Supplementary Information

Supplementary Information Supramolecular polymerization of hydrogen-bonded rosettes with anthracene chromophores: regioisomeric effect on nanostructures Deepak D. Prabhu, Keisuke Aratsu, Mitsuaki Yamauchi, Xu Lin, Bimalendu Adhikari, and Shiki Yagai* Graduate School of Engineering, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan E-mail: yagai@faculty.chiba-u.jp Tel: +81-43-290-3169 Fax: +81-43-290-3039 S1

Contents Experimental Section S3 General Synthesis and Characterization Supporting Figures S8 Figure. S1: Concentration dependent dynamic light scattering of 1 and 2 in MCH Figure. S2: Temperature dependence of the fraction of aggregates for 1 and 2 and the corresponding cooperative nucleation-elongation fits Figure. S3: UV-Vis absorption spectra and CD spectra of 2 with different volume fraction of (R)-limonene (c = 2.5 10 5 M). Figure. S4: AFM image of 2 spin-coated from a MCH:(R)-limonene mixture (80:20 v/v%; c = 1 10 4 M). Figure. S5: UV-Vis absorption spectrum and CD spectra of 2 with different volume fraction of (S)-limonene (c = 2.5 10 5 M). Figure. S6: AFM image of 2 spin-coated from a MCH:(S)-limonene mixture (80:20 v/v%; c = 1 10 4 M). Figure. S7: UV-Vis absorption spectrum of 1 with different volume fraction of (R)-limonene (c = 2.5 10 5 M) Figure. S8: AFM image of 1 spin-coated from a MCH:(R)-limonene mixture (80:20 v/v%; c = 1 10 4 M). Table. S1: Thermodynamic parameters of the cooperative self-assembly of 1 and 2 at c = 2.5 10 5 M in MCH. References S12 S2

Experimental Section General All the commercially available reagents and solvents were of reagent grade and used without further purification. The solvents for the preparation of the assemblies were all spectral grade and used without further purification. Column chromatography was performed using 63 210 µm silica gel. 1 H NMR and 13 C NMR spectra were recorded on JEOL JNM-ECA500 NMR spectrometer and chemical shifts are reported in ppm (δ) with the signal of TMS as the internal standard. ESI-MS spectra were measured on an Exactive (Thermo Fisher). UV-Vis absorption spectra were recorded on a JASCO V660 spectrophotometer with Peltier device temperature-control unit. Dynamic light scattering (DLS) measurements were performed on a Zetasizer Nano S (Malvern Instruments) using non-invasive back-scatter technology (NIBS) under 4.0 mw He-Ne laser (633 nm). The scattering angle was set at 173º. Atomic force microscopic (AFM) images were acquired under ambient conditions using Multimode 8 Nanoscope V (Bruker Instruments) in Peak Force Tapping (Scanasyst) or tapping mode. Silicon cantilevers (SCANASYST-AIR) with a spring constant of 0.4 N/m and frequency of 70 khz (nominal value, Bruker, Japan) were used for scanasyst mode. Silicon cantilevers (OMCL-AC240TS-C2) with a spring constant of 2 N/m and frequency of 70 khz (nominal value, S2 Olympus, Japan) were used for tapping mode. The scan rate was varied from 1 to 2 Hz. The samples were prepared by spin-coating the solutions (3000 rpm) onto freshly cleaved highly-oriented pyrolytic graphite (HOPG). Circular dichroism (CD) spectra were recorded on a JASCO J840 spectropolarimeter equipped with a Peltier device temperature control unit. Molecular mechanics calculations were performed on MacroModel version 10.2 using MMFF force field. S3

