Taming Tris(bipyridine)ruthenium(II) and Its Reactions in Water by Capture/Release with Shape-Switchable Symmetry-Matched Cyclophanes

Electron/proton transfers in water proceeding from ground/excited states are the elementary reactions of chemistry. These reactions of an iconic class of molecules—polypyridineRu(II)—are now controlled by capturing or releasing three of them with hosts that are shape-switchable. Reversible erection or collapse of the host walls allows such switchability. Some reaction rates are suppressed by factors of up to 120 by inclusive binding of the metal complexes. This puts nanometric coordination chemistry in a box that can be open or shut as necessary. Such second-sphere complexation can allow considerable control to be exerted on photocatalysis, electrocatalysis, and luminescent sensing involving polypyridineRu(II) compounds. The capturing states of hosts are symmetry-matched to guests for selective binding and display submicromolar affinities. A perching complex, which is an intermediate state between capturing and releasing states, is also demonstrated.

Materials and Methods S1. Synthesis schemes, preparative procedures and characterization data of all compounds used.
Scheme S1. Synthesis steps and subsequent measurements on these compounds conducted by C.Y.Y. No stereochemistry is intended in the molecular structures.  Scheme S2. Synthesis steps and subsequent measurements on these compounds conducted by H.Y.L., except where noted otherwise in section S8. No stereochemistry is intended in the molecular structures. S1.1. 1 H and 13 C NMR Spectra for 2-5, 10.
These are given in Figs. S1-S5 respectively. S1.2. Synthesis of bis(4-((5-bromopentyl)oxy)phenyl)methanone (13). 4,4'-dihydroxybenzophenone (2.0 g, 9.3 mmol) was dissolved in acetone (300 mL, HPLC grade) and added dropwise with the aid of a dropping funnel over 3 hours to a mixture of acetone (100 mL, HPLC grade), 1,5-dibromopentane (3.18 mL, 1.688 g/cm 3 , 23.3 mmol) and potassium carbonate (6.45 g, 46.7 mmol) being refluxed in a three-neck flask by heating in an oil bath. The dropping funnel and reflux condenser were connected to drying tubes. The mixture was then refluxed for 12 hours. The hot reaction mixture was then filtered under gravity. TLC on silica of the filtrate showed two spots, one of which corresponded to 4,4'-dihydroxybenzophenone. Then the solution was evaporated to give a white solid. The solid was purified using flash silica chromatography eluting with 70% petroleum ether and 30% ethyl acetate yielding the desired white plate-like solid (2.635 g, 55%).
The residual solid was then treated with chloroform (150 mL). The mixture was filtered, and the filtrate was collected. The solvent was evaporated. The residual solid was dissolved in chloroform (20 mL) and heated until boiling. After cooling, methanol (200 mL) was added which turned the transparent solution cloudy. The white solidified oil (0.40 g, 0.47 mmol) was then collected by filtration under suction (0.40 g, 32.9%).

S1.8.
