2-Isopropyl-6-methyl-4-oxo-3,4-dihydro­pyrimidin-1-ium 2-carb­oxy-4,6-dinitro­phenolate monohydrate

Madhukar Hemamalini; Hoong-Kun Fun

doi:10.1107/S1600536810042571

. 2010 Oct 30;66(Pt 11):o2950–o2951. doi: 10.1107/S1600536810042571

2-Isopropyl-6-methyl-4-oxo-3,4-dihydropyrimidin-1-ium 2-carboxy-4,6-dinitrophenolate monohydrate

Madhukar Hemamalini ^a, Hoong-Kun Fun ^a,^*,^‡

PMCID: PMC3009185 PMID: 21589119

Abstract

In the title molecular salt, C₈H₁₃N₂O⁺·C₇H₃N₂O₇ ⁻·H₂O, the pyrimidinium cation is essentially planar, with a maximum deviation of 0.009 (1) Å. The cation undergoes an enol–keto tautomerism during the crystallization. In the crystal, the ion pairs and water molecules are connected via O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds, forming two-dimensional networks parallel to the bc plane. There is an intramolecular O—H⋯O hydrogen bond in the 3,5-dinitrosalicylate anion, which generates an S(6) ring motif.

Related literature

For applications of pyrimidine derivaties, see: Condon et al. (1993 ▶); Maeno et al. (1990 ▶); Gilchrist (1997 ▶). For a related structure, see: Hemamalini & Fun (2010 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶). For bond-length data, see: Allen et al. (1987 ▶). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 ▶).

Experimental

Crystal data

C₈H₁₃N₂O⁺·C₇H₃N₂O₇ ⁻·H₂O
M _r = 398.33
Triclinic,
a = 6.6691 (3) Å
b = 11.3831 (4) Å
c = 12.2900 (5) Å
α = 89.727 (2)°
β = 76.771 (2)°
γ = 76.930 (2)°
V = 883.62 (6) Å³
Z = 2
Mo Kα radiation
μ = 0.13 mm⁻¹
T = 100 K
0.52 × 0.13 × 0.10 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T _min = 0.937, T _max = 0.987
17014 measured reflections
4061 independent reflections
3279 reflections with I > 2σ(I)
R _int = 0.030

Refinement

R[F ² > 2σ(F ²)] = 0.040
wR(F ²) = 0.105
S = 1.03
4061 reflections
273 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.53 e Å⁻³
Δρ_min = −0.30 e Å⁻³

Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶).

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810042571/fj2355sup1.cif

e-66-o2950-sup1.cif^{(20.7KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810042571/fj2355Isup2.hkl

e-66-o2950-Isup2.hkl^{(195KB, 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
N3—H1N3⋯O6ⁱ	0.91 (2)	1.817 (19)	2.7180 (16)	170 (2)
N4—H1N4⋯O1W	0.90 (2)	1.84 (2)	2.7309 (17)	171 (2)
O1W—H2W1⋯O1ⁱⁱ	0.85 (2)	1.97 (2)	2.7878 (16)	162 (2)
O1W—H1W1⋯O3ⁱⁱⁱ	0.84 (2)	2.11 (2)	2.9381 (17)	170 (2)
O7—H7⋯O1	0.82	1.67	2.4370 (16)	156
C9—H9A⋯O5^iv	0.93	2.54	3.4312 (18)	161
C12—H12A⋯O7ⁱ	0.98	2.41	3.3023 (18)	152
C14—H14B⋯O4^v	0.96	2.60	3.2318 (19)	124
C15—H15C⋯O3^vi	0.96	2.60	3.471 (2)	152

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

Acknowledgments

MH and HKF thank the Malaysian Government and Universiti Sains Malaysia for the Research University grant No. 1001/PFIZIK/811160. MH also thanks Universiti Sains Malaysia for a post-doctoral research fellowship.

supplementary crystallographic information

Comment

Pyrimidine derivatives are very important molecules in biology and have many application in the areas of pesticide and pharmaceutical agents (Condon et al., 1993). For example, imazosulfuron, ethirmol and mepanipyrim have been commercialized as agrochemicals (Maeno et al., 1990). Pyrimidine derivatives have also been developed as antiviral agents, such as AZT, which is the most widely-used anti-AIDS drug (Gilchrist, 1997). The nitro-substituted aromatic acid 3,5-dinitrosalicylic acid (DNSA) has proven potential for formation of proton-transfer compounds, particularly because of its acid strength (pK_a = 2.18), its interactive ortho-related phenolic substituent group together with the nitro substituents which have potential for both π···π interactions as well as hydrogen-bonding interactions. Since our aim is to study some interesting hydrogen bonding interactions, the crystal structure of the title compound is presented here.

The asymmetric unit of (I) (Fig 1), contains a 2-isopropyl-6-methyl pyrimidinium-4(3H)-one cation, a 3,5-dinitrosalicylate anion and a water molecule. In the cation, the proton transfer from the hydroxyl group of the anion to the N4 atom leads to a slight increase in the C8—N4—C11 angle to 124.54 (12)°, compared to 116.83 (8)° in (Hemamalini & Fun, 2010). The phenol oxygen atoms are bent slightly away from the mean plane of the benzene ring [torsion angle O1-C7-C8-C9 = 177.02 (13)°]. The Pyrimidine ring is essentially planar, with a maximum deviation of 0.009 (1) Å for atom N4. The bond lengths (Allen et al., 1987) and angles are normal. The cation undergoes an enol-keto tautomerism during the crystallization. Similar tautomerism was also observed in the crystal structure of 2-Isopropyl-6-methylpyrimidinium-4(3H)-one (Hemamalini & Fun, 2010).

In the crystals structure (Fig. 2), the ion pairs and water molecules are connected via N3—H1N3···O6, N4—H1N4···O1W, O1W—H2W1···O1, O1W—H1W1···O3, C9—H9A···O5, C12—H12A···O7, C14—H14B···O4 and C15—H15C···O3 hydrogen bonds, forming two-dimensional networks parallel to the bc plane. There is an intramolecular O7—H7···O1 hydrogen bond in the 3,5-dinitrosalicylate anion which generates an S(6) (Bernstein et al., 1995) ring motif.

Experimental

A hot methanol solution (20 ml) of 2-isopropyl-4-hydroxy-6-methylpyrimidine (46 mg, Aldrich) and 3,5-dinitrosalicylic acid (58 mg, Merck) were mixed and warmed over a heating magnetic stirrer for a few minutes. The resulting solution was allowed to cool slowly at room temperature and yellow blocks of (I) appeared after a few days.