organic compounds
of ethyl 4-(2-methoxyphenyl)-6-methyl-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carboxylate
aChemistry and Environmental Division, Manchester Metropolitan University, Manchester M1 5GD, England, bChemistry Department, Faculty of Science, Minia University, 61519 El-Minia, Egypt, cDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA, dDepartment of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Turkey, and eChemistry Department, Faculty of Science, Sohag University, 82524 Sohag, Egypt
*Correspondence e-mail: abdala_15@yahoo.com
In the title compound, C15H18N2O3S, the hydropyrimidine ring adopts a sofa conformation with the methine C atom as the flap. The benzene ring is almost perpendicular to the mean plane of the hydropyrimidine ring, making a dihedral angle of 85.51 (8)°, and the methoxy O atom lies over the centre of the pyrimidine ring. In the crystal, weak N—H⋯S interactions form a zigzag chain running along the b-axis direction.
Keywords: crystal structure; Biginelli reactions; dihyropyrimidinones; three-component reactions; N—H⋯S interactions.
CCDC reference: 1402530
1. Related literature
For syntheses of dihydropyrimidinones and their analogous, see: Biginelli (1893); Varala et al. (2003); Gohain et al. (2004); Ahmed et al. (2009). For biological activities of hydropyrimidinones, see: Salehi et al. (2006); Singh et al. (2010); Hed et al. (2009); Russowsky et al. (2007); Shah et al. (2009). For the synthesis of the title compound, see: Ahmed et al. (2012).
2. Experimental
2.1. Crystal data
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2.3. Refinement
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Data collection: APEX2 (Bruker, 2014); cell SAINT (Bruker, 2014); data reduction: SAINT; program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXL2014.
Supporting information
CCDC reference: 1402530
10.1107/S2056989015010026/is5401sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S2056989015010026/is5401Isup2.hkl
Supporting information file. DOI: 10.1107/S2056989015010026/is5401Isup3.cml
The title compound was prepared according to our reported method (Ahmed et al., 2012). Colourless crystals suitable for X-ray analysis were grown from ethanol (m.p. 473–475 K, yield 98%).
H-atoms attached to C were placed in calculated positions (C—H = 0.95–1.00 Å), while those attached to N were placed in a difference map and their parameters adjusted to give N—H = 0.91 Å. All were included as riding contributions with isotropic displacement parameters 1.2 or 1.5 times those of the attached atoms.
Data collection: APEX2 (Bruker, 2014); cell
SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015b).C15H18N2O3S | Z = 2 |
Mr = 306.37 | F(000) = 324 |
Triclinic, P1 | Dx = 1.343 Mg m−3 |
a = 7.9791 (2) Å | Cu Kα radiation, λ = 1.54178 Å |
b = 8.2031 (2) Å | Cell parameters from 7936 reflections |
