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Acta Crystallogr Sect E Struct Rep Online. 2009 December 1; 65(Pt 12): o3024.
Published online 2009 November 7. doi:  10.1107/S1600536809045681
PMCID: PMC2971748

(Z)-Amino­(2-methyl-3-oxoisoindolin-1-yl­idene)acetonitrile

Abstract

The asymmetric unit of the title compound, C11H9N3O, contains two independent and nearly identical mol­ecules (A and B). Mol­ecule A can be transformed to B using a rotation of approximately 85° around the [111] direction. Each A mol­ecule is connected to three B mol­ecules via N—H(...)N and N—H(...)O hydrogen bonds and vice versa. Centrosymmetric­ally related mol­ecules of the same residue form π–π inter­actions with centroid–centroid distances of 4.326 (1) and 3.826 (1) Å for the benzene rings of mol­ecules A and B, respectively.

Related literature

For the preparation of the compound as well as the crystal structure of the corresponding 2-benzyl derivative, see: Opatz & Ferenc (2004 [triangle]). For the crystal structure of the distantly related compound N-(2-amino-1,2-dicyano­vinyl)acetamide, see: Al-Azmi et al., (2001 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o3024-scheme1.jpg

Experimental

Crystal data

  • C11H9N3O
  • M r = 199.21
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o3024-efi1.jpg
  • a = 8.5021 (7) Å
  • b = 8.5080 (6) Å
  • c = 14.0412 (11) Å
  • α = 80.741 (5)°
  • β = 80.797 (5)°
  • γ = 68.329 (4)°
  • V = 925.98 (12) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 298 K
  • 0.44 × 0.30 × 0.24 mm

Data collection

  • Bruker SMART APEXII diffractometer
  • Absorption correction: none
  • 13710 measured reflections
  • 4570 independent reflections
  • 3668 reflections with I > 2σ(I)
  • R int = 0.095

Refinement

  • R[F 2 > 2σ(F 2)] = 0.047
  • wR(F 2) = 0.114
  • S = 0.97
  • 4570 reflections
  • 274 parameters
  • H-atom parameters constrained
  • Δρmax = 0.24 e Å−3
  • Δρmin = −0.29 e Å−3

Data collection: APEX2 (Bruker, 2006 [triangle]); cell refinement: SAINT (Bruker, 2006 [triangle]); data reduction: SAINT; program(s) used to solve structure: SIR97 (Altomare et al., 1999 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: PLATON.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809045681/bt5125sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809045681/bt5125Isup2.hkl

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

Acknowledgments

The authors thank the Deutsche Forschungsgemeinschaft and the Fonds der Chemischen Industrie for Financial Support.

supplementary crystallographic information

Comment

Amino(2-alkyl-3-oxo-2,3-dihydro-1H-isoindol-1-ylidene)acetonitriles are readily obtained in a three-component reaction between 2-carboxybenzaldehyde (2-formylbenzoic acid), aliphatic amines and cyanide in acidic medium. While steric hindrance is a decisive factor and the reaction fails for α-branched primary amines such as isopropylamine, all tested unbranched primary amines give the desired products. Consequently, the highest yield of 53% is found for the preparation of the title compound, in which unfavorable steric interactions are reduced to a minimum. Despite the fact that this compound had been obtained as the prototype example of the series, the determination of its crystal structure was hampered by twinning of the crystals. Compared to the N-benzyl derivative described earlier (Opatz & Ferenc, 2004), the exocyclic aminoacetonitrile unit is even less twisted against the plane of the bicyclic π-system (5.0 (1)° and 1.7 (2)°) (Fig. 1). Furthermore, the compound forms a hydrogen bonded network, in which both exocyclic nitrogen atoms as well as the oxygen atom act as acceptors and the NH2 group is the double donor. Centrosymetrically related molecules of the same residue form π-π-interactions. The distances between the centroids are 4.326 (1)Å and 3.826 (1)Å for the rings C1–C6 of A and B respectively (Fig. 2).

Experimental

The preparation was carried out as described in the procedure reported by Opatz and Ferenc (2004). The (Z)-isomer was obtained by recrystallization of the isomeric mixture from hexanes/ethyl acetate. Single crystals suitable for X-ray crystallography were grown by evaporation from a CH2Cl2 solution.

Refinement

Hydrogen atoms attached to carbons were placed at calculated positions with C—H = 0.95 Å (aromatic) or 0.98–0.99 Å (sp3 C-atom). Hydrogen atoms attached to N were located in difference Fourier maps. All H atoms were refined in the riding-model approximation with isotropic displacement parameters (set at 1.2–1.5 times of the Ueq of the parent atom). The crystal used for data collection was twinned. Using the twin matrix 0 - 1 0, -1 0 0, 0 0 - 1 with BSAF 0.468 (1) the structure refinement was succesful.

