amount of CH3I. Suitable crystal of compound (I) was obtained by slow evaporation from a water/methanol solution at room temperature, and X-ray crystallographic analysis confirmed the structural assignment (Fig. 1).
All non-H atoms were refined with anisotropic atomic displacement parameters. All H atoms were localized on Fourier maps but introduced in calculated positions and treated as riding on their parent C or N atom. (with C—H = 0.93 and 0.96 Å and Uiso(H) = 1.5 or 1.2 (carrier atom).
Data collection: APEX2 (Bruker, 2006); cell
SAINT (Bruker, 2006); data reduction: SAINT (Bruker, 2006); program(s) used to solve structure: SIR2002 (Burla et al., 2005); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and DIAMOND (Brandenburg & Berndt, 2001); software used to prepare material for publication: WinGX (Farrugia, 2012).Fig. 1. The structure of the title compound with the atomic labelling scheme. Displacement are drawn at the 50% probability level. | |
Fig. 2. A diagram of the layered crystal packing of (I) viewed down the a axis and showing hydrogen bond [C—H···O] as dashed line. |
C13H13N3O3 | Z = 2 |
Mr = 259.26 | F(000) = 272 |
Triclinic, P1 | Dx = 1.424 Mg m−3 |
a = 7.9339 (18) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 8.1994 (19) Å | Cell parameters from 1356 reflections |
c = 10.452 (3) Å | θ = 2.7–24.6° |
α = 68.877 (17)° | µ = 0.10 mm−1 |
β = 75.037 (17)° | T = 150 K |
γ = 76.182 (17)° | Block, yellow |
V = 604.7 (2) Å3 | 0.19 × 0.12 × 0.08 mm |
Bruker APEXII diffractometer | 3712 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0 |
CCD rotation images, thin slices scans | θmax = 25.3°, θmin = 2.7° |
Absorption correction: multi-scan (SADABS; Sheldrick, 2002) | h = −9→9 |
Tmin = 0.754, Tmax = 1.000 | k = −9→9 |
5177 measured reflections | l = −12→12 |
5177 independent reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.088 | H-atom parameters constrained |
wR(F2) = 0.282 | w = 1/[σ2(Fo2) + (0.1745P)2 + 0.1919P] where P = (Fo2 + 2Fc2)/3 |
S = 1.06 | (Δ/σ)max < 0.001 |
5171 reflections | Δρmax = 0.49 e Å−3 |
176 parameters | Δρmin = −0.42 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.045 (12) |
C13H13N3O3 | γ = 76.182 (17)° |
Mr = 259.26 | V = 604.7 (2) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.9339 (18) Å | Mo Kα radiation |
b = 8.1994 (19) Å | µ = 0.10 mm−1 |
c = 10.452 (3) Å | T = 150 K |
α = 68.877 (17)° | 0.19 × 0.12 × 0.08 mm |
β = 75.037 (17)° |
Bruker APEXII diffractometer | 5177 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2002) | 3712 reflections with I > 2σ(I) |
Tmin = 0.754, Tmax = 1.000 | Rint = 0 |
5177 measured reflections |
R[F2 > 2σ(F2)] = 0.088 | 0 restraints |
wR(F2) = 0.282 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.49 e Å−3 |
5171 reflections | Δρmin = −0.42 e Å−3 |
176 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 | ||
O1 | 0.4178 (3) | 0.2400 (3) | 0.2786 (3) | 0.0256 (6) | |
O3 | 1.0969 (3) | 0.6148 (3) | 0.0846 (2) | 0.0219 (6) | |
