organic compounds
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
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); Seefeld et al. (2003). For details of the synthesis, see: Pedras & Soledade (2006).
Experimental
Crystal data
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Refinement
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Data collection: RAPID-AUTO (Rigaku Corporation, 1998); cell RAPID-AUTO; 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.
Supporting information
10.1107/S1600536811028595/gk2396sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536811028595/gk2396Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536811028595/gk2396Isup3.cml
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.
Carbon-bound H-atoms were placed in calculated positions (C—H 0.93 and 0.97 Å) and were included in the
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).Data collection: RAPID-AUTO (Rigaku Corporation, 1998); cell
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).C12H13NO2 | F(000) = 432 |
Mr = 203.23 | Dx = 1.273 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 5849 reflections |
a = 6.893 (5) Å | θ = 3.2–27.4° |
b = 9.146 (8) Å | µ = 0.09 mm−1 |
c = 18.052 (10) Å | T = 296 K |
β = 111.27 (3)° | Block, colorless |
V = 1060.5 (13) Å3 | 0.46 × 0.19 × 0.18 mm |
Z = 4 |
Rigaku R-AXIS RAPID diffractometer | 2414 independent reflections |
Radiation source: fine-focus sealed tube | 1509 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.048 |
ω scans | θmax = 27.5°, θmin = 3.2° |
Absorption correction: multi-scan (ABSCOR; Higashi, 1995) | h = −8→8 |
Tmin = 0.961, Tmax = 0.984 | k = −11→11 |
10015 measured reflections | l = −23→23 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.052 | H-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 reflections | Δρmax = 0.16 e Å−3 |
138 parameters | Δρmin = −0.16 e Å−3 |
1 restraint | Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.036 (5) |
C12H13NO2 | V = 1060.5 (13) Å3 |
Mr = 203.23 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 6.893 (5) Å | µ = 0.09 mm−1 |
b = 9.146 (8) Å | T = 296 K |
c = 18.052 (10) Å | 0.46 × 0.19 × 0.18 mm |
β = 111.27 (3)° |
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 = 0.984 | Rint = 0.048 |
10015 measured reflections |
R[F2 > 2σ(F2)] = 0.052 | 1 restraint |
wR(F2) = 0.138 | H-atom parameters constrained |
S = 1.04 | Δρmax = 0.16 e Å−3 |
2414 reflections | Δρmin = −0.16 e Å−3 |
138 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | −0.1892 (2) | 0.69967 (17) | 0.43997 (8) | 0.0762 (5) | |
O2 | −0.3213 (2) | 0.88674 (17) | 0.48330 (8) | 0.0760 (5) | |
N1 | 0.5979 (2) | 0.80147 (17) | 0.76433 (8) | 0.0566 (4) | |
H1 | 0.6448 | 0.8259 | 0.8192 | 0.085* | |
C1 | 0.5726 (3) | 0.65764 (19) | 0.66104 (9) | 0.0469 (4) | |
C2 | 0.6478 (3) | 0.5573 (2) | 0.61952 (11) | 0.0585 (5) | |
H2 | 0.5628 | 0.5253 | 0.5693 | 0.070* | |
C3 | 0.8477 (3) | 0.5065 (2) | 0.65345 (13) | 0.0668 (6) | |
H3 | 0.8984 | 0.4403 | 0.6258 | 0.080* | |
C4 | 0.9761 (3) | 0.5526 (2) | 0.72877 (13) | 0.0671 (6) | |
H4 | 1.1109 | 0.5161 | 0.7507 | 0.080* | |
C5 | 0.9079 (3) | 0.6506 (2) | 0.77134 (11) | 0.0598 (5) | |