Figures

Fig. 1.
View of compound I. Displacement ellipsoids are drawn at the 50% probability level.
Fig. 2.
Part of the packing diagram. Hydrogen bonds with dashed lines.

Crystal data

C11H9N3OZ = 4
Mr = 199.21F(000) = 416
Triclinic, P1Dx = 1.429 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 8.5021 (7) ÅCell parameters from 5592 reflections
b = 8.5080 (6) Åθ = 2.5–27.8°
c = 14.0412 (11) ŵ = 0.10 mm1
α = 80.741 (5)°T = 298 K
β = 80.797 (5)°Block, yellow
γ = 68.329 (4)°0.44 × 0.30 × 0.24 mm
V = 925.98 (12) Å3

Data collection

Bruker SMART APEXII diffractometer3668 reflections with I > 2σ(I)
Radiation source: sealed tubeRint = 0.095
graphiteθmax = 28.4°, θmin = 2.6°
CCD scanh = −11→11
13710 measured reflectionsk = −11→11
4570 independent reflectionsl = −18→18

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.114H-atom parameters constrained
S = 0.97w = 1/[σ2(Fo2) + (0.0637P)2] where P = (Fo2 + 2Fc2)/3
4570 reflections(Δ/σ)max = 0.001
274 parametersΔρmax = 0.24 e Å3
0 restraintsΔρmin = −0.29 e Å3

Special details

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)

