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Acta Cryst. (2008). E64, o1890    [ doi:10.1107/S1600536808027682 ]

3-Cyclohexylsulfanyl-2-(4-methylphenyl)-5,7-dinitro-1H-indole

P. Ramesh, A. Subbiahpandi, R. Manikannan, S. Muthusubramanian and M. N. Ponnuswamy

Abstract top

In the title compound, C21H21N3O4S, the cyclohexane ring adopts a chair conformation. The nitro and methylphenyl groups are all coplanar with the indole ring system. Intramolecular N-H...O and C-H...S hydrogen bonds generate S(6) ring motifs. The molecules form R22(20) centrosymmetric dimers via intermolecular C-H...O hydrogen bonds. A short O...O contact [2.842 (2) Å] is observed in the dimer.

Comment top

Indole, being an integral part of many natural products of therapeutic importance, possesses potentially reactive sites for a variety of chemical reactions to generate molecular diversity (Farhanullah et al., 2004). The spiro-indole ring system is a frequently encountered structural motif in many biologically important and pharmacologically relevant alkaloids, e.g. vincrinstine, vinblastine and spirotypostatins (Cordell, 1981). Against this background and to ascertain the detailed information on its molecular conformation, the structure determination of the title compound was carried out.

The indole ring system is planar and the two nitro groups are coplanar with it. The cyclohexane ring adopts a chair conformation, with puckering parameters (Cremer & Pople, 1975) q2 = 0.010 (3) Å, q3 = 0.574 (3) Å and φ = 51 (18)°. The methylphenyl group is also coplanar with the indole ring system [dihedral angle 1.98 (9)°]. Each of the intramolecular N1—H1···O1 and C19—H19···S1 hydrogen bonds generates an S(6) ring motif (Bernstein et al. 1995).

In the crystal structure, molecules at (x, y, z) and (-x, 1-y, -z) are linked into a centrosymmetric R22(20) dimer by C22—H22···O2 hydrogen bonds. Within the dimer, a short O1···O1 contact [2.842 (2) Å] is observed.

Related literature top

For related literature, see: Cordell (1981); Farhanullah et al. (2004). For details of hydrogen-bond motifs, see: Bernstein et al. (1995). For puckering parameters, see: Cremer & Pople (1975).

Experimental top

A solution of 2-(cyclohexylsulfanyl)-1-(4-methylphenyl)-1-ethanone- N-(2,4-dinitrophenyl)hydrazone (0.001 mol) in dimethylforamide (5 ml) was allowed to cool in an ice bath with stirring. To this stirred solution, phosphorus oxychloride (0.008 mol) was added dropwise and the mixture was subjected to microwave irritation for 30–60 sec under 40% power with a pulse rate of 15 s. The reaction was monitored by TLC and after completion of the reaction, the reaction mixture was poured onto the crushed ice. The solid was filtered and washed with plenty of water. The different compounds present in the mixture were separated by column chromatography using petroleum ether and ethyl acetate mixture as eluent. The title compound was recrystallized in dichloromethane in 10% yield.

Refinement top

The N-bound H atom was located in a difference map and refined freely. C-bound H atoms were positioned geometrically (C-H = 0.93–0.98 Å) and allowed to ride on their parent atoms, with Uiso(H) = 1.5Ueq(C) for methyl H and 1.2Ueq(C) for other H atoms.

