On-Surface Azide-Alkyne Cycloaddition on Au(111) Oscar Díaz Arado,,, Harry Mönig,,, Hendrik Wagner, Jörn-Holger Franke, Gernot Langewisch,, Philipp Alexander Held, Armido Studer,, and Harald Fuchs,,, Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Strasse 10, 48149 Münster, Germany, Center for Nanotechnology (CeNTech), Heisenbergstrasse 11, 48149 Münster, Germany, Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany, and Department of Physics, Université Libre de Bruxelles, Campus Plaine-CP 231, 1050 Brussels, Belgium E-mail: harry.moenig@uni-muenster.de; studer@uni-muenster.de; fuchsh@uni-muenster.de To whom correspondence should be addressed Physikalisches Institut, Westfälische Wilhelms-Universität Münster Center for Nanotechnology (CeNTech) Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster Department of Physics, Université Libre de Bruxelles Centro de Estudios Avanzados de Cuba (CEAC), Carretera San Antonio de los Baños Km 3 1 /2, 17100 La Habana, (Cuba) Institut für Nanotechnology, KIT, 76344 Karlsruhe, (Germany) 1
Table of contents: 1. AEB monomers deposition and on-surface reaction. 2. Mass Spectrometry data for the sublimation of the AEB monomers. 3. STM manipulation of the AEB trimers. 4. Synthesis of the AEB monomer and ex-situ AEB dimer. 5. Dimension Analysis for the AEB compounds. 6. Schematic of the out-of-plane rotation of the 1,5 regioisomer. 7. Mass spectrometry and STM study of the sublimation of ex-situ AEB dimers. 2
AEB monomers deposition and on-surface reaction Figure S1: STM images of different depositions of AEB molecules at 85. Underlying reacted products can be observed, ranging from monomers to trimers. (A) 16 16 nm 2 ; V = 600 mv; I = 50 pa; T 5K. (B) 28 28 nm 2 ; V = 600 mv; I = 35 pa; T 5K. 3
Mass Spectrometry data for the sublimation of the AEB monomers Figure S2: Mass Spectrometry data for the AEB molecules sublimation. Strong signal corresponds to the monomer mass detected in a range between 80 and 180. Temperature around the 2.90 mark was increased manually and not by TIC control. 4
Figure S3: Mass signal corresponding to the AEB molecules was detected. 5
Figure S4: Regions corresponding to the mass signals of AEB dimers and trimers. corresponding signal was detected during the evaporation. No 6
STM manipulation of the AEB trimers All STM manipulations were carried out at T 5K with 100pA I 3.5 na and V = 5mV. In every case, a strong Van-der-Waals interaction and/or probable hydrogen bonding between the manipulated objects was observed. Such effect, in most cases, made impossible to successfully isolate an AEB trimer. Figure S5: Successful manipulation of an AEB trimer. Section E shows a full relaxation of the trimer back to its initial state, altogether with a formerly manipulated dimer structure. 7
