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

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

doi:10.1107/S1600536808025610

organic compounds

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ISSN: 2056-9890

Volume 64| Part 9| September 2008| Page o1752

doi:10.1107/S1600536808025610

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

M. Nizam Mohideen,^a ^* A. Rasheeth,^b C. A. M. A. Huq ^b and S. Syed Nizar ^b

^aDepartment of Physics, The New College (Autonomous), Chennai 600 014, India, and ^bDepartment of Chemistry, The New College (Autonomous), Chennai 600 014, India
^*Correspondence e-mail: mnizam_new@yahoo.in

(Received 26 July 2008; accepted 8 August 2008; online 13 August 2008)

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.

Related literature

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

Crystal data

C₁₄H₁₆N₂O₃
M_r = 260.29
Triclinic, $[P \overline 1]$
a = 7.5495 (2) Å
b = 8.9797 (3) Å
c = 11.0812 (3) Å
α = 107.843 (2)°
β = 108.603 (1)°
γ = 98.244 (2)°
V = 653.07 (4) Å³
Z = 2
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 293 (2) K
0.3 × 0.2 × 0.2 mm

Data collection

Bruker APEXII CCD area-detector diffractometer
Absorption correction: none
16135 measured reflections
3710 independent reflections
2972 reflections with I > 2σ(I)
R_int = 0.023

Refinement

R[F² > 2σ(F²)] = 0.047
wR(F²) = 0.159
S = 1.00
3710 reflections
174 parameters
H-atom parameters constrained
Δρ_max = 0.34 e Å⁻³
Δρ_min = −0.33 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O2ⁱ	0.86	2.37	3.1773 (13)	156
N2—H2⋯O1ⁱⁱ	0.86	2.00	2.8568 (13)	178
C11—H11A⋯O1ⁱⁱⁱ	0.96	2.58	3.1785 (16)	121
C11—H11C⋯O2	0.96	2.44	2.8379 (17)	105
Symmetry codes: (i) x-1, y, z; (ii) -x, -y+2, -z+1; (iii) x+1, y, z.

Data collection: APEX2 (Bruker, 2004 ); cell refinement: APEX2 and SAINT (Bruker, 2004); data reduction: SAINT; 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 and PLATON (Spek, 2003 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808025610/bt2758sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536808025610/bt2758Isup2.hkl

checkCIF report

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 Δ_S(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).

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

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

C₁₄H₁₆N₂O₃	Z = 2
M_r = 260.29	F(000) = 276
Triclinic, P1	D_x = 1.324 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 7.5495 (2) Å	Cell parameters from 5321 reflections
b = 8.9797 (3) Å	θ = 2.5–24.1°
c = 11.0812 (3) Å	µ = 0.09 mm⁻¹
α = 107.843 (2)°	T = 293 K
β = 108.603 (1)°	Needle, colourless
γ = 98.244 (2)°	0.3 × 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 tube	R_int = 0.023
Graphite monochromator	θ_max = 29.7°, θ_min = 2.5°
ω and ϕ scans	h = −9→10
16135 measured reflections	k = −12→12
3710 independent reflections	l = −15→15

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.047	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.159	H-atom parameters constrained
S = 1.00	w = 1/[σ²(F_o²) + (0.0959P)² + 0.106P] where P = (F_o² + 2F_c²)/3
3710 reflections	(Δ/σ)_max < 0.001
174 parameters	Δρ_max = 0.34 e Å⁻³
0 restraints	Δρ_min = −0.33 e Å⁻³

Crystal data top

C₁₄H₁₆N₂O₃	γ = 98.244 (2)°
M_r = 260.29	V = 653.07 (4) Å³
Triclinic, P1	Z = 2
a = 7.5495 (2) Å	Mo Kα radiation
b = 8.9797 (3) Å	µ = 0.09 mm⁻¹
c = 11.0812 (3) Å	T = 293 K
α = 107.843 (2)°	0.3 × 0.2 × 0.2 mm
β = 108.603 (1)°

