Crystal structure of methyl (E)-2-(1-methyl-2-oxoindolin-3-yl­idene)acetate

Savithri, M.P.; Yuvaraj, P.S.; Reddy, B.S.R.; Raja, R.; SubbiahPandi, A.

doi:10.1107/S2056989015003217

organic compounds

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Volume 71| Part 3| March 2015| Pages o188-o189

doi:10.1107/S2056989015003217

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Crystal structure of methyl (E)-2-(1-methyl-2-oxoindolin-3-ylidene)acetate

M. P. Savithri,^a P. S. Yuvaraj,^b B. S. R. Reddy,^b R. Raja ^c and A. SubbiahPandi ^c ^*

^aDepartment of Physics, Queen Mary's College (Autonomous), Chennai 600 004, India, ^bUniversity of Madras, Industrial Chemistry Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India, and ^cDepartment of Physics, Presidency College (Autonomous), Chennai 600 005, India
^*Correspondence e-mail: aspandian59@gmail.com

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 11 February 2015; accepted 15 February 2015; online 21 February 2015)

The title compound, C₁₂H₁₁NO₃, is essentially planar, with the mean plane of the acetate side chain [–C—C(=O)—O—C] being inclined to the mean plane of the indole ring system by 12.49 (7)°. The five- and six-membered rings of the indole group are almost coplanar, making a dihedral angle of 1.76 (8)°. The conformation about the C=C bond is E and there is an intramolecular C—H⋯O hydrogen bond present. In the crystal, molecules are linked by pairs of C—H⋯O hydrogen bonds forming inversion dimers, with an R₂²(16) ring motif. The dimers are linked by a second pair of C—H⋯O hydrogen bonds, enclosing R₂²(16) ring motifs, forming ribbons lying parallel to (-114). The ribbons are linked via C—H⋯π interactions, forming a three-dimensional structure.

Keywords: crystal structure; indole; 3-substituted indoles; C—H⋯O hydrogen bonds; C—H⋯π interactions; π–π stacking interactions.

CCDC reference: 1049502

1. Related literature

For general background to the synthesis of 3-substituted indole derivatives as precursors of potent anti-inflammatory and analgesic agents, see: Radwan et al. (2007 ). For related structures, see: Bhella et al. (2009 ); Hou & Li (2011 ).

2. Experimental

2.1. Crystal data

C₁₂H₁₁NO₃
M_r = 217.22
Monoclinic, P 2₁ /n
a = 11.6814 (7) Å
b = 5.6106 (4) Å
c = 16.5299 (11) Å
β = 108.713 (2)°
V = 1026.09 (12) Å³
Z = 4
Mo Kα radiation
μ = 0.10 mm⁻¹
T = 293 K
0.35 × 0.30 × 0.30 mm

2.2. Data collection

Bruker Kappa APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2004 ) T_min = 0.948, T_max = 0.955
14793 measured reflections
1809 independent reflections
1528 reflections with I > 2σ(I)
R_int = 0.023

2.3. Refinement

R[F² > 2σ(F²)] = 0.033
wR(F²) = 0.093
S = 1.05
1809 reflections
148 parameters
H-atom parameters constrained
Δρ_max = 0.18 e Å⁻³
Δρ_min = −0.13 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of ring C6–C11.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C8—H8⋯O2	0.93	2.29	2.988 (2)	132
C9—H9⋯O2ⁱ	0.93	2.50	3.387 (2)	159
C1—H1A⋯O3ⁱⁱ	0.96	2.57	3.526 (2)	175
C11—H11⋯Cgⁱⁱⁱ	0.93	2.83	3.558 (2)	135
Symmetry codes: (i) -x+2, -y, -z+1; (ii) -x+1, -y-1, -z+1; (iii) $[-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: APEX2 (Bruker, 2004); cell refinement: APEX2 and SAINT (Bruker, 2004); data reduction: SAINT and XPREP (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015 ); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ), PLATON (Spek, 2009 ) and Mercury (Macrae et al., 2008 ); software used to prepare material for publication: SHELXL2014 and PLATON.

