supplementary materials


bt5708 scheme

Acta Cryst. (2012). E68, o66    [ doi:10.1107/S1600536811051762 ]

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

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

Abstract top

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.

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.

Refinement top

All H atoms attached to C atoms and N atoms were fixed geometrically and treated as riding with C—H = 0.93 Å (CH), C—H = 0.97 Å (CH2), C—H = 0.96 Å (CH3)and N—H = 0.86 Å with Uiso(H) = 1.2Ueq(CH, CH2 and NH) and Uiso(H) = 1.5Ueq(CH3).

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
[Figure 1] 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.
[Figure 2] 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
C11H10N2OF(000) = 392
Mr = 186.21Dx = 1.308 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 2164 reflections
a = 8.9242 (18) Åθ = 3.0–27.5°
b = 11.461 (2) ŵ = 0.09 mm1
c = 9.889 (2) ÅT = 293 K
β = 110.77 (3)°Prism, white
V = 945.7 (3) Å30.20 × 0.20 × 0.20 mm
Z = 4
Data collection top
Rigaku SCXmini
diffractometer
2164 independent reflections
Radiation source: fine-focus sealed tube1225 reflections with I > 2σ(I)
graphiteRint = 0.085
Detector resolution: 13.6612 pixels mm-1θmax = 27.5°, θmin = 3.0°
CCD_Profile_fitting scansh = 1111
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)
k = 1414
Tmin = 0.983, Tmax = 0.983l = 1212
9617 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.064Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.162H-atom parameters constrained
S = 1.01 w = 1/[σ2(Fo2) + (0.0742P)2]
where P = (Fo2 + 2Fc2)/3
2164 reflections(Δ/σ)max < 0.001
127 parametersΔρmax = 0.16 e Å3
0 restraintsΔρmin = 0.23 e Å3
Crystal data top
C11H10N2OV = 945.7 (3) Å3
Mr = 186.21Z = 4
Monoclinic, P21/nMo Kα radiation
a = 8.9242 (18) ŵ = 0.09 mm1
b = 11.461 (2) ÅT = 293 K
c = 9.889 (2) Å0.20 × 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)
Tmin = 0.983, Tmax = 0.983Rint = 0.085
9617 measured reflectionsθmax = 27.5°
Refinement top
R[F2 > 2σ(F2)] = 0.064H-atom parameters constrained
wR(F2) = 0.162Δρmax = 0.16 e Å3
S = 1.01Δρmin = 0.23 e Å3
2164 reflectionsAbsolute structure: ?
127 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
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
xyzUiso*/Ueq
O10.08200 (19)0.23891 (13)0.92113 (17)0.0519 (5)
N10.4881 (3)0.52233 (16)0.7682 (2)0.0518 (6)
H1A0.47450.58340.71460.062*
C110.3678 (3)0.45969 (19)0.7916 (2)0.0427 (6)
C70.1867 (3)0.30957 (19)0.8827 (2)0.0411 (6)
C60.3486 (3)0.29199 (18)0.9310 (2)0.0397 (6)
H6A0.39530.23060.99320.048*
C50.4415 (3)0.36821 (17)0.8848 (2)0.0375 (5)
C90.1145 (3)0.40038 (19)0.7890 (2)0.0471 (6)
H9A0.00390.40970.75780.056*
C20.6091 (3)0.37808 (19)0.9158 (2)0.0435 (6)
C100.2039 (3)0.4759 (2)0.7425 (2)0.0493 (7)
H10A0.15590.53660.67950.059*
C40.7188 (3)0.1836 (2)0.9369 (3)0.0512 (7)
N20.7006 (3)0.0969 (2)0.8796 (3)0.0763 (8)
