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1 Stereochemical nversion in Difunctionalized Pillar[5]arenes Nathan L. Strutt, Severin T. Schneebeli, J. Fraser Stoddart* Department of hemistry, Northwestern University, Evanston, L U.S.A. stoddart@northwestern.edu Supporting nformation ontents S1. General Methods S2 S2. 1H NMR Spectra of ompounds 2 and 3 S3 S3. Variable Temperature 1H NMR Spectra of 1 S4 6 S4. Variable Temperature 1H NMR Spectra of 2 S7 8 S5. Variable Temperature 1H NMR Spectra of 3 S9 10 S6. 2-D NMR Experiments with 1 S11 14 S7. 2-D NMR Experiments with 2 S15 17 S8. 2-D NMR Experiments with 3 S18 21 S9. Simulated 1H NMR spectra of 1 S22 23 S10. Eyring Plot for 3 S24 S11. X-Ray rystallography of 3 S25 S12. Molecular Mechanics alculations S26 S13. Quantum Mechanical alculations S27 S14. DFT-ptimized Structures and Energies S28 51
2 S1. General Methods Analytical thin-layer chromatography (TL) was carried out using glass plates, precoated with silica gel 60 and fluorescent indicator (Whatman LK6F). The plates were inspected by UV light (254 nm). Flash chromatography was carried out using silica gel 60 (Silicycle) as the stationary phase. Nuclear magnetic resonance (NMR) spectra were recorded on Bruker Avance 500 and 600 MHz spectrometers, with working frequencies of and MHz for 1 H, and and MHz for 13 nuclei, respectively. hemical shifts are reported in ppm relative to the signals corresponding to the residual non-deuterated solvent and coupling constants were recorded in Hertz (Hz). Temperatures for VT 1 H NMR experiments were calibrated using either 100% MeH or 100% ethylene glycol. Simulated 1 H NMR spectra were created using inmr version Single crystal X-ray data was collected on a Bruker Kappa APEX D Diffractometer equipped with a ukα microsource with Quazar optics. Molecular mechanics calculations were performed with the PLS-2005 force field using the program MacroModel software package. alculations were performed with the chloroform GB/SA solvation model. Density functional theory (DFT) calculations were performed with the B3LYP functional using the Jaguar software package. Single point calculations were conducted with the Poisson-Boltzmann continuum-solvation model implemented in Jaguar using either the 6-311G**++ or LAV3P**++ basis set. Geometry optimizations and frequency calculations were conducted with either the 6-31G* or LAVP*basis set. Default grids and SF convergence criteria as implemented in Jaguar were used. S2
3 S2. 1 H NMR Spectra of ompounds 2 and 3 H % H 3 H 3 H 3 V H 3 H % H 3 V H 3 H 3 H 3 2 +V Hl3 H$ H" H% H# H! H2l2 Hc+d He Ha+b δ (ppm) Figure S1. 1 H NMR (600 MHz, 318 K, Dl 3 ) spectrum of compound 2. H 3 H 3 H Br H 3 V H 3 Br H H 3 V H 3 H 3 H 3 3 +V H Hl3 H! H" H# H$ H2l2 Hb Hc+d Ha He δ (ppm) Figure S2. 1 H NMR (600 MHz, 318 K, Dl 3 ) spectrum of compound 3. S3
4 S3. Variable Temperature 1 H NMR Spectra of 1 H % H 3 H 3 H H 3 V H 3 H H % H 3 V H 3 H 3 H Temperature (K) δ (ppm) Figure S3. Variable temperature (VT) 1 H NMR (600 MHz, Dl 3 ) spectra of 1. S4
5 H % H 3 H 3 H H 3 V H 3 H H % H 3 V H 3 H 3 H Temperature (K) δ (ppm) Figure S4. Variable temperature (VT) 1 H NMR (600 MHz, Dl 2 Dl 2 ) spectra of 1. S5
6 H % H 3 H 3 H H 3 V H 3 H H % H 3 V H 3 H 3 H Ha + Hb Temperature (K) δ (ppm) Figure S5. Variable temperature (VT) 1 H NMR (600 MHz, 4:1 Dl 3 / D 3 D) spectra of 1. S6