Supporting information

CCDC reference: 1049502

Crystal structure: contains datablocks global, I. DOI: 10.1107/S2056989015003217/su5085sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989015003217/su5085Isup2.hkl

Supporting information file. DOI: 10.1107/S2056989015003217/su5085Isup3.cml

checkCIF report

Comment top

The indole skeleton is a key component of many biologically active compounds and 3-substituted indole derivatives have been evaluated as precursors of potent anti-inflammatory and analgesic agents (Radwan et al., 2007). Herein, we report on the synthesis and crystal structure of the title compound.

In the title compound (Fig. 1), all bond lengths and angles are normal and comparable with those reported for similar structures (Bhella et al., 2009; Hou & Li, 2011). The five-membered ring (N1/C4-C7) and the six-membered ring (C6-C11) of the the indole group are almost co-planar, with a dihedral angle of 1.76 (8)°.

In the crystal, molecules are linked by pairs of C-H···O hydrogen bonds forming inversion dimers, with an R²₂(16) ring motif (Table 1 and Fig. 2). The dimers are linked by a second pair of C-H···O hydrogen bonds, enclosing R²₂(16) ring motifs, forming ribbons lying parallel to (114); see Table 1 and Fig. 2. The ribbons are linked via C-H···π interactions (Table 1 and Fig. 3) forming a three-dimensional structure.

Related literature top

For general background to the synthesis of 3-substituted indole derivatives as precursors of potent anti-inflammatory and analgesic agents, see: Radwan et al. (2007). For related structures, see: Bhella et al. (2009); Hou & Li (2011).

Experimental top

A mixture of isatin and 1.5 eq of methylbromoacetate were dissolved in DMF with potassium tert-butoxide as catalyst. Th reaction mixture was refluxed at 353 K for 2 h. On completion of the reaction, monitored by thin layer chromatography, the mixture was extracted with ethyl acetate and water. The product was dried and purified by column chromatography using ethyl acetate and hexane (1:9) as an elutent to afford the title compound (yield: 90 %). Colourless block-like crystals were obtained by slow evaporation of a solution in ethyl acetate at room temperature.

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: APEX2 and SAINT (Bruker, 2004); data reduction: SAINT and XPREP (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012), PLATON (Spek, 2009) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015) and PLATON (Spek, 2009).

Figures top

	Fig. 1. The molecular structure of the title compound, with atom labelling. Displacement ellipsoids are drawn at the 30% probability level.
	Fig. 2. A partial view along the b axis of the crystal packing of the title compound. The hydrogen bonds are shown as dashed lines (see Table 1 for details; H atoms not involved in hydrogen bonding have been omitted for clarity).
	Fig. 3. The crystal packing of the title compound viewed along the b axis. The hydrogen bonds are shown as dashed lines (see Table 1 for details; H atoms not involved in hydrogen bonding have been omitted for clarity).

Methyl (E)-2-(1-methyl-2-oxoindolin-3-ylidene)acetate top

Crystal data top

C₁₂H₁₁NO₃	F(000) = 456
M_r = 217.22	D_x = 1.406 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 1809 reflections
a = 11.6814 (7) Å	θ = 2.6–25.0°
b = 5.6106 (4) Å	µ = 0.10 mm⁻¹
c = 16.5299 (11) Å	T = 293 K
β = 108.713 (2)°	Block, colourless
V = 1026.09 (12) Å³	0.35 × 0.30 × 0.30 mm
Z = 4

Data collection top

Bruker Kappa APEXII CCD diffractometer	1809 independent reflections
Radiation source: fine-focus sealed tube	1528 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.023
ω and ϕ scans	θ_max = 25.0°, θ_min = 2.6°
Absorption correction: multi-scan (SADABS; Bruker, 2004)	h = −13→13
T_min = 0.948, T_max = 0.955	k = −6→6
14793 measured reflections	l = −19→19

