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Acta Crystallogr Sect E Struct Rep Online. 2008 November 1; 64(Pt 11): o2143.
Published online 2008 October 18. doi:  10.1107/S1600536808033497
PMCID: PMC2959681

4-Phenyl-1,2,3,4-tetra­hydro­pyrimido[1,2-a]benzimidazol-2-one

Abstract

In the title compound, C16H13N3O, the tetrahydropyrimidin­one ring adopts a sofa conformation. In the crystal structure, mol­ecules are linked by N—H(...)N hydrogen bonds and C—H(...)π inter­actions.

Related literature

For background information on the biological activities of derivatives of benzo[4,5]imidazo[1,2-a]pyrimidine, see: Abdel-Hafez (2007 [triangle]); Cheung et al. (2002 [triangle]); Nunes, Zhu, Amouzegh et al. (2005 [triangle]); Nunes, Zhu, Ermann et al. (2005 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-o2143-scheme1.jpg

Experimental

Crystal data

  • C16H13N3O
  • M r = 263.29
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-64-o2143-efi1.jpg
  • a = 13.606 (3) Å
  • b = 7.5674 (15) Å
  • c = 24.578 (5) Å
  • V = 2530.6 (9) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.09 mm−1
  • T = 113 (2) K
  • 0.18 × 0.16 × 0.12 mm

Data collection

  • Rigaku Saturn diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2002 [triangle]) T min = 0.984, T max = 0.989
  • 18521 measured reflections
  • 2232 independent reflections
  • 2075 reflections with I > 2σ(I)
  • R int = 0.035

Refinement

  • R[F 2 > 2σ(F 2)] = 0.037
  • wR(F 2) = 0.112
  • S = 1.15
  • 2232 reflections
  • 185 parameters
  • 1 restraint
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.21 e Å−3
  • Δρmin = −0.28 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/S1600536808033497/bt2811sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808033497/bt2811Isup2.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 Education Department, China (grant No. 2007150036), for financial support.

supplementary crystallographic information

Comment

Among the derivatives of dihydropyrimidine, the derivatives of benzo[4,5]imidazo[1,2-a]-pyrimidine 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). This led us to pay much attention to the synthesis and bioactivity of these important fused heterocyclic compounds. To further study the relationship between structure and bioactivity, we synthesised a series of derivatives of benzo[4,5]imidazo[1,2-a]-pyrimidine. Here we report the crystal structure of the title compound.

In the title molecule (Fig.1), the pyrimidine ring adopts a sofa conformation. The phenyl ring is almost perpendicular to the pyrimidine plane [dihedral angle 89.00 (3)°].

The crystal packing is stabilized by an N—H···N hydrogen bond, and a C—H···π interaction (Table 1, Fig. 2).

Experimental

The title compound was synthesized by the reaction of benzaldehyde (1 mmol), 2,2-dimethyl-1,3-dioxane-4,6-dione (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

The hydrogen atom bonded to the nitrogen atom was located in a Fourier difference map and was refined with a distance restraint of 0.90 Å with an estimated standard deviation of 0.01 Å. Other H atoms were placed in calculated positions (C—H = 0.93–0.98 Å) and included in the final cycles of refinement using a riding model, with Uiso(H) = 1.2Ueq(C).

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

C16H13N3ODx = 1.382 Mg m3
Mr = 263.29Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, PbcaCell parameters from 5932 reflections
a = 13.606 (3) Åθ = 1.5–27.9°
b = 7.5674 (15) ŵ = 0.09 mm1
c = 24.578 (5) ÅT = 113 K
V = 2530.6 (9) Å3Block, colourless
Z = 80.18 × 0.16 × 0.12 mm
F(000) = 1104

Data collection

Rigaku Saturn diffractometer2232 independent reflections
Radiation source: rotating anode2075 reflections with I > 2σ(I)
confocalRint = 0.035
ω scansθmax = 25.0°, θmin = 1.7°
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2002)h = −14→16
Tmin = 0.984, Tmax = 0.989k = −9→9
18521 measured reflectionsl = −29→29

