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

Sampath Natarajan; Rita Mathews

doi:10.1107/S1600536811035501

. 2011 Sep 14;67(Pt 10):o2567. doi: 10.1107/S1600536811035501

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

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

PMCID: PMC3201463 PMID: 22065507

Abstract

In the title salt, C₁₂H₁₄ClN₄ ⁺·C₁₀H₁₀NO₃ ⁻, zwitterionic N—H⋯O interactions form an R ₂ ²(8) ring. The crystal structure is stabilized by N—H⋯O and N—H⋯N hydrogen bonds involving two different eight-membered rings. An N—H⋯O interaction occurs between the pyrimidine ring (donor) and carboxylate group (acceptor) while the other ring is formed by N—H⋯N interactions, which form a dimer between two symmetry-related salts. An intramolecular N—H⋯O hydrogen bond forms a six-membered ring in the benzoate. Intermolecular C—H⋯O interactions are also observed.

Related literature

For aminopyrimidine carboxylates, see: Chinnakali et al. (1999 ▶); Lynch & Jones (2004 ▶); Stanley et al. (2005 ▶). For aminopyrimidine and benzoic acid adducts, see: Balasubramani et al. (2005 ▶, 2006 ▶); Thanigaimani et al. (2006 ▶, 2007 ▶). For hydrogen bonding in molecular recognition and crystal engineering, see: Desiraju (1989 ▶). For puckering and asymmetry parameters, see: Cremer & Pople, (1975 ▶); Nardelli (1995 ▶).

Experimental

Crystal data

C₁₂H₁₄ClN₄ ⁺·C₁₀H₁₀NO₃ ⁻
M _r = 441.91
Monoclinic,
a = 22.144 (3) Å
b = 9.4915 (14) Å
c = 21.844 (3) Å
β = 99.071 (3)°
V = 4533.7 (12) Å³
Z = 8
Mo Kα radiation
μ = 0.20 mm⁻¹
T = 293 K
0.50 × 0.45 × 0.42 mm

Data collection

Bruker SMART APEX CCD area-detector diffractometer
17933 measured reflections
5077 independent reflections
2719 reflections with I > 2σ(I)
R _int = 0.039

Refinement

R[F ² > 2σ(F ²)] = 0.088
wR(F ²) = 0.228
S = 1.06
5077 reflections
281 parameters
H-atom parameters constrained
Δρ_max = 0.29 e Å⁻³
Δρ_min = −0.24 e Å⁻³

Data collection: APEX2 (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/S1600536811035501/ff2025sup1.cif

e-67-o2567-sup1.cif^{(21.8KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811035501/ff2025Isup2.hkl

e-67-o2567-Isup2.hkl^{(243.7KB, hkl)}

Supplementary material file. DOI: 10.1107/S1600536811035501/ff2025Isup3.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⋯O2	0.86	1.89	2.605 (4)	140
N2—H2A⋯O3ⁱ	0.86	2.15	2.977 (4)	163
N4—H4A⋯N1ⁱⁱ	0.86	2.16	2.988 (4)	163
N3—H3⋯O1ⁱⁱⁱ	0.86	1.80	2.660 (4)	178
C14—H14C⋯O1ⁱⁱⁱ	0.96	2.53	3.323 (6)	140
N2—H2B⋯O2ⁱⁱⁱ	0.86	1.91	2.746 (4)	164
N4—H4B⋯O3^iv	0.86	2.35	3.017 (3)	134

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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 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 are also 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 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-propanamidobenzoate which forms a zwitterionic interaction between the molecules of aminopyrimidine and benzoate exhibit a motif R₂²(8) ring.

The asymmetric unit of crystal contains a single molecule of each component of salt (Fig. 1). Interactions are found between the salt of aminopyrimidin-1-ium and benzoate via hydrogen bonds N2—H2B···O2 and N3—H3···O1 (Fig. 2). Here the pyrimidine acts as a donor which donates two H atoms to carboxylate O atoms (acceptor). In addition, a dimeric interaction through centre of inverted symmetry related salts via a hydrogen bond N4—H4A···N1 (Fig. 2) forms an eight membered ring. The dihedral angle between the rings, 4-chlorophenyl and 2,4-diaminopyrimidine is 63.8 (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 propanamido group is slightly deviating from the plane of benzoate moiety and the dihedral angle between these two is 10.8 (1)° (Cremer & Pople, 1975; Nardelli, 1995).

The packing diagram of the molecule viewed down b-axis is shown in Fig. 3. Two symmetry related molecules of salt form the dimer and organize as a sheet. This sheet like dimers are connected through the hydrogen bonds N4—H4B···O3 & N2—H2A···O3 interactions. In addition, a six membered ring is formed by an intra-molecular interaction (N5—H5···O2)in benzoate molecule which also controls the molecules in crystal packing. Molecular packing is stabilized by many N—H···O and N—H···N types 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-(propanoylamino)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