(E)-6-Amino-1,3-dimethyl-5-[(pyridin-2-yl­methyl­idene)amino]­pyrimidine-2,4(1H,3H)-dione

Irvin Booysen; Thulani Hlela; Muhammed Ismail; Thomas Gerber; Eric Hosten; Richard Betz

doi:10.1107/S1600536811031618

. 2011 Aug 11;67(Pt 9):o2289. doi: 10.1107/S1600536811031618

(E)-6-Amino-1,3-dimethyl-5-[(pyridin-2-ylmethylidene)amino]pyrimidine-2,4(1H,3H)-dione

Irvin Booysen ^a, Thulani Hlela ^a, Muhammed Ismail ^a, Thomas Gerber ^b, Eric Hosten ^b, Richard Betz ^b,^*

PMCID: PMC3200715 PMID: 22065567

Abstract

In the title compound, C₁₂H₁₃N₅O₂, a Schiff-base-derived chelate ligand, the non-aromatic heterocycle and its substituents essentially occupy one common plane (r.m.s. of fitted non-H atoms = 0.0503 Å). The N=C bond is E-configured. Intracyclic angles in the pyridine moiety cover the range 117.6 (2)–124.1 (2)°. Intra- and intermolecular N—H⋯N and N—H⋯O hydrogen bonds are observed in the crystal structure, as are intra- and intermolecular C—H⋯O contacts which, in total, connect the molecules into a three-dimensional network. The shortest ring-centroid-to-ring-centroid distance of 3.5831 (14) Å is between the two different types of six-membered rings.

Related literature

For the crystal structures of two polymorphs of 6-amino-1,3-dimethyl-5-[(E-2-(methylsulfanyl)benzylideneamino]pyrimidine-2,4(1H,3H)-dione, see: Booysen et al. (2011a ▶,b ▶). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990 ▶); Bernstein et al. (1995 ▶). For puckering analysis, see: Cremer & Pople (1975 ▶). For general information about the chelate effect in coordination chemistry, see: Gade (1998 ▶).

Experimental

Crystal data

C₁₂H₁₃N₅O₂
M _r = 259.27
Orthorhombic,
a = 26.5036 (8) Å
b = 28.9987 (14) Å
c = 6.2193 (1) Å
V = 4780.0 (3) Å³
Z = 16
Mo Kα radiation
μ = 0.10 mm⁻¹
T = 200 K
0.27 × 0.14 × 0.06 mm

Data collection

Bruker APEXII CCD diffractometer
11316 measured reflections
1620 independent reflections
1171 reflections with I > 2σ(I)
R _int = 0.049

Refinement

R[F ² > 2σ(F ²)] = 0.039
wR(F ²) = 0.079
S = 0.94
1620 reflections
182 parameters
1 restraint
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.17 e Å⁻³
Δρ_min = −0.19 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

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536811031618/lh5299sup1.cif

e-67-o2289-sup1.cif^{(17.2KB, cif)}

Supplementary material file. DOI: 10.1107/S1600536811031618/lh5299Isup2.cdx

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811031618/lh5299Isup3.hkl

e-67-o2289-Isup3.hkl^{(80.1KB, hkl)}

Supplementary material file. DOI: 10.1107/S1600536811031618/lh5299Isup4.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—H71⋯N5ⁱ	0.93 (3)	2.08 (3)	2.928 (3)	151 (3)
N4—H72⋯N3	0.84 (2)	2.25 (2)	2.661 (3)	110.2 (18)
N4—H72⋯O2ⁱⁱ	0.84 (2)	2.54 (2)	3.108 (3)	125.8 (19)
C7—H7⋯O2	0.95	2.17	2.847 (3)	127
C11—H11⋯O1ⁱⁱⁱ	0.95	2.54	3.313 (3)	138

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

Acknowledgments

The authors thank Mr David Neale-Shutte 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. Two crystal structures of 6-amino-1,3-dimethyl-5-[(E-2- (methylsulfanyl)benzylideneamino]pyrimidine-2,4(1H,3H)-dione are apparent in the literature (Booysen et al., 2011a; Booysen et al., 2011b).

The molecule is a Schiff-base composed of a pyridyl moiety and a 6-amino-1,3- dimethylpyrimidine-2,4(1H,3H)-dione moiety. The C=N double-bond is (E)-configured. A conformation analysis of the non-aromatic six-membered ring (Cremer & Pople, 1975) fails due to the low puckering amplitude (τ = 2.9 °; r.m.s. of fitted non-hydrogen atoms – including the exocyclic substituents – = 0.0503 Å). Intracyclic angles in the pyridyl moiety cover a range from 117.6 (2)–124.1 (2) ° with the smallest angle found on the nitrogen atom and the largest angle found on the unsubstituted carbon atom in ortho position to the nitrogen atom. The least-squares planes defined by the respective atoms of the six-membered heterocycles intersect at an angle of 8.11 (12) °. The amino group is almost planar. The plane defined by its atoms and the least-squares plane defined by the atoms of its six-membered carrier ring enclose an angle of 9.56(2.54) ° (Fig. 1).

In the crystal structure, hydrogen bonds of N–H···N type as well as N–H···O type are observed. These are intra- as well as intermolecular and, in the case of N–H···N hydrogen bonds, involve only the nitrogen atom of the aromatic system and the Schiff base's double bonded nitrogen atom as acceptor. The intramolecular hydrogen bond shows bifurcation involving an oxygen atom. Apart from these classical hydrogen bonds, intra- as well as intermolecular C–H···O contacts can be observed whose range falls by more than 0.5 Å (in the former case) and by almost 0.2 Å (in the latter case) below the sum of van-der-Waals radii of the atoms participating. While the intramolecular C–H···O contact is apparent between the vinylic hydrogen atom and the neighbouring oxygen atom, the intermolecular C–H···O contacts are supported by the C–H group in para position to the Schiff-base substituent on the aromatic system and the keto group's oxygen atom that is not involved in the intramolecular C–H···O contacts. In terms of graph-set analysis (Etter et al., 1990; Bernstein et al., 1995), the descriptor for the classical hydrogen bonds is S(5)C¹₁(6)C¹₁(8) on the unitary level while a description of the C–H···O contacts necessitates a S(6)C¹₁(12) descriptor on the same level. In total, the molecules are connected to a three-dimensional network. The shortest intercentroid distance between two centers of gravity was measured at 3.5831 (14) Å while the shortest intercentroid distance between two aromatic systems was found at 5.2956 (14) Å. (Fig. 2).

The packing of the title compound in the crystal is shown in Figure 3.

Experimental

Equimolar amounts of picolinaldehyde (1.00 g, 9.36 mmol) and 5,6-diamino-1,3-dimethylpyrimidine-2,4(1H,3H)-dione (1.59 g) in anhydrous methanol (50 cm³) were refluxed for 3 h. The reaction mixture was allowed to cool to room temperature. An orange precipitate was isolated, which was recrystallized from anhydrous acetonitrile to give orange crystals. The crystals were filtered and dried under vacuum.