Synthesis of 2,12,22-trihydroxy-4,10,14,20,24,30-hexaoxa-1,3,11,13,21,23(1,4)hexabenzenacyclotriacontaphane-1 3 ,3 3 ,11 2 ,13 3 ,21 2 ,23 3 -hexacarboxylic acid (3) 2 (0.170 g, 0.153 mmol) was dissolved in water (8.3 mL) with aid of a few drops of dilute sodium hydroxide and then sodium borohydride (0.174 g, 4.59 mmol) added and stirred overnight at room temperature. A few drops of acetic acid were then added to destroy any unreacted sodium borohydride. The mixture was then acidified to approximately pH 1 with 4 M hydrochloric acid. The precipitated product was then filtered, washed with water and dried (0.150 g, 87.8%). S1.8a. Optimized NaBH 4 reduction procedure for conversion of 2 to 3. 2 (56 mg, 0.05 mmol) was dissolved in 0.4 M NaOH (5.0 mL) and then sodium borohydride (10 equiv.) added and kept at 60 o C for 5 min with vigorous stirring. The mixture was then cautiously neutralized with dilute HCl. This was centrifuged, the supernatant was decanted, more distilled water was added and the process repeated. The pellet was then flushed from the centrifuge vial with distilled water and dried under reduced pressure at 60 o C to give a white solid. (52 mg, 93%). 1 H-NMR analysis in D 2 O-NaOD confirmed that 3 is the sole component. S1.9. KMnO 4 oxidation procedure for conversion of 3 back to 2. 3 (10 mg, 0.009 mmol) was dissolved in distilled water (13.4 mL) with NaOH (96.7 mg, 2.4 mmol). KMnO 4 (4.2 mg, 0.028 mmol) was then added and the mixture was kept at 40 o C for 24 hours with vigorous stirring. After this time, methanol (0.67 ml) was added and kept for 1 hour when the purple color faded. The solution was filtered and acidified with dilute HCl. This was centrifuged, the supernatant was decanted, more distilled water was added and the process repeated. The pellet was then flushed from the centrifuge vial with distilled water and dried under reduced pressure at 60 o C to give a white solid. (8 mg, 80%). 1 H-NMR analysis in D 2 O-NaOD confirmed that 2 is the sole component. S1.9a. Optimized KMnO 4 oxidation procedure for conversion of 3 back to 2. 3 (56 mg, 0.05 mmol) was dissolved in 0.4 M NaOH (5.0 mL). KMnO 4 (3 equiv.) was then added and the solution was kept at 60 o C for 5 min with vigorous stirring. For work-up, methanol (0.4 mL) was added and kept 60 o C for 5 min with vigorous stirring. The dark mixture was centrifuged and the supernatant was acidified with dilute HCl. This was centrifuged again, the supernatant was decanted, more distilled water was added and the process repeated. The pellet was then flushed from the centrifuge vial with distilled water and dried under reduced pressure at 60 o C to give a white solid. (54 mg, 96%). 1 H-NMR analysis in D 2 O-NaOD confirmed that 2 is the sole component. S1.10. Stability test of 1 under the oxidation conditions which were applied to 3 with KMnO 4 in water. Judging by its smaller-sized relative, 12 trialcohol 3 is less oxidizable in one-electron processes than 1 (E ox +1.7 c.f. +1.3 V 29 vs sce respectively). However, our oxidation condition of KMnO 4 with methanol work-up leaves 1 with no nett change.
1 (dichloride salt hexahydrate, 5 mg, 0.0067 mmol) was dissolved in distilled water (1.5 mL) with NaOH (72.1 mg, 1.8 mmol). KMnO 4 (1.1 mg, 0.007 mmol) was then added and the mixture was kept at 40 o C for 24 hours with vigorous stirring. After this time, methanol (0.075 ml) was added and kept until the green colour changed to red. The solution was filtered through cotton, hydrochloric acid added and evaporated to dryness under reduced pressure. 1 H-NMR analysis confirmed that 1 was the sole component. S1.10a. In situ KMnO 4 oxidation procedure for conversion of 3 to 2 in the presence of 1.
3 (100 mg, 0.089 mmol) was dissolved in distilled water (5 mL) with NaOH (0.2 g) and 1 (dichloride salt hexahydrate, 67 mg, 0.089 mmol). KMnO 4 (0.0424 g, 0.27 mmol) was then added and the mixture was kept at 60 o C for 5 minutes with vigorous stirring. After this time, methanol (0.67 mL) was added until the purple color faded. The solution was filtered to remove MnO 2 , dilute HCl and NaPF 6 were added. This was centrifuged, the supernatant was decanted, more distilled water was added and the process repeated. The pellet was then flushed from the centrifuge vial with distilled water and dried under reduced pressure at 60 o C to give a red solid (167 mg, 95%). 1 H-NMR analysis in dmso-d 6 confirmed that 2 and 1 are the sole components. S1.11. Stability test of 1 under the reduction conditions which were applied to 2 with NaBH 4 in water.