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: APEX2 (Bruker, 2004); data reduction: SAINT (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP3 (Farrugia, (1997)); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2003).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound, showing the atomic numbering and 50% probability displacement ellipsoids. Dashed lines indicate hydrogen bonds.
3-(Cyclohexylsulfanyl)-2-(4-methylphenyl)-5,7-dinitro-1H-indole top
Crystal data top
C21H21N3O4SZ = 2
Mr = 411.47F(000) = 432
Triclinic, P1Dx = 1.403 Mg m−3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.1009 (3) ÅCell parameters from 4582 reflections
b = 8.5237 (4) Åθ = 1.1–27.9°
c = 19.1522 (10) ŵ = 0.20 mm−1
α = 83.551 (3)°T = 293 K
β = 84.184 (3)°Block, colourless
γ = 81.157 (2)°0.30 × 0.20 × 0.16 mm
V = 974.30 (8) Å3
Data collection top
Bruker Kappa APEXII area-detector
diffractometer		4586 independent reflections
Radiation source: fine-focus sealed tube3424 reflections with I > 2σ(I)
graphiteRint = 0.036
ω and φ scansθmax = 27.9°, θmin = 1.1°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2001)		h = −7→8
Tmin = 0.953, Tmax = 0.969k = −11→11
21439 measured reflectionsl = −25→25
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.049Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.170H atoms treated by a mixture of independent and constrained refinement
S = 1.05 w = 1/[σ2(Fo2) + (0.0969P)2 + 0.289P]
where P = (Fo2 + 2Fc2)/3
4586 reflections(Δ/σ)max = 0.043
267 parametersΔρmax = 0.54 e Å−3
0 restraintsΔρmin = −0.31 e Å−3
Crystal data top
C21H21N3O4Sγ = 81.157 (2)°
Mr = 411.47V = 974.30 (8) Å3
Triclinic, P1Z = 2
a = 6.1009 (3) ÅMo Kα radiation
b = 8.5237 (4) ŵ = 0.20 mm−1
c = 19.1522 (10) ÅT = 293 K
α = 83.551 (3)°0.30 × 0.20 × 0.16 mm
β = 84.184 (3)°
Data collection top
Bruker Kappa APEXII area-detector
diffractometer		4586 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2001)		3424 reflections with I > 2σ(I)
Tmin = 0.953, Tmax = 0.969Rint = 0.036
21439 measured reflectionsθmax = 27.9°
Refinement top
R[F2 > 2σ(F2)] = 0.049H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.170Δρmax = 0.54 e Å−3
S = 1.05Δρmin = −0.31 e Å−3
4586 reflectionsAbsolute structure: ?
267 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.37693 (9)0.57116 (6)0.32294 (3)0.04681 (19)
O1−0.1393 (3)0.6217 (2)0.03507 (9)0.0579 (4)
O2−0.4543 (3)0.7672 (3)0.05530 (10)0.0796 (7)
O3−0.6221 (3)1.0174 (3)0.26759 (12)0.0825 (6)
O4−0.3829 (4)0.9921 (3)0.34373 (11)0.0856 (7)
N10.1558 (3)0.5458 (2)0.13764 (10)0.0390 (4)
H10.157 (4)0.513 (3)0.0989 (13)0.038 (6)*
C2−0.0106 (3)0.6496 (2)0.16537 (10)0.0372 (4)
C3−0.2102 (3)0.7282 (2)0.14075 (10)0.0394 (4)
C4−0.3508 (3)0.8295 (2)0.18166 (12)0.0442 (5)
H4−0.48430.88200.16570.053*
C5−0.2909 (4)0.8521 (2)0.24679 (11)0.0444 (5)
C6−0.0973 (4)0.7772 (2)0.27392 (11)0.0444 (5)
