organic compounds
8-(2-Hydroxyphenyl)-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione
aUniversity of Kwazulu-Natal, School of Chemistry, Private Bag X01, Scottsville 3209, Pietermaritzburg, South Africa, and bNelson Mandela Metropolitan University, Summerstrand Campus, Department of Chemistry, University Way, Summerstrand, PO Box 77000, Port Elizabeth 6031, South Africa
*Correspondence e-mail: richard.betz@webmail.co.za
The title compound, C13H12N4O3, is an imidazole derivative featuring an annealed purine ring system. The benzimidazole-inspired moiety is essentially planar (r.m.s. of all fitted non-H atoms = 0.0205 Å). An intramolecular O—H⋯N hydrogen bond occurs. In the crystal, intermolecular N—H⋯O and C—H⋯O hydrogen bonds are observed, which connect the molecules into chains along [110]. The shortest centroid–centroid distance between two aromatic systems is 3.7771 (11) Å.
Related literature
For the ). For the of hypoxanthinium nitrate monohydrate as an example of an oxopurine compound, see: Schmalle et al. (1990). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990); Bernstein et al. (1995). For puckering analysis, see: Cremer & Pople (1975). For general information about the chelate effect in coordination chemistry, see: Gade (1998).
of benzimidazole, see: Krawczyk & Gdaniec (2005Experimental
Crystal data
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Refinement
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Data collection: APEX2 (Bruker, 2010); cell SAINT (Bruker, 2010); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009).
Supporting information
10.1107/S1600536811032417/si2369sup1.cif
contains datablocks I, global. DOI:Supporting information file. DOI: 10.1107/S1600536811032417/si2369Isup2.cdx
Structure factors: contains datablock I. DOI: 10.1107/S1600536811032417/si2369Isup3.hkl
Supporting information file. DOI: 10.1107/S1600536811032417/si2369Isup4.cml
The title compound was prepared by reacting 6-amino-1,3-dimethyl-5-[(E)- 2-(hydroxy)benzylideneamino]pyrimidine-2,4-(1H,3H)-dione and NH4VO3 in methanol. A bright yellow precipitate was filtered, washed with methanol and dried under reduced pressure. Single-crystals suitable for the X-ray diffraction study were obtained by recrystallization from ethanol-dichlormethane (v:v = 1:1) mixture which was left in a fridge for several days.
Carbon-bound H atoms were placed in calculated positions (C—H 0.95 Å) and were included in the
in the riding model approximation, with U(H) set to 1.2Ueq(C). The H atoms of the methyl groups were allowed to rotate with a fixed angle around the C—C bond to best fit the experimental electron density (HFIX 137 in the SHELX program suite (Sheldrick, 2008)), with U(H) set to 1.5Ueq(C). The nitrogen-bound H atom was located on a difference Fourier map and refined freely.Data collection: APEX2 (Bruker, 2010); cell
SAINT (Bruker, 2010); data reduction: SAINT (Bruker, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).C13H12N4O3 | F(000) = 568 |
Mr = 272.27 | Dx = 1.502 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 1955 reflections |
a = 8.6418 (5) Å | θ = 2.4–27.2° |
b = 5.9415 (3) Å | µ = 0.11 mm−1 |
c = 23.4475 (10) Å | T = 200 K |
β = 91.275 (2)° | Platelet, yellow |
