organic compounds
6,9-Dimethoxy-3,4-dihydro-1H-1,4-oxazino[4,3-a]indol-1-one
aDepartamento de Química Orgánica, Facultad de Química, Pontificia Universidad Católica de Chile, 702843 Santiago de Chile, Chile
*Correspondence e-mail: cosalas@puc.cl
The title compound, C13H13NO4, is one product of the reaction of ethyl 1-(2-bromoethyl)-4,7-dimethoxy-1H-indole-2-carboxylate with sodium azide in refluxing dioxane and was synthesized with the aim of finding new compounds with biological properties. Bond lengths and angles are within the expected values and confirm the bond orders giving in the scheme. The shortest contacts between molecules are set along the a axis, where stacked molecules related by an inversion center form an ABAB array through π–π stacking interactions with centroid–centroid distances ranging from 3.922 (2) to 4.396 (2) Å. Weak C—H⋯O hydrogen bonds further stabilize the structure.
Related literature
For background to oxazinoindoles as intermediates in the chemistry of bioactive compounds, see: Demerson et al. (1975); Fedouloff et al. (2001); Shchekotikhin et al. (2004). Several synthetic strategies for the preparation of oxazinoindoles have been reported, for some examples, see: Abbiati et al. (2005); Brudeli et al. (2010); Fu et al. (2010).
Experimental
Crystal data
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Refinement
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Data collection: APEX2 (Bruker, 2007); cell SAINT (Bruker, 2007); data reduction: SAINT; program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).
Supporting information
10.1107/S1600536811000249/sj5085sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536811000249/sj5085Isup2.hkl
6,9-Dimethoxy-3,4-dihydro-1H-[1,4]oxazino[4,3-a]indol-1-one (2)
Sodium azide (40 mg, 0.62 mmol) was added to a solution of ethyl 1-(2-bromoethyl)-4,7-dimethoxy-1H-indole-2-carboxylate 1 (100 mg, 0.28 mmol) in dioxane (5.0 ml) and the mixture was stirred at reflux for 4 days. The suspension was filtered and the solvent was removed in vacuum to give a residue, which was purified by flash
(CH2Cl2) to give 6,9-dimethoxy-3,4-dihydro-1H-[1,4]oxazino[4,3-a]indol-1-one (2) (27 mg, 39%) as a white solid. mp: 419.0–419.5 K (Fig. 3).H atoms were placed in idealized positions with C—H distances 0.95 – 0.98 Å and thereafter treated as riding. A torsional parameter was refined for each methyl group. Uiso for H were assigned as 1.2 times Ueq of the attached C atom (1.5 for the methyl groups).
Data collection: APEX2 (Bruker, 2007); cell
SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).C13H13NO4 | Dx = 1.477 Mg m−3 |
Mr = 247.24 | Melting point = 419.0–419.5 K |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
a = 8.414 (2) Å | Cell parameters from 1832 reflections |
b = 6.9722 (19) Å | θ = 2.5–27.5° |
c = 19.331 (5) Å | µ = 0.11 mm−1 |
β = 101.276 (4)° | T = 100 K |
V = 1112.1 (5) Å3 | Prism, colourless |
Z = 4 | 0.72 × 0.27 × 0.26 mm |
F(000) = 520 |
