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Acta Cryst. (2009). E65, o489    [ doi:10.1107/S1600536809003821 ]

3-(4-Bromophenyl)-3-(4-hydroxy-6-oxo-1,6-dihydropyrimidin-5-yl)-N-[(S)-1-phenylethyl]propanamide

J.-H. Peng, W.-J. Hao and S.-J. Tu

Abstract top

In the molecule of the title compound, C21H20BrN3O3, the pyrimidine ring is oriented at dihedral angles of 80.87 (3) and 15.99 (3)°, respectively, to the pyrimidine and bromophenyl rings. The dihedral angle between the two benzene rings is 88.37 (3)°. In the crystal structure, intermolecular N-H...O and O-H...N hydrogen bonds link the molecules. A [pi]-[pi] contact between pyrimidine and phenyl rings [centroid-centroid distance = 3.776 (3) Å] may further stabilize the structure. The methine H and the methyl C and H atoms are disordered over two positions and were refined with occupancies of 0.522 (13) and 0.478 (13).

Comment top

The pyrimidines and their derivatives as a class of extremely important heterocyclic compounds are used in a wide array of synthetic and industrial applications. Not only they are an integral part of the genetic materials, viz. DNA and RNA as nucleotides and nucleosides but also play critical roles especially in pharmaceutical fields (Johar et al., 2005; Janeba et al., 2005). Some pyrimidine derivatives can give stable and good quality nanomaterials having many important electrical and optical properties (Soloducho et al., 2003; Mathews & Asokan, 2007), and also used as functional materials (Lagoja, 2005; Michael, 2005; Erian, 1993). We report herein the crystal structure of the title compound.

In the molecule of the title compound (Fig 1), the bond lengths (Allen et al., 1987) and angles are within normal ranges. Rings A (N1/N2/C1-C4), B (C8-C13) and C (C15-C20) are, of course, planar, and they are oriented at dihedral angles of A/B = 80.87 (3)°, A/C = 15.99 (3)° and B/C = 88.37 (3)°.

In the crystal structure, intermolecular N—H···O and O—H···N hydrogen bonds (Table 1) link the molecules, in which they may be effective in the stabilization of the structure. The π-π contact between the pyrimidine and the phenyl rings, Cg1—Cg2 [where Cg1 and Cg2 are centroids of the rings A (N1/N2/C1-C4) and C (C15-C20), respectively] may further stabilize the structure, with centroid-centroid distance of 3.776 (3) Å.

Related literature top

For general background, see: Johar et al. (2005); Janeba et al. (2005); Soloducho et al. (2003); Mathews & Asokan (2007); Lagoja (2005); Michael (2005); Erian (1993). For bond-length data, see: Allen et al. (1987).

Experimental top

The title compound was prepared by the reaction of 4-bromophenylidene-Meldrum's acid (1 mmol) with 6-hydroxypyrimidin-4(3H)-one (1 mmol) and (S)-1-phenylethanamine (1 mmol) at 373 K in glacial acetic acid under microwave irradiation (maximum power 250 W, initial power 100 W) for 18 min (yield; 85%, m.p. 551–553 K). Crystals suitable for X-ray analysis were obtained from an ethanol solution by slow evaporation.

Refinement top

Atoms C21, H21A, H21B, H21C and H14 were disordered over two positions. During the refinement process the disordered atoms were refined with occupancies of 0.522 (13) and 0.478 (13). H atoms were positioned geometrically, with O-H = 0.82 Å (for OH), N-H = 0.86 Å (for NH) and C-H = 0.93, 0.98, 0.97 and 0.96 Å for aromatic, methine, methylene and methyl H, respectively, and constrained to ride on their parent atoms, with Uiso(H) = xUeq(C,N,O), where x = 1.5 for methyl and OH H and x = 1.2 for all other H atoms.

