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Acta Cryst. (2008). E64, o2143    [ doi:10.1107/S1600536808033497 ]

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

G.-C. Li, F.-L. Yang and C.-S. Yao

Abstract top

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...[pi] interactions.

Comment top

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).

Related literature top

For related literature, see: Abdel-Hafez (2007); Cheung et al. (2002); Nunes, Zhu, Amouzegh et al. (2005); Nunes, Zhu, Ermann et al. (2005).

Experimental top

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 top

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).

Computing details top

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

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, showing 30% probability displacement ellipsoids and the atom-numbering scheme.
[Figure 2] Fig. 2. The packing diagram of the title compound. Intermolecular hydrogen bonds are shown as dashed lines.
4-Phenyl-1,2,3,4-tetrahydropyrimido[1,2-a]benzimidazol-2-one top
Crystal data top
C16H13N3ODx = 1.382 Mg m−3
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 mm−1
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 top
Rigaku Saturn
diffractometer		2232 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 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)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.112H atoms treated by a mixture of independent and constrained refinement
S = 1.15 w = 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 Å−3
1 restraintΔρmin = −0.28 e Å−3
Crystal data top
C16H13N3OV = 2530.6 (9) Å3
Mr = 263.29Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 13.606 (3) ŵ = 0.09 mm−1
b = 7.5674 (15) ÅT = 113 K
c = 24.578 (5) Å0.18 × 0.16 × 0.12 mm
Data collection top
Rigaku Saturn
diffractometer		2075 reflections with I > 2σ(I)
Absorption correction: multi-scan
(CrystalClear; Rigaku/MSC, 2002)		Rint = 0.035
Tmin = 0.984, Tmax = 0.989θmax = 25.0°
18521 measured reflectionsStandard reflections: 0
2232 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.037H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.112Δρmax = 0.21 e Å−3
S = 1.15Δρmin = −0.28 e Å−3
2232 reflectionsAbsolute structure: ?
185 parametersFlack parameter: ?
1 restraintRogers 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
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) top
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, °) top
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, °) top
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.
Table 1
Hydrogen-bond geometry (Å, °) top
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.
Acknowledgements top

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.

references
References top

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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.