Bruker APEXII CCD diffractometer | 2277 independent reflections |
Radiation source: fine-focus sealed tube | 1922 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.030 |
ϕ and ω scans | θmax = 26.4°, θmin = 2.2° |
Absorption correction: multi-scan (SADABS; Bruker, 2001) | h = −10→10 |
Tmin = 0.925, Tmax = 0.972 | k = 0→8 |
10088 measured reflections | l = 0→24 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.038 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.102 | H-atom parameters constrained |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0537P)2 + 0.3721P] where P = (Fo2 + 2Fc2)/3 |
2277 reflections | (Δ/σ)max = 0.001 |
165 parameters | Δρmax = 0.32 e Å−3 |
0 restraints | Δρmin = −0.23 e Å−3 |
C13H13NO4 | V = 1112.1 (5) Å3 |
Mr = 247.24 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 8.414 (2) Å | µ = 0.11 mm−1 |
b = 6.9722 (19) Å | T = 100 K |
c = 19.331 (5) Å | 0.72 × 0.27 × 0.26 mm |
β = 101.276 (4)° |
Bruker APEXII CCD diffractometer | 2277 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2001) | 1922 reflections with I > 2σ(I) |
Tmin = 0.925, Tmax = 0.972 | Rint = 0.030 |
10088 measured reflections |
R[F2 > 2σ(F2)] = 0.038 | 0 restraints |
wR(F2) = 0.102 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.32 e Å−3 |
2277 reflections | Δρmin = −0.23 e Å−3 |
165 parameters |
Experimental. 6,9-Dimethoxy-3,4-dihydro-1H-[1,4]oxazino[4,3-a]indol-1-one (2) IR (NaCl, cm-1): 1730 (CO). 1H RMN (CDCl3, 200 MHz) d 3.89 (s, 6H, 3xOCH3); 4.63–4.76 (m, 4H, 2xCH2); 6.34 (d, 1H, J =8.3 Hz, H-6); 6.61 (d, 1H, J =8.3 Hz, H7); 7.50 (s, 1H, H9). 13C RMN (CDCl3, 50 MHz) d 42.8 (CH2); 55.6 (OCH3); 55.7 (OCH3); 66.9 (CH2); 99.1 (C9); 105.5 (C6); 108.5 (C7); 120.3 (C8a); 123.0 (C9a); 128.1 (C5a); 142.1 (C5); 148.7 (C8); 159.7 (CO). MS (CI) m/z 248.1 [(M+1)+, 100]. |
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 | ||
N1 | 0.79680 (13) | 0.12018 (17) | 0.99864 (6) | 0.0178 (3) | |
C2 | 0.86881 (15) | 0.3060 (2) | 1.02003 (7) | 0.0199 (3) | |
H2A | 0.8631 | 0.3907 | 0.9785 | 0.024* | |
H2B | 0.9839 | 0.2908 | 1.0432 | 0.024* | |
C3 | 0.77300 (16) | 0.3898 (2) | 1.07063 (7) | 0.0212 (3) | |
H3A | 0.8196 | 0.5157 | 1.0874 | 0.025* | |
H3B | 0.6598 | 0.4110 | 1.0458 | 0.025* | |
O4 | 0.77361 (12) | 0.26469 (14) | 1.13077 (5) | 0.0230 (2) | |
O5 | 0.69846 (12) | −0.01995 (15) | 1.16341 (5) | 0.0258 (3) | |
C5 | 0.72921 (15) | 0.0798 (2) | 1.11666 (7) | 0.0197 (3) | |
C6 | 0.72754 (15) | 0.0118 (2) | 1.04487 (7) | 0.0183 (3) | |
C7 | 0.66807 (15) | −0.1555 (2) | 1.01289 (7) | 0.0182 (3) | |
H7 | 0.6138 | −0.2542 | 1.0330 | 0.022* | |
C8 | 0.70291 (15) | −0.1534 (2) | 0.94399 (7) | 0.0179 (3) | |
C9 | 0.67102 (15) | −0.2832 (2) | 0.88665 (7) | 0.0192 (3) | |
C10 | 0.72240 (16) | −0.2367 (2) | 0.82573 (7) | 0.0221 (3) | |
H10 | 0.7025 | −0.3227 | 0.7869 | 0.026* | |
C11 | 0.80488 (16) | −0.0619 (2) | 0.81999 (8) | 0.0225 (3) | |
H11 | 0.8394 | −0.0340 | 0.7771 | 0.027* | |