O2 | 0.1531 (3) | 0.2922 (3) | 0.3961 (3) | 0.0238 (6) | |
N1 | 0.3026 (4) | 0.3303 (4) | 0.3420 (3) | 0.0167 (7) | |
N2 | 0.5059 (3) | 0.5331 (4) | 0.2979 (3) | 0.0162 (7) | |
N3 | 0.3292 (3) | 0.7076 (3) | 0.4156 (3) | 0.0134 (6) | |
C1 | 0.3460 (4) | 0.4809 (4) | 0.3545 (3) | 0.0142 (7) | |
C2 | 0.4934 (4) | 0.6726 (4) | 0.3362 (3) | 0.0125 (7) | |
C5 | 0.6299 (4) | 0.7796 (5) | 0.3004 (3) | 0.0172 (8) | |
H5 | 0.6018 | 0.8867 | 0.319 | 0.021* | |
C6 | 0.7973 (4) | 0.7279 (4) | 0.2408 (3) | 0.0151 (7) | |
H6 | 0.8198 | 0.6187 | 0.2261 | 0.018* | |
C7 | 0.9464 (4) | 0.8227 (4) | 0.1968 (3) | 0.0139 (7) | |
C8 | 1.1027 (4) | 0.7634 (4) | 0.1144 (3) | 0.0159 (8) | |
C13 | 1.2438 (4) | 0.5580 (5) | −0.0106 (4) | 0.0273 (9) | |
H13C | 1.2622 | 0.6542 | −0.0961 | 0.041* | |
H13A | 1.22 | 0.4604 | −0.0296 | 0.041* | |
H13B | 1.3478 | 0.5214 | 0.0299 | 0.041* | |
C4 | 0.2711 (4) | 0.8439 (5) | 0.4845 (3) | 0.0196 (8) | |
H4A | 0.1465 | 0.8508 | 0.5215 | 0.029* | |
H4B | 0.2948 | 0.9563 | 0.418 | 0.029* | |
H4C | 0.3339 | 0.814 | 0.5591 | 0.029* | |
C3 | 0.2328 (4) | 0.5873 (4) | 0.4277 (3) | 0.0139 (7) | |
H3 | 0.117 | 0.5778 | 0.4744 | 0.017* | |
C9 | 1.2469 (4) | 0.8506 (5) | 0.0702 (3) | 0.0207 (8) | |
H9 | 1.349 | 0.81 | 0.0154 | 0.025* | |
C10 | 1.2392 (5) | 0.9970 (5) | 0.1072 (3) | 0.0233 (8) | |
H10 | 1.3369 | 1.0544 | 0.0781 | 0.028* | |
C11 | 1.0871 (4) | 1.0600 (5) | 0.1876 (3) | 0.0211 (8) | |
H11 | 1.0818 | 1.1602 | 0.2116 | 0.025* | |
C12 | 0.9434 (4) | 0.9723 (5) | 0.2317 (3) | 0.0199 (8) | |
H12 | 0.8418 | 1.0144 | 0.2863 | 0.024* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0232 (13) | 0.0238 (14) | 0.0331 (14) | −0.0046 (11) | 0.0055 (11) | −0.0199 (12) |
O3 | 0.0169 (13) | 0.0238 (14) | 0.0257 (13) | −0.0036 (10) | 0.0029 (10) | −0.0135 (11) |
O2 | 0.0142 (13) | 0.0280 (15) | 0.0313 (14) | −0.0066 (11) | 0.0037 (11) | −0.0154 (12) |
N1 | 0.0173 (15) | 0.0150 (15) | 0.0183 (14) | −0.0021 (12) | −0.0013 (12) | −0.0077 (12) |
N2 | 0.0144 (14) | 0.0181 (15) | 0.0159 (14) | −0.0007 (12) | −0.0022 (11) | −0.0070 (12) |
N3 | 0.0139 (14) | 0.0113 (14) | 0.0162 (13) | −0.0006 (11) | −0.0005 (11) | −0.0083 (11) |
C1 | 0.0135 (16) | 0.0166 (17) | 0.0122 (16) | −0.0007 (13) | −0.0053 (13) | −0.0032 (13) |
C2 | 0.0120 (16) | 0.0162 (17) | 0.0099 (14) | −0.0020 (13) | −0.0029 (13) | −0.0043 (13) |
C5 | 0.0170 (18) | 0.0181 (17) | 0.0207 (17) | −0.0027 (14) | −0.0072 (14) | −0.0086 (15) |
C6 | 0.0155 (17) | 0.0144 (17) | 0.0177 (16) | 0.0010 (14) | −0.0055 (13) | −0.0084 (14) |
C7 | 0.0154 (17) | 0.0165 (17) | 0.0089 (15) | −0.0037 (14) | −0.0028 (13) | −0.0018 (13) |
C8 | 0.0143 (17) | 0.0193 (18) | 0.0134 (16) | −0.0016 (14) | −0.0034 (14) | −0.0047 (14) |
C13 | 0.0200 (19) | 0.033 (2) | 0.0253 (19) | 0.0037 (17) | 0.0043 (15) | −0.0167 (17) |
C4 | 0.0171 (17) | 0.0219 (18) | 0.0232 (17) | −0.0021 (15) | −0.0010 (14) | −0.0137 (15) |
C3 | 0.0126 (17) | 0.0178 (18) | 0.0129 (15) | −0.0037 (14) | −0.0026 (13) | −0.0058 (13) |
C9 | 0.0150 (17) | 0.029 (2) | 0.0163 (17) | −0.0043 (15) | −0.0043 (14) | −0.0036 (15) |
