organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

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

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

[Scheme 1]

Experimental

Crystal data
  • C11H10N2O

  • Mr = 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[Rigaku. (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.983, Tmax = 0.983

  • 9617 measured reflections

  • 2164 independent reflections

  • 1225 reflections with I > 2σ(I)

  • Rint = 0.085

Refinement
  • R[F2 > 2σ(F2)] = 0.064

  • wR(F2) = 0.162

  • S = 1.01

  • 2164 reflections

  • 127 parameters

  • H-atom parameters constrained

  • Δρmax = 0.16 e Å−3

  • Δρmin = −0.23 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Rigaku. (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: DIAMOND (Brandenburg & Putz, 2005[Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: SHELXL97.

Supporting information


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)
Graphite monochromatorRint = 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 reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0640 restraints
wR(F2) = 0.162H-atom parameters constrained
S = 1.01Δρmax = 0.16 e Å3
2164 reflectionsΔρmin = 0.23 e Å3
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
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, º) 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, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···O1i0.862.183.038 (3)175
Symmetry code: (i) x+1/2, y+1/2, z+3/2.

Experimental details

Crystal data
Chemical formulaC11H10N2O
Mr186.21
Crystal system, space groupMonoclinic, P21/n
Temperature (K)293
a, b, c (Å)8.9242 (18), 11.461 (2), 9.889 (2)
β (°) 110.77 (3)
V3)945.7 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.20 × 0.20 × 0.20
Data collection
DiffractometerRigaku SCXmini
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku, 2005)
Tmin, Tmax0.983, 0.983
No. of measured, independent and
observed [I > 2σ(I)] reflections
9617, 2164, 1225
Rint0.085
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.064, 0.162, 1.01
No. of reflections2164
No. of parameters127
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
N1—H1A···O1i0.862.183.038 (3)174.8
Symmetry code: (i) x+1/2, y+1/2, z+3/2.
 

References

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

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.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
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