organic compounds
(Z)-N-Methyl-2-(5-nitro-2-oxoindolin-3-ylidene)hydrazinecarbothioamide
aSchool of Chemical Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia, bFaculty of Science, Sabha University, Libya, cDepartment of Chemistry, International University of Africa, Sudan, and dX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: sgteoh@usm.my
In the title compound, C10H9N5O3S, an intramolecular N—H⋯O hydrogen bond generates an S(6) ring motif. In the crystal, molecules are linked via N—H⋯S hydrogen bonds into a zigzag chain along the b axis. C—H⋯O interactions are observed between the chains.
Related literature
For related structures, see: Qasem Ali et al. (2011a,b); Ferrari et al. (2002); Pervez et al. (2010); Ramzan et al. (2010). For various biological activities of see: Bhandari et al. (2008); Bhardwaj et al. (2010); Pandeya et al. (1999); Sridhar et al. (2002); Suryavanshi & Pai (2006). For the cytotoxic and anticancer activity of isatin and its derivatives, see: Vine et al. (2009). For graph-set analysis, see: Bernstein et al. (1995).
Experimental
Crystal data
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Refinement
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Data collection: APEX2 (Bruker, 2005); cell SAINT (Bruker, 2005); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009).
Supporting information
10.1107/S1600536812001183/is5048sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812001183/is5048Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812001183/is5048Isup3.cml
The Schiff base have been synthesized by refluxing the reaction mixture of hot ethanolic solution (30 ml) of 5-methyl-3-thiosemicarbazide (0.01 mol) and hot ethanolic solution (30 ml) of 5-nitroisatin (0.01 mol) for 2 hrs. The precipitate formed during reflux was filtered, washed with cold EtOH and recrystallized from hot EtOH (yield 80%, m.p. 579.8–580.3 K). The orange crystals were grown in an acetone-DMF (3:1) solution by slow evaporation at room temperature.
N-bound H atoms were located in a difference Fourier map and were refined freely. The remaining H atoms were positioned geometrically and refined using a riding model, with C—H = 0.95 Å for aromatic ring and C—H = 0.98 Å for methyl group, and with Uiso(H) = 1.2Ueq(C) and Uiso(H) = 1.5Ueq(C) for aromatic ring and methyl group, respectively. The highest residual electron density peak is located at 0.81 Å from C6 and the deepest hole is located at 0.36 Å from Sl.
Isatin (2,3-dioxindole) is an endogenous compound identified in humans, and its effect has been studied in a variety of systems. Biological properties of isatin and its derivatives include a range of actions in the brain, offer protection against bacterial (Suryavanshi & Pai, 2006) and antifungal infections and possess anticonvulsant, anti-HIV (Pandeya et al., 1999), anti-depressant and anti-inflammatory activities (Bhandari et al., 2008). Recently, we reported the
of (Z)-2-(5-chloro-2-oxoindolin-3-ylidene)-N-phenylhydrazinecarbothioamide (Qasem Ali et al., 2011a). In the present paper we describe the single-crystal X-ray diffraction study of title compound, Fig. 1.In this compound (Fig. 1), the chain N2/N3//C9/S1/N4/C10 connected to the nine-membered 5-nitroindolin-2-one ring system in C7. In this chain, C7—N2—N3—C9 and C10—N4—C9—S1 have torsion angles 177.82 (19) and -0.9 (3)°, respectively. The essentially planar conformation of the molecule is maintained by an intramolecular N3—H1N3···O1 hydrogen bond (Table 1) with a graph-set S(6) (Bernstein et al., 1995) In the crystal, molecules are linked via an intermolecular N1—H1N1···S1i hydrogen bond into an infinite one-dimensional chain along the b axis (Table 1 and Fig. 2). C2—H2A···O1ii and C10—H10A···O2iii hydrogen bonds (Table 1) are also observed between the chains.
For related structures, see: Qasem Ali et al. (2011a,b); Ferrari et al. (2002); Pervez et al. (2010); Ramzan et al. (2010). For various biological activities of
see: Bhandari et al. (2008); Bhardwaj et al. (2010); Pandeya et al. (1999); Sridhar et al. (2002); Suryavanshi & Pai (2006). For the cytotoxic and anticancer activity of isatin and its derivatives, see: Vine et al. (2009). For graph-set analysis, see: Bernstein et al. (1995).Data collection: APEX2 (Bruker, 2005); cell
SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).C10H9N5O3S | F(000) = 576 |
Mr = 279.28 | Dx = 1.630 Mg m−3 |
Monoclinic, P21/c | Melting point = 579.8–580.3 K |
Hall symbol: -P 2ybc | Mo Kα radiation, λ = 0.71073 Å |
a = 4.6316 (4) Å | Cell parameters from 3870 reflections |
b = 9.3157 (8) Å | θ = 2.7–30.1° |
c = 26.458 (2) Å | µ = 0.30 mm−1 |
β = 94.485 (2)° | T = 100 K |
V = 1138.09 (17) Å3 | Needle, orange |
Z = 4 | 0.36 × 0.12 × 0.07 mm |
Bruker APEXII CCD diffractometer | 2710 independent reflections |
Radiation source: fine-focus sealed tube | 2177 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.045 |
φ and ω scans | θmax = 28.0°, θmin = 2.3° |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | h = −6→6 |
Tmin = 0.900, Tmax = 0.979 | k = −11→12 |
10734 measured reflections | l = −34→34 |
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)] = 0.048 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.102 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.10 | w = 1/[σ2(Fo2) + (0.0189P)2 + 1.8143P] where P = (Fo2 + 2Fc2)/3 |
2710 reflections | (Δ/σ)max = 0.001 |
185 parameters | Δρmax = 0.40 e Å−3 |
0 restraints | Δρmin = −0.29 e Å−3 |
C10H9N5O3S | V = 1138.09 (17) Å3 |
Mr = 279.28 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 4.6316 (4) Å | µ = 0.30 mm−1 |
b = 9.3157 (8) Å | T = 100 K |
c = 26.458 (2) Å | 0.36 × 0.12 × 0.07 mm |
β = 94.485 (2)° |
Bruker APEXII CCD diffractometer | 2710 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | 2177 reflections with I > 2σ(I) |
Tmin = 0.900, Tmax = 0.979 | Rint = 0.045 |
10734 measured reflections |
R[F2 > 2σ(F2)] = 0.048 | 0 restraints |
wR(F2) = 0.102 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.10 | Δρmax = 0.40 e Å−3 |
2710 reflections | Δρmin = −0.29 e Å−3 |
185 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 | ||
S1 | 1.21633 (12) | 0.51362 (6) | 0.32848 (2) | 0.01849 (15) | |
O1 | 0.5410 (3) | 0.21885 (18) | 0.25632 (6) | 0.0199 (4) | |
O2 | −0.1914 (4) | −0.2525 (2) | 0.47157 (8) | 0.0409 (5) | |
O3 | 0.1838 (4) | −0.1372 (2) | 0.50290 (7) | 0.0304 (4) | |
N1 | 0.2084 (4) | 0.0484 (2) | 0.27784 (8) | 0.0187 (4) | |
N2 | 0.6885 (4) | 0.2193 (2) | 0.36918 (7) | 0.0159 (4) | |
N3 | 0.8430 (4) | 0.3086 (2) | 0.34179 (7) | 0.0166 (4) | |
N4 | 1.0960 (4) | 0.3840 (2) | 0.41442 (7) | 0.0189 (4) | |
