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Acta Cryst. (2008). E64, o1752    [ doi:10.1107/S1600536808025610 ]

Ethyl 6-methyl-2-oxo-4-phenyl-1,2,3,4-tetrahydropyrimidine-5-carboxylate

M. Nizam Mohideen, A. Rasheeth, C. A. M. A. Huq and S. S. Nizar

Abstract top

The title compound, C14H16N2O3, belongs to a group of esters of 2-oxo- and 1,2,3,4-tetrahydropyrimidine-5-carboxylic acids, which exhibit a wide spectrum of biological activities. The dihydropyrimidine ring adopts a screw-boat conformation. The crystal packing is stabilized by strong N-H...O and weak C-H...O intermolecular hydrogen bonds. An intramolecular C-H...O hydrogen bond is also present.

Comment top

The title compound belongs to the group of esters of 2-oxo and -1,2,3,4-tetrahydropyrimidine-5-carboxylic acids, which are known as `Biginelli compounds' (Kappe et al., 1997). It has been suggested that the substituent effect may be attributable to intramolecular hydrogen bonding between the alkoxy oxygen and the proton of the pyrimidine ring NH group (Broughton et al., 1975). Several marine alkaloids having the dihydropyrimidine core unit have been found to show interesting biological activities, such as antiviral, antibacterial and anti-inflammatory (Overman et al., 1995). Many functionalized derivatives are used as calcium channel blockers and antihypertensive agents (Atwal et al., 1991). Against this background and in order to obtain detailed information on its molecular conformation, the structure of the title compound has been determined and the results are presented here.

The bond lengths and angles are comparable with the similar structure reported in the literature (Li et al., 2005). The six membered ring (atoms N1, N2, C7, C8, C9, C10) of the dihydropyrimidine group adopts a screw boat conformation; the puckering parameters are q2 = 0.257 (1) Å and φ = 211.7 (2)° (Cremer & Pople, 1975), and the lowest displacement asymmetry parameters ΔS(N1) is 14.4 (1)° (Nardelli, 1983), with atom O1 deviating by -0.116 (1) Å from the least squares plane of the ring.

The dihedral angle between the pyrimidine and benzene rings is 86.5 (1)°, close to the value of 82.8 (6)° found in ethyl 4-(4-hydroxyphenyl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5- carboxylate.

The crystal packing is stabilized by strong N—H···O and C—H···O intermolecular hydrogen bonds (Table 1).

Related literature top

For related literature, see: Atwal et al. (1991); Broughton et al. (1975); Cremer & Pople (1975); Kappe et al. (1997); Li et al. (2005); Nardelli (1983); Overman et al. (1995).

Experimental top

A mixture of benzaldehyde (0.106 g, 1 mmol), ethyl acetoacetate (0.130 g, 1 mmol) and urea (0.070 g, 1.17 mmol) was ground with four drops of ortho phosphoric acid for about 30 minutes. The reaction mixture was cooled for 15 minutes and poured into a beaker containing 50 ml of cold water. The precipitate obtained was filtered, washed with water and ethanol to get white solid. Single crystals of the title compound suitable for X-ray diffraction were obtained by slow evaporation of a solution in ethanol (0.26 g, 92% yield; mp 203–204).

Refinement top

All H atoms were positioned geometrically and allowed to ride on their parent C atoms, with C—H distances fixed in the range 0.93–0.98 Å and N—H distance of 0.86 Å, with Uiso(H) = 1.5Ueq(C) for methyl H atoms and Uiso(H) = 1.2Ueq(C, N) for other H atoms.

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: APEX2 and SAINT (Bruker, 2004); data reduction: SAINT (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2003).

