Supporting Information

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1 Supporting Information Wiley-VCH Weinheim, Germany

2 Suitanes Avril R. Williams, Brian H. Northrop, Theresa Chang, J. Fraser Stoddart,* Andrew J. P. White and David J. Williams* [*] Prof. J. F. Stoddart, Dr. A. R. Williams, Dr. T. Chang, B. H. Northrop California NanoSystems Institute and Department of Chemistry and Biochemistry University of California, Los Angeles 405 Hilgard Avenue, Los Angeles, CA (USA) Fax: Int. Code +(310) [*] Prof. D. J. Williams, Dr. A. J. P. White Department of Chemistry Imperial College South Kensington, London SW7 2AY (UK) Supporting Information Correspondence Address Dr J Fraser Stoddart Department of Chemistry and Biochemistry University of California, Los Angeles 405 Hilgard Avenue, Los Angeles CA (USA) Tel: Int. Code +(310) Fax: Int. Code +(310) stoddart@chem.ucla.edu

3 Synthesis of the Linear Body Template and the Functionalized Crown Ether. Reductive amination (Scheme S1) of the known [S1] 9-aminomethyl-10-bromoanthracene (1) with 3,5-difluorobenzaldehyde, followed by treatment of the resulting secondary amine with di-tert-butyldicarbonate gave the Boc-protected amine 2. Two molecules of 2 were linked together by a phenylene group using a Suzuki coupling with 1,4- diphenylenebisboronic acid on a gram scale. Deprotection with hydrochloric acid, followed by counterion exchange with ammonium hexafluorophosphate, gave the desired linear biped LBT-H 2 2PF 6. Dimethyl 4-dimethoxymethylpyridine (4) is a known compound. [S2] The ester functions at the 2- and 6-positions of 4 were reduced (Scheme S2) and the resulting diol 5 was tosylated to afford the bistosylate 6. Reaction of 6 with dietthylene glycol resulted in a [2+2] macrocyclization to yield the masked diformyl crown ether 7. Deprotection of the acetal functions was achieved by refluxing an aqueous tetrahydrofuran solution of the crown ether 7 in the presence of hydrochloric acid to give diformyl-dp24c8, (CHO) 2 - DP24C8. Experimental Section General: Chemicals were purchased from Aldrich and used as received unless indicated otherwise. Solvents were dried according to literature procedures. [S3] Thin layer chromatography was carried out using aluminum sheets precoated with silica gel 60F (Merck 5554). The plates were inspected by UV light and, if required, developed in I 2

4 vapor. Column chromatography was carried out using silica gel 60F (Merck 9385, mm). Melting points were determined on an electrothermal 9100 apparatus and are uncorrected. 1 H and 13 C NMR spectra were recorded on either a Bruker ARX400 (400MHz and 100 MHz, respectively), or Bruker ARX500 (500 MHz and 125 MHz, respectively) or Bruker Avance500 (500 MHz and 125 MHz, respectively) spectrometer, using residual solvent as the internal standard. All chemical shifts are quoted on the δ scale, and all coupling constants are expressed in Hertz (Hz). Fast atom bombardment (FAB) mass spectra were obtained using a ZAB-SE mass spectrometer, equipped with a krypton primary atom beam, utilizing a m-nitrobenzyl alcohol matrix. Cesium iodide or poly(ethylene glycol) were employed as reference compounds. Electrospray mass spectra (ESMS) were measured on a VG ProSpec triple focusing mass spectrometer with MeCN as the mobile phase. High resolution matrix-assisted laser desorption ionization spectra (HR-MALDI) were measured on an IonSpec Fourier transform mass spectrometer. 2: PhMe (300 ml) was added to 10-bromo-9-anthracenemetthylamine (1) (4.5 g, 15.7 mmol) and 3,5-difluorobenzaldehyde (2.2 g, 15.7 mmol) in a 500 ml round-bottomed flask. The mixture was heated under reflux overnight and the H 2 O collected using a Dean-Stark apparatus. The mixture was cooled down to room temperature and the solvents were removed under reduced pressure. NaBH 4 (5.9 g, 157 mmol) was added to the residue dissolved in warm MeOH (200 ml). The mixture was allowed to stir overnight at room temperature, after which 2 M HCl (10 ml) was added and the solvents were evaporated. The residue was suspended in 8 M NaOH (100 ml) and extracted with CHCl 3 (2 x 75 ml). The organic layers were combined, dried (MgSO 4 ) and the solvents

