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Acta Crystallographica Section E: Structure Reports Online logoLink to Acta Crystallographica Section E: Structure Reports Online
. 2013 May 11;69(Pt 6):o856. doi: 10.1107/S1600536813011768

Methyl 2-(5-chloro-1-methyl-2-oxo-2,3-di­hydro-1H-indol-3-ylidene)acetate

Piskala Subburaman Kannan a, PanneerSelvam Yuvaraj b, Karthikeyan Manivannan b, Boreddy S R Reddy b, A SubbiahPandi c,*
PMCID: PMC3684938  PMID: 23795040

Abstract

The title compound, C12H10ClNO3, the indoline ring system is essentially planar, with a maximum deviation of 0.009 Å for the N atom. The indoline ring and acetate group are essentially coplanar, with a maximum deviation of 0.086 Å for the O atom. The mean plane through the methoxy­carbonyl­methyl group forms a dihedral angle of 3.68 (5)° with the plane of the indoline ring system. The mol­ecular structure is stabilized by an intra­molecular C—H⋯O hydrogen-bond inter­action. In the crystal, π–π stacking inter­actions [centroid–centroid distance = 3.7677 (8) Å] occur between benzene rings, forming a chain running along the c-axis direction.

Related literature  

For the biological activity of indole derivatives, see: Chai et al. (2006 ▶); Nieto et al. (2005 ▶); Singh et al. (2000 ▶); Andreani et al. (2001 ▶); Quetin-Leclercq (1994 ▶); Mukhopadhyay et al. (1981 ▶); Taylor et al. (1999 ▶). For closely related structures, see: Hu et al. (2011 ▶); Han & Luo (2012 ▶); Deng (2011 ▶). For puckering parameters, see: Cremer & Pople (1975 ▶).graphic file with name e-69-0o856-scheme1.jpg

Experimental  

Crystal data  

  • C12H10ClNO3

  • M r = 251.66

  • Monoclinic, Inline graphic

  • a = 8.4709 (7) Å

  • b = 17.1658 (13) Å

  • c = 7.9481 (6) Å

  • β = 107.228 (4)°

  • V = 1103.88 (15) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.34 mm−1

  • T = 293 K

  • 0.30 × 0.25 × 0.20 mm

Data collection  

  • Bruker SMART APEXII area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2008 ▶) T min = 0.903, T max = 0.934

  • 10447 measured reflections

  • 2815 independent reflections

  • 2410 reflections with I > 2σ(I)

  • R int = 0.031

Refinement  

  • R[F 2 > 2σ(F 2)] = 0.038

  • wR(F 2) = 0.138

  • S = 1.13

  • 2815 reflections

  • 157 parameters

  • H-atom parameters constrained

  • Δρmax = 0.34 e Å−3

  • Δρmin = −0.21 e Å−3

Data collection: APEX2 (Bruker, 2008 ▶); cell refinement: SAINT (Bruker, 2008 ▶); 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 for Windows (Farrugia, 2012 ▶); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009 ▶).

Supplementary Material

Click here for additional data file. (16.8KB, cif)

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536813011768/bx2438sup1.cif

e-69-0o856-sup1.cif (16.8KB, cif)
Click here for additional data file. (135.4KB, hkl)

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813011768/bx2438Isup2.hkl

e-69-0o856-Isup2.hkl (135.4KB, hkl)
Click here for additional data file. (4.5KB, cml)

Supplementary material file. DOI: 10.1107/S1600536813011768/bx2438Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C6—H6⋯O2 0.93 2.30 3.0181 (17) 134
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Acknowledgments

The authors thank the TBI X-ray facility, CAS in Crystallography and BioPhysics, University of Madras, Chennai, India, for the data collection.

supplementary crystallographic information

Comment

Indole derivatives exhibit antihepatitis B virus (Chai et al., 2006) and antibacterial (Nieto et al., 2005) activities. Indole derivatives have been found to exhibit antibacterial, antifungal (Singh et al., 2000) and antitumour activities (Andreani et al., 2001). Some of the indole alkaloids extracted from plants possess interesting cytotoxic, antitumour or antiparasitic properties (Quetin-Leclercq, 1994; Mukhopadhyay et al., 1981). Pyrido[1,2-a]indole derivatives have been identified as potent inhibitors of human immunodeficiency virus type 1 (Taylor et al., 1999).

In the title compound, C12H10Cl1N1O3,Figure 1 the indole ring system [C1-C8/N1] is essentially co-planar, with maxmium deviations of -0.009 Å for N1 atom. The indole ring and acetate group systems are essentially co-planar, with maxmium deviations of 0.086 Å for O2 atom. The mean plane through the methyl 4-oxobutanoate(acetate) group forms a dihedral angle of 3.68 (5)° with the plane of the indole ring system.

