Rubidium 2,4,6-trioxo-1,3-diazinan-5-ide–1,3-diazinane-2,4,6-trione–water (1/1/1)

Marlena Gryl; Katarzyna Stadnicka

doi:10.1107/S1600536811012657

. 2011 Apr 13;67(Pt 5):m571–m572. doi: 10.1107/S1600536811012657

Rubidium 2,4,6-trioxo-1,3-diazinan-5-ide–1,3-diazinane-2,4,6-trione–water (1/1/1)

Marlena Gryl ^a,^*, Katarzyna Stadnicka ^a

PMCID: PMC3089342 PMID: 21754300

Abstract

The asymmetric unit of the title compound, Rb⁺·C₄H₃N₂O₃ ⁻·C₄H₄N₂O₃·H₂O, consists of one rubidium cation, a barbituric acid molecule, a barbiturate anion and one water molecule. The rubidium ion has seven close-contact interactions with O atoms, with Rb⋯O distances ranging from 2.8594 (16) to 3.2641 (14) Å. These seven O atoms together with an eighth O atom at 3.492 (2) Å away from Rb form a distorted polyhedron with shape intermediate between an antiprism and a dodecahedron. The Rb⁺ ions connect layers built of organic components and water molecules linked via N—H⋯O and O—H⋯O hydrogen bonds.

Related literature

For the crystal structures of selected barbiturates, see: Xiong et al. (2003 ▶); Gryl et al. (2008 ▶, 2011 ▶); Braga et al. (2010 ▶); Garcia et al. (2010 ▶); Ivanova & Spiteller (2010 ▶) and for those of rubidium salts, see: Clegg & Liddle (2004 ▶); Yıldırım et al. (2008 ▶). For classification of hydrogen-bond systems according to graph-set theory, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

Rb⁺·C₄H₃N₂O₃ ⁻·C₄H₄N₂O₃·H₂O
M _r = 358.66
Monoclinic,
a = 9.8810 (1) Å
b = 19.6790 (5) Å
c = 6.4530 (3) Å
β = 108.26 (2)°
V = 1191.59 (15) Å³
Z = 4
Mo Kα radiation
μ = 4.20 mm⁻¹
T = 293 K
0.43 × 0.23 × 0.21 mm

Data collection

Nonius KappaCCD diffractometer
Absorption correction: multi-scan (DENZO and SCALEPACK; Otwinowski & Minor, 1997 ▶) T _min = 0.266, T _max = 0.473
17623 measured reflections
2555 independent reflections
2239 reflections with I > 2σ(I)
R _int = 0.037

Refinement

R[F ² > 2σ(F ²)] = 0.024
wR(F ²) = 0.059
S = 1.03
2555 reflections
199 parameters
6 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.27 e Å⁻³
Δρ_min = −0.30 e Å⁻³

Data collection: COLLECT (Nonius, 1998 ▶); cell refinement: SCALEPACK (Otwinowski & Minor, 1997 ▶); data reduction: DENZO (Otwinowski & Minor, 1997 ▶) and SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: Mercury (Macrae et al., 2006 ▶) and ORTEP-3 (Farrugia, 1997 ▶); software used to prepare material for publication: SHELXL97 and WinGX (Farrugia, 1999 ▶).

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811012657/vm2087sup1.cif

e-67-0m571-sup1.cif^{(19.8KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536811012657/vm2087Isup2.hkl

e-67-0m571-Isup2.hkl^{(122.9KB, 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
N1A—H1A⋯O6Bⁱ	0.88 (1)	1.90 (1)	2.769 (2)	172 (2)
N3A—H3A⋯O4B	0.86 (1)	1.84 (1)	2.694 (2)	175 (2)
N1B—H1B⋯O2Aⁱⁱ	0.88 (1)	1.94 (1)	2.820 (2)	175 (2)
N3B—H3B⋯O4A	0.87 (1)	2.12 (1)	2.975 (2)	169 (2)
O1W—H1W⋯O6Bⁱⁱⁱ	0.84 (1)	1.87 (1)	2.700 (2)	171 (2)
O1W—H2W⋯O4A^iv	0.83 (1)	2.08 (1)	2.898 (2)	170 (3)

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

Acknowledgments

The authors thank the X-ray Diffraction Laboratory. Faculty of Chemistry, Jagiellonian University, for making the Nonius KappaCCD diffractometer available. This work was partially supported by the Polish Ministry of Science and Higher Education: grant No. N N204 316537.

supplementary crystallographic information

Comment

Recently we have reported structures for three polymorphic forms of barbituric acid and urea addition compounds (Gryl et al., 2008) for two of which a charge density analysis was also performed (Gryl et al., 2011). Barbituric acid appeared as a valuable component in designing new, functional materials and in particular polar materials (Xiong, et al., 2003). However many attempts to design and obtain polar barbiturates failed (see for example Ivanova & Spiteller, 2010). Herein we report the structure of the title addition compound (I), the asymmetric unit of which is comprised of a rubidium cation, barbiturate anion, barbituric acid molecule and one water molecule (Fig. 1). Unfortunately, like for many barbiturates, the structure is centrosymmetric (space group P2₁/c). Each Rb1 cation is surrounded by seven oxygen atoms and bridged by O6a (x - 1, y, z) and O2b (-x + 1, y + 1/2, -z + 1/2) to Rb1 (x, -y+1/2, z + 1/2) and by O2b (x, -y + 1/2, z - 1/2) and O6a (x-1, -y + 1/2, z - 1/2) to Rb1 (x, -y + 1/2, z - 1/2) (Fig. 2).

All barbiturate NH groups and water molecules act as hydrogen bond donors. The hydrogen bond geometry is given in Table 1. There are considerable differences in the accepting properties of the carbonyl oxygen atoms. In the barbituric acid molecule, only atom O4a is a hydrogen bond acceptor from O1W, whereas atoms O2a and O6a interact with Rb ions. A different situation is observed in the barbituriate ion: atom O6b is an acceptor of two hydrogen bonds from O1W and N1a whereas atoms O2b and O4b are both involved in interactions with rubidium ions. The structure is comprised of layers built of barbituric acid molecules and barbiturate anions connected by hydrogen bonds (Fig. 3). Graph-set descriptors R₂²(8) and R₈⁶(28) were assigned to the hydrogen bonds according to Bernstein et al., (1995). The two ring systems of R₂²(8) are formed between barbiturate anions and barbituric acid molecules by crystallographically different hydrogen bonds. In the R₈⁶(28) ring formation additionally two water molecules act as hydrogen bond donors. The layers, parallel to ab, are joined together into a three dimensional structure due to interactions of Rb1 cations with oxygen atoms from barbiturate anions, barbituric acid molecules and water molecules (Fig. 4).

Experimental

The title compound was synthesized by mixing aqueous solutions of barbituric acid and rubidium carbonate prepared at 323 K using a water bath. Single crystals suitable for X-ray diffraction were obtained from ethanol solution by slow evaporation at ambient conditions.