Figure S6: Cases A to C show an island containing AEB monomers, dimers and trimers together, densely packed. Through STM manipulation, two AEB dimers were able to be removed from the island. Furthermore, two AEB trimers could be bent downwards. A complete detachment could not be achieved for the reasons previously discussed. Figure S7: Example of a successful AEB trimer detachment. (A) An island containing a mixture of AEB species was separated. (B) AEB trimer observed after the manipulation. 8
Synthesis of the AEB monomer and ex-situ AEB dimer General All reactions involving air -or moisture- sensitive reagents or intermediates were carried out in heat-gun-dried glassware under an argon atmosphere and were performed using standard Schlenk techniques. All solvents for extraction and flash chromatography (FC) were distilled before use. All chemicals were purchased from Sigma Aldrich, Acros Organics, ABCR, Alfa Aesar, TCI or Fluka and were used as received. Gas chromatography (GC) was performed on an Agilent 7890A chromatograph equipped with a HP-5 column (30 m 0.32 mm, film thickness 0.25 µm) using H 2 ( 1 bar) as carrier gas. 1 H-NMR and 13 C-NMR spectra were recorded on a Bruker DPX-300 (300 MHz), a Bruker AV 400 (400 MHz) and Varian Unity plus (600 MHz). Chemical shifts δ in ppm are referenced to the solvent residual peak (CDCl 3 : 1 H, δ = 7.26; 13 C, δ = 77.0; CD 3 OD: 1 H, δ = 4.87; 13 C, δ = 49.0; DMSO-d 6 : 1 H, δ = 2.50; 13 C, δ = 39.5) as an internal standard. Peak multiplicities are given as follows: s, singlet; d, doublet; t, triplet; q, quartett; m, multiplet; br, broad. HRMS ESI (m/z) spectra were recorded on a Bruker MicroTof, an Orbitrap LTQ XL (Nanospray) of Thermo Scientific and MALDI-MS was performed using an Autoflex speed TOF-MS of Bruker Daltonics. Melting points (MP) were determined on a Stuart SMP10 and are uncorrected. IR-spectra were recorded on a Digilab Varian 3100 FT-IR Excalibur Series. IR signals are described as w (weak), m (middle), s (strong), br (broad) in cm 1. Thin layer chromatography (TLC) was carried out on Merck silica gel 60 F254 plates; detection with UV light or by dipping into a solution of KMnO 4 (1.5 g) and NaHCO 3 (5.0 g) in H 2 O (0.40 L) followed by heating. FC was carried out on Merck silica gel 60 (40-63 µm) with an argon excess pressure of about 0.5 bar. 9
Synthesis 4-((Trimethylsilyl)ethynyl)benzonitrile (4) Under an atmosphere of argon 4-iodobenzonitrile (440 mg, 1.92 mmol, 1.00 eq), CuI (29 mg, 0.15 mmol, 8.0 mol%), PdCl 2 (PPh 3 ) 2 (54 mg, 80 µmol, 4.0 mol%) and ethynyltrimethylsilane (189 mg, 1.92 mmol, 1.00 eq) were dissolved in THF (20 ml) and NEt 3 (9.6 ml, 69 mmol, 36 eq) was added. The resulting mixture was stirred at room temperature for 15 h. Water (30 ml) was added and the phases were separated. The aqueous phase was extracted with CH 2 Cl 2 (3 20 ml) and the combined organic phases were washed with NH 4 Cl (aq. sat., 50 ml), HCl (aq. 1M, 50 ml), NaHCO 3 (aq. sat., 50 ml) and NaCl (aq. sat., 50 ml) in turn. It was dried over MgSO 4 and the solvent was evaporated under reduced pressure. The crude material was purified by flash chromatography (pentane/mtbe; 100:1) and 4 was obtained as a colorless solid (256 mg, 1.28 mmol, 67%). 