supplementary materials


ng5344 scheme

Acta Cryst. (2013). E69, o1745    [ doi:10.1107/S1600536813029589 ]

Ethyl N-(3-cyano-1H-indol-2-yl)form­imidate

Y. Ruchun, Z. Hui and C. BanPeng

Abstract top

In the title compound, C12H11N3O, the C=N imino bond is in an E conformation. In the crystal, adjacent mol­ecules are linked by N-H...Ncyano hydrogen bonds, forming a chain running along [110].

Comment top

The indole compounds play an important role in the pharmaceutical and agrochemical industries. Introduction of different groups into indole molecules can generate a series of bioactive derivatives, which have been the subject of much attention in anti-cancer drugs (Laird et al., 2000; Li et al., 2005). In our study, we report an indole compound.

Related literature top

The starting reactant was synthesized according to a literature method (Yang et al., 2010). Introduction of different groups into indole molecules can generate a series of bioactive derivatives, which have been the subject of much attention in anti-cancer drugs (Laird et al., 2000; Li et al., 2005).

Experimental top

The starting reactant 1 was synthesized according to a literature method (Yang et al., 2010).

Synthesis of (2)

2-amino-1H-indole-3-carbonitrile (6.29 g, 40 mmol) was suspended in dry acetonitrile (150 ml). Triethylorthoformate (10.92 ml, 9.73 g, 60 mmol) was added and the mixture was heated at reflux temperature for 1 hour. The dark brown solution was cooled to room temperature and filtered through filter paper. The acetonitrile was removed on a rotoevaporator to afford 2 as a brown solid. 1H NMR (400 MHz, CDCl3, TMS): δ 1.41(t, 3H, J=7.2 Hz, OCH2CH3), 4.40 (q, 2H, J=7.2 Hz, OCH2CH3), 7.20-7.31 (m, 3H, aromatic H), 7.61 (dd, 1H, aromatic H), 8.51 (s, 1H, N=CH) ppm; 13C NMR (100 MHz, CDCl3): δ 14.0, 64.0, 72.7, 111.0, 116.7, 118.9, 122.2, 123.2, 127.5, 132.2, 149.8, 160.7 ppm. Crystals were grown from an acetonitrile solution.

Refinement top

H atoms bond to N were located in a difference map and refined with distance of N—H = 0.866 Å (18) and Uiso(H) = 1.2Ueq(N). other H atoms attached to C were fixed geometrically and treated as riding with C—H = 0.96 Å (methyl) or 0.93 Å (aromatic) and with Uiso(H) = 1.2Ueq(aromatic) or Uiso(H) = 1.5Ueq(methyl).