c = 11.8405 (3) Å | θ = 3.8–72.2° |
α = 81.987 (1)° | µ = 2.00 mm−1 |
β = 87.975 (1)° | T = 150 K |
γ = 80.850 (1)° | Thick plate, colourless |
V = 757.60 (3) Å3 | 0.25 × 0.21 × 0.12 mm |
Bruker D8 VENTURE PHOTON 100 CMOS diffractometer | 2929 independent reflections |
Radiation source: INCOATEC IµS micro–focus source | 2773 reflections with I > 2σ(I) |
Mirror monochromator | Rint = 0.021 |
Detector resolution: 10.4167 pixels mm-1 | θmax = 72.2°, θmin = 3.8° |
ω scans | h = −9→9 |
Absorption correction: multi-scan (SADABS; Bruker, 2014) | k = −10→10 |
Tmin = 0.73, Tmax = 0.79 | l = −14→14 |
9145 measured reflections |
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)] = 0.039 | Hydrogen site location: mixed |
wR(F2) = 0.101 | H-atom parameters constrained |
S = 1.08 | w = 1/[σ2(Fo2) + (0.0487P)2 + 0.4254P] where P = (Fo2 + 2Fc2)/3 |
2929 reflections | (Δ/σ)max = 0.001 |
193 parameters | Δρmax = 0.43 e Å−3 |
0 restraints | Δρmin = −0.26 e Å−3 |
C15H18N2O3S | γ = 80.850 (1)° |
Mr = 306.37 | V = 757.60 (3) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.9791 (2) Å | Cu Kα radiation |
b = 8.2031 (2) Å | µ = 2.00 mm−1 |
c = 11.8405 (3) Å | T = 150 K |
α = 81.987 (1)° | 0.25 × 0.21 × 0.12 mm |
β = 87.975 (1)° |
Bruker D8 VENTURE PHOTON 100 CMOS diffractometer | 2929 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2014) | 2773 reflections with I > 2σ(I) |
Tmin = 0.73, Tmax = 0.79 | Rint = 0.021 |
9145 measured reflections |
R[F2 > 2σ(F2)] = 0.039 | 0 restraints |
wR(F2) = 0.101 | H-atom parameters constrained |
S = 1.08 | Δρmax = 0.43 e Å−3 |
2929 reflections | Δρmin = −0.26 e Å−3 |
193 parameters |
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. H-atoms attached to carbon were placed in calculated positions (C—H = 0.95 - 0.98 Å) while those attached to nitrogen were placed in locations derived from a difference map and their parameters adjusted to give N—H = 0.91 Å. All were included as riding contributions with isotropic displacement parameters 1.2 - 1.5 times those of the attached atoms. |
x | y | z | Uiso*/Ueq | ||
S1 | 1.08339 (5) | 0.22865 (4) | 1.02799 (3) | 0.02400 (13) | |
O1 | 0.64475 (15) | 0.28798 (15) | 0.86937 (10) | 0.0312 (3) | |
O2 | 0.8568 (2) | 0.26940 (18) | 0.47910 (11) | 0.0494 (4) | |
O3 | 0.75790 (16) | 0.52294 (15) | 0.52331 (9) | 0.0304 (3) | |
N1 | 0.96037 (16) | 0.42742 (15) | 0.84338 (11) | 0.0213 (3) | |
H1A | 0.9617 | 0.5109 | 0.8864 | 0.026* | |
N2 | 0.99441 (17) | 0.14788 (16) | 0.83198 (11) | 0.0240 (3) | |
H2A | 1.0080 | 0.0431 | 0.8710 | 0.029* | |
C1 | 0.85934 (19) | 0.47576 (19) | 0.73835 (13) | 0.0216 (3) | |
H1 | 0.9084 | 0.5685 | 0.6916 | 0.026* | |
C2 | 1.00503 (19) | 0.27318 (19) | 0.89394 (13) | 0.0209 (3) | |
C3 | 0.9414 (2) | 0.1739 (2) | 0.71936 (13) | 0.0247 (3) | |
C4 | 0.9585 (3) | 0.0158 (2) | 0.66684 (15) | 0.0351 (4) | |
H4A | 0.8722 | 0.0271 | 0.6082 | 0.053* | |
H4B | 0.9429 | −0.0770 | 0.7259 | 0.053* | |
