(5-Meth­oxy-1H-indol-3-yl)acetonitrile

Ge, Y.-H.; Li, J.-F.; Luo, Y.-H.

doi:10.1107/S1600536811051762

organic compounds

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Volume 68| Part 1| January 2012| Page o66

doi:10.1107/S1600536811051762

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(5-Methoxy-1H-indol-3-yl)acetonitrile

Yu-Hua Ge,^a ^* Jin-Feng Li ^a and Yang-Hui Luo ^a

^aOrdered Matter Science Research Center, College of Chemistry and Chemical Engineering, Southeast University, Nanjing 210096, People's Republic of China
^*Correspondence e-mail: peluoyh@sina.com

(Received 5 November 2011; accepted 1 December 2011; online 10 December 2011)

In the title compound, C₁₁H₁₀N₂O, the O atom and the C atom of the methylene group deviate only slightly [0.029 (3) and 0.055 (3) Å, respectively] from the approximately planar ring system (r.m.s. deviation = 0.013 Å). In the crystal, N—H⋯O hydrogen bonds link the molecules into zigzag chains running along the b axis.

Related literature

Indole-3-acetic acid is recognized as the key auxin in most plants, see: see: Woodward & Bartel (2005 ).

Experimental

Crystal data

C₁₁H₁₀N₂O
M_r = 186.21
Monoclinic, P 2₁ /n
a = 8.9242 (18) Å
b = 11.461 (2) Å
c = 9.889 (2) Å
β = 110.77 (3)°
V = 945.7 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 293 K
0.20 × 0.20 × 0.20 mm

Data collection

Rigaku SCXmini diffractometer
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 ) T_min = 0.983, T_max = 0.983
9617 measured reflections
2164 independent reflections
1225 reflections with I > 2σ(I)
R_int = 0.085

Refinement

R[F² > 2σ(F²)] = 0.064
wR(F²) = 0.162
S = 1.01
2164 reflections
127 parameters
H-atom parameters constrained
Δρ_max = 0.16 e Å⁻³
Δρ_min = −0.23 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯O1ⁱ	0.86	2.18	3.038 (3)	175
Symmetry code: (i) $[-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg & Putz, 2005 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811051762/bt5708sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811051762/bt5708Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811051762/bt5708Isup3.cml

checkCIF report

Comment top

The derivatives of indole are important chemical materials, because they are excellent drug intermediates for many pharmaceutical products. As part of our interest in these materials, we report here the crystal structure of the title compound.

The molecular structure of the title compound is shown in Fig. 1. The atoms O1 and N3 are located in the indole plane. The title compound formed zigzag chain structure via intermolecular N—H···O hydrogen bonds interactions (Fig. 2).

Related literature top

Indole-3-acetic acid is recognized as the key auxin in most plants, see: see: Woodward & Bartel (2005)

Experimental top

Crystals of 3-cyano-5-methoxyindole suitable for X-ray diffraction were obstained by slow evaporation of a methanol solution.

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg & Putz, 2005); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of the title compound with the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are represented as small spheres of arbitrary radii.
	Fig. 2. A packing view down the a axis showing the three dimensionnal network. Intermolecular hydrogen bonds are shown as dashed lines.

(5-Methoxy-1H-indol-3-yl)acetonitrile top

Crystal data top

C₁₁H₁₀N₂O	F(000) = 392
M_r = 186.21	D_x = 1.308 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 2164 reflections
a = 8.9242 (18) Å	θ = 3.0–27.5°
b = 11.461 (2) Å	µ = 0.09 mm⁻¹
c = 9.889 (2) Å	T = 293 K
β = 110.77 (3)°	Prism, white
V = 945.7 (3) Å³	0.20 × 0.20 × 0.20 mm
Z = 4

Data collection top

Rigaku SCXmini diffractometer	2164 independent reflections
Radiation source: fine-focus sealed tube	1225 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.085
Detector resolution: 13.6612 pixels mm^-1	θ_max = 27.5°, θ_min = 3.0°
CCD_Profile_fitting scans	h = −11→11
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	k = −14→14
T_min = 0.983, T_max = 0.983	l = −12→12
9617 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.064	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.162	H-atom parameters constrained
S = 1.01	w = 1/[σ²(F_o²) + (0.0742P)²] where P = (F_o² + 2F_c²)/3
2164 reflections	(Δ/σ)_max < 0.001
127 parameters	Δρ_max = 0.16 e Å⁻³
0 restraints	Δρ_min = −0.23 e Å⁻³