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.033	w = 1/[σ²(F_o²) + (0.0431P)² + 0.3282P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.093	(Δ/σ)_max < 0.001
S = 1.05	Δρ_max = 0.18 e Å⁻³
1809 reflections	Δρ_min = −0.13 e Å⁻³
148 parameters	Extinction correction: SHELXL2014 (Sheldrick, 2015), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
0 restraints	Extinction coefficient: 0.008 (2)

Crystal data top

C₁₂H₁₁NO₃	V = 1026.09 (12) Å³
M_r = 217.22	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 11.6814 (7) Å	µ = 0.10 mm⁻¹
b = 5.6106 (4) Å	T = 293 K
c = 16.5299 (11) Å	0.35 × 0.30 × 0.30 mm
β = 108.713 (2)°

Data collection top

Bruker Kappa APEXII CCD diffractometer	1809 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2004)	1528 reflections with I > 2σ(I)
T_min = 0.948, T_max = 0.955	R_int = 0.023
14793 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.033	0 restraints
wR(F²) = 0.093	H-atom parameters constrained
S = 1.05	Δρ_max = 0.18 e Å⁻³
1809 reflections	Δρ_min = −0.13 e Å⁻³
148 parameters

Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.65902 (9)	−0.46212 (19)	0.54283 (6)	0.0431 (3)
O2	0.80169 (10)	−0.1929 (2)	0.54829 (8)	0.0552 (4)
O3	0.39479 (9)	0.0890 (2)	0.33278 (7)	0.0482 (3)
N1	0.53182 (11)	0.3529 (2)	0.31063 (8)	0.0373 (3)
C1	0.74710 (16)	−0.5928 (3)	0.60928 (11)	0.0522 (5)
H1A	0.7104	−0.7341	0.6227	0.078*
H1B	0.7760	−0.4949	0.6593	0.078*
H1C	0.8135	−0.6366	0.5901	0.078*
C2	0.69963 (13)	−0.2616 (3)	0.51875 (9)	0.0361 (4)
C3	0.60129 (13)	−0.1379 (3)	0.45343 (9)	0.0365 (4)
H3	0.5236	−0.1964	0.4439	0.044*
C4	0.61193 (12)	0.0491 (3)	0.40656 (9)	0.0337 (3)
C5	0.49776 (13)	0.1589 (3)	0.34670 (9)	0.0354 (3)
C6	0.65784 (13)	0.3756 (3)	0.33871 (9)	0.0353 (4)
C7	0.71103 (13)	0.1927 (3)	0.39651 (9)	0.0344 (3)
C8	0.83571 (14)	0.1806 (3)	0.42921 (10)	0.0418 (4)
H8	0.8729	0.0592	0.4667	0.050*
C9	0.90449 (15)	0.3510 (3)	0.40554 (11)	0.0473 (4)
H9	0.9884	0.3436	0.4272	0.057*
C10	0.84974 (16)	0.5317 (3)	0.35007 (11)	0.0489 (4)
H10	0.8975	0.6462	0.3358	0.059*
C11	0.72544 (15)	0.5465 (3)	0.31528 (10)	0.0442 (4)
H11	0.6889	0.6676	0.2774	0.053*
C12	0.44906 (15)	0.5083 (3)	0.24895 (11)	0.0480 (4)
H12A	0.4669	0.5039	0.1962	0.072*
H12B	0.4579	0.6684	0.2706	0.072*
H12C	0.3676	0.4554	0.2393	0.072*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0453 (6)	0.0360 (6)	0.0424 (6)	−0.0008 (5)	0.0062 (5)	0.0067 (5)
O2	0.0384 (7)	0.0578 (8)	0.0610 (8)	−0.0034 (6)	0.0042 (5)	0.0181 (6)
O3	0.0353 (6)	0.0460 (7)	0.0569 (7)	−0.0001 (5)	0.0060 (5)	0.0046 (5)
N1	0.0380 (7)	0.0339 (7)	0.0364 (7)	0.0047 (5)	0.0071 (5)	0.0032 (5)
C1	0.0551 (10)	0.0466 (10)	0.0482 (10)	0.0047 (8)	0.0073 (8)	0.0154 (8)
C2	0.0381 (8)	0.0345 (8)	0.0356 (8)	0.0018 (7)	0.0118 (6)	0.0009 (6)
C3	0.0348 (8)	0.0346 (8)	0.0388 (8)	0.0014 (6)	0.0102 (6)	−0.0010 (6)
C4	0.0352 (8)	0.0329 (8)	0.0320 (7)	0.0034 (6)	0.0092 (6)	−0.0037 (6)
C5	0.0371 (8)	0.0331 (8)	0.0342 (8)	0.0022 (6)	0.0087 (6)	−0.0038 (6)
C6	0.0405 (8)	0.0342 (8)	0.0318 (7)	0.0019 (6)	0.0122 (6)	−0.0040 (6)
C7	0.0381 (8)	0.0338 (8)	0.0317 (7)	0.0013 (6)	0.0117 (6)	−0.0034 (6)
C8	0.0371 (8)	0.0461 (9)	0.0407 (8)	0.0022 (7)	0.0105 (7)	0.0007 (7)
C9	0.0384 (9)	0.0563 (11)	0.0479 (9)	−0.0064 (8)	0.0147 (7)	−0.0029 (8)
C10	0.0518 (10)	0.0488 (10)	0.0500 (10)	−0.0118 (8)	0.0219 (8)	−0.0011 (8)
C11	0.0552 (10)	0.0386 (9)	0.0404 (8)	−0.0013 (8)	0.0175 (7)	0.0016 (7)
C12	0.0505 (10)	0.0393 (9)	0.0464 (9)	0.0080 (7)	0.0046 (7)	0.0053 (7)