H6−0.06190.79560.31810.053*
C70.0435 (3)0.6731 (2)0.23291 (11)0.0395 (4)
C80.2509 (3)0.5755 (2)0.24487 (11)0.0403 (4)
C90.3180 (3)0.4986 (2)0.18474 (10)0.0383 (4)
N10−0.2723 (3)0.7050 (2)0.07243 (10)0.0481 (4)
N11−0.4432 (4)0.9614 (2)0.28929 (11)0.0577 (5)
C120.3142 (3)0.3850 (2)0.37195 (10)0.0419 (4)
H120.40200.29590.34890.050*
C130.0732 (4)0.3632 (3)0.37755 (15)0.0607 (6)
H13A0.02680.35860.33090.073*
H13B−0.01750.45310.39810.073*
C140.0406 (5)0.2098 (3)0.42342 (17)0.0743 (8)
H14A−0.11610.19820.42830.089*
H14B0.12190.11970.40070.089*
C150.1201 (6)0.2090 (4)0.49543 (16)0.0852 (10)
H15A0.02990.29330.51990.102*
H15B0.10240.10800.52270.102*
C160.3607 (6)0.2331 (4)0.49010 (16)0.0825 (9)
H16A0.45280.14290.47030.099*
H16B0.40520.23900.53680.099*
C170.3957 (5)0.3857 (3)0.44377 (13)0.0603 (6)
H17A0.31610.47680.46620.072*
H17B0.55280.39590.43850.072*
C180.5160 (3)0.3879 (2)0.16483 (11)0.0400 (4)
C190.6844 (4)0.3372 (3)0.20963 (12)0.0499 (5)
H190.67060.37380.25400.060*
C200.8705 (4)0.2343 (3)0.18971 (13)0.0530 (5)
H200.98010.20290.22090.064*
C210.8985 (3)0.1762 (3)0.12438 (13)0.0467 (5)
C220.7331 (4)0.2260 (3)0.07958 (14)0.0560 (6)
H220.74800.18900.03520.067*
C230.5454 (4)0.3299 (3)0.09918 (12)0.0518 (5)
H230.43670.36150.06770.062*
C241.1020 (4)0.0629 (3)0.10306 (16)0.0616 (6)
H24A1.07680.01500.06210.092*
H24B1.1321−0.01880.14100.092*
H24C1.22690.12020.09240.092*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0558 (3)0.0444 (3)0.0442 (3)−0.0110 (2)−0.0198 (2)−0.0025 (2)
O10.0530 (9)0.0732 (11)0.0447 (9)0.0112 (8)−0.0118 (7)−0.0152 (8)
O20.0584 (11)0.1142 (16)0.0618 (11)0.0323 (10)−0.0311 (9)−0.0277 (11)
O30.0664 (12)0.0930 (15)0.0803 (14)0.0314 (11)−0.0120 (10)−0.0287 (11)
O40.1046 (16)0.0878 (14)0.0585 (12)0.0318 (12)−0.0201 (11)−0.0321 (11)
N10.0373 (8)0.0439 (9)0.0351 (9)−0.0011 (7)−0.0091 (7)−0.0024 (7)
C20.0382 (9)0.0360 (9)0.0368 (10)−0.0057 (7)−0.0047 (7)0.0006 (7)
C30.0396 (10)0.0408 (10)0.0368 (10)−0.0033 (8)−0.0070 (8)0.0009 (8)
C40.0414 (10)0.0416 (10)0.0474 (12)−0.0011 (8)−0.0062 (8)0.0013 (9)
C50.0493 (11)0.0386 (10)0.0427 (11)−0.0002 (8)−0.0021 (9)−0.0028 (8)
C60.0542 (12)0.0401 (10)0.0388 (11)−0.0042 (9)−0.0080 (9)−0.0026 (8)
C70.0435 (10)0.0369 (10)0.0385 (10)−0.0079 (8)−0.0080 (8)0.0020 (8)
C80.0425 (10)0.0386 (10)0.0406 (11)−0.0074 (8)−0.0103 (8)0.0012 (8)
C90.0364 (9)0.0395 (10)0.0394 (10)−0.0065 (7)−0.0103 (7)0.0017 (8)
N100.0442 (9)0.0563 (11)0.0421 (10)0.0028 (8)−0.0110 (7)−0.0045 (8)
N110.0683 (13)0.0500 (11)0.0498 (12)0.0095 (9)−0.0056 (9)−0.0080 (9)
C120.0511 (11)0.0393 (10)0.0353 (10)−0.0009 (8)−0.0099 (8)−0.0050 (8)
C130.0592 (14)0.0618 (15)0.0637 (16)−0.0165 (12)−0.0139 (11)0.0015 (12)
C140.0739 (18)0.0625 (16)0.086 (2)−0.0213 (14)0.0013 (15)0.0030 (15)
C150.123 (3)0.0659 (18)0.0593 (18)−0.0139 (18)0.0167 (18)0.0067 (14)
C160.117 (3)0.0775 (19)0.0515 (16)−0.0137 (18)−0.0255 (16)0.0155 (14)