Synthesis and Characterization Compounds 1 and 2 were synthesized according to Scheme S1. The synthesis of intermediate compounds 3 S1 and 7 S2 were reported previously. Scheme S1 Synthesis of 1 and 2. Synthetic Details: a) 4-iodophenol, K 2 CO 3, DMF, 80 C, 6 h; b) (trimethylsilyl)acetylene, Pd(PPh 3 ) 2 Cl 2, CuI, PPh 3, diisopropylamine, r.t., 6 h; c) TBAF, THF, r.t., 6 h; d) n-buli, DMF, THF, 78 C, 12 h; e) Pd(PPh 3 ) 2 Cl 2, CuI, PPh 3, DIPA, 80 C, 6 h; f) barbituric acid, ethanol, reflux, 16 h. Synthesis of 1,2,3-tris(dodecyloxy)-5-((4-iodophenoxy)methyl)benzene (4): In a 100 ml round bottom flask connected with refluxing condenser, 5-(chloromethyl)-1,2,3-tris(dodecyloxy)benzene (1 equiv.), 4-iodophenol (1 equiv.), K 2 CO 3 (3 equiv.) were mixed in 30 ml of dry DMF. The mixture was heated at 80 C with stirring for 12 h. The reaction the reaction mixture was poured into ice and extracted with dichloromethane. The organic layer was washed several times with water and dried over anhydrous Na 2 SO 4. The solvent was removed under reduced pressure. The crude product was further purified by column chromatography (silica gel as the stationary phase and 5% ethyl acetate-hexane as the eluent) to give the titled compound (white low melting solid, yield 83%). 1 H NMR (500 MHz, CDCl 3 ): δ 7.56 7.54 (d, 2H, J = 7 Hz), 6.75 6.74 (d, 2H, J = 6.8 Hz), 6.58 (s, 2H) 4.90 (s, 2H, benzylic), 3.98 3.93 (t, 6H, OCH 2 ), 1.81 1.71 (m, 6H), 1.47 1.26 (m, 54H), 0.89 0.86 (t, 9H) ppm. 13 C NMR (125 MHz, CDCl 3 ): δ 158.62, 153.31, 138.21, 137.9, 117.49, 106.03, 83.07, S4

73.45, 70.50, 69.13, 32.37, 29.78, 29.69, 26.16, 22.74, 13.47 ppm. HRMS-EI: m/z calcd for C 49 H 83 IO 4 Na: 886.1035; found: 886.5244. Synthesis of trimethyl((4-((3,4,5-tris(dodecyloxy)benzyl)oxy)phenyl)ethynyl)silane (5): In a 100 ml round bottom flask kept under N 2 atmosphere, 1,2,3-tris(dodecyloxy)-5-((4-iodophenoxy)methyl)benzene (1 equiv.) Pd(PPh 3 ) 2 Cl 2 (2 mol%), CuI (4 mol%), PPh 3 (4 mol%) were mixed in 20 ml of dry diisopropylamine. The reaction mixture was stirred in an ice bath. To this mixture (trimethylsilyl)acetylene (2 equiv.) was added dropwise under N 2 atmosphere and stirred for 6 h. The reaction mixture was passed through a small pad of celite column. The crude product was further purified by column chromatography (silica gel as the stationary phase and 5% ethyl acetate-hexane as the eluent) to give the titled compound. The product was used for the next reaction without further characterization. Synthesis of 1,2,3-tris(dodecyloxy)-5-((4-ethynylphenoxy)methyl)benzene (6): In a 100 ml round bottom flask trimethyl((4-((3,4,5-tris(dodecyloxy)benzyl)oxy)phenyl)ethynyl)silane was dissolved in dry THF. To this mixture tetrabutylammonium fluoride (1 equiv.) was added and the mixture was stirred at room temperature for 6 h. The reaction mixture was extracted with dichloromethane and the organic layer was dried over anhydrous Na 2 SO 4. The solvent was removed under reduced pressure and the crude product was further purified by column chromatography (silica gel as the stationary phase and 5% ethyl acetate-hexane as the eluent) to give the titled compound (white solid, yield 78%). 1 H NMR (500 MHz, CDCl 3 ): δ 7.44 7.42 (d, 2H, J = 8.5 Hz), 6.92 6.90 (d, 2H, J = 9 Hz), 6.59 (s, 2H), 4.94 (s, 2H, benzylic), 3.98 3.93 (t, 6H, OCH 2 ), 3.00 (s, 1H, acetylenic), 1.81 1.71 (m, 6H), 1.47 1.42 (m, 6H), 1.29 1.26 (m, 48H), 0.89 0.87 (t, 9H) ppm. 13 C NMR (125 MHz, CDCl 3 ): δ 159.15, 153.31, 137.98, 133.59, 131.34, 114.81, 114.42, 106.07, 83.60, 76.78, 75.91, 73.45, 70.44, 69.13, 31.97, 29.80, 29.41, 26.17, 22.74, 22.60, 14.17 ppm. HRMS-EI: m/z calcd for C 51 H 85 O 4 : 762.329; found: 761.6449. General procedure for the synthesis of compound 8 and 9: A 100 ml three neck round bottom flask kept under N 2 atmosphere was charged with dibromoanthracene (1 equiv.) dissolved in 15 ml of anhydrous THF. The reaction mixture was cooled to 78 C, producing a yellow suspension. To the resulting yellow suspension, n-buli (1.1 equiv.) was added dropwise to give an orange solution which was further stirred for 30 minutes. To this mixture anhydrous DMF (2 equiv.) was slowly added and the resultant solution was warmed slowly to room temperature and stirred for another 12 h. The reaction mixture was then quenched with H 2 O and extracted with dichloromethane. The combined organic phases were washed with aqueous NH 4 Cl solution and H 2 O, and dried over Na 2 SO 4. The solvent was then removed under S5

