Cucurbit[6]uril p-xylylenediammonium diiodide decahydrate inclusion complex

The title inclusion complex, C36H36N24O12·C8H14N2 2+·2I−·10H2O, displays a large ellipsoidal deformation of the cucurbit[6]uril (CB[6]) skeleton upon complex formation. The benzene ring of the cation is rotationally disordered between two orientations in a ratio of 3:1. The solvent H2O molecules form a hydrogen-bonded network by interaction with the carbonyl groups of CB[6] and the I− counterions. The crystal studied exhibited non-merohedral twinning. Both CB[6] and the cation are centrosymmetric.

The asymmetric unit of complex (I) comprises one half of a CB[6] molecule and one half of a p-xylylenediammonium cation both disposed about a center of inversion, an iodide counterion and five water molecules. The majority of the structural features of complex (I) are as expected based on its molecular structure, but several deserve some comment. For example, the p-xylylenediammonium ions are held in the cavity of CB[6] by H-bonds to its ureidyl C═O portals ( Fig. 1 and Table   1). The solvating H 2 O molecules form a cap on the complex by H-bonding to CB[6], the diammonium ion, themselves, and finally terminated by H-bonding to the Icounterion (Fig. 2). Complex (I) packs in the crystal by formation of a square array in the bc plane (Fig. 3).
Most interesting is the substantial ellipsoidal deformation observed in complex (I). We quantify this distortion for complex (I) as 0.88 Å (non-bonded C-C range 9.852-10.730 Å) by determining the distances between opposing C-atoms along the equator of the molecule as suggested previously by Samsonenko (Samsonenko et al., 2002). Although this ellipsoidal deformation is modest relative to those previously reported for complexes of CB[6] and other CB[n]-type receptors, taken together the results highlight the ability of CB[n]-type receptors to respond to the size and shape of their guests.

Experimental
Complex (I) was prepared by mixing cucurbit[6]uril with 1,4-xylylenediamine dihydrochloride in water according to the literature procedure (Freeman et al., 1981;Freeman, 1984;Liu et al., 2005) followed by the addition of KI. Single crystals suitable for structure determination were obtained by allowing the aqueous solution of complex (I) to stand at room temperature for several days.

Refinement
The N-and C-bound H atoms were included in the riding-model approximation with N-H = 0.90 Å and C-H = 0.98 to 0.99 Å, and with U iso (H) = 1.5U eq (N) and U iso (H) = 1.2U eq (C). The water H atoms were refined with soft restraints (2)° in a riding model approximation, with U iso (H) = 1.5U eq (O). The benzene ring of the cation is rotationally disordered between two orientations in a ratio of 3:1. The highest residual peak (1.68 e Å -3 ) is located 0.95 Å from I1 atom and is due to either partial disorder of I1 atom or truncation effect. The crystal studied is non-merohedral twin consisting of two components (domains). The twinning law is 180° rotation around 100 reciprocal direction with approximate 7:1 domain ratio.

Special details
Geometry. All e.s. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > σ(F 2 ) is used only for calculating Rfactors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.