xyzUiso*/Ueq
C1A0.2396 (3)0.2747 (2)0.03598 (13)0.0253 (4)
C2A0.0717 (3)0.2796 (3)0.05168 (15)0.0336 (5)
H2A0.02730.24030.00790.040*
C3A−0.0270 (3)0.3451 (3)0.13471 (15)0.0383 (5)
H3A−0.13900.34870.14640.046*
C4A0.0353 (3)0.4049 (3)0.20035 (15)0.0368 (5)
H4A−0.03450.44740.25540.044*
C5A0.2019 (3)0.4024 (2)0.18496 (14)0.0331 (4)
H5A0.24540.44230.22890.040*
C6A0.3004 (3)0.3385 (2)0.10205 (13)0.0269 (4)
C7A0.4779 (3)0.3235 (2)0.06796 (13)0.0270 (4)
N8A0.5196 (2)0.2477 (2)−0.01665 (11)0.0260 (3)
C9A0.3809 (2)0.2157 (2)−0.04199 (13)0.0244 (4)
O10A0.5747 (2)0.36850 (19)0.10405 (10)0.0367 (3)
C11A0.6877 (3)0.2169 (3)−0.07052 (14)0.0334 (5)
H11A0.75390.2569−0.03750.050*
H11B0.67610.2765−0.13460.050*
H11C0.74390.0971−0.07490.050*
C12A0.3794 (3)0.1446 (2)−0.12086 (13)0.0274 (4)
N13A0.5046 (2)0.1033 (2)−0.19937 (12)0.0378 (4)
H13A0.49290.0314−0.24280.057*
H13B0.62480.0872−0.18580.057*
C14A0.2264 (3)0.1156 (3)−0.13240 (14)0.0333 (5)
N15A0.1094 (3)0.0862 (3)−0.14296 (14)0.0497 (5)
C1B0.2361 (2)0.7692 (2)0.48593 (13)0.0255 (4)
C2B0.2327 (3)0.9368 (2)0.46907 (14)0.0315 (5)
H2B0.27760.97930.51110.038*
C3B0.1607 (3)1.0388 (3)0.38784 (15)0.0365 (5)
H3B0.15751.15060.37600.044*
C4B0.0932 (3)0.9777 (3)0.32407 (15)0.0364 (5)
H4B0.04541.04870.27060.044*
C5B0.0971 (3)0.8124 (3)0.33976 (14)0.0340 (5)
H5B0.05270.77020.29750.041*
C6B0.1689 (3)0.7110 (2)0.42024 (13)0.0273 (4)
C7B0.1883 (3)0.5323 (2)0.45288 (13)0.0285 (4)
N8B0.2650 (2)0.49057 (19)0.53725 (11)0.0283 (4)
C9B0.2977 (2)0.6286 (2)0.56289 (13)0.0257 (4)
O10B0.1472 (2)0.43614 (19)0.41427 (10)0.0382 (4)
C11B0.2984 (3)0.3212 (2)0.58994 (15)0.0356 (5)
H11D0.26020.25480.55610.053*
H11E0.23860.33060.65400.053*
H11F0.41840.26670.59440.053*
C12B0.3717 (3)0.6276 (2)0.64150 (14)0.0285 (4)
N13B0.4376 (3)0.4959 (2)0.71336 (13)0.0409 (4)
H13C0.45490.52040.77300.061*
H13D0.41770.39430.70530.061*
C14B0.3965 (3)0.7805 (3)0.65574 (14)0.0334 (4)
N15B0.4204 (3)0.8972 (3)0.67200 (14)0.0483 (5)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C1A0.0268 (10)0.0205 (9)0.0297 (9)−0.0101 (8)−0.0021 (7)−0.0029 (7)
C2A0.0313 (12)0.0356 (11)0.0376 (10)−0.0165 (10)−0.0019 (9)−0.0049 (9)
C3A0.0289 (12)0.0403 (12)0.0448 (12)−0.0153 (9)0.0048 (9)−0.0037 (9)
C4A0.0401 (12)0.0329 (11)0.0346 (10)−0.0133 (9)0.0080 (9)−0.0067 (9)
C5A0.0417 (13)0.0291 (10)0.0306 (10)−0.0159 (9)0.0012 (9)−0.0059 (8)
C6A0.0340 (11)0.0199 (9)0.0292 (9)−0.0135 (8)−0.0020 (8)−0.0011 (7)
C7A0.0326 (10)0.0240 (9)0.0273 (9)−0.0128 (8)−0.0046 (8)−0.0026 (7)
N8A0.0269 (9)0.0262 (8)0.0288 (7)−0.0139 (7)−0.0008 (6)−0.0047 (6)
C9A0.0278 (10)0.0203 (9)0.0276 (9)−0.0120 (8)−0.0032 (7)−0.0006 (7)
O10A0.0405 (9)0.0431 (8)0.0372 (7)−0.0240 (7)−0.0049 (6)−0.0111 (6)
C11A0.0295 (11)0.0376 (11)0.0373 (11)−0.0169 (9)0.0020 (8)−0.0095 (9)
C12A0.0324 (11)0.0239 (9)0.0281 (9)−0.0127 (8)−0.0047 (8)−0.0011 (7)
N13A0.0425 (11)0.0443 (11)0.0347 (9)−0.0227 (9)0.0054 (8)−0.0183 (8)
C14A0.0397 (12)0.0357 (11)0.0288 (9)−0.0171 (10)−0.0050 (8)−0.0054 (8)
N15A0.0510 (13)0.0666 (14)0.0468 (11)−0.0343 (11)−0.0064 (9)−0.0153 (10)
C1B0.0258 (10)0.0236 (9)0.0286 (9)−0.0122 (8)0.0058 (7)−0.0078 (7)
C2B0.0379 (12)0.0260 (10)0.0358 (10)−0.0179 (9)0.0021 (9)−0.0082 (8)
C3B0.0420 (12)0.0244 (10)0.0425 (11)−0.0148 (9)0.0040 (9)−0.0034 (8)
C4B0.0419 (13)0.0308 (11)0.0345 (10)−0.0130 (10)−0.0013 (9)0.0001 (8)
C5B0.0379 (12)0.0370 (11)0.0313 (10)−0.0183 (10)0.0010 (8)−0.0079 (8)
C6B0.0316 (11)0.0269 (9)0.0265 (9)−0.0153 (8)0.0052 (7)−0.0083 (7)
C7B0.0337 (11)0.0263 (10)0.0296 (9)−0.0159 (8)0.0056 (8)−0.0111 (7)
N8B0.0372 (10)0.0213 (8)0.0313 (8)−0.0159 (7)0.0017 (7)−0.0081 (6)
C9B0.0273 (10)0.0208 (9)0.0317 (9)−0.0118 (8)0.0038 (7)−0.0098 (7)
O10B0.0548 (10)0.0354 (8)0.0357 (7)−0.0260 (8)−0.0021 (6)−0.0137 (6)
C11B0.0492 (13)0.0227 (10)0.0393 (10)−0.0184 (9)−0.0031 (9)−0.0038 (8)
C12B0.0296 (10)0.0250 (10)0.0332 (10)−0.0123 (8)0.0029 (8)−0.0095 (7)
N13B0.0592 (13)0.0316 (10)0.0369 (9)−0.0181 (9)−0.0131 (9)−0.0052 (8)
C14B0.0392 (12)0.0346 (11)0.0320 (10)−0.0171 (9)−0.0033 (8)−0.0100 (8)
N15B0.0668 (14)0.0387 (11)0.0526 (11)−0.0287 (10)−0.0115 (10)−0.0127 (9)