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 1998); data reduction: SAINT (Bruker, 1998); 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 molecule, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
3-(4-Bromophenyl)-3-(4-hydroxy-6-oxo-1,6-dihydropyrimidin-5-yl)-N- [(S)-1-phenylethyl]propanamide top
Crystal data top
C21H20BrN3O3Z = 2
Mr = 442.31F(000) = 452
Triclinic, P1Dx = 1.463 Mg m−3
Hall symbol: -P 1Melting point = 551–553 K
a = 7.147 (1) ÅMo Kα radiation, λ = 0.71073 Å
b = 12.5010 (14) ÅCell parameters from 1260 reflections
c = 13.0940 (16) Åθ = 3.1–25.2°
α = 118.506 (2)°µ = 2.07 mm−1
β = 99.047 (1)°T = 298 K
γ = 93.074 (1)°Block, colorless
V = 1004.0 (2) Å30.20 × 0.18 × 0.17 mm
Data collection top
Bruker SMART CCD area-detector
diffractometer		3498 independent reflections
Radiation source: fine-focus sealed tube1810 reflections with I > 2σ(I)
graphiteRint = 0.029
φ and ω scansθmax = 25.0°, θmin = 1.8°
Absorption correction: multi-scan
(SADABS; Bruker, 1998)		h = −8→8
Tmin = 0.682, Tmax = 0.719k = −14→14
5285 measured reflectionsl = −15→12
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)] = 0.062Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.162H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0673P)2]
where P = (Fo2 + 2Fc2)/3
3498 reflections(Δ/σ)max = 0.001
265 parametersΔρmax = 0.38 e Å−3
0 restraintsΔρmin = −0.43 e Å−3
Crystal data top
C21H20BrN3O3γ = 93.074 (1)°
Mr = 442.31V = 1004.0 (2) Å3
Triclinic, P1Z = 2
a = 7.147 (1) ÅMo Kα radiation
b = 12.5010 (14) ŵ = 2.07 mm−1
c = 13.0940 (16) ÅT = 298 K
α = 118.506 (2)°0.20 × 0.18 × 0.17 mm
β = 99.047 (1)°
Data collection top
Bruker SMART CCD area-detector
diffractometer		3498 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 1998)		1810 reflections with I > 2σ(I)
Tmin = 0.682, Tmax = 0.719Rint = 0.029
5285 measured reflectionsθmax = 25.0°
Refinement top
R[F2 > 2σ(F2)] = 0.062H-atom parameters constrained
wR(F2) = 0.162Δρmax = 0.38 e Å−3
S = 1.06Δρmin = −0.43 e Å−3
3498 reflectionsAbsolute structure: ?
265 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'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 > σ(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*/UeqOcc. (<1)
Br10.19659 (12)−0.19766 (6)0.27241 (8)0.1005 (4)
O10.5807 (5)0.4123 (3)0.5600 (3)0.0571 (10)
O20.3046 (5)0.4229 (4)0.8648 (3)0.0636 (11)
H20.34060.44550.93560.095*
O30.0791 (5)0.5971 (3)0.7386 (3)0.0556 (10)
N10.7505 (6)0.4888 (4)0.7474 (4)0.0428 (11)
H10.85120.50630.72670.051*
N20.6202 (6)0.4935 (4)0.9004 (4)0.0478 (11)
N30.3055 (6)0.6437 (4)0.6606 (4)0.0475 (11)
H30.36440.61600.60260.057*
C10.5815 (7)0.4342 (4)0.6618 (5)0.0408 (12)
C20.4203 (7)0.4109 (4)0.7041 (4)0.0394 (12)
C30.4498 (7)0.4424 (5)0.8225 (4)0.0417 (13)
C40.7634 (7)0.5149 (5)0.8586 (5)0.0450 (13)