5 evaporated to yield the amine as a yellow solid (5.6 g, 90 %). The amine (4.6 g, 10.9 mmol) was dissolved in CH 2 Cl 2 (40 ml) followed by the addition of di-tertbutyldicarbonate (2.4 g, 10.9 mmol) and DMAP (0.01g, 0.11mmol). The reaction mixture was stirred at ambient temperature for 24 h. The solution was washed with 2 M HCl (10 ml), H 2 O (10 ml), brine (10 ml) and dried (MgSO 4 ). The solvents were evaporated to yield 2 as a clear yellow oil (5.8 g, 83 %) that solidified on standing. This crude product was used without further purification; 1 H NMR (500 MHz, CDCl 3 ) δ = 1.55 (s, 9H), 3.98 (br s, 2H), 5.59 (br s, 2H), 6.22 (br s, 2H), 6.55 (br s, 1H), (m, 4H), 8.21 (d, J = 10 Hz, 2H), 8.61 (d, J = 10 Hz, 2H). LBT-H 2 2PF 6 : A degassed round-bottomed flask was charged with dry THF (80 ml) followed by 2 (1.7 g, 3.7 mmol) and tetrakis-triphenylphosphinepalladium(0) (0.3 g, 0.2 mmol) and the solution was purged with argon and sealed. 2 M Na 2 CO 3 (25 ml) and a solution of 1,4-phenylenebisboronic acid (0.3 g, 1.9 mmol) in EtOH (30 ml) was injected into the vessel. The mixture was stirred at 80 C for 2 days during which time a yellow solid precipitated. The reaction mixture was cooled down to room temperature and filtered. The residue was washed with H 2 O (25 ml), MeOH (25 ml) and CH 2 Cl 2 (25 ml). This residue was then subjected to column chromatography (EtOAc:CH 2 Cl 2, 10:1) to yield the Boc-protected diamine 3 as a yellow powder (1.2 g, 76 %). Trifluoroacetic acid (3 ml) was added to a solution of the Boc-protected diamine (1.0 g, 1.2 mmol) in CHCl 3 (15 ml). The reaction mixture was stirred at room temperature overnight. The solvents were removed under pressure and the solid was suspended in 6 M NaOH (40 ml) and extracted with CHCl 3 (2 x 40 ml). The combined organic phases were washed

6 with brine (30 ml), dried (MgSO 4 ) and the solvents were evaporated off to yield a brown solid, which was subsequently dissolved in CHCl 3 (10 ml). To this solution was added concentrated HBr (10 drops) and the reaction mixture was vigorously stirred at room temperature for 5 h. The solvents were removed and the bromide salt was dissolved in MeOH (15 ml) to which saturated aqueous NH 4 PF 6 was added. The solvents were then removed under pressure and the solid was washed with copious amounts of H 2 O followed by MeOH and CH 2 Cl 2 and then air dried to yield LBT-H 2 2 PF 6 a light yellow powder (0.6 g, 79 %); mp 184 C (dec.); 1 H NMR (500 MHz, CD 3 CN) δ = 4.59 (s, 4H), 5.46 (s, 4H), (m, 2H), 7.22 (d, J = 10 Hz, 4H), (m, 4H), 7.71 (s, 4H), (m, 4H), 8.05 (d, J = 10 Hz, 4H), 8.39 (d, J = 10 Hz, 4H); 13 C NMR (125 MHz, CD 3 CN) δ = 43.8, 50.8, 105.2, 113.4, 120.9, 123.4, 125.8, 127.4, 127.9, 129.9, 130.6, 130.9, 137.9, 140.7, 161.9, : Dimethyl 4-dimethoxymethylpyridine-2,6-dicarboxylate (4) (2.5 g, 9.29 mmol) was dissolved in MeOH (150 ml). Upon addition of NaBH 4 (1.5 g, mol) the solution turned a dark burgundy color. The color gradually subsided as the reaction was stirred for 18 h. The solvent was evaporated and the residue partitioned between H 2 O and EtOAc. The aqueous layer was extracted with further amounts of EtOAc (2 x 200 ml) and the combined organic layers dried with MgSO 4 and evaporated to give the diol 5 as a pale yellow oil (1.55 g, 78 %); 1 H NMR (500 MHz, MeOD): δ = 3.32 (s, 6H), 4.66 (s, 4H), 5.42 (s, 1H), 7.47 (s, 2H); 13 C NMR (125 MHz, CDCl 3 ) δ = 52.7, 64.4, 101.1, 117.2, 148.4, 158.8; HRMS (MALDI): calcd for C 10 H 15 NO 4 m/z = ; found m/z = [M + H] +, [M + Na] +.

