organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

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

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[Zeynep, A. A., Tulay, C. & Sibel, S. (2005). Med. Chem. Res. 14, 169-179.]). For details of the synthesis, see García-Rubia et al. (2010[García-Rubia, A., Urones, B., Arrayás, R. G. & Carretero, J. C. (2010). Chem. Eur. J. 16, 9676-9685.]).

[Scheme 1]

Experimental

Crystal data
  • C12H11NO2

  • Mr = 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[Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.966, Tmax = 0.980

  • 18445 measured reflections

  • 2326 independent reflections

  • 1555 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.14 e Å−3

  • Δρmin = −0.19 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Rigaku (1998). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.]); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002[Rigaku/MSC (2002). CrystalStructure. Rigaku/MSC Inc., The Woodlands, Texas, USA.]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXL97.

Supporting information


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.

Refinement top

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 Uiso(H) = 1.5 or 1.2 Ueq(C). The N-bound H atom was located from a difference map and refined with the distance restraints N—H = 0.90 Å and Uiso(H) = 1.5 Ueq(N).

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
[Figure 1] 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
C12H11NO2F(000) = 848
Mr = 201.22Dx = 1.313 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 10451 reflections
a = 7.735 (5) Åθ = 3.2–27.5°
b = 11.324 (5) ŵ = 0.09 mm1
c = 23.236 (10) ÅT = 296 K
V = 2035.4 (17) Å3Block, colorless
Z = 80.39 × 0.27 × 0.22 mm
Data collection top
Rigaku R-AXIS RAPID
diffractometer
2326 independent reflections
Radiation source: fine-focus sealed tube1555 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.065
ω scansθmax = 27.5°, θmin = 3.2°
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
h = 1010
Tmin = 0.966, Tmax = 0.980k = 1413
18445 measured reflectionsl = 3029
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) = 0.133H-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 parametersΔρmax = 0.14 e Å3
1 restraintΔρmin = 0.19 e Å3
Crystal data top
C12H11NO2V = 2035.4 (17) Å3
Mr = 201.22Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 7.735 (5) ŵ = 0.09 mm1
b = 11.324 (5) ÅT = 296 K
c = 23.236 (10) Å0.39 × 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)
Tmin = 0.966, Tmax = 0.980Rint = 0.065
18445 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0491 restraint
wR(F2) = 0.133H-atom parameters constrained
S = 1.04Δρmax = 0.14 e Å3
2326 reflectionsΔρmin = 0.19 e Å3
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
xyzUiso*/Ueq
C10.5285 (2)0.89360 (14)0.82265 (7)0.0413 (4)
C20.6101 (3)0.86472 (16)0.77057 (7)0.0505 (5)
H20.62920.92240.74280.061*
C30.6611 (3)0.75051 (17)0.76123 (8)0.0571 (5)
H30.71580.73100.72690.068*
C40.6323 (3)0.66264 (17)0.80249 (9)0.0592 (6)
H40.66620.58550.79460.071*
C50.5548 (3)0.68769 (16)0.85450 (8)0.0511 (5)
H50.53740.62930.88210.061*
C60.5037 (2)0.80400 (14)0.86409 (7)0.0399 (4)
C70.4614 (2)0.99847 (15)0.84673 (7)0.0448 (4)
H70.45851.07210.82900.054*
C80.4012 (2)0.97292 (14)0.90079 (7)0.0401 (4)
C90.3182 (2)1.05130 (14)0.94093 (7)0.0421 (4)
H90.30521.12920.92900.051*
C100.2580 (2)1.02608 (14)0.99292 (7)0.0422 (4)
H100.26930.94981.00720.051*
C110.1744 (2)1.11639 (13)1.02804 (7)0.0397 (4)
C120.0416 (3)1.15364 (17)1.11785 (8)0.0573 (5)
H12A0.10571.22601.12060.086*
H12B0.03321.11801.15520.086*
H12C0.07231.16991.10350.086*
N10.4262 (2)0.85400 (11)0.91135 (6)0.0409 (4)
H10.39970.81300.94730.061*
O10.1477 (2)1.21728 (10)1.01398 (5)0.0635 (4)
O20.12888 (17)1.07412 (10)1.07924 (5)0.0484 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0440 (11)0.0430 (9)0.0370 (8)0.0047 (7)0.0065 (7)0.0006 (7)
C20.0554 (13)0.0565 (11)0.0394 (9)0.0110 (9)0.0013 (8)0.0037 (8)
C30.0526 (13)0.0653 (12)0.0533 (11)0.0077 (10)0.0060 (9)0.0191 (9)
C40.0546 (14)0.0508 (11)0.0724 (13)0.0036 (9)0.0002 (10)0.0176 (10)
C50.0531 (12)0.0391 (9)0.0609 (11)0.0005 (8)0.0035 (9)0.0007 (8)
C60.0383 (10)0.0387 (8)0.0428 (9)0.0013 (7)0.0046 (7)0.0006 (7)
C70.0548 (12)0.0391 (8)0.0405 (9)0.0009 (8)0.0044 (8)0.0066 (7)
C80.0431 (10)0.0365 (8)0.0406 (9)0.0011 (7)0.0039 (7)0.0014 (7)
C90.0462 (11)0.0359 (8)0.0443 (9)0.0017 (7)0.0035 (8)0.0016 (7)
C100.0475 (11)0.0351 (8)0.0440 (9)0.0019 (7)0.0035 (8)0.0037 (7)
C110.0442 (10)0.0370 (9)0.0377 (8)0.0009 (7)0.0048 (7)0.0025 (7)
C120.0559 (13)0.0626 (12)0.0533 (11)0.0067 (10)0.0079 (9)0.0038 (9)
N10.0468 (9)0.0362 (7)0.0396 (7)0.0000 (6)0.0003 (6)0.0048 (6)
O10.0983 (12)0.0409 (7)0.0514 (8)0.0168 (7)0.0050 (7)0.0073 (6)
O20.0572 (9)0.0428 (6)0.0452 (7)0.0047 (6)0.0062 (6)0.0043 (5)
Geometric parameters (Å, º) top
C1—C21.403 (2)C8—N11.383 (2)
C1—C71.412 (2)C8—C91.439 (2)
C1—C61.412 (2)C9—C101.326 (2)
C2—C31.370 (3)C9—H90.9300
C2—H20.9300C10—C111.460 (2)
C3—C41.400 (3)C10—H100.9300
C3—H30.9300C11—O11.2060 (19)
C4—C51.378 (3)C11—O21.330 (2)
C4—H40.9300C12—O21.439 (2)
C5—C61.393 (2)C12—H12A0.9600
C5—H50.9300C12—H12B0.9600
C6—N11.373 (2)C12—H12C0.9600
C7—C81.371 (2)N1—H10.9772
C7—H70.9300
C2—C1—C7134.69 (16)C7—C8—C9127.99 (15)
C2—C1—C6118.79 (16)N1—C8—C9123.26 (15)
C7—C1—C6106.51 (15)C10—C9—C8127.91 (16)
C3—C2—C1119.11 (17)C10—C9—H9116.0
C3—C2—H2120.4C8—C9—H9116.0
C1—C2—H2120.4C9—C10—C11120.93 (15)
C2—C3—C4121.12 (18)C9—C10—H10119.5
C2—C3—H3119.4C11—C10—H10119.5
C4—C3—H3119.4O1—C11—O2122.54 (15)
C5—C4—C3121.56 (17)O1—C11—C10126.04 (15)
C5—C4—H4119.2O2—C11—C10111.42 (13)
C3—C4—H4119.2O2—C12—H12A109.5
C4—C5—C6117.27 (17)O2—C12—H12B109.5
C4—C5—H5121.4H12A—C12—H12B109.5
C6—C5—H5121.4O2—C12—H12C109.5
N1—C6—C5129.91 (16)H12A—C12—H12C109.5
N1—C6—C1107.97 (14)H12B—C12—H12C109.5
C5—C6—C1122.13 (16)C6—N1—C8108.71 (13)
C8—C7—C1108.11 (15)C6—N1—H1125.4
C8—C7—H7125.9C8—N1—H1125.8
C1—C7—H7125.9C11—O2—C12117.17 (13)
C7—C8—N1108.70 (15)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.981.932.900 (2)174
C5—H5···O2ii0.932.573.390 (3)147
Symmetry codes: (i) x+1/2, y1/2, z; (ii) x+1/2, y+3/2, z+2.