1 H-NMR (300 MHz, CDCl 3 ): δ = 7.62-7.50 (m, 4H, Aryl-H); 0.26 (s, 9H, Si(CH 3 ) 3 ) ppm. The analytical data is in accordance with data reported in literature. 1 4-Ethynylbenzoic acid (5) Alkyne 4 (250 mg, 1.25 mmol, 1.00 eq) was dissolved in MeOH (5 ml) and a solution of Ba(OH) 2 8H 2 O (1.26 g, 4.00 mmol, 3.20 eq) and NaOH (55 mg, 1.4 mmol, 1.1 eq) in water (20 ml) was added. The reaction mixture was refluxed for 18 h and allowed to cool to room temperature afterwards. The mixture was extracted with CH 2 Cl 2 (20 ml) and the aqueous phase was acidified with (aq. 1M, 20 ml; a ph = 4 was adjusted). The resulting aqueous layer was extracted with CH 2 Cl 2 (3 50 ml). The combined organic phases of the second extraction were dried over MgSO 4 and 10
the solvent was removed in vacuo. The crude material was purified by flash chromatography FC (MTBE/pentane; 1:1) and 5 was isolated as a brown solid (151 mg, 1.03 mmol, 83%). 1 H-NMR (300 MHz, CD 3 OD): δ = 8.03 (d, J = 8.6 Hz, 2H, Aryl-H); 7.59 (d, J = 8.4 Hz, 2H, Aryl-H); 3.74 (s, 1H, Alkin-H) ppm. The analytical data is in accordance with data reported in literature. 2 N-(4-aminophenyl)-4-ethynylbenzamide (6) Benzoic acid 5 (149 mg, 1.02 mmol, 1.00 eq), benzene-1,4- diamin (553 mg, 5.11 mmol, 5.01 eq), N-methylmorpholine (125 µl, 1.13 mmol, 1.11 eq), HOBT HCl (152 mg, 1.12 mmol, 1.10 eq) and EDCI HCl (216 mg, 1.13 mmol, 1.11 eq) were dissolved in CH 2 Cl 2 (20 ml). The resulting solution was stirred at room temperature for 13 h. The reaction was stopped by the addition of water. The phases were separated and the aqueous phase was extracted with CH 2 Cl 2 (3 30 ml). The combined organic phases were dried over MgSO 4 and the solvent was removed under reduced pressure. The crude material was purified by flash chromatography (pentane/etoac; 1:1 1:2) and 6 was obtained as a brown solid (135 mg, 0.571 mmol, 56%). Mp.: 177. IR (neat): 3378w, 3324m, 3286w, 3129m,br, 3041w, 1643s, 1606m, 1561w, 1516s, 1500s, 1422s, 1317m, 1288m, 1248m, 1182m, 1133w, 1106w, 1092w, 1016m, 977w, 959w, 877m, 857s, 836m, 791m, 763m, 702m, 652m, 635m, 624m, 610w cm 1. 1 H-NMR (400 MHz, CD 3 OD): δ = 7.86 (d, J = 8.5 Hz, 2H, Aryl-H); 7.56 (d, J = 8.5 Hz, 2H, Aryl-H); 7.36 (d, J = 8.8 Hz, 2H, Aryl-H); 6.72 (d, J = 8.8 Hz, 2H, Aryl-H); 3.67 (s, 1H, Alkin-H) ppm. 13 C-NMR (100 MHz, CD 3 OD): δ = 167.6 (C), 146.2 (C), 136.4 (C), 133.1 (CH), 130.3 (C), 128.6 (CH), 127.0 (C), 124.1 (CH), 116.6 (CH), 83.6 (C), 81.1 (CH) ppm. MS (ESI): m/z: 237 [M+H] +, 259 [M+ Na] +. HRMS (ESI): m/z calculated for [M+H] + : 237.1022; found: 237.1030. 11
N-(4-azidophenyl)-4-ethynylbenzamide (1) Alkyne 6 (135 mg, 0.571 mmol, 1.00 eq) was dissolved in dry CH 3 CN (7 ml) and at 0 tert-butylnitrite (206 µl, 1.72 mmol, 3.01 eq) and azidotrimethylsilane (226 µl, 1.72 mmol, 3.01 eq.) were added in turn. The reaction mixture was stirred at RT for 3 h and subsequently the solvent was removed under reduced pressure. The crude product was purified without further work up by flash chromatography (pentane/et 2 O; 5:1 1:2) and 1 was obtained as a yellow-brown solid (125 mg, 477 µmol, 84%). Mp.: 177. IR (neat): 3357w, 3297w, 3264m, 2922w, 2851w, 2481w, 2407w, 2263w, 2251w, 2108s, 1642s, 1607m, 1597m, 1583m, 1559w, 1526m, 1506s, 1441m, 1388m, 1324w, 1303w, 1281m, 1181w, 1141w, 1126m, 1109m, 1016w, 986m, 895w, 883w, 862m, 831s, 795w, 761s, 734w, 708m, 650m, 633m cm 1. 