C170.0774 (17)0.0627 (14)0.0435 (13)−0.0102 (12)−0.0243 (11)0.0011 (11)
C180.0365 (9)0.0397 (10)0.0435 (11)−0.0053 (8)−0.0088 (8)0.0022 (8)
C190.0439 (11)0.0604 (13)0.0445 (12)−0.0005 (10)−0.0111 (9)−0.0040 (10)
C200.0392 (11)0.0626 (14)0.0554 (13)−0.0009 (9)−0.0161 (9)0.0039 (11)
C210.0387 (10)0.0424 (11)0.0575 (13)−0.0035 (8)−0.0095 (9)0.0031 (9)
C220.0504 (12)0.0610 (14)0.0555 (14)0.0068 (10)−0.0132 (10)−0.0142 (11)
C230.0463 (11)0.0566 (13)0.0514 (13)0.0081 (9)−0.0184 (9)−0.0093 (10)
C240.0446 (12)0.0570 (14)0.0777 (18)0.0057 (10)−0.0055 (11)−0.0003 (12)
Geometric parameters (Å, °) top
S1—C81.744 (2)C13—H13B0.97
S1—C121.823 (2)C14—C151.507 (4)
O1—N101.223 (2)C14—H14A0.97
O2—N101.215 (2)C14—H14B0.97
O3—N111.216 (3)C15—C161.505 (5)
O4—N111.208 (3)C15—H15A0.97
N1—C21.347 (2)C15—H15B0.97
N1—C91.390 (2)C16—C171.521 (4)
N1—H10.82 (2)C16—H16A0.97
C2—C31.396 (3)C16—H16B0.97
C2—C71.409 (3)C17—H17A0.97
C3—C41.373 (3)C17—H17B0.97
C3—N101.441 (3)C18—C231.387 (3)
C4—C51.377 (3)C18—C191.392 (3)
C4—H40.93C19—C201.373 (3)
C5—C61.375 (3)C19—H190.93
C5—N111.464 (3)C20—C211.382 (4)
C6—C71.388 (3)C20—H200.93
C6—H60.93C21—C221.377 (3)
C7—C81.427 (3)C21—C241.502 (3)
C8—C91.384 (3)C22—C231.383 (3)
C9—C181.460 (3)C22—H220.93
C12—C131.502 (3)C23—H230.93
C12—C171.510 (3)C24—H24A0.96
C12—H120.98C24—H24B0.96
C13—C141.519 (4)C24—H24C0.96
C13—H13A0.97
C8—S1—C12103.22 (9)C15—C14—H14A109.3
C2—N1—C9110.57 (17)C13—C14—H14A109.3
C2—N1—H1124.1 (16)C15—C14—H14B109.3
C9—N1—H1125.3 (16)C13—C14—H14B109.3
N1—C2—C3133.05 (19)H14A—C14—H14B108.0
N1—C2—C7107.39 (17)C16—C15—C14111.1 (2)
C3—C2—C7119.55 (18)C16—C15—H15A109.4
C4—C3—C2120.10 (19)C14—C15—H15A109.4
C4—C3—N10118.89 (18)C16—C15—H15B109.4
C2—C3—N10121.01 (18)C14—C15—H15B109.4
C3—C4—C5118.86 (19)H15A—C15—H15B108.0
C3—C4—H4120.6C15—C16—C17110.5 (2)
C5—C4—H4120.6C15—C16—H16A109.5
C6—C5—C4123.55 (19)C17—C16—H16A109.5
C6—C5—N11118.6 (2)C15—C16—H16B109.5
C4—C5—N11117.81 (19)C17—C16—H16B109.5
C5—C6—C7117.57 (19)H16A—C16—H16B108.1
C5—C6—H6121.2C12—C17—C16111.0 (2)
C7—C6—H6121.2C12—C17—H17A109.4
C6—C7—C2120.35 (18)C16—C17—H17A109.4
C6—C7—C8132.23 (19)C12—C17—H17B109.4
C2—C7—C8107.42 (17)C16—C17—H17B109.4
C9—C8—C7106.84 (17)H17A—C17—H17B108.0
C9—C8—S1131.38 (15)C23—C18—C19116.87 (19)
C7—C8—S1121.76 (16)C23—C18—C9120.83 (18)
C8—C9—N1107.76 (17)C19—C18—C9122.3 (2)
C8—C9—C18132.49 (18)C20—C19—C18121.5 (2)
N1—C9—C18119.74 (18)C20—C19—H19119.3
O2—N10—O1123.43 (19)C18—C19—H19119.3
O2—N10—C3118.61 (18)C19—C20—C21121.4 (2)
O1—N10—C3117.96 (17)C19—C20—H20119.3
O4—N11—O3123.6 (2)C21—C20—H20119.3
O4—N11—C5118.0 (2)C22—C21—C20117.5 (2)
O3—N11—C5118.3 (2)C22—C21—C24121.3 (2)
C13—C12—C17111.4 (2)C20—C21—C24121.2 (2)
C13—C12—S1114.70 (15)C21—C22—C23121.4 (2)
C17—C12—S1105.15 (15)C21—C22—H22119.3
C13—C12—H12108.5C23—C22—H22119.3
C17—C12—H12108.5C22—C23—C18121.3 (2)
S1—C12—H12108.5C22—C23—H23119.3
