4-Meth­oxy-4-methyl-6-phenyl-1,3-diazinane-2-thione

Seranthimata Samshuddin; Badiadka Narayana; Hemmige S Yathirajan; Thomas Gerber; Eric Hosten; Richard Betz

doi:10.1107/S1600536812044662

. 2012 Nov 3;68(Pt 12):o3271. doi: 10.1107/S1600536812044662

4-Methoxy-4-methyl-6-phenyl-1,3-diazinane-2-thione

Seranthimata Samshuddin ^a, Badiadka Narayana ^a, Hemmige S Yathirajan ^b, Thomas Gerber ^c, Eric Hosten ^c, Richard Betz ^c,^*

PMCID: PMC3588820 PMID: 23468785

Abstract

In the title pyrimidine derivative, C₁₂H₁₆N₂OS, the tetrahydropyrimidine ring adopts an envelope conformation with the C atom of the methylene –CH₂– group as the flap. In the crystal, N—H⋯O and N—H⋯S hydrogen bonds connect molecules into undulating sheets perpendicular to the a axis.

Related literature

For the pharmacological importance of pyrimidines, see: Selvam et al. (2012 ▶); Gupta et al. (2010 ▶); Lagoja (2005 ▶). For the crystal structures of related compounds, see: Kant et al. (2012 ▶); Fun et al. (2012 ▶); Betz et al. (2012 ▶). For puckering analysis of six-membered rings, see: Cremer & Pople (1975 ▶); Boeyens (1978 ▶). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990 ▶); Bernstein et al. (1995 ▶).

Experimental

Crystal data

C₁₂H₁₆N₂OS
M _r = 236.33
Monoclinic,
a = 10.1894 (3) Å
b = 14.6889 (4) Å
c = 9.2026 (2) Å
β = 111.719 (1)°
V = 1279.58 (6) Å³
Z = 4
Mo Kα radiation
μ = 0.24 mm⁻¹
T = 200 K
0.47 × 0.41 × 0.33 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2008 ▶) T _min = 0.898, T _max = 0.926
12126 measured reflections
3173 independent reflections
2876 reflections with I > 2σ(I)
R _int = 0.011

Refinement

R[F ² > 2σ(F ²)] = 0.032
wR(F ²) = 0.089
S = 1.07
3173 reflections
155 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.33 e Å⁻³
Δρ_min = −0.23 e Å⁻³

Data collection: APEX2 (Bruker, 2010 ▶); cell refinement: SAINT (Bruker, 2010 ▶); 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 (Farrugia, 1997 ▶) and Mercury (Macrae et al., 2008 ▶); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009 ▶).

Supplementary Material

Click here for additional data file.^{(20.5KB, cif)}

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536812044662/lh5545sup1.cif

e-68-o3271-sup1.cif^{(20.5KB, cif)}

Click here for additional data file.^{(1.9KB, cdx)}

Supplementary material file. DOI: 10.1107/S1600536812044662/lh5545Isup2.cdx

Click here for additional data file.^{(155.7KB, hkl)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812044662/lh5545Isup3.hkl

e-68-o3271-Isup3.hkl^{(155.7KB, hkl)}

Click here for additional data file.^{(4.8KB, cml)}

Supplementary material file. DOI: 10.1107/S1600536812044662/lh5545Isup4.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯S1ⁱ	0.862 (15)	2.503 (16)	3.3527 (9)	168.8 (12)
N2—H2⋯O1ⁱⁱ	0.841 (15)	2.076 (16)	2.8863 (12)	161.7 (13)

Open in a new tab

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

Acknowledgments

BN thanks the UGC for financial assistance through a BSR one-time grant for the purchase of chemicals. HSY thanks Mysore University for the research facilities.

supplementary crystallographic information

Comment

Pyrimidine and its derivatives exhibit remarkable pharmacological activities including anticonvulsant, antiinflammatory, antibacterial, antifungal, antiviral and anticancer properties (Selvam et al., 2012; Gupta et al., 2010). They constitute important building blocks of natural biologically active compounds like nucleic acids, several vitamins, coenzymes, purines and some marine microorganisms (Lagoja, 2005). Pyrimidine and its derivatives form a component in a number of marketed drugs including flucytosine (antimycotic), floxuridine (antimetabolite), ambrisentan (endothelin receptor antagonist), fluorouracil (antimetabolite), pyrimethamine (antimalarial), piribedil (antiparkinsonian), minoxidil (antihypertensive), carmofur (antineoplastic), bosentan (endothelin receptor antagonist) and many more. The crystal structures of some pyrimidine derivatives such as 2-[3,5-bis(4-methoxyphenyl)-4,5- dihydro-1H-pyrazol-1-yl]-4,6-bis(4-methoxyphenyl)pyrimidine (Kant et al., 2012) and 2-[3,5-bis(4-fluorophenyl)-4,5-dihydro-1H-pyrazol-1-yl]- 4,6-bis(4-fluorophenyl)pyrimidine (Fun et al., 2012) have been reported. In view of the pharmacological importance of pyrimidine derivatives and in continuation of our work on synthesis of pyrimidine derivatives (Betz et al., 2012), we have determined the crystal structure of the title compound, 4-methoxy-4-methyl-6-phenyl-1,3-diazinane-2-thione.

According to a puckering analysis (Cremer & Pople, 1975; Boeyens, 1978), the tetrahydropyrimidine ring adopts an ⁵E conformation with atom C4 as the flap (^C(4)E). The aromatic substituent is found in a nearly perpendicular conformation with respect to the tetrahydropyrimidine ring with the least-squares planes defined by the intracyclic atoms of the phenyl group on the one hand and the five essentially planar atoms [C1/C2/C3/N1/N2] of the 1,3-diazacyclohexane ring on the other hand intersecting at an angle of 74.95 (7) ° (Fig. 1).

In the crystal, N–H···O and N–H···S hydrogen bonds connect molecules into undulating sheets perpendicular to the crystallographic a axis. In terms of graph-set analysis (Etter et al., 1990; Bernstein et al., 1995), the descriptor for these contacts is C¹₁(6)R²₂(8) on the unary level. Metrical parameters as well as information about the symmetry of these contacts are summarized in Table 1. The shortest intercentroid distance between two aromatic systems is 4.9991 (9) Å (Fig. 2).

Experimental

To a mixture of benzylidene acetone (1.46 g, 0.01 mol) and thiourea (1.1 g, 0.015 mol) in methanol (20 ml), sodium methoxide solution (1 ml) was added and the batch was refluxed for 8 h. The precipitate formed was collected by filtration and dried, yield: 82%. The single crystal was grown from a DMF solution of the title compound by slow evaporation at room temperature.