6-Amino-1,3-dimethyl-5-[(E)-2-(methyl­sulfan­yl)benzyl­idene­amino]­pyrimidine-2,4(1H,3H)-dione

Irvin Booysen; Ismail Muhammed; Anna Soares; Thomas Gerber; Eric Hosten; Richard Betz

doi:10.1107/S1600536811020903

. 2011 Jun 11;67(Pt 7):o1592. doi: 10.1107/S1600536811020903

6-Amino-1,3-dimethyl-5-[(E)-2-(methylsulfanyl)benzylideneamino]pyrimidine-2,4(1H,3H)-dione

Irvin Booysen ^a, Ismail Muhammed ^a, Anna Soares ^a, Thomas Gerber ^b, Eric Hosten ^b, Richard Betz ^b,^*

PMCID: PMC3151916 PMID: 21837000

Abstract

The title compound, C₁₄H₁₆N₄O₂S, is a Schiff base derivative of 2-(methylsulfanyl)benzaldehyde. The configuration about the C=N double bond is E. The heterocyclic ring is essentially planar (τ = 3.1°) and makes a dihedral angle of 12.24 (7)° with the benzene ring. An intramolecular N—H⋯S hydrogen bond is observed. In the crystal, N—H⋯O and C—H⋯O hydrogen bonds link molecules into layers perpendicular to [101]. The closest distance between the centroids of two heterocyclic rings was found to be 3.5268 (8) Å.

Related literature

For background on chelating ligands, see: Gade (1998 ▶). For the crystal structures of other Schiff bases derived from ortho-(thiomethyl)benzaldehyde, see: Yan et al. (2007 ▶); Baidina et al. (1987 ▶). For details of graph-set analysis of hydrogen bonds, see: Etter et al. (1990 ▶); Bernstein et al. (1995 ▶). For details of puckering analysis, see: Cremer & Pople (1975 ▶).

Experimental

Crystal data

C₁₄H₁₆N₄O₂S
M _r = 304.37
Monoclinic,
a = 7.9740 (2) Å
b = 12.4630 (3) Å
c = 13.9870 (3) Å
β = 94.384 (1)°
V = 1385.96 (6) Å³
Z = 4
Mo Kα radiation
μ = 0.24 mm⁻¹
T = 100 K
0.45 × 0.25 × 0.13 mm

Data collection

Bruker APEXII CCD diffractometer
13383 measured reflections
3441 independent reflections
2912 reflections with I > 2σ(I)
R _int = 0.025

Refinement

R[F ² > 2σ(F ²)] = 0.036
wR(F ²) = 0.094
S = 1.09
3441 reflections
201 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.43 e Å⁻³
Δρ_min = −0.26 e Å⁻³

Data collection: APEX2 (Bruker, 2010 ▶); cell refinement: SAINT (Bruker, 2010 ▶); data reduction: SAINT; program(s) used to solve structure: SIR97 (Altomare et al., 1999 ▶); 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

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536811020903/wn2434sup1.cif

e-67-o1592-sup1.cif^{(18KB, cif)}

Supplementary material file. DOI: 10.1107/S1600536811020903/wn2434Isup2.cdx

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811020903/wn2434Isup3.hkl

e-67-o1592-Isup3.hkl^{(168.8KB, hkl)}

Supplementary material file. DOI: 10.1107/S1600536811020903/wn2434Isup4.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
N4—H741⋯S1	0.88 (2)	2.63 (2)	3.5117 (14)	178.4 (17)
N4—H742⋯O2ⁱ	0.86 (2)	2.07 (2)	2.8463 (16)	150 (2)
C9—H9⋯O1ⁱⁱ	0.95	2.61	3.2807 (18)	128

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

Acknowledgments

The authors thank Mrs Isolda Williams for helpful discussions.

supplementary crystallographic information

Comment

Chelate ligands have found widespread use in coordination chemistry due to the enhanced thermodynamic stability of resultant coordination compounds in relation to coordination compounds exclusively applying comparable monodentate ligands (Gade, 1998). Combining different sets of donor atoms in one chelate ligand molecule, a probe for testing and accomodating metal centers of different Lewis acidities is at hand. To enable comparative studies with envisioned coordination compounds, we determined the crystal structure of the title compound. Other crystal structures of Schiff-bases derived from ortho-(thiomethyl)-benzaldehyde are reported in the literature (Yan et al., 2007; Baidina et al. 1987).

The molecule is a Schiff-base featuring an ortho-(thiomethyl)phenyl moiety and a 6-amino-1,3-dimethylpyrimidine-2,4(1H,3H)-dione moiety. The double-bond is (E)-configured. A conformational analysis of the non-aromatic six-membered ring (Cremer & Pople, 1975) fails due to the low puckering amplitude. The molecule, excluding methyl hydrogen atoms is essentially planar, the least-squares planes defined by the respective atoms of both six-membered ring systems intersecting at an angle of only 12.24 (7)° (Fig. 1).

In the crystal structure, intra- as well as intermolecular hydrogen bonds can be observed, both supported by the amino group. While the intramolecular hydrogen bond is formed to the sulfur atom of the thiomethyl group, the intermolecular hydrogen bond uses one of the ketonic oxygen atoms as acceptor. Apart from these hydrogen bonds, C—H···O contacts whose range falls by more than 0.1 Å below the sum of van-der-Waals radii of the atoms participating are apparent. These stem from the H atom bonded to the C atom in para-position to the Schiff-base functionality on the aromatic ring and have the second ketonic O atom as acceptor. A description of the hydrogen bonding system in terms of graph-set analysis (Etter et al., 1990; Bernstein et al., 1995) is possible with a DC¹₁(6) descriptor on the unitary level, whereas the C—H···O contacts necessitate a C¹₁(10) descriptor on the same level. In total, the molecules are linked in planes perpendicular to [1 0 1]. The shortest distance between the centroids of two heterocyclic rings was found to be 3.5268 (8) Å (Fig. 2). The packing of the title compound is shown in Fig. 3.

Experimental

Equimolar amounts of ortho-(thiomethyl)-benzaldehyde (1.00 g, 6.57 mmol) and 5,6-diamino-1,3-dimethylpyrimidine-2,4(1H,3H)-dione (1.12 g) in 50 cm³ anhydrous methanol were refluxed for three hours. The reaction mixture was allowed to cool to room temperature. A yellow precipitate was isolated which was recrystallized from anhydrous acetonitrile to give yellow crystals, which were suitable for X-ray analysis.