Multiple molecular logic gate arrays in one system of (2-(2′-pyridyl)imidazole)Ru(ii) complexes and trimeric cyclophanes in water

Shape-switchable cyclophane hosts allow the controlled capture and release of reactive polypyridineRu(ii) complexes in water. This gives rise to a network of host–guest binding, acid–base reactions in ground and excited states, and chemical redox interconversions. In the case of (2-(2′-pyridyl)imidazole)Ru(ii) complexes, several molecular logic gate arrays of varying complexity emerge as a result. Cyclophane-induced ‘off–on’ switching of luminescence in neutral solution is found to originate from two features of these aromatic hosts: enhancement of radiative decay by the polarizable host and the suppression of nonradiative decay involving deprotonation by reducing the water content within the deep host cavity. These are examples of nanometric coordination chemistry/physics being controlled by inclusion in an open box. The aromatic units of the macrocycle are also responsible for the shape-switching mechanism of wall collapse/erection.

The base-induced red-shift of 23 nm seen in the absorption spectrum of host-free 6 is stretched to 50 nm in the emission spectrum ( Figure S2), as might be expected by the water reorganization during the excited state lifetime. The host-bound cases also show similarly large red-shifts.

Section S4. Luminescence lifetime determinations
Measurements are performed on 5x10 -5 M Ru(II) complexes and 10 -3 M host solutions in water at pH 7 or at pH 12 on a PicoQuant FluoTime 100 Compact FLS TCSPC system using a 450 nm pulsed laser source generated from a PicoQuant PDL800-B box and an external Thurlby Thandar Instruments TGP110 10 MHz pulse generator to enable acquisition of long lifetime data. A band-pass filter (>520 nm) is used to exclude excitation light. Data is collected up to 40,000 counts and decay curves are analysed using PicoQuant Fluofit software and tail-fit statistical modelling. In all cases the minimum number of exponents are used for the fit and Chi-squared values are employed to assess the goodness-of-fit to the exponential decay along with visual inspection of the residuals.
Representative cases are given in Figure S5.
Radiative (k r ) and non-radiative (k nr ) are calculated from the luminescence lifetimes () and the quantum yields () after allowing for the effects of air on the luminescence of 6 40 and (bipyridine) 3 Ru(II) 109,110 according to the following equations. The corresponding values in the absence of air are  0 and  0 .
= k r /[k r + k nr + k O2 (O 2 )] = 1/[k r + k nr + k O2 (O 2 )]  0 = k r /(k r + k nr )  0 = 1/(k r + k nr ) k r = /=  0 / 0  0 /=  0 / Electronic Supplementary Material (ESI) for Chemical Science. This journal is © The Royal Society of Chemistry 2022 k nr = (1/ 0 ) -k r Section S5. Resonance Raman spectroscopy Resonance Raman spectroscopy is carried out on a Horiba Labram HR confocal microscope, using a 10x objective with a 473 nm diode laser (5 µW) as resonant excitation source. Conventional Raman is carried out on a Horiba Jobin Yvon HR800 UV spectrometer using 785 nm laser excitation. A 600 lines/mm diffraction grating is employed, providing data at 0.5 cm -1 resolution. The x-axis is calibrated versus the Rayleigh line (0 nm) and the phonon mode from silicon wafer (520.7 cm -1 ). Typically, an exposure time of 4 s and accumulation for 6 s are used for spectral recording and spectra are collected across a 200-2000 cm -1 spectral range. Spectra for 6 under various conditions are given in Figure S6. A spectrum for (bipyridine) 3 Ru(II) is included for comparison.
When excited at 474 nm, the resonance concerns 6's MLCT state involving Ru(II) and the bipyridines so that the imidazole modes are not observed among the Raman bands. Therefore, the spectra ( Figure  S6) of 6 and (bipyridine) 3 Ru(II) S1,S2 are essentially identical. Deprotonation of the imidazole N-H has an indirect effect on the MLCT state which shows up in the electronic spectra (e.g. Figure 4) but only very weakly in the resonance Raman spectrum where ca. 2 cm -1 shifts to lower frequency are observed in the signature bipyridine modes ( Figure S6). Since the host-induced effects in Figure 4 are smaller than pH effects, it is understandable that hosts 1&2 show no noticeable influence on the resonance Raman spectrum of 6 ( Figure S6).