H40.88160.55080.91040.054*
C50.1767 (7)0.5650 (5)0.6613 (4)0.0420 (13)
C60.1587 (8)0.4333 (4)0.5658 (4)0.0445 (13)
H6A0.23530.42750.50880.053*
H6B0.02620.40260.52410.053*
C70.2281 (7)0.3561 (4)0.6225 (4)0.0429 (13)
H70.13780.35850.67250.051*
C80.2223 (7)0.2209 (5)0.5337 (5)0.0457 (13)
C90.2544 (10)0.1396 (5)0.5734 (6)0.0734 (19)
H90.27860.16820.65480.088*
C100.2523 (11)0.0158 (6)0.4969 (7)0.084 (2)
H100.2783−0.03690.52710.101*
C110.2120 (9)−0.0288 (5)0.3769 (6)0.0642 (17)
C120.1737 (11)0.0496 (6)0.3352 (6)0.088 (2)
H120.14440.02000.25370.105*
C130.1777 (11)0.1740 (5)0.4129 (5)0.079 (2)
H130.14960.22630.38260.094*
C140.3576 (10)0.7744 (6)0.7498 (6)0.0682 (17)
H140.23800.79460.77760.082*0.522 (13)
H14'0.44280.80490.71460.082*0.478 (13)
C150.4908 (10)0.7923 (5)0.8600 (6)0.0644 (17)
C160.4207 (11)0.7902 (7)0.9509 (7)0.085 (2)
H160.28900.77820.94490.102*
C170.5439 (14)0.8058 (7)1.0516 (7)0.099 (2)
H170.49490.80391.11250.119*
C180.7363 (16)0.8239 (7)1.0612 (8)0.105 (3)
H180.81820.83441.12890.126*
C190.8110 (12)0.8270 (7)0.9733 (10)0.108 (3)
H190.94300.83940.98040.129*
C200.6863 (11)0.8114 (7)0.8724 (8)0.090 (2)
H200.73650.81380.81210.108*
C210.3839 (18)0.8563 (10)0.6965 (11)0.072 (5)0.522 (13)
H21A0.26890.84430.64100.108*0.522 (13)
H21B0.48880.83600.65620.108*0.522 (13)
H21C0.41080.94080.75850.108*0.522 (13)
C21'0.211 (2)0.8496 (13)0.7670 (15)0.096 (7)0.478 (13)
H21D0.15340.84330.69260.144*0.478 (13)
H21E0.26470.93360.82300.144*0.478 (13)
H21F0.11520.82260.79700.144*0.478 (13)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.0949 (6)0.0471 (4)0.1247 (8)0.0142 (4)0.0106 (5)0.0183 (4)
O10.064 (3)0.080 (3)0.037 (2)0.007 (2)0.0134 (19)0.035 (2)
O20.045 (2)0.106 (3)0.037 (2)−0.023 (2)−0.0018 (18)0.040 (2)
O30.046 (2)0.062 (2)0.052 (2)−0.0011 (19)0.018 (2)0.020 (2)
N10.036 (3)0.052 (3)0.040 (3)0.003 (2)0.008 (2)0.023 (2)
N20.045 (3)0.060 (3)0.032 (3)−0.008 (2)−0.001 (2)0.021 (2)
N30.051 (3)0.051 (3)0.039 (3)0.001 (2)0.014 (2)0.020 (2)
C10.045 (3)0.045 (3)0.038 (3)0.006 (3)0.014 (3)0.023 (3)
C20.045 (3)0.040 (3)0.034 (3)−0.001 (2)0.004 (2)0.020 (3)
C30.039 (3)0.052 (3)0.035 (3)−0.004 (3)0.004 (3)0.024 (3)
C40.036 (3)0.058 (3)0.039 (4)0.003 (3)0.002 (3)0.025 (3)
C50.039 (3)0.049 (3)0.038 (3)0.006 (3)0.006 (3)0.023 (3)
C60.050 (3)0.047 (3)0.034 (3)0.002 (3)0.001 (2)0.020 (3)
C70.045 (3)0.043 (3)0.036 (3)−0.001 (3)0.005 (3)0.018 (3)
C80.047 (3)0.047 (3)0.041 (3)−0.002 (3)0.003 (3)0.022 (3)
C90.109 (6)0.056 (4)0.054 (4)0.007 (4)0.000 (4)0.031 (4)
C100.110 (6)0.055 (4)0.081 (5)0.012 (4)0.002 (4)0.034 (4)
C110.062 (4)0.048 (3)0.068 (5)0.004 (3)0.007 (3)0.020 (4)
C120.130 (7)0.057 (4)0.059 (5)0.007 (4)0.000 (4)0.020 (4)
C130.131 (6)0.048 (4)0.044 (4)0.008 (4)−0.006 (4)0.020 (3)
C140.079 (5)0.057 (4)0.063 (4)−0.005 (4)0.005 (4)0.030 (4)
