Experimental and Theoretical Investigations of. Surface-Assisted Graphene Nanoribbon Synthesis
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1 Experimental and Theoretical Investigations of Surface-Assisted Graphene Nanoribbon Synthesis Featuring Carbon Fluorine Bond Cleavage Hironobu Hayashi,,, * Junichi Yamaguchi,, Hideyuki Jippo, Ryunosuke Hayashi, Naoki Aratani, Mari Ohfuchi, Shintaro Sato,, * and Hiroko Yamada, * Graduate School of Materials Science, Nara Institute of Science and Technology, Takayama-cho, Ikoma , Japan Fujitsu Laboratories Ltd and Fujitsu Limited, 10-1 Morinosato-Wakamiya, Atsugi, Kanagawa , Japan Supporting Information Table of Content 1. Materials and Methods S3 2. Abbreviations S3 3. Synthesis of HFH-DBTA S4 4. Single-crystal X-ray data of HFH-DBTA S6 5. On-surface reaction of anthracene based precursors S7 1
2 6. Single-crystal X-ray structure S8 7. DFT-calculated STM images S9 8. STM image after annealing at 350 C for 3 h S10 9. DFT simulated optimized structure of poly-h on Au(111) S DFT calculations for activation energy S Discussion for other possible paths S Arrhenius plots S NMR spectra S HRMS S17 2
3 1. Materials and Methods Reagents for synthesis were purchased from Wako, Nacalai Tesque, and Sigma Aldrich, and were reagent-grade quality, obtained commercially, and used without further purification. For spectral measurements, spectral-grade solvents were purchased from Nacalai Tesque. Unless stated otherwise, column chromatography was carried out on silica gel 60N (Kanto Chemical, µm). Analytical thin layer chromatography (TLC) was performed on Art (Merck, KGaA). Melting points (m.p.) were measured with a YAMAKO MP-J3. IR spectra were recorded on a JASCO FP-6600 and are reported as wavenumbers ν in cm -1 with band intensities indicated as s (strong), m (medium), w (weak). 1 H NMR (400 MHz and 600 MHz) and 19 F NMR (564 MHz) spectra were recorded (as indicated) either on a JEOL JNM-ECX 400 and JEOL JNM-ECX 600 spectrometer and are reported as chemical shifts (δ) in ppm relative to TMS (δ = 0). Broad peaks are marked as br. High resolution MS was performed on a MALDI-TOF (Bruker Autoflex II) or JEOL AccuTOF JMS-T100LC. X-ray crystallographic data were recorded at 90 K on a Bruker APEX II X-Ray diffractometer equipped with a large area CCD detector by using graphite monochromated Mo-Kα radiation (λ = Å). 2. Abbreviations. AcOH: Acetic acid; Ar: Argon; n-buli: n-butyllithium; DCM: Dichloromethane; DFT: Density functional theory; HRMS: High resolution mass spectroscopy; MALDI-TOF: Matrix assisted laser desorption ionization-time of flight; m.p.: Melting point; NBS: N-bromosuccinimide; rt: Room temperature; STM; Scanning tunneling microscopy; THF: Tetrahydrofuran; TLC: Thin layer chromatography; TMEDA: N,N,N,N -Tetramethylethylenediamine; TMS: Tetramethylsilane; XPS: X-ray photoelectron spectroscopy. 3
4 3. Synthesis of HFH-DBTA Compound 1. To a solution of 9-bromoanthracene (925 mg, 3.6 mmol) and TMEDA (2.4 ml, 16.1 mmol) in anhydrous THF (120 ml) was added n-buli (1.6 M in hexane, 2.4 ml, 3.84 mmol) dropwise at 50 C under Ar atmosphere. The solution was stirred for 4 h at 50 C. To a solution of 2,3,6,7-tetrafuoroanthraquinone (257 mg, 0.9 mmol) in anhydrous THF (40 ml) was added the prepared lithium reagent at 50 C. The mixture was slowly warmed to rt over 3 h and kept stirring over night, and then the reaction mixture