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Acta Crystallogr Sect E Struct Rep Online. 2010 December 1; 66(Pt 12): o3305.
Published online 2010 November 27. doi:  10.1107/S1600536810048373
PMCID: PMC3011633

12-(4-Chloro­phen­yl)-7-methyl-10-phenyl-3,4,5,6,8,10-hexa­aza­tricyclo­[7.3.0.02,6]dodeca-1(9),2,4,7,11-penta­ene

Abstract

The 12 non-H atoms defining the triple-fused-ring system in the title compound, C19H13ClN6, are almost coplanar (r.m.s. deviation = 0.023 Å). The chloro-substituted ring is almost effectively coplanar with the central atoms [dihedral angle = 6.74 (13)°], but the N-bound benzene ring is not [dihedral angle = 54.38 (13)°]. In the crystal, supra­molecular chains along the a axis sustained by C—H(...)π and π–π [centroid–centroid distance between N4C and C4N five-membered rings = 3.484 (2) Å] stacking occur. A very long C—Cl(...)π contact is also seen.

Related literature

For biological activity of imidazoles, see: Yohjiro et al. (1990 [triangle]). For related structures, see: Jotani et al. (2010a [triangle],b [triangle]). Semi-empirical quantum chemical calculations were performed using MOPAC2009, see: Stewart (2009 [triangle]).

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Object name is e-66-o3305-scheme1.jpg

Experimental

Crystal data

  • C19H13ClN6
  • M r = 360.80
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o3305-efi1.jpg
  • a = 6.9459 (5) Å
  • b = 9.7010 (8) Å
  • c = 24.0382 (16) Å
  • V = 1619.7 (2) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.25 mm−1
  • T = 293 K
  • 0.40 × 0.22 × 0.15 mm

Data collection

  • Bruker SMART APEX CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.928, T max = 0.975
  • 8751 measured reflections
  • 1677 independent reflections
  • 1405 reflections with I > 2σ(I)
  • R int = 0.047

Refinement

  • R[F 2 > 2σ(F 2)] = 0.035
  • wR(F 2) = 0.096
  • S = 0.98
  • 1677 reflections
  • 236 parameters
  • H-atom parameters constrained
  • Δρmax = 0.17 e Å−3
  • Δρmin = −0.22 e Å−3

Data collection: APEX2 (Bruker, 2004 [triangle]); cell refinement: APEX2 and SAINT (Bruker, 2004 [triangle]); data reduction: SAINT and XPREP (Bruker, 2004 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]) and DIAMOND (Brandenburg, 2006 [triangle]); software used to prepare material for publication: publCIF (Westrip, 2010 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810048373/hb5751sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810048373/hb5751Isup2.hkl

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

Acknowledgments

The authors are thankful to the Department of Science and Technology (DST), and the SAIF, IIT Madras, India, for the X-ray data collection.

supplementary crystallographic information

Comment

The crystal structure of the title compound, (I), was examined in connection with on-going structural studies of imidazoles (Jotani et al., 2010a; Jotani et al., 2010b), which are known to possess a wide spectrum of biological activities such as herbicidal, anti-bacterial, anti-fungal, etc. (Yohjiro et al., 1990).

In (I), the 12 non-hydrogen atoms comprising the three ring fused system are co-planar with a r.m.s. deviation of 0.023 Å [max. and min. deviations = 0.033 (3) Å for atom N1 and -0.039 (4) Å for C3]. Whereas the chloro-substituted benzene ring is co-planar with the fused ring system [the C2–C3–C14–C15 torsion angle = -173.1 (4) °], the N-bound benzene ring is twisted out of the plane [the C1–N1–C8–C9 torsion angle = -54.0 (6) °]. Other features in the molecule match recently determined literature precedents (Jotani et al., 2010a; Jotani et al., 2010b)

The presence of C—H···π, Table 1, and π–π interactions between five-membered rings [ring centroid(N1,C1–C4)···ring centroid(N3–N6,C6) = 3.484 (2) Å with an angle of inclination = 2.2 (2) ° for i: 1/2 + x, 1/2 - y, 1 - z] lead to supramolecular chains along the a axis. The major interactions involving the Cl atom are of the type C—Cl···π, Table 1, which serve to connect molecules along the b axis.

