2-Amino-4-methyl-6-oxo-3,6-dihydro­pyrimidin-1-ium perchlorate–2-amino-6-methyl­pyrimidin-4(1H)-one–water (1/1/1)

Kamel Kaabi; Maher El Glaoui; Valeria Ferretti; Matthias Zeller; Cherif Ben Nasr

doi:10.1107/S1600536811034106

. 2011 Aug 27;67(Pt 9):o2507–o2508. doi: 10.1107/S1600536811034106

2-Amino-4-methyl-6-oxo-3,6-dihydropyrimidin-1-ium perchlorate–2-amino-6-methylpyrimidin-4(1H)-one–water (1/1/1)

Kamel Kaabi ^a, Maher El Glaoui ^a, Valeria Ferretti ^b, Matthias Zeller ^c, Cherif Ben Nasr ^a,^*

PMCID: PMC3200758 PMID: 22065517

Abstract

In the title compound, C₅H₈N₃O⁺·ClO₄ ⁻·C₅H₇N₃O·H₂O, each perchlorate anion is paired with a protonated cationic 2-amino-6-methylpyrimidin-4(1H)-one and another non-protonated entity of the same organic pyrimidinone. The crystal structure is stabilized by N—H⋯O_org, N—H⋯O_water, N—H⋯O_ClO4, O—H⋯O_ClO4, N—H⋯N and C—H⋯O_ClO4 hydrogen bonds between the anions, organic entities and water molecules. Intermolecular π–π stacking interactions between neighbouring organic rings are observed with a face-to-face distance of 3.776 (2) Å, and O—H⋯O hydrogen bonds link the perchlorate anions and the water molecules into chains along the b-axis direction. The perchlorate anion and the interstitial water molecule are disordered over two mutually incompatible positions with a common occupancy ratio of 0.678 (16):0.322 (16).

Related literature

For general background to perchlorate salts with organic cations, see: Czarnecki et al. (1994 ▶); Czupinski et al. (2002 ▶, 2006 ▶). For enamine-imino resonance, see: Oueslati et al. (2007 ▶). For π–π stacking interactions, see: Janiak (2000 ▶).

Experimental

Crystal data

C₅H₈N₃O⁺·ClO₄ ⁻·C₅H₇N₃O·H₂O
M _r = 368.75
Monoclinic,
a = 10.3669 (3) Å
b = 10.4342 (3) Å
c = 15.0780 (5) Å
β = 92.751 (2)°
V = 1629.11 (9) Å³
Z = 4
Mo Kα radiation
μ = 0.28 mm⁻¹
T = 295 K
0.30 × 0.15 × 0.12 mm

Data collection

Nonius Kappa CCD diffractometer
7792 measured reflections
4739 independent reflections
2765 reflections with I > 2σ(I)
R _int = 0.027

Refinement

R[F ² > 2σ(F ²)] = 0.059
wR(F ²) = 0.184
S = 1.02
4739 reflections
279 parameters
64 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.38 e Å⁻³
Δρ_min = −0.47 e Å⁻³

Data collection: Kappa CCD server software (Nonius, 1997 ▶); cell refinement: DENZO-SMN (Otwinowski & Minor, 1997 ▶); data reduction: DENZO-SMN; program(s) used to solve structure: SIR97 (Altomare et al.,1999 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEPIII (Burnett & Johnson, 1996 ▶); software used to prepare material for publication: SHELXL97, PARST (Nardelli, 1983 ▶, 1995 ▶), WinGX (Farrugia, 1999 ▶).

