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Acta Crystallogr Sect E Struct Rep Online. 2008 December 1; 64(Pt 12): o2469.
Published online 2008 November 29. doi:  10.1107/S160053680803941X
PMCID: PMC2960121

Ethyl 4-(4-nitro­phen­yl)-2-(trifluoro­meth­yl)pyrimido[1,2-a]benzimidazole-3-carboxyl­ate

Abstract

In the title compound, C20H13F3N4O4, the fused pyrimido[1,2-a]benzimidazole ring system is nearly planar, with a maximum deviation from the mean plane of 0.126 (1) Å. Mol­ecules are linked by C—H(...)N and C—H(...)O hydrogen bonds and by π–π inter­actions with inter­planar distances of 3.2661 (6) and 3.2775 (6) Å.

Related literature

For the bioactivity of benzo[4,5] imidazo[1,2-a]-pyrimidine derivatives, see: Abdel-Hafez (2007 [triangle]); Cheung et al. (2002 [triangle]); Nunes, Zhu, Amouzegh et al. (2005 [triangle]); Nunes, Zhu, Ermann et al. (2005 [triangle] [triangle]). For the bioactivity of organofluorine compounds, see: Hermann et al. (2003 [triangle]); Ulrich (2004 [triangle]).

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Object name is e-64-o2469-scheme1.jpg

Experimental

Crystal data

  • C20H13F3N4O4
  • M r = 430.34
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o2469-efi1.jpg
  • a = 8.4075 (5) Å
  • b = 26.6904 (14) Å
  • c = 9.0559 (5) Å
  • β = 111.027 (2)°
  • V = 1896.82 (18) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.13 mm−1
  • T = 113 (2) K
  • 0.32 × 0.30 × 0.26 mm

Data collection

  • Rigaku Saturn diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2002 [triangle]) T min = 0.961, T max = 0.968
  • 18499 measured reflections
  • 4492 independent reflections
  • 3911 reflections with I > 2σ(I)
  • R int = 0.039

Refinement

  • R[F 2 > 2σ(F 2)] = 0.045
  • wR(F 2) = 0.116
  • S = 1.11
  • 4492 reflections
  • 282 parameters
  • H-atom parameters constrained
  • Δρmax = 0.34 e Å−3
  • Δρmin = −0.22 e Å−3

Data collection: CrystalClear (Rigaku/MSC, 2002 [triangle]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053680803941X/fj2169sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680803941X/fj2169Isup2.hkl

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

Acknowledgments

The authors thank the Natural Science Foundation of Henan Province, China (grant No. 082300420110) and the Natural Science Foundation of Henan Province Eduation Department, China (grant No. 2007150036) for financial support.

supplementary crystallographic information

Comment

Among the derivatives of the dihydropyrimidine, the derivatives of pyrimido[1,2-a]benzimidazole have been reported to have a variety of biological activities, such as antineoplastic activity (Abdel-Hafez, 2007), protein kinase inhibitor (Nunes, Zhu, Amouzegh et al., 2005), T cell activation (Nunes, Zhu, Ermann et al., 2005), TIE-2 and/or VEGFR2 inhibitory activities (Cheung et al, 2002). Besides, compounds that contain fluorine have special bioactivity, for example, flumioxazin is a widely used herbicide (Hermann et al., 2003; Ulrich,2004). This led us to pay much attention to the synthesis and bioactivity of these important fused perfluoroalkylated heterocyclic compounds. To further study the relationship between the structure and bioactivity, we synthesised series of derivatives of benzo[4,5] pyrimido[1,2-a]benzimidazole. Here we report the crystal structure of the title compound, (I).

In the title molecule (Fig.1), the fused ring are near planar, for the dihedral angle between the phenyl ring/imidazole ring/pyrimidine ring are 3.68 (9) and 3.65 (8)°, respectively. The conformation of the attachment of the phenyl ring to the fused ring is described by the torsion angle of N2-C2-C11-C16 of 123.17 (14)°.

The crystal packing is stabilized by C—H···N and C—H···O intermolecular hydrogen bond (Table 1, Fig. 2). In addition, there are the intermolecular π–π stacking interacions between the two neighbouring parallel imidazole rings(symmetry code: 1-x,1-y,1-z; centroid-to-centroid distance: 3.3386 (9)Å, plane-plane distance: 3.2661 (6)Å, displacement distance: 0.692Å) and phenyl rings (C5-C10, symmetry code: -x,1-y,1-z; centroid-to-centroid distance: 3.9822 (9)Å, plane-plane distance: 3.2775 (6)Å, displacement distance: 2.262Å) in the title compound.

