organic compounds
(Z)-N-Methyl-2-(5-methyl-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, Khartoum, 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, C11H12N4OS, an intramolecular N—H⋯O hydrogen bond generates an S(6) ring motif. In the crystal, the molecules form a helical chain along the a axis through an N—H⋯O hydrogen bond. These chains are extended by an N—H⋯S hydrogen bond and a C—H⋯π interaction into a three-dimensional network.
Related literature
For related structures, see: Ali et al. (2012); Qasem Ali et al. (2012, 2011a,b). 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 cytotoxic and anticancer activities 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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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/S1600536812005417/is5066sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812005417/is5066Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812005417/is5066Isup3.cml
The Schiff base has 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-methylisatin (0.01 mol) for 2 h. The precipitate formed during reflux was filtered, washed with cold EtOH and recrystallized from hot EtOH (yield 94%, m.p. 551.7–552.2 K). The yellow crystals were grown in acetone–DMF (3:1) 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 1.5Ueq(C) for aromatic ring and methyl group, respectively. The highest residual electron density peak is located at 0.76 Å from C9 and the deepest hole is located at 0.16 Å from H11C.
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 fungal 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)-N-methyl-2-(5-nitro-2-oxoindolin-3-ylidene) hydrazinecarbothioamide (Ali et al., 2012). In the present paper we describe the single-crystal X-ray diffraction study of title compound.In this compound (Fig. 1), the chain N2/N3/C9/S1/N4/C10 connects to the nine-membered 5-methylindolin-2-one ring system at C7. In this chain, C7/N2/N3/C9 and C10/N4/C9/S1 have torsion angles -176.69 (13) and -1.4 (2)°, respectively. The essentially planar conformation of the molecule is maintained by the cyclic intramolecular N3—H1N3···O1 hydrogen-bond (Table 1) [graph set S(6); Bernstein et al., 1995)]. In the crystal, the molecules form a helical chain through an intermolecular N1—H1N1···O1 hydrogen bond and are extended by an N4—H1N4···S1 hydrogen bond and a weak C3—H3A···Cg2 interaction into a three-dimensional network (Table 1, Fig. 2). Cg2 is the centroid of the C1–C6 ring.
For related structures, see: Ali et al. (2012); Qasem Ali et al. (2012, 2011a,b). 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 cytotoxic and anticancer activities 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).C11H12N4OS | Dx = 1.368 Mg m−3 |
Mr = 248.31 | Melting point = 551.7–552.2 K |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 5511 reflections |
a = 6.2826 (2) Å | θ = 2.3–30.7° |
b = 10.0341 (3) Å | µ = 0.26 mm−1 |
c = 19.1315 (5) Å | T = 100 K |
V = 1206.05 (6) Å3 | Block, orange |
Z = 4 | 0.51 × 0.18 × 0.13 mm |
F(000) = 520 |
Bruker APEXII CCD diffractometer | 3780 independent reflections |
Radiation source: fine-focus sealed tube | 3463 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.050 |
φ and ω scans | θmax = 31.0°, θmin = 2.1° |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | h = −8→9 |
