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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 64| Part 11| November 2008| Page o2143
doi:10.1107/S1600536808033497

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

Gong-Chun Li,a* Feng-Ling Yanga and Chang-Sheng Yaob

aCollege of Chemistry and Chemical Engineering, Xuchang University, Xuchang, Henan Province 461000, People's Republic of China, and bSchool of Chemistry and Chemical Engineering, Xuzhou Normal University, Xuzhou 221116, People's Republic of China, and Key Laboratory of Biotechnology for Medicinal Plants, Xuzhou Normal University, Xuzhou 221116, People's Republic of China
*Correspondence e-mail: actaeli@gmail.com

(Received 13 October 2008; accepted 15 October 2008; online 18 October 2008)

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[Abdel-Hafez, A. A. M. (2007). Arch. Pharm. Res. 30, 678-684.]); Cheung et al. (2002[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, Zhu, Amouzegh et al. (2005[Nunes, J. J., Zhu, X. T., Amouzegh, P., Ghiron, C., Johnston, D. N. & Power, E. C. (2005). WO Patent No. 2005009443.]); Nunes, Zhu, Ermann et al. (2005[Nunes, J. J., Zhu, X. T., Ermann, M., Ghiron, C., Johnston, D. N. & Saluste, C. G. P. (2005). WO Patent No. 2005021551.]).

[Scheme 1]

Experimental

Crystal data

  • C16H13N3O

  • Mr = 263.29

  • Orthorhombic, P b c a

  • 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[Rigaku/MSC (2002). CrystalClear. Rigaku/MSC, The Woodlands, Texas, USA.]) Tmin = 0.984, Tmax = 0.989

  • 18521 measured reflections

  • 2232 independent reflections

  • 2075 reflections with I > 2σ(I)

  • Rint = 0.035
Refinement

  • R[F2 > 2σ(F2)] = 0.037

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the C11–C16 ring.
D—H⋯A D—H H⋯A D⋯A D—H⋯A
N1—H1⋯N3i 0.901 (9) 1.909 (10) 2.8027 (17) 171.0 (19)
C13—H13⋯Cgii 0.93 2.85 3.6296 (18) 143
Symmetry codes: (i) -x+2, -y, -z+1; (ii) [-x+{\script{3\over 2}}, y+{\script{1\over 2}}, z].

Data collection: CrystalClear (Rigaku/MSC, 2002[Rigaku/MSC (2002). CrystalClear. Rigaku/MSC, The Woodlands, Texas, USA.]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808033497/bt2811sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536808033497/bt2811Isup2.hkl

checkCIF report


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)
Confocal monochromatorRint = 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		2232 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku/MSC, 2002)		2075 reflections with I > 2σ(I)
Tmin = 0.984, Tmax = 0.989Rint = 0.035
18521 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0371 restraint
wR(F2) = 0.112H atoms treated by a mixture of independent and constrained refinement
S = 1.15Δρmax = 0.21 e Å−3
2232 reflectionsΔρmin = −0.28 e Å−3
185 parameters
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, º) 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, º) 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.

Experimental details

Crystal data
Chemical formulaC16H13N3O
Mr263.29
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)113
a, b, c (Å)13.606 (3), 7.5674 (15), 24.578 (5)
V (Å3)2530.6 (9)
Z8
Radiation typeMo Kα
µ (mm−1)0.09
Crystal size (mm)0.18 × 0.16 × 0.12
Data collection
DiffractometerRigaku Saturn
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku/MSC, 2002)
Tmin, Tmax0.984, 0.989
No. of measured, independent and
observed [I > 2σ(I)] reflections		18521, 2232, 2075
Rint0.035
(sin θ/λ)max (Å−1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.037, 0.112, 1.15
No. of reflections2232
No. of parameters185
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.21, −0.28

Computer programs: CrystalClear (Rigaku/MSC, 2002), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N3i0.901 (9)1.909 (10)2.8027 (17)171.0 (19)
C13—H13···Cgii0.932.853.6296 (18)143.00
Symmetry codes: (i) −x+2, −y, −z+1; (ii) −x+3/2, y+1/2, z.
 

Acknowledgements

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

First citationAbdel-Hafez, A. A. M. (2007). Arch. Pharm. Res. 30, 678–684.  Web of Science CrossRef PubMed CAS Google Scholar
 First citationCheung, 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.  Google Scholar
 First citationNunes, J. J., Zhu, X. T., Amouzegh, P., Ghiron, C., Johnston, D. N. & Power, E. C. (2005). WO Patent No. 2005009443.  Google Scholar
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Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 64| Part 11| November 2008| Page o2143
doi:10.1107/S1600536808033497
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