Data collection top

Bruker APEXII CCD area-detector diffractometer	2972 reflections with I > 2σ(I)
16135 measured reflections	R_int = 0.023
3710 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.047	0 restraints
wR(F²) = 0.159	H-atom parameters constrained
S = 1.00	Δρ_max = 0.34 e Å⁻³
3710 reflections	Δρ_min = −0.33 e Å⁻³
174 parameters

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

	x	y	z	U_iso*/U_eq
O1	−0.18468 (12)	0.90274 (12)	0.54481 (10)	0.0472 (2)
O2	0.51966 (14)	0.59340 (12)	0.67258 (11)	0.0546 (3)
O3	0.30937 (13)	0.47104 (11)	0.73822 (10)	0.0473 (2)
N1	−0.09885 (13)	0.70875 (12)	0.62494 (10)	0.0389 (2)
H1	−0.2165	0.6651	0.6107	0.047*
N2	0.10294 (14)	0.85056 (13)	0.55737 (11)	0.0413 (2)
H2	0.1288	0.9264	0.5285	0.050*
C1	0.2277 (2)	0.89996 (17)	0.91862 (15)	0.0542 (3)
H1A	0.2782	0.9495	0.8699	0.065*
C2	0.2660 (3)	0.9866 (2)	1.05616 (17)	0.0711 (5)
H2A	0.3398	1.0942	1.0982	0.085*
C3	0.1961 (3)	0.9148 (3)	1.12917 (17)	0.0757 (5)
H3	0.2226	0.9726	1.2212	0.091*
C4	0.0872 (4)	0.7575 (3)	1.0669 (2)	0.0860 (6)
H4	0.0400	0.7079	1.1170	0.103*
C5	0.0461 (3)	0.6709 (2)	0.93002 (18)	0.0663 (4)
H5	−0.0292	0.5638	0.8885	0.080*
C6	0.11595 (16)	0.74226 (14)	0.85451 (12)	0.0380 (2)
C7	0.05617 (15)	0.65119 (13)	0.70151 (12)	0.0351 (2)
H7	0.0032	0.5360	0.6808	0.042*
C8	−0.06779 (16)	0.82505 (14)	0.57613 (12)	0.0363 (2)
C9	0.23610 (16)	0.76219 (13)	0.58195 (12)	0.0371 (2)
C10	0.22084 (15)	0.66550 (13)	0.65175 (11)	0.0353 (2)
C11	0.3835 (2)	0.7861 (2)	0.52121 (17)	0.0556 (4)
H11A	0.5017	0.8612	0.5918	0.083*
H11B	0.3354	0.8286	0.4511	0.083*
H11C	0.4080	0.6839	0.4817	0.083*
C12	0.36538 (16)	0.57600 (13)	0.68571 (12)	0.0387 (2)
C13	0.4443 (2)	0.37945 (18)	0.77957 (16)	0.0533 (3)
H13A	0.5686	0.4526	0.8461	0.064*
H13B	0.4638	0.3116	0.7006	0.064*
C14	0.3605 (3)	0.2774 (2)	0.8412 (2)	0.0736 (5)
H14A	0.3373	0.3455	0.9171	0.110*
H14B	0.4495	0.2185	0.8729	0.110*
H14C	0.2403	0.2023	0.7733	0.110*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0364 (4)	0.0620 (5)	0.0619 (5)	0.0227 (4)	0.0271 (4)	0.0348 (5)
O2	0.0412 (5)	0.0638 (6)	0.0791 (7)	0.0260 (4)	0.0348 (5)	0.0359 (5)
O3	0.0454 (5)	0.0496 (5)	0.0621 (6)	0.0229 (4)	0.0290 (4)	0.0276 (4)
N1	0.0265 (4)	0.0462 (5)	0.0487 (5)	0.0090 (4)	0.0175 (4)	0.0211 (4)
N2	0.0337 (5)	0.0488 (5)	0.0569 (6)	0.0163 (4)	0.0268 (4)	0.0281 (5)
C1	0.0591 (8)	0.0482 (7)	0.0481 (7)	0.0069 (6)	0.0199 (6)	0.0127 (6)
C2	0.0693 (11)	0.0669 (9)	0.0531 (8)	0.0156 (8)	0.0146 (7)	0.0016 (7)
C3	0.0706 (11)	0.1122 (15)	0.0470 (8)	0.0445 (11)	0.0283 (8)	0.0187 (9)
C4	0.1003 (15)	0.1211 (18)	0.0684 (11)	0.0388 (14)	0.0585 (11)	0.0462 (12)
C5	0.0736 (10)	0.0732 (10)	0.0667 (9)	0.0123 (8)	0.0443 (8)	0.0307 (8)
C6	0.0327 (5)	0.0453 (6)	0.0446 (6)	0.0160 (4)	0.0208 (4)	0.0195 (5)
C7	0.0300 (5)	0.0336 (5)	0.0453 (6)	0.0088 (4)	0.0185 (4)	0.0152 (4)
C8	0.0290 (5)	0.0425 (5)	0.0397 (5)	0.0100 (4)	0.0162 (4)	0.0150 (4)
C9	0.0304 (5)	0.0407 (5)	0.0434 (6)	0.0112 (4)	0.0194 (4)	0.0138 (4)
C10	0.0306 (5)	0.0357 (5)	0.0410 (5)	0.0109 (4)	0.0182 (4)	0.0109 (4)
C11	0.0466 (7)	0.0753 (9)	0.0742 (9)	0.0281 (7)	0.0421 (7)	0.0416 (8)
C12	0.0353 (5)	0.0382 (5)	0.0436 (6)	0.0133 (4)	0.0184 (4)	0.0116 (4)
C13	0.0531 (8)	0.0576 (7)	0.0645 (8)	0.0292 (6)	0.0289 (7)	0.0302 (7)
C14	0.0817 (12)	0.0773 (11)	0.0928 (13)	0.0373 (9)	0.0446 (10)	0.0539 (10)