C30.7349 (3)0.2968 (2)1.0056 (3)0.0499 (7)
H3A0.83990.32881.01920.060*
H3B0.72580.28841.10000.060*
C10.6310 (3)0.4726 (2)0.8428 (2)0.0488 (6)
H1B0.72970.49930.84380.059*
C120.1430 (3)0.1826 (2)1.0567 (3)0.0674 (8)
H12A0.06030.13611.07070.101*
H12B0.17920.24011.13190.101*
H12C0.23120.13341.05960.101*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0497 (10)0.0531 (11)0.0501 (10)0.0009 (8)0.0141 (9)0.0083 (8)
N10.0763 (15)0.0387 (11)0.0433 (11)0.0030 (11)0.0248 (11)0.0039 (9)
C110.0580 (15)0.0334 (13)0.0369 (12)0.0000 (11)0.0171 (12)0.0018 (10)
C70.0483 (14)0.0359 (13)0.0375 (12)0.0007 (10)0.0132 (11)0.0029 (10)
C60.0510 (15)0.0296 (12)0.0354 (12)0.0022 (10)0.0116 (11)0.0016 (9)
C50.0482 (14)0.0336 (12)0.0297 (11)0.0016 (10)0.0127 (10)0.0052 (9)
C90.0496 (15)0.0413 (14)0.0422 (13)0.0042 (11)0.0063 (12)0.0013 (11)
C20.0533 (15)0.0397 (14)0.0387 (13)0.0006 (11)0.0181 (12)0.0064 (10)
C100.0649 (17)0.0367 (14)0.0393 (13)0.0084 (12)0.0098 (13)0.0051 (10)
C40.0540 (16)0.0443 (16)0.0596 (16)0.0075 (12)0.0253 (13)0.0017 (13)
N20.0910 (19)0.0520 (16)0.0877 (18)0.0086 (13)0.0337 (15)0.0115 (14)
C30.0490 (14)0.0445 (15)0.0569 (15)0.0016 (11)0.0197 (12)0.0065 (12)
C10.0589 (16)0.0443 (15)0.0497 (14)0.0050 (12)0.0274 (13)0.0078 (11)
C120.0650 (18)0.0741 (19)0.0598 (17)0.0023 (15)0.0180 (14)0.0212 (15)
Geometric parameters (Å, °) top
O1—C71.387 (3)C9—H9A0.9300
O1—C121.411 (3)C2—C11.353 (3)
N1—C11.352 (3)C2—C31.487 (3)
N1—C111.378 (3)C10—H10A0.9300
N1—H1A0.8600C4—N21.127 (3)
C11—C51.397 (3)C4—C31.448 (3)
C11—C101.381 (3)C3—H3A0.9700
C7—C61.366 (3)C3—H3B0.9700
C7—C91.391 (3)C1—H1B0.9300
C6—C51.389 (3)C12—H12A0.9600
C6—H6A0.9300C12—H12B0.9600
C5—C21.420 (3)C12—H12C0.9600
C9—C101.363 (3)
C7—O1—C12117.14 (18)C5—C2—C3126.4 (2)
C1—N1—C11109.2 (2)C9—C10—C11118.0 (2)
C1—N1—H1A125.4C9—C10—H10A121.0
C11—N1—H1A125.4C11—C10—H10A121.0
N1—C11—C5106.8 (2)N2—C4—C3177.3 (3)
N1—C11—C10131.5 (2)C4—C3—C2110.65 (19)
C5—C11—C10121.7 (2)C4—C3—H3A109.5
C6—C7—O1123.33 (19)C2—C3—H3A109.5
C6—C7—C9121.7 (2)C4—C3—H3B109.5
O1—C7—C9114.9 (2)C2—C3—H3B109.5
C7—C6—C5118.2 (2)H3A—C3—H3B108.1
C7—C6—H6A120.9C2—C1—N1110.0 (2)
C5—C6—H6A120.9C2—C1—H1B125.0
C6—C5—C11119.5 (2)N1—C1—H1B125.0
C6—C5—C2133.2 (2)O1—C12—H12A109.5
C11—C5—C2107.2 (2)O1—C12—H12B109.5
C10—C9—C7120.8 (2)H12A—C12—H12B109.5
C10—C9—H9A119.6O1—C12—H12C109.5
C7—C9—H9A119.6H12A—C12—H12C109.5
C1—C2—C5106.8 (2)H12B—C12—H12C109.5
C1—C2—C3126.8 (2)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···O1i0.862.183.038 (3)175.
Symmetry codes: (i) −x+1/2, y+1/2, −z+3/2.
Table 1
Hydrogen-bond geometry (Å, °)
top
D—H···AD—HH···AD···AD—H···A
N1—H1A···O1i0.862.183.038 (3)175.
Symmetry codes: (i) −x+1/2, y+1/2, −z+3/2.
Acknowledgements top

none

references
References top

Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany.

Rigaku. (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Woodward, A. W. & Bartel, B. (2005). Ann. Bot. 95, 707–735.