Experimental

The title compound was synthesized by the reaction of 4-nitrobenzaldehyde (1 mmol), ethyl 4,4,4-trifluoro-3-oxobutanoate (1 mmol) and 1H-benzo[d]imidazol-2-amine (1 mmol) in 3-butyl-1-methyl-1H- imidazol-3-ium chloride (1.5 mL) at 363 K for a certain time (monitered by TLC). After cooling, the reaction mixture was washed with water and recrystallized from ethanol, to obtain single crystals suitable for X-ray diffraction.

Refinement

H atoms were placed in calculated positions (C-H = 0.95–0.99 Å) and included in the final cycles of refinement using a riding model, with Uiso(H) = 1.2Ueq(parent atom).

Figures

Fig. 1.
The molecular structure of the title compound, showing 30% probability displacement ellipsoids and the atom-numbering scheme.
Fig. 2.
The packing diagram of the title compound. Intermolecular hydrogen bonds are shown as dashed lines.

Crystal data

C20H13F3N4O4F000 = 880
Mr = 430.34Dx = 1.507 Mg m3
Monoclinic, P21/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 4213 reflections
a = 8.4075 (5) Åθ = 2.3–27.9º
b = 26.6904 (14) ŵ = 0.13 mm1
c = 9.0559 (5) ÅT = 113 (2) K
β = 111.027 (2)ºBlock, orange
V = 1896.82 (18) Å30.32 × 0.30 × 0.26 mm
Z = 4

Data collection

Rigaku Saturn diffractometer4492 independent reflections
Radiation source: rotating anode3911 reflections with I > 2σ(I)
Monochromator: confocalRint = 0.039
Detector resolution: 7.31 pixels mm-1θmax = 27.9º
T = 113(2) Kθmin = 2.5º
ω scansh = −11→11
Absorption correction: multi-scan(CrystalClear; Rigaku/MSC, 2002)k = −34→35
Tmin = 0.961, Tmax = 0.968l = −11→11
18499 measured reflections

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.045  w = 1/[σ2(Fo2) + (0.0565P)2 + 0.3435P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.116(Δ/σ)max = 0.001
S = 1.11Δρmax = 0.35 e Å3
4492 reflectionsΔρmin = −0.22 e Å3
282 parametersExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0129 (15)
Secondary atom site location: difference Fourier map

Special details

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)