Figures top
[Figure 1] Fig. 1. The molecular configuration and atom-numbering scheme for (I). Displacement ellipsoids are drawn at the 50% probability level.
Ethyl 6-methyl-2-oxo-4-phenyl-1,2,3,4-tetrahydropyrimidine-5-carboxylate top
Crystal data top
C14H16N2O3Z = 2
Mr = 260.29F000 = 276
Triclinic, P1Dx = 1.324 Mg m−3
Hall symbol: -P 1Mo Kα radiation
λ = 0.71073 Å
a = 7.5495 (2) ÅCell parameters from 5321 reflections
b = 8.9797 (3) Åθ = 2.5–24.1º
c = 11.0812 (3) ŵ = 0.09 mm−1
α = 107.843 (2)ºT = 293 (2) K
β = 108.603 (1)ºNeedle, colourless
γ = 98.244 (2)º0.3 × 0.2 × 0.2 mm
V = 653.07 (4) Å3
Data collection top
Bruker APEXII CCD area-detector
diffractometer		2972 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.023
Monochromator: graphiteθmax = 29.7º
T = 293(2) Kθmin = 2.5º
ω and φ scansh = −9→10
Absorption correction: Nonek = −12→12
16135 measured reflectionsl = −15→15
3710 independent reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.047H-atom parameters constrained
wR(F2) = 0.159  w = 1/[σ2(Fo2) + (0.0959P)2 + 0.106P]
where P = (Fo2 + 2Fc2)/3
S = 1.00(Δ/σ)max < 0.001
3710 reflectionsΔρmax = 0.34 e Å−3
174 parametersΔρmin = −0.33 e Å−3
Primary atom site location: structure-invariant direct methodsExtinction correction: none
Crystal data top
C14H16N2O3γ = 98.244 (2)º
Mr = 260.29V = 653.07 (4) Å3
Triclinic, P1Z = 2
a = 7.5495 (2) ÅMo Kα
b = 8.9797 (3) ŵ = 0.09 mm−1
c = 11.0812 (3) ÅT = 293 (2) K
α = 107.843 (2)º0.3 × 0.2 × 0.2 mm
β = 108.603 (1)º
Data collection top
Bruker APEXII CCD area-detector
diffractometer		3710 independent reflections
Absorption correction: None2972 reflections with I > 2σ(I)
16135 measured reflectionsRint = 0.023
Refinement top
R[F2 > 2σ(F2)] = 0.047174 parameters
wR(F2) = 0.159H-atom parameters constrained
S = 1.00Δρmax = 0.34 e Å−3
3710 reflectionsΔρmin = −0.33 e Å−3
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*/Ueq
O1−0.18468 (12)0.90274 (12)0.54481 (10)0.0472 (2)
O20.51966 (14)0.59340 (12)0.67258 (11)0.0546 (3)
O30.30937 (13)0.47104 (11)0.73822 (10)0.0473 (2)
N1−0.09885 (13)0.70875 (12)0.62494 (10)0.0389 (2)
H1−0.21650.66510.61070.047*
N20.10294 (14)0.85056 (13)0.55737 (11)0.0413 (2)
H20.12880.92640.52850.050*
C10.2277 (2)0.89996 (17)0.91862 (15)0.0542 (3)
H1A0.27820.94950.86990.065*
C20.2660 (3)0.9866 (2)1.05616 (17)0.0711 (5)
H2A0.33981.09421.09820.085*
C30.1961 (3)0.9148 (3)1.12917 (17)0.0757 (5)
H30.22260.97261.22120.091*
C40.0872 (4)0.7575 (3)1.0669 (2)0.0860 (6)
H40.04000.70791.11700.103*
C50.0461 (3)0.6709 (2)0.93002 (18)0.0663 (4)
H5−0.02920.56380.88850.080*
C60.11595 (16)0.74226 (14)0.85451 (12)0.0380 (2)
