(E)-Methyl 3-(1H-indol-2-yl)acrylate

Abstract

The title compound, C₁₂H₁₁NO₂, is close to being planar (r.m.s. deviation for the non-H atoms = 0.033 Å). In the crystal, mol­ecules are linked by N—H⋯O hydrogen bonds, generating C(7) chains running along the b axis. A weak C—H⋯O interaction helps to establish the packing.

Related literature

For background literature related to indoles in medicinal chemistry, see: Zeynep et al. (2005 ▶). For details of the synthesis, see García-Rubia et al. (2010 ▶).

Experimental

Crystal data

• C₁₂H₁₁NO₂

• M _r = 201.22

• Orthorhombic,

• a = 7.735 (5) Å

• b = 11.324 (5) Å

• c = 23.236 (10) Å

• V = 2035.4 (17) ų

• Z = 8

• Mo Kα radiation

• μ = 0.09 mm⁻¹

• T = 296 K

• 0.39 × 0.27 × 0.22 mm

Data collection

• Rigaku R-AXIS RAPID diffractometer

• Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ▶) T _min = 0.966, T _max = 0.980

• 18445 measured reflections

• 2326 independent reflections

• 1555 reflections with I > 2σ(I)

• R _int = 0.065

Refinement

• R[F ² > 2σ(F ²)] = 0.049

• wR(F ²) = 0.133

• S = 1.04

• 2326 reflections

• 137 parameters

• 1 restraint

• H-atom parameters constrained

• Δρ_max = 0.14 e Å⁻³

• Δρ_min = −0.19 e Å⁻³

Data collection: RAPID-AUTO (Rigaku, 1998 ▶); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002 ▶); 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: SHELXL97.

Supplementary Material

Supplementary material file. DOI: 10.1107/S1600536811030121/hb5951Isup3.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
N1—H1⋯O1i	0.98	1.93	2.900 (2)	174
C5—H5⋯O2ii	0.93	2.57	3.390 (3)	147

Symmetry codes: (i) ; (ii) .

supplementary crystallographic information

Comment

Indole derivatives constitute an important class of therapeutic agents in medicinal chemistry including anticancer, antioxidant, antirheumatoidal and anti-HIVv (e.g. Zeynep et al., 2005). We recently synthesized some indole derivatives as histone deacetylase (HDAC) inhibitors with the precursor. In this paper, we report the crystal structure of the title compound, (I).

The molecular structure of title compound, C₁₂H₁₃O₂N, as shown in Fig. 1, all bond lengths and angles are in the normal ranges. All non-hydrogen atoms are nearly coplanar. In the crystal, the intermolecular N—H···O hydrogen bonds link the molecules into chains along b direction.

Experimental

The title compound was prepared according to the literature method (García-Rubia et al., 2010). Colourless blocks of (I) were prepared by slow evaporation of a solution in a mixture of dichloromethane and petroleum (60–90 °C) at room temperature.

Refinement

Carbon-bound H-atoms were placed in calculated positions (C—H 0.93 and 0.97 Å) and were included in the refinement in the riding model with U_iso(H) = 1.5 or 1.2 U_eq(C). The N-bound H atom was located from a difference map and refined with the distance restraints N—H = 0.90 Å and U_iso(H) = 1.5 U_eq(N).

Figures

Fig. 1.

The title compound, with displacement ellipsoids of non-H atoms drawn at the 30% probalility level.