Experimental details

Crystal data
Chemical formulaC12H11NO2
Mr201.22
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)296
a, b, c (Å)7.735 (5), 11.324 (5), 23.236 (10)
V3)2035.4 (17)
Z8
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.39 × 0.27 × 0.22
Data collection
DiffractometerRigaku R-AXIS RAPID
diffractometer
Absorption correctionMulti-scan
(ABSCOR; Higashi, 1995)
Tmin, Tmax0.966, 0.980
No. of measured, independent and
observed [I > 2σ(I)] reflections
18445, 2326, 1555
Rint0.065
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.049, 0.133, 1.04
No. of reflections2326
No. of parameters137
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
N1—H1···O1i0.981.932.900 (2)174
C5—H5···O2ii0.932.573.390 (3)147
Symmetry codes: (i) x+1/2, y1/2, 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

First citationGarcía-Rubia, A., Urones, B., Arrayás, R. G. & Carretero, J. C. (2010). Chem. Eur. J. 16, 9676–9685.  Web of Science PubMed Google Scholar
First citationHigashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.  Google Scholar
First citationRigaku (1998). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.  Google Scholar
First citationRigaku/MSC (2002). CrystalStructure. Rigaku/MSC Inc., The Woodlands, Texas, USA.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationZeynep, A. A., Tulay, C. & Sibel, S. (2005). Med. Chem. Res. 14, 169–179.  Google Scholar

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