Judging by its smaller-sized relative, 12 triketone 2 is less reducible than 1 (E red -2.3 c.f. -1.3 V 29 respectively). However, our reduction condition of NaBH 4 with aqueous work-up leaves 1 with no nett change.
1 (dichloride salt hexahydrate, 5 mg, 0.0067 mmol) was dissolved in water (1.5 mL), sodium borohydride (7.6 mg, 0.2 mmol) added and stirred for 24 hours at room temperature (ca. 20 o C). After that, the reaction mixture was still red in colour. Hydrochloric acid was then added to destroy unreacted sodium borohydride and evaporated to dryness under reduced pressure. 1 H-NMR analysis confirmed that 1 was the sole component. Thus, under our chemical redox conditions, 2 and 3 can be interconverted without affecting 1. S1.11a. In situ NaBH 4 reduction procedure for conversion of 2 to 3 in the presence of 1. 2 (50 mg, 0.045 mmol) and 1 (dichloride salt hexahydrate, 33.7 mg, 0.045 mmol) was dissolved in water (2.5 mL) with aid of a few drops of dilute NaOH and then NaBH 4 (17 mg, 0.45 mmol) was added and stirred 5 minutes at 60 o C. A few drops of acetic acid were then added to destroy any unreacted NaBH 4 . Then dilute HCl and NaPF 6 were added. The red precipitate was then filtered, washed with water and dried. (85 mg, 96%). 1 H-NMR analysis in dmso-d 6 confirmed that 3 and 1 are the sole components. S1.12. Synthesis of Tetraethyl 5,5'-methylenebis(2-((5-bromopentyl)oxy)isophthalate) (17) 1,5-Dibromopentane (16.73 ml, 1.688 g/ml, 0.123 mol) and potassium carbonate (16.97 g, 0.123 mol) were added to a round bottom flask with dmf (100 ml, HPLC grade) and heated to 70 o C. 16 65 (6 g, 6.94 mmol) was added into a dropping funnel with dmf (300 ml, HPLC grade), then added dropwise over 3 hours and heated for a further hour. The dropping funnel and reflux condenser were connected to drying tubes. Then, the solution was filtered and saturated brine (800 ml) was added. Diethyl ether (325 ml, HPLC grade) was added and the solution was extracted, followed by another 325 ml and then 175 ml. Then, ethereal extracts were combined. The ether layer was dried with sodium sulfate and then filtered. The solvent was reduced by rotavapor to a small volume. The product was purified using flash silica chromatography eluting with ethyl acetate: hexane (1:5 v/v) yielding the desired oily product 17 (59.8%
S2. X-ray crystallography of 8.  Fig. S7(ii) (packing diagram in plan view) give ball-and-stick representation, with calculated hydrogen positions included. Carbon atoms are shown in grey, oxygen atoms in red and hydrogen atoms in white. The structure was solved using Olex2, 66 with the ShelXS 67 structure solution programme using direct methods and refined with the ShelXL 67 refinement package using least squares minimization. All non-hydrogen atoms in Fig. 1B are close to the mean macrocycle plane. The mean macrocycle plane is the mean plane passing through the atoms noted in red circles in the structure below.
The crystallography information file (cif file) for 8 is given in Fig. S6.

S3. NMR Δδ maps and 2-D ROESY spectra.
Δδ maps are reported in Fig. S8 alongside the corresponding sets of 1 H NMR spectra in D 2 O under various conditions. In contrast, negligible  values are seen in d-dmso solution which shows lack of binding and confirms the importance of hydrophobicity for binding in water. 2-D ROESY spectra are reported in Fig. S8a. barostat was used to maintain the pressure at 1 bar and the SHAKE algorithm was used to constrain bonds involving hydrogen atoms. A time step of 2 fs was used for all MD simulations. For each host-guest complex, a 500-ns production MD simulation was performed in an NPT ensemble with a target pressure of 1 bar and a pressure coupling constant of 2 ps. Two replica runs were conducted for each complex. Clustering analysis was conducted for the equilibrated MD trajectories of the various host-guest complexes and the top three most populated snapshots were selected for the subsequent QM/MM calculations.