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536811034106/bx2369sup1.cif

e-67-o2507-sup1.cif^{(26.8KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811034106/bx2369Isup2.hkl

e-67-o2507-Isup2.hkl^{(227.5KB, hkl)}

Supplementary material file. DOI: 10.1107/S1600536811034106/bx2369Isup3.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
O1WA—H2WA⋯O2	0.82 (2)	2.26 (6)	3.07 (4)	169 (16)
C5—H5B⋯O3′	0.96	2.55	3.509 (6)	173
N5—H5⋯O1WB	0.86	1.95	2.797 (8)	166
O1WB—H2WB⋯O4′	0.82 (2)	2.30 (4)	3.071 (14)	159 (6)
N1—H1⋯N4ⁱ	0.86	1.98	2.839 (2)	174
N3—H3B⋯O6ⁱ	0.86	1.93	2.787 (2)	178
N6—H6A⋯O5ⁱ	0.86	2.05	2.895 (2)	168
N2—H2⋯O6ⁱⁱ	0.86	1.84	2.6560 (18)	158
N3—H3A⋯O5ⁱⁱ	0.86	2.24	3.0363 (18)	154
N6—H6B⋯O1ⁱⁱⁱ	0.86	2.35	3.095 (17)	145
C3—H3⋯O1^iv	0.93	2.56	3.466 (17)	166

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

Acknowledgments

The authors acknowledge the support provided by the Secretary of State for Scientific Research and Technology of Tunisia.

supplementary crystallographic information

Comment

Perchlorate salts containing organic cations have been studied extensively in recent years owing to some of their interesting properties such as e.g. ferroelectric and dielectric behaviour (Czarnecki et al., 1994; Czupinski et al., 2002; Czupinski et al., 2006). Here, we report the synthesis and the crystal structure of one such compound, (C₅H₈N₃O)(C₅H₇N₃O)ClO₄.H₂O.

The crystal structure of the title compound (Fig.1) contains one perchlorate anion, one water molecule, and two 2-amino-6-methylpyrimidin-4(1H)-one molecules. One of these molecules is protonated at the nitrogen atom of the six membered ring, thus formally changing the molecule into a 2-amino-4-methyl-6-oxo-3,6-dihydropyrimidin-1-ium cation. The atomic arrangement of (C₅H₈N₃O)(C₅H₇N₃O)ClO₄.H₂O can be divided into an organic and an inorganic part. The inorganic section is composed of chains of [ClO₄]^- tetrahedra and water molecules that extend along the b axis direction, held together by O_water—H···O(ClO₄) hydrogen bonds. Two such chains cross the unit cell at z = (2n +1)/4 and x = 0.5 (Fig. 2, Table 1). The organic groups are located between these chains and connect to them through N—H···O_water, N—H···O(ClO₄) and C—H···O(ClO₄) hydrogen bonds to form a three dimensional infinite network (Fig. 3, Table 1). Of the hydrogen bonds, one is bifurcted: O1WA—H2WA···(O2, O4) (Fig. 2, Table 1). The organic entities are associated with each other via N—H···O_org and N—H···N hydrogen bonds (Fig. 3, Table 1). Intermolecular π-π stacking interactions between neighbouring organic rings are observed with a face-to-face distance of 3.776 (2) Å, less than 3.8 Å, the maximum regarded as relevant for π-π interactions (Janiak, 2000).

The C—N bond distances of the NH₂ groups, N3—C1 and N6—C6, are 1.311 (2) and 1.327 (2) Å, respectively, which is short for a C—N single bond, but still not quite as contracted as one would expect for a fully established C=N double bond. These bond length features are consistent with an imino resonance form as it is commonly found for C—N single bonds involving sp² hybridized C and N atoms (Oueslati et al., 2007). The distance values of C2—O5 [1.233 (2) Å] and C7—O6 [1.260 (2) Å] clearly indicate two C=O double bonds. This confirms that the first step of the formation of the title compound consists in the tautomerization of the starting material 2-amino-4-hydroxy-6-methylpyrimidine into 2-amino-6-methylpyrimidin-4(1H)-one.

Experimental

An aqueous solution of Cu(ClO₄)₂ (1 mmol, 0.263 g) was added dropwise to a solution of 2-amino-4-hydroxy-6-methylpyrimidine (1 mmol, 0.125 g) in ethanol. The resultant mixture was evaporated at room temperature. Crystals of the title compound, which remained stable under normal conditions of temperature and humidity, were isolated after several days and subjected to X-ray diffraction analysis (yield 56%).