C150.067 (5)0.049 (3)0.060 (4)−0.004 (3)0.007 (4)0.017 (3)
C160.076 (5)0.099 (6)0.063 (5)−0.004 (4)0.009 (4)0.029 (4)
C170.105 (7)0.100 (6)0.066 (6)−0.007 (5)0.000 (5)0.028 (5)
C180.107 (8)0.081 (5)0.082 (7)0.006 (5)−0.016 (6)0.016 (5)
C190.070 (6)0.098 (6)0.110 (8)0.006 (5)−0.005 (6)0.024 (6)
C200.070 (5)0.092 (5)0.091 (6)0.003 (4)0.018 (5)0.032 (5)
C210.071 (9)0.059 (7)0.088 (10)0.001 (6)0.007 (7)0.042 (7)
C21'0.094 (13)0.066 (9)0.104 (13)0.014 (9)−0.007 (10)0.031 (9)
Geometric parameters (Å, °) top
Br1—C111.874 (6)C10—H100.9300
O1—C11.225 (5)C11—C121.352 (8)
O2—C31.314 (5)C12—C131.389 (8)
O2—H20.8200C12—H120.9300
O3—C51.239 (5)C13—H130.9300
N1—C41.318 (6)C14—C21'1.418 (15)
N1—C11.391 (6)C14—C211.507 (12)
N1—H10.8600C14—C151.508 (9)
N2—C41.305 (6)C14—H140.9800
N2—C31.355 (6)C14—H14'0.9800
N3—C51.315 (6)C15—C161.373 (9)
N3—C141.467 (7)C15—C201.375 (9)
N3—H30.8600C16—C171.387 (10)
C1—C21.428 (7)C16—H160.9300
C2—C31.381 (6)C17—C181.358 (11)
C2—C71.495 (7)C17—H170.9300
C4—H40.9300C18—C191.357 (11)
C5—C61.500 (7)C18—H180.9300
C6—C71.534 (6)C19—C201.394 (11)
C6—H6A0.9700C19—H190.9300
C6—H6B0.9700C20—H200.9300
C7—C81.520 (7)C21—H14'0.8878
C7—H70.9800C21—H21A0.9600
C8—C91.360 (7)C21—H21B0.9600
C8—C131.372 (8)C21—H21C0.9600
C9—C101.382 (8)C21'—H21D0.9600
C9—H90.9300C21'—H21E0.9600
C10—C111.366 (9)C21'—H21F0.9600
C3—O2—H2109.5C11—C12—C13120.6 (6)
C4—N1—C1123.0 (4)C11—C12—H12119.7
C4—N1—H1118.5C13—C12—H12119.7
C1—N1—H1118.5C8—C13—C12121.2 (6)
C4—N2—C3116.3 (4)C8—C13—H13119.4
C5—N3—C14125.9 (5)C12—C13—H13119.4
C5—N3—H3117.1C21'—C14—N3117.5 (8)
C14—N3—H3117.1C21'—C14—C2169.8 (8)
O1—C1—N1119.3 (4)N3—C14—C21113.2 (7)
O1—C1—C2125.8 (5)C21'—C14—C15116.8 (9)
N1—C1—C2114.9 (5)N3—C14—C15111.5 (5)
C3—C2—C1117.2 (5)C21—C14—C15122.5 (7)
C3—C2—C7122.2 (4)N3—C14—H14102.1
C1—C2—C7120.5 (4)C21—C14—H14102.1
O2—C3—N2116.5 (4)C15—C14—H14102.1
O2—C3—C2119.0 (5)C21'—C14—H14'103.5
N2—C3—C2124.6 (4)N3—C14—H14'102.5
N2—C4—N1124.0 (5)C15—C14—H14'102.1
N2—C4—H4118.0C16—C15—C20118.0 (7)
N1—C4—H4118.0C16—C15—C14121.0 (6)
O3—C5—N3121.8 (5)C20—C15—C14120.9 (7)
O3—C5—C6121.8 (5)C15—C16—C17120.8 (7)
N3—C5—C6116.3 (4)C15—C16—H16119.6
C5—C6—C7109.1 (4)C17—C16—H16119.6
C5—C6—H6A109.9C18—C17—C16119.9 (8)
C7—C6—H6A109.9C18—C17—H17120.0
C5—C6—H6B109.9C16—C17—H17120.0
C7—C6—H6B109.9C19—C18—C17121.0 (8)
H6A—C6—H6B108.3C19—C18—H18119.5
C2—C7—C8111.5 (4)C17—C18—H18119.5
C2—C7—C6112.3 (4)C18—C19—C20118.8 (8)
C8—C7—C6114.0 (4)C18—C19—H19120.6
C2—C7—H7106.1C20—C19—H19120.6
C8—C7—H7106.1C15—C20—C19121.5 (8)
C6—C7—H7106.1C15—C20—H20119.2
C9—C8—C13117.0 (5)C19—C20—H20119.2
C9—C8—C7119.6 (5)C14—C21—H21A109.5
C13—C8—C7123.3 (5)C14—C21—H21B109.5
C8—C9—C10122.2 (6)C14—C21—H21C109.5
C8—C9—H9118.9H14'—C21—H21C114.6
C10—C9—H9118.9C14—C21'—H21D109.5