Crystal data

C12H11NO2	F(000) = 848
Mr = 201.22	Dx = 1.313 Mg m−3
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 10451 reflections
a = 7.735 (5) Å	θ = 3.2–27.5°
b = 11.324 (5) Å	µ = 0.09 mm−1
c = 23.236 (10) Å	T = 296 K
V = 2035.4 (17) Å3	Block, colorless
Z = 8	0.39 × 0.27 × 0.22 mm

Data collection

Rigaku R-AXIS RAPID diffractometer	2326 independent reflections
Radiation source: fine-focus sealed tube	1555 reflections with I > 2σ(I)
graphite	Rint = 0.065
ω scans	θmax = 27.5°, θmin = 3.2°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −10→10
Tmin = 0.966, Tmax = 0.980	k = −14→13
18445 measured reflections	l = −30→29

Refinement

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)] = 0.049	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.133	H-atom parameters constrained
S = 1.04	w = 1/[σ2(Fo2) + (0.0668P)2 + 0.2072P] where P = (Fo2 + 2Fc2)/3
2326 reflections	(Δ/σ)max = 0.003
137 parameters	Δρmax = 0.14 e Å−3
1 restraint	Δρmin = −0.19 e Å−3

Special details

Experimental. (See detailed section in the paper)

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 (Ų)

	x	y	z	Uiso*/Ueq
C1	0.5285 (2)	0.89360 (14)	0.82265 (7)	0.0413 (4)
C2	0.6101 (3)	0.86472 (16)	0.77057 (7)	0.0505 (5)
H2	0.6292	0.9224	0.7428	0.061*
C3	0.6611 (3)	0.75051 (17)	0.76123 (8)	0.0571 (5)
H3	0.7158	0.7310	0.7269	0.068*
C4	0.6323 (3)	0.66264 (17)	0.80249 (9)	0.0592 (6)
H4	0.6662	0.5855	0.7946	0.071*
C5	0.5548 (3)	0.68769 (16)	0.85450 (8)	0.0511 (5)
H5	0.5374	0.6293	0.8821	0.061*
C6	0.5037 (2)	0.80400 (14)	0.86409 (7)	0.0399 (4)
C7	0.4614 (2)	0.99847 (15)	0.84673 (7)	0.0448 (4)
H7	0.4585	1.0721	0.8290	0.054*
C8	0.4012 (2)	0.97292 (14)	0.90079 (7)	0.0401 (4)
C9	0.3182 (2)	1.05130 (14)	0.94093 (7)	0.0421 (4)
H9	0.3052	1.1292	0.9290	0.051*
C10	0.2580 (2)	1.02608 (14)	0.99292 (7)	0.0422 (4)
H10	0.2693	0.9498	1.0072	0.051*
C11	0.1744 (2)	1.11639 (13)	1.02804 (7)	0.0397 (4)
C12	0.0416 (3)	1.15364 (17)	1.11785 (8)	0.0573 (5)
H12A	0.1057	1.2260	1.1206	0.086*
H12B	0.0332	1.1180	1.1552	0.086*
H12C	−0.0723	1.1699	1.1035	0.086*
N1	0.4262 (2)	0.85400 (11)	0.91135 (6)	0.0409 (4)
H1	0.3997	0.8130	0.9473	0.061*
O1	0.1477 (2)	1.21728 (10)	1.01398 (5)	0.0635 (4)
O2	0.12888 (17)	1.07412 (10)	1.07924 (5)	0.0484 (4)

