Crystal structure of ethyl 4-(2-meth­oxy­phen­yl)-6-methyl-2-sulfanyl­idene-1,2,3,4-tetra­hydro­pyrimidine-5-carboxyl­ate

Shaaban K Mohamed; Joel T Mague; Mehmet Akkurt; Ahmed Khodairy; Eman A Ahmed

doi:10.1107/S2056989015010026

. 2015 Jun 3;71(Pt 7):o444–o445. doi: 10.1107/S2056989015010026

Crystal structure of ethyl 4-(2-methoxyphenyl)-6-methyl-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carboxylate

Shaaban K Mohamed ^a,^b, Joel T Mague ^c, Mehmet Akkurt ^d, Ahmed Khodairy ^e, Eman A Ahmed ^e,^*

PMCID: PMC4518927 PMID: 26279898

Abstract

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

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 ▸). graphic file with name e-71-0o444-scheme1.jpg

Experimental

Crystal data

C₁₅H₁₈N₂O₃S
M _r = 306.37
Triclinic,
a = 7.9791 (2) Å
b = 8.2031 (2) Å
c = 11.8405 (3) Å
α = 81.987 (1)°
β = 87.975 (1)°
γ = 80.850 (1)°
V = 757.60 (3) Å³
Z = 2
Cu Kα radiation
μ = 2.00 mm⁻¹
T = 150 K
0.25 × 0.21 × 0.12 mm

Data collection

Bruker D8 VENTURE PHOTON 100 CMOS diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2014 ▸) T _min = 0.73, T _max = 0.79
9145 measured reflections
2929 independent reflections
2773 reflections with I > 2σ(I)
R _int = 0.021

Refinement

R[F ² > 2σ(F ²)] = 0.039
wR(F ²) = 0.101
S = 1.08
2929 reflections
193 parameters
H-atom parameters constrained
Δρ_max = 0.43 e Å⁻³
Δρ_min = −0.26 e Å⁻³

Data collection: APEX2 (Bruker, 2014 ▸); cell refinement: 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.

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015010026/is5401sup1.cif

e-71-0o444-sup1.cif^{(283.5KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015010026/is5401Isup2.hkl

e-71-0o444-Isup2.hkl^{(234.1KB, hkl)}

Click here for additional data file.^{(6KB, cml)}

Supporting information file. DOI: 10.1107/S2056989015010026/is5401Isup3.cml

Click here for additional data file.^{(1.6MB, tif)}

. DOI: 10.1107/S2056989015010026/is5401fig1.tif

The molecular structure of the title compound showing labeling scheme and 50% probability ellipsoids.

Click here for additional data file.^{(1.1MB, tif)}

. DOI: 10.1107/S2056989015010026/is5401fig2.tif

A section of the chain formed by N—H⋯S hydrogen bonds (dashed lines).

Click here for additional data file.^{(1.2MB, tif)}

b . DOI: 10.1107/S2056989015010026/is5401fig3.tif

A packing diagram viewed along the b axis. N—H⋯S interactions are shown as dotted lines.

CCDC reference: 1402530

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
N1H1AS1ⁱ	0.91	2.46	3.3539(13)	167
N2H2AS1ⁱⁱ	0.91	2.58	3.4327(14)	157

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Symmetry codes: (i) Inline graphic ; (ii) .

Acknowledgments

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.

supplementary crystallographic information

S1. Comment

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).

S2. Experimental

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%).