V = 1203.62 (11) Å3 | 0.41 × 0.10 × 0.05 mm |
Z = 4 |
Bruker APEXII CCD diffractometer | 2975 independent reflections |
Radiation source: fine-focus sealed tube | 1752 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.043 |
ϕ and ω scans | θmax = 28.3°, θmin = 2.4° |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | h = −11→11 |
Tmin = 0.860, Tmax = 1.000 | k = −7→6 |
10068 measured reflections | l = −31→27 |
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)] = 0.049 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.124 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.01 | w = 1/[σ2(Fo2) + (0.0584P)2 + 0.0815P] where P = (Fo2 + 2Fc2)/3 |
2975 reflections | (Δ/σ)max < 0.001 |
188 parameters | Δρmax = 0.25 e Å−3 |
0 restraints | Δρmin = −0.21 e Å−3 |
C13H12N4O3 | V = 1203.62 (11) Å3 |
Mr = 272.27 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 8.6418 (5) Å | µ = 0.11 mm−1 |
b = 5.9415 (3) Å | T = 200 K |
c = 23.4475 (10) Å | 0.41 × 0.10 × 0.05 mm |
β = 91.275 (2)° |
Bruker APEXII CCD diffractometer | 2975 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | 1752 reflections with I > 2σ(I) |
Tmin = 0.860, Tmax = 1.000 | Rint = 0.043 |
10068 measured reflections |
R[F2 > 2σ(F2)] = 0.049 | 0 restraints |
wR(F2) = 0.124 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.01 | Δρmax = 0.25 e Å−3 |
2975 reflections | Δρmin = −0.21 e Å−3 |
188 parameters |
x | y | z | Uiso*/Ueq | ||
O1 | 0.47991 (16) | 0.4606 (2) | 0.07866 (5) | 0.0356 (4) | |
O2 | 0.66823 (16) | −0.0720 (2) | 0.20267 (6) | 0.0390 (4) | |
O3 | 0.94790 (18) | −0.3204 (3) | −0.06725 (6) | 0.0454 (4) | |
H3 | 0.9105 | −0.2923 | −0.0353 | 0.068* | |
N1 | 0.65931 (17) | 0.2091 (3) | −0.01367 (6) | 0.0260 (4) | |
H71 | 0.615 (2) | 0.330 (4) | −0.0365 (9) | 0.049 (7)* | |
N2 | 0.79184 (18) | −0.1028 (3) | 0.00928 (6) | 0.0273 (4) | |
N3 | 0.73063 (17) | −0.1106 (3) | 0.10978 (6) | 0.0269 (4) | |
N4 | 0.57335 (17) | 0.1913 (3) | 0.13977 (6) | 0.0259 (4) | |
C1 | 0.6392 (2) | 0.1685 (3) | 0.04385 (7) | 0.0247 (4) | |
C2 | 0.7221 (2) | −0.0211 (3) | 0.05591 (7) | 0.0238 (4) | |
C3 | 0.6584 (2) | −0.0024 (3) | 0.15408 (8) | 0.0267 (4) | |
C4 | 0.5573 (2) | 0.2871 (3) | 0.08562 (7) | 0.0254 (4) | |
C5 | 0.8231 (2) | −0.3115 (3) | 0.12198 (8) | 0.0323 (5) | |
H5A | 0.8296 | −0.4032 | 0.0874 | 0.048* | |
H5B | 0.7742 | −0.3993 | 0.1520 | 0.048* | |
H5C | 0.9274 | −0.2668 | 0.1347 | 0.048* | |
C6 | 0.4923 (2) | 0.3034 (4) | 0.18658 (8) | 0.0342 (5) | |
H6A | 0.5389 | 0.4513 | 0.1938 | 0.051* | |
H6B | 0.5012 | 0.2112 | 0.2212 | 0.051* | |
H6C | 0.3827 | 0.3221 | 0.1759 | 0.051* | |
C7 | 0.7514 (2) | 0.0418 (3) | −0.03268 (8) | 0.0254 (4) | |
C8 | 0.8012 (2) | 0.0162 (3) | −0.09136 (8) | 0.0258 (4) | |
C9 | 0.7563 (2) | 0.1677 (3) | −0.13407 (8) | 0.0307 (5) | |
H9 | 0.6913 | 0.2908 | −0.1248 | 0.037* | |
C10 | 0.8043 (2) | 0.1426 (4) | −0.18967 (8) | 0.0352 (5) | |
H10 | 0.7732 | 0.2476 | −0.2182 | 0.042* | |
C11 | 0.8985 (2) | −0.0377 (4) | −0.20303 (8) | 0.0383 (5) | |
H11 | 0.9316 | −0.0568 | −0.2411 | 0.046* | |
C12 | 0.9443 (2) | −0.1892 (4) | −0.16178 (8) | 0.0391 (5) | |
H12 | 1.0093 | −0.3115 | −0.1716 | 0.047* | |