Crystal data top

C₁₁H₁₀N₂O	V = 945.7 (3) Å³
M_r = 186.21	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 8.9242 (18) Å	µ = 0.09 mm⁻¹
b = 11.461 (2) Å	T = 293 K
c = 9.889 (2) Å	0.20 × 0.20 × 0.20 mm
β = 110.77 (3)°

Data collection top

Rigaku SCXmini diffractometer	2164 independent reflections
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	1225 reflections with I > 2σ(I)
T_min = 0.983, T_max = 0.983	R_int = 0.085
9617 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.064	0 restraints
wR(F²) = 0.162	H-atom parameters constrained
S = 1.01	Δρ_max = 0.16 e Å⁻³
2164 reflections	Δρ_min = −0.23 e Å⁻³
127 parameters

Special details top

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	0.08200 (19)	0.23891 (13)	0.92113 (17)	0.0519 (5)
N1	0.4881 (3)	0.52233 (16)	0.7682 (2)	0.0518 (6)
H1A	0.4745	0.5834	0.7146	0.062*
C11	0.3678 (3)	0.45969 (19)	0.7916 (2)	0.0427 (6)
C7	0.1867 (3)	0.30957 (19)	0.8827 (2)	0.0411 (6)
C6	0.3486 (3)	0.29199 (18)	0.9310 (2)	0.0397 (6)
H6A	0.3953	0.2306	0.9932	0.048*
C5	0.4415 (3)	0.36821 (17)	0.8848 (2)	0.0375 (5)
C9	0.1145 (3)	0.40038 (19)	0.7890 (2)	0.0471 (6)
H9A	0.0039	0.4097	0.7578	0.056*
C2	0.6091 (3)	0.37808 (19)	0.9158 (2)	0.0435 (6)
C10	0.2039 (3)	0.4759 (2)	0.7425 (2)	0.0493 (7)
H10A	0.1559	0.5366	0.6795	0.059*
C4	0.7188 (3)	0.1836 (2)	0.9369 (3)	0.0512 (7)
N2	0.7006 (3)	0.0969 (2)	0.8796 (3)	0.0763 (8)
C3	0.7349 (3)	0.2968 (2)	1.0056 (3)	0.0499 (7)
H3A	0.8399	0.3288	1.0192	0.060*
H3B	0.7258	0.2884	1.1000	0.060*
C1	0.6310 (3)	0.4726 (2)	0.8428 (2)	0.0488 (6)
H1B	0.7297	0.4993	0.8438	0.059*
C12	0.1430 (3)	0.1826 (2)	1.0567 (3)	0.0674 (8)
H12A	0.0603	0.1361	1.0707	0.101*
H12B	0.1792	0.2401	1.1319	0.101*
H12C	0.2312	0.1334	1.0596	0.101*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0497 (10)	0.0531 (11)	0.0501 (10)	−0.0009 (8)	0.0141 (9)	0.0083 (8)
N1	0.0763 (15)	0.0387 (11)	0.0433 (11)	−0.0030 (11)	0.0248 (11)	0.0039 (9)
C11	0.0580 (15)	0.0334 (13)	0.0369 (12)	0.0000 (11)	0.0171 (12)	−0.0018 (10)
C7	0.0483 (14)	0.0359 (13)	0.0375 (12)	−0.0007 (10)	0.0132 (11)	−0.0029 (10)
C6	0.0510 (15)	0.0296 (12)	0.0354 (12)	0.0022 (10)	0.0116 (11)	0.0016 (9)
C5	0.0482 (14)	0.0336 (12)	0.0297 (11)	0.0016 (10)	0.0127 (10)	−0.0052 (9)
C9	0.0496 (15)	0.0413 (14)	0.0422 (13)	0.0042 (11)	0.0063 (12)	−0.0013 (11)
C2	0.0533 (15)	0.0397 (14)	0.0387 (13)	0.0006 (11)	0.0181 (12)	−0.0064 (10)
C10	0.0649 (17)	0.0367 (14)	0.0393 (13)	0.0084 (12)	0.0098 (13)	0.0051 (10)
C4	0.0540 (16)	0.0443 (16)	0.0596 (16)	0.0075 (12)	0.0253 (13)	0.0017 (13)
N2	0.0910 (19)	0.0520 (16)	0.0877 (18)	0.0086 (13)	0.0337 (15)	−0.0115 (14)
C3	0.0490 (14)	0.0445 (15)	0.0569 (15)	0.0016 (11)	0.0197 (12)	−0.0065 (12)
C1	0.0589 (16)	0.0443 (15)	0.0497 (14)	−0.0050 (12)	0.0274 (13)	−0.0078 (11)
C12	0.0650 (18)	0.0741 (19)	0.0598 (17)	−0.0023 (15)	0.0180 (14)	0.0212 (15)