Tmin = 0.879, Tmax = 0.967 | k = −14→13 |
13743 measured reflections | l = −26→27 |
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)] = 0.037 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.097 | w = 1/[σ2(Fo2) + (0.0489P)2 + 0.2287P] where P = (Fo2 + 2Fc2)/3 |
S = 1.07 | (Δ/σ)max = 0.001 |
3780 reflections | Δρmax = 0.32 e Å−3 |
168 parameters | Δρmin = −0.24 e Å−3 |
0 restraints | Absolute structure: Flack (1983), with 1584 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: −0.08 (7) |
C11H12N4OS | V = 1206.05 (6) Å3 |
Mr = 248.31 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 6.2826 (2) Å | µ = 0.26 mm−1 |
b = 10.0341 (3) Å | T = 100 K |
c = 19.1315 (5) Å | 0.51 × 0.18 × 0.13 mm |
Bruker APEXII CCD diffractometer | 3780 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | 3463 reflections with I > 2σ(I) |
Tmin = 0.879, Tmax = 0.967 | Rint = 0.050 |
13743 measured reflections |
R[F2 > 2σ(F2)] = 0.037 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.097 | Δρmax = 0.32 e Å−3 |
S = 1.07 | Δρmin = −0.24 e Å−3 |
3780 reflections | Absolute structure: Flack (1983), with 1584 Friedel pairs |
168 parameters | Absolute structure parameter: −0.08 (7) |
0 restraints |
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 | −0.25429 (6) | 0.29169 (3) | 0.213725 (19) | 0.02077 (10) | |
O1 | 0.31886 (18) | 0.26735 (11) | 0.06564 (6) | 0.0214 (2) | |
N1 | 0.6103 (2) | 0.39581 (13) | 0.03384 (7) | 0.0191 (3) | |
N2 | 0.2245 (2) | 0.50945 (11) | 0.15475 (6) | 0.0159 (2) | |
N3 | 0.0861 (2) | 0.40757 (13) | 0.16284 (7) | 0.0171 (2) | |
N4 | −0.1126 (2) | 0.54025 (13) | 0.23530 (7) | 0.0181 (2) | |
C1 | 0.6888 (2) | 0.52394 (15) | 0.05069 (8) | 0.0170 (3) | |
C2 | 0.8718 (2) | 0.58576 (17) | 0.02731 (8) | 0.0206 (3) | |
H2A | 0.9661 | 0.5427 | −0.0042 | 0.025* | |
C3 | 0.9124 (2) | 0.71447 (17) | 0.05206 (8) | 0.0217 (3) | |
H3A | 1.0386 | 0.7586 | 0.0374 | 0.026* | |
C4 | 0.7740 (2) | 0.78049 (15) | 0.09758 (7) | 0.0202 (3) | |
C5 | 0.5903 (2) | 0.71534 (15) | 0.12059 (7) | 0.0175 (3) | |
H5A | 0.4945 | 0.7585 | 0.1516 | 0.021* | |
C6 | 0.5498 (2) | 0.58673 (15) | 0.09747 (7) | 0.0157 (3) | |
C7 | 0.3812 (2) | 0.49169 (14) | 0.11202 (7) | 0.0158 (3) | |
C8 | 0.4287 (2) | 0.37009 (15) | 0.06883 (8) | 0.0175 (3) | |
C9 | −0.0900 (2) | 0.42245 (14) | 0.20479 (7) | 0.0163 (3) | |
C10 | −0.2903 (2) | 0.57322 (17) | 0.28065 (9) | 0.0246 (3) | |
H10A | −0.3009 | 0.6702 | 0.2853 | 0.037* | |
H10B | −0.2675 | 0.5333 | 0.3268 | 0.037* | |
H10C | −0.4223 | 0.5383 | 0.2604 | 0.037* | |
C11 | 0.8227 (3) | 0.92103 (18) | 0.12193 (9) | 0.0288 (4) | |
H11A | 0.9767 | 0.9361 | 0.1204 | 0.043* | |
H11B | 0.7716 | 0.9327 | 0.1699 | 0.043* | |
H11C | 0.7511 | 0.9851 | 0.0912 | 0.043* | |
H1N1 | 0.675 (4) | 0.345 (2) | 0.0091 (12) | 0.030 (6)* | |
H1N3 | 0.105 (3) | 0.337 (2) | 0.1401 (10) | 0.022 (5)* | |
H1N4 | −0.027 (4) | 0.598 (2) | 0.2289 (11) | 0.028 (6)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.01781 (16) | 0.01833 (15) | 0.02616 (18) | −0.00367 (14) | 0.00191 (16) | 0.00281 (13) |
O1 | 0.0245 (5) | 0.0189 (5) | 0.0207 (5) | −0.0035 (4) | −0.0012 (4) | −0.0036 (4) |
N1 | 0.0210 (6) | 0.0189 (6) | 0.0173 (6) | 0.0018 (5) | 0.0025 (5) | −0.0022 (5) |
N2 | 0.0162 (6) | 0.0145 (5) | 0.0171 (5) | −0.0021 (4) | −0.0010 (5) | 0.0021 (4) |