H5 | 0.9941 | 0.6810 | 0.8217 | 0.072* | |
C6 | 0.7059 (3) | 0.70276 (19) | 0.73679 (10) | 0.0481 (4) | |
C7 | 0.4000 (3) | 0.8150 (2) | 0.70877 (10) | 0.0546 (5) | |
H7 | 0.2961 | 0.8736 | 0.7145 | 0.066* | |
C8 | 0.3779 (3) | 0.7306 (2) | 0.64415 (9) | 0.0491 (5) | |
C9 | 0.1912 (3) | 0.7142 (2) | 0.56905 (10) | 0.0606 (5) | |
H9A | 0.1467 | 0.6129 | 0.5639 | 0.073* | |
H9B | 0.2316 | 0.7372 | 0.5242 | 0.073* | |
C10 | 0.0095 (3) | 0.8096 (2) | 0.56507 (10) | 0.0558 (5) | |
H10A | −0.0319 | 0.7868 | 0.6097 | 0.067* | |
H10B | 0.0529 | 0.9111 | 0.5699 | 0.067* | |
C11 | −0.1734 (3) | 0.7903 (2) | 0.48976 (10) | 0.0532 (5) | |
C12 | −0.5084 (3) | 0.8803 (3) | 0.41298 (12) | 0.0820 (7) | |
H12A | −0.4753 | 0.9036 | 0.3671 | 0.123* | |
H12B | −0.6080 | 0.9494 | 0.4178 | 0.123* | |
H12C | −0.5661 | 0.7836 | 0.4074 | 0.123* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0724 (10) | 0.0813 (11) | 0.0522 (7) | 0.0196 (8) | −0.0047 (7) | −0.0124 (7) |
O2 | 0.0590 (9) | 0.0844 (11) | 0.0673 (8) | 0.0192 (8) | 0.0020 (7) | −0.0161 (7) |
N1 | 0.0537 (9) | 0.0640 (10) | 0.0445 (8) | −0.0005 (8) | 0.0087 (7) | −0.0074 (7) |
C1 | 0.0477 (10) | 0.0480 (10) | 0.0424 (8) | −0.0038 (8) | 0.0132 (8) | 0.0026 (7) |
C2 | 0.0677 (13) | 0.0552 (12) | 0.0516 (10) | −0.0013 (10) | 0.0204 (9) | −0.0030 (8) |
C3 | 0.0675 (14) | 0.0577 (13) | 0.0807 (14) | 0.0070 (10) | 0.0338 (11) | −0.0018 (10) |
C4 | 0.0520 (12) | 0.0571 (13) | 0.0878 (14) | 0.0035 (10) | 0.0202 (11) | 0.0053 (11) |
C5 | 0.0475 (11) | 0.0566 (12) | 0.0635 (11) | −0.0053 (9) | 0.0060 (9) | 0.0001 (9) |
C6 | 0.0458 (10) | 0.0459 (10) | 0.0486 (9) | −0.0054 (8) | 0.0124 (8) | 0.0030 (8) |
C7 | 0.0476 (11) | 0.0620 (12) | 0.0485 (9) | 0.0046 (9) | 0.0107 (8) | −0.0029 (8) |
C8 | 0.0487 (10) | 0.0542 (11) | 0.0401 (9) | −0.0019 (8) | 0.0109 (8) | −0.0001 (7) |
C9 | 0.0529 (11) | 0.0744 (14) | 0.0440 (9) | 0.0054 (10) | 0.0050 (8) | −0.0041 (9) |
C10 | 0.0574 (12) | 0.0549 (11) | 0.0464 (9) | −0.0020 (9) | 0.0084 (8) | 0.0004 (8) |
C11 | 0.0542 (11) | 0.0548 (11) | 0.0460 (9) | 0.0027 (9) | 0.0126 (8) | 0.0045 (8) |
C12 | 0.0555 (13) | 0.0987 (19) | 0.0722 (13) | 0.0191 (12) | −0.0002 (11) | −0.0103 (12) |
O1—C11 | 1.198 (2) | C5—C6 | 1.388 (3) |
O2—C11 | 1.321 (2) | C5—H5 | 0.9300 |
O2—C12 | 1.446 (2) | C7—C8 | 1.361 (3) |
N1—C6 | 1.373 (2) | C7—H7 | 0.9300 |
N1—C7 | 1.375 (2) | C8—C9 | 1.500 (2) |
N1—H1 | 0.9498 | C9—C10 | 1.507 (3) |
C1—C2 | 1.398 (3) | C9—H9A | 0.9700 |
C1—C6 | 1.404 (2) | C9—H9B | 0.9700 |
C1—C8 | 1.429 (3) | C10—C11 | 1.491 (2) |
C2—C3 | 1.371 (3) | C10—H10A | 0.9700 |
C2—H2 | 0.9300 | C10—H10B | 0.9700 |
C3—C4 | 1.392 (3) | C12—H12A | 0.9600 |
C3—H3 | 0.9300 | C12—H12B | 0.9600 |
C4—C5 | 1.370 (3) | C12—H12C | 0.9600 |
C4—H4 | 0.9300 | ||
C11—O2—C12 | 117.67 (16) | C7—C8—C1 | 106.12 (15) |
C6—N1—C7 | 108.66 (15) | C7—C8—C9 | 128.62 (17) |
C6—N1—H1 | 120.5 | C1—C8—C9 | 125.26 (16) |
C7—N1—H1 | 127.7 | C8—C9—C10 | 114.27 (16) |
C2—C1—C6 | 118.42 (17) | C8—C9—H9A | 108.7 |
C2—C1—C8 | 133.97 (16) | C10—C9—H9A | 108.7 |
C6—C1—C8 | 107.61 (16) | C8—C9—H9B | 108.7 |
C3—C2—C1 | 119.42 (18) | C10—C9—H9B | 108.7 |
C3—C2—H2 | 120.3 | H9A—C9—H9B | 107.6 |
C1—C2—H2 | 120.3 | C11—C10—C9 | 112.84 (16) |