Computing details top

Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 1997); data reduction: SAINT (Bruker, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. Thermal ellipsoid plot of C12H11N3O. Ellipsoids are drawn at the 30% probability level and H atoms are represented as small spheres of arbitrary radius.
[Figure 2] Fig. 2. Synthesis method of the title compound.
[Figure 3] Fig. 3. The packing of the title compound, viewed down the c axis. Dashed lines indicate hydrogen bonds.
Ethyl N-(3-cyano-1H-indol-2-yl)formimidate top
Crystal data top
C12H11N3OF(000) = 896
Mr = 213.24Dx = 1.288 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 1934 reflections
a = 12.7884 (6) Åθ = 3.0–26.2°
b = 8.0546 (6) ŵ = 0.09 mm1
c = 21.4116 (10) ÅT = 296 K
β = 94.069 (4)°Block, colorless
V = 2200.0 (2) Å30.30 × 0.20 × 0.20 mm
Z = 8
Data collection top
Bruker SMART APEX
diffractometer
1934 independent reflections
Radiation source: fine-focus sealed tube1579 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.031
ω scansθmax = 25.0°, θmin = 3.0°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 1515
Tmin = 0.997, Tmax = 0.998k = 99
14358 measured reflectionsl = 2525
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)] = 0.040Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.110H atoms treated by a mixture of independent and constrained refinement
S = 1.12 w = 1/[σ2(Fo2) + (0.0524P)2 + 0.9005P]
where P = (Fo2 + 2Fc2)/3
1934 reflections(Δ/σ)max < 0.001
149 parametersΔρmax = 0.18 e Å3
379 restraintsΔρmin = 0.19 e Å3
Crystal data top
C12H11N3OV = 2200.0 (2) Å3
Mr = 213.24Z = 8
Monoclinic, C2/cMo Kα radiation
a = 12.7884 (6) ŵ = 0.09 mm1
b = 8.0546 (6) ÅT = 296 K
c = 21.4116 (10) Å0.30 × 0.20 × 0.20 mm
β = 94.069 (4)°
Data collection top
Bruker SMART APEX
diffractometer
1934 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
1579 reflections with I > 2σ(I)
Tmin = 0.997, Tmax = 0.998Rint = 0.031
14358 measured reflectionsθmax = 25.0°
Refinement top
R[F2 > 2σ(F2)] = 0.040H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.110Δρmax = 0.18 e Å3
S = 1.12Δρmin = 0.19 e Å3
1934 reflectionsAbsolute structure: ?
149 parametersAbsolute structure parameter: ?
379 restraintsRogers parameter: ?
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
N10.49318 (10)0.29181 (16)0.48715 (6)0.0443 (3)
H10.5435 (14)0.348 (2)0.4722 (8)0.053*
N20.19409 (11)0.05378 (19)0.46004 (7)0.0594 (4)
N30.40141 (10)0.25137 (15)0.38870 (6)0.0452 (3)
O10.34656 (11)0.16502 (16)0.29081 (6)0.0700 (4)
C10.48809 (11)0.25080 (18)0.54931 (7)0.0421 (4)
C20.54626 (13)0.3073 (2)0.60195 (8)0.0529 (4)
H20.60220.37970.59870.063*
C30.51832 (15)0.2523 (2)0.65929 (9)0.0618 (5)
H30.55570.28930.69550.074*
C40.43506 (15)0.1423 (2)0.66423 (8)0.0618 (5)
H40.41860.10610.70360.074*
C50.37706 (13)0.0865 (2)0.61200 (8)0.0525 (4)
H50.32140.01370.61570.063*
C60.40314 (11)0.14121 (17)0.55334 (7)0.0396 (4)
C70.35841 (10)0.11823 (17)0.49076 (7)0.0393 (4)
C80.41570 (11)0.21415 (17)0.45158 (7)0.0401 (4)
C90.26740 (12)0.02327 (19)0.47287 (7)0.0436 (4)
C100.36983 (15)0.1409 (2)0.35136 (8)0.0589 (5)
H100.36210.03430.36700.071*
C110.35402 (15)0.3329 (2)0.26845 (8)0.0627 (5)
H11A0.42220.37880.28140.075*
H11B0.30080.40140.28570.075*
C120.33881 (17)0.3308 (3)0.19911 (9)0.0765 (6)
H12A0.39290.26530.18230.115*
H12B0.34200.44230.18340.115*
H12C0.27160.28360.18670.115*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0337 (7)0.0414 (7)0.0582 (8)0.0134 (6)0.0058 (6)0.0020 (6)
N20.0426 (8)0.0631 (9)0.0725 (10)0.0232 (7)0.0051 (6)0.0006 (7)
N30.0391 (7)0.0447 (7)0.0523 (8)0.0114 (6)0.0070 (5)0.0010 (5)
O10.0946 (10)0.0603 (8)0.0553 (8)0.0194 (7)0.0057 (7)0.0082 (6)
C10.0338 (8)0.0366 (8)0.0557 (9)0.0016 (6)0.0025 (6)0.0021 (6)
C20.0446 (9)0.0448 (9)0.0678 (11)0.0089 (8)0.0064 (8)0.0016 (8)
C30.0642 (11)0.0599 (11)0.0592 (11)0.0026 (9)0.0107 (8)0.0003 (8)
C40.0637 (11)0.0688 (12)0.0527 (10)0.0039 (10)0.0037 (8)0.0083 (9)
C50.0443 (9)0.0529 (10)0.0611 (10)0.0072 (8)0.0083 (7)0.0083 (8)
C60.0300 (7)0.0342 (7)0.0547 (9)0.0005 (6)0.0047 (6)0.0010 (6)
C70.0284 (7)0.0349 (7)0.0551 (9)0.0055 (6)0.0069 (6)0.0008 (6)
C80.0322 (7)0.0337 (7)0.0548 (9)0.0039 (6)0.0068 (6)0.0021 (6)
C90.0354 (8)0.0412 (8)0.0550 (9)0.0062 (7)0.0087 (6)0.0015 (7)
C100.0729 (12)0.0487 (9)0.0563 (11)0.0157 (8)0.0117 (8)0.0050 (7)
C110.0639 (11)0.0637 (12)0.0609 (11)0.0036 (9)0.0071 (8)0.0010 (8)
C120.0734 (13)0.0910 (15)0.0636 (12)0.0029 (12)0.0056 (10)0.0011 (10)
Geometric parameters (Å, º) top
N1—C81.3587 (19)C4—C51.373 (2)
N1—C11.377 (2)C4—H40.9300
N1—H10.866 (18)C5—C61.393 (2)
N2—C91.1415 (19)C5—H50.9300
N3—C101.244 (2)C6—C71.431 (2)
N3—C81.379 (2)C7—C81.387 (2)
O1—C101.324 (2)C7—C91.422 (2)
O1—C111.440 (2)C10—H100.9300
C1—C21.383 (2)C11—C121.484 (3)
C1—C61.407 (2)C11—H11A0.9700
C2—C31.376 (2)C11—H11B0.9700
C2—H20.9300C12—H12A0.9600
C3—C41.395 (3)C12—H12B0.9600
C3—H30.9300C12—H12C0.9600
C8—N1—C1110.41 (12)C8—C7—C9126.43 (14)
C8—N1—H1124.4 (11)C8—C7—C6107.52 (12)
C1—N1—H1124.7 (11)C9—C7—C6125.92 (13)
C10—N3—C8119.12 (14)N1—C8—N3119.22 (13)
C10—O1—C11116.60 (14)N1—C8—C7108.23 (13)
N1—C1—C2130.48 (14)N3—C8—C7132.25 (13)
N1—C1—C6107.42 (13)N2—C9—C7178.31 (16)
C2—C1—C6121.97 (15)N3—C10—O1124.39 (16)
C3—C2—C1117.56 (16)N3—C10—H10117.8
C3—C2—H2121.2O1—C10—H10117.8
C1—C2—H2121.2O1—C11—C12108.37 (16)
C2—C3—C4121.33 (16)O1—C11—H11A110.0
C2—C3—H3119.3C12—C11—H11A110.0
C4—C3—H3119.3O1—C11—H11B110.0
C5—C4—C3121.14 (16)C12—C11—H11B110.0
C5—C4—H4119.4H11A—C11—H11B108.4
C3—C4—H4119.4C11—C12—H12A109.5
C4—C5—C6118.74 (15)C11—C12—H12B109.5
C4—C5—H5120.6H12A—C12—H12B109.5
C6—C5—H5120.6C11—C12—H12C109.5
C5—C6—C1119.25 (14)H12A—C12—H12C109.5
C5—C6—C7134.24 (14)H12B—C12—H12C109.5
C1—C6—C7106.42 (13)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N2i0.87 (2)2.12 (2)2.9490 (19)161 (2)
Symmetry code: (i) x+1/2, y+1/2, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N2i0.87 (2)2.12 (2)2.9490 (19)161 (2)
Symmetry code: (i) x+1/2, y+1/2, z.
Acknowledgements top

This work was supported by the Science Fund of the Education Office of Jiangxi (GJJ12583) and the Bureau of Science and Technology of Nanchang City.

references
References top

Bruker (1997). SAINT and SMART. Bruker AXS Inc., Madison, Wisconsin, USA.

Laird, D., Vajkoczy, P., Shawver, L. K., Thurnher, A., Liang, C. X. & Mohammadi, M. (2000). Cancer Res. 60 4152–4160.

Li, P.-K., Xiao, Z., Hu, Z., Pandit, B., Sun, Y., Sacket, D. L., Werbovetz, K., Lewis, A. & Johnsamuel, J. (2005). Bioorg. Med. Chem. Lett. 15 5382–5385.

Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.

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

Yang, X. B., Fu, H., Qiao, R. Z., Jiang, Y. Y. & Zhao, Y. F. (2010). Adv. Synth. Catal. 352, 1033–1038.