CB[7]- and CB[8]-Based [2]-(Pseudo)rotaxanes with Triphenylphosphonium-Capped Threads: Serendipitous Discovery of a New High-Affinity Binding Motif

The synthesis of new triphenylphosphonium-capped cucurbit[7]uril (CB[7])- and cucurbit[8]uril (CB[8])-based [2]rotaxanes was achieved by a simultaneous threading-capping strategy. While the use of CB[7] produced the designed [2]rotaxane, attempts to obtain the CB[8] analogue were unsuccessful due to the unexpected strong interaction found between the host and the phosphonium caps leading to pseudo-heteroternary host–guest complexes. This unusual binding motif has been extensively studied experimentally, with results in good agreement with those obtained by dispersion-corrected DFT methods.


General
The chemicals used in this work were purchased from commercial suppliers and used without further purification. The purity of the CB [7] and CB [8] was assessed as previously reported by Kaifer et al. 1 Milli-Q water was purified with a Millipore Gradient A10 apparatus. Merck 60 F254 foils were used for thin layer chromatography, and Merck 60 (230-400 mesh) silica gel was used for flash chromatography. NMR spectra were recorder on a Bruker Advance 400 or 500 MHz for 1 H, 125 MHz for 13 C equipped each other with a dual cryoprobe and 160 MHz for 31 P. The solvent for NMR experiments was deuterated water (D2O) and acetonitrile (CD3CN). Mass spectrometry experiments were carried out in a LCQ-q-TOF Applied Biosystems QSTAR Elite spectrometer for low and high resolution ESI. UV/Vis spectra were recorded on a Jasco V-650 spectrometer. Structural assignments were made with additional information from gCOSY, gHSQC, and gHMBC experiments.     A mixture of semiaxle 1 a •2Br (9.4 mg, 0.014 mmol) and semiaxle 1 b •2Br (9.7 mg, 0.014 mmol), cucurbit [7]uril (45 mg, 0.026 mmol) was dissolved in water (6.0 mL) and trifluoroacetic acid (1.8 L, 0.028 mmol) was added to assure the acidic conditions. The yellow solution was heated under reflux using a heating mantle for 18 hours. Then, the solvent was removed in vacuum to leave a yellow crude, which was subjected to flash chromatography (SiO2) with two different eluent  Rotaxane 2•4PF 6 ⊂CB[7] (10 mg, 0.004 mmol) was dissolved in 3 mL of a mixture of CH 3 CN/ KCl aq (1M). The mixture was stirred for 72 hours and the solvent was removed in order to obtain the rotaxane soluble in pure water as a chloride salt 2•4Cl⊂CB [7]. 1   A solution of 1 a •2Br (2.6 mg, 0.004 mmol) in 2 mL of D 2 O was prepared. Then, cucurbit [8]uril was added in excess and the mixture was sonicated and heated using an oil bath at 60 °C for 15 min.

SP1: Synthesis of precursor P1•Br
Finally, the sample was filtered off to remove the excess of CB [8] to yield the inclusion complex

SP9: Synthesis of pseudorotaxane 1b•2Br⊂CB[8]:
A solution of 1 b •2Br (2.7 mg, 0.004 mmol) in 2 mL of D 2 O was prepared. Then, cucurbit [8]uril was added in excess and the mixture was sonicated and heated using an oil bath at 60 °C for 15 min.
Finally, the sample was filtered off to remove the excess of CB [8] to yield the inclusion complex  A solution of 2•4Cl (4.3 mg, 0.004 mmol) in 2 mL of D2O was prepared. Then, cucurbit [8]uril was added in excess and the mixture was sonicated and heated using an oil bath at 60 °C for 15 min.

S19
Calculation of Host-Guest Binding Constant by Competitive 1H NMR spectroscopy with ferrocenylmethyl trimethylammonium iodide (Fc•I):

S24
Computational details: Semiempirical (pm6), and Density Functional Theory (DFT) calculations reported in this work were carried out using the G16 C.01 program. 2 Geometry optimizations at the DFT level of theory were performed using the BLYP-D3(BJ) functional: combination of the Becke exchange functional B and LYP correlation functional, 3,4 dispersion corrected by using the D3 version of Grimme's empirical dispersion scheme with Becke-Johnson damping (D3(BJ)). 5 The BLYP-D3(BJ) functional was used in combination with the valence double-zeta size polarization basis set def2-SVP for the energy minimizations this work, as it has been recently proven to afford reliable optimized geometries for CB[n]-based complexes at a reasonable computational cost. 6 Truhlar´s SMD model was used to account for solvation effects in water, 7 and the quadruple zeta valence quality basis set def2-QZVP was used in single point calculations, to more accurately evaluate the energy differences between isomeric species. 8 In order to predict initial binding modes for 1 a 2+ ⊂CB [7,8], hosts and guest were geometrically minimized in vacuum at the PM6 semiempirical level. Then, docking experiments were carried out for each host-guest pair on a 1:1 stoichiometry, employing the program AutoDock Vina, 9 as implemented in UCSF Chimera 1.15. 10 For each docking experiment, cubes of 15 Å 3 /1 Å grids centered on the hosts were used as search volume. The best 10 ranked poses obtained for each complex, 1a 2+ ⊂CB [7] and 1a 2+ ⊂CB [8], where then geometrically optimized at the BLYP-D3(BJ)/def2-SVP/SMD(water) level of theory, resulting in 2 unique conformers for 1 a 2+ ⊂CB [7] and 4 for 1 a 2+ ⊂CB [8], which were confirmed as local minima on the corresponding potential energy surface by running frequency calculations at the same level of theory. The total electronic energy of each unique isomer was then calculated at the BLYP-D3(BJ)/def2-QZVP/SMD(water) level of theory, in order to more accurately compare their relative energies. The starting geometry for the [2]rotaxane 2 4+ ⊂CB [7] was produced with the aid of the software Avogadro, 11 by manually centering the structure of the CB [7] host to the center of mass of the thread 2 4+ , both minimized at the pm6 semiempirical level of theory. The obtained geometry was firstly re-optimized using the pm6 method to avoid steric clashes and, finally, at the BLYP-D3(BJ)/def2-SVP/SMD(water) level. The later structure was corroborated as a local minimum by running the appropriate frequency calculations at the same level of theory.                      Figure S47 1 H NMR (500 MHz, CD 3 CN) spectrum of 2•4PF 6 . Figure S48 13 C{ 1 H} NMR (125 MHz, CD 3 CN) spectrum of 2•4PF 6 .⊂CB [7].