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)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.112H atoms treated by a mixture of independent and constrained refinement
S = 1.15w = 1/[σ2(Fo2) + (0.0639P)2 + 0.7741P] where P = (Fo2 + 2Fc2)/3
2232 reflections(Δ/σ)max < 0.001
185 parametersΔρmax = 0.21 e Å3
1 restraintΔρmin = −0.28 e Å3

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
O11.17082 (8)−0.08466 (14)0.37667 (4)0.0259 (3)
N11.05925 (9)0.04671 (16)0.43091 (5)0.0194 (3)
N20.98285 (9)0.31430 (15)0.40471 (4)0.0169 (3)
N30.95726 (9)0.21752 (16)0.48971 (5)0.0174 (3)
C11.11740 (10)0.0412 (2)0.38584 (6)0.0197 (3)
C21.11420 (10)0.2022 (2)0.34972 (6)0.0207 (3)
H2A1.13140.16730.31300.025*
H2B1.16350.28560.36210.025*
C31.01412 (10)0.29573 (19)0.34843 (5)0.0183 (3)
H31.02340.41410.33310.022*
C41.00072 (10)0.18918 (18)0.44299 (5)0.0168 (3)
C50.93882 (10)0.19885 (19)0.31400 (6)0.0187 (3)
C60.93352 (11)0.2371 (2)0.25863 (6)0.0225 (4)
H60.97480.32250.24380.027*
C70.86734 (12)0.1491 (2)0.22546 (6)0.0257 (4)
H70.86390.17640.18860.031*
C80.80641 (11)0.0207 (2)0.24712 (6)0.0261 (4)
H80.7624−0.03920.22480.031*
C90.81109 (11)−0.0182 (2)0.30193 (6)0.0259 (4)
H90.7702−0.10450.31650.031*
C100.87656 (11)0.0711 (2)0.33525 (6)0.0229 (4)
H100.87880.04510.37220.028*
C110.92020 (10)0.43649 (18)0.42860 (6)0.0169 (3)
C120.87700 (10)0.58958 (19)0.40932 (6)0.0211 (3)
H120.88680.62870.37390.025*
C130.81828 (11)0.6814 (2)0.44562 (6)0.0239 (4)
H130.78730.78460.43430.029*
C140.80457 (11)0.6224 (2)0.49899 (6)0.0220 (4)
H140.76460.68730.52230.026*
C150.84877 (10)0.47015 (19)0.51797 (6)0.0189 (3)
H150.84030.43290.55370.023*
C160.90620 (10)0.37505 (19)0.48182 (5)0.0164 (3)
H11.0597 (14)−0.043 (2)0.4548 (6)0.040 (5)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0249 (6)0.0282 (6)0.0246 (6)0.0092 (5)0.0023 (4)−0.0037 (5)
N10.0215 (7)0.0183 (7)0.0185 (6)0.0044 (5)0.0020 (5)0.0009 (5)
N20.0180 (6)0.0174 (6)0.0154 (6)0.0013 (5)0.0003 (5)−0.0006 (5)
N30.0171 (6)0.0169 (7)0.0182 (6)0.0007 (5)0.0000 (5)−0.0007 (5)
C10.0158 (7)0.0241 (8)0.0192 (7)0.0005 (6)−0.0014 (6)−0.0036 (6)
C20.0171 (7)0.0247 (8)0.0202 (7)−0.0016 (6)0.0021 (6)−0.0015 (6)
C30.0197 (7)0.0190 (8)0.0161 (7)−0.0006 (6)0.0030 (5)0.0007 (6)
C40.0151 (7)0.0169 (7)0.0184 (7)−0.0004 (5)−0.0015 (5)−0.0009 (5)
C50.0174 (7)0.0192 (8)0.0195 (7)0.0041 (5)0.0010 (6)−0.0009 (6)
C60.0263 (8)0.0209 (8)0.0204 (7)0.0035 (6)0.0023 (6)0.0024 (6)
C70.0313 (9)0.0273 (8)0.0186 (7)0.0087 (7)−0.0048 (6)−0.0012 (6)
C80.0240 (8)0.0237 (8)0.0306 (8)0.0057 (6)−0.0082 (6)−0.0069 (7)
C90.0220 (8)0.0252 (8)0.0303 (8)−0.0023 (6)−0.0007 (6)−0.0012 (6)
C100.0225 (8)0.0264 (8)0.0199 (7)−0.0009 (6)−0.0001 (6)0.0022 (6)
C110.0136 (7)0.0170 (7)0.0200 (7)−0.0018 (5)−0.0016 (5)−0.0024 (6)
C120.0209 (8)0.0199 (8)0.0224 (7)−0.0003 (6)−0.0022 (6)0.0021 (6)
C130.0221 (8)0.0179 (8)0.0316 (8)0.0039 (6)−0.0032 (6)0.0009 (6)
C140.0169 (7)0.0200 (8)0.0291 (8)0.0014 (6)0.0007 (6)−0.0054 (6)
C150.0162 (7)0.0199 (8)0.0208 (7)−0.0029 (6)0.0000 (6)−0.0025 (6)
C160.0141 (7)0.0154 (7)0.0197 (7)−0.0019 (5)−0.0019 (5)−0.0007 (5)

