Methyl 3-(1H-indol-3-yl)propano­ate

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

doi:10.1107/S1600536811028595

organic compounds

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ISSN: 2056-9890

Volume 67| Part 8| August 2011| Page o2121

doi:10.1107/S1600536811028595

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Methyl 3-(1H-indol-3-yl)propanoate

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

^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 ); Seefeld et al. (2003 ). For details of the synthesis, see: Pedras & Soledade (2006 ).

Experimental

Crystal data

C₁₂H₁₃NO₂
M_r = 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 ) T_min = 0.961, T_max = 0.984
10015 measured reflections
2414 independent reflections
1509 reflections with I > 2σ(I)
R_int = 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
Δρ_max = 0.16 e Å⁻³
Δρ_min = −0.16 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1ⁱ	0.95	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 ); cell refinement: 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

Crystal structure: contains datablock I. DOI: 10.1107/S1600536811028595/gk2396sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811028595/gk2396Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811028595/gk2396Isup3.cml

checkCIF report

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.

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

	Fig. 1. Molecular structure of the title compound with displacement ellipsoids drawn at the 30% probalility level.
	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

C₁₂H₁₃NO₂	F(000) = 432
M_r = 203.23	D_x = 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

Data collection top

Rigaku R-AXIS RAPID diffractometer	2414 independent reflections
Radiation source: fine-focus sealed tube	1509 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.048
ω scans	θ_max = 27.5°, θ_min = 3.2°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −8→8
T_min = 0.961, T_max = 0.984	k = −11→11
10015 measured reflections	l = −23→23

Refinement top

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(F_o²) + (0.0614P)² + 0.1289P] where P = (F_o² + 2F_c²)/3
S = 1.04	(Δ/σ)_max < 0.001
2414 reflections	Δρ_max = 0.16 e Å⁻³
138 parameters	Δρ_min = −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)

Crystal data top

C₁₂H₁₃NO₂	V = 1060.5 (13) Å³
M_r = 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)°

Data collection top

Rigaku R-AXIS RAPID diffractometer	2414 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	1509 reflections with I > 2σ(I)
T_min = 0.961, T_max = 0.984	R_int = 0.048
10015 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.052	1 restraint
wR(F²) = 0.138	H-atom parameters constrained
S = 1.04	Δρ_max = 0.16 e Å⁻³
2414 reflections	Δρ_min = −0.16 e Å⁻³
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

	x	y	z	U_iso*/U_eq
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*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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
M_r	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)
T_min, T_max	0.961, 0.984
No. of measured, independent and observed [I > 2σ(I)] reflections	10015, 2414, 1509
R_int	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
Δρ_max, Δρ_min (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).

Hydrogen-bond geometry (Å, º) top

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).

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