Semi-empirical Quantum Chemical Calculations were performed using the MOPAC2009 programme (Stewart, 2009) to optimize the experimental structure with the Parametrization Model 6 (PM6) approximation together with restricted the Hartree Folk closed shell wavefunction; the minimizations were terminated at a r.m.s. gradient less than 0.01 kJ-mol-1 Å-1. These calculations gave an optimized structure which had different conformations for the chloro-substituted and the N-bound benzene rings, as seen in the C2—C3—C14—C15 and C1—N1—C8—C9 torsion angles of 146.1 and -38.5 °, respectively.

Experimental

To a well stirred mixture of 2-methyl-4-chloro-5-(4-chlorophenyl)-7-phenyl-7H-pyrrolo[2,3-d]pyrimidine (5 mmol) and Aliquat 336 (0.202 g, 0.5 mmol) in toluene (25 ml) was added sodium azide (0.390 g, 6 mmol) in water (5 ml). The reaction mixture was stirred under reflux conditions for 1–1.5 h. Thereafter, the two phases were separated, the aqueous phase was extracted with toluene (15 ml) and combined organic layers were washed with water (10 x 2 ml) and passed through anhydrous sodium sulfate. The excess of solvent was distilled under reduced pressure. The oily residue was treated with cold methanol. The obtained solid was filtered, dried, and crystallized from dioxane to yield colourless blocks; m.pt: 251–253 K.

Refinement

The C-bound H atoms were geometrically placed (C–H = 0.93–0.96 Å) and refined as riding with Uiso(H) = 1.2–1.5Ueq(parent atom). In the absence of significant anomalous scattering effects, 1165 Friedel pairs were averaged in the final refinement. In the final refinement a low angle reflection evidently effected by the beam stop was omitted, i.e. (002).

Figures

Fig. 1.
The molecular structure of (I) showing displacement ellipsoids at the 35% probability level.
Fig. 2.
A supramolecular chain aligned along the a axis in (I), mediated by C–H···π and π–π interactions, both shown as purple dashed lines.

Crystal data

C19H13ClN6F(000) = 744
Mr = 360.80Dx = 1.480 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 3699 reflections
a = 6.9459 (5) Åθ = 2.3–29.6°
b = 9.7010 (8) ŵ = 0.25 mm1
c = 24.0382 (16) ÅT = 293 K
V = 1619.7 (2) Å3Block, colourless
Z = 40.40 × 0.22 × 0.15 mm

Data collection

Bruker SMART APEX CCD diffractometer1677 independent reflections
Radiation source: fine-focus sealed tube1405 reflections with I > 2σ(I)
graphiteRint = 0.047
ω and [var phi] scansθmax = 25.0°, θmin = 1.7°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −8→4
Tmin = 0.928, Tmax = 0.975k = −11→11
8751 measured reflectionsl = −27→28

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)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.096H-atom parameters constrained
S = 0.98w = 1/[σ2(Fo2) + (0.066P)2] where P = (Fo2 + 2Fc2)/3
1677 reflections(Δ/σ)max < 0.001
236 parametersΔρmax = 0.17 e Å3
0 restraintsΔρmin = −0.22 e Å3

