N-(4,6-Dimethyl­pyrimidin-2-yl)-1H-benzimidazol-2-amine

Shaaban Kamel Mohamed; Mahmoud A A El-Remaily; Atash V Gurbanov; Ali N Khalilov; Seik Weng Ng

doi:10.1107/S1600536811006507

. 2011 Feb 26;67(Pt 3):o719. doi: 10.1107/S1600536811006507

N-(4,6-Dimethylpyrimidin-2-yl)-1H-benzimidazol-2-amine

Shaaban Kamel Mohamed ^a, Mahmoud A A El-Remaily ^b, Atash V Gurbanov ^c, Ali N Khalilov ^c, Seik Weng Ng ^d,^*

PMCID: PMC3052168 PMID: 21522461

Abstract

There are two independent molecules in the asymmetric unit of the title compound, C₁₃H₁₃N₅. In each molecule, an amino N atom is connected to a benzimidazole fused-ring system and a pyrimidine ring [these are aligned at 1.3 (1)° in one independent molecule and at 5.4 (1)° in the other]. The amino N atom of the fused ring forms an intramolecular N—H⋯O hydrogen bond to a pyrimidine N atom in each molecule. The amino N atom connecting the two ring systems interacts with the other N atom of the pyrimidine ring of an adjacent molecule, generating centrosymmetric hydrogen-bonded dimers.

Related literature

For the synthesis, see: Bossio et al. (1985 ▶); Shestakov et al. (2006 ▶).

Experimental

Crystal data

C₁₃H₁₃N₅
M _r = 239.28
Triclinic,
a = 8.2836 (4) Å
b = 9.6135 (5) Å
c = 16.5694 (8) Å
α = 92.121 (1)°
β = 96.100 (1)°
γ = 112.597 (1)°
V = 1206.94 (10) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 295 K
0.30 × 0.20 × 0.20 mm

Data collection

Bruker APEXII diffractometer
13373 measured reflections
5550 independent reflections
4124 reflections with I > 2σ(I)
R _int = 0.019

Refinement

R[F ² > 2σ(F ²)] = 0.044
wR(F ²) = 0.136
S = 1.01
5550 reflections
345 parameters
4 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.25 e Å⁻³
Δρ_min = −0.18 e Å⁻³

Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: SAINT (Bruker, 2005 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: X-SEED (Barbour, 2001 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶).

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811006507/hg5003sup1.cif

e-67-0o719-sup1.cif^{(23.2KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536811006507/hg5003Isup2.hkl

e-67-0o719-Isup2.hkl^{(271.7KB, hkl)}

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⋯N5	0.86 (1)	2.05 (2)	2.664 (2)	128 (2)
N3—H3⋯N2ⁱ	0.87 (1)	2.05 (1)	2.912 (2)	170 (2)
N7—H7⋯N10	0.87 (1)	2.10 (2)	2.695 (2)	125 (2)
N8—H8⋯N6ⁱⁱ	0.87 (1)	2.05 (1)	2.908 (2)	170 (2)

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

Acknowledgments

We thank Manchester Metropolitan University, Baku State University and the University of Malaya for supporting this study.

supplementary crystallographic information

Comment

The reported synthesis involves the reaction of 4,6-dimethylpyrimidin-2-ylcyanamide with o-phenylenediamine, and it illustrates the type of heterocycles that are formed by the reaction of cyanamides with N,N-binucleophiles (Shestakov et al., 2006). The unsubstituted compound was reported earlier (Bossio et al., 1985). The present synthesis is a more convenient synthesis that uses acetylacetone as one of the reactants. An amino N atom in the approximately planar C₁₃H₁₃N₅ molecule is connected to a benzimidazoyl fused-ring and a pyrimidyl ring; the amino N atom of the fused ring forms an intramolecular N–H···O hydrogen bond to a pyridmidyl N atom (Scheme I, Fig. 1). There are two independent molecules; each molecule is connected to an inversion-related molecule by an N–H···O hydrogen bond.

Experimental

1H-Benzo[d]imidazol-2-yliminomethanediamine (0.05 mol) and acetylacetone (0.10 mol, approx.10 ml) along with several drops of acetic acid were heated at 473 for 1 h. The solid that formed on cooling was collected and recrystallized from ethanol to give the title compound in 80% yield; m.p. 623 K.