2,4-Diamino-5-(4-chloro­phen­yl)-6-ethyl­pyrimidin-1-ium 2-acet­amido­benzoate

Sampath Natarajan; Rita Mathews

doi:10.1107/S1600536811032570

. 2011 Aug 17;67(Pt 9):o2357–o2358. doi: 10.1107/S1600536811032570

2,4-Diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium 2-acetamidobenzoate

Sampath Natarajan ^a,^*, Rita Mathews ^a

PMCID: PMC3200980 PMID: 22065484

Abstract

The title compound, C₁₂H₁₄ClN₄ ⁺·C₉H₈NO₃ ⁻, is a salt with a 1:1 ratio of cation and anion components interacting with each other forming an R ₂ ²(8) ring motif. The crystal structure is stabilized by hydrogen bonds (N—H⋯O) involving two different eight-membered rings. One of them is formed between the pyrimidine ring (donor) and the carboxylate group (acceptor) from the benzoate, whereas the other ring is formed by N—H⋯O interactions, which help to form a dimer between two symmetry-related salts in the unit cell. In addition, an intramolecular C—H⋯N and intermolecular C—H⋯Cl interactions help to control the molecules in the unit-cell packing.

Related literature

For related literature on aminopyrimidine–carboxylate interactions, see: Baker & Santi (1965 ▶); Chinnakali et al. (1999 ▶); Desiraju (1989 ▶); Hunt et al. (1980 ▶); Lynch & Jones (2004 ▶); Stanley et al. (2005 ▶). For literature on aminopyrimidine and benzoic acid adducts, see: Thanigaimani et al. (2006 ▶, 2007 ▶); Balasubramani et al. (2005 ▶, 2006 ▶). For puckering parameters, see: Cremer & Pople, (1975 ▶); Nardelli (1995 ▶).

Experimental

Crystal data

C₁₂H₁₄ClN₄ ⁺·C₉H₈NO₃ ⁻
M _r = 427.89
Monoclinic,
a = 25.226 (4) Å
b = 9.0666 (16) Å
c = 20.688 (4) Å
β = 113.400 (3)°
V = 4342.5 (13) Å³
Z = 8
Mo Kα radiation
μ = 0.21 mm⁻¹
T = 293 K
0.4 × 0.35 × 0.32 mm

Data collection

Bruker SMART APEX CCD area-detector diffractometer
14400 measured reflections
3937 independent reflections
3079 reflections with I > 2σ(I)
R _int = 0.019

Refinement

R[F ² > 2σ(F ²)] = 0.046
wR(F ²) = 0.123
S = 1.04
3937 reflections
272 parameters
H-atom parameters constrained
Δρ_max = 0.20 e Å⁻³
Δρ_min = −0.19 e Å⁻³

Data collection: SMART (Bruker, 2004 ▶); cell refinement: SAINT (Bruker, 2004 ▶); 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 ▶); software used to prepare material for publication: PLATON (Spek, 2009 ▶).

Supplementary Material

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536811032570/ng5209sup1.cif

e-67-o2357-sup1.cif^{(21.4KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811032570/ng5209Isup2.hkl

e-67-o2357-Isup2.hkl^{(189.2KB, hkl)}

Supplementary material file. DOI: 10.1107/S1600536811032570/ng5209Isup3.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
N5—H5⋯O1	0.86	1.90	2.614 (2)	140
C9—H9B⋯N5	0.97	2.87	3.683 (3)	142
N1—H1⋯O1ⁱ	0.86	1.86	2.715 (2)	177
N3—H3B⋯O2ⁱ	0.86	1.96	2.802 (3)	165
N3—H3A⋯O2ⁱⁱ	0.86	2.16	2.897 (2)	143
N4—H4A⋯O3ⁱⁱⁱ	0.86	2.01	2.859 (2)	168
C10—H10B⋯Cl1^iv	0.96	2.95	3.864 (3)	160

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

supplementary crystallographic information

Comment

Aminopyrimidine-Carboxylate interactions are important since they are involved in protein-nucleic acids recognition and protein-drug binding. Hydrogen bonding plays a key role in molecular recognition and crystal engineering research (Desiraju, 1989). In general, aminopyrimidines posses self complementary hydrogen-bonded motifs forming a base pair which in itself is a unique property. The adducts of carboxylic acid with 2-aminopyrimidine system form a graph-set motif R₂²(8) (Lynch & Jones, 2004). This motif is very robust in aminopyrimidine-carboxylic acid/carboxylates systems. The crystal structures of many aminopyrimidine carboxylates (Stanley et al., 2005) and co-crystal structures (Chinnakali et al.,1999) have been reported. Many structures of aminopyrimidine and benzoic acid adducts have been reported. Few of them are 2-amino-4,6-dimethoxy pyrimidine: 4-aminobenzoic acid (Thanigaimani et al., 2006), 2-amino-4,6-dimethoxypyrimidine: phthalic acid (Thanigaimani et al., 2007), 2-amino-4,6-dimethylpyrimidine: cinnamic acid (Balasubramani et al., 2005) and 2-amino-4,6-dimethylpyrimidine: 4-hydroxybenzoic acid (Balasubramani et al., 2006). All these reported structures also have common features of heterosynthone formation. In the present study we report a salt (1:1) namely, 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium- 2-(acetylamino)benzoate and its interactions are studied extensively.

The asymmetric unit of crystal contains a single molecule of each component of salt (Fig. 1) and does not have any direct interactions each other. The interactions were found between the symmetry related molecules of aminopyrimidin-1-ium and benzoate salt via hydrogen bonds N1—H1···O1 and N3—H3B···O2 (-x + 1/2, -y + 1/2, -z + 1) (Fig. 2). Here the pyrimidine acts as a donor which donates two H atoms and carboxylate O atoms as acceptors. In addition dimeric interactions by the atoms O2 and N3 form an eight membered ring through the Hydrogen bonds N3—H3A···O2 (x - 1/2, -y + 1/2, z - 1/2) and N3—H3B···O2 (-x + 1/2, -y + 1/2, -z + 1) (Fig. 2). The dihedral angle between the rings, 4-chlorophenyl and 2,4-diaminopyrimidine is 80.6 (1)°. This value is higher than that in a biphenyl ring system. This may be due to the substitution of ethyl and amine groups at C4 and C6, respectively. An extended moiety of acetylamino group is coplanar with phenyl carboxylate and the dihedral angle between these two is 1.59 (1)° (Cremer & Pople, 1975; Nardelli, 1995).

In the crystal packing, the molecules are arranged as sheets along the a direction (Fig. 3). These sheets are organized as two layers in the unit cell and both layer molecules are connected to each other through N4—H4A···O3 hydrogen bond. In addition, a six membered ring is formed by an intra-molecular interaction (N5—H5···O1)in benzoate molecule which also controls the molecules in crystal packing. Molecular packing is stabilized by many N—H···O and a C—H···Cl (x, -y, z - 1/2) intra and intermolecular interactions (Table 1, Fig. 2).

Experimental

A hot methanolic solution (20 ml) of 2,4-diamino-5-(4-chlorophenyl)-6- ethylpyrimidine and 2-(acetylamino)benzoic acid in the ratio of 1:1 was warmed for 0.5 h over a water bath. The mixture was cooled slowly and kept at room temperature and after a few days, colourless crystals were obtained