7 6: Aqueous sodium hydroxide (2 M, 30 ml) was added to a round-bottomed flask fitted with a pressure-equalized dropping funnel and the solution was subsequently chilled in a ice-water bath to 0 o C while being stirred. 4-Dimethoxymethyl-2,6-bis(hydroxymethyl)- pyridine (5) (1.55 g, 7.27 mmol) and tosyl chloride (3.5 g, 18 mmol) were dissolved in THF (150 ml) and added to the dropping funnel. The diol/tosyl chloride solution was added dropwise over 1 h. The reaction mixture was warmed to ambient temperature and stirred for a further 16 h. The solvent was evaporated and the residue partitioned between distilled H 2 O (200 ml) and CH 2 Cl 2 (150 ml). The layers were separated and the organic layer was extracted with further amounts of CH 2 Cl 2 (2 x 150 ml). The combined organic layers were dried (MgSO 4 ) and evaporated to give a white residue which was purified by column chromatography (EtOAc: pet. ether 2:1) to give 6 as a white solid (3.16 g, 83 %); 1 H NMR (500 MHz, CDCl 3 ): δ = 2.44 (s, 6H), 3.29 (s, 6H), 5.05 (s, 4H), 7.33 (d, J = 8.4 Hz, 4H), 7.39 (s, 2H), 7.82 (d, J = 8.4 Hz, 4H); 13 C NMR (125 MHz, CDCl 3 ) δ = 21.5, 52.7, 71.1, 100.7, 119.5, 127.9, 129.8, 132.6, 145.0, 149.2, 153.7; HRMS (MALDI): calcd for C 24 H 27 NO 8 S 2 m/z = ; found m/z = [M + H] +, [M + Na] +. 7: NaH (0.20 g, 9.3 mmol) was added to dry THF (500 ml) and the suspension was brought to reflux. A solution of diethylene glycol (0.30 g, 3.1 mmol) and 4- dimethoxymethyl-2,6-bis(p-toluenesulfonylmethyl)pyridine (6) (1.61 g, 3.1 mmol) in dry THF (160 ml) was added dropwise to the refluxing suspension. After addition was complete (24 h), the mixture was heated under reflux for a further 48 h. The resulting suspension was cooled down and the remaining NaH was quenched with MeOH and