C12 | 0.83662 (15) | 0.0683 (2) | 0.87398 (7) | 0.0195 (3) | |
C13 | 0.78441 (15) | 0.0205 (2) | 0.93686 (7) | 0.0176 (3) | |
O14 | 0.59004 (11) | −0.44721 (14) | 0.89811 (5) | 0.0225 (2) | |
C15 | 0.52860 (17) | −0.5606 (2) | 0.83664 (8) | 0.0259 (3) | |
H15A | 0.4598 | −0.4806 | 0.8012 | 0.039* | |
H15B | 0.4647 | −0.6675 | 0.8496 | 0.039* | |
H15C | 0.6194 | −0.6109 | 0.8172 | 0.039* | |
O16 | 0.91115 (11) | 0.24306 (15) | 0.87236 (5) | 0.0228 (3) | |
C17 | 0.94995 (18) | 0.2967 (2) | 0.80615 (7) | 0.0256 (3) | |
H17A | 1.0370 | 0.2142 | 0.7961 | 0.038* | |
H17B | 0.9856 | 0.4307 | 0.8083 | 0.038* | |
H17C | 0.8538 | 0.2819 | 0.7687 | 0.038* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0153 (5) | 0.0198 (6) | 0.0184 (6) | −0.0006 (4) | 0.0035 (4) | 0.0009 (4) |
C2 | 0.0163 (6) | 0.0198 (7) | 0.0227 (7) | −0.0024 (5) | 0.0019 (5) | 0.0000 (6) |
C3 | 0.0218 (7) | 0.0199 (7) | 0.0212 (7) | 0.0007 (5) | 0.0023 (5) | 0.0006 (6) |
O4 | 0.0275 (5) | 0.0220 (5) | 0.0192 (5) | −0.0008 (4) | 0.0039 (4) | −0.0007 (4) |
O5 | 0.0297 (5) | 0.0293 (6) | 0.0185 (5) | −0.0027 (4) | 0.0049 (4) | 0.0024 (4) |
C5 | 0.0145 (6) | 0.0228 (7) | 0.0208 (7) | 0.0019 (5) | 0.0010 (5) | 0.0003 (6) |
C6 | 0.0143 (6) | 0.0220 (7) | 0.0185 (7) | 0.0032 (5) | 0.0031 (5) | 0.0034 (5) |
C7 | 0.0137 (6) | 0.0200 (7) | 0.0204 (7) | 0.0020 (5) | 0.0023 (5) | 0.0024 (5) |
C8 | 0.0115 (6) | 0.0215 (7) | 0.0201 (7) | 0.0035 (5) | 0.0013 (5) | 0.0014 (5) |
C9 | 0.0127 (6) | 0.0209 (7) | 0.0235 (7) | 0.0018 (5) | 0.0020 (5) | −0.0010 (6) |
C10 | 0.0175 (7) | 0.0271 (8) | 0.0214 (7) | 0.0021 (6) | 0.0032 (5) | −0.0051 (6) |
C11 | 0.0180 (6) | 0.0299 (8) | 0.0206 (7) | 0.0029 (6) | 0.0062 (5) | 0.0010 (6) |
C12 | 0.0134 (6) | 0.0241 (7) | 0.0213 (7) | 0.0013 (5) | 0.0040 (5) | 0.0024 (6) |
C13 | 0.0127 (6) | 0.0214 (7) | 0.0180 (7) | 0.0028 (5) | 0.0013 (5) | 0.0002 (5) |
O14 | 0.0210 (5) | 0.0230 (5) | 0.0232 (5) | −0.0037 (4) | 0.0040 (4) | −0.0039 (4) |
C15 | 0.0229 (7) | 0.0273 (8) | 0.0273 (8) | −0.0038 (6) | 0.0044 (6) | −0.0083 (6) |
O16 | 0.0222 (5) | 0.0270 (6) | 0.0200 (5) | −0.0043 (4) | 0.0063 (4) | 0.0019 (4) |
C17 | 0.0237 (7) | 0.0331 (9) | 0.0212 (7) | −0.0012 (6) | 0.0076 (6) | 0.0053 (6) |
N1—C13 | 1.3678 (17) | C9—C10 | 1.370 (2) |
N1—C6 | 1.3830 (17) | C9—O14 | 1.3712 (17) |
N1—C2 | 1.4557 (18) | C10—C11 | 1.418 (2) |
C2—C3 | 1.5019 (19) | C10—H10 | 0.9500 |
C2—H2A | 0.9900 | C11—C12 | 1.369 (2) |
C2—H2B | 0.9900 | C11—H11 | 0.9500 |
C3—O4 | 1.4525 (17) | C12—O16 | 1.3736 (18) |
C3—H3A | 0.9900 | C12—C13 | 1.4108 (19) |
C3—H3B | 0.9900 | O14—C15 | 1.4365 (17) |
O4—C5 | 1.3552 (18) | C15—H15A | 0.9800 |
O5—C5 | 1.2077 (17) | C15—H15B | 0.9800 |
C5—C6 | 1.4638 (19) | C15—H15C | 0.9800 |
C6—C7 | 1.368 (2) | O16—C17 | 1.4310 (17) |
C7—C8 | 1.4188 (19) | C17—H17A | 0.9800 |
C7—H7 | 0.9500 | C17—H17B | 0.9800 |
C8—C13 | 1.413 (2) | C17—H17C | 0.9800 |
C8—C9 | 1.4156 (19) | ||
C13—N1—C6 | 108.48 (12) | C10—C9—C8 | 118.59 (13) |
C13—N1—C2 | 131.04 (12) | O14—C9—C8 | 115.52 (12) |