was concentrated in vacuo. A mixture of crude product diol 1, NaI (810 mg, 5.4 mmol), and NaH 2 PO 2 H 2 O (834 mg, 7.9 mmol) in AcOH (100 ml) was heated to reflux for 2.5 h. After cooling to rt, the mixture was diluted with H 2 O. The resulting precipitate was filtered, and washed with H 2 O and MeOH, and dried in vacuo. The residue was recrystallized from CHCl 3 /MeOH to give a pure compound 1 (269 mg, 45%, R f = 0.5 with CHCl 3 /hexane 1:4) as a yellow solid. m.p.: >300 C; IR (KBr): 3078 (m), 3052 (s), 2700 (s), 2371 (s), 1931 (s), 1788 (s), 1520 (m), 1486 (s), 1453 (s), 1442 (s), 1309 (s), 1245 (s), 1215 (s), 1159 (s), 1143 (s), 1021 (s); 1 H NMR (400 MHz, CDCl 3 ): 8.80 (s, 2H), 8.25 (d, 8.0 Hz, 4H), 7.57 (dq, 8.0 Hz, 4.0 Hz, 4H), 7.39 (dt, 8.0 Hz, 4H), 7.24 (d, 8.0 Hz, 4H), 6.86 (t, 10.0 Hz, 4H); 19 F NMR (564 MHz, CDCl 3 ): (t, 10.2 Hz, 4F); HRMS (EI, +ve) calcd for C 42 H 22 F 4 : , found: HFH-DBTA. To a refluxed solution of 1 (200 mg, 0.33 mmol) in CHCl 3 (60 ml) and anhydrous acetonitrile (120 ml) was added NBS (125 mg, 0.70 mmol) under Ar atmosphere. The mixture was refluxed for 15 h, and then additional NBS (125 mg, 0.70 mmol) was added to the reaction mixture. The mixture was refluxed for 20 h. After cooling to rt, the 4
5 reaction mixture was diluted with CHCl 3 and washed successively with Na 2 S 2 O 3 aq and then dried over Na 2 SO 4. The residue was concentrated in vacuo and then purified by flash chromatography (CHCl 3 /hexane 1:4, R f = 0.6) and recrystallized from CHCl 3 /MeOH to give a pure compound HFH-DBTA (65 mg, 26%) as a yellow crystal. m.p.: >300 C; IR (KBr): 3073 (s), 3058 (s), 2924 (m), 2699 (m), 2360 (m), 1902 (m), 1728 (m), 1522 (s), 1488 (s), 1438 (s), 1365 (s), 1303 (s), 1258 (s), 1218 (s), 1146 (s), 1024 (s); 1 H NMR (600 MHz, CDCl 3 ): 8.81 (d, 9.0 Hz, 4H), (m, 4H), (m, 4H), 7.24 (d, 8.4 Hz, 4H), 6.86 (t, 9.6 Hz, 4H); 19 F NMR (564 MHz, CDCl 3 ): (t, 10.2 Hz, 4F); HRMS (EI, +ve) calcd for C 42 H 20 Br 2 F 4 : , found:
6 4. Single-crystal X-ray data of HFH-DBTA Empirical formula C 42 H 20 Br 2 F 4 Formula weight Temperature Wavelength Crystal system 90 K Å Space group P2 1 /n Unit cell dimensions Monoclinic a = (12) Å b = (12) Å β = (9) c = (12) Å Volume 4629(6) Å 3 Z 6 Density (calculated) g/cm 3 Absorption coefficient mm 1 F(000) 2268 Crystal size x x mm 3 Theta range for data collection to Index ranges 19 h 19, 0 k 19, 19 l 19 Reflections collected Independent reflections 6821 [R(int) = ] Completeness to theta = % Absorption correction Max. and min. transmission and Semi-empirical from equivalents Refinement method Full-matrix least-squares on F 2 Data / restraints / parameters 6821 / 444 / 649 Goodness-of-fit on F Final R indices [I > 2σ(I)] R 1 = , wr 2 = R indices (all data) R 1 = , wr 2 = Extinction coefficient Largest diff. peak and hole and e.å 3 n/a 6
7 5. On-surface reaction of anthracene based precursors Figure S1. Schemes of chemical reactions of precursor molecules. 7
8 6. Single-crystal X-ray structure Figure S2. Single crystal X-ray structure of HFH-DBTA. ORTEP representation of X-ray crystal structure of HFH-DBTA. Thermal ellipsoids represent 50% probability. 8
9 7. DFT-calculated STM images Figure S3. DFT-calculated STM images of a) HFH-7-GNR and b) H-7-GNR. The structural mode was overlaid on the image. 9
10 8. STM image after annealing at 350 C for 3 h Figure S4. STM topographic image of species after annealing at 350 C for 3 h (Vs = 1.6 V, It = 30 pa). 10