The geometric parameters of the title molecule (Fig. 1) agree well with the reported similar structures (Han et al., 2012). The sum of the angles at N1 [359.98 (1)°] of the pyrrolidine rings are in accordance with sp2 hybridizations.The crystal structure is stabilized by intramolecular C-H···O hydrogen bond interaction and π -π stacking interactions [centroid–centroid distance = 3.7677 (8) Å] between benzene rings [Cg1–Cg1i (Cg1:C1–C6) (i):symmetry code: -x,1-y,1-z]

Experimental

To a mixture of 1eq of (E)-methyl 2-(5-chloro-1-methyl-2-oxoindolin- 3-ylidene) acetate, 1eq of isatin and 1.5eq of sarcosine were dissolved in acetonitrile. This reaction mixture refluxed at 80°C for 8hours. Completion of reaction monitor by Thin layar chromatography. The reaction mixture was extracted with ethyl acetate and water. The product was dried and purified by coloumn chromatography using ethyl acetate and hexane (1:9) as an elutent to afford pure Dispiro oxindole. Yield (90%). Single crystals suitable for X-ray diffraction were obtained by slow evaporation of a solution of the title compound in ethyl acetate at room temperature.

Refinement

All H atoms were fixed geometrically and allowed to ride on their parent C atoms, with C—H distances fixed in the range 0.93–0.97 Å with Uiso(H) = 1.5Ueq(C) for methyl H 1.2Ueq(C) for other H atoms. The positions of methyl hydrogens were optimized rotationally.

Figures

Fig. 1.

Fig. 1.

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The structure of showing the atom-numbering scheme. The displacement ellipsoids are drawn at the 30% probability level.

Crystal data

C12H10ClNO3 F(000) = 520
Mr = 251.66 Dx = 1.514 Mg m−3
Monoclinic, P21/c Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc Cell parameters from 2857 reflections
a = 8.4709 (7) Å θ = 2.4–28.6°
b = 17.1658 (13) Å µ = 0.34 mm−1
c = 7.9481 (6) Å T = 293 K
β = 107.228 (4)° Block, colourless
V = 1103.88 (15) Å3 0.30 × 0.25 × 0.20 mm
Z = 4
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Data collection

Bruker SMART APEXII area-detector diffractometer 2815 independent reflections
Radiation source: fine-focus sealed tube 2410 reflections with I > 2σ(I)
Graphite monochromator Rint = 0.031
ω and φ scans θmax = 28.6°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2008) h = −11→11
Tmin = 0.903, Tmax = 0.934 k = −23→23
10447 measured reflections l = −10→10
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Refinement