C6—N1—C2 | 120.48 (12) | C9—C10—C11 | 120.80 (13) |
N1—C2—C3 | 106.52 (11) | C9—C10—H10 | 119.6 |
N1—C2—H2A | 110.4 | C11—C10—H10 | 119.6 |
C3—C2—H2A | 110.4 | C12—C11—C10 | 122.39 (13) |
N1—C2—H2B | 110.4 | C12—C11—H11 | 118.8 |
C3—C2—H2B | 110.4 | C10—C11—H11 | 118.8 |
H2A—C2—H2B | 108.6 | C11—C12—O16 | 126.33 (13) |
O4—C3—C2 | 111.70 (11) | C11—C12—C13 | 116.95 (13) |
O4—C3—H3A | 109.3 | O16—C12—C13 | 116.70 (12) |
C2—C3—H3A | 109.3 | N1—C13—C12 | 130.47 (13) |
O4—C3—H3B | 109.3 | N1—C13—C8 | 107.84 (12) |
C2—C3—H3B | 109.3 | C12—C13—C8 | 121.69 (12) |
H3A—C3—H3B | 107.9 | C9—O14—C15 | 115.79 (11) |
C5—O4—C3 | 116.89 (11) | O14—C15—H15A | 109.5 |
O5—C5—O4 | 119.21 (13) | O14—C15—H15B | 109.5 |
O5—C5—C6 | 124.02 (14) | H15A—C15—H15B | 109.5 |
O4—C5—C6 | 116.73 (12) | O14—C15—H15C | 109.5 |
C7—C6—N1 | 109.68 (12) | H15A—C15—H15C | 109.5 |
C7—C6—C5 | 129.72 (13) | H15B—C15—H15C | 109.5 |
N1—C6—C5 | 120.58 (13) | C12—O16—C17 | 115.93 (11) |
C6—C7—C8 | 106.91 (12) | O16—C17—H17A | 109.5 |
C6—C7—H7 | 126.5 | O16—C17—H17B | 109.5 |
C8—C7—H7 | 126.5 | H17A—C17—H17B | 109.5 |
C13—C8—C9 | 119.58 (13) | O16—C17—H17C | 109.5 |
C13—C8—C7 | 107.08 (12) | H17A—C17—H17C | 109.5 |
C9—C8—C7 | 133.33 (13) | H17B—C17—H17C | 109.5 |
C10—C9—O14 | 125.89 (13) | ||
C13—N1—C2—C3 | 149.07 (13) | O14—C9—C10—C11 | 179.79 (12) |
C6—N1—C2—C3 | −32.03 (15) | C8—C9—C10—C11 | −0.4 (2) |
N1—C2—C3—O4 | 57.70 (13) | C9—C10—C11—C12 | −0.3 (2) |
C2—C3—O4—C5 | −52.35 (15) | C10—C11—C12—O16 | −177.91 (12) |
C3—O4—C5—O5 | −166.24 (12) | C10—C11—C12—C13 | 0.5 (2) |
C3—O4—C5—C6 | 15.92 (16) | C6—N1—C13—C12 | −179.71 (13) |
C13—N1—C6—C7 | −1.05 (15) | C2—N1—C13—C12 | −0.7 (2) |
C2—N1—C6—C7 | 179.83 (11) | C6—N1—C13—C8 | 1.00 (14) |
C13—N1—C6—C5 | 177.50 (11) | C2—N1—C13—C8 | 180.00 (12) |
C2—N1—C6—C5 | −1.62 (18) | C11—C12—C13—N1 | −179.28 (13) |
O5—C5—C6—C7 | 12.2 (2) | O16—C12—C13—N1 | −0.7 (2) |
O4—C5—C6—C7 | −170.05 (13) | C11—C12—C13—C8 | −0.07 (19) |
O5—C5—C6—N1 | −166.01 (12) | O16—C12—C13—C8 | 178.48 (11) |
O4—C5—C6—N1 | 11.72 (18) | C9—C8—C13—N1 | 178.81 (11) |
N1—C6—C7—C8 | 0.66 (14) | C7—C8—C13—N1 | −0.59 (14) |
C5—C6—C7—C8 | −177.72 (12) | C9—C8—C13—C12 | −0.56 (19) |
C6—C7—C8—C13 | −0.04 (14) | C7—C8—C13—C12 | −179.96 (12) |
C6—C7—C8—C9 | −179.33 (13) | C10—C9—O14—C15 | −12.25 (19) |
C13—C8—C9—C10 | 0.77 (18) | C8—C9—O14—C15 | 167.92 (12) |
C7—C8—C9—C10 | 179.98 (13) | C11—C12—O16—C17 | 3.90 (19) |
C13—C8—C9—O14 | −179.38 (11) | C13—C12—O16—C17 | −174.50 (11) |
C7—C8—C9—O14 | −0.2 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2a···O16 | 0.99 | 2.40 | 2.9776 (18) | 117 |
C3—H3B···O14i | 0.99 | 2.56 | 3.2524 (19) | 127 (4) |
C15—H15B···O5ii | 0.98 | 2.56 | 3.493 (2) | 159 (4) |
C17—H17A···O5iii | 0.98 | 2.59 | 3.484 (2) | 151 (4) |
Symmetry codes: (i) −x+1, −y, −z+2; (ii) −x+1, −y−1, −z+2; (iii) −x+2, −y, −z+2. |
Experimental details
Crystal data | |
Chemical formula | C13H13NO4 |
Mr | 247.24 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 100 |