Geometric parameters (Å, °)

O1—C11.2192 (18)C6—H60.9300
N1—C11.3619 (18)C7—C81.384 (2)
N1—C41.3728 (18)C7—H70.9300
N1—H10.901 (9)C8—C91.380 (2)
N2—C41.3568 (18)C8—H80.9300
N2—C111.3879 (18)C9—C101.386 (2)
N2—C31.4541 (17)C9—H90.9300
N3—C41.3091 (18)C10—H100.9300
N3—C161.3933 (19)C11—C121.383 (2)
C1—C21.508 (2)C11—C161.4013 (19)
C2—C31.535 (2)C12—C131.385 (2)
C2—H2A0.9700C12—H120.9300
C2—H2B0.9700C13—C141.398 (2)
C3—C51.518 (2)C13—H130.9300
C3—H30.9800C14—C151.381 (2)
C5—C101.388 (2)C14—H140.9300
C5—C61.393 (2)C15—C161.385 (2)
C6—C71.385 (2)C15—H150.9300
C1—N1—C4122.48 (12)C8—C7—C6120.03 (14)
C1—N1—H1120.3 (13)C8—C7—H7120.0
C4—N1—H1117.2 (13)C6—C7—H7120.0
C4—N2—C11106.36 (11)C9—C8—C7119.84 (14)
C4—N2—C3122.67 (12)C9—C8—H8120.1
C11—N2—C3130.28 (12)C7—C8—H8120.1
C4—N3—C16104.09 (11)C8—C9—C10120.16 (15)
O1—C1—N1121.37 (14)C8—C9—H9119.9
O1—C1—C2122.66 (13)C10—C9—H9119.9
N1—C1—C2115.93 (12)C9—C10—C5120.64 (14)
C1—C2—C3114.22 (12)C9—C10—H10119.7
C1—C2—H2A108.7C5—C10—H10119.7
C3—C2—H2A108.7C12—C11—N2132.40 (13)
C1—C2—H2B108.7C12—C11—C16122.69 (13)
C3—C2—H2B108.7N2—C11—C16104.91 (12)
H2A—C2—H2B107.6C11—C12—C13116.43 (14)
N2—C3—C5112.30 (11)C11—C12—H12121.8
N2—C3—C2106.53 (11)C13—C12—H12121.8
C5—C3—C2112.82 (12)C12—C13—C14121.39 (14)
N2—C3—H3108.3C12—C13—H13119.3
C5—C3—H3108.3C14—C13—H13119.3
C2—C3—H3108.3C15—C14—C13121.71 (14)
N3—C4—N2114.39 (12)C15—C14—H14119.1
N3—C4—N1125.47 (13)C13—C14—H14119.1
N2—C4—N1120.13 (12)C14—C15—C16117.56 (13)
C10—C5—C6118.75 (13)C14—C15—H15121.2
C10—C5—C3122.61 (13)C16—C15—H15121.2
C6—C5—C3118.62 (13)C15—C16—N3129.56 (13)
C7—C6—C5120.56 (14)C15—C16—C11120.20 (13)
C7—C6—H6119.7N3—C16—C11110.24 (12)
C5—C6—H6119.7
C4—N1—C1—O1177.97 (13)C5—C6—C7—C8−0.6 (2)
C4—N1—C1—C20.3 (2)C6—C7—C8—C90.6 (2)
O1—C1—C2—C3149.84 (14)C7—C8—C9—C100.0 (2)