Geometric parameters (Å, º) top

O1—C7	1.387 (3)	C9—H9A	0.9300
O1—C12	1.411 (3)	C2—C1	1.353 (3)
N1—C1	1.352 (3)	C2—C3	1.487 (3)
N1—C11	1.378 (3)	C10—H10A	0.9300
N1—H1A	0.8600	C4—N2	1.127 (3)
C11—C5	1.397 (3)	C4—C3	1.448 (3)
C11—C10	1.381 (3)	C3—H3A	0.9700
C7—C6	1.366 (3)	C3—H3B	0.9700
C7—C9	1.391 (3)	C1—H1B	0.9300
C6—C5	1.389 (3)	C12—H12A	0.9600
C6—H6A	0.9300	C12—H12B	0.9600
C5—C2	1.420 (3)	C12—H12C	0.9600
C9—C10	1.363 (3)

C7—O1—C12	117.14 (18)	C5—C2—C3	126.4 (2)
C1—N1—C11	109.2 (2)	C9—C10—C11	118.0 (2)
C1—N1—H1A	125.4	C9—C10—H10A	121.0
C11—N1—H1A	125.4	C11—C10—H10A	121.0
N1—C11—C5	106.8 (2)	N2—C4—C3	177.3 (3)
N1—C11—C10	131.5 (2)	C4—C3—C2	110.65 (19)
C5—C11—C10	121.7 (2)	C4—C3—H3A	109.5
C6—C7—O1	123.33 (19)	C2—C3—H3A	109.5
C6—C7—C9	121.7 (2)	C4—C3—H3B	109.5
O1—C7—C9	114.9 (2)	C2—C3—H3B	109.5
C7—C6—C5	118.2 (2)	H3A—C3—H3B	108.1
C7—C6—H6A	120.9	C2—C1—N1	110.0 (2)
C5—C6—H6A	120.9	C2—C1—H1B	125.0
C6—C5—C11	119.5 (2)	N1—C1—H1B	125.0
C6—C5—C2	133.2 (2)	O1—C12—H12A	109.5
C11—C5—C2	107.2 (2)	O1—C12—H12B	109.5
C10—C9—C7	120.8 (2)	H12A—C12—H12B	109.5
C10—C9—H9A	119.6	O1—C12—H12C	109.5
C7—C9—H9A	119.6	H12A—C12—H12C	109.5
C1—C2—C5	106.8 (2)	H12B—C12—H12C	109.5
C1—C2—C3	126.8 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1ⁱ	0.86	2.18	3.038 (3)	175

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

Experimental details

Crystal data
Chemical formula	C₁₁H₁₀N₂O
M_r	186.21
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	293
a, b, c (Å)	8.9242 (18), 11.461 (2), 9.889 (2)
β (°)	110.77 (3)
V (Å³)	945.7 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.20 × 0.20 × 0.20

Data collection
Diffractometer	Rigaku SCXmini diffractometer
Absorption correction	Multi-scan (CrystalClear; Rigaku, 2005)
T_min, T_max	0.983, 0.983
No. of measured, independent and observed [I > 2σ(I)] reflections	9617, 2164, 1225
R_int	0.085
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.064, 0.162, 1.01
No. of reflections	2164
No. of parameters	127
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.16, −0.23

Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg & Putz, 2005).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1ⁱ	0.86	2.18	3.038 (3)	174.8

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

References

Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Rigaku. (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Woodward, A. W. & Bartel, B. (2005). Ann. Bot. 95, 707–735. Web of Science CrossRef PubMed CAS Google Scholar

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 68| Part 1| January 2012| Page o66

doi:10.1107/S1600536811051762

Open

access