Geometric parameters (Å, º) top

O1—C8	1.2310 (14)	C5—C6	1.3793 (18)
O2—C12	1.2133 (14)	C5—H5	0.9300
O3—C12	1.3359 (15)	C6—C7	1.5176 (16)
O3—C13	1.4481 (15)	C7—C10	1.5168 (14)
N1—C8	1.3398 (15)	C7—H7	0.9800
N1—C7	1.4716 (15)	C9—C10	1.3436 (16)
N1—H1	0.8600	C9—C11	1.4950 (15)
N2—C8	1.3684 (14)	C10—C12	1.4673 (15)
N2—C9	1.3788 (14)	C11—H11A	0.9600
N2—H2	0.8600	C11—H11B	0.9600
C1—C6	1.3712 (18)	C11—H11C	0.9600
C1—C2	1.393 (2)	C12—O2	1.2133 (14)
C1—H1A	0.9300	C13—C14	1.483 (2)
C2—C3	1.357 (3)	C13—H13A	0.9700
C2—H2A	0.9300	C13—H13B	0.9700
C3—C4	1.362 (3)	C14—H14A	0.9600
C3—H3	0.9300	C14—H14B	0.9600
C4—C5	1.382 (3)	C14—H14C	0.9600
C4—H4	0.9300

C12—O3—C13	116.09 (10)	O1—C8—N2	120.40 (10)
C8—N1—C7	123.94 (9)	N1—C8—N2	115.72 (10)
C8—N1—H1	118.0	C10—C9—N2	119.72 (10)
C7—N1—H1	118.0	C10—C9—C11	127.49 (11)
C8—N2—C9	124.03 (10)	N2—C9—C11	112.77 (10)
C8—N2—H2	118.0	C9—C10—C12	121.18 (10)
C9—N2—H2	118.0	C9—C10—C7	120.31 (10)
C6—C1—C2	120.50 (14)	C12—C10—C7	118.47 (10)
C6—C1—H1A	119.8	C9—C11—H11A	109.5
C2—C1—H1A	119.8	C9—C11—H11B	109.5
C3—C2—C1	120.33 (17)	H11A—C11—H11B	109.5
C3—C2—H2A	119.8	C9—C11—H11C	109.5
C1—C2—H2A	119.8	H11A—C11—H11C	109.5
C2—C3—C4	119.62 (15)	H11B—C11—H11C	109.5
C2—C3—H3	120.2	O2—C12—O3	122.18 (11)
C4—C3—H3	120.2	O2—C12—O3	122.18 (11)
C3—C4—C5	120.60 (17)	O2—C12—C10	126.44 (11)
C3—C4—H4	119.7	O2—C12—C10	126.44 (11)
C5—C4—H4	119.7	O3—C12—C10	111.36 (9)
C6—C5—C4	120.44 (17)	O3—C13—C14	107.69 (12)
C6—C5—H5	119.8	O3—C13—H13A	110.2
C4—C5—H5	119.8	C14—C13—H13A	110.2
C1—C6—C5	118.50 (13)	O3—C13—H13B	110.2
C1—C6—C7	121.28 (11)	C14—C13—H13B	110.2
C5—C6—C7	120.04 (12)	H13A—C13—H13B	108.5
N1—C7—C10	109.36 (9)	C13—C14—H14A	109.5
N1—C7—C6	109.37 (9)	C13—C14—H14B	109.5
C10—C7—C6	114.22 (9)	H14A—C14—H14B	109.5
N1—C7—H7	107.9	C13—C14—H14C	109.5
C10—C7—H7	107.9	H14A—C14—H14C	109.5
C6—C7—H7	107.9	H14B—C14—H14C	109.5
O1—C8—N1	123.84 (10)

C6—C1—C2—C3	1.3 (3)	C8—N2—C9—C11	165.78 (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—C12	4.52 (19)
C3—C4—C5—C6	0.4 (3)	N2—C9—C10—C7	0.98 (17)
C2—C1—C6—C5	−1.3 (2)	C11—C9—C10—C7	−177.57 (12)