N3 | 0.0167 (6) | 0.0147 (5) | 0.0200 (6) | −0.0019 (5) | 0.0022 (5) | −0.0016 (4) |
N4 | 0.0145 (5) | 0.0195 (6) | 0.0204 (6) | −0.0004 (5) | 0.0015 (5) | −0.0009 (5) |
C1 | 0.0175 (6) | 0.0185 (6) | 0.0149 (6) | 0.0012 (5) | −0.0009 (5) | 0.0020 (5) |
C2 | 0.0171 (7) | 0.0255 (7) | 0.0191 (7) | 0.0031 (6) | 0.0023 (5) | 0.0038 (6) |
C3 | 0.0162 (6) | 0.0277 (7) | 0.0213 (7) | −0.0036 (6) | −0.0010 (5) | 0.0069 (6) |
C4 | 0.0211 (7) | 0.0220 (6) | 0.0174 (6) | −0.0062 (6) | −0.0035 (5) | 0.0031 (5) |
C5 | 0.0180 (6) | 0.0185 (6) | 0.0161 (6) | −0.0013 (6) | −0.0002 (5) | 0.0003 (5) |
C6 | 0.0148 (6) | 0.0184 (6) | 0.0140 (6) | 0.0005 (5) | −0.0001 (5) | 0.0013 (5) |
C7 | 0.0167 (6) | 0.0164 (6) | 0.0143 (6) | −0.0005 (5) | −0.0021 (5) | −0.0008 (5) |
C8 | 0.0197 (7) | 0.0175 (6) | 0.0154 (6) | 0.0015 (5) | −0.0018 (5) | −0.0015 (5) |
C9 | 0.0151 (6) | 0.0170 (6) | 0.0169 (6) | 0.0004 (5) | −0.0026 (5) | 0.0019 (5) |
C10 | 0.0195 (7) | 0.0294 (7) | 0.0251 (7) | 0.0036 (6) | 0.0031 (6) | −0.0041 (6) |
C11 | 0.0322 (8) | 0.0273 (8) | 0.0271 (8) | −0.0129 (7) | −0.0012 (7) | −0.0017 (7) |
S1—C9 | 1.6781 (15) | C2—H2A | 0.9500 |
O1—C8 | 1.2419 (18) | C3—C4 | 1.398 (2) |
N1—C8 | 1.348 (2) | C3—H3A | 0.9500 |
N1—C1 | 1.414 (2) | C4—C5 | 1.398 (2) |
N1—H1N1 | 0.81 (2) | C4—C11 | 1.516 (2) |
N2—C7 | 1.2920 (19) | C5—C6 | 1.388 (2) |
N2—N3 | 1.3510 (17) | C5—H5A | 0.9500 |
N3—C9 | 1.3749 (19) | C6—C7 | 1.452 (2) |
N3—H1N3 | 0.84 (2) | C7—C8 | 1.503 (2) |
N4—C9 | 1.3259 (19) | C10—H10A | 0.9800 |
N4—C10 | 1.4520 (19) | C10—H10B | 0.9800 |
N4—H1N4 | 0.80 (2) | C10—H10C | 0.9800 |
C1—C2 | 1.381 (2) | C11—H11A | 0.9800 |
C1—C6 | 1.400 (2) | C11—H11B | 0.9800 |
C2—C3 | 1.399 (2) | C11—H11C | 0.9800 |
C8—N1—C1 | 110.85 (13) | C5—C6—C1 | 120.52 (14) |
C8—N1—H1N1 | 127.0 (16) | C5—C6—C7 | 133.10 (14) |
C1—N1—H1N1 | 122.0 (16) | C1—C6—C7 | 106.37 (13) |
C7—N2—N3 | 117.30 (12) | N2—C7—C6 | 125.90 (13) |
N2—N3—C9 | 120.18 (12) | N2—C7—C8 | 127.65 (13) |
N2—N3—H1N3 | 119.1 (15) | C6—C7—C8 | 106.44 (12) |
C9—N3—H1N3 | 120.6 (15) | O1—C8—N1 | 127.21 (14) |
C9—N4—C10 | 123.25 (13) | O1—C8—C7 | 126.20 (13) |
C9—N4—H1N4 | 120.3 (16) | N1—C8—C7 | 106.59 (13) |
C10—N4—H1N4 | 116.4 (16) | N4—C9—N3 | 116.09 (13) |
C2—C1—C6 | 121.61 (15) | N4—C9—S1 | 125.91 (11) |
C2—C1—N1 | 128.67 (15) | N3—C9—S1 | 118.00 (11) |
C6—C1—N1 | 109.72 (13) | N4—C10—H10A | 109.5 |
C1—C2—C3 | 117.20 (15) | N4—C10—H10B | 109.5 |
C1—C2—H2A | 121.4 | H10A—C10—H10B | 109.5 |
C3—C2—H2A | 121.4 | N4—C10—H10C | 109.5 |
C4—C3—C2 | 122.33 (14) | H10A—C10—H10C | 109.5 |
C4—C3—H3A | 118.8 | H10B—C10—H10C | 109.5 |
C2—C3—H3A | 118.8 | C4—C11—H11A | 109.5 |
C3—C4—C5 | 119.23 (14) | C4—C11—H11B | 109.5 |
C3—C4—C11 | 120.45 (14) | H11A—C11—H11B | 109.5 |
C5—C4—C11 | 120.31 (15) | C4—C11—H11C | 109.5 |
C6—C5—C4 | 119.07 (14) | H11A—C11—H11C | 109.5 |
C6—C5—H5A | 120.5 | H11B—C11—H11C | 109.5 |
C4—C5—H5A | 120.5 | ||
C7—N2—N3—C9 | −176.69 (13) | N3—N2—C7—C6 | −178.16 (13) |
C8—N1—C1—C2 | 178.42 (15) | N3—N2—C7—C8 | 0.6 (2) |
C8—N1—C1—C6 | −1.59 (17) | C5—C6—C7—N2 | −2.0 (3) |
C6—C1—C2—C3 | −0.3 (2) | C1—C6—C7—N2 | 177.54 (14) |
N1—C1—C2—C3 | 179.68 (14) | C5—C6—C7—C8 | 178.97 (15) |
C1—C2—C3—C4 | −1.1 (2) | C1—C6—C7—C8 | −1.48 (15) |
C2—C3—C4—C5 | 1.3 (2) | C1—N1—C8—O1 | 179.56 (15) |