reduced pressure and the crude product was purified by column chromatography (silica gel as the stationary phase and 10% ethyl acetate-hexane as the eluent). The product was further purified by crystallizing from toluene. 4-bromoanthracene-1-carboxaldehyde (8): Yellow solid, yield 47 %. 1 H NMR (500 MHz, CDCl 3 ): δ 10.36 (s, 1H, CHO), 9.99 (s, 1H), 8.94 (s, 1H), 8.17 8.11 (m, 2H), 7.96 7.97 (d, 1H, J = 7.5 Hz), 7.81 7.79 (d, 1H, J = 7 Hz), 7.62 7.61 (m, 2H) ppm. 13 C NMR (125 MHz, CDCl 3 ): δ 193.14, 131.74, 131.71, 130.07, 128.89, 127.27, 125.43, 123.69 ppm. HRMS-EI: m/z calcd. for C 15 H 10 BrO: 286.1400; found: 286.5244. 10-bromoanthracene-9-carboxaldehyde (9): Yellow solid, yield 56 %. 1 H NMR (500 MHz, CDCl 3 ): δ 11.30 (s, 1H, CHO), 8.72 8.70 (d, 2H, J = 9.5 Hz), 8.49 8.48 (d, 2H, J = 9.5 Hz), 7.57 7.49 (m, 4H) ppm. 13 C NMR (125 MHz, CDCl 3 ): δ 193.14, 131.74, 131.71, 130.07, 128.89, 127.27, 125.43, 123.69 ppm. HRMS-EI: m/z calcd for C 15 H 10 BrO: 286.1400; found: 286.4133. General procedure for the synthesis of compound 10 and 11: In a 100 ml three neck round bottom flask kept under N 2 atmosphere, corresponding bromoanthracenecarboxaldehyde (1 equiv.), Pd(PPh 3 ) 2 Cl 2 (2 mol%), CuI (4 mol%), PPh 3 (4 mol%) were mixed in 20 ml of dry diisopropylamine. The reaction mixture was stirred in an ice bath. To this mixture 1,2,3-tris(dodecyloxy)-5-((4-ethynylphenoxy)methyl)benzene (1. 2 equiv.) was added and stirred for 6 h. The reaction mixture was passed through a small pad of celite column. The crude product was further purified by column chromatography (silica gel as the stationary phase and 5% ethyl acetate-hexane as the eluent). 4-((4-((3,4,5-tris(dodecyloxy)benzyl)oxy)phenyl)ethynyl)anthracene-1-carbaldehyde (10): Yellow orange solid, yield: 68%. 1 H NMR (500 MHz, CDCl 3 ): δ 10.38 (s, 1H, CHO), 9.97 (s, 1H), 9.08 (s, 1H), 8.17 8.11 (m, 2H), 7.99 7.97 (d, 1H, J = 7 Hz), 7.87 7.86 (d, 1H, J = 7.5 Hz), 7.70 7.69 (d, 2H, J = 8.5 Hz), 7.60 7.59 (d, 2H, J = 8.5 Hz), 7.07 7.06 (d, 2H, J = 9 Hz), 6.65 (s, 2H), 5.03 (s, 2H, benzylic), 4.01 3.95 (t, 6H, OCH 2 ), 1.84 1.73 (m, 6H), 1.47 1.45 (m, 6H), 1.34 1.26 (m, 47H), 0.89 0.86 (t, 9H) ppm. 13 C NMR (125 MHz, CDCl 3 ): δ 192.91, 159.64, 153.35, 138.05, 133.45, 131.62, 131.39, 131.20, 128.98, 127.78, 126.46, 126.24, 124.58, 123.86, 115.21, 115.12, 106.11, 105.14, 85.35, 73.46, 70.57, 69.15, 31.94, 30.366, 29.78, 29.39, 26.16, 26.12, 26.02, 22.72, 14.15 ppm. HRMS-EI: m/z calcd. for C 66 H 93 O 5 : 965.4570; found: 965.7033. 10-((4-((3,4,5-tris(dodecyloxy)benzyl)oxy)phenyl)ethynyl)anthracene-9-carbaldehyde (11): Yellow orange solid, yield: 75%. 1 H NMR (500 MHz, CDCl 3 ): δ 11.49 (s, 1H, CHO), 8.96 8.95 (d, 2H, J = 8.85 Hz), 8.76 8.74 (d, 2H, J = 9 Hz), 7.74 7.73 (d, 2H, J = 8.8 Hz), 7.72 7.68 (m, 2H), 7.65 7.62 S6