1 H-NMR (300 MHz, CDCl 3 ): δ = 7.70 (d, J = 8.4 Hz, 2H, Aryl-H); 7.52 (d, J = 8.8 Hz, 2H, Aryl-H); 7.40 (d, J = 8.4 Hz, 2H, Aryl-H); 6.84 (d, J = 8.9 Hz, 2H, Aryl-H); 3.17 (s, 1H, Alkin-H) ppm. 13 C-NMR (75 MHz, CDCl 3 ): δ = 166.1 (C), 135.9 (C), 135.2 (C), 134.6 (C), 132.0 (CH), 127.3 (CH), 125.6 (C), 122.3 (CH), 119.1 (CH), 82.5 (C), 79.6 (CH) ppm. MS (ESI): m/z: 285 [M+Na] +, 547 [2M+ Na] +. HRMS (ESI): m/z calculated for [M+Na] + : 285.0747; found: 285.0740. N-(4-azidophenyl)-4-[(trimethylsilyl)ethynyl]benzamide (7) Under an atmosphere of argon, 4-[(trimethylsilyl)ethynyl]benzoic TMS O HN N 3 acid (327 mg, 1.50 mmol, 1.00 eq) and 4-azidoaniline hydrochloride (512 mg, 3.00 mmol, 2.00 eq) were dissolved in THF (100 ml). Then N-methylmorpholine (0.49 ml, 0.45 g, 4.5 mmol, 3.0 eq) and 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (498 mg, 1.80 mmol, 1.20 eq) were added and the resulting mixture was stirred for 18 h at room tempera- 12
ture. The solvent was removed under reduced pressure and the crude product was purified without further work up by flash chromatography (pentane/mtbe; 1:1). Azide 7 was isolated as a red-brown solid (308 mg, 0.921 mmol, 61%). Mp.: 185. IR (neat): 3356w, 2959w, 2900w, 2413w, 2266w, 2162w, 2106s, 1650s, 1600m, 1506s, 1411m, 1321w, 1285m, 1248s, 1220m, 1184w, 1131w, 1110w, 1017w, 830s, 786m, 761m, 703w, 674m, 647m, 628m cm 1. 1 H-NMR (400 MHz, DMSO-d 6 ): δ = 10.40 (s, 1H, Amide-H), 7.96 (d, J = 8.5 Hz, 2H, Aryl-H), 7.83 (d, J = 8.9 Hz, 2H, Aryl-H), 7.61 (d, J = 8.5 Hz, 2H, Aryl-H), 7.12 (d, J = 8.9 Hz, 2H, Aryl-H), 0.25 (s, 9H, Si(CH 3 ) 3 ) ppm. 13 C-NMR (100 MHz, DMSO-d 6 ): δ = 164.5 (C), 136.3 (C), 134.6 (C), 134.4 (C), 131.6 (CH), 128.0 (CH) 125.2 (C) 121.9 (CH), 119.3 (CH), 104.4 (C), 96.8 (C), 0.2 (CH) ppm. HRMS (ESI): m/z calculated for [M+Na] + : 357.1142; found: 357.1143. N-(4-aminophenyl)-4-(1-(4-(4-((trimethylsilyl)ethynyl)benzamido)phenyl)-1H- 1,2,3-triazol-4-yl)benzamide (8) Under an atmosphere of argon, azide 7 (101 TMS O HN N N N mg, 0.302 mmol, 1.00 eq) and alkyne 6 (72 mg, 0.30 mmol, 1.0 eq) were dissolved in O H N NH 2 MeCN (25 ml). Copper(I) iodide (7.0 mg, 37 µmol, 12 mol%) and ( i Pr) 2 NEt (0.1 ml) were added and the solution was stirred for 16 h at room temperature. The resulting slurry was filtered and the solid was washed with MeCN (2 10 ml), which yielded without further purification amine 8 as a brown solid (102 mg, 0.179 mmol, 59%). Mp.: > 300. IR (neat): 3370w, 3127w, 3112w, 2957w, 2900w, 2155w, 2114w, 1664s, 1647s, 1607m, 1532s, 1517s, 1437m, 1427m, 1416m, 1326m, 1286w, 1244m, 1190w, 1122w, 13