C2—C3—C4 | 120.9 (2) | C11—C10—H10A | 109.0 |
C2—C3—H3 | 119.5 | C9—C10—H10A | 109.0 |
C4—C3—H3 | 119.5 | C11—C10—H10B | 109.0 |
C5—C4—C3 | 121.4 (2) | C9—C10—H10B | 109.0 |
C5—C4—H4 | 119.3 | H10A—C10—H10B | 107.8 |
C3—C4—H4 | 119.3 | O1—C11—O2 | 122.57 (17) |
C4—C5—C6 | 117.73 (18) | O1—C11—C10 | 125.61 (18) |
C4—C5—H5 | 121.1 | O2—C11—C10 | 111.82 (16) |
C6—C5—H5 | 121.1 | O2—C12—H12A | 109.5 |
N1—C6—C5 | 130.60 (17) | O2—C12—H12B | 109.5 |
N1—C6—C1 | 107.26 (15) | H12A—C12—H12B | 109.5 |
C5—C6—C1 | 122.14 (17) | O2—C12—H12C | 109.5 |
C8—C7—N1 | 110.32 (16) | H12A—C12—H12C | 109.5 |
C8—C7—H7 | 124.8 | H12B—C12—H12C | 109.5 |
N1—C7—H7 | 124.8 | ||
C6—C1—C2—C3 | −0.2 (3) | N1—C7—C8—C1 | 1.2 (2) |
C8—C1—C2—C3 | −179.77 (19) | N1—C7—C8—C9 | −178.59 (18) |
C1—C2—C3—C4 | 0.5 (3) | C2—C1—C8—C7 | 179.6 (2) |
C2—C3—C4—C5 | −0.4 (3) | C6—C1—C8—C7 | −0.1 (2) |
C3—C4—C5—C6 | −0.1 (3) | C2—C1—C8—C9 | −0.6 (3) |
C7—N1—C6—C5 | −178.76 (18) | C6—C1—C8—C9 | 179.73 (17) |
C7—N1—C6—C1 | 1.8 (2) | C7—C8—C9—C10 | 2.6 (3) |
C4—C5—C6—N1 | −179.00 (18) | C1—C8—C9—C10 | −177.13 (17) |
C4—C5—C6—C1 | 0.4 (3) | C8—C9—C10—C11 | −179.92 (16) |
C2—C1—C6—N1 | 179.23 (15) | C12—O2—C11—O1 | 0.1 (3) |
C8—C1—C6—N1 | −1.06 (19) | C12—O2—C11—C10 | −179.83 (17) |
C2—C1—C6—C5 | −0.3 (3) | C9—C10—C11—O1 | 7.5 (3) |
C8—C1—C6—C5 | 179.44 (16) | C9—C10—C11—O2 | −172.55 (16) |
C6—N1—C7—C8 | −1.9 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1i | 0.95 | 2.08 | 2.972 (3) | 157 |
Symmetry code: (i) x+1, −y+3/2, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C12H13NO2 |
Mr | 203.23 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 296 |
a, b, c (Å) | 6.893 (5), 9.146 (8), 18.052 (10) |
β (°) | 111.27 (3) |
V (Å3) | 1060.5 (13) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.46 × 0.19 × 0.18 |
Data collection | |
Diffractometer | Rigaku R-AXIS RAPID diffractometer |
Absorption correction | Multi-scan (ABSCOR; Higashi, 1995) |
Tmin, Tmax | 0.961, 0.984 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 10015, 2414, 1509 |
Rint | 0.048 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.052, 0.138, 1.04 |
No. of reflections | 2414 |
No. of parameters | 138 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 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).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1i | 0.95 | 2.08 | 2.972 (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
Brandenburg, K. & Berndt, M. (2001). DIAMOND. Crystal Impact, Bonn, Germany. Google Scholar
Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan. Google Scholar
MSC & Rigaku (2002). CrystalStructure. MSC, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan. Google Scholar
Pedras, M. & Soledade, C. (2006). Med. Chem. 14, 4958–4979. CrossRef CAS Google Scholar
Rigaku Corporation (1998). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan. Google Scholar
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. Web of Science CrossRef PubMed CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Zeynep, A. A., Tulay, C. & Sibel, S. (2005). Med. Chem. Res. 14, 169–179. Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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.