Geometric parameters (Å, º) top

O1—C2	1.3303 (18)	C4—C5	1.513 (2)
O1—C1	1.4415 (18)	C6—C11	1.374 (2)
O2—C2	1.1980 (18)	C6—C7	1.404 (2)
O3—C5	1.2149 (17)	C7—C8	1.383 (2)
N1—C5	1.3604 (19)	C8—C9	1.384 (2)
N1—C6	1.4001 (19)	C8—H8	0.9300
N1—C12	1.4498 (19)	C9—C10	1.379 (2)
C1—H1A	0.9600	C9—H9	0.9300
C1—H1B	0.9600	C10—C11	1.382 (2)
C1—H1C	0.9600	C10—H10	0.9300
C2—C3	1.474 (2)	C11—H11	0.9300
C3—C4	1.333 (2)	C12—H12A	0.9600
C3—H3	0.9300	C12—H12B	0.9600
C4—C7	1.463 (2)	C12—H12C	0.9600

C2—O1—C1	114.99 (12)	C11—C6—C7	122.19 (14)
C5—N1—C6	110.60 (12)	N1—C6—C7	110.34 (13)
C5—N1—C12	124.50 (13)	C8—C7—C6	118.85 (14)
C6—N1—C12	124.84 (13)	C8—C7—C4	134.50 (14)
O1—C1—H1A	109.5	C6—C7—C4	106.64 (12)
O1—C1—H1B	109.5	C7—C8—C9	119.33 (15)
H1A—C1—H1B	109.5	C7—C8—H8	120.3
O1—C1—H1C	109.5	C9—C8—H8	120.3
H1A—C1—H1C	109.5	C10—C9—C8	120.56 (15)
H1B—C1—H1C	109.5	C10—C9—H9	119.7
O2—C2—O1	123.65 (14)	C8—C9—H9	119.7
O2—C2—C3	125.93 (14)	C9—C10—C11	121.47 (15)
O1—C2—C3	110.41 (13)	C9—C10—H10	119.3
C4—C3—C2	126.90 (14)	C11—C10—H10	119.3
C4—C3—H3	116.5	C6—C11—C10	117.57 (15)
C2—C3—H3	116.5	C6—C11—H11	121.2
C3—C4—C7	136.38 (14)	C10—C11—H11	121.2
C3—C4—C5	118.26 (13)	N1—C12—H12A	109.5
C7—C4—C5	105.36 (12)	N1—C12—H12B	109.5
O3—C5—N1	125.89 (14)	H12A—C12—H12B	109.5
O3—C5—C4	127.13 (14)	N1—C12—H12C	109.5
N1—C5—C4	106.98 (12)	H12A—C12—H12C	109.5
C11—C6—N1	127.47 (14)	H12B—C12—H12C	109.5