Geometric parameters (Å, °)

C1A—C2A1.395 (3)C1B—C6B1.395 (3)
C1A—C6A1.395 (3)C1B—C2B1.398 (3)
C1A—C9A1.485 (2)C1B—C9B1.475 (3)
C2A—C3A1.387 (3)C2B—C3B1.393 (3)
C2A—H2A0.9300C2B—H2B0.9300
C3A—C4A1.377 (3)C3B—C4B1.391 (3)
C3A—H3A0.9300C3B—H3B0.9300
C4A—C5A1.391 (3)C4B—C5B1.377 (3)
C4A—H4A0.9300C4B—H4B0.9300
C5A—C6A1.381 (3)C5B—C6B1.383 (3)
C5A—H5A0.9300C5B—H5B0.9300
C6A—C7A1.473 (3)C6B—C7B1.471 (3)
C7A—O10A1.228 (2)C7B—O10B1.225 (2)
C7A—N8A1.377 (2)C7B—N8B1.377 (3)
N8A—C9A1.412 (2)N8B—C9B1.412 (2)
N8A—C11A1.458 (2)N8B—C11B1.458 (2)
C9A—C12A1.348 (3)C9B—C12B1.352 (3)
C11A—H11A0.9600C11B—H11D0.9600
C11A—H11B0.9600C11B—H11E0.9600
C11A—H11C0.9600C11B—H11F0.9600
C12A—N13A1.395 (2)C12B—N13B1.393 (3)
C12A—C14A1.447 (3)C12B—C14B1.441 (2)
N13A—H13A0.9688N13B—H13C0.9399
N13A—H13B1.0251N13B—H13D0.9669
C14A—N15A1.148 (3)C14B—N15B1.147 (3)
C2A—C1A—C6A119.47 (17)C6B—C1B—C2B118.63 (19)
C2A—C1A—C9A133.57 (17)C6B—C1B—C9B107.85 (15)
C6A—C1A—C9A106.95 (16)C2B—C1B—C9B133.53 (18)
C3A—C2A—C1A117.81 (19)C3B—C2B—C1B118.40 (18)
C3A—C2A—H2A121.1C3B—C2B—H2B120.8
C1A—C2A—H2A121.1C1B—C2B—H2B120.8
C4A—C3A—C2A122.2 (2)C4B—C3B—C2B121.68 (18)
C4A—C3A—H3A118.9C4B—C3B—H3B119.2
C2A—C3A—H3A118.9C2B—C3B—H3B119.2
C3A—C4A—C5A120.48 (19)C5B—C4B—C3B120.3 (2)
C3A—C4A—H4A119.8C5B—C4B—H4B119.9
C5A—C4A—H4A119.8C3B—C4B—H4B119.9
C6A—C5A—C4A117.56 (19)C4B—C5B—C6B118.06 (19)
C6A—C5A—H5A121.2C4B—C5B—H5B121.0
C4A—C5A—H5A121.2C6B—C5B—H5B121.0
C5A—C6A—C1A122.42 (18)C5B—C6B—C1B122.93 (17)
C5A—C6A—C7A128.57 (17)C5B—C6B—C7B128.61 (17)
C1A—C6A—C7A109.01 (16)C1B—C6B—C7B108.46 (17)
O10A—C7A—N8A124.46 (18)O10B—C7B—N8B125.50 (18)
O10A—C7A—C6A129.24 (18)O10B—C7B—C6B128.30 (19)
N8A—C7A—C6A106.30 (15)N8B—C7B—C6B106.20 (14)
C7A—N8A—C9A111.70 (15)C7B—N8B—C9B112.07 (15)
C7A—N8A—C11A120.31 (15)C7B—N8B—C11B119.95 (14)
C9A—N8A—C11A127.93 (15)C9B—N8B—C11B127.95 (16)
C12A—C9A—N8A126.48 (17)C12B—C9B—N8B126.16 (17)
C12A—C9A—C1A127.51 (17)C12B—C9B—C1B128.42 (16)
N8A—C9A—C1A106.01 (14)N8B—C9B—C1B105.42 (15)
N8A—C11A—H11A109.5N8B—C11B—H11D109.5
N8A—C11A—H11B109.5N8B—C11B—H11E109.5
H11A—C11A—H11B109.5H11D—C11B—H11E109.5
N8A—C11A—H11C109.5N8B—C11B—H11F109.5
H11A—C11A—H11C109.5H11D—C11B—H11F109.5
H11B—C11A—H11C109.5H11E—C11B—H11F109.5
C9A—C12A—N13A128.35 (17)C9B—C12B—N13B130.12 (17)