C2—C3—C4—C11 | −178.82 (15) | C1—N1—C8—C7 | 0.58 (16) |
C3—C4—C5—C6 | −0.1 (2) | N2—C7—C8—O1 | 2.6 (2) |
C11—C4—C5—C6 | −179.99 (14) | C6—C7—C8—O1 | −178.43 (14) |
C4—C5—C6—C1 | −1.2 (2) | N2—C7—C8—N1 | −178.43 (14) |
C4—C5—C6—C7 | 178.28 (15) | C6—C7—C8—N1 | 0.57 (16) |
C2—C1—C6—C5 | 1.5 (2) | C10—N4—C9—N3 | 179.39 (14) |
N1—C1—C6—C5 | −178.51 (13) | C10—N4—C9—S1 | −1.4 (2) |
C2—C1—C6—C7 | −178.14 (13) | N2—N3—C9—N4 | 0.19 (19) |
N1—C1—C6—C7 | 1.87 (16) | N2—N3—C9—S1 | −179.14 (10) |
Cg2 is the centroid of the C1–C6 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···O1i | 0.81 (2) | 2.03 (2) | 2.8319 (17) | 171 (2) |
N3—H1N3···O1 | 0.84 (2) | 2.079 (19) | 2.7525 (17) | 136.9 (17) |
N4—H1N4···S1ii | 0.80 (2) | 2.85 (2) | 3.5538 (13) | 148.5 (19) |
C3—H3A···Cg2iii | 0.95 | 2.62 | 3.4165 (16) | 142 |
Symmetry codes: (i) x+1/2, −y+1/2, −z; (ii) −x, y+1/2, −z+1/2; (iii) x+1/2, −y+3/2, −z. |
Experimental details
Crystal data | |
Chemical formula | C11H12N4OS |
Mr | 248.31 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 100 |
a, b, c (Å) | 6.2826 (2), 10.0341 (3), 19.1315 (5) |
V (Å3) | 1206.05 (6) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.26 |
Crystal size (mm) | 0.51 × 0.18 × 0.13 |
Data collection | |
Diffractometer | Bruker APEXII CCD |
Absorption correction | Multi-scan (SADABS; Bruker, 2005) |
Tmin, Tmax | 0.879, 0.967 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 13743, 3780, 3463 |
Rint | 0.050 |
(sin θ/λ)max (Å−1) | 0.724 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.097, 1.07 |
No. of reflections | 3780 |
No. of parameters | 168 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.32, −0.24 |
Absolute structure | Flack (1983), with 1584 Friedel pairs |
Absolute structure parameter | −0.08 (7) |
Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
Cg2 is the centroid of the C1–C6 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···O1i | 0.81 (2) | 2.03 (2) | 2.8319 (17) | 171 (2) |
N3—H1N3···O1 | 0.84 (2) | 2.079 (19) | 2.7525 (17) | 136.9 (17) |
N4—H1N4···S1ii | 0.80 (2) | 2.85 (2) | 3.5538 (13) | 148.5 (19) |
C3—H3A···Cg2iii | 0.95 | 2.62 | 3.4165 (16) | 142 |
Symmetry codes: (i) x+1/2, −y+1/2, −z; (ii) −x, y+1/2, −z+1/2; (iii) x+1/2, −y+3/2, −z. |
Acknowledgements
The authors thank the Malaysian Government and Universiti Sains Malaysia for an RU research grant (No. 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 fungal 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)-N-methyl-2-(5-nitro-2-oxoindolin-3-ylidene) hydrazinecarbothioamide (Ali et al., 2012). In the present paper we describe the single-crystal X-ray diffraction study of title compound.
In this compound (Fig. 1), the chain N2/N3/C9/S1/N4/C10 connects to the nine-membered 5-methylindolin-2-one ring system at C7. In this chain, C7/N2/N3/C9 and C10/N4/C9/S1 have torsion angles -176.69 (13) and -1.4 (2)°, respectively. The essentially planar conformation of the molecule is maintained by the cyclic intramolecular N3—H1N3···O1 hydrogen-bond (Table 1) [graph set S(6); Bernstein et al., 1995)]. In the crystal, the molecules form a helical chain through an intermolecular N1—H1N1···O1 hydrogen bond and are extended by an N4—H1N4···S1 hydrogen bond and a weak C3—H3A···Cg2 interaction into a three-dimensional network (Table 1, Fig. 2). Cg2 is the centroid of the C1–C6 ring.