a, b, c (Å) | 8.414 (2), 6.9722 (19), 19.331 (5) |
β (°) | 101.276 (4) |
V (Å3) | 1112.1 (5) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.72 × 0.27 × 0.26 |
Data collection | |
Diffractometer | Bruker APEXII CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2001) |
Tmin, Tmax | 0.925, 0.972 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 10088, 2277, 1922 |
Rint | 0.030 |
(sin θ/λ)max (Å−1) | 0.625 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.038, 0.102, 1.06 |
No. of reflections | 2277 |
No. of parameters | 165 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.32, −0.23 |
Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2a···O16 | 0.99 | 2.40 | 2.9776 (18) | 117 |
C3—H3B···O14i | 0.99 | 2.56 | 3.2524 (19) | 127 (4) |
C15—H15B···O5ii | 0.98 | 2.56 | 3.493 (2) | 159 (4) |
C17—H17A···O5iii | 0.98 | 2.59 | 3.484 (2) | 151 (4) |
Symmetry codes: (i) −x+1, −y, −z+2; (ii) −x+1, −y−1, −z+2; (iii) −x+2, −y, −z+2. |
CgI-CgJ* | CgI-CgJ(Å)** | Alpha(°)*** | Beta(°)**** | CgI_Perp(Å)***** |
Cg(1)-Cg(1) | 4.1164 (14)(a) | 0 | 34.50 | -3.3925 (6) |
Cg(1)-Cg(1) | 4.3962 (14)(b) | 0 | 35.72 | 3.5692 (6) |
Cg(1)-Cg(3) | 4.6434 (15)(b) | 0.50 (7) | 40.18 | 3.5476 (6) |
*Centroid plane numbers **Distance between ring centroids of planar cycles I and J. ***Dihedral angle between stacking planes. ****Angle CgI-->CgJ and normal to plane I. *****Perpendicular distance of CgI on ring J. Symmetry relationships: (a)1-x,-y,2-z (b)2-x,-y,2-z |
Acknowledgements
We gratefully acknowledge the Unidade de Raios X, RIAIDT, University of Santiago de Compostela, Spain.
References
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Oxazinoindoles are very important as precursors of a wide range of natural and synthetic products with relevant biological properties such as antidepressant activity (Demerson et al., 1975), 5-HT4 Receptor Antagonist (Fedouloff et al., 2001), antiproliferative activity (Shchekotikhin et al., 2004). The oxazinoindolone 2 is the product of the cyclization of ethyl 1-(2-bromoethyl)-4,7-dimethoxy-1H-indole-2-carboxylate mediated by the azido intermediate in dioxane at reflux (Fig. 2). Other efficient cyclizations have been reported also (Abbiati et al.,2005; Brudeli et al., 2010; Fu et al., 2010). The molecular structure of the title compound is represented in Fig. 1. Bond lengths and angles are within the expected values and confirm the bond orders giving in the Scheme. The e.s.d. for the molecular plane, as well as the bond distances and angles for the indol fragment, are within the expected values for bicyclic aromatic systems [r.m.s deviation = 0.006 (1) Å]. The shortest contacts between molecules are set along the crystallographic axis a, where the stacked molecules related by an inversion center form an ABAB array. Centroid to centroid distances range from 3.922 (2) to 4.396 (2)Å (Table 2). Weak C–H···O hydrogen bonds further stabilize the structure (Table 1).