As described in the previous Chapters, the self-assembled [Pd2L24] cage shows an interesting dy-namic motion of the adamantyl groups and a rich host-guest chemistry (encapsulation of a large selection of bis-anionic guest molecules, see Chapter 4.4). In a further study, the influence of the guest uptake on the flipping rate of the steric adamantyl groups was investigated. The rate constant of the dynamic motion in the [G1@Pd2L24] and [G2@Pd2L24] host-guest complexes was measured via high resolution NMR spectroscopy on a 900 MHz machine from Dr. M. John (2D NOESY meas-urement at 298 K, see Figure 7.129 and Figure 7.130). As a counter cation [K(18-crown-6)]+ was used, since the 1H NMR signals of the NBu4+ species overlapped with relevant ligand signals. The
rate constants of the flipping motion of the adamantyl groups in the host-guest systems [G1@Pd2L24] and [G2@Pd2L24] were determined to be k < 0.03 s−1 and k < 0.02 s−1, respectively.
When compared, with the rate constant in the tetrafluoroborate-containing [Pd2L24] cage (k < 0.32 s−1), the flipping dynamics in the host guest systems are more than ten times slower. The exchange rate of the guests G1 and G2 were determined to be in the range of k ≈ 4-7 s−1 (see Chapter 4.4), which is several hundred times faster than the flipping motion. Thus, it can be as-sumed that a flipping of the adamantyl groups does not occur while the host-guest complex is intact.
Instead, the bis-anionic guest will leave the cage, before the adamantyl groups undergo the flipping motion.
4.6 X-ray Structure Analysis
The formation of the supramolecular [Pd2L24] coordination cage and the corresponding host-guest complexes [G1-5@Pd2L24] in solution were confirmed via intensive NMR spectroscopy and HR-MS spectrometry. Furthermore, the presence of these structures in the solid state were examined with X-ray radiation. Single crystals of [Pd2L24] suitable for X-ray structure determination were grown by slow vapor diffusion of diethyl ether into an acetonitrile solution (0.7 mM) of the self-assembled cage. PD Dr. B. Dittrich and co-workers collected diffraction data for all crystals at the SLS syn-chrotron source.
Figure 4.14 X-ray crystal structures of (a) [Pd2L24], (b) [G1@Pd2L24], (c) [G4@Pd2L24] and (d) [G5@Pd2L24]. Color scheme:
C, grey; N: blue; O: red; S: yellow; F: green; B: salmon; Pd: orange Fe: forest green. For clarity, solvent molecules and free (non encapsulated) anions are omitted. Appendix section 7.5.5 and CCDC numbers 1053080-83 contain details of the crystallographic data. Reprinted with permission from reference [107]. Copyright © 2016 Royal Society of Chemistry.
The cationic coordination cage [Pd2L24] crystalized in the triclinic space group P
1 ̅
with unit cell dimension of a = 16.196(3), b = 16.375(3) Å and c = 17.065(3) Å. The central cavity of the supra-molecular assembly is occupied by two tetrafluoroborate anions, which are positioned in close61 proximity to the Pd(II) cation (~4.1 Å from Pd(II) to the boron atom). The Pd-Pd distance in the monomeric coordination cage was measured to be 16.20 Å (see Figure 4.14). A fact worth discuss-ing is the arrangement of the ligand within the cage structure. Due to the attachment of the sterically demanding adamantyl group, the ligand shows a remarkable bent shape. This arises from a strong deformation of the tricyclic acridone backbone, in which the central ring arranges in a boat confor-mation. The connecting double bond between the acridone backbone and the adamantyl residue is not bent. Thus, all six carbon atoms constituting the tetra-substituted double bond system occupy a common plane.
In the cage structure, all adamantyl groups are bent to one side with radial symmetry and block the openings of the supramolecular assembly. The crystal structure is highly packed and short inter-ligand distances are found. For example, proton Ha from one ligand and proton Hj’ from the neigh-boring ligand are only 3.11 Å apart.
The central cavity of the coordination cage provides a rather spacious environment close to the Pd(pyridine)4-planes. These spaces are occupied by the tetrafluoroborate counter anions. In con-trast, the bulky adamantyl groups reach into the center of the cage cavity, which results in a quite narrow channel with a diameter of about 6.3 Å (see appendix section 7.5.5 for further views of the X-ray structure).
In addition, single crystals of the host-guest systems [G1@Pd2L24], [G4@Pd2L24] and [G5@Pd2L24] were obtained by slow vapor diffusion of methanol (for [G1@Pd2L24]), benzene (for [G4@Pd2L24]) and diethyl ether (for [G5@Pd2L24]) into acetonitrile solutions (0.7 M) of these supramolecular as-semblies. The crystal structures of the host-guest complexes confirm the encapsulation of the bis-anionic guest molecules G1, G4 and G5 (see Figure 4.14b-d). The negatively charged sulfonate groups of the guest molecules are in close proximity to the positively charged Pd(II) cations. The palladium−sulphur distances in the [G5@Pd2L24] host-guest complex are 4.42 Å and 4.03 Å (similar values were measured for G4@Pd2L24]). Due to the smaller size of the ferrocene-based guest G1, only one sulfonate group shows a close Pd−S contact of 4.12 Å. The distance between the second sulfonate group and the palladium(II) cation was measured to be 6.73 Å. Surprisingly, the encap-sulation of the ionic guest molecules inside the central cavity of the coordination cage forced the adamantyl groups of the ligand to bend further towards the outside of the cage (see Figure 4.14 b-d anb-d Table 4.1). Accorb-ding to DFT computational results (performeb-d from Prof. Dr. R. Mata anb-d coworkers), this guest-induced overstretching of the ligand should not cost an energetic penalty of more than 4 kJ·mol−1. In the “empty” [Pd2L24] cage, the average distance between the adamantyl sp2-carbon atom and the center of the cage is 5.3 Å, while in the host-guest complex [G1@Pd2L24] the distance is 6.0 Å. In addition, the size of the cage shrinks along the Pd-Pd axis. For example from 16.2 Å for [Pd2L24] to 16.0 Å in the [G1@Pd2L24] complex. The packing coefficient (PC) of the three encapsulated guest molecules G1,4,5 are calculated to be PC ~ 70-80 %, which exceeds Re-bek’s rule of 55 %,[132] indicating the formation of a densely packed complex.
In conclusion, the more bulky guests push the adamantyl groups further away from the center of the cage, which results in an overall shortening of the cage along the palladium axis. The cage
seems to be a flexible container, which can adapt to the size and shape of the “cargo” (see Table 4.1 for selected distances extracted from the X-ray structure analysis).
Table 4.1 Selected distances extracted from the X-ray structures of [Pd2L24] and some of its host-guest complexes.
[Pd2L24] [G4@Pd2L24] [G5@Pd2L24] [G1@Pd2L24]
a calculated from the DFT (B3LYP/6-31G*)[133] structure of the anions, b distance between adamantyl sp2-C atom and the center of the cage as defined by the middle of the line connecting the two palladium atoms, c The packing coefficient (PC) was calculated as the quotient of Vguest/Vcavity*100. The volume of the cavity was calculated using VOIDOO (details see experimental section p. 162),d the longest distance each is highlighted in bold font.