C2—C1—C6—C7	173.94 (13)	N1—C7—C10—C9	18.31 (14)
C4—C5—C6—C1	0.4 (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—C12	73.35 (12)
C8—N1—C7—C6	94.75 (12)	C13—O3—C12—O2	0.36 (18)
C1—C6—C7—N1	−75.26 (14)	C13—O3—C12—O2	0.36 (18)
C5—C6—C7—N1	99.89 (14)	C13—O3—C12—C10	−178.13 (10)
C1—C6—C7—C10	47.66 (15)	C9—C10—C12—O2	10.07 (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—O2	10.07 (19)
C7—N1—C8—N2	22.03 (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—N1	1.82 (17)	C7—C10—C12—O3	10.53 (14)
C8—N2—C9—C10	−12.97 (18)	C12—O3—C13—C14	177.11 (13)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2ⁱ	0.86	2.37	3.1773 (13)	156
N2—H2···O1ⁱⁱ	0.86	2.00	2.8568 (13)	178
C11—H11A···O1ⁱⁱⁱ	0.96	2.58	3.1785 (16)	121
C11—H11C···O2	0.96	2.44	2.8379 (17)	105

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

Experimental details

Crystal data
Chemical formula	C₁₄H₁₆N₂O₃
M_r	260.29
Crystal system, space group	Triclinic, P1
Temperature (K)	293
a, b, c (Å)	7.5495 (2), 8.9797 (3), 11.0812 (3)
α, β, γ (°)	107.843 (2), 108.603 (1), 98.244 (2)
V (Å³)	653.07 (4)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.3 × 0.2 × 0.2

Data collection
Diffractometer	Bruker APEXII CCD area-detector diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	16135, 3710, 2972
R_int	0.023
(sin θ/λ)_max (Å⁻¹)	0.698

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.047, 0.159, 1.00
No. of reflections	3710
No. of parameters	174
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.34, −0.33

Computer programs: APEX2 (Bruker, 2004), APEX2 and SAINT (Bruker, 2004), SAINT (Bruker, 2004), SHELXS97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2003).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2ⁱ	0.86	2.37	3.1773 (13)	156.0
N2—H2···O1ⁱⁱ	0.86	2.00	2.8568 (13)	178.2
C11—H11A···O1ⁱⁱⁱ	0.96	2.58	3.1785 (16)	120.5
C11—H11C···O2	0.96	2.44	2.8379 (17)	104.5

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

Acknowledgements

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

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