7 S4. Variable Temperature 1 H NMR Spectra of 2 H % H 3 H 3 H 3 V H 3 H % H 3 V H 3 H 3 H Temperature (K) δ (ppm) Figure S6. Variable temperature (VT) 1 H NMR (600 MHz, Dl 3 ) spectra of 2. S7
8 H % H 3 H 3 H 3 V H 3 H % H 3 V H 3 H 3 H 3 2 Temperature (K) Figure S7. Variable temperature (VT) 1 H NMR (600 MHz, Dl 2 Dl 2 ) spectra of 2. S8
9 S5. Variable Temperature 1 H NMR Spectra of 3 H 3 H 3 H Br H 3 V H 3 Br H H 3 V H 3 H 3 H Temperature (K) δ (ppm) Figure S8. Variable temperature 1 H NMR (600 MHz, Dl 3 ) spectra of 3. S9
10 H 3 H 3 H Br H 3 V H 3 Br H H 3 V H 3 H 3 H Temperature (K) δ (ppm) Figure S9. Variable temperature (VT) 1 H NMR (600 MHz, Dl 2 Dl 2 ) spectra of 3. S10
11 S6. 2-D NMR Experiments with 1 H % H 3 H 3 H H 3 V H 3 H H % H 3 V H 3 H 3 H 3 1 V + + He Hc+d Ha Hb 2D HSQ 233 K Dl3 600 MHz ! (ppm) ! (ppm) Figure S10. Phase-sensitive multiplicity-edited 2-D HSQ spectrum (600 MHz, 233 K, Dl 3 ) of 1 (left). Enlargement of aliphatic section of HSQ spectrum (right). Red crosspeaks indicate H 2 groups and blue crosspeaks indicate H 3 groups. S11
12 H % H 3 H 3 H H 3 V H 3 H H % H 3 V H 3 H 3 H 3 1 V + + He Hc+d Ha Hb 2D NESY 228 K Dl3 600 MHz H! H% H$ H# H" (H! Ha) (H% Ha) (H% ) (H# V) (H" ) (H! ) (H" Hc+d) (H$ ) (H" ) (H! Hb) (H% Hb) Hl3 7.0 H (H Ha) (H ) (H Hb) ! (ppm) ! (ppm) Figure S11. 2-D NESY Spectrum (600 MHz, 228 K, Dl 3 ) of 1 (left). Enlargement of the bottom right section of the spectrum (blue box in full spectrum) with annotated crosspeaks (right). S12
13 H % H 3 H 3 H H 3 V H 3 H H % H 3 V H 3 H 3 H 3 1 Hc+d He Ha+b V 2D HSQ 348 K Dl2Dl2 600 MHz ! (ppm) ! (ppm) Figure S12. 2-D HSQ Spectrum (600 MHz, 348 K, Dl 2 Dl 2 ) of 1 (left). Enlargement of aliphatic section of HSQ spectrum (right). S13
14 H % H 3 H 3 H H 3 V H 3 H H % H 3 V H 3 H 3 H 3 1 Hc+d He V Ha+b 2D NESY 350 K Dl2Dl2 600 MHz 4.0 H (H ) (H Ha+b) (H$ He) (H$ V) 5.0 H$ (H% Ha+b) 6.6 H% H! H# (H# Hc+d) (H! Ha+b) (H$ ) H" (H" Hc+d) (H! ) (H# V) (H" ) (H" ) ! (ppm) ! (ppm) Figure S13. 2-D NESY Spectrum (600 MHz, 350 K, Dl 2 Dl 2 ) of 1 (left). Enlargement of the bottom right section (blue box in full spectrum) with annotated crosspeaks (right). S14
15 S7. 2-D NMR Experiments with 2 H % H 3 H 3 H 3 V H 3 H % H 3 V H 3 H 3 H 3 2 V He Hc+d Ha+b 2D HSQ 318 K Dl3 600 MHz ! (ppm) ! (ppm) Figure S14. 2-D HSQ Spectrum (600 MHz, 318 K, Dl 3 ) of 2 (left). Enlargement of aliphatic section of HSQ spectrum (right). S15
16 H % H 3 H 3 H 3 V H 3 H % H 3 V H 3 H 3 H 3 2 H# H! Hl3 H$ H" H% 2D NESY 318 K Dl2Dl2 600 MHz ( H") V + Hc+d Ha+b He (V H#) ( H$) (He H$) (Ha+b H!) (Ha+b H%) ( H!) (Hc+d H#) (Hc+d H") ! (ppm) ! (ppm) Figure S15. 2-D NESY Spectrum (600 MHz, 318 K, Dl 3 ) of 2 (left). Enlargement of the top left section (blue box in full spectrum) with annotated crosspeaks (right). S16
17 H % H 3 H 3 H 3 V H 3 H % H 3 V H 3 H 3 H 3 2 Hc+d V He Ha+b 2D HSQ 298 K Dl2Dl2 600 MHz ! (ppm) ! (ppm) Figure S16. 2-D HSQ Spectrum (600 MHz, 298 K, Dl 2 Dl 2 ) of 2 (left). Enlargement of the aliphatic section of the HSQ spectrum (right). S17
18 S8. 2-D NMR Experiments with 3 H 3 H 3 H Br H 3 V H 3 Br H H 3 V H 3 H 3 H 3 3 V + Hc+d Hb Ha He 2D HSQ 300 K Dl3 600 MHz ! (ppm) ! (ppm) Figure S17. 2-D HSQ Spectrum (600 MHz, 300 K, Dl 3 ) of 3 (left). Enlargement of aliphatic section of HSQ spectrum (right). S18
19 H 3 H 3 H Br H 3 V H 3 Br H H 3 V H 3 H 3 H 3 3 V + Hc+d Hb Ha He 2D NESY 300 K Dl3 600 MHz H$ H# H" Hl3 H! (H$ V) (H$ He) (H$ ) (H" ) (H# V) (H" ) (H" Hc+d) (H# Hc+d) (H! Ha) (H! Hb) (H! ) H (H Hb) (H ) (H Hb) ! (ppm) ! (ppm) Figure S18. 2-D NESY Spectrum (600 MHz, 300 K, Dl 3 ) of 3 (left). Enlargement of the bottom right section (blue box in full spectrum) showing annotated crosspeaks. S19