C9A—C12A—C14A118.38 (17)C9B—C12B—C14B118.57 (18)
N13A—C12A—C14A113.12 (16)N13B—C12B—C14B111.26 (17)
C12A—N13A—H13A116.8C12B—N13B—H13C120.2
C12A—N13A—H13B115.0C12B—N13B—H13D111.4
H13A—N13A—H13B118.1H13C—N13B—H13D123.8
N15A—C14A—C12A177.1 (2)N15B—C14B—C12B175.9 (2)
C6A—C1A—C2A—C3A−1.5 (3)C6B—C1B—C2B—C3B0.7 (3)
C9A—C1A—C2A—C3A−179.98 (19)C9B—C1B—C2B—C3B−178.89 (19)
C1A—C2A—C3A—C4A0.4 (3)C1B—C2B—C3B—C4B−0.1 (3)
C2A—C3A—C4A—C5A0.3 (3)C2B—C3B—C4B—C5B−0.3 (3)
C3A—C4A—C5A—C6A0.1 (3)C3B—C4B—C5B—C6B0.2 (3)
C4A—C5A—C6A—C1A−1.3 (3)C4B—C5B—C6B—C1B0.4 (3)
C4A—C5A—C6A—C7A179.10 (18)C4B—C5B—C6B—C7B179.96 (19)
C2A—C1A—C6A—C5A2.1 (3)C2B—C1B—C6B—C5B−0.9 (3)
C9A—C1A—C6A—C5A−179.10 (16)C9B—C1B—C6B—C5B178.83 (17)
C2A—C1A—C6A—C7A−178.31 (16)C2B—C1B—C6B—C7B179.50 (16)
C9A—C1A—C6A—C7A0.5 (2)C9B—C1B—C6B—C7B−0.8 (2)
C5A—C6A—C7A—O10A−2.3 (3)C5B—C6B—C7B—O10B1.3 (3)
C1A—C6A—C7A—O10A178.13 (19)C1B—C6B—C7B—O10B−179.04 (19)
C5A—C6A—C7A—N8A178.35 (18)C5B—C6B—C7B—N8B−179.13 (19)
C1A—C6A—C7A—N8A−1.3 (2)C1B—C6B—C7B—N8B0.5 (2)
O10A—C7A—N8A—C9A−177.91 (18)O10B—C7B—N8B—C9B179.60 (18)
C6A—C7A—N8A—C9A1.5 (2)C6B—C7B—N8B—C9B0.1 (2)
O10A—C7A—N8A—C11A−0.6 (3)O10B—C7B—N8B—C11B−2.1 (3)
C6A—C7A—N8A—C11A178.87 (16)C6B—C7B—N8B—C11B178.37 (16)
C7A—N8A—C9A—C12A179.28 (17)C7B—N8B—C9B—C12B−179.94 (18)
C11A—N8A—C9A—C12A2.2 (3)C11B—N8B—C9B—C12B1.9 (3)
C7A—N8A—C9A—C1A−1.2 (2)C7B—N8B—C9B—C1B−0.5 (2)
C11A—N8A—C9A—C1A−178.31 (17)C11B—N8B—C9B—C1B−178.69 (17)
C2A—C1A—C9A—C12A−1.5 (3)C6B—C1B—C9B—C12B−179.79 (18)
C6A—C1A—C9A—C12A179.87 (18)C2B—C1B—C9B—C12B−0.2 (4)
C2A—C1A—C9A—N8A179.0 (2)C6B—C1B—C9B—N8B0.8 (2)
C6A—C1A—C9A—N8A0.4 (2)C2B—C1B—C9B—N8B−179.6 (2)
N8A—C9A—C12A—N13A−7.3 (3)N8B—C9B—C12B—N13B2.2 (3)
C1A—C9A—C12A—N13A173.28 (18)C1B—C9B—C12B—N13B−177.04 (19)
N8A—C9A—C12A—C14A177.50 (17)N8B—C9B—C12B—C14B179.39 (17)
C1A—C9A—C12A—C14A−1.9 (3)C1B—C9B—C12B—C14B0.1 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N13A—H13A···N15Bi0.972.083.035 (3)169
N13B—H13C···O10Aii0.942.042.948 (2)163
N13B—H13D···N13Aiii0.972.523.238 (3)131

Symmetry codes: (i) x, y−1, z−1; (ii) −x+1, −y+1, −z+1; (iii) x, y, z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BT5125).

References

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