QM/MM calculations
The representative snapshots obtained from the MD simulations were first subjected to 1,000 steps of steepest descent energy minimisation, followed by 1,000 steps of conjugate gradient minimisation using Amber18. 78 The QM/MM geometry optimisations were performed using Chemshell 3.7 81 for all the host-guest complex systems. The QM region is consisted of a total of 184-196 atoms, depending on the host molecule and was calculated using DFT UB3LYP functional 69,70 with D3 dispersion correction and BJ damping set. 82,83 The singlet state of 1 was calculated using def2-TZVP and rest of the atoms in the complex were calculated using def2-SVP basis set. The QM calculations were performed using ORCA 4.2.0 84,85 and the MM region was defined using DL_POLY. RIJCOSX approximation and TightSCF criteria were used in the QM calculations. The effect of the solvent environment on the polarization of the QM wavefunction was considered using the electronic embedding scheme. The QM/MM optimised structures were then used for subsequent structural analysis. Although not studied experimentally due to their aqueous insolubility, 8 and its trialcohol counterpart (11) are also examined for their interaction with 1 via MD simulation [ Fig. S10 and videos S2 and S4 respectively]. These are broadly similar to those for 2·1 and 3·1 [ Fig. 1D and videos S1 and S3 respectively], although the binding interactions are weakened in the absence of carboxylate moieties.

S5.
Host-dependent luminescence spectroscopy. Conditions for these experiments are reported in the caption to Fig. S16.

S6.
In situ switching of host system 2/3 in the presence of 1 by redox cycling and observation of the luminescence signal. 3 (56 mg, 0.05 mmol) was dissolved in 0.4 M NaOH (5.0 mL) which was 10 -4 M in 1. KMnO 4 (3 equiv.) was then added and the solution was kept at 60 o C for 5 min with vigorous stirring. This is the oxidation step of the first redox cycle. For work-up, methanol (0.4 mL) was added and kept 60 o C for 5 min with vigorous stirring. After centrifugation, the pale orange supernatant was decanted. An aliquot (0.1 mL) was diluted 10-fold and analyzed in microcuvets by uv-vis absorption spectroscopy and luminescence spectroscopy. The relative luminescence quantum yield was obtained by excitation at 453 nm, using 1 in water as the reference at the same absorbance. NaBH 4 (10 equiv.) was then added and the pale orange solution was kept at 60 o C for 5 min with stirring. This is the reduction step of the first redox cycle. The solution was cautiously neutralized with 10 M H 2 SO 4 and then made alkaline (NaOH). An aliquot (0.1 mL) was diluted 10-fold and the relative luminescence quantum yield was obtained as before. The oxidation step was then repeated to launch the second redox cycle. Work-up and spectroscopic analysis was carried out as before. The reduction step was then conducted to complete the second redox cycle. Work-up and spectroscopic analysis was carried out as before. The third redox cycle was achieved similarly. Salt accumulation, usually found in such experiments involving chemical switching, 16 does not interfere significantly with the spectroscopic measurements leading to Figure 5A. Clear 'high-lowhigh-low-high-low' switching of the relative luminescence quantum yield is found. The luminescence enhancement(LE) factors seen here are slightly smaller than those reported in Table  1 because the concentration conditions are different in the two situations. For control purposes, the same series of redox cycles were carried out on another sample of 1 with the host omitted. These are also shown in Figure 5A and their relative luminescence quantum yields remain essentially constant. For reference, the absolute luminescence quantum yield of 1 in water is 0.042. 29 S7. In situ switching of host system 4/5 in the presence of 1 by redox cycling and observation of the luminescence signal. 5 (68.5 mg, 0.05 mmol) was put through the sequence in Section S6 and the results are shown in Figure 5B. Strong 'high-low-high-low-high-low' switching of the relative luminescence quantum yield is found. The luminescence enhancement(LE) factors seen here are slightly smaller than those reported in Table 1 because the concentration conditions are different in the two situations. For control purposes, the same series of redox cycles were carried out on another sample of 1 with the host omitted. These are also shown in Figure 5B and their relative luminescence quantum yields remain essentially constant.