20 H 3 H 3 H Br H 3 V H 3 Br H H 3 V H 3 H 3 H 3 3 Ha+b Hc+d He V 2D HSQ 368 K Dl2Dl2 600 MHz ! (ppm) ! (ppm) Figure S19. 2-D HSQ Spectrum (600 MHz, 368 K, Dl 2 Dl 2 ) of 3 (left). Enlargement of the aliphatic section of the HSQ spectrum (right). S20
21 H 3 H 3 H Br H 3 V H 3 Br H H 3 V H 3 H 3 H 3 3 Ha+b Hc+d He V 2D NESY 348 K 3.0 Dl2Dl2 600 MHz H# (H# Hc+d) (H# ) (H# V) H$ (H$ He) (H$ ) (H# V) H" (H" Hc+d) (H" ) (H! Ha+b) (H" Hc+d) 6.9 H! H (H Ha+b) (H ) (H! ) ! (ppm) ! (ppm) Figure S20. 2-D NESY Spectrum (600 MHz, 348 K, Dl 2 Dl 2 ) of 3 (left). Enlargement of bottom right section (blue box in full spectrum) showing annotated crosspeaks (right). S21
22 S9. Simulated 1 H NMR Spectra of 1 Dynamic 1 H NMR simulations were conducted for protons and on the methylene bridges of 1 using inmr (version 3.2.1). The magnetic field, B 0, for the simulated spectra was set to a frequency of for 1 H, while the experimental spectra were conducted using a B 0 of MHz. Figures S20 - S24 contain the experimental 1 H NMR spectra for the aliphatic portion of 1 directly above the simulated spectra at the same temperature. T = 328 K k = 119,000 s -1 Experimental Simulated δ (ppm) Figure S21. Experimental (above) and simulated (below) 1 H NMR spectra (600 MHz, 328 K, Dl 3 ) of the aliphatic portion of 1. T = 298 K k = 19,800 s -1 Experimental Simulated δ (ppm) Figure S22. Experimental (above) and simulated (below) 1 H NMR spectra (600 MHz, 298 K, Dl 3 ) of the aliphatic portion of 1. S22
23 T = 268 K k = 1057 s -1 Experimental Simulated δ (ppm) Figure S23. Experimental (above) and simulated (below) 1 H NMR spectra (600 MHz, 268 K, Dl 3 ) of the aliphatic portion of 1. T = 238 K k = 33 s -1 Experimental Simulated δ (ppm) Figure S24. Experimental (above) and simulated (below) 1 H NMR spectra (600 MHz, 238 K, Dl 3 ) of the aliphatic portion of 1. T = 218 K k = 6.0 s -1 Experimental Simulated δ (ppm) Figure S25. Experimental (above) and simulated (below) 1 H NMR spectra (600 MHz, 218 K, Dl 3 ) of the aliphatic portion of 1. S23
24 S10. Eyring Plot for 3 Dynamic 1 H NMR simulations were conducted for protons and on the methylene bridges of 3 using the same method described for the simulation of the dynamic 1 H NMR of 1. The rates obtained through the 1H NMR simulations were used to generate an Eyring plot (Figure S26). The Eyring plot was used to calculate ΔH and ΔS for the inversion process in 3. ln (k / T) = ( ± 133.6) + (27.59 ± 0.44) R 2 = H = 18.2 ± 0.3 kcal mol -1 S = 7.6 ± 0.9 cal mol -1 K -1 Figure S26. Eyring plot of the stereochemical inversion process of 3 using simulated 1 H NMR spectroscopic data to determine the rate of the process at multiple temperatures. The equation of the linear curve was used to calculate ΔH and ΔS for this process. S24
25 S11. X-Ray rystallography of 3 a) Methods. Single crystals of 3 were grown by slow evaporation of H 2 l 2. Data was collected at 100 K on a Bruker Kappa APEX D Diffractometer equipped with a ukα microsource with Quazar optics. The SQUEEZE function of PLATN was used to remove the contribution of disordered solvent molecules to the data. b) rystal Parameters. Formula: 43 H 44 Br 2 10, orange block, mm 3, monoclinic, space group P2 1 /n; a = (3), b = (9), and c = (7) Å; β = (2) ; V = (4) Å 3 ; T = 100(2) K, Z = 8, ρ calc = g cm 3, µ(u Kα) = mm 1, F(000) = 3616; independent measured reflections = 92,194; R 1 = and wr 2 = for independent observed reflections [2θ 124, > 2σ ()]. D# Figure S27. X-Ray crystal structure of 3 with thermal ellipsoids shown at a 50% probability level. atoms are black, atoms are red, Br atoms are gold, toms are white. S25