8 H 2 O. The solvent was evaporated and the residue partitioned between H 2 O (75 ml) and EtOAc (50 ml). The layers were separated and the aqueous layer extracted with further amounts of EtOAc (2 x 50 ml). The organic layers were then combined, dried with Na 2 SO 4, filtered and evaporated to give a crude off-white solid. The off-white solid was washed with cold MeOH to give 7 as a white solid (0.60 g, 35 % yield); 1 H NMR (CDCl 3, 500 MHz) δ = 3.27 (s, 12 H), (m, 16 H), 4.64 (s, 8H), 5.34 (s, 2H), 7.38 (s, 4H); 13 C NMR (125 MHz, CDCl 3 ) δ = 52.5, 70.1, 70.9, 73.9, 101.3, 118.1, 147.7, 158.2; HRMS (MALDI): calcd for C 28 H 42 N 2 O 10 m/z = ; found m/z = (CHO) 2 -DP24C8: 2N HCl (1 ml) was added to a THF (25 ml) solution of 4,4'- dimethoxydipyrido[24]crown-8 (6) (0.64 g, 1.12 mmol) and the mixture was heated under reflux for 5 h. The mixture was cooled and the solvents evaporated. The residue was neutralized by addition of saturated NaHCO 3 and the aqueous solution extracted with CH 2 Cl 2 (3 x 50 ml). The organic layers were combined, dried with Na 2 SO 4, filtered and evaporated to give an off-white solid. The crude product was purified by recrystallization from MeOH to give the (CHO) 2 -DP24C8 (0.40 g, 75 % yield). 1 H NMR (500 MHz, CDCl 3 ) δ = (m, 16 H), 4.68 (s, 8H), 7.73 (s, 4H), 9.78 (s, 2H); 13 C NMR (125 MHz, CDCl 3 ) δ = 70.7, 71.1, 3.2, 118.1, 142.5, 160.3, 191.4; HRMS (MALDI): calcd for C 24 H 30 N 2 O 8 m/z = ; found m/z = [M + H] +, [M + Na] +.

9 Evaluation of Binding Energies by Computation: Stochastic conformational and coconformational searches of 1000 randomly generated structures were performed in order to obtain the lowest energy conformation, or co-conformation, of the five molecules shown in Figure S1 namely: a) suit[2]ane, b) the 2:1 (macrocycle:thread) model complex, c) LBT H 2 2PF 6, d) DP24C8, and e) the macrobicyclic suit of suit[2]ane. Computational force-field modeling was performed using the program Maestro v [S4] with the AMBER* force field [S5] and GB/SA solvent model [S6] for CHCl 3. From the results of these conformational searches it is possible to determine the binding energy in suit[2]ane and in the 2:1 model complex. The binding energy of suit[2]ane was determined as: ΔE binding = [E suit[2]ane (E LBT H2 2PF 6 + E macro-bicyclic suit )] = 82.5 kcal mol 1 The binding energy of the 2:1 complex was determined as: ΔE 2:1 complex = [E 2:1 complex (E LBT H2 2PF 6 + 2*E DP24C8 )] = 81.4 kcal mol 1 The 1.1 kcal/mol difference in binding energy is within the error in these calculations, and so the binding energies of the two should be taken to be roughly identical. It must also be noted that a systematic overestimation of binding energy of approximately 30 kcal mol 1 per binding site has been observed [S7] when the AMBER* force field is used to study dialkylammonium crown ether binding. Binding energies of the 2:1 complex and suit[2]ane are still comparable because of there structural similarities. Calculations suggest that there is no energetic cost associated with linking the two (CHO) 2 -DP24C8 macrocycles of the 2:1 complex in order to dynamically assemble the suit[2]ane.

10 References [S1] H. Zhang, W. Verboom, D. N. Reinhoudt, Tetrahedron Lett. 2001, 42, [S2] M. Chavarot, S. Socquet, M. Kotera, J. Lhomme, Tetrahedron 1997, 53, [S3] D. D. Perrin, W. F. L. Armarego, Purification of Laboratory Chemicals, Pergamon: Oxford [S4] F. Mohamadi, N. G. J. Richards, W. C. Guida, R. Liskamp, M. Lipton, C. Caufield, G. Chand, T. Hendrickson, W. C. Still, J. Comput. Chem. 1990, 11, [S5] P. S. J. Weiner, P. A. Kollman, D. A. Case, V. C. Singh, C. Ghio, G. Alagona, S. Profeta, Jr., P. Weinre, J. Am. Chem. Soc. 1986, 106, [S6] W. C. Still, A. Tempczyk, R. C. Hawler, T. Hendrickson, J. Am. Chem. Soc. 1990, 112, [S7] A. R. Williams, B. H. Northrop, K. N. Houk, J. F. Stoddart, D. J. Williams, Chem. Eur. J. 2004, 10,

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