N5 | 0.0142 (5) | −0.1717 (2) | 0.46698 (8) | 0.0242 (5) | |
C1 | 0.1322 (5) | −0.0181 (2) | 0.32196 (8) | 0.0167 (5) | |
C2 | −0.0740 (5) | −0.1225 (3) | 0.32723 (9) | 0.0198 (5) | |
H2A | −0.1871 | −0.1592 | 0.2986 | 0.024* | |
C3 | −0.1108 (5) | −0.1721 (3) | 0.37559 (9) | 0.0212 (5) | |
H3A | −0.2502 | −0.2444 | 0.3807 | 0.025* | |
C4 | 0.0580 (5) | −0.1154 (3) | 0.41667 (9) | 0.0198 (5) | |
C5 | 0.2677 (5) | −0.0110 (3) | 0.41212 (9) | 0.0185 (5) | |
H5A | 0.3813 | 0.0249 | 0.4408 | 0.022* | |
C6 | 0.3033 (5) | 0.0383 (2) | 0.36375 (8) | 0.0166 (5) | |
C7 | 0.4952 (5) | 0.1430 (2) | 0.34383 (8) | 0.0155 (4) | |
C8 | 0.4257 (5) | 0.1451 (2) | 0.28722 (8) | 0.0166 (5) | |
C9 | 1.0477 (5) | 0.3984 (2) | 0.36484 (8) | 0.0164 (5) | |
C10 | 1.3117 (5) | 0.4679 (3) | 0.44437 (9) | 0.0257 (6) | |
H10A | 1.2463 | 0.4842 | 0.4782 | 0.039* | |
H10B | 1.3383 | 0.5604 | 0.4277 | 0.039* | |
H10C | 1.4959 | 0.4157 | 0.4473 | 0.039* | |
H1N3 | 0.803 (6) | 0.317 (3) | 0.3104 (11) | 0.020 (7)* | |
H1N4 | 1.013 (6) | 0.318 (3) | 0.4291 (10) | 0.021 (7)* | |
H1N1 | 0.123 (6) | 0.039 (3) | 0.2501 (11) | 0.024 (7)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0212 (3) | 0.0194 (3) | 0.0137 (3) | 0.0002 (2) | −0.0055 (2) | 0.0021 (2) |
O1 | 0.0248 (8) | 0.0222 (9) | 0.0117 (8) | 0.0021 (7) | −0.0052 (7) | −0.0004 (7) |
O2 | 0.0460 (12) | 0.0433 (12) | 0.0332 (11) | −0.0198 (10) | 0.0027 (9) | 0.0087 (10) |
O3 | 0.0335 (10) | 0.0384 (11) | 0.0183 (9) | −0.0006 (8) | −0.0046 (8) | 0.0046 (8) |
N1 | 0.0225 (10) | 0.0215 (10) | 0.0107 (10) | 0.0014 (8) | −0.0081 (8) | −0.0037 (8) |
N2 | 0.0173 (9) | 0.0160 (9) | 0.0135 (9) | 0.0022 (7) | −0.0039 (7) | −0.0008 (8) |
N3 | 0.0211 (10) | 0.0193 (10) | 0.0082 (9) | 0.0007 (8) | −0.0062 (7) | 0.0012 (8) |
N4 | 0.0221 (10) | 0.0222 (11) | 0.0111 (10) | −0.0047 (8) | −0.0055 (8) | −0.0006 (8) |
N5 | 0.0274 (11) | 0.0227 (11) | 0.0224 (11) | 0.0017 (9) | 0.0013 (9) | 0.0036 (9) |
C1 | 0.0173 (10) | 0.0165 (11) | 0.0153 (11) | 0.0060 (9) | −0.0047 (8) | −0.0041 (9) |
C2 | 0.0190 (11) | 0.0189 (12) | 0.0203 (12) | 0.0019 (9) | −0.0066 (9) | −0.0068 (10) |
C3 | 0.0216 (11) | 0.0155 (11) | 0.0258 (13) | 0.0013 (9) | −0.0015 (10) | −0.0016 (10) |
C4 | 0.0226 (11) | 0.0186 (12) | 0.0177 (12) | 0.0045 (9) | −0.0012 (9) | 0.0010 (9) |
C5 | 0.0183 (10) | 0.0188 (12) | 0.0176 (11) | 0.0039 (9) | −0.0037 (9) | −0.0020 (9) |
C6 | 0.0165 (10) | 0.0170 (11) | 0.0155 (11) | 0.0037 (8) | −0.0041 (9) | −0.0034 (9) |
C7 | 0.0175 (10) | 0.0170 (11) | 0.0111 (11) | 0.0053 (8) | −0.0043 (8) | −0.0016 (9) |
C8 | 0.0190 (11) | 0.0182 (11) | 0.0113 (11) | 0.0049 (9) | −0.0063 (8) | −0.0032 (9) |
C9 | 0.0174 (10) | 0.0156 (11) | 0.0152 (11) | 0.0047 (9) | −0.0048 (9) | −0.0036 (9) |
C10 | 0.0283 (13) | 0.0315 (14) | 0.0157 (12) | −0.0081 (11) | −0.0086 (10) | −0.0036 (11) |
S1—C9 | 1.675 (2) | C1—C2 | 1.378 (3) |