xyzUiso*/Ueq
F10.84705 (13)0.60521 (4)0.95949 (11)0.0426 (3)
F20.69893 (13)0.67273 (4)0.89880 (11)0.0385 (3)
F30.89019 (12)0.65773 (4)0.79846 (11)0.0409 (3)
O10.62940 (15)0.71967 (4)0.55129 (14)0.0356 (3)
O20.75651 (13)0.66746 (4)0.43224 (12)0.0274 (2)
O30.21549 (16)0.71512 (4)−0.24329 (13)0.0346 (3)
O40.26759 (14)0.64080 (4)−0.30905 (12)0.0308 (3)
N10.57725 (14)0.56861 (4)0.74106 (13)0.0219 (3)
N20.37814 (14)0.56650 (4)0.47093 (13)0.0189 (2)
N30.37200 (15)0.50437 (4)0.64198 (13)0.0229 (3)
N40.26160 (15)0.67171 (4)−0.21060 (14)0.0223 (3)
C10.44825 (17)0.54571 (5)0.62568 (15)0.0202 (3)
C20.45006 (17)0.60793 (5)0.43043 (15)0.0191 (3)
C30.57796 (17)0.63165 (5)0.54926 (16)0.0209 (3)
C40.63487 (17)0.61029 (5)0.70372 (15)0.0215 (3)
C50.24130 (17)0.53536 (5)0.38824 (16)0.0204 (3)
C60.24395 (18)0.49711 (5)0.49625 (17)0.0220 (3)
C70.12231 (19)0.45881 (5)0.45180 (18)0.0266 (3)
H70.12440.43220.52220.032*
C8−0.00046 (19)0.46102 (6)0.30259 (18)0.0293 (3)
H8−0.08370.43530.26940.035*
C9−0.0057 (2)0.50043 (6)0.19808 (18)0.0293 (3)
H9−0.09460.50110.09730.035*
C100.11445 (18)0.53821 (6)0.23755 (16)0.0255 (3)
H100.11120.56470.16640.031*
C110.39418 (17)0.62415 (5)0.26248 (15)0.0200 (3)
C120.41635 (18)0.59172 (5)0.15022 (16)0.0223 (3)
H120.46050.55900.18040.027*
C130.37390 (18)0.60735 (5)−0.00523 (16)0.0218 (3)
H130.38830.5857−0.08280.026*
C140.30986 (17)0.65537 (5)−0.04460 (15)0.0204 (3)
C150.28857 (18)0.68848 (5)0.06432 (16)0.0235 (3)
H150.24570.72130.03370.028*
C160.33160 (18)0.67247 (5)0.21975 (16)0.0226 (3)
H160.31840.69450.29700.027*
C170.65622 (18)0.67848 (5)0.51235 (16)0.0246 (3)
C180.8334 (2)0.71015 (6)0.3818 (2)0.0351 (4)
H18A0.89540.73170.47350.042*
H18B0.74450.73050.30320.042*
C190.9537 (2)0.68897 (7)0.3101 (2)0.0422 (4)
H19A1.04690.67160.39180.063*
H19B1.00030.71620.26520.063*
H19C0.89280.66530.22630.063*
C200.76917 (19)0.63640 (6)0.84092 (17)0.0284 (3)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
F10.0462 (6)0.0400 (6)0.0245 (5)0.0004 (5)−0.0079 (4)0.0038 (4)
F20.0469 (6)0.0361 (5)0.0305 (5)−0.0008 (4)0.0115 (4)−0.0114 (4)
F30.0288 (5)0.0560 (6)0.0329 (5)−0.0142 (4)0.0050 (4)−0.0033 (4)
O10.0452 (7)0.0252 (6)0.0389 (6)−0.0043 (5)0.0181 (5)−0.0062 (5)
O20.0309 (6)0.0254 (5)0.0283 (5)−0.0041 (4)0.0135 (5)0.0027 (4)
O30.0516 (7)0.0228 (5)0.0276 (6)0.0064 (5)0.0121 (5)0.0081 (4)
O40.0405 (6)0.0326 (6)0.0199 (5)0.0078 (5)0.0116 (5)0.0013 (4)
N10.0222 (6)0.0260 (6)0.0176 (5)0.0036 (5)0.0073 (5)0.0012 (5)
N20.0210 (6)0.0200 (5)0.0162 (5)0.0018 (4)0.0073 (4)0.0010 (4)
N30.0240 (6)0.0228 (6)0.0238 (6)0.0041 (5)0.0109 (5)0.0038 (5)
N40.0244 (6)0.0225 (6)0.0202 (6)0.0011 (5)0.0082 (5)0.0039 (5)
C10.0220 (6)0.0225 (6)0.0183 (6)0.0055 (5)0.0097 (5)0.0035 (5)
C20.0215 (6)0.0188 (6)0.0190 (6)0.0026 (5)0.0097 (5)0.0006 (5)
C30.0227 (7)0.0219 (7)0.0182 (6)0.0010 (5)0.0074 (5)0.0002 (5)
C40.0216 (6)0.0247 (7)0.0180 (6)0.0037 (5)0.0069 (5)−0.0001 (5)
C50.0203 (6)0.0208 (6)0.0217 (7)0.0003 (5)0.0096 (5)−0.0024 (5)
C60.0231 (7)0.0210 (7)0.0248 (7)0.0034 (5)0.0122 (6)0.0003 (5)
C70.0299 (7)0.0210 (7)0.0352 (8)0.0005 (6)0.0193 (6)−0.0006 (6)
C80.0281 (7)0.0271 (7)0.0365 (8)−0.0064 (6)0.0163 (7)−0.0085 (6)
C90.0279 (8)0.0344 (8)0.0254 (7)−0.0046 (6)0.0093 (6)−0.0053 (6)
C100.0262 (7)0.0285 (7)0.0216 (7)−0.0021 (6)0.0084 (6)−0.0012 (6)
C110.0199 (6)0.0219 (6)0.0176 (6)−0.0010 (5)0.0062 (5)0.0003 (5)
C120.0269 (7)0.0196 (6)0.0209 (7)0.0032 (5)0.0090 (6)0.0019 (5)
C130.0261 (7)0.0212 (7)0.0198 (6)0.0021 (5)0.0102 (5)0.0010 (5)
C140.0205 (6)0.0232 (7)0.0166 (6)−0.0010 (5)0.0057 (5)0.0028 (5)
C150.0273 (7)0.0194 (6)0.0227 (7)0.0028 (5)0.0079 (6)0.0022 (5)
C160.0261 (7)0.0215 (7)0.0198 (7)0.0019 (5)0.0077 (6)−0.0008 (5)
C170.0248 (7)0.0276 (7)0.0191 (6)−0.0024 (6)0.0051 (6)−0.0003 (5)
C180.0380 (9)0.0335 (8)0.0348 (9)−0.0097 (7)0.0142 (7)0.0076 (7)
C190.0411 (10)0.0533 (11)0.0367 (9)−0.0086 (8)0.0195 (8)0.0058 (8)
C200.0301 (8)0.0311 (8)0.0205 (7)−0.0003 (6)0.0047 (6)−0.0005 (6)