C13 | 0.8968 (2) | −0.1664 (3) | −0.10562 (8) | 0.0316 (5) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0444 (8) | 0.0353 (8) | 0.0272 (8) | 0.0189 (7) | 0.0052 (6) | 0.0019 (6) |
O2 | 0.0474 (9) | 0.0435 (9) | 0.0265 (8) | 0.0104 (7) | 0.0069 (6) | 0.0106 (7) |
O3 | 0.0634 (10) | 0.0420 (10) | 0.0311 (8) | 0.0278 (8) | 0.0109 (7) | 0.0036 (7) |
N1 | 0.0290 (9) | 0.0272 (9) | 0.0219 (8) | 0.0080 (7) | 0.0029 (6) | 0.0010 (7) |
N2 | 0.0320 (9) | 0.0256 (9) | 0.0245 (8) | 0.0059 (7) | 0.0016 (7) | −0.0002 (7) |
N3 | 0.0296 (9) | 0.0270 (9) | 0.0240 (8) | 0.0059 (7) | 0.0022 (6) | 0.0037 (7) |
N4 | 0.0284 (8) | 0.0283 (9) | 0.0212 (8) | 0.0062 (7) | 0.0047 (6) | 0.0010 (7) |
C1 | 0.0278 (10) | 0.0251 (10) | 0.0212 (9) | 0.0041 (8) | 0.0024 (7) | 0.0008 (8) |
C2 | 0.0248 (9) | 0.0243 (10) | 0.0224 (9) | 0.0006 (8) | 0.0029 (7) | −0.0011 (8) |
C3 | 0.0261 (10) | 0.0269 (11) | 0.0270 (10) | 0.0011 (8) | 0.0028 (8) | 0.0032 (8) |
C4 | 0.0252 (10) | 0.0270 (11) | 0.0241 (10) | 0.0034 (9) | 0.0015 (8) | 0.0006 (8) |
C5 | 0.0356 (11) | 0.0274 (11) | 0.0339 (11) | 0.0090 (9) | 0.0015 (8) | 0.0052 (9) |
C6 | 0.0396 (11) | 0.0399 (13) | 0.0233 (10) | 0.0084 (10) | 0.0088 (8) | 0.0003 (9) |
C7 | 0.0246 (10) | 0.0257 (10) | 0.0257 (10) | 0.0038 (8) | 0.0012 (7) | −0.0019 (8) |
C8 | 0.0274 (10) | 0.0282 (10) | 0.0219 (9) | 0.0036 (8) | 0.0031 (7) | −0.0025 (8) |
C9 | 0.0309 (10) | 0.0341 (12) | 0.0271 (10) | 0.0063 (9) | 0.0028 (8) | −0.0014 (9) |
C10 | 0.0370 (11) | 0.0425 (13) | 0.0261 (10) | 0.0046 (10) | 0.0019 (9) | 0.0018 (10) |
C11 | 0.0439 (12) | 0.0475 (14) | 0.0239 (11) | 0.0060 (11) | 0.0067 (9) | −0.0053 (10) |
C12 | 0.0458 (13) | 0.0388 (13) | 0.0330 (12) | 0.0124 (11) | 0.0090 (9) | −0.0070 (10) |
C13 | 0.0352 (11) | 0.0308 (11) | 0.0289 (11) | 0.0058 (9) | 0.0026 (8) | −0.0012 (9) |
O1—C4 | 1.237 (2) | C5—H5A | 0.9800 |
O2—C3 | 1.213 (2) | C5—H5B | 0.9800 |
O3—C13 | 1.351 (2) | C5—H5C | 0.9800 |
O3—H3 | 0.8400 | C6—H6A | 0.9800 |
N1—C7 | 1.355 (2) | C6—H6B | 0.9800 |
N1—C1 | 1.385 (2) | C6—H6C | 0.9800 |
N1—H71 | 0.97 (2) | C7—C8 | 1.459 (2) |
N2—C7 | 1.346 (2) | C8—C9 | 1.395 (3) |
N2—C2 | 1.351 (2) | C8—C13 | 1.409 (3) |
N3—C2 | 1.371 (2) | C9—C10 | 1.385 (3) |
N3—C3 | 1.382 (2) | C9—H9 | 0.9500 |
N3—C5 | 1.461 (2) | C10—C11 | 1.385 (3) |
N4—C4 | 1.396 (2) | C10—H10 | 0.9500 |
N4—C3 | 1.402 (2) | C11—C12 | 1.373 (3) |
N4—C6 | 1.474 (2) | C11—H11 | 0.9500 |
C1—C2 | 1.361 (3) | C12—C13 | 1.394 (3) |
C1—C4 | 1.410 (3) | C12—H12 | 0.9500 |
C13—O3—H3 | 109.5 | H5B—C5—H5C | 109.5 |
C7—N1—C1 | 106.25 (15) | N4—C6—H6A | 109.5 |
C7—N1—H71 | 126.1 (13) | N4—C6—H6B | 109.5 |
C1—N1—H71 | 127.6 (13) | H6A—C6—H6B | 109.5 |
C7—N2—C2 | 104.41 (15) | N4—C6—H6C | 109.5 |
C2—N3—C3 | 119.72 (16) | H6A—C6—H6C | 109.5 |
C2—N3—C5 | 121.03 (15) | H6B—C6—H6C | 109.5 |
C3—N3—C5 | 119.14 (15) | N2—C7—N1 | 111.87 (15) |
C4—N4—C3 | 126.42 (15) | N2—C7—C8 | 123.05 (16) |
C4—N4—C6 | 116.97 (15) | N1—C7—C8 | 125.08 (16) |
C3—N4—C6 | 116.61 (15) | C9—C8—C13 | 118.81 (17) |
C2—C1—N1 | 105.66 (16) | C9—C8—C7 | 121.77 (17) |
C2—C1—C4 | 122.63 (17) | C13—C8—C7 | 119.42 (17) |
N1—C1—C4 | 131.69 (17) | C10—C9—C8 | 121.44 (18) |
N2—C2—C1 | 111.80 (16) | C10—C9—H9 | 119.3 |
N2—C2—N3 | 126.19 (17) | C8—C9—H9 | 119.3 |
C1—C2—N3 | 122.00 (16) | C9—C10—C11 | 119.09 (19) |
O2—C3—N3 | 121.57 (17) | C9—C10—H10 | 120.5 |