11 9. DFT simulated optimized structure of poly-h on Au(111) Figure S5. DFT-simulated optimized structure of poly-h on Au(111). Grey, pale pink, blue, and orange spheres represent C, H, F, and Au atoms, respectively. 11
12 10. DFT calculations for activation energy Figure S6. DFT calculations for the activation energy of (A D) C F bond and (E) C H bond dissociation. Grey, pale pink, blue, and orange spheres represent C, H, and F atoms, respectively. The H atom of H C F structure is represented by a yellow sphere. 12
13 11. Discussion for other possible paths Figure S7A shows the optimized structures of P1 and P2 states. The P1 is the geometry of poly-hfh on Au(111), whose details are shown in Figure 3A. In the P2 state, the one of the edge F atoms is detached from poly-hfh and adsorbed to the hcp hollow site of Au(111). The distance between the radical C atom at the edge and the topmost Au atom is 2.10 Å, indicating a chemical bond of C Au. The P2 state is less stable than the P1 state by 189 kj/mol. The activation energy for reaction from P1 to P2 would be higher than 189 kj/mol. Figure S7B shows the optimized structures of R1 and R2 states. The R1 is the geometry of HFH-7-GNR on Au(111). The center C atom of the ribbon, the edge H atom and the edge F atom are located far from Au(111) surface with the distance of 0.38 nm, 0.33 nm and 0.45 nm, respectively. In the R2 state, the one of the edge F atoms is detached from HFH-7-GNR and adsorbed to the fcc hollow site of Au(111). The radical C atom in the HFH-7-GNR cannot make a chemical bond with the Au surface unlike the P2 state, causing the R2 state highly unstable. The R2 state is less stable than R1 state by 291 kj/mol. The activation energy for the reaction from R1 to R2 would be higher than 291 kj/mol. Figure S7C shows the optimized structures of I1 state. The H atom pointing outward the surface in the I0 state, which is indicated by the red arrow, is migrated to the neighbor C atom in the same row for the I1 state. If a reaction proceeds irreversibly from I0 to I1 instead of I1, the F atom at the edge cannot be detached based on an analogy with the reactions from P1 to P2 and from R1 to R2. The I1 state is more stable than the I0 state by only 6 kj/mol. The small energy difference between I0 and I1 indicates the reversible reaction of I0 to I1 with almost the same activation energies. 13
14 Figure S7. Optimized geometries of (A) poly-hfh and (B) HFH-7-GNR before and after the defluorination reaction. (C) Optimized geometries of intermediate state before and after H atom migration. 14
15 12. Arrhenius plots Rate constants (k) of reactions were calculated by use of equation 1 k = Aexp E a (1) k B T where A is the frequency factor (A = s 1 ), E a is the activation energy (ev), k B is Boltzmann constant (J K 1 ), and T is the temperature of the substrate (400 C). The calculated values were summarized in Table S1. Table S1. Calculated activation energies and rate constants by Arrhenius plots. Reaction E a (kj/mol) k (s 1 ) P1 P2 >189 <10 2 R1 R2 >291 <10 10 I0 I1 ~ I1 I0 ~ E a (I0 I1 ) ~ E a (I1 I0) I0 I1 I1 I2 ~
16 13. NMR spectra Figure S8. 1 H NMR spectrum of HFH-DBTA in CDCl 3. 16
17 Figure S9. 19 F NMR spectrum of HFH-DBTA in CDCl 3. 17
18 14. HRMS Figure S10. HRMS spectrum of HFH-DBTA. 18
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