C10 | 0.026 (2) | 0.030 (2) | 0.0173 (17) | −0.0148 (16) | −0.0081 (15) | −0.0020 (16) |
C11 | 0.0237 (19) | 0.025 (2) | 0.0201 (17) | −0.0062 (16) | −0.0086 (15) | −0.0092 (16) |
C12 | 0.0187 (18) | 0.025 (2) | 0.0176 (17) | −0.0039 (15) | −0.0067 (14) | −0.0068 (15) |
O1—N1 | 1.241 (3) | C7—C8 | 1.406 (4) |
O3—C8 | 1.375 (4) | C8—C9 | 1.383 (5) |
O3—C13 | 1.429 (4) | C13—H13C | 0.96 |
O2—N1 | 1.236 (3) | C13—H13A | 0.96 |
N1—C1 | 1.415 (4) | C13—H13B | 0.96 |
N2—C2 | 1.317 (4) | C4—H4A | 0.96 |
N2—C1 | 1.354 (4) | C4—H4B | 0.96 |
N3—C3 | 1.339 (4) | C4—H4C | 0.96 |
N3—C2 | 1.380 (4) | C3—H3 | 0.93 |
N3—C4 | 1.464 (4) | C9—C10 | 1.372 (5) |
C1—C3 | 1.380 (4) | C9—H9 | 0.93 |
C2—C5 | 1.445 (5) | C10—C11 | 1.386 (5) |
C5—C6 | 1.351 (5) | C10—H10 | 0.93 |
C5—H5 | 0.93 | C11—C12 | 1.382 (5) |
C6—C7 | 1.455 (5) | C11—H11 | 0.93 |
C6—H6 | 0.93 | C12—H12 | 0.93 |
C7—C12 | 1.394 (5) | ||
C8—O3—C13 | 117.1 (3) | O3—C13—H13A | 109.5 |
O2—N1—O1 | 122.5 (3) | H13C—C13—H13A | 109.5 |
O2—N1—C1 | 119.0 (3) | O3—C13—H13B | 109.5 |
O1—N1—C1 | 118.4 (3) | H13C—C13—H13B | 109.5 |
C2—N2—C1 | 103.9 (3) | H13A—C13—H13B | 109.5 |
C3—N3—C2 | 108.4 (2) | N3—C4—H4A | 109.5 |
C3—N3—C4 | 124.7 (3) | N3—C4—H4B | 109.5 |
C2—N3—C4 | 126.7 (3) | H4A—C4—H4B | 109.5 |
N2—C1—C3 | 112.9 (3) | N3—C4—H4C | 109.5 |
N2—C1—N1 | 123.0 (3) | H4A—C4—H4C | 109.5 |
C3—C1—N1 | 124.1 (3) | H4B—C4—H4C | 109.5 |
N2—C2—N3 | 111.1 (3) | N3—C3—C1 | 103.7 (3) |
N2—C2—C5 | 125.9 (3) | N3—C3—H3 | 128.1 |
N3—C2—C5 | 123.0 (3) | C1—C3—H3 | 128.1 |
C6—C5—C2 | 121.7 (3) | C10—C9—C8 | 120.0 (3) |
C6—C5—H5 | 119.2 | C10—C9—H9 | 120 |
C2—C5—H5 | 119.2 | C8—C9—H9 | 120 |
C5—C6—C7 | 127.7 (3) | C9—C10—C11 | 120.6 (3) |
C5—C6—H6 | 116.1 | C9—C10—H10 | 119.7 |
C7—C6—H6 | 116.1 | C11—C10—H10 | 119.7 |
C12—C7—C8 | 117.2 (3) | C12—C11—C10 | 119.2 (3) |
C12—C7—C6 | 123.3 (3) | C12—C11—H11 | 120.4 |
C8—C7—C6 | 119.5 (3) | C10—C11—H11 | 120.4 |
O3—C8—C9 | 124.8 (3) | C11—C12—C7 | 121.9 (3) |
O3—C8—C7 | 114.1 (3) | C11—C12—H12 | 119 |
C9—C8—C7 | 121.1 (3) | C7—C12—H12 | 119 |
O3—C13—H13C | 109.5 | ||
C2—N2—C1—C3 | 0.3 (3) | C13—O3—C8—C9 | −6.8 (5) |
C2—N2—C1—N1 | −178.3 (3) | C13—O3—C8—C7 | 173.6 (3) |
O2—N1—C1—N2 | −179.5 (3) | C12—C7—C8—O3 | 179.6 (3) |
O1—N1—C1—N2 | 1.5 (4) | C6—C7—C8—O3 | −0.6 (4) |
O2—N1—C1—C3 | 2.0 (5) | C12—C7—C8—C9 | −0.1 (5) |
O1—N1—C1—C3 | −176.9 (3) | C6—C7—C8—C9 | 179.8 (3) |
C1—N2—C2—N3 | 0.1 (3) | C2—N3—C3—C1 | 0.6 (3) |
C1—N2—C2—C5 | −179.2 (3) | C4—N3—C3—C1 | −175.4 (3) |
C3—N3—C2—N2 | −0.5 (3) | N2—C1—C3—N3 | −0.5 (3) |
C4—N3—C2—N2 | 175.4 (3) | N1—C1—C3—N3 | 178.1 (3) |
C3—N3—C2—C5 | 178.9 (3) | O3—C8—C9—C10 | −179.3 (3) |
C4—N3—C2—C5 | −5.3 (5) | C7—C8—C9—C10 | 0.3 (5) |
N2—C2—C5—C6 | −10.8 (5) | C8—C9—C10—C11 | −0.7 (5) |
N3—C2—C5—C6 | 170.0 (3) | C9—C10—C11—C12 | 0.8 (5) |
C2—C5—C6—C7 | 178.6 (3) | C10—C11—C12—C7 | −0.5 (5) |
C5—C6—C7—C12 | 11.0 (5) | C8—C7—C12—C11 | 0.1 (5) |
C5—C6—C7—C8 | −168.8 (3) | C6—C7—C12—C11 | −179.7 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