O2—C3—N4 | 122.01 (17) | C11—C10—H10 | 120.5 |
N3—C3—N4 | 116.43 (16) | C12—C11—C10 | 120.61 (18) |
O1—C4—N4 | 120.16 (16) | C12—C11—H11 | 119.7 |
O1—C4—C1 | 127.08 (17) | C10—C11—H11 | 119.7 |
N4—C4—C1 | 112.74 (16) | C11—C12—C13 | 121.01 (19) |
N3—C5—H5A | 109.5 | C11—C12—H12 | 119.5 |
N3—C5—H5B | 109.5 | C13—C12—H12 | 119.5 |
H5A—C5—H5B | 109.5 | O3—C13—C12 | 117.67 (18) |
N3—C5—H5C | 109.5 | O3—C13—C8 | 123.27 (17) |
H5A—C5—H5C | 109.5 | C12—C13—C8 | 119.05 (18) |
C7—N1—C1—C2 | 0.44 (19) | C2—C1—C4—O1 | 179.62 (19) |
C7—N1—C1—C4 | 179.0 (2) | N1—C1—C4—O1 | 1.2 (3) |
C7—N2—C2—C1 | 0.3 (2) | C2—C1—C4—N4 | 1.1 (3) |
C7—N2—C2—N3 | −179.25 (17) | N1—C1—C4—N4 | −177.26 (18) |
N1—C1—C2—N2 | −0.5 (2) | C2—N2—C7—N1 | 0.0 (2) |
C4—C1—C2—N2 | −179.25 (17) | C2—N2—C7—C8 | −179.54 (17) |
N1—C1—C2—N3 | 179.11 (16) | C1—N1—C7—N2 | −0.3 (2) |
C4—C1—C2—N3 | 0.4 (3) | C1—N1—C7—C8 | 179.23 (17) |
C3—N3—C2—N2 | 177.08 (17) | N2—C7—C8—C9 | 179.44 (17) |
C5—N3—C2—N2 | 0.9 (3) | N1—C7—C8—C9 | 0.0 (3) |
C3—N3—C2—C1 | −2.5 (3) | N2—C7—C8—C13 | −0.4 (3) |
C5—N3—C2—C1 | −178.64 (17) | N1—C7—C8—C13 | −179.78 (18) |
C2—N3—C3—O2 | −177.22 (18) | C13—C8—C9—C10 | −0.4 (3) |
C5—N3—C3—O2 | −1.0 (3) | C7—C8—C9—C10 | 179.85 (18) |
C2—N3—C3—N4 | 2.8 (2) | C8—C9—C10—C11 | 0.3 (3) |
C5—N3—C3—N4 | 179.07 (16) | C9—C10—C11—C12 | −0.3 (3) |
C4—N4—C3—O2 | 178.72 (17) | C10—C11—C12—C13 | 0.3 (3) |
C6—N4—C3—O2 | −1.7 (3) | C11—C12—C13—O3 | −179.3 (2) |
C4—N4—C3—N3 | −1.3 (3) | C11—C12—C13—C8 | −0.4 (3) |
C6—N4—C3—N3 | 178.23 (16) | C9—C8—C13—O3 | 179.20 (18) |
C3—N4—C4—O1 | −179.24 (17) | C7—C8—C13—O3 | −1.0 (3) |
C6—N4—C4—O1 | 1.2 (3) | C9—C8—C13—C12 | 0.4 (3) |
C3—N4—C4—C1 | −0.6 (3) | C7—C8—C13—C12 | −179.82 (18) |
C6—N4—C4—C1 | 179.82 (16) |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3···N2 | 0.84 | 1.86 | 2.611 (2) | 148 |
N1—H71···O1i | 0.97 (2) | 1.78 (2) | 2.746 (2) | 175.4 (19) |
C9—H9···O1i | 0.95 | 2.37 | 3.294 (2) | 164 |
C5—H5A···O3ii | 0.98 | 2.58 | 3.234 (2) | 124 |
Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x+2, −y−1, −z. |
Experimental details
Crystal data | |
Chemical formula | C13H12N4O3 |
Mr | 272.27 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 200 |
a, b, c (Å) | 8.6418 (5), 5.9415 (3), 23.4475 (10) |
β (°) | 91.275 (2) |
V (Å3) | 1203.62 (11) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.41 × 0.10 × 0.05 |
Data collection | |
Diffractometer | Bruker APEXII CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2008) |
Tmin, Tmax | 0.860, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 10068, 2975, 1752 |
Rint | 0.043 |
(sin θ/λ)max (Å−1) | 0.667 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.049, 0.124, 1.01 |
No. of reflections | 2975 |
No. of parameters | 188 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.25, −0.21 |
Computer programs: APEX2 (Bruker, 2010), SAINT (Bruker, 2010), SHELXS97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2008), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3···N2 | 0.84 | 1.86 | 2.611 (2) | 148.2 |
N1—H71···O1i | 0.97 (2) | 1.78 (2) | 2.746 (2) | 175.4 (19) |
C9—H9···O1i | 0.95 | 2.37 | 3.294 (2) | 164.3 |
C5—H5A···O3ii | 0.98 | 2.58 | 3.234 (2) | 124.2 |
Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x+2, −y−1, −z. |