Geometric parameters (Å, °)

F1—C201.3304 (17)C7—C81.376 (2)
F2—C201.3365 (17)C7—H70.9500
F3—C201.3372 (18)C8—C91.405 (2)
O1—C171.2004 (18)C8—H80.9500
O2—C171.3277 (17)C9—C101.381 (2)
O2—C181.4617 (17)C9—H90.9500
O3—N41.2239 (15)C10—H100.9500
O4—N41.2289 (15)C11—C161.3941 (19)
N1—C41.3056 (18)C11—C121.3978 (18)
N1—C11.3522 (18)C12—C131.3865 (18)
N2—C21.3719 (17)C12—H120.9500
N2—C51.3989 (17)C13—C141.3864 (19)
N2—C11.4235 (16)C13—H130.9500
N3—C11.3108 (18)C14—C151.3830 (19)
N3—C61.3851 (19)C15—C161.3890 (19)
N4—C141.4755 (16)C15—H150.9500
C2—C31.3729 (19)C16—H160.9500
C2—C111.4861 (18)C18—C191.495 (2)
C3—C41.4248 (18)C18—H18A0.9900
C3—C171.5049 (19)C18—H18B0.9900
C4—C201.516 (2)C19—H19A0.9800
C5—C101.4004 (19)C19—H19B0.9800
C5—C61.4084 (19)C19—H19C0.9800
C6—C71.399 (2)
C17—O2—C18115.89 (12)C16—C11—C12120.43 (12)
C4—N1—C1117.02 (12)C16—C11—C2120.19 (12)
C2—N2—C5133.83 (11)C12—C11—C2119.22 (12)
C2—N2—C1120.72 (11)C13—C12—C11119.95 (13)
C5—N2—C1105.42 (11)C13—C12—H12120.0
C1—N3—C6104.76 (11)C11—C12—H12120.0
O3—N4—O4123.49 (12)C14—C13—C12118.30 (12)
O3—N4—C14118.27 (11)C14—C13—H13120.9
O4—N4—C14118.23 (11)C12—C13—H13120.9
N3—C1—N1125.63 (12)C15—C14—C13123.03 (12)
N3—C1—N2113.11 (12)C15—C14—N4118.63 (12)
N1—C1—N2121.23 (12)C13—C14—N4118.34 (12)
N2—C2—C3117.29 (12)C14—C15—C16118.21 (13)
N2—C2—C11120.05 (12)C14—C15—H15120.9
C3—C2—C11122.61 (12)C16—C15—H15120.9
C2—C3—C4118.54 (13)C15—C16—C11120.07 (13)
C2—C3—C17119.40 (12)C15—C16—H16120.0
C4—C3—C17122.05 (12)C11—C16—H16120.0
N1—C4—C3124.75 (13)O1—C17—O2125.91 (14)
N1—C4—C20114.58 (12)O1—C17—C3123.53 (13)
C3—C4—C20120.66 (13)O2—C17—C3110.57 (12)
N2—C5—C10132.99 (13)O2—C18—C19106.55 (13)
N2—C5—C6104.70 (12)O2—C18—H18A110.4
C10—C5—C6122.20 (13)C19—C18—H18A110.4
N3—C6—C7127.89 (13)O2—C18—H18B110.4
N3—C6—C5111.94 (12)C19—C18—H18B110.4
C7—C6—C5120.13 (13)H18A—C18—H18B108.6
C8—C7—C6117.67 (13)C18—C19—H19A109.5
C8—C7—H7121.2C18—C19—H19B109.5
C6—C7—H7121.2H19A—C19—H19B109.5
C7—C8—C9121.65 (14)C18—C19—H19C109.5
C7—C8—H8119.2H19A—C19—H19C109.5
C9—C8—H8119.2H19B—C19—H19C109.5
C10—C9—C8121.95 (14)F1—C20—F2107.24 (12)
