Methyl 3-(1H-indol-3-yl)propano­ate

Abstract

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,

• a = 6.893 (5) Å

• b = 9.146 (8) Å

• c = 18.052 (10) Å

• β = 111.27 (3)°

• V = 1060.5 (13) ų

• 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[F ² > 2σ(F ²)] = 0.052

• wR(F ²) = 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

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.

Supplementary Material

Supplementary material file. DOI: 10.1107/S1600536811028595/gk2396Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

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) .

supplementary crystallographic information

Comment

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.

Experimental

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

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

Figures

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.

Crystal data

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

Data collection

Rigaku R-AXIS RAPID diffractometer	2414 independent reflections
Radiation source: fine-focus sealed tube	1509 reflections with I > 2σ(I)
graphite	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

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)

Special details

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 (Ų)

	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*

Atomic displacement parameters (Ų)

	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, °)

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, °)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1i	0.95	2.08	2.972 (3)	157

Symmetry codes: (i) x+1, −y+3/2, z+1/2.