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

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Methyl 3-(1H-indol-3-yl)propano­ate

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

(Received 13 July 2011; accepted 16 July 2011; online 23 July 2011)

The mol­ecule of the title compound, C12H13NO2, adopts an essentially planar conformation (r.m.s. deviation = 0.057 Å). In the crystal, the mol­ecules are linked by inter­molecular N—H⋯O hydrogen bonds, generating chains along [201].

Related literature

For the biological activity of indole derivatives, see: Zeynep et al. (2005[Zeynep, A. A., Tulay, C. & Sibel, S. (2005). Med. Chem. Res. 14, 169-179.]); Seefeld et al. (2003[Seefeld, M. A., Miler, W. H., Newlander, K. A., Burgess, W. J., DeWolf, W. E. Jr, Elkins, P. A., Head, M. S., Jakas, D. R., Janson, C. A., Keller, P. M., Manley, P. J., Moore, T. D., Payne, D. J., Pearson, S., Polizzi, B. J., Qiu, X., Rittenhouse, S. F., Uzinskas, I. N., Wallis, N. G. & Huffman, W. F. (2003). J. Med. Chem. 46, 1627-1635.]). For details of the synthesis, see: Pedras & Soledade (2006[Pedras, M. & Soledade, C. (2006). Med. Chem. 14, 4958-4979.]).

[Scheme 1]

Experimental

Crystal data
  • C12H13NO2

  • Mr = 203.23

  • Monoclinic, P 21 /c

  • a = 6.893 (5) Å

  • b = 9.146 (8) Å

  • c = 18.052 (10) Å

  • β = 111.27 (3)°

  • V = 1060.5 (13) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 296 K

  • 0.46 × 0.19 × 0.18 mm

Data collection
  • Rigaku R-AXIS RAPID diffractometer

  • Absorption correction: multi-scan (ABSCOR; Higashi, 1995[Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.961, Tmax = 0.984

  • 10015 measured reflections

  • 2414 independent reflections

  • 1509 reflections with I > 2σ(I)

  • Rint = 0.048

Refinement
  • R[F2 > 2σ(F2)] = 0.052

  • wR(F2) = 0.138

  • S = 1.04

  • 2414 reflections

  • 138 parameters

  • 1 restraint

  • H-atom parameters constrained

  • Δρmax = 0.16 e Å−3

  • Δρmin = −0.16 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯O1i 0.95 2.08 2.972 (3) 157
Symmetry code: (i) [x+1, -y+{\script{3\over 2}}, z+{\script{1\over 2}}].

Data collection: RAPID-AUTO (Rigaku Corporation, 1998[Rigaku Corporation (1998). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.]); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (MSC & Rigaku, 2002[MSC & Rigaku (2002). CrystalStructure. MSC, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan.]); 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.]) and DIAMOND (Brandenburg & Berndt, 2001[Brandenburg, K. & Berndt, M. (2001). DIAMOND. Crystal Impact, Bonn, Germany.]); 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-HIV (Zeynep et al., 2005; Seefeld et al., 2003). We have 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.

The molecular structure of tiltle compound, C12H13O2N, as shown in Fig. 1, all bond lengths and angles are in the normal ranges. All non-hydrogen atoms except for O1 are nearly coplanar. In the crystal, the intermolecular N—H···O hydrogen bonds link the molecules into chains along the [201] direction.

Related literature top

For the biological activity of indole derivatives, see: Zeynep et al. (2005); Seefeld et al. (2003). For details of the synthesis, see: Pedras & Soledade (2006).

Experimental top

The title compound was prepared according to the literature (Pedras & Soledade, 2006). Single crystals suitable for X-ray diffraction were prepared by slow evaporation method from a solution in dichloromethane/ 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 restraint N—H = 0.90 Å and Uiso(H) = 1.5 Ueq(N).