1103w, 1044m, 1018w, 996m, 897w, 856m, 836s, 824s, 761m, 710w, 696w, 641m, 626m, 540m, 510m cm 1. 1 H-NMR (400 MHz, DMSO-d 6 ): δ = 10.62 (s, 1H, Amide-H), 9.94 (s, 1H, Amide-H), 9.39 (s, 1H, Triazole-H), 8.10-7.99 (m, 8H, Aryl-H), 7.96 (d, J = 9.0 Hz, 2H, Aryl-H), 7.65 (d, J = 8.3 Hz, 2H, Aryl-H), 7.40 (d, J = 8.6 Hz, 2H, Aryl-H), 6.55 (d, J = 8.6 Hz, 2H, Aryl-H), 4.94 (br s, 2H, Amin-H), 0.26 (s, 9H, Si(CH 3 ) 3 ) ppm. MS (MALDI): m/z: 571.22 [M+H] +, 593.21 [M+Na] +. HRMS (ESI): m/z calculated for [M+H] + : 571.22723; found: 571.22736. N-(4-azidophenyl)-4-(1-(4-(4-((trimethylsilyl)ethynyl)benzamido)phenyl)-1H- 1,2,3-triazol-4-yl)benzamide (9) Under an atmosphere of argon, amine 8 (34 TMS O HN N N N mg, 60 µmol, 1.0 eq) was dissolved in DMSO H N (25 ml). Isopentyl nitrite (120 µl, 105 mg, O N 3 900 µmol, 15.0 eq) was added drop wise and the mixture was stirred at room temperature for 30 min. Azidotrimethylsilane (120 µl, 106 mg, 920 µmol, 15.0 eq) was added, which led to a gentle gas development. After 6 h of stirring isopentyl nitrite (120 µl, 104 mg, 900 µmol, 15.0 eq) and azidotrimethylsilane (120 µl, 104 mg, 900 µmol, 15.0 eq) were added once more and the mixture was keep up stirring for another 16 h at room temperature. The solvent was removed at 65 under reduced pressure ( 8 10 2 mbar). Without further purification azide 9 (35 mg, 59 µmol, 98%) was obtained as a light-brown solid. IR (neat): 3370w, 3127w, 3111w, 2958w, 2413w, 2156w, 2110m, 1943w, 1914w, 1663s, 1606m, 1526s, 1509s, 1438m, 1413m, 1325m, 1288m, 1245m, 1188w, 1105w, 1044m, 1018m, 995m, 952w, 896w, 857m, 836s, 825s, 761m, 711m, 696m, 686m, 642m, 626m, 540m, 507m cm 1. 1 H-NMR (600 MHz, DMSO-d 6 ): δ = 10.60 (s, 1H, Amide-H), 10.38 (s, 1H, Amide- H), 9.41 (s, 1H, Triazole-H), 8.10 (s, 4H, Aryl-H), 8.05 (d, J = 9.1 Hz, 2H, Aryl-H), 8.01 14
(d, J = 8.5 Hz, 2H, Aryl-H), 7.96 (d, J = 9.1 Hz, 2H, Aryl-H), 7.86 (d, J = 9.0 Hz, 2H, Aryl-H), 7.65 (d, J = 8.5 Hz, 2H, Aryl-H), 7.15 (d, J = 9.0 Hz, 2H, Aryl-H), 0.27 (s, 9H, Si(CH 3 ) 3 ) ppm. N-(4-azidophenyl)-4-(1-(4-(4-ethynylbenzamido)phenyl)-1H-1,2,3-triazol-4- yl)benzamide (2) N-(4-aminophenyl)-4-(1-(4-(4-ethynylbenzamido)phenyl)-1H-1,2,3-triazol-4- yl)benzamide (10) Under an atmosphere of argon, azide 9 (22 mg, 37 µmol, 1.0 eq) was widely dissolved in a solvent mixture consisting of DMSO (15 ml) and MeOH (2 ml). Caesium fluoride (10 mg, 66 µmol, 1.8 eq) was added and the resulting mixture was stirred for 1.5 h at room temperature. The solvent was removed at 45 under reduced pressure ( 6 10 2 mbar). The dark red solid was washed with THF/MeOH (7 ml/2 ml) and centrifuged (5300 rpm, 10 min). This step was repeated and the solid was dried under reduced pressure. A 1:1 mixture of the desired azide 2 and a side-product amine 10 was obtained as a dark red-brown solid (overall 19 mg; azide 2: 10 mg, 18.5 µmol, 50%; amine 10: 9 mg, 18.5 µmol, 50%). IR (neat): 3360w, 3293w, 3127w, 2112m, 1982w, 1656m, 1605m, 1515s, 1437w, 1409m, 1320m, 1288m, 1241m, 1181w, 1105w, 1042m, 1018w, 994w, 896w, 856m, 826s, 761m, 710w, 694w, 642m, 623m cm 1. 15