Special details

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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
Cl10.39113 (13)0.63434 (9)0.75124 (3)0.0425 (3)
N10.4515 (4)0.4484 (3)0.42147 (10)0.0298 (6)
N20.4434 (4)0.2102 (3)0.39545 (10)0.0298 (6)
N30.4374 (4)0.0610 (3)0.47095 (10)0.0283 (6)
N40.4365 (5)−0.0648 (3)0.49607 (11)0.0376 (7)
N50.4374 (5)−0.0389 (3)0.54866 (12)0.0425 (8)
N60.4393 (5)0.0980 (3)0.56050 (11)0.0361 (7)
C10.4475 (5)0.3117 (3)0.43459 (12)0.0278 (7)
C20.4411 (5)0.2987 (3)0.49267 (11)0.0245 (7)
C30.4383 (5)0.4353 (3)0.51533 (12)0.0273 (7)
C40.4465 (5)0.5218 (3)0.47005 (13)0.0301 (7)
H40.44840.61750.47220.036*
C50.4366 (5)0.0842 (3)0.41388 (13)0.0300 (7)
C60.4393 (5)0.1602 (3)0.51112 (12)0.0281 (7)
C70.4230 (6)−0.0361 (4)0.37716 (14)0.0405 (9)
H7A0.2920−0.06740.37580.061*
H7B0.5037−0.10850.39120.061*
H7C0.4645−0.01110.34040.061*
C80.4640 (5)0.5089 (3)0.36712 (12)0.0289 (8)
C90.6114 (5)0.4716 (4)0.33131 (13)0.0349 (8)
H90.70110.40510.34160.042*
C100.6221 (6)0.5346 (4)0.28045 (13)0.0408 (9)
H100.71860.50870.25570.049*
C110.4940 (5)0.6351 (4)0.26511 (13)0.0394 (9)
H110.50540.67850.23080.047*
C120.3477 (5)0.6713 (4)0.30125 (13)0.0396 (9)
H120.25960.73900.29120.048*
C130.3322 (5)0.6070 (4)0.35236 (13)0.0358 (8)
H130.23290.63040.37650.043*
C140.4292 (5)0.4834 (3)0.57356 (12)0.0276 (7)
C150.4074 (5)0.6233 (3)0.58553 (13)0.0315 (7)
H150.39970.68600.55640.038*
C160.3968 (5)0.6708 (3)0.63951 (13)0.0336 (8)
H160.38240.76440.64670.040*
C170.4079 (5)0.5776 (3)0.68284 (12)0.0300 (7)
C180.4282 (5)0.4389 (3)0.67246 (13)0.0340 (8)
H180.43420.37680.70190.041*
C190.4397 (5)0.3921 (3)0.61828 (12)0.0319 (7)
H190.45480.29830.61150.038*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0529 (6)0.0401 (5)0.0344 (4)−0.0031 (4)0.0028 (4)−0.0066 (4)
N10.0367 (16)0.0210 (15)0.0317 (14)−0.0009 (13)0.0002 (12)0.0045 (12)
N20.0289 (15)0.0257 (16)0.0348 (14)−0.0007 (14)−0.0003 (12)−0.0003 (12)
N30.0281 (15)0.0209 (14)0.0358 (14)−0.0017 (12)0.0016 (12)−0.0010 (12)
N40.0465 (19)0.0210 (15)0.0453 (18)−0.0009 (15)0.0005 (14)0.0049 (13)
N50.061 (2)0.0213 (17)0.0457 (18)−0.0007 (16)0.0016 (16)0.0061 (14)
N60.0501 (18)0.0232 (16)0.0349 (16)−0.0033 (14)0.0033 (13)0.0065 (12)
C10.0252 (17)0.0243 (18)0.0339 (17)0.0003 (15)0.0006 (14)0.0015 (14)
C20.0231 (17)0.0235 (17)0.0269 (15)0.0006 (15)0.0011 (13)0.0036 (13)
C30.0260 (17)0.0229 (17)0.0329 (17)0.0016 (15)−0.0016 (14)0.0033 (14)
C40.0365 (19)0.0214 (18)0.0323 (17)−0.0015 (15)0.0007 (15)−0.0013 (14)
C50.0238 (18)0.0308 (19)0.0355 (18)0.0000 (15)0.0017 (14)−0.0022 (15)
C60.0233 (17)0.0260 (18)0.0350 (17)0.0001 (15)0.0020 (13)0.0004 (14)
C70.043 (2)0.030 (2)0.048 (2)0.0006 (18)0.0033 (18)−0.0072 (16)
C80.0356 (19)0.0227 (18)0.0286 (17)−0.0026 (15)−0.0030 (14)0.0036 (14)
C90.035 (2)0.031 (2)0.0384 (18)0.0043 (16)0.0018 (15)0.0023 (16)
C100.044 (2)0.045 (2)0.0336 (19)−0.0009 (19)0.0070 (15)0.0038 (17)
C110.054 (2)0.031 (2)0.0338 (19)−0.0061 (17)−0.0049 (15)0.0061 (17)
C120.053 (2)0.032 (2)0.0336 (18)0.0090 (17)−0.0063 (16)0.0038 (16)
C130.043 (2)0.031 (2)0.0330 (18)0.0033 (16)0.0013 (14)−0.0008 (16)
C140.0256 (18)0.0259 (18)0.0314 (16)−0.0047 (15)0.0011 (14)−0.0022 (14)
C150.038 (2)0.0224 (17)0.0341 (17)0.0005 (16)−0.0012 (14)0.0057 (15)
C160.035 (2)0.0216 (18)0.0443 (19)−0.0005 (14)0.0002 (15)−0.0034 (16)
C170.0268 (18)0.033 (2)0.0304 (16)−0.0015 (14)−0.0010 (13)−0.0010 (14)
C180.041 (2)0.0290 (19)0.0325 (17)−0.0014 (17)0.0019 (15)0.0067 (15)
C190.0369 (18)0.0220 (18)0.0366 (18)−0.0036 (16)−0.0021 (15)0.0037 (14)