Acknowledgements
The authors thank Mrs Patricia Pono for helpful discussions.
References
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Chelate ligands have found widespread use in coordination chemistry due to the enhanced thermodynamic stability of resultant coordination compounds in relation to metal complexes exclusively applying comparable monodentate ligands (Gade 1998). Combining different sets of donor atoms in one chelate ligand molecule, a probe for testing and accomodating metal centers of different Lewis acidities is at hand. To enable comparative studies with envisioned coordination compounds, we determined the crystal structure of the title compound. The crystal structure of benzimidazole has been reported various times in the literature (e.g. Krawczyk & Gdaniec, 2005). In addition, several oxopurine derivatives have been the topic of crystal structure determinations (e.g. Schmalle et al., 1990).
The molecule features a benzimidazole-inspired backbone comprised of a 6-amino-1,3-dimethylpyrimidine-2,4(1H,3H)-dione moiety which is annealed to a five-membered aromatic ring. This part of the molecule is essentially planar (r.m.s. of its fitted non-hydrogen atoms = 0.0205 Å). The small puckering amplitude (τ = 1.6 °) of the six-membered heterocycle precludes a conformation analysis (Cremer & Pople, 1975). The least-squares planes defined by the atoms of the phenyl ring on the one hand and the benzimidazole-type ring system on the other hand enclose an angle of 0.45 (10) ° (Fig. 1). Both C–N–C angles in the five-membered heterocycle are similar in value with 106.25 (15)° and 104.41 (15)°, with the smaller value found on the non-protonated nitrogen atom. However, these angles are smaller in value than the corresponding ones in hypoxanthinium nitrate monohydrate – invariably above 108 ° – where both nitrogen atoms bear a hydrogen atom (Schmalle et al., 1990).
In the crystal structure, intra- as well as intermolecular hydrogen bonds and C–H···O contacts whose range falls by more than 0.1 Å below the sum of van-der-Waals radii of atoms participating are observed. While the intramolecular hydrogen bonds are exclusively made up by the proton of the hydroxyl group as donor and the non-protonated nitrogen atom of the five-membered heterocycle, intermolecular hydrogen bonds are solely apparent between the amino group and one of the double-bonded oxygen atoms (Table 1). The C–H···O contacts can be separated in two groups: while one of the nitrogen-bound methyl groups forms a C–H···O contact involving the oxygen atom of the hydroxyl group, one of the aromatic C–H groups acts as donor for the double-bonded oxygen atom that is already part of the N–H···O type hydrogen bonds. In terms of graph-set analysis (Etter et al., 1990; Bernstein et al., 1995), the descriptor for the classical hydrogen bonds is S(6)R22(10) on the unitary level. For the C–H···O contacts, a R22(16)R22(18) descriptor on the same level is needed for description. In total, the molecules are connected to chains along [1 1 0]. The shortest intercentroid distance between two aromatic systems was measured at 3.7771 (11) Å (Fig. 2).
The packing of the title compound in the crystal is shown in Figure 3.