Computing details top

Data collection: RAPID-AUTO (Rigaku Corporation, 1998); cell refinement: RAPID-AUTO (Rigaku Corporation, 1998); data reduction: CrystalStructure (MSC & Rigaku, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008) and DIAMOND (Brandenburg & Berndt, 2001); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound with displacement ellipsoids drawn at the 30% probalility level.
[Figure 2] Fig. 2. Hydrogen-bonded chain in the title compound. Dashed lines indicate hydrogen bonds.
Methyl 3-(1H-indol-3-yl)propanoate top
Crystal data top
C12H13NO2F(000) = 432
Mr = 203.23Dx = 1.273 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 5849 reflections
a = 6.893 (5) Åθ = 3.2–27.4°
b = 9.146 (8) ŵ = 0.09 mm1
c = 18.052 (10) ÅT = 296 K
β = 111.27 (3)°Block, colorless
V = 1060.5 (13) Å30.46 × 0.19 × 0.18 mm
Z = 4
Data collection top
Rigaku R-AXIS RAPID
diffractometer
2414 independent reflections
Radiation source: fine-focus sealed tube1509 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.048
ω scansθmax = 27.5°, θmin = 3.2°
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
h = 88
Tmin = 0.961, Tmax = 0.984k = 1111
10015 measured reflectionsl = 2323
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.052H-atom parameters constrained
wR(F2) = 0.138 w = 1/[σ2(Fo2) + (0.0614P)2 + 0.1289P]
where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
2414 reflectionsΔρmax = 0.16 e Å3
138 parametersΔρmin = 0.16 e Å3
1 restraintExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.036 (5)
Crystal data top
C12H13NO2V = 1060.5 (13) Å3
Mr = 203.23Z = 4
Monoclinic, P21/cMo Kα radiation
a = 6.893 (5) ŵ = 0.09 mm1
b = 9.146 (8) ÅT = 296 K
c = 18.052 (10) Å0.46 × 0.19 × 0.18 mm
β = 111.27 (3)°
Data collection top
Rigaku R-AXIS RAPID
diffractometer
2414 independent reflections
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
1509 reflections with I > 2σ(I)
Tmin = 0.961, Tmax = 0.984Rint = 0.048
10015 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0521 restraint
wR(F2) = 0.138H-atom parameters constrained
S = 1.04Δρmax = 0.16 e Å3
2414 reflectionsΔρmin = 0.16 e Å3
138 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
O10.1892 (2)0.69967 (17)0.43997 (8)0.0762 (5)
O20.3213 (2)0.88674 (17)0.48330 (8)0.0760 (5)
N10.5979 (2)0.80147 (17)0.76433 (8)0.0566 (4)
H10.64480.82590.81920.085*
C10.5726 (3)0.65764 (19)0.66104 (9)0.0469 (4)
C20.6478 (3)0.5573 (2)0.61952 (11)0.0585 (5)
H20.56280.52530.56930.070*
C30.8477 (3)0.5065 (2)0.65345 (13)0.0668 (6)
H30.89840.44030.62580.080*
C40.9761 (3)0.5526 (2)0.72877 (13)0.0671 (6)
H41.11090.51610.75070.080*
C50.9079 (3)0.6506 (2)0.77134 (11)0.0598 (5)
H50.99410.68100.82170.072*
C60.7059 (3)0.70276 (19)0.73679 (10)0.0481 (4)
C70.4000 (3)0.8150 (2)0.70877 (10)0.0546 (5)
H70.29610.87360.71450.066*
C80.3779 (3)0.7306 (2)0.64415 (9)0.0491 (5)
C90.1912 (3)0.7142 (2)0.56905 (10)0.0606 (5)
H9A0.14670.61290.56390.073*
H9B0.23160.73720.52420.073*
C100.0095 (3)0.8096 (2)0.56507 (10)0.0558 (5)
H10A0.03190.78680.60970.067*
H10B0.05290.91110.56990.067*
C110.1734 (3)0.7903 (2)0.48976 (10)0.0532 (5)
C120.5084 (3)0.8803 (3)0.41298 (12)0.0820 (7)
H12A0.47530.90360.36710.123*
H12B0.60800.94940.41780.123*
H12C0.56610.78360.40740.123*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0724 (10)0.0813 (11)0.0522 (7)0.0196 (8)0.0047 (7)0.0124 (7)
O20.0590 (9)0.0844 (11)0.0673 (8)0.0192 (8)0.0020 (7)0.0161 (7)
N10.0537 (9)0.0640 (10)0.0445 (8)0.0005 (8)0.0087 (7)0.0074 (7)
C10.0477 (10)0.0480 (10)0.0424 (8)0.0038 (8)0.0132 (8)0.0026 (7)
C20.0677 (13)0.0552 (12)0.0516 (10)0.0013 (10)0.0204 (9)0.0030 (8)
C30.0675 (14)0.0577 (13)0.0807 (14)0.0070 (10)0.0338 (11)0.0018 (10)
C40.0520 (12)0.0571 (13)0.0878 (14)0.0035 (10)0.0202 (11)0.0053 (11)
C50.0475 (11)0.0566 (12)0.0635 (11)0.0053 (9)0.0060 (9)0.0001 (9)
C60.0458 (10)0.0459 (10)0.0486 (9)0.0054 (8)0.0124 (8)0.0030 (8)
C70.0476 (11)0.0620 (12)0.0485 (9)0.0046 (9)0.0107 (8)0.0029 (8)
C80.0487 (10)0.0542 (11)0.0401 (9)0.0019 (8)0.0109 (8)0.0001 (7)
C90.0529 (11)0.0744 (14)0.0440 (9)0.0054 (10)0.0050 (8)0.0041 (9)
C100.0574 (12)0.0549 (11)0.0464 (9)0.0020 (9)0.0084 (8)0.0004 (8)
C110.0542 (11)0.0548 (11)0.0460 (9)0.0027 (9)0.0126 (8)0.0045 (8)
C120.0555 (13)0.0987 (19)0.0722 (13)0.0191 (12)0.0002 (11)0.0103 (12)
Geometric parameters (Å, º) top
O1—C111.198 (2)C5—C61.388 (3)
O2—C111.321 (2)C5—H50.9300
O2—C121.446 (2)C7—C81.361 (3)
N1—C61.373 (2)C7—H70.9300
N1—C71.375 (2)C8—C91.500 (2)
N1—H10.9498C9—C101.507 (3)
C1—C21.398 (3)C9—H9A0.9700
C1—C61.404 (2)C9—H9B0.9700
C1—C81.429 (3)C10—C111.491 (2)
C2—C31.371 (3)C10—H10A0.9700
C2—H20.9300C10—H10B0.9700
C3—C41.392 (3)C12—H12A0.9600
C3—H30.9300C12—H12B0.9600
C4—C51.370 (3)C12—H12C0.9600
C4—H40.9300
C11—O2—C12117.67 (16)C7—C8—C1106.12 (15)
C6—N1—C7108.66 (15)C7—C8—C9128.62 (17)
C6—N1—H1120.5C1—C8—C9125.26 (16)
C7—N1—H1127.7C8—C9—C10114.27 (16)
C2—C1—C6118.42 (17)C8—C9—H9A108.7
C2—C1—C8133.97 (16)C10—C9—H9A108.7
C6—C1—C8107.61 (16)C8—C9—H9B108.7
C3—C2—C1119.42 (18)C10—C9—H9B108.7
C3—C2—H2120.3H9A—C9—H9B107.6
C1—C2—H2120.3C11—C10—C9112.84 (16)
C2—C3—C4120.9 (2)C11—C10—H10A109.0
C2—C3—H3119.5C9—C10—H10A109.0
C4—C3—H3119.5C11—C10—H10B109.0
C5—C4—C3121.4 (2)C9—C10—H10B109.0
C5—C4—H4119.3H10A—C10—H10B107.8
C3—C4—H4119.3O1—C11—O2122.57 (17)
C4—C5—C6117.73 (18)O1—C11—C10125.61 (18)
C4—C5—H5121.1O2—C11—C10111.82 (16)
C6—C5—H5121.1O2—C12—H12A109.5
N1—C6—C5130.60 (17)O2—C12—H12B109.5
N1—C6—C1107.26 (15)H12A—C12—H12B109.5
C5—C6—C1122.14 (17)O2—C12—H12C109.5
C8—C7—N1110.32 (16)H12A—C12—H12C109.5
C8—C7—H7124.8H12B—C12—H12C109.5
N1—C7—H7124.8
C6—C1—C2—C30.2 (3)N1—C7—C8—C11.2 (2)
C8—C1—C2—C3179.77 (19)N1—C7—C8—C9178.59 (18)
C1—C2—C3—C40.5 (3)C2—C1—C8—C7179.6 (2)
C2—C3—C4—C50.4 (3)C6—C1—C8—C70.1 (2)
C3—C4—C5—C60.1 (3)C2—C1—C8—C90.6 (3)
C7—N1—C6—C5178.76 (18)C6—C1—C8—C9179.73 (17)
C7—N1—C6—C11.8 (2)C7—C8—C9—C102.6 (3)
C4—C5—C6—N1179.00 (18)C1—C8—C9—C10177.13 (17)
C4—C5—C6—C10.4 (3)C8—C9—C10—C11179.92 (16)
C2—C1—C6—N1179.23 (15)C12—O2—C11—O10.1 (3)
C8—C1—C6—N11.06 (19)C12—O2—C11—C10179.83 (17)
C2—C1—C6—C50.3 (3)C9—C10—C11—O17.5 (3)
C8—C1—C6—C5179.44 (16)C9—C10—C11—O2172.55 (16)
C6—N1—C7—C81.9 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.952.082.972 (3)157
Symmetry code: (i) x+1, y+3/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC12H13NO2
Mr203.23
Crystal system, space groupMonoclinic, P21/c
Temperature (K)296
a, b, c (Å)6.893 (5), 9.146 (8), 18.052 (10)
β (°) 111.27 (3)
V3)1060.5 (13)
Z4
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.46 × 0.19 × 0.18
Data collection
DiffractometerRigaku R-AXIS RAPID
diffractometer
Absorption correctionMulti-scan
(ABSCOR; Higashi, 1995)
Tmin, Tmax0.961, 0.984
No. of measured, independent and
observed [I > 2σ(I)] reflections
10015, 2414, 1509
Rint0.048
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.052, 0.138, 1.04
No. of reflections2414
No. of parameters138
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.16, 0.16