C11—C10—C9119.9 (6)C14—C21'—H21E109.5
C11—C10—H10120.1H21D—C21'—H21E109.5
C9—C10—H10120.1C14—C21'—H21F109.5
C12—C11—C10118.9 (6)H21D—C21'—H21F109.5
C12—C11—Br1120.8 (5)H21E—C21'—H21F109.5
C10—C11—Br1120.2 (5)
C4—N1—C1—O1−179.8 (5)C13—C8—C9—C103.2 (10)
C4—N1—C1—C21.4 (7)C7—C8—C9—C10−179.5 (6)
O1—C1—C2—C3−179.8 (5)C8—C9—C10—C11−1.8 (11)
N1—C1—C2—C3−1.0 (6)C9—C10—C11—C12−0.4 (11)
O1—C1—C2—C7−0.6 (8)C9—C10—C11—Br1−176.9 (5)
N1—C1—C2—C7178.1 (4)C10—C11—C12—C130.9 (11)
C4—N2—C3—O2−178.8 (5)Br1—C11—C12—C13177.4 (6)
C4—N2—C3—C21.0 (8)C9—C8—C13—C12−2.6 (10)
C1—C2—C3—O2179.6 (4)C7—C8—C13—C12−179.8 (6)
C7—C2—C3—O20.5 (7)C11—C12—C13—C80.7 (12)
C1—C2—C3—N2−0.1 (8)C5—N3—C14—C21'−59.8 (11)
C7—C2—C3—N2−179.3 (5)C5—N3—C14—C21−138.3 (7)
C3—N2—C4—N1−0.7 (8)C5—N3—C14—C1578.9 (7)
C1—N1—C4—N2−0.5 (8)C21'—C14—C15—C1651.4 (11)
C14—N3—C5—O32.8 (8)N3—C14—C15—C16−87.7 (8)
C14—N3—C5—C6−175.3 (5)C21—C14—C15—C16133.6 (8)
O3—C5—C6—C7−65.8 (6)C21'—C14—C15—C20−128.6 (10)
N3—C5—C6—C7112.3 (5)N3—C14—C15—C2092.4 (7)
C3—C2—C7—C8−108.8 (5)C21—C14—C15—C20−46.4 (10)
C1—C2—C7—C872.1 (6)C20—C15—C16—C17−0.5 (10)
C3—C2—C7—C6121.9 (5)C14—C15—C16—C17179.5 (6)
C1—C2—C7—C6−57.2 (6)C15—C16—C17—C180.3 (12)
C5—C6—C7—C2−50.3 (6)C16—C17—C18—C190.0 (13)
C5—C6—C7—C8−178.3 (4)C17—C18—C19—C200.1 (13)
C2—C7—C8—C960.7 (7)C16—C15—C20—C190.6 (11)
C6—C7—C8—C9−170.9 (5)C14—C15—C20—C19−179.5 (7)
C2—C7—C8—C13−122.2 (6)C18—C19—C20—C15−0.4 (12)
C6—C7—C8—C136.2 (8)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O3i0.861.882.694 (3)158
O2—H2···N2ii0.821.872.681 (3)170
N3—H3···O1iii0.862.092.892 (3)155
Symmetry codes: (i) x+1, y, z; (ii) −x+1, −y+1, −z+2; (iii) −x+1, −y+1, −z+1.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O3i0.861.882.694 (3)158
O2—H2···N2ii0.821.872.681 (3)170
N3—H3···O1iii0.862.092.892 (3)155
Symmetry codes: (i) x+1, y, z; (ii) −x+1, −y+1, −z+2; (iii) −x+1, −y+1, −z+1.
Acknowledgements top

We thank the Natural Science Foundation of China (grant No. 20672090) and Natural Science Foundation of Jiangsu Province (grant No. BK2006033).

references
References top

Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. 1–S19.

Bruker (1998). SMART, SAINT, SHELXTL and SADABS. Bruker AXS, Inc., Madison, Wisconsin, USA.

Erian, A. W. (1993). Chem. Rev. 93, 1991–2005.

Janeba, Z., Balzarini, J., Andrei, G., Robert Snoeck, R., De Clercq, E. & Robins, M. J. (2005). J. Med. Chem. 48, 4690–4696.

Johar, M., Manning, T., Kunimoto, D. Y. & Kumar, R. (2005). Bioorg. Med. Chem. 13, 6663–6671.

Lagoja, I. M. (2005). Chem. Biodivers. 2, 1–50.

Mathews, A. & Asokan, C. V. (2007). Tetrahedron, 63, 7845–7849.

Michael, J. P. (2005). Nat. Prod. Rep. 22, 627–646.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Soloducho, J., Doskocz, J., Cabaj, J. & Roszak, S. (2003). Tetrahedron, 59, 4761–4766.