H4C | 1.0717 | −0.0061 | 0.6320 | 0.053* | |
C5 | 0.88282 (19) | 0.3296 (2) | 0.66990 (13) | 0.0230 (3) | |
C6 | 0.8339 (2) | 0.3648 (2) | 0.54883 (14) | 0.0277 (3) | |
C7 | 0.6888 (2) | 0.5701 (2) | 0.40933 (14) | 0.0331 (4) | |
H7A | 0.6051 | 0.4980 | 0.3959 | 0.040* | |
H7B | 0.7806 | 0.5588 | 0.3512 | 0.040* | |
C8 | 0.6050 (3) | 0.7480 (3) | 0.40272 (18) | 0.0486 (5) | |
H8A | 0.5172 | 0.7580 | 0.4625 | 0.073* | |
H8B | 0.5529 | 0.7841 | 0.3278 | 0.073* | |
H8C | 0.6900 | 0.8183 | 0.4136 | 0.073* | |
C9 | 0.6761 (2) | 0.5437 (2) | 0.76670 (13) | 0.0255 (3) | |
C10 | 0.6100 (2) | 0.7098 (2) | 0.72635 (15) | 0.0304 (4) | |
H10 | 0.6797 | 0.7785 | 0.6817 | 0.036* | |
C11 | 0.4425 (3) | 0.7744 (2) | 0.75156 (17) | 0.0382 (4) | |
H11 | 0.3972 | 0.8861 | 0.7228 | 0.046* | |
C12 | 0.3434 (2) | 0.6753 (2) | 0.81827 (16) | 0.0370 (4) | |
H12 | 0.2298 | 0.7205 | 0.8357 | 0.044* | |
C13 | 0.4043 (2) | 0.5117 (2) | 0.86057 (15) | 0.0320 (4) | |
H13 | 0.3342 | 0.4452 | 0.9068 | 0.038* | |
C14 | 0.5720 (2) | 0.4459 (2) | 0.83384 (13) | 0.0269 (3) | |
C15 | 0.5435 (2) | 0.1762 (2) | 0.93170 (16) | 0.0361 (4) | |
H15A | 0.4988 | 0.2205 | 1.0013 | 0.054* | |
H15B | 0.6133 | 0.0671 | 0.9521 | 0.054* | |
H15C | 0.4489 | 0.1642 | 0.8845 | 0.054* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0304 (2) | 0.0195 (2) | 0.0222 (2) | −0.00308 (15) | −0.00427 (14) | −0.00340 (14) |
O1 | 0.0296 (6) | 0.0277 (6) | 0.0355 (6) | −0.0073 (5) | 0.0044 (5) | 0.0011 (5) |
O2 | 0.0744 (10) | 0.0443 (8) | 0.0274 (7) | 0.0095 (7) | −0.0101 (6) | −0.0165 (6) |
O3 | 0.0391 (7) | 0.0314 (6) | 0.0209 (6) | −0.0055 (5) | −0.0058 (5) | −0.0026 (5) |
N1 | 0.0255 (6) | 0.0180 (6) | 0.0217 (6) | −0.0048 (5) | −0.0032 (5) | −0.0046 (5) |
N2 | 0.0309 (7) | 0.0181 (6) | 0.0238 (6) | −0.0034 (5) | −0.0014 (5) | −0.0056 (5) |
C1 | 0.0237 (7) | 0.0218 (7) | 0.0202 (7) | −0.0052 (6) | −0.0020 (6) | −0.0033 (6) |
C2 | 0.0202 (7) | 0.0206 (7) | 0.0227 (7) | −0.0045 (6) | 0.0013 (6) | −0.0044 (6) |
C3 | 0.0261 (8) | 0.0261 (8) | 0.0241 (8) | −0.0069 (6) | 0.0019 (6) | −0.0084 (6) |
C4 | 0.0497 (11) | 0.0273 (9) | 0.0309 (9) | −0.0059 (8) | −0.0026 (8) | −0.0121 (7) |
C5 | 0.0235 (7) | 0.0256 (8) | 0.0217 (7) | −0.0063 (6) | 0.0014 (6) | −0.0067 (6) |
C6 | 0.0278 (8) | 0.0332 (9) | 0.0233 (8) | −0.0059 (7) | 0.0010 (6) | −0.0066 (6) |
C7 | 0.0370 (9) | 0.0430 (10) | 0.0199 (8) | −0.0104 (8) | −0.0046 (7) | 0.0000 (7) |
C8 | 0.0683 (14) | 0.0410 (11) | 0.0346 (10) | −0.0088 (10) | −0.0160 (10) | 0.0062 (8) |
C9 | 0.0268 (8) | 0.0292 (8) | 0.0222 (7) | −0.0048 (6) | −0.0031 (6) | −0.0081 (6) |
C10 | 0.0335 (9) | 0.0276 (8) | 0.0289 (8) | 0.0007 (7) | −0.0053 (7) | −0.0055 (7) |
C11 | 0.0398 (10) | 0.0284 (9) | 0.0436 (10) | 0.0035 (8) | −0.0066 (8) | −0.0041 (8) |
C12 | 0.0352 (9) | 0.0377 (10) | 0.0367 (9) | 0.0019 (8) | 0.0000 (7) | −0.0094 (8) |
C13 | 0.0320 (9) | 0.0368 (9) | 0.0278 (8) | −0.0069 (7) | −0.0017 (7) | −0.0049 (7) |