26 S12. Molecular Mechanics alculations Molecular mechanics coordinate scans were performed with MacroModel to determine approximate structures for the transition states between intermediate conformations. The coordinate scans were conducted by rotating the respective aromatic unit at 1 intervals over 180 through the pillar[5]arene cavity. The PLS 2005 energies of the highest energy structures of the coordinate scans (approximate transition states) are listed in Table S1. The molecular mechanics calculations were conducted with the chloroform GB/SA solvation model implemented in Macromodel. Due to the symmetry of the system, the reverse pathways involving enantiomers of the transformations listed were assumed to have the same transition state and energy barrier, e.g. the tranformation of conformer 1 to conformer 1 a1 would have a transition state which is the enantiomer of the transformation of conformer 1* to conformer 1 a1 *. Table S1. PLS 2005 energies of approximate transition states. Transformation (1 st conformer to 2 nd conformer) Relative PLS 2005 Energy (in Hl 3 ) (kcal mol -1 ) 1 to 1 a a1 to 1 b b1 to 1 b3 * a3 to 1 b a3 to b1 to 1 b6* b6 to 1 a to 1 a a2 to 1 b a2 to 1 b a3 to 1 b S26
27 S13. Quantum Mechanical alculations Density functional theory (DFT) calculations were performed with the B3LYP exchangecorrelation functional using the Jaguar software package. Geometry optimization and frequency calculations were conducted with either the 6-31G* or LAVP* basis set. Table S2 lists the lowest calculated vibrational frequency and zero point energies for each intermediate conformer and transition state. Single point calculations (Table S2) were conducted with a Poisson-Boltzmann continuum-solvation model using either the 6-311G**++ or LAV3P**++ basis set. Default grids and SF convergence criteria as implemented in Jaguar were used. Table S2. DFT calculated properties for intermediate conformers and transition states ntermediate onformer Single Point Energy (Hartrees) Zero Point Energy (Hartrees) Total Energy (Hartrees) Energy Relative to onformer 1 (kcal mol -1 ) a b b6 * a3 * Transition State Single Point Energy (Hartrees) Zero Point Energy (Hartrees) Total Energy (Hartrees) Energy Relative to onformer 1 (kcal mol -1 ) TS 1 (1 / 1 a2 ) TS 2 (1 a2 / 1 b1 ) TS 3 (1 b1 / 1 b6 *) TS 4 (1 b6 * / 1 a3 *) TS 5 (1 a3 * / 1*) S27
28 S14. DFT ptimized Structures and Energies onformer 1 Energy [B3LYP (solvation)/ 6-311g**++// B3LYP/ 6-31g*] = Hartrees (oordinates in Ångströms) atom x y z H H H H H H H H H H H H H H H H H H H H H H H H H H H S28
29 H H H H H H H H H H H H H H H H H H H Figure S28. Side view (left) and top view (right) of the DFT optimized structure for 1. S29
30 onformer 1 a2 Energy [B3LYP (solvation)/ 6-311g**++// B3LYP/ 6-31g*]= Hartrees (oordinates in Ångströms) atom x y z H H H H H H H H H H H H H H H H H H H H H H H H H H H H S30
31 H H H H H H H H H H H H H H H H H H Figure S29. Side view (left) and top view (right) of the DFT optimized structure for 1 a2. S31
32 onformer 1 b1 Energy [B3LYP (solvation)/ 6-311g**++// B3LYP/ 6-31g*] = Hartrees (oordinates in Ångströms) atom x y z H H H H H H H H H H H H H H H H H H H H H H H H H H H H H S32