Azide 2: 1 H-NMR (600 MHz, DMSO-d 6 ): δ = 10.61 (s, 1H, Amide-H), 10.39 (s, 1H, Amide-H), 941 (s, 1H, Triazole-H), 8.11 (s, 4H, Aryl-H), 8.06-8.03 (m, 2H, Aryl-H), 8.01 (d, J = 8.4 Hz, 2H, Aryl-H) 7.98-7.95 (m, 2H, Aryl-H), 7.86 (d, J = 8.9 Hz, 2H, Aryl-H), 7.67 (d, J = 8.3 Hz, 2H, Aryl-H), 7.15 (d, J = 8.9 Hz, 2H, Aryl-H), 4.43 (s, 1H, Alkyne-H) ppm. Amine 10: 1 H-NMR (600 MHz, DMSO-d 6 ): δ = 10.61 (s, 1H, Amide-H), 9.93 (s, 1H, Amide-H), 939 (s, 1H, Triazole-H), 8.07 (s, 4H, Aryl-H), 8.06-8.03 (m, 2H, Aryl-H), 8.01 (d, J = 8.4 Hz, 2H, Aryl-H) 7.98-7.95 (m, 2H, Aryl-H), 7.67 (d, J = 8.3 Hz, 2H, Aryl-H), 7.40 (d, J = 8.7 Hz, 2H, Aryl-H), 6.56 (d, J = 8.7 Hz, 2H, Aryl-H), 4.93 (br s, 2H, Amine-H), 4.43 (s, 1H, Alkyne-H) ppm. HRMS (ESI): m/z calculated for [M+H] + : 499.18770; found: 499.18756. References (1) Zehner, R.; Parsons, B.; Hsung, R.; Sita, L. Langmuir 1999, 15, 1121 1127. (2) Feng, K.; Peng, M.-L.; Wang, D.-H.; Zhang, L.-P.; Tung, C.-H.; Wu, L.-Z. Dalton Trans. 2009, 9794 9799. 16
NMR Spectra 17
18
19
IR Spectra corresponding to the ex-situ synthesis of AEB dimers 20
21
Dimension Analysis for the AEB compounds Figure S8: A good quantitative agreement was found between the experimental and the center-to-center theoretical distances for the three AEB species observed. 22
Schematic of the out-of-plane rotation of the 1,5 regioisomer Figure S9: Representation of the steric hindrance effect that affects the 1,5 regioisomer. 23
Mass spectrometry and STM study of the sublimation of ex-situ AEB dimers Figure S10: Mass Spectrometry data for the ex-situ AEB dimers sublimation. Only the mass of the THF solvent used during the synthesis is detected around 85. 24
Figure S11: Regions corresponding to the mass signals detected. THF mass visible at 85. 25
Figure S12: STM images of the deposition on ex-situ AEB dimers at 85 of a Au(111) surface kept at room temperature. Two phases of small absorbates ascribed to THF are observed. Images recorded at T 78K. (A) 300 300 nm 2 ; V = 650 mv; I = 10 pa (B) 100 100 nm 2 ; V = 650 mv; I = 5 pa (C) 35 35 nm 2 ; V = 650 mv; I = 5 pa (D-E) High resolution images of both phases. 12 12 nm 2 ; V = 650 mv; I = 5 pa. Figure S13: Defects could be found in both self-assembled arrangements. Images recorded at T 78K. (A) 8 8 nm 2 ; V = 650 mv; I = 5 pa (B) 12 12 nm 2 ; V = 650 mv; I = 5 pa. 26
Controlled STM tip manipulations were conducted to demonstrate the weak interaction between the constituents of both phases. Figure S14: Successful STM tip manipulations resulted in the dissociation of the selfassembled "honeycomb" phase. White arrows represent the manipulation vectors. Images recorded at T 78K and manipulations performed with V = 50mV and 100pA I 3.5 na. (A-C) 20 20 nm 2. (D-F) 25 25 nm 2. Figure S15: Successful STM tip manipulations also resulted in the dissociation of the selfassembled "linear" phase. White arrows represent the manipulation vectors. Images recorded at T 78K and manipulations performed with V = 50mV and 100pA I 3.5 na. (A-C) 13 13 nm 2. (D-F) 20 20 nm 2. 27