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)] = 0.038 H-atom parameters constrained
wR(F2) = 0.138 w = 1/[σ2(Fo2) + (0.1P)2] where P = (Fo2 + 2Fc2)/3
S = 1.13 (Δ/σ)max < 0.001
2815 reflections Δρmax = 0.34 e Å−3
157 parameters Δρmin = −0.21 e Å−3
0 restraints Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methods Extinction coefficient: 0.008 (3)
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Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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.
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Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq
C1 0.18640 (15) 0.52152 (8) 0.41988 (16) 0.0337 (3)
C2 0.22645 (18) 0.44379 (9) 0.44263 (18) 0.0400 (3)
H2 0.3224 0.4283 0.5281 0.048*
C3 0.12324 (18) 0.38846 (8) 0.33765 (19) 0.0396 (3)
H3 0.1487 0.3357 0.3514 0.047*
C4 −0.01720 (16) 0.41357 (7) 0.21330 (17) 0.0321 (3)
C5 −0.05973 (15) 0.49301 (7) 0.18943 (15) 0.0287 (3)
C6 0.04383 (15) 0.54819 (7) 0.29523 (15) 0.0317 (3)
H6 0.0187 0.6010 0.2831 0.038*
C7 −0.21570 (16) 0.49743 (7) 0.04971 (15) 0.0306 (3)
C8 −0.25984 (18) 0.41402 (7) −0.00755 (18) 0.0344 (3)
C9 −0.1339 (2) 0.28462 (9) 0.0829 (2) 0.0509 (4)
H9A −0.2332 0.2668 −0.0022 0.076*
H9B −0.1267 0.2625 0.1960 0.076*
H9C −0.0398 0.2687 0.0476 0.076*
C10 −0.31915 (15) 0.55312 (8) −0.03603 (16) 0.0349 (3)
H10 −0.4126 0.5363 −0.1232 0.042*
C11 −0.30207 (15) 0.63753 (7) −0.00835 (16) 0.0341 (3)
C12 −0.4227 (2) 0.75770 (8) −0.1167 (2) 0.0499 (4)
H12A −0.4311 0.7724 −0.0031 0.075*
H12B −0.5155 0.7782 −0.2068 0.075*
H12C −0.3222 0.7783 −0.1314 0.075*
N1 −0.13690 (14) 0.36835 (6) 0.09414 (14) 0.0370 (3)
O1 −0.38178 (14) 0.39168 (7) −0.12194 (15) 0.0484 (3)
O2 −0.19597 (13) 0.67151 (6) 0.10265 (16) 0.0503 (3)
O3 −0.42172 (12) 0.67452 (6) −0.12966 (13) 0.0426 (3)
Cl1 0.31706 (4) 0.58922 (2) 0.55565 (4) 0.04557 (17)
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Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
C1 0.0283 (6) 0.0363 (7) 0.0319 (6) −0.0017 (5) 0.0015 (5) 0.0008 (4)
C2 0.0347 (7) 0.0386 (7) 0.0406 (6) 0.0058 (6) 0.0016 (5) 0.0059 (5)
C3 0.0409 (7) 0.0302 (6) 0.0437 (7) 0.0054 (5) 0.0065 (6) 0.0047 (5)
C4 0.0331 (7) 0.0284 (6) 0.0340 (6) −0.0013 (4) 0.0084 (5) −0.0007 (4)
C5 0.0277 (6) 0.0265 (6) 0.0306 (5) 0.0001 (4) 0.0065 (4) −0.0003 (4)
C6 0.0285 (6) 0.0303 (6) 0.0324 (6) −0.0003 (5) 0.0031 (4) −0.0001 (4)
C7 0.0289 (6) 0.0299 (6) 0.0307 (6) −0.0030 (4) 0.0052 (4) −0.0027 (4)
C8 0.0372 (7) 0.0298 (6) 0.0346 (6) −0.0055 (5) 0.0084 (5) −0.0045 (4)
C9 0.0618 (10) 0.0273 (7) 0.0595 (9) −0.0019 (6) 0.0116 (7) −0.0034 (6)
C10 0.0298 (6) 0.0344 (7) 0.0346 (6) −0.0026 (5) 0.0003 (5) −0.0025 (5)
C11 0.0298 (6) 0.0345 (7) 0.0332 (6) 0.0040 (5) 0.0021 (4) 0.0012 (5)
C12 0.0546 (9) 0.0351 (8) 0.0501 (8) 0.0081 (6) 0.0003 (7) 0.0075 (6)
N1 0.0406 (6) 0.0272 (6) 0.0399 (6) −0.0034 (4) 0.0068 (5) −0.0045 (4)
O1 0.0443 (6) 0.0404 (5) 0.0503 (6) −0.0094 (4) −0.0018 (5) −0.0099 (4)
O2 0.0423 (6) 0.0347 (5) 0.0547 (6) 0.0022 (4) −0.0151 (4) −0.0065 (4)
O3 0.0408 (6) 0.0336 (5) 0.0406 (5) 0.0029 (4) −0.0074 (4) 0.0021 (4)
Cl1 0.0370 (2) 0.0450 (3) 0.0434 (2) −0.00716 (13) −0.00546 (16) −0.00314 (13)
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Geometric parameters (Å, º)

C1—C2 1.3753 (19) C8—O1 1.2183 (18)
C1—C6 1.3932 (16) C8—N1 1.3615 (18)
C1—Cl1 1.7415 (13) C9—N1 1.4408 (18)
C2—C3 1.389 (2) C9—H9A 0.9600
C2—H2 0.9300 C9—H9B 0.9600
C3—C4 1.3717 (18) C9—H9C 0.9600
C3—H3 0.9300 C10—C11 1.4661 (19)
C4—N1 1.3995 (16) C10—H10 0.9300
C4—C5 1.4089 (17) C11—O2 1.2070 (16)
C5—C6 1.3917 (16) C11—O3 1.3346 (15)
C5—C7 1.4545 (17) C12—O3 1.4320 (16)
C6—H6 0.9300 C12—H12A 0.9600
C7—C10 1.3389 (19) C12—H12B 0.9600
C7—C8 1.5153 (17) C12—H12C 0.9600
C2—C1—C6 122.71 (12) N1—C8—C7 106.77 (11)
C2—C1—Cl1 118.64 (10) N1—C9—H9A 109.5
C6—C1—Cl1 118.64 (10) N1—C9—H9B 109.5
C1—C2—C3 119.83 (13) H9A—C9—H9B 109.5
C1—C2—H2 120.1 N1—C9—H9C 109.5
C3—C2—H2 120.1 H9A—C9—H9C 109.5
C4—C3—C2 118.36 (12) H9B—C9—H9C 109.5
C4—C3—H3 120.8 C7—C10—C11 127.50 (11)
C2—C3—H3 120.8 C7—C10—H10 116.3
C3—C4—N1 127.82 (11) C11—C10—H10 116.3
C3—C4—C5 122.27 (12) O2—C11—O3 122.67 (12)
N1—C4—C5 109.92 (11) O2—C11—C10 127.33 (11)
C6—C5—C4 119.15 (11) O3—C11—C10 109.98 (11)
C6—C5—C7 133.90 (11) O3—C12—H12A 109.5
C4—C5—C7 106.94 (11) O3—C12—H12B 109.5
C5—C6—C1 117.68 (11) H12A—C12—H12B 109.5
C5—C6—H6 121.2 O3—C12—H12C 109.5
C1—C6—H6 121.2 H12A—C12—H12C 109.5
C10—C7—C5 137.34 (12) H12B—C12—H12C 109.5
C10—C7—C8 117.12 (12) C8—N1—C4 110.84 (10)
C5—C7—C8 105.52 (11) C8—N1—C9 124.20 (12)
O1—C8—N1 126.31 (12) C4—N1—C9 124.94 (12)
O1—C8—C7 126.92 (13) C11—O3—C12 116.21 (11)
C6—C1—C2—C3 0.6 (2) C5—C7—C8—O1 179.90 (14)
Cl1—C1—C2—C3 179.16 (10) C10—C7—C8—N1 178.76 (11)
C1—C2—C3—C4 −0.1 (2) C5—C7—C8—N1 0.12 (13)
C2—C3—C4—N1 179.68 (12) C5—C7—C10—C11 −0.4 (2)
C2—C3—C4—C5 −0.2 (2) C8—C7—C10—C11 −178.48 (12)
C3—C4—C5—C6 0.01 (19) C7—C10—C11—O2 −4.1 (2)
N1—C4—C5—C6 −179.87 (10) C7—C10—C11—O3 174.29 (13)
C3—C4—C5—C7 −179.19 (12) O1—C8—N1—C4 −179.33 (13)
N1—C4—C5—C7 0.93 (13) C7—C8—N1—C4 0.45 (14)
C4—C5—C6—C1 0.42 (17) O1—C8—N1—C9 −0.9 (2)
C7—C5—C6—C1 179.36 (11) C7—C8—N1—C9 178.84 (12)
C2—C1—C6—C5 −0.71 (19) C3—C4—N1—C8 179.24 (13)
Cl1—C1—C6—C5 −179.32 (9) C5—C4—N1—C8 −0.88 (14)
C6—C5—C7—C10 2.1 (2) C3—C4—N1—C9 0.9 (2)
C4—C5—C7—C10 −178.84 (15) C5—C4—N1—C9 −179.26 (13)
C6—C5—C7—C8 −179.66 (13) O2—C11—O3—C12 −2.8 (2)
C4—C5—C7—C8 −0.63 (12) C10—C11—O3—C12 178.73 (12)
C10—C7—C8—O1 −1.5 (2)
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Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
C6—H6···O2 0.93 2.30 3.0181 (17) 134
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Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BX2438).

References

  1. Andreani, A., Granaiola, M., Leoni, A., Locatelli, A., Morigi, R., Rambaldi, M., Giorgi, G., Salvini, L. & Garaliene, V. (2001). Anticancer Drug Des. 16, 167–174. [PubMed]
  2. Bruker (2008). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
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  4. Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354–1358.
  5. Deng, Q. (2011). Acta Cryst. E67, o897. [DOI] [PMC free article] [PubMed]
  6. Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854.
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  10. Nieto, M. J., Alovero, F. L., Manzo, R. H. & Mazzieri, M. R. (2005). Eur. J. Med. Chem. 40, 361–369. [DOI] [PubMed]
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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Click here for additional data file. (16.8KB, cif)

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536813011768/bx2438sup1.cif

e-69-0o856-sup1.cif (16.8KB, cif)
Click here for additional data file. (135.4KB, hkl)

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813011768/bx2438Isup2.hkl

e-69-0o856-Isup2.hkl (135.4KB, hkl)
Click here for additional data file. (4.5KB, cml)

Supplementary material file. DOI: 10.1107/S1600536813011768/bx2438Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography

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