2-Amino-4,6-dimethyl­pyrimidinium 3,5-dinitro­benzoate dihydrate

Annamalai Subashini; Packianathan Thomas Muthiah; Daniel E Lynch

doi:10.1107/S1600536808000524

. 2008 Jan 11;64(Pt 2):o426. doi: 10.1107/S1600536808000524

2-Amino-4,6-dimethylpyrimidinium 3,5-dinitrobenzoate dihydrate

Annamalai Subashini ^a, Packianathan Thomas Muthiah ^a,^*, Daniel E Lynch ^b

PMCID: PMC2960285 PMID: 21201453

Abstract

In the title compound, C₆H₁₀N₃ ⁺·C₇H₃N₂O₆ ⁻·2H₂O, the aminopyrimidine molecule is protonated at one of the pyrimidine N atoms. The carboxylate group of the 3,5-dinitrobenzoate anion interacts with the protonated pyrimidine N atom and the 2-amino group through a pair of N—H⋯O hydrogen bonds, forming an R ₂ ²(8) motif. Two inversion-related pyrimidine rings are linked via a pair of N—H⋯N hydrogen bonds, also forming an R ₂ ²(8) ring motif.

Related literature

For related literature, see: Allen et al. (1998 ▶); Baker & Santi (1965 ▶); Baskar Raj et al. (2003 ▶); Desiraju (1989 ▶); Hunt et al. (1980 ▶); Lynch & Jones (2004 ▶); Panneerselvam et al. (2004 ▶); Prince et al. (1991 ▶); Stanley et al. (2005 ▶); Subashini et al. (2006 ▶).

Experimental

Crystal data

C₆H₁₀N₃ ⁺·C₇H₃N₂O₆ ⁻·2H₂O
M _r = 371.32
Triclinic,
a = 7.1465 (3) Å
b = 11.0215 (5) Å
c = 11.1531 (4) Å
α = 99.473 (3)°
β = 101.322 (3)°
γ = 100.826 (2)°
V = 827.33 (6) Å³
Z = 2
Mo Kα radiation
μ = 0.13 mm⁻¹
T = 120 K
0.44 × 0.36 × 0.23 mm

Data collection

Bruker–Nonius KappaCCD area-detector diffractometer
Absorption correction: none
15739 measured reflections
3235 independent reflections
2283 reflections with I > 2σ(I)
R _int = 0.043

Refinement

R[F ² > 2σ(F ²)] = 0.059
wR(F ²) = 0.171
S = 1.04
3235 reflections
238 parameters
H-atom parameters constrained
Δρ_max = 0.50 e Å⁻³
Δρ_min = −0.55 e Å⁻³

Data collection: COLLECT (Nonius, 1998 ▶); cell refinement: DENZO (Otwinowski & Minor, 1997 ▶) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: PLATON (Spek, 2003 ▶); software used to prepare material for publication: PLATON.

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808000524/rz2189sup1.cif

e-64-0o426-sup1.cif^{(23.3KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808000524/rz2189Isup2.hkl

e-64-0o426-Isup2.hkl^{(155.4KB, 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⋯O1	0.88	1.73	2.605 (3)	174
N2—H2A⋯N3ⁱ	0.88	2.17	3.041 (3)	172
N2—H2B⋯O2	0.88	1.92	2.787 (3)	168

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Symmetry code: (i) Inline graphic .

Acknowledgments

AS thanks Bharathidasan University for the award of a Research Student Fellowship (Reference CCCD/PhD-2/15504/2004). DEL thanks the EPSRC National Crystallography Service (Southampton, England) for the X-ray data collection.

supplementary crystallographic information

Comment

Hydrogen-bonding patterns involving aminopyrimidine and carboxylates have been observed in drug–receptor interactions, protein–nucleic acid interactions and supramolecular architectures (Desiraju, 1989). Studies of such interactions are also of current interest because of their applications in drug design and the crystal engineering of pharmaceuticals (Stanley et al., 2005). Pyrimidine and aminopyrimidine derivatives are biologically important compounds as they occur in nature as components of nucleic acids. Some aminopyrimidine derivatives are used as antifolate drugs (Hunt et al., 1980; Baker & Santi, 1965). Two monoclinic polymorphic forms of 3,5-dinitrobenzoic acid (Prince et al., 1991) have already been reported. From our laboratory, the crystal structures of 2-amino-4,6-dimethylpyrimidinium bromide 2-amino-4,6-dimethyl pyrimidine monohydrate (Panneerselvam et al., 2004) and 2-amino-4,6-dimethylpyrimidinium picrate (Subashini et al., 2006) have been reported. The present study was undertaken to explore the hydrogen-bonding patterns involving aminopyrimidine–carboxylate interactions.

The asymmetric unit of the title compound contains one 2-amino-4,6-dimethylpyrimidinium cation, one 3,5-dinitrobenzoate anion and two water molecules (Fig. 1). Protonation of the pyrimidine base on the N1 site is reflected in a change in bond angle. The C2—N3—C4 angle at unprotonated atom N3 is 117.6 (2)°, while for protonated atom N1, the C2—N1—C6 angle is 120.5 (2)°. The carboxylate group of the 3,5-dinitrobenzoate anion (O1 and O2) interacts with the protonated N1 atom and the 2-amino group of the pyrimidine moiety through a pair of N—H···O hydrogen bonds, forming a fork-like interaction with graph-set R₂²(8) (Lynch & Jones, 2004). This R₂²(8) motif is one of the 24 most frequently observed bimolecular cyclic hydrogen-bonded motifs in organic crystal structures (Allen et al., 1998). The aminopyrimidinium cations are centrosymmetrically paired through two N—H···N hydrogen hydrogen bonds involving the 2-amino group and the N3 nitrogen atom (graph-set R₂²(8)) (Fig. 2). A similar type of interaction has been observed in crystal structure of trimethoprim m-chlorobenzoate and trimethoprim m-chlorobenzoate dihydrate (Baskar Raj et al., 2003).

Experimental

A hot ethanol solution of 2-amino-4,6-dimethylpyrimidine (31 mg, Aldrich) was added to a hot aqueous solution of 3,5-dinitrobenzoic acid (53 mg, LOBA) in a 1:1 molar ratio. The resultant solution was warmed over a water bath for an hour. After a few days brown colored block shaped crystals were obtained as a result of slow evaporation.