Geometric parameters (Å, °)

Cl1—C171.738 (3)C8—C131.368 (5)
N1—C11.364 (4)C8—C91.386 (5)
N1—C41.368 (4)C9—C101.369 (5)
N1—C81.435 (4)C9—H90.9300
N2—C51.301 (4)C10—C111.370 (5)
N2—C11.362 (4)C10—H100.9300
N3—C61.364 (4)C11—C121.382 (5)
N3—N41.361 (4)C11—H110.9300
N3—C51.390 (4)C12—C131.382 (5)
N4—N51.289 (4)C12—H120.9300
N5—N61.359 (4)C13—H130.9300
N6—C61.332 (4)C14—C191.395 (4)
C1—C21.402 (4)C14—C151.395 (4)
C2—C61.415 (4)C15—C161.379 (4)
C2—C31.433 (4)C15—H150.9300
C3—C41.376 (4)C16—C171.382 (4)
C3—C141.477 (4)C16—H160.9300
C4—H40.9300C17—C181.375 (5)
C5—C71.466 (4)C18—C191.382 (4)
C7—H7A0.9600C18—H180.9300
C7—H7B0.9600C19—H190.9300
C7—H7C0.9600
C1—N1—C4108.0 (3)C13—C8—N1118.7 (3)
C1—N1—C8127.6 (3)C9—C8—N1120.2 (3)
C4—N1—C8124.5 (3)C10—C9—C8118.6 (3)
C5—N2—C1116.4 (3)C10—C9—H9120.7
C6—N3—N4108.6 (2)C8—C9—H9120.7
C6—N3—C5125.8 (3)C9—C10—C11121.5 (3)
N4—N3—C5125.7 (3)C9—C10—H10119.2
N5—N4—N3105.1 (3)C11—C10—H10119.2
N4—N5—N6113.3 (3)C10—C11—C12119.3 (3)
C6—N6—N5104.9 (3)C10—C11—H11120.4
N2—C1—N1122.9 (3)C12—C11—H11120.4
N2—C1—C2128.5 (3)C11—C12—C13120.1 (3)
N1—C1—C2108.5 (3)C11—C12—H12120.0
C1—C2—C6113.4 (3)C13—C12—H12120.0
C1—C2—C3107.2 (3)C8—C13—C12119.5 (3)
C6—C2—C3139.4 (3)C8—C13—H13120.2
C4—C3—C2105.2 (3)C12—C13—H13120.2
C4—C3—C14124.0 (3)C19—C14—C15117.7 (3)
C2—C3—C14130.8 (3)C19—C14—C3121.9 (3)
N1—C4—C3111.0 (3)C15—C14—C3120.5 (3)
N1—C4—H4124.5C16—C15—C14121.7 (3)
C3—C4—H4124.5C16—C15—H15119.2
N2—C5—N3119.2 (3)C14—C15—H15119.2
N2—C5—C7123.0 (3)C17—C16—C15119.2 (3)
N3—C5—C7117.7 (3)C17—C16—H16120.4
N6—C6—N3108.1 (3)C15—C16—H16120.4
N6—C6—C2135.2 (3)C18—C17—C16120.6 (3)
N3—C6—C2116.7 (3)C18—C17—Cl1119.2 (2)
C5—C7—H7A109.5C16—C17—Cl1120.1 (3)
C5—C7—H7B109.5C17—C18—C19119.9 (3)
H7A—C7—H7B109.5C17—C18—H18120.0
C5—C7—H7C109.5C19—C18—H18120.0
H7A—C7—H7C109.5C18—C19—C14121.0 (3)
H7B—C7—H7C109.5C18—C19—H19119.5
C13—C8—C9121.0 (3)C14—C19—H19119.5
C6—N3—N4—N50.2 (4)N4—N3—C6—C2179.8 (3)
C5—N3—N4—N5−179.9 (3)C5—N3—C6—C2−0.1 (5)
N3—N4—N5—N6−0.1 (4)C1—C2—C6—N6177.8 (4)
N4—N5—N6—C60.1 (4)C3—C2—C6—N6−2.2 (8)
C5—N2—C1—N1−178.9 (3)C1—C2—C6—N3−2.2 (4)
C5—N2—C1—C2−1.5 (5)C3—C2—C6—N3177.9 (4)
C4—N1—C1—N2177.4 (3)C1—N1—C8—C13128.3 (4)
C8—N1—C1—N2−4.1 (5)C4—N1—C8—C13−53.5 (5)
C4—N1—C1—C2−0.4 (4)C1—N1—C8—C9−54.1 (5)
C8—N1—C1—C2178.1 (3)C4—N1—C8—C9124.2 (4)
N2—C1—C2—C63.2 (5)C13—C8—C9—C10−0.4 (5)
N1—C1—C2—C6−179.1 (3)N1—C8—C9—C10−178.0 (3)
N2—C1—C2—C3−176.8 (3)C8—C9—C10—C111.6 (5)
N1—C1—C2—C30.9 (4)C9—C10—C11—C12−1.6 (6)
C1—C2—C3—C4−1.0 (4)C10—C11—C12—C130.4 (5)
C6—C2—C3—C4179.0 (4)C9—C8—C13—C12−0.8 (5)
C1—C2—C3—C14179.1 (3)N1—C8—C13—C12176.8 (3)
C6—C2—C3—C14−1.0 (7)C11—C12—C13—C80.8 (5)
C1—N1—C4—C3−0.3 (4)C4—C3—C14—C19−173.7 (3)
C8—N1—C4—C3−178.8 (3)C2—C3—C14—C196.2 (6)
C2—C3—C4—N10.8 (4)C4—C3—C14—C157.0 (5)
C14—C3—C4—N1−179.3 (3)C2—C3—C14—C15−173.1 (3)
C1—N2—C5—N3−1.1 (5)C19—C14—C15—C160.1 (5)
C1—N2—C5—C7177.3 (3)C3—C14—C15—C16179.5 (3)
C6—N3—C5—N22.0 (5)C14—C15—C16—C17−0.1 (5)
N4—N3—C5—N2−178.0 (3)C15—C16—C17—C18−0.3 (5)
C6—N3—C5—C7−176.5 (3)C15—C16—C17—Cl1−179.0 (3)
N4—N3—C5—C73.5 (5)C16—C17—C18—C190.7 (5)
N5—N6—C6—N30.0 (4)Cl1—C17—C18—C19179.3 (3)
N5—N6—C6—C2−179.9 (4)C17—C18—C19—C14−0.6 (5)
N4—N3—C6—N6−0.1 (4)C15—C14—C19—C180.2 (5)
C5—N3—C6—N6179.9 (3)C3—C14—C19—C18−179.1 (3)