(m, 2H), 7.08 7.06 (d, 2H, J = 8.5 Hz), 6.65 (s, 2H), 5.03 (s, 2H, benzylic), 4.01 3.95 (t, 6H, OCH 2 ), 1.84 1.73 (m, 6H), 1.47 1.44 (m, 6H), 1.33 1.25 (m, 47H), 0.89 0.86 (t, 9H) ppm. 13 C NMR (125 MHz, CDCl 3 ): δ 192.91, 159.64, 153.35, 138.05, 133.45, 131.62, 131.39, 131.20, 128.97, 127.78, 126.46, 126.23, 124.58, 123.86, 115.21, 115.12, 106.11, 105.14, 85.35, 73.46, 70.57, 69.15, 31.94, 30.36, 29.78, 29.39, 26.16, 26.12, 26.02, 22.72, 14.15 ppm. HRMS-EI: m/z calcd. for C 66 H 93 O 5 : 965.4570; found: 965.6503. General procedure for the synthesis of compound 1 and 2: In a 100 ml round bottom flask kept under N 2 atmosphere, corresponding aldehyde derivatives (1 equiv.), barbituric acid (5 equiv.) were mixed in 20 ml of dry ethanol. The reaction mixture was refluxed for 16 h. The reaction mixture was cooled to room temperature, the precipitate formed were filtered, washed with hot ethanol and dried under vacuum to give pure compound. 5-((4-((4-((3,4,5-tris(dodecyloxy)benzyl)oxy)phenyl)ethynyl)anthracen-1-yl)methylene)pyrimidine- 2,4,6(1H,3H,5H)-trione [1]: Red color solid, yield: 84%. 1 H NMR (500 MHz, CDCl 3 ): δ 9.42 (s, 1H), 9.02 (s, 1H), 8.61 (1s, 1H, NH), 8.48 (s, 1H), 8.28 8.26 (d, 1H, J = 7.5 Hz), 8.24 (s, 1H, NH), 8.09 8.02 (m, 2H), 7.74 7.73 (d, 1H, J = 7.5 Hz), 7.67 7.65 (d, 2H, J = 8.5 Hz), 7.55 7.53 (d, 2H, J = 8 Hz), 7.05 7.03 (d, 2H, J = 8.5 Hz), 6.64 (s, 2H), 5.01 (s, 2H, benzylic), 4.00 3.94 (t, 6H, OCH 2 ), 1.83 1.72 (m, 6H), 1.47 1.44 (m, 6H), 1.33 1.25 (m, 47H), 0.89 0.62 (t, 9H) ppm. 13 C NMR (125 MHz, CDCl 3 ): δ 160.39, 158.65, 157.51, 156.54, 152.56, 147.59, 137.83, 132.22, 132.25, 130.72, 130.50, 127.60, 126.97, 126.95, 126.19, 125.51, 124.23, 121.39, 121.15, 114.84, 114.45, 105.81, 102.53, 84.43, 72.57, 69.76, 68.69, 30.97, 29.43, 28.78, 28.74, 28.69, 28.63, 28.50, 28.46, 28.37, 25.39, 25.24, 25.21, 21.78, 21.70, 13.03 ppm. HRMS-EI: m/z calcd. for C 70 H 94 N 2 O 7 : 1075.5290; found: 1075.7134. 5-((10-((4-((3,4,5-tris(dodecyloxy)benzyl)oxy)phenyl)ethynyl)anthracen-9-yl)methylene)pyrimidine -2,4,6(1H,3H,5H)-trione [2]: Purple color solid, yield: 87%. 1 H NMR (500 MHz, CDCl 3 ): δ 9.35 (s, 1H), 8.62 8.60 (d, 2H, J = 8.65 Hz), 7.74 7.72 (d, 2H, J = 8.5 Hz), 7.61 7.59 (d, 2H, J = 8.5 Hz), 7.50 7.47 (m, 2H), 7.43 7.40 (m, 2H), 6.96 6.94 (d, 2H, J = 8.5 Hz), 6.58 (s, 2H), 4.93 (s, 2H, benzylic), 3.92 3.88 (t, 6H, OCH 2 ), 1.74 1.65 (m, 6H), 1.41 1.37 (m, 6H), 1.27 1.19 (m, 47H), 0.81 0.78 (t, 9H) ppm. 13 C NMR (125 MHz, CDCl 3 ): δ 160.39, 158.65, 157.51, 156.54, 152.56, 147.59, 137.83, 132.22, 132.25, 130.72, 130.50, 127.60, 126.97, 126.95, 126.19, 125.51, 124.236, 121.33, 121.15, 114.84, 114.47, 105.85, 102.53, 84.46, 72.57, 69.76, 68.61, 30.97, 29.48, 28.78, 28.74, 28.69, 28.63, 28.52, 28.40, 28.37, 25.33, 25.24, 25.21, 21.78, 21.70, 13.03 ppm. HRMS-EI: m/z calcd. for C 70 H 94 N 2 O 7 : 1075.5290; found: 1075.6243. S7