33 H H H H H H H H H H H H H H H H H Figure S30. Side view (left) and top view (right) of the DFT optimized structure for 1 b1. S33
34 onformer 1 b6 * Energy [B3LYP (solvation)/ 6-311g**++// B3LYP/ 6-31g*] = Hartrees (oordinates in Ångströms) atom x y z H H H H H H H H H H H H H H H H H H H H H H H H H H H H S34
35 H H H H H H H H H H H H H H H H H H Figure S31. Side view (left) and top view (right) of the DFT optimized structure of 1 b6 * S35
36 onformer 1 a3 * Energy [B3LYP (solvation)/ 6-311g**++// B3LYP/ 6-31g*] = Hartrees (oordinates in Ångströms) atom x y z H H H H H H H H H H H H H H H H H H H H H H H H H H H H H S36
37 H H H H H H H H H H H H H H H H H Figure S32. Side view (left) and top view (right) of DFT optimized structure 1 a3 *. S37
38 Transition state in the conversion of conformer 1 to 1 a2 Energy [B3LYP (solvation)/ 6-311g**++// B3LYP/ 6-31g*] = Hartrees (oordinates in Ångströms) atom x y z H H H H H H H H H H H H H H H H H H H H H H H H H H H H S38
39 H H H H H H H H H H H H H H H H H H Figure S33. Side view (left) and top view (right) of the optimized transition state between conformers 1 and 1 a2. S39
40 Transition state in the conversion of conformer 1 a2 conformer 1 b1 Energy [B3LYP (solvation)/ 6-311g**++// B3LYP/ 6-31g*]= Hartrees (oordinates in Ångströms) atom x y z H H H H H H H H H H H H H H H H H H H H H H H H H H H H S40
41 H H H H H H H H H H H H H H H H H H Figure S34. Side view (left) and top view (right) of the optimized transition state between conformers 1 a2 and 1 b1. S41
42 Transition state in the conversion of conformer 1 b1 conformer 1 b6 * Energy [B3LYP (solvation)/ 6-311g**++// B3LYP/ 6-31g*] = Hartrees (oordinates in Ångströms) atom x y z H H H H H H H H H H H H H H H H H H H H H H H H H H H H H S42
43 H H H H H H H H H H H H H H H H H Figure S35. Side view (left) and top view (right) of the optimized transition state between conformers 1 b1 and 1 b6 *. S43
44 Transition state in the conversion of conformer 1 b6 * conformer 1 a3 * Energy [B3LYP (solvation)/ 6-311g**++// B3LYP/ 6-31g*] = Hartrees (oordinates in Ångströms) atom x y z H H H H H H H H H H H H H H H H H H H H H H H H H H H H S44
45 H H H H H H H H H H H H H H H H H H Figure S36. Side view (left) and top view (right) of the optimized transition state between conformers 1 b6 * and 1 a3 *. S45
46 Transition state in the conversion of conformer 1 a3 * conformer 1* Energy [B3LYP (solvation)/ 6-311g**++// B3LYP/ 6-31g*] = Hartrees (oordinates in Ångströms) atom x y z H H H H H H H H H H H H H H H H H H H H H H H H H H H H S46
47 H H H H H H H H H H H H H H H H H H Figure S37. Side view (left) and top view (right) of the optimized transition state between conformers 1 a3 * and 1*. S47
48 Ground state of 3 Energy [B3LYP (solvation)/ LAV3P**++// B3LYP/ LAVP*] = Hartrees (oordinates in Ångströms) atom x y z Br Br H H H H H H H H H H H H H H H H H H H H S48
49 H H H H H H H H H H H H H H H H H H H H H H H H Figure S38. Side view (left) and top view (right) of the optimized ground state of 3. S49
50 Assumed highest energy transition state of 3 Energy [B3LYP (solvation)/ LAV3P**++// B3LYP/ LAVP*] = Hartrees (oordinates in Ångströms) atom x y z Br Br H H H H H H H H H H H H H H H H H H H H S50
51 H H H H H H H H H H H H H H H H H H H H H H H H Figure S39. Side view (left) and top view (right) of the highest energy transition state of 3. S51
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