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

Hou, R.-B.; Li, D.-F.

doi:10.1107/S1600536811030121

organic compounds

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ISSN: 2056-9890

Volume 67| Part 8| August 2011| Page o2197

doi:10.1107/S1600536811030121

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

Rui-Bin Hou ^a and Dong-Feng Li ^a ^*

^aSchool of Chemistry and Life Sciences, Changchun University of Technology, Changchun 130012, People's Republic of China
^*Correspondence e-mail: lidongfeng@mail.ccut.edu.cn

(Received 14 July 2011; accepted 26 July 2011; online 30 July 2011)

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, P b c a
a = 7.735 (5) Å
b = 11.324 (5) Å
c = 23.236 (10) Å
V = 2035.4 (17) Å³
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[F² > 2σ(F²)] = 0.049
wR(F²) = 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

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) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, z]$ ; (ii) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+2]$ .

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.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811030121/hb5951sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811030121/hb5951Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811030121/hb5951Isup3.cml

checkCIF report

Comment top

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.

Related literature top

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 top

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.

Computing details top

Data collection: RAPID-AUTO (Rigaku, 1998); cell refinement: RAPID-AUTO (Rigaku, 1998); 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 (Sheldrick, 2008).

Figures top

Fig. 1. The title compound, with displacement ellipsoids of non-H atoms drawn at the 30% probalility level.

(E)-Methyl 3-(1H-indol-2-yl)prop-2-enoate top

Crystal data top

C₁₂H₁₁NO₂	F(000) = 848
M_r = 201.22	D_x = 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 top

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

Refinement top

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(F_o²) + (0.0668P)² + 0.2072P] where P = (F_o² + 2F_c²)/3
2326 reflections	(Δ/σ)_max = 0.003
137 parameters	Δρ_max = 0.14 e Å⁻³
1 restraint	Δρ_min = −0.19 e Å⁻³

Crystal data top

C₁₂H₁₁NO₂	V = 2035.4 (17) Å³
M_r = 201.22	Z = 8
Orthorhombic, Pbca	Mo Kα radiation
a = 7.735 (5) Å	µ = 0.09 mm⁻¹
b = 11.324 (5) Å	T = 296 K
c = 23.236 (10) Å	0.39 × 0.27 × 0.22 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	2326 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	1555 reflections with I > 2σ(I)
T_min = 0.966, T_max = 0.980	R_int = 0.065
18445 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.049	1 restraint
wR(F²) = 0.133	H-atom parameters constrained
S = 1.04	Δρ_max = 0.14 e Å⁻³
2326 reflections	Δρ_min = −0.19 e Å⁻³
137 parameters

Special details top

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 (Å²) top

	x	y	z	U_iso*/U_eq
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 (Å²) top

	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, º) top

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, º) top

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.

Experimental details

Crystal data
Chemical formula	C₁₂H₁₁NO₂
M_r	201.22
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	296
a, b, c (Å)	7.735 (5), 11.324 (5), 23.236 (10)
V (Å³)	2035.4 (17)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.39 × 0.27 × 0.22

Data collection
Diffractometer	Rigaku R-AXIS RAPID diffractometer
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995)
T_min, T_max	0.966, 0.980
No. of measured, independent and observed [I > 2σ(I)] reflections	18445, 2326, 1555
R_int	0.065
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.049, 0.133, 1.04
No. of reflections	2326
No. of parameters	137
No. of restraints	1
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.14, −0.19

Computer programs: RAPID-AUTO (Rigaku, 1998), CrystalStructure (Rigaku/MSC, 2002), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

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.

Acknowledgements

The authors acknowledge financial support from the National Natural Science Foundation of Jilin Province (grant No. 20101548).

References

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