C70.05617 (15)0.65119 (13)0.70151 (12)0.0351 (2)
H70.00320.53600.68080.042*
C8−0.06779 (16)0.82505 (14)0.57613 (12)0.0363 (2)
C90.23610 (16)0.76219 (13)0.58195 (12)0.0371 (2)
C100.22084 (15)0.66550 (13)0.65175 (11)0.0353 (2)
C110.3835 (2)0.7861 (2)0.52121 (17)0.0556 (4)
H11A0.50170.86120.59180.083*
H11B0.33540.82860.45110.083*
H11C0.40800.68390.48170.083*
C120.36538 (16)0.57600 (13)0.68571 (12)0.0387 (2)
C130.4443 (2)0.37945 (18)0.77957 (16)0.0533 (3)
H13A0.56860.45260.84610.064*
H13B0.46380.31160.70060.064*
C140.3605 (3)0.2774 (2)0.8412 (2)0.0736 (5)
H14A0.33730.34550.91710.110*
H14B0.44950.21850.87290.110*
H14C0.24030.20230.77330.110*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0364 (4)0.0620 (5)0.0619 (5)0.0227 (4)0.0271 (4)0.0348 (5)
O20.0412 (5)0.0638 (6)0.0791 (7)0.0260 (4)0.0348 (5)0.0359 (5)
O30.0454 (5)0.0496 (5)0.0621 (6)0.0229 (4)0.0290 (4)0.0276 (4)
N10.0265 (4)0.0462 (5)0.0487 (5)0.0090 (4)0.0175 (4)0.0211 (4)
N20.0337 (5)0.0488 (5)0.0569 (6)0.0163 (4)0.0268 (4)0.0281 (5)
C10.0591 (8)0.0482 (7)0.0481 (7)0.0069 (6)0.0199 (6)0.0127 (6)
C20.0693 (11)0.0669 (9)0.0531 (8)0.0156 (8)0.0146 (7)0.0016 (7)
C30.0706 (11)0.1122 (15)0.0470 (8)0.0445 (11)0.0283 (8)0.0187 (9)
C40.1003 (15)0.1211 (18)0.0684 (11)0.0388 (14)0.0585 (11)0.0462 (12)
C50.0736 (10)0.0732 (10)0.0667 (9)0.0123 (8)0.0443 (8)0.0307 (8)
C60.0327 (5)0.0453 (6)0.0446 (6)0.0160 (4)0.0208 (4)0.0195 (5)
C70.0300 (5)0.0336 (5)0.0453 (6)0.0088 (4)0.0185 (4)0.0152 (4)
C80.0290 (5)0.0425 (5)0.0397 (5)0.0100 (4)0.0162 (4)0.0150 (4)
C90.0304 (5)0.0407 (5)0.0434 (6)0.0112 (4)0.0194 (4)0.0138 (4)
C100.0306 (5)0.0357 (5)0.0410 (5)0.0109 (4)0.0182 (4)0.0109 (4)
C110.0466 (7)0.0753 (9)0.0742 (9)0.0281 (7)0.0421 (7)0.0416 (8)
C120.0353 (5)0.0382 (5)0.0436 (6)0.0133 (4)0.0184 (4)0.0116 (4)
C130.0531 (8)0.0576 (7)0.0645 (8)0.0292 (6)0.0289 (7)0.0302 (7)
C140.0817 (12)0.0773 (11)0.0928 (13)0.0373 (9)0.0446 (10)0.0539 (10)
Geometric parameters (Å, °) top
O1—C81.2310 (14)C5—C61.3793 (18)
O2—C121.2133 (14)C5—H50.9300
O3—C121.3359 (15)C6—C71.5176 (16)
O3—C131.4481 (15)C7—C101.5168 (14)
N1—C81.3398 (15)C7—H70.9800
N1—C71.4716 (15)C9—C101.3436 (16)
N1—H10.8600C9—C111.4950 (15)
N2—C81.3684 (14)C10—C121.4673 (15)
N2—C91.3788 (14)C11—H11A0.9600
N2—H20.8600C11—H11B0.9600
C1—C61.3712 (18)C11—H11C0.9600
C1—C21.393 (2)C12—O21.2133 (14)
C1—H1A0.9300C13—C141.483 (2)
C2—C31.357 (3)C13—H13A0.9700
C2—H2A0.9300C13—H13B0.9700
C3—C41.362 (3)C14—H14A0.9600
C3—H30.9300C14—H14B0.9600
C4—C51.382 (3)C14—H14C0.9600
C4—H40.9300
C12—O3—C13116.09 (10)O1—C8—N2120.40 (10)
C8—N1—C7123.94 (9)N1—C8—N2115.72 (10)
C8—N1—H1118.0C10—C9—N2119.72 (10)