Hydrogen-bond geometry (Å, °)

Cg1 and Cg2 are the centroids of the C14–C19 and C8–C13 rings, respectively.
D—H···AD—HH···AD···AD—H···A
C7—H7a···Cg1i0.962.623.509 (5)154
C17—Cl1···Cg2ii1.737 (4)3.608 (2)4.423 (4)106.34 (13)

Symmetry codes: (i) x−1/2, −y+1/2, −z+1; (ii) −x+1/2, −y+1, z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HB5751).

References

  • Brandenburg, K. (2006). DIAMOND Crystal Impact GbR, Bonn, Germany.
  • Bruker (2004). APEX2, SAINT and XPREP Bruker AXS Inc., Madison, Wisconsin, USA.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Jotani, M. M., Shah, R. D. & Jasinski, J. P. (2010a). Acta Cryst. E66, o212–o213. [PMC free article] [PubMed]
  • Jotani, M. M., Shah, R. D. & Tiekink, E. R. T. (2010b). Acta Cryst. E66, o805. [PMC free article] [PubMed]
  • Sheldrick, G. M. (1996). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Stewart, J. P. (2009). MOPAC2009. Stewart Computational Chemistry http://OpenMOPAC.net.
  • Westrip, S. P. (2010). J. Appl. Cryst.43, 920–925.
  • Yohjiro, H., Hiasao, S., Nobuyuki, K., Takuo, W. & Kazukuki, T. (1990). US Patent 4902705.

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