Single crystals of [3BF4@Pd4L18] suitable for X-ray diffraction were obtained via slow vapor diffu-sion of benzene into an acetonitrile solution of the interpenetrated cage. The supramolecular as-sembly crystallizes in the tetragonal space group P4/n with unit cell dimension of a = b = 22.065(4) Å and c = 33.491(6) Å. The structure consists of four square planar coordinated Pd(II) cations aligned in one axis and eight banana-shaped ligands L1. The interpenetrated double cage structure is composed of two monomeric cages with the formula [Pd2L14], which are quadruply interpenetrated to form the thermodynamically stable [3BF4@Pd4L18] cage. Looking at the topology of the assembly, the [3BF4@Pd4L18] cage belongs to the class of “catenanes” (see Chapter 1.1 and Figure 1.2), which are defined as “a molecules which contain two or more intertwined rings.[15] The structure features three internal pockets, which are all filled with one tetrafluoroborate anion. Fur-ther BF4− anions are located at the outside of the interpenetrated cage in close proximity to the palladium(II) cations. The distance between the palladium cations in the outer voids was measured to be 8.24 and 8.26 Å and the Pd−Pd distance in the inner cavity was determined to be 8.44 Å (Figure 2.7a). These values are in accordance with the previously reported dibenzosuberone and phenothiazine containing interpenetrated cages.[75,78]
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Figure 2.7 X-ray crystal structures of cage (a) [3BF4@Pd4L18], (b) [2Cl+benzene@Pd4L18] and c) [2Cl+DABCO@Pd4L18] with disordered DABCO guest. Color scheme: C: light/dark gray; N: blue; O: red; Cl: yellow; F: green; B: salmon; Pd:
orange. Hydrogen atoms, some of the solvent molecules and disordered components have been removed for clarity.
Benzene molecules were highlighted in red.
Slow vapor diffusion of benzene into an acetonitrile solution of the chloride-incorporated coordina-tion cage [2Cl@Pd4L18] gave suitable crystals for X-ray determination. The halide containing coor-dination cage crystallized in the monoclinic space group P21/n, with cell dimensions of a = b = 22.065(4) Å and c = 33.491(5) Å. Due to the smaller size of the chloride anion in compari-son to the larger tetrafluoroborate anion, the overall size of the coordination cage is decreased from 24.94 Å for [3BF4@Pd4L18] to 23.69 Å in the [2Cl@Pd4L18] cage (distance measured between the outer two palladium cations). The Pd−Pd distance in the outer cavities of the interpenetrated double cage decreases to 6.59 Å and 6.62 Å. In contrast, the central cavity enlarges, which is indicated by the increase of the Pd−Pd distance from 8.44 Å to 10.48 Å (see Figure 2.7b). Surprisingly, benzene molecules were not only found at the exterior of the cage, but also one benzene molecule is en-capsulated in the central pocket of the interpenetrated coordination cage, thereby forming the host-guest complex [2Cl+benzene@Pd4L18]. Stabilizing cation-π interaction between the cationic coor-dination cage and the neutral guest molecule can be excluded, because the closet distance be-tween one of the central palladium cations and the benzene ring center was measured to be 4.64 Å (and 5.02 Å to the center of the ring). Furthermore, the closest distance from the benzene hydrogen atoms to the next carbonyl oxygen is 2.68 Å and all pyridine hydrogen atoms are more than 3.0 Å away. Consequently, substantial CH-π or hydrogen bond interaction are unlikely to contribute to the stabilization of the benzene molecule. Based on the position of the benzene molecule in the interior of the coordination cage, it is assumed, that the main interaction for stabilizing the neutral
guest molecule in the cationic coordination cage are dispersion interaction, with further contribution of solvophobic effects.[89]
A closer look at the crystal structure of [2Cl+benzene@Pd4L18] along the Pd4-axis shows a quite asymmetric arrangement of the eight ligands around the palladium centers. It therefore can be assumed, that the acridone-based ligands are to some degree flexible. This observation is in con-trast with the previously reported interpenetrated cage structures based on dibenzosuberone and phenothiazine. Those ligands have twisted or bent backbones, which result in more rigidly inter-locked cage structures. The conformational flexibility of the acridone-derived ligand might be an important requirement of the interpenetrated coordination cage to enable the uptake of the relatively large neutral guest molecule in its central cavity (Figure 2.7b). On the basis of the unique guest-uptake behavior of the interpenetrated coordination cage, a series of neutral guest molecules was tested for their capability to be encapsulated in the chloride-containing coordination cage [2Cl@Pd4L18] (see Chapter 2.5 about Neutral Guest Uptake for a more detailed description).
Figure 2.8 Central pockets of the X-ray structure of the host-guest complexes [2Cl+NG@Pd4L18] (NG = neutral guest) with a) benzene and b) one selected orientation of DACBO. While the benzene molecules is oriented perpendicular to the Pd4 axis, the DABCO molecules stands upright in the central pocket of the interpenetrated coordination cage. Reproduced from reference [90] with permission from The Royal Society of Chemistry.
Further crystals suitable for X-ray structure determination were obtained for the host-guest complex [2Cl+DABCO@Pd4L18] from slow vapor diffusion of ethanol into an acetonitrile solution of the com-plex (see Figure 2.7c) (DABCO = 1,4-Diazabicyclo[2.2.2]octane). The supramolecular assembly crystallizes in the tetragonal space group P4/ncc with unit cell dimension of a = b = 22.064(3) Å and c = 62.075(1) Å. The structure has a fourfold crystallographic symmetry axis along the Pd4 – axis, which complicated the modeling of the axially disordered D3h symmetric DABCO molecule.
Nevertheless, refinement showed clearly, that the DABCO molecule stands upright inside the cen-tral cavity with its nitrogen-axis aligned with the Pd4-axis of the interpenetrated coordination cage (see Figure 2.7c for visualization of the disordered DABCO molecule). Comparison with the zene-containing complex, the binding mode of these two neutral guest are quite different. The ben-zene molecular plane is oriented perpendicular to the Pd4-axis, exposing its π-surface towards the palladium(II) cations (see Figure 2.8a), while DABCO stands upright in the central pocket (see Figure 2.8b). A close contact of 4.13 Å between the positively-charged palladium cation and the nitrogen atom of the DABCO molecule indicates an interaction of the free lone pair (from DABCO)
27 with the Pd(II) cation from the interpenetrated coordination cage. Furthermore, close contacts of
~2.5 Å between the hydrogen atoms of the encapsulated neutral guest molecule and the ligands of the coordination cage were found in the crystal structure. One can assume that both of these interactions contribute to the stability of the host-guest system.
The distances between the palladium cations in the outer voids of [2Cl+DABCO@Pd4L18] were measured to be 6.40 Å and 6.49 Å and the Pd-Pd distance in the central cavity is 10.93 Å (Figure 2.7c, top). These values are in a similar range compared to the benzene-containing coordination cage. Nevertheless, it is noteworthy that the central pocket of the DABCO-containing cage (Pd-Pd:
10.93 Å) is larger compared to the host-guest complex incorporating benzene (Pd-Pd: 10.48 Å) (see Figure 2.7b and c), while the outer pockets are smaller. This change in size might be due to the overall size of the encapsulated neutral guest. While benzene is a rather small, plate-like neutral molecule (Vbenzene = 99.0 Å3), DABCO has a larger and three-dimensional shape (VDABCO =126.4 Å3). Due to the observed trends, it seems that the interpenetrated coordination cage is able to adapt to a certain extend towards the size and shape of the neutral guest molecule.