Section S6. Time-resolved emission anisotropy measurements
Time-resolved emission anisotropy measurements are carried out on the PicoQuant Fluotime 100 Time-Correlated Single Photon Counting (TCSPC) system (excitation wavelength of 450 nm with a 510 nm narrow band pass dielectric filter) using a Thurlby Thandar Instruments TGP110 10MHz pulse generator with sheet polarisers to select V polarized excitation from the diode source. The G-factor is estimated by tail matching the VV and VH emission decays. Typical pulse rates of the excitation source are 1x10 5 s -1 with typical pulse widths of 300 ps. 20,000 counts were collected for each anisotropy measurement. All measurements are performed in duplicate. Time resolved luminescence anisotropy measurements are analyzed using Picoquant Fluofit software to yield anisotropy (rotational correlation time,  rot ) values using the mono-exponential model shown in (Equation S1).
where r(t) is the time-dependent anisotropy, r 0 is the limiting anisotropy, τ is the luminescent lifetime of the sample and φ rot is the rotational correlation time.
Representative cases are given in Figure S7.
Following a suggestion from a Referee, time resolved luminescence anisotropy measurements were conducted to provide a novel approach to investigate the binding of Ru(II) complex 6 with cyclophane hosts 1&2. A weak anisotropy decay is noticeable when 6 is bound by host 1 or by host 2 in water. This reflects anisotropy relaxation due to the host-guest assembly and its solvation shell, where each host adds 1100 Da when bound to 6. It also suggests that 6 cannot rotate when assembled inside each host. However, as seen in Figure S7, the rotational time constant could not be measured as it was shorter than the temporal limit of our instrumentation (1 ns). The addition of 1100 Da would be expected to cause rotational correlation times in the picosecond range, as found in fluorophores bound to cyclodextrins. S3 Importantly, host-free 6 shows no anisotropy decay. For comparison, stronger anisotropy decays in the microsecond range are seen S4 when polypyridineRu(II) complexes are bound to an integrin of molecular mass 240,000 Da. Section S7. Further studies on 7 Section 7a. 1 H NMR spectroscopy of 7 7 tends to precipitate in phosphate buffer. Although perdeuterated versions of some other buffers 94 are available, phosphate is simplest at serving our overall needs of a wide pD range, especially for studies with guest 6. Precipitation of 7 is found, though to a lesser extent, even in the presence of host 1. However, host 2 protects guest 7 against interaction with phosphate. Still, log values of 5.4 and ca. 4.6 can be inferred for host-guest complexes 2·7 and 1·7 respectively, at pD 7 (see Table S1). The NMR  maps of the hosts can be analyzed (Figure 2), but the guest signals are not easy to unravel.
Section 7b. UV-visible absorption spectroscopy of 7 A base-induced red-shift is found for 7 82 (Table S1). The  Abs value in the UV-visible absorption spectrum of 7 is not changed upon adding 1 or 2 (Table S1), once samples are well-annealed in 0.1 M NaOH. Since pH variation on samples so annealed show time-dependent spectra, quantitation of pH dependence to obtain pK a values is not attempted.
Section 7c. Steady-state luminescence spectroscopy of 7 Compound 7 remains non-emissive even in the presence of hosts 1 or 2. Host-binding does not alter the energy of the low-lying metal-centred (MC) excited state responsible for this non-emissivity. 81 Each replacement of a bipyridine with a pyridyl imidazole reduces the ligand field strength and three such replacements makes the MC state thermally-accessible at room temperature. _______________________________________________________ Section S8. Schematic representations of Inclusive (or nesting) and perching binding Inclusive (nesting) and perching binding modes are represented schematically in Figure S8. These modes are deduced from the 1 H NMR  maps in this paper (Figures 2 and S1) 4.8, 5.4, 6.5, 7.1, 7.7, 8.4, 9.1, 9.4, 9.7, 10.1, 10.4, 10.7, 11.0, 11.3, 11.5, 11.7, 12.0, 12.2 and 13.0.  Figure S3. Host(5) -dependent luminescence spectra of 10 -6 M 6 in water at pH 7. Host concentration in order of increasing intensity: 0, 1, 1. 6, 2.5, 4, 6.3, 10, 16, 25, 40, 63, 100, 160, 250, 400, 630 and 1000x10 -6 M.     Figure S6. B. Resonance Raman spectra of 10 -3 M 6 in water at pH 12 (orange) and at pH 7 (blue). It is easier to see the small, but noticeable, movement to lower frequencies at pH 12 in the zoomed-in lower panel.     Excitation wavelength is 450 nm and solid line shows fit to anisotropy decay that yields an R 0 of 0.028 and decay time of <3 ns. The exciting pulse is applied at 30.67 ns. Figure S8. Schematic representations of host-guest complexes where all three ligands around Ru(II) are assumed to be bipyridine and where the hosts' carboxylate groups are omitted for clarity. Left: side view of 1·6 with perching binding. Middle: side view of 2·6 with inclusive/nesting binding. Right: top view of 2·6 with inclusive/nesting binding (gold ball = Ru(II), green box = bipyridine, red-brown box = phenylene, blue ball = corner oxygen, brown-yellow string = alkyl chain).