C10—C9—H9119.0F1—C20—F3107.08 (12)
C8—C9—H9119.0F2—C20—F3107.02 (12)
C9—C10—C5116.31 (13)F1—C20—C4112.34 (12)
C9—C10—H10121.8F2—C20—C4110.55 (12)
C5—C10—H10121.8F3—C20—C4112.33 (12)
C6—N3—C1—N1176.80 (12)C7—C8—C9—C101.9 (2)
C6—N3—C1—N2−1.36 (15)C8—C9—C10—C5−0.5 (2)
C4—N1—C1—N3−178.44 (13)N2—C5—C10—C9−177.67 (14)
C4—N1—C1—N2−0.42 (18)C6—C5—C10—C9−2.0 (2)
C2—N2—C1—N3−175.64 (11)N2—C2—C11—C16123.17 (14)
C5—N2—C1—N32.61 (15)C3—C2—C11—C16−59.60 (18)
C2—N2—C1—N16.11 (18)N2—C2—C11—C12−61.32 (17)
C5—N2—C1—N1−175.64 (11)C3—C2—C11—C12115.92 (15)
C5—N2—C2—C3174.80 (13)C16—C11—C12—C13−0.8 (2)
C1—N2—C2—C3−7.54 (18)C2—C11—C12—C13−176.33 (12)
C5—N2—C2—C11−7.8 (2)C11—C12—C13—C140.0 (2)
C1—N2—C2—C11169.83 (11)C12—C13—C14—C150.9 (2)
N2—C2—C3—C43.79 (18)C12—C13—C14—N4−178.87 (12)
C11—C2—C3—C4−173.52 (12)O3—N4—C14—C154.90 (19)
N2—C2—C3—C17−177.54 (11)O4—N4—C14—C15−174.11 (13)
C11—C2—C3—C175.16 (19)O3—N4—C14—C13−175.37 (13)
C1—N1—C4—C3−3.5 (2)O4—N4—C14—C135.63 (18)
C1—N1—C4—C20175.22 (12)C13—C14—C15—C16−0.8 (2)
C2—C3—C4—N11.9 (2)N4—C14—C15—C16178.91 (12)
C17—C3—C4—N1−176.76 (13)C14—C15—C16—C11−0.1 (2)
C2—C3—C4—C20−176.79 (12)C12—C11—C16—C150.9 (2)
C17—C3—C4—C204.6 (2)C2—C11—C16—C15176.33 (13)
C2—N2—C5—C10−8.5 (2)C18—O2—C17—O1−3.0 (2)
C1—N2—C5—C10173.60 (14)C18—O2—C17—C3176.91 (12)
C2—N2—C5—C6175.31 (13)C2—C3—C17—O1106.37 (17)
C1—N2—C5—C6−2.60 (13)C4—C3—C17—O1−75.00 (19)
C1—N3—C6—C7−178.26 (13)C2—C3—C17—O2−73.58 (16)
C1—N3—C6—C5−0.43 (15)C4—C3—C17—O2105.05 (14)
N2—C5—C6—N31.99 (14)C17—O2—C18—C19174.18 (13)
C10—C5—C6—N3−174.73 (12)N1—C4—C20—F122.08 (18)
N2—C5—C6—C7−179.99 (12)C3—C4—C20—F1−159.12 (13)
C10—C5—C6—C73.3 (2)N1—C4—C20—F2−97.67 (14)
N3—C6—C7—C8175.79 (13)C3—C4—C20—F281.13 (16)
C5—C6—C7—C8−1.88 (19)N1—C4—C20—F3142.87 (13)
C6—C7—C8—C9−0.6 (2)C3—C4—C20—F3−38.33 (18)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C12—H12···N3i0.952.413.2987 (18)156
C16—H16···O3ii0.952.553.2096 (18)127

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x, −y+3/2, z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FJ2169).

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