Host concentration-dependent luminescence intensities of guests like 1 (I L ) also yield binding constants () for host-guest pairs (Table 1, Figure S16 Analysis of the scan rate dependence of current in the cyclic voltammograms (Fig. S17) gives the diffusion coefficients of 1, 2·1 and 3·1 as 1.8x10 -6 , 2.1x10 -6 and 1.9x10 -8 cm 2 s -1 respectively, when 1 is in the Ru(II) form. In terms of this parameter, the protection factors offered by hosts 2 and 3 towards electron transfer from 1 to the electrode are 0.9 and 93 respectively. The host protection factor 93 arises from the ratio of diffusion coefficients 1.8x10 -6 /1.9x10 -8 . When 1 is in the Ru(III) form, the diffusion coefficients of 1, 2·1 and 3·1 are 7.5x10 -7 , 7.7x10 -7 and 8.7x10 -8 cm 2 s -1 respectively. This corresponds to host protection factors of 1 (which means no protection) and 9 for 2 and 3 respectively. Conditions for differential pulse voltammetry are given in Fig. S18.

S9.
Phenolate quenching of polypyridineRu(II) luminescence. When a host binds with polypyridineRu(II) complex 1 or 6, the latter is protected to some extent from colliding with phenolates and the degree of luminescence quenching would become smaller. In order to extract the host protection factors (HPF) caused by complexation, the Stern-Volmer equation 31 is used to obtain quenching rates in 0.1 M NaOH in water. Without host or phenolate being present, the only quencher of the luminescence is O 2 in air. Equation (S2) is our starting point: When phenolate is added, we get equation (S3): Combining equations (S2) and (S3), we get equation (S4): I no phenolate k ′ q = ( I no phenolate I phenolate -1 )( I 0 I no phenolate ) 1 where = phenolate quenching rate constant involving 1 or 6 without host, = O 2 quenching k ′ q k q rate constant involving 1 or 6 without host, I no phenolate = luminescence intensity of 1 or 6 in water, I phenolate = luminescence intensity of 1 or 6 and various phenolates in water, I 0 = luminescence intensity of 1 or 6 in argon-bubbled water, luminescence lifetime of 1,  0 = 560 ns (in water) 29 and luminescence lifetime of 6, τ 0 = 960 ns (in water). 29 When a host is added, a new set of equations (S5)-(S7) arise in a similar way, but with a new lifetime  host : Combining equations (S5) and (S6), we get equation (S7): I no phenolate with host k ′′′ q = ( I no phenolate with host I phenolate with host -1 )( I 0 with host I no phenolate with host ) 1 where = phenolate quenching rate constant to 1 or 6 with host, = O 2 quenching rate constant k ′′′ q k ′′ q to 1 or 6 with host. I no phenolate with host = luminescence intensity of 1 or 6 in water with host, I phenolate with host = luminescence intensity of 1 or 6 and phenolate in water with host, I 0 with host = luminescence intensity of 1 or 6 in argon-bubbled water.
We note that  host / 0 = LE, which is the host-induced luminescence enhancement factor. These values are given in Table 1.
