Electronic Supplementary Material (ESI) for New Journal of Chemistry. This journal is The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2014 Electronic Supplementary Information for: Effect of 1,3-adamantane bridging units within the surrounding macrocycle of squaraine rotaxanes Carleton G. Collins, Andrew T. Johnson, ǂ Richard D. Connell, Ruth A. Nelson, ǂ Ivan Murgu, Allen G. Oliver, Bradley Smith * Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA. ǂ Math and Science Department, Concordia University-Portland, 2811 NE Holman Street, Portland, OR 97211 *Email: smith.115@nd.edu, andjohnson@cu-portland.edu Contents: Page A. Photophysical Spectra... S2 B. 1 H NMR Titrations to Macrocycles 8-10... S2 C. Cycloreversion of 5EP... S3 D. Molecular Dynamics Simulation of Rotaxanes... S3 E. Crystallographic Analysis of Rotaxane 5... S4 F. 1 H NMR and 13 C NMR Spectra... S7 G. References... S14 S1
A. Photophysical Spectra Figure S1. Absorption and emission spectra for adamantyl-containing SR (a) 2 and (b) 5 in CHCl 3 (rotaxane concentration of 5 µm). B. 1 H NMR Titrations to Macrocycles 8-10 Figure S2. (a) Quantified summary of the titration results using two separate fitting programs. Data and fit curves using the K. Hirose spreadsheet software for titration with macrocycle (b) 10, (c) 9, and (d) 8 with xanthone thread 11. S2
C. Cycloreversion of 5EP Figure S3. (top) Thermolysis of 5EP (50 µm) at 38 C over 60 h in o-xylene by monitoring the increasing anthracene absorbance band at 374 nm; (bottom) Cycloreversion obeys first-order kinetics. D. Molecular Dynamics Simulation of Rotaxanes Table S1. Dimensions of each system and the number of solvent molecules. SR Dimensions (Å) Number of 2- mercaptoethanol molecules Number of chloroform molecules 2 47x43x36 2 538 3 47x39x35 2 481 4 47x40x35 2 491 S3
b c d Figure S4. (a) Diagram of the measured bond distance d. Change in d over simulation timescale for SR (b) 2, (c) 3, and (d) 4. As seen in Figure S5 below, the histogram of NH O angles for isopthaloyl SR 3 (b) and pyridyl SR 4 (c) are centered around 140 degrees while the corresponding histogram for adamantyl SR 2 (a) is more widely distributed and centered around 125 degrees. a b c Figure S5. Histogram of NH O angles formed by one of the macrocycle NH residues hydrogen bonded to a squaraine oxygen atom. (a) 2, (b) 3, and (c) 4. E. Crystallographic Analysis of Rotaxane 5 The compound crystallizes as turquoise thin, blade-like crystals. There is one molecule of the rotaxane (wheel and thread molecules), two molecules of water of crystallization and one molecule of chloroform of crystallization in the unit cell of the primitive, centrosymmetric, triclinic space group P-1. S4
The chloroform was found to be partial occupancy. Refinement of the occupancy of the atoms in this molecule yielded an occupancy of approximately one half per asymmetric unit. In the final refinement the occupancy was set to a half. The hydrogens on the water of crystallization could not be located or calculated. They are however, included in the chemical formula to correctly account for Mr, mu, density F(000) etc. The structure of the SR 5 is as expected. Due to the extremely thin crystals synchrotron intensity data were required. In spite of the increased intensity, the diffraction quality is still poor. The high R-factor (12.2%) is indicative of this. The connectivity is confirmed and the wheel molecule consists of anthracene and adamantly moieties. The compound crystallizes about the center of symmetry at [0, 0, 0]. The bond distance and angles have large estimated standard deviations and are thus not as valuable as the connectivity information. All hydrogens were included in calculated positions. The amides are oriented towards the oxygens of the cyclobutadione of the thread molecule. The enlarged thermal ellipsoids also demonstrate that the molecule is not well located in a rigid position within the lattice. Figure S6 shows thermal ellipses depicted at 25% probability. Figure S6. ORTEP of SR 5. S5
Table S2. Crystal data and structure refinement. Identification code nd041b Empirical formula C 101 H 97 Cl 3 N 6 O 8 Formula weight 1629.20 Temperature 150(2) K Wavelength 0.77490 Å Crystal system Triclinic Space group P-1 Unit cell dimensions a = 11.1735(15) Å α = 100.460(8) b = 11.7304(13) Å β = 99.693(9) c = 17.822(3) Å γ = 107.086(6) Volume 2133.7(5) Å 3 Z 1 Density (calculated) 1.268 g.cm -3 Absorption coefficient (µ) 0.176 mm -1 F(000) 860 Crystal size 0.08 0.03 0.005 mm 3 θ range for data collection 2.04 to 24.07 Index ranges -11 h 11, -12 k 12, -18 l 18 Reflections collected 25755 Independent reflections 5094 [R int = 0.1228] Completeness to θ = 24.07 97.5 % Absorption correction Semi-empirical from equivalents Max. and min. transmission 0.7458 and 0.5875 Refinement method Full-matrix least-squares on F 2 Data / restraints / parameters 5094 / 0 / 551 Goodness-of-fit on F 2 1.087 Final R indices [I>2σ(I)] R 1 = 0.1220, wr 2 = 0.3117 R indices (all data) R 1 = 0.1785, wr 2 = 0.3490 Extinction coefficient 0.043(6) Largest diff. peak and hole 1.072 and -0.359 e.å -3 S6
F. 1 H NMR and 13 C NMR Spectra Figure S7. 1 H NMR (500 MHz, CDCl 3) spectrum of macrocycle 8. S7
Figure S8. 1 H NMR (600 MHz, CDCl 3) spectrum of SR 2. S8
Figure S9. 13 C NMR (150 MHz, CDCl 3) spectrum of SR 2. S9
Figure S10. 1 H NMR (600 MHz, CDCl 3) spectrum of SR 5. S10
Figure S11. 13 C NMR (150 MHz, CDCl 3) spectrum of SR 5. S11
Figure S12. 1 H NMR (600 MHz, CDCl 3) spectrum of SR 5EP. S12
Figure S13. 13 C NMR (150 MHz, CDCl 3, 0 C) spectrum of SR 5EP. S13
G. References S1. Schmidt, M. W., Baldridge, K. K., Boatz, J. A., Elbert, S. T., Gordon, M. S., Jensen, J. H., Koseki, S., Matsunaga, N., Nguyen, K. A., Su, S. J., Windus, T.L., Dupuis, M., Montgomery, J. A., J. Comput. Chem. 1993, 14, 1347-1363 S2. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K., J. Comput. Chem., 2005, 26, 1781-1802 S3. Martinez, L.; Andrade, R.; Birgin, E. G.; Martinez, J. M., J. Comput. Chem., 2009, 13, 2157-2169 S14