C14 | 0.0294 (8) | 0.0286 (8) | 0.0233 (8) | −0.0044 (7) | −0.0036 (6) | −0.0049 (6) |
C15 | 0.0366 (10) | 0.0323 (9) | 0.0386 (10) | −0.0106 (8) | 0.0047 (8) | 0.0033 (8) |
S1—C2 | 1.6969 (15) | C5—C6 | 1.476 (2) |
O1—C14 | 1.349 (2) | C7—C8 | 1.498 (3) |
O1—C15 | 1.430 (2) | C7—H7A | 0.9900 |
O2—C6 | 1.205 (2) | C7—H7B | 0.9900 |
O3—C6 | 1.340 (2) | C8—H8A | 0.9800 |
O3—C7 | 1.4541 (19) | C8—H8B | 0.9800 |
N1—C2 | 1.322 (2) | C8—H8C | 0.9800 |
N1—C1 | 1.4783 (18) | C9—C14 | 1.397 (2) |
N1—H1A | 0.9098 | C9—C10 | 1.403 (2) |
N2—C2 | 1.3580 (19) | C10—C11 | 1.395 (3) |
N2—C3 | 1.391 (2) | C10—H10 | 0.9500 |
N2—H2A | 0.9098 | C11—C12 | 1.376 (3) |
C1—C5 | 1.522 (2) | C11—H11 | 0.9500 |
C1—C9 | 1.523 (2) | C12—C13 | 1.382 (3) |
C1—H1 | 1.0000 | C12—H12 | 0.9500 |
C3—C5 | 1.347 (2) | C13—C14 | 1.403 (2) |
C3—C4 | 1.501 (2) | C13—H13 | 0.9500 |
C4—H4A | 0.9800 | C15—H15A | 0.9800 |
C4—H4B | 0.9800 | C15—H15B | 0.9800 |
C4—H4C | 0.9800 | C15—H15C | 0.9800 |
C14—O1—C15 | 118.77 (14) | C8—C7—H7A | 110.4 |
C6—O3—C7 | 116.45 (13) | O3—C7—H7B | 110.4 |
C2—N1—C1 | 125.30 (12) | C8—C7—H7B | 110.4 |
C2—N1—H1A | 117.1 | H7A—C7—H7B | 108.6 |
C1—N1—H1A | 114.7 | C7—C8—H8A | 109.5 |
C2—N2—C3 | 123.59 (14) | C7—C8—H8B | 109.5 |
C2—N2—H2A | 116.2 | H8A—C8—H8B | 109.5 |
C3—N2—H2A | 119.5 | C7—C8—H8C | 109.5 |
N1—C1—C5 | 108.79 (12) | H8A—C8—H8C | 109.5 |
N1—C1—C9 | 110.68 (12) | H8B—C8—H8C | 109.5 |
C5—C1—C9 | 115.38 (12) | C14—C9—C10 | 118.77 (16) |
N1—C1—H1 | 107.2 | C14—C9—C1 | 121.76 (15) |
C5—C1—H1 | 107.2 | C10—C9—C1 | 119.46 (15) |
C9—C1—H1 | 107.2 | C11—C10—C9 | 120.32 (17) |
N1—C2—N2 | 117.28 (14) | C11—C10—H10 | 119.8 |
N1—C2—S1 | 122.70 (11) | C9—C10—H10 | 119.8 |
N2—C2—S1 | 119.94 (12) | C12—C11—C10 | 119.55 (17) |
C5—C3—N2 | 119.62 (14) | C12—C11—H11 | 120.2 |
C5—C3—C4 | 127.50 (15) | C10—C11—H11 | 120.2 |
N2—C3—C4 | 112.89 (14) | C11—C12—C13 | 121.84 (17) |
C3—C4—H4A | 109.5 | C11—C12—H12 | 119.1 |
C3—C4—H4B | 109.5 | C13—C12—H12 | 119.1 |
H4A—C4—H4B | 109.5 | C12—C13—C14 | 118.62 (17) |
C3—C4—H4C | 109.5 | C12—C13—H13 | 120.7 |
H4A—C4—H4C | 109.5 | C14—C13—H13 | 120.7 |
H4B—C4—H4C | 109.5 | O1—C14—C9 | 115.19 (15) |
C3—C5—C6 | 121.63 (14) | O1—C14—C13 | 123.92 (15) |
C3—C5—C1 | 120.93 (14) | C9—C14—C13 | 120.89 (16) |
C6—C5—C1 | 117.42 (14) | O1—C15—H15A | 109.5 |
O2—C6—O3 | 122.34 (16) | O1—C15—H15B | 109.5 |
O2—C6—C5 | 126.96 (16) | H15A—C15—H15B | 109.5 |
O3—C6—C5 | 110.70 (13) | O1—C15—H15C | 109.5 |
O3—C7—C8 | 106.67 (14) | H15A—C15—H15C | 109.5 |
O3—C7—H7A | 110.4 | H15B—C15—H15C | 109.5 |
C2—N1—C1—C5 | −25.4 (2) | C3—C5—C6—O3 | 171.37 (14) |
C2—N1—C1—C9 | 102.32 (16) | C1—C5—C6—O3 | −6.8 (2) |
C1—N1—C2—N2 | 16.9 (2) | C6—O3—C7—C8 | 177.69 (16) |
C1—N1—C2—S1 | −166.47 (11) | N1—C1—C9—C14 | −61.89 (18) |
C3—N2—C2—N1 | 0.7 (2) | C5—C1—C9—C14 | 62.18 (19) |
C3—N2—C2—S1 | −176.02 (12) | N1—C1—C9—C10 | 116.92 (15) |