N1—C1—C2—C3−32.47 (18)C8—C9—C10—C5−0.7 (2)
C4—N2—C3—C587.47 (16)C6—C5—C10—C90.7 (2)
C11—N2—C3—C5−81.67 (17)C3—C5—C10—C9−177.88 (14)
C4—N2—C3—C2−36.51 (17)C4—N2—C11—C12−179.39 (15)
C11—N2—C3—C2154.34 (14)C3—N2—C11—C12−8.9 (2)
C1—C2—C3—N247.56 (15)C4—N2—C11—C161.18 (15)
C1—C2—C3—C5−76.11 (15)C3—N2—C11—C16171.67 (13)
C16—N3—C4—N2−0.06 (16)N2—C11—C12—C13−179.24 (14)
C16—N3—C4—N1−179.26 (13)C16—C11—C12—C130.1 (2)
C11—N2—C4—N3−0.74 (16)C11—C12—C13—C140.6 (2)
C3—N2—C4—N3−172.13 (12)C12—C13—C14—C150.0 (2)
C11—N2—C4—N1178.50 (12)C13—C14—C15—C16−1.2 (2)
C3—N2—C4—N17.1 (2)C14—C15—C16—N3−178.84 (13)
C1—N1—C4—N3−166.90 (14)C14—C15—C16—C111.8 (2)
C1—N1—C4—N213.9 (2)C4—N3—C16—C15−178.53 (14)
N2—C3—C5—C10−30.14 (19)C4—N3—C16—C110.85 (15)
C2—C3—C5—C1090.27 (16)C12—C11—C16—C15−1.3 (2)
N2—C3—C5—C6151.27 (13)N2—C11—C16—C15178.17 (12)
C2—C3—C5—C6−88.32 (16)C12—C11—C16—N3179.23 (12)
C10—C5—C6—C70.0 (2)N2—C11—C16—N3−1.28 (15)
C3—C5—C6—C7178.60 (13)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···N3i0.90 (1)1.91 (1)2.8027 (17)171 (2)
C13—H13···Cgii0.932.853.6296 (18)143

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BT2811).

References

  • Abdel-Hafez, A. A. M. (2007). Arch. Pharm. Res.30, 678–684. [PubMed]
  • Cheung, M., Harris, P. A., Hasegawa, M., Ida, S., Kano, K., Nishigaki, N., Sato, H., Veal, J. M., Washio, Y. & West, R. I. (2002). WO Patent No. 2002044156.
  • Nunes, J. J., Zhu, X. T., Amouzegh, P., Ghiron, C., Johnston, D. N. & Power, E. C. (2005). WO Patent No. 2005009443.
  • Nunes, J. J., Zhu, X. T., Ermann, M., Ghiron, C., Johnston, D. N. & Saluste, C. G. P. (2005). WO Patent No. 2005021551.
  • Rigaku/MSC (2002). CrystalClear Rigaku/MSC, The Woodlands, Texas, USA.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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