C7—N1—H1118.0C10—C9—C11127.49 (11)
C8—N2—C9124.03 (10)N2—C9—C11112.77 (10)
C8—N2—H2118.0C9—C10—C12121.18 (10)
C9—N2—H2118.0C9—C10—C7120.31 (10)
C6—C1—C2120.50 (14)C12—C10—C7118.47 (10)
C6—C1—H1A119.8C9—C11—H11A109.5
C2—C1—H1A119.8C9—C11—H11B109.5
C3—C2—C1120.33 (17)H11A—C11—H11B109.5
C3—C2—H2A119.8C9—C11—H11C109.5
C1—C2—H2A119.8H11A—C11—H11C109.5
C2—C3—C4119.62 (15)H11B—C11—H11C109.5
C2—C3—H3120.2O2—C12—O3122.18 (11)
C4—C3—H3120.2O2—C12—O3122.18 (11)
C3—C4—C5120.60 (17)O2—C12—C10126.44 (11)
C3—C4—H4119.7O2—C12—C10126.44 (11)
C5—C4—H4119.7O3—C12—C10111.36 (9)
C6—C5—C4120.44 (17)O3—C13—C14107.69 (12)
C6—C5—H5119.8O3—C13—H13A110.2
C4—C5—H5119.8C14—C13—H13A110.2
C1—C6—C5118.50 (13)O3—C13—H13B110.2
C1—C6—C7121.28 (11)C14—C13—H13B110.2
C5—C6—C7120.04 (12)H13A—C13—H13B108.5
N1—C7—C10109.36 (9)C13—C14—H14A109.5
N1—C7—C6109.37 (9)C13—C14—H14B109.5
C10—C7—C6114.22 (9)H14A—C14—H14B109.5
N1—C7—H7107.9C13—C14—H14C109.5
C10—C7—H7107.9H14A—C14—H14C109.5
C6—C7—H7107.9H14B—C14—H14C109.5
O1—C8—N1123.84 (10)
C6—C1—C2—C31.3 (3)C8—N2—C9—C11165.78 (12)
C1—C2—C3—C4−0.4 (3)N2—C9—C10—C12−176.93 (10)
C2—C3—C4—C5−0.4 (3)C11—C9—C10—C124.52 (19)
C3—C4—C5—C60.4 (3)N2—C9—C10—C70.98 (17)
C2—C1—C6—C5−1.3 (2)C11—C9—C10—C7−177.57 (12)
C2—C1—C6—C7173.94 (13)N1—C7—C10—C918.31 (14)
C4—C5—C6—C10.4 (3)C6—C7—C10—C9−104.61 (12)
C4—C5—C6—C7−174.83 (16)N1—C7—C10—C12−163.72 (9)
C8—N1—C7—C10−31.02 (15)C6—C7—C10—C1273.35 (12)
C8—N1—C7—C694.75 (12)C13—O3—C12—O20.36 (18)
C1—C6—C7—N1−75.26 (14)C13—O3—C12—O20.36 (18)
C5—C6—C7—N199.89 (14)C13—O3—C12—C10−178.13 (10)
C1—C6—C7—C1047.66 (15)C9—C10—C12—O210.07 (19)
C5—C6—C7—C10−137.19 (13)C7—C10—C12—O2−167.88 (12)
C7—N1—C8—O1−160.27 (11)C9—C10—C12—O210.07 (19)
C7—N1—C8—N222.03 (16)C7—C10—C12—O2−167.88 (12)
C9—N2—C8—O1−175.96 (11)C9—C10—C12—O3−171.52 (10)
C9—N2—C8—N11.82 (17)C7—C10—C12—O310.53 (14)
C8—N2—C9—C10−12.97 (18)C12—O3—C13—C14177.11 (13)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.862.373.1773 (13)156
N2—H2···O1ii0.862.002.8568 (13)178
C11—H11A···O1iii0.962.583.1785 (16)121
C11—H11C···O20.962.442.8379 (17)105
Symmetry codes: (i) x−1, y, z; (ii) −x, −y+2, −z+1; (iii) x+1, y, z.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.862.373.1773 (13)156
N2—H2···O1ii0.862.002.8568 (13)178
C11—H11A···O1iii0.962.583.1785 (16)121
C11—H11C···O20.962.442.8379 (17)105
Symmetry codes: (i) x−1, y, z; (ii) −x, −y+2, −z+1; (iii) x+1, y, z.
Acknowledgements top

MNM, AR, CAMAH and SSN thank the management of The New College, Chennai, India, for providing the necessary facilities.

references
References top

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