Equations (S4) and (S7) allow us to calculate phenolate quenching rate constant in 1 or 6 without k ′ q host and in 1 or 6 with host. The right hand sides of equations (S4) and (S7), can be divided k ′′′ q into two factors, and in equation (S4)  analysis of Fig. S19A, for example, because the phenolates are good quenchers of the luminescence of 1. Sample calculations are shown in Fig. S20 in terms of the processed graphs obtained from the data in Fig. S19A. The graphs in each panel's main set are the phenolatedependent luminescence changes of 1, 2·1 and 3·1 in which the ordinate is the total luminescence intensity. The inset graphs in each panel have or as the ordinate. In I no phenolate I phenolate -1 I no phenolate with host I phenolate with host -1 these graphs, only the points whose phenolate concentrations are lower than 2x10 -3 M are analysed in order to obtain the initial slopes from the Stern-Volmer plots. The quenching rate constants obtained from Fig. S20 are given in Table S1. These allow us to calculate the factors of protection offered by host 2 or 3 against quenching by phenolates. The largest factor seen is 120 for the case of 5·6 with 2,6-dimethylphenolate. It shows the potential of controlling the catalytic processes of coordination complexes by inclusively binding them. The perching complex 2·1 shows a relatively smaller protection factor of 9.9 with 2,6dimethylphenolate. This allows a degree of tunable control over the properties of polypyridineRu(II) complexes. S10. pH-dependent luminescence of 7 57,90 without/with various hosts. This study was conducted by C.Y.Y. Conditions for Fig. 8: pH-dependent luminescence quantum yields of 10 -5 M 7 without/with various hosts (10 -3 M each) in aerated water with 0.1 M phosphate buffers excited at isosbestic points. 1 in water is used as the luminescence quantum yield standard. 29 2 and 3 begin to precipitate at pH<6.3, whereas 4 and 5 begin to precipitate at pH<4.0. The green line marks pH=7 which roughly demarcates the lower pH region of excited state deprotonation from the higher pH region of ground state deprotonation. The green line also connects with the photograph. Conditions for photograph: Luminescence emission of 10 -4 M 7 alone and in the presence of 2, 3, 4 and 5 (10 -3 M each) in aerated water with 0.1 M phosphate buffer at pH 7.0. Luminescence excited from above at 366 nm. Ground state pK a values of 7 are also ordered according to perturbation of its deprotonation equilibrium by the local environment caused by hosts. These values are 10.4 (in the presence of 5), 9.6 (3), 9.1 (2), 9.0 (4) and 8.8 (free). [continued]  Signs of  values, whether negative or positive, are symbolized by green or red circles respectively. B. As in A, but guest=1, host=3. C. As in A, but in 0.1 M NaOD/D 2 O instead of pD 7.0 buffer, and where guest=6, host=2. D. As in C, but guest=6, host=3. E. As in A, but guest=1, host=4. F. As in A, but guest=1, host=5. G. As in A, but guest=1, host=10. H. As in C, but guest=6, host=4. I. As in C, but guest=6, host=5. J. As in C, but guest=6, host=10. K. As in C, but guest=6, host=5 and at 60 o C rather than the usual 27 o C. L. As in K, but guest=6, host=10. The last two cases were conducted because some signals which were broad at 27 o C were sharpened under these conditions.

Fig. S8a.
A. 2-D ROESY spectrum of a mixture of guest 1 and host 2. Conditions are as given in the caption to Figure 2. Peak assignments are also to be found in Figure 2. B. As in A, but for host 3 instead of 2. C. As in A, but for host 4 instead of 2. Peak assignments are to be found in Figure  6. D. As in C, but for host 5 instead of 4. E. As in C, but for host 10 instead of 4.   1.6x10 -6 , 2.5x10 -6 , 3.16x10 -6 , 4x10 -6 , 5x10 -6 , 6.3x10 -6 , 8x10 -6 , 1x10 -5 , 1.26x10 -5 , 1.6x10 -5 , 2x10 -5 , 2.5x10 -5 , 5x10 -5 , 1x10 -4 , 2x10 -4 and 1x10 -3 M). The corresponding spectra of the hypothetical mixtures are also shown, where the individual spectra of 6 and the host 5 are summed. The small but significant differences in absorbance at 262 nm between actual mixture and the arithmetic sum of host and guest's absorbances can be analysed to yield logβ=5.0. D. As in C, but with 10 instead of 5, yielding logβ=5.3.   Table  1.  Intensity(a.u.)   Fig. 2A. B. As in A, but with 5x10 -3 M 1 + 5x10 -3 M 2, so that the D value of 1 in the presence of 2 is produced. C. As in A, but with 5x10 -3 M 1 + 5x10 -3 M 3, so that the D value of 1 in the presence of 3 is produced. This value is markedly smaller than that found in A. Red data points in inset allows calculation of D values in the Ru(III) form for each case.