C12—C13—C14109.6 (2)C18—C23—H23119.3
C12—C13—H13A109.8C21—C24—H24A109.5
C14—C13—H13A109.8C21—C24—H24B109.5
C12—C13—H13B109.8H24A—C24—H24B109.5
C14—C13—H13B109.8C21—C24—H24C109.5
H13A—C13—H13B108.2H24A—C24—H24C109.5
C15—C14—C13111.5 (2)H24B—C24—H24C109.5
C9—N1—C2—C3−178.5 (2)C2—C3—N10—O2175.0 (2)
C9—N1—C2—C70.4 (2)C4—C3—N10—O1175.8 (2)
N1—C2—C3—C4179.9 (2)C2—C3—N10—O1−4.1 (3)
C7—C2—C3—C41.1 (3)C4—C3—N10—O1175.8 (2)
N1—C2—C3—N10−0.2 (3)C2—C3—N10—O1−4.1 (3)
C7—C2—C3—N10−179.03 (18)C6—C5—N11—O46.6 (3)
C2—C3—C4—C50.2 (3)C4—C5—N11—O4−173.8 (2)
N10—C3—C4—C5−179.71 (19)C6—C5—N11—O3−174.2 (2)
C3—C4—C5—C6−0.6 (3)C4—C5—N11—O35.4 (3)
C3—C4—C5—N11179.72 (19)C8—S1—C12—C13−50.48 (19)
C4—C5—C6—C7−0.2 (3)C8—S1—C12—C17−173.23 (16)
N11—C5—C6—C7179.44 (19)C17—C12—C13—C14−57.0 (3)
C5—C6—C7—C21.5 (3)S1—C12—C13—C14−176.27 (18)
C5—C6—C7—C8−178.8 (2)C12—C13—C14—C1556.9 (3)
N1—C2—C7—C6178.97 (18)C13—C14—C15—C16−56.9 (3)
C3—C2—C7—C6−1.9 (3)C14—C15—C16—C1755.5 (4)
N1—C2—C7—C8−0.8 (2)C13—C12—C17—C1657.0 (3)
C3—C2—C7—C8178.26 (17)S1—C12—C17—C16−178.1 (2)
C6—C7—C8—C9−178.8 (2)C15—C16—C17—C12−55.6 (3)
C2—C7—C8—C91.0 (2)C8—C9—C18—C23−178.5 (2)
C6—C7—C8—S1−0.1 (3)N1—C9—C18—C230.5 (3)
C2—C7—C8—S1179.67 (14)C8—C9—C18—C190.7 (4)
C12—S1—C8—C9−79.3 (2)N1—C9—C18—C19179.66 (19)
C12—S1—C8—C7102.35 (17)C23—C18—C19—C20−0.1 (3)
C7—C8—C9—N1−0.7 (2)C9—C18—C19—C20−179.3 (2)
S1—C8—C9—N1−179.26 (15)C18—C19—C20—C21−0.2 (4)
C7—C8—C9—C18178.3 (2)C19—C20—C21—C220.3 (4)
S1—C8—C9—C18−0.2 (4)C19—C20—C21—C24−179.7 (2)
C2—N1—C9—C80.2 (2)C20—C21—C22—C23−0.2 (4)
C2—N1—C9—C18−178.97 (17)C24—C21—C22—C23179.8 (2)
O1—O1—N10—O20.00 (4)C21—C22—C23—C18−0.1 (4)
O1—O1—N10—C30.00 (14)C19—C18—C23—C220.2 (3)
C4—C3—N10—O2−5.1 (3)C9—C18—C23—C22179.5 (2)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O10.82 (2)2.30 (2)2.755 (2)115 (2)
C19—H19···S10.932.623.347 (2)135
C22—H22···O2i0.932.583.224 (3)127
Symmetry codes: (i) −x, −y+1, −z.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O10.82 (2)2.30 (2)2.755 (2)115 (2)
C19—H19···S10.932.623.347 (2)135
C22—H22···O2i0.932.583.224 (3)127
Symmetry codes: (i) −x, −y+1, −z.
Acknowledgements top

PR thanks Dr Babu Varghese, SAIF, IIT-Madras, Chennai, India, for his help with the data collection.

references
References top

Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N. L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.

Bruker (2004). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.

Cordell, G. (1981). Introduction to Alkaloids: A Biogenic Approach. New York: Wiley International.

Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354–1358.

Farhanullah, S. A., Maulik, P. R. & Ji Ram, V. (2004). Tetrahedron Lett. 45, 5099–5102

Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.

Sheldrick, G. M. (2001). SADABS. University of Göttingen, Germany.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13.