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
C1	0.0440 (11)	0.0430 (9)	0.0370 (8)	−0.0047 (7)	−0.0065 (7)	−0.0006 (7)
C2	0.0554 (13)	0.0565 (11)	0.0394 (9)	−0.0110 (9)	−0.0013 (8)	−0.0037 (8)
C3	0.0526 (13)	0.0653 (12)	0.0533 (11)	−0.0077 (10)	0.0060 (9)	−0.0191 (9)
C4	0.0546 (14)	0.0508 (11)	0.0724 (13)	0.0036 (9)	−0.0002 (10)	−0.0176 (10)
C5	0.0531 (12)	0.0391 (9)	0.0609 (11)	−0.0005 (8)	−0.0035 (9)	0.0007 (8)
C6	0.0383 (10)	0.0387 (8)	0.0428 (9)	−0.0013 (7)	−0.0046 (7)	−0.0006 (7)
C7	0.0548 (12)	0.0391 (8)	0.0405 (9)	−0.0009 (8)	−0.0044 (8)	0.0066 (7)
C8	0.0431 (10)	0.0365 (8)	0.0406 (9)	−0.0011 (7)	−0.0039 (7)	0.0014 (7)
C9	0.0462 (11)	0.0359 (8)	0.0443 (9)	0.0017 (7)	−0.0035 (8)	0.0016 (7)
C10	0.0475 (11)	0.0351 (8)	0.0440 (9)	0.0019 (7)	−0.0035 (8)	0.0037 (7)
C11	0.0442 (10)	0.0370 (9)	0.0377 (8)	−0.0009 (7)	−0.0048 (7)	0.0025 (7)
C12	0.0559 (13)	0.0626 (12)	0.0533 (11)	0.0067 (10)	0.0079 (9)	−0.0038 (9)
N1	0.0468 (9)	0.0362 (7)	0.0396 (7)	0.0000 (6)	0.0003 (6)	0.0048 (6)
O1	0.0983 (12)	0.0409 (7)	0.0514 (8)	0.0168 (7)	0.0050 (7)	0.0073 (6)
O2	0.0572 (9)	0.0428 (6)	0.0452 (7)	0.0047 (6)	0.0062 (6)	0.0043 (5)

Geometric parameters (Å, °)

C1—C2	1.403 (2)	C8—N1	1.383 (2)
C1—C7	1.412 (2)	C8—C9	1.439 (2)
C1—C6	1.412 (2)	C9—C10	1.326 (2)
C2—C3	1.370 (3)	C9—H9	0.9300
C2—H2	0.9300	C10—C11	1.460 (2)
C3—C4	1.400 (3)	C10—H10	0.9300
C3—H3	0.9300	C11—O1	1.2060 (19)
C4—C5	1.378 (3)	C11—O2	1.330 (2)
C4—H4	0.9300	C12—O2	1.439 (2)
C5—C6	1.393 (2)	C12—H12A	0.9600
C5—H5	0.9300	C12—H12B	0.9600
C6—N1	1.373 (2)	C12—H12C	0.9600
C7—C8	1.371 (2)	N1—H1	0.9772
C7—H7	0.9300
C2—C1—C7	134.69 (16)	C7—C8—C9	127.99 (15)
C2—C1—C6	118.79 (16)	N1—C8—C9	123.26 (15)
C7—C1—C6	106.51 (15)	C10—C9—C8	127.91 (16)
C3—C2—C1	119.11 (17)	C10—C9—H9	116.0
C3—C2—H2	120.4	C8—C9—H9	116.0
C1—C2—H2	120.4	C9—C10—C11	120.93 (15)
C2—C3—C4	121.12 (18)	C9—C10—H10	119.5
C2—C3—H3	119.4	C11—C10—H10	119.5
C4—C3—H3	119.4	O1—C11—O2	122.54 (15)
C5—C4—C3	121.56 (17)	O1—C11—C10	126.04 (15)
C5—C4—H4	119.2	O2—C11—C10	111.42 (13)
C3—C4—H4	119.2	O2—C12—H12A	109.5
C4—C5—C6	117.27 (17)	O2—C12—H12B	109.5
C4—C5—H5	121.4	H12A—C12—H12B	109.5
C6—C5—H5	121.4	O2—C12—H12C	109.5
N1—C6—C5	129.91 (16)	H12A—C12—H12C	109.5
N1—C6—C1	107.97 (14)	H12B—C12—H12C	109.5
C5—C6—C1	122.13 (16)	C6—N1—C8	108.71 (13)
C8—C7—C1	108.11 (15)	C6—N1—H1	125.4
C8—C7—H7	125.9	C8—N1—H1	125.8
C1—C7—H7	125.9	C11—O2—C12	117.17 (13)
C7—C8—N1	108.70 (15)

Hydrogen-bond geometry (Å, °)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1i	0.98	1.93	2.900 (2)	174
C5—H5···O2ii	0.93	2.57	3.390 (3)	147

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