C3—H3···O2i | 0.93 | 2.45 | 3.271 (4) | 147 |
C4—H4B···O1ii | 0.96 | 2.53 | 3.465 (5) | 165 |
C6—H6···O3 | 0.93 | 2.31 | 2.685 (4) | 103 |
C6—H6···N2 | 0.93 | 2.60 | 2.935 (4) | 102 |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) x, y+1, z. |
D—H···A | D—H | H···A | D···A | D—H···A |
C3—H3···O2i | 0.9300 | 2.4500 | 3.271 (4) | 147.00 |
C4—H4B···O1ii | 0.9600 | 2.5300 | 3.465 (5) | 165.00 |
C6—H6···O3 | 0.9300 | 2.3100 | 2.685 (4) | 103.00 |
C6—H6···N2 | 0.9300 | 2.6000 | 2.935 (4) | 102.00 |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) x, y+1, z. |
Acknowledgements
We are grateful to the personnel of the PHYSYNOR Laboratory, Universite Constantine 1, Algeria, for their assistance. Thanks are due to the MESRS (Ministére de l'Enseignement Supérieur et de la Recherche Scientifique, Algérie) for financial support.
References
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Nitroimidazoles are a class of N-heterocyclic compounds which have a wide range of applications in the drug synthesis (Hori, et al., 1997) In fact, Metronidazole (Flagyl) and related N-1 substituted 5-nitroimidazoles such as Tinidazole (Fasigyne), Ornidazole (Tiberal) and Secnidazole (Secnol) still commonly used in medicine. Despite their fewer biological activities compared with 5-nitroimidazoles, a number of 4-nitroimidazoles were reported to exhibit antileishmanial, antiamebic and anti-parasitic activities (Bourdin-Trunz, et al. 2011). However, only some limited investigations have been carried out using methyl iodide (Alliouche, et al. 2014). In previous work, we have reported the synthesis and structure determination of some new heterocyclic compounds bearing an imidazole unit (Zama, et al., 2013; Bahnous, et al., 2012). Herein, we describe the synthesis and the structure determination of (E)-1-methyl-2-[(2-methoxphenyl)-1-ethenyl]-4-nitroimidazole resulting from the intramolecular transposition reaction of its 5-nitro isomer in the presence of catalytic amounts of methyl iodide in nitrobenzene. The molecular geometry and the atom-numbering scheme of (I) are shown in Fig. 1. In the asymmetric unit of title compound the methoxphenyl-1-ethenyl unit is linked to methyl-nitroimidazole moiety. The molecule is quasi-planar and the two rings of phenyl and imidazol form a dihedral angle of 0.92 (11)°. The crystal packing can be described as layers parallel to (011) plane, along the a axis (Fig. 2). It is stabilized by intermolecular hydrogen bond C—H···O, resulting in the formation of an infinite three-dimensional network linking these layers together and reinforcing cohesion in the structure (Fig. 2). Hydrogen-bonding parameters are listed in Table 1. Strong π-π stacking interactions are observed between phenyl-phenyl, imidazol-imidazol and phenyl-imidazol rings, distances centroid-centroid are Cg—Cg = 3.528 (2), 3.457 (2) and 3.544 (2) Å respetively. The crystal used was a non-merohedral twin, the refined ratio of twin components being 0.3687:0.6313.