Supporting Figures a) b) Figure S1 Dynamic light scattering of (a) 1 and (b) 2 in MCH at concentrations of 1 10 5 M (red), 3 10 5 M (green), 4 10 5 M (blue) and 5 10 5 M (pink). a) b) Figure S2 Temperature dependence of the fraction of aggregates (α) calculated from apparent absorption intensity at (a) λ = 585 nm for 1 (c = 2.5 10 5 M) and (b) λ = 600 nm for 2 (c = 2.5 10 5 M) in the cooling process at a rate of 1 K min 1. Green and blue curve in (a) and (b) were obtained by fitting analysis based on the cooperative nucleation-elongation model in the elongation and nucleation regimes respectively. S8

a) b) Figure S3 (a) UV-Vis absorption spectra of 2 (c = 2.5 10 5 M) in pure MCH and MCH:(R)-limonene mixtures with different (R)-limonene volume fraction (0 50%). Dotted line in the figure show the absorption spectrum of monomeric 2 in pure MCH at 363 K. (b) CD spectra of 2 (c = 2.5 10 5 M) with different (R)-limonene fraction in MCH:(R)-limonene solvent mixtures. Red curve (0% (R)-limonene), green curve (10% (R)-limonene) and blue curve (20% (R)-limonene). 200 nm Figure S4 AFM image of 2 spin-coated from a MCH:(R)-limonene mixture (80:20 v/v%; c = 1 10 4 M) onto HOPG. S9

a) b) Figure S5 (a) UV-Vis absorption spectra of 2 (c = 2.5 10 5 M) in pure MCH and MCH:(S)-limonene mixtures with different (S)-limonene volume fraction (0 50%). (b) CD spectra of 2 (c = 2.5 10 5 M) with different (S)-limonene fraction in MCH:(S)-limonene solvent mixtures. Red curve (0% (S)-limonene), green curve (10% (S)-limonene) and blue curve (20% (S)-limonene). a) b) 100 nm 100 nm Figure S6 (a) AFM tapping mode height image of 2 spin-coated from a solutions of MCH:(S)-limonene mixture (80:20 v/v%; c = 1 10 4 M) onto HOPG. (b) Corresponding phase image of (a). S10

Figure S7 UV-Vis absorption spectrum of 1 (c = 2.5 10 5 M) in pure MCH and MCH:(R)-limonene solvent mixtures with different (R)-limonene volume fraction (0 50%). 100 nm Figure S8 AFM height image of 1 spin-coated from a solution of MCH:(R)-limonene mixture (80:20, c = 1 10 4 M) onto HOPG. S11

Table S1 Thermodynamic parameters of the cooperative self-assembly of 1 and 2 at c = 2.5 10 5 M in MCH. Compound ΔH e /kj mol 1 T e /K K a 1-96.7 335.2 6.9 x 10 5 2-75.5 323.4 5.3 x 10 5 References [S1] Balagurusamy, V. S. K., Ungar, G., Percec, V. & Johnsson, G. J. Am. Chem. Soc. 119, 1539 1555 (1997). [S2] Ho, J. H., Chen, Y., Chou, L., Lai, P-W. & Chen, P-S. Tetrahedron Lett. 55, 5727 5731 (2014). S12