Computer programs: RAPID-AUTO (Rigaku Corporation, 1998), CrystalStructure (MSC & Rigaku, 2002), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008) and DIAMOND (Brandenburg & Berndt, 2001).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.952.082.972 (3)157
Symmetry code: (i) x+1, y+3/2, z+1/2.
 

Acknowledgements

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

References

First citationBrandenburg, K. & Berndt, M. (2001). DIAMOND. Crystal Impact, Bonn, Germany.
First citationHigashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.
First citationMSC & Rigaku (2002). CrystalStructure. MSC, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan.
First citationPedras, M. & Soledade, C. (2006). Med. Chem. 14, 4958–4979.  CrossRef CAS
First citationRigaku Corporation (1998). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.
First citationSeefeld, M. A., Miler, W. H., Newlander, K. A., Burgess, W. J., DeWolf, W. E. Jr, Elkins, P. A., Head, M. S., Jakas, D. R., Janson, C. A., Keller, P. M., Manley, P. J., Moore, T. D., Payne, D. J., Pearson, S., Polizzi, B. J., Qiu, X., Rittenhouse, S. F., Uzinskas, I. N., Wallis, N. G. & Huffman, W. F. (2003). J. Med. Chem. 46, 1627–1635.  Web of Science CrossRef PubMed CAS
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationZeynep, A. A., Tulay, C. & Sibel, S. (2005). Med. Chem. Res. 14, 169–179.

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