O1—C8 | 1.222 (3) | C1—C6 | 1.410 (3) |
O2—N5 | 1.227 (3) | C2—C3 | 1.383 (3) |
O3—N5 | 1.227 (3) | C2—H2A | 0.9500 |
N1—C8 | 1.359 (3) | C3—C4 | 1.392 (3) |
N1—C1 | 1.391 (3) | C3—H3A | 0.9500 |
N1—H1N1 | 0.81 (3) | C4—C5 | 1.387 (3) |
N2—C7 | 1.289 (3) | C5—C6 | 1.382 (3) |
N2—N3 | 1.346 (3) | C5—H5A | 0.9500 |
N3—C9 | 1.371 (3) | C6—C7 | 1.446 (3) |
N3—H1N3 | 0.84 (3) | C7—C8 | 1.507 (3) |
N4—C9 | 1.320 (3) | C10—H10A | 0.9800 |
N4—C10 | 1.454 (3) | C10—H10B | 0.9800 |
N4—H1N4 | 0.84 (3) | C10—H10C | 0.9800 |
N5—C4 | 1.460 (3) | ||
C8—N1—C1 | 112.00 (19) | C5—C4—N5 | 118.6 (2) |
C8—N1—H1N1 | 123 (2) | C3—C4—N5 | 117.8 (2) |
C1—N1—H1N1 | 125 (2) | C6—C5—C4 | 116.7 (2) |
C7—N2—N3 | 115.95 (19) | C6—C5—H5A | 121.7 |
N2—N3—C9 | 121.06 (19) | C4—C5—H5A | 121.7 |
N2—N3—H1N3 | 120.3 (18) | C5—C6—C1 | 120.1 (2) |
C9—N3—H1N3 | 118.3 (18) | C5—C6—C7 | 133.1 (2) |
C9—N4—C10 | 122.9 (2) | C1—C6—C7 | 106.81 (19) |
C9—N4—H1N4 | 119.1 (19) | N2—C7—C6 | 127.1 (2) |
C10—N4—H1N4 | 117.7 (19) | N2—C7—C8 | 126.5 (2) |
O2—N5—O3 | 122.6 (2) | C6—C7—C8 | 106.34 (19) |
O2—N5—C4 | 118.3 (2) | O1—C8—N1 | 127.4 (2) |
O3—N5—C4 | 119.1 (2) | O1—C8—C7 | 127.0 (2) |
C2—C1—N1 | 128.5 (2) | N1—C8—C7 | 105.67 (19) |
C2—C1—C6 | 122.4 (2) | N4—C9—N3 | 116.0 (2) |
N1—C1—C6 | 109.2 (2) | N4—C9—S1 | 125.82 (18) |
C1—C2—C3 | 117.8 (2) | N3—C9—S1 | 118.22 (17) |
C1—C2—H2A | 121.1 | N4—C10—H10A | 109.5 |
C3—C2—H2A | 121.1 | N4—C10—H10B | 109.5 |
C2—C3—C4 | 119.5 (2) | H10A—C10—H10B | 109.5 |
C2—C3—H3A | 120.2 | N4—C10—H10C | 109.5 |
C4—C3—H3A | 120.2 | H10A—C10—H10C | 109.5 |
C5—C4—C3 | 123.6 (2) | H10B—C10—H10C | 109.5 |
C7—N2—N3—C9 | 177.82 (19) | C2—C1—C6—C7 | 179.3 (2) |
C8—N1—C1—C2 | −178.9 (2) | N1—C1—C6—C7 | −0.7 (2) |
C8—N1—C1—C6 | 1.1 (3) | N3—N2—C7—C6 | 179.3 (2) |
N1—C1—C2—C3 | −179.9 (2) | N3—N2—C7—C8 | −0.4 (3) |
C6—C1—C2—C3 | 0.0 (3) | C5—C6—C7—N2 | −0.5 (4) |
C1—C2—C3—C4 | 0.3 (3) | C1—C6—C7—N2 | −179.7 (2) |
C2—C3—C4—C5 | −0.7 (4) | C5—C6—C7—C8 | 179.3 (2) |
C2—C3—C4—N5 | −179.4 (2) | C1—C6—C7—C8 | 0.1 (2) |
O2—N5—C4—C5 | 172.4 (2) | C1—N1—C8—O1 | 179.1 (2) |
O3—N5—C4—C5 | −7.9 (3) | C1—N1—C8—C7 | −1.0 (2) |
O2—N5—C4—C3 | −8.9 (3) | N2—C7—C8—O1 | 0.2 (4) |
O3—N5—C4—C3 | 170.8 (2) | C6—C7—C8—O1 | −179.6 (2) |
C3—C4—C5—C6 | 0.8 (3) | N2—C7—C8—N1 | −179.7 (2) |
N5—C4—C5—C6 | 179.5 (2) | C6—C7—C8—N1 | 0.5 (2) |
C4—C5—C6—C1 | −0.5 (3) | C10—N4—C9—N3 | 178.2 (2) |
C4—C5—C6—C7 | −179.5 (2) | C10—N4—C9—S1 | −0.9 (3) |
C2—C1—C6—C5 | 0.1 (3) | N2—N3—C9—N4 | 4.5 (3) |
N1—C1—C6—C5 | 180.0 (2) | N2—N3—C9—S1 | −176.25 (16) |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H1N3···O1 | 0.84 (3) | 2.02 (3) | 2.697 (2) | 137 (3) |
N1—H1N1···S1i | 0.81 (3) | 2.52 (3) | 3.320 (2) | 171 (3) |
C2—H2A···O1ii | 0.95 | 2.39 | 3.317 (3) | 165 |
C10—H10A···O2iii | 0.98 | 2.56 | 3.079 (3) | 113 |
Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) −x, y−1/2, −z+1/2; (iii) −x+1, −y, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C10H9N5O3S |
Mr | 279.28 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 100 |
a, b, c (Å) | 4.6316 (4), 9.3157 (8), 26.458 (2) |
β (°) | 94.485 (2) |
V (Å3) | 1138.09 (17) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.30 |
Crystal size (mm) | 0.36 × 0.12 × 0.07 |
Data collection | |
Diffractometer | Bruker APEXII CCD |
Absorption correction | Multi-scan (SADABS; Bruker, 2005) |
Tmin, Tmax | 0.900, 0.979 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 10734, 2710, 2177 |
Rint | 0.045 |
(sin θ/λ)max (Å−1) | 0.661 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.048, 0.102, 1.10 |
No. of reflections | 2710 |
No. of parameters | 185 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.40, −0.29 |
Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H1N3···O1 | 0.84 (3) | 2.02 (3) | 2.697 (2) | 137 (3) |
N1—H1N1···S1i | 0.81 (3) | 2.52 (3) | 3.320 (2) | 171 (3) |
C2—H2A···O1ii | 0.9500 | 2.3900 | 3.317 (3) | 165.00 |
C10—H10A···O2iii | 0.9800 | 2.5600 | 3.079 (3) | 113.00 |
Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) −x, y−1/2, −z+1/2; (iii) −x+1, −y, −z+1. |
Acknowledgements
The authors thank the Malaysian Government and Universiti Sains Malaysia for the RU research grant (1001/PKIMIA/815067). AQA thanks the Ministry of Higher Education and the University of Sabha (Libya) for a scholarship.
References
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Isatin (2,3-dioxindole) is an endogenous compound identified in humans, and its effect has been studied in a variety of systems. Biological properties of isatin and its derivatives include a range of actions in the brain, offer protection against bacterial (Suryavanshi & Pai, 2006) and antifungal infections and possess anticonvulsant, anti-HIV (Pandeya et al., 1999), anti-depressant and anti-inflammatory activities (Bhandari et al., 2008). Recently, we reported the crystal structure of (Z)-2-(5-chloro-2-oxoindolin-3-ylidene)-N-phenylhydrazinecarbothioamide (Qasem Ali et al., 2011a). In the present paper we describe the single-crystal X-ray diffraction study of title compound, Fig. 1.
In this compound (Fig. 1), the chain N2/N3//C9/S1/N4/C10 connected to the nine-membered 5-nitroindolin-2-one ring system in C7. In this chain, C7—N2—N3—C9 and C10—N4—C9—S1 have torsion angles 177.82 (19) and -0.9 (3)°, respectively. The essentially planar conformation of the molecule is maintained by an intramolecular N3—H1N3···O1 hydrogen bond (Table 1) with a graph-set S(6) (Bernstein et al., 1995) In the crystal, molecules are linked via an intermolecular N1—H1N1···S1i hydrogen bond into an infinite one-dimensional chain along the b axis (Table 1 and Fig. 2). C2—H2A···O1ii and C10—H10A···O2iii hydrogen bonds (Table 1) are also observed between the chains.