C1—O1—C2—O2	1.0 (2)	C12—N1—C6—C7	−178.31 (13)
C1—O1—C2—C3	−177.63 (13)	C11—C6—C7—C8	−1.7 (2)
O2—C2—C3—C4	11.4 (3)	N1—C6—C7—C8	177.86 (12)
O1—C2—C3—C4	−170.09 (14)	C11—C6—C7—C4	179.26 (13)
C2—C3—C4—C7	2.6 (3)	N1—C6—C7—C4	−1.18 (15)
C2—C3—C4—C5	−176.20 (13)	C3—C4—C7—C8	4.6 (3)
C6—N1—C5—O3	−177.71 (14)	C5—C4—C7—C8	−176.43 (16)
C12—N1—C5—O3	−0.1 (2)	C3—C4—C7—C6	−176.56 (16)
C6—N1—C5—C4	2.20 (15)	C5—C4—C7—C6	2.39 (14)
C12—N1—C5—C4	179.83 (13)	C6—C7—C8—C9	1.2 (2)
C3—C4—C5—O3	−3.7 (2)	C4—C7—C8—C9	179.95 (15)
C7—C4—C5—O3	177.08 (14)	C7—C8—C9—C10	0.1 (2)
C3—C4—C5—N1	176.35 (13)	C8—C9—C10—C11	−1.2 (3)
C7—C4—C5—N1	−2.83 (15)	N1—C6—C11—C10	−178.78 (14)
C5—N1—C6—C11	178.83 (14)	C7—C6—C11—C10	0.7 (2)
C12—N1—C6—C11	1.2 (2)	C9—C10—C11—C6	0.7 (2)
C5—N1—C6—C7	−0.70 (16)

Hydrogen-bond geometry (Å, º) top

Cg1 is the centroid of ring C6–C11.

D—H···A	D—H	H···A	D···A	D—H···A
C8—H8···O2	0.93	2.29	2.988 (2)	132
C9—H9···O2ⁱ	0.93	2.50	3.387 (2)	159
C1—H1A···O3ⁱⁱ	0.96	2.57	3.526 (2)	175
C11—H11···Cgⁱⁱⁱ	0.93	2.83	3.558 (2)	135

Symmetry codes: (i) −x+2, −y, −z+1; (ii) −x+1, −y−1, −z+1; (iii) −x+3/2, y+1/2, −z+1/2.

Hydrogen-bond geometry (Å, º) top

Cg1 is the centroid of ring C6–C11.

D—H···A	D—H	H···A	D···A	D—H···A
C8—H8···O2	0.93	2.29	2.988 (2)	132
C9—H9···O2ⁱ	0.93	2.50	3.387 (2)	159
C1—H1A···O3ⁱⁱ	0.96	2.57	3.526 (2)	175
C11—H11···Cgⁱⁱⁱ	0.93	2.83	3.558 (2)	135

Symmetry codes: (i) −x+2, −y, −z+1; (ii) −x+1, −y−1, −z+1; (iii) −x+3/2, y+1/2, −z+1/2.

Acknowledgements

The authors thank Dr Babu Vargheese, SAIF, IIT, Madras, India, for the data collection.

References

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