C2—N2—C3—C5 | −6.0 (2) | C5—C1—C9—C10 | −119.01 (16) |
C2—N2—C3—C4 | 173.96 (15) | C14—C9—C10—C11 | −1.1 (2) |
N2—C3—C5—C6 | 176.60 (14) | C1—C9—C10—C11 | −179.90 (15) |
C4—C3—C5—C6 | −3.3 (3) | C9—C10—C11—C12 | 1.3 (3) |
N2—C3—C5—C1 | −5.3 (2) | C10—C11—C12—C13 | −0.7 (3) |
C4—C3—C5—C1 | 174.72 (16) | C11—C12—C13—C14 | −0.3 (3) |
N1—C1—C5—C3 | 18.7 (2) | C15—O1—C14—C9 | −175.65 (14) |
C9—C1—C5—C3 | −106.35 (17) | C15—O1—C14—C13 | 4.3 (2) |
N1—C1—C5—C6 | −163.15 (13) | C10—C9—C14—O1 | −179.93 (14) |
C9—C1—C5—C6 | 71.79 (18) | C1—C9—C14—O1 | −1.1 (2) |
C7—O3—C6—O2 | 5.8 (2) | C10—C9—C14—C13 | 0.1 (2) |
C7—O3—C6—C5 | −174.41 (13) | C1—C9—C14—C13 | 178.93 (14) |
C3—C5—C6—O2 | −8.9 (3) | C12—C13—C14—O1 | −179.41 (16) |
C1—C5—C6—O2 | 172.98 (18) | C12—C13—C14—C9 | 0.5 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···S1i | 0.91 | 2.46 | 3.3539 (13) | 167 |
N2—H2A···S1ii | 0.91 | 2.58 | 3.4327 (14) | 157 |
Symmetry codes: (i) −x+2, −y+1, −z+2; (ii) −x+2, −y, −z+2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···S1i | 0.91 | 2.46 | 3.3539 (13) | 167 |
N2—H2A···S1ii | 0.91 | 2.58 | 3.4327 (14) | 157 |
Symmetry codes: (i) −x+2, −y+1, −z+2; (ii) −x+2, −y, −z+2. |
Acknowledgements
The support of NSF–MRI grant No. 1228232 for the purchase of the diffractometer and Tulane University for support of the Tulane Crystallography Laboratory are gratefully acknowledged.
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Dihydropyrimidin-2(1H)-one scaffold compounds are an important class of substances in organic and medicinal chemistry. Aryl-substituted 3, 4-dihydropyrimidin-2(1H)-ones and their sulfur analogue have been reported to possess diverse range of pharmacological activity (Salehi et al., 2006) such as anticancer, anti HIV, antibacterial, antimalarial, antihypertensive, sedative, hypnotics, anticonvulsant, antithyroid,antihistaminic agents and antibiotics (Singh et al., 2010; Hed et al., 2009; Russowsky et al., 2007; Shah et al., 2009). This stimulated the invention of a wide range of synthetic methods for their preparation and chemical transformations. In recent years, several modified procedures have been reported to improve the efficiency of the Biginelli dihydropyrimidine synthesis (Biginelli, 1893) by using different catalysts e.g. Lewis acids (Varala et al., 2003; Gohain et al., 2004) or by using basic condition via phase transfer catalysis (Ahmed et al., 2009). In this context, we report in this study the crystal structure of the title compound.
In the title compound (Fig. 1), the plane of the benzene ring is almost parallel to the C1···N2 vector with the methoxy oxygen atom (O1) lying over the centre of the pyrimidine ring. The pyrimidine ring has Cremer-Pople puckering parameters Q = 0.201 (2) Å, θ = 62.2 (5)° and ϕ = 42.9 (2)°. In the crystal, weak N—H···S interactions (Table 1) form a chain running parallel to the b axis (Figs. 2 & 3).