On-surface generation and imaging of arynes by atomic force microscopy

DOI: 0.038/NCHEM.2300 On-surface generation and imaging of arynes by atomic force microscopy Niko Pavliček, Bruno Schuler, Sara Collazos, 2 Nikolaj Moll, Dolores Pérez, 2 Enrique Guitián, 2 Gerhard Meyer, Diego Peña, 2 and Leo Gross. IBM Research Zurich, 8803 Rüschlikon, Switzerland 2. CIQUS, Universidad de Santiago de Compostela, 5782 Santiago de Compostela, Spain 2st May 205 This supplemental material presents complementary scanning tunnelling and atomic force microscopy experiments of 0,-diiodonaphtho[,2,3,4-ghi]perylene (DINP) and related 0-iodonaphtho- [,2,3,4-ghi]perylene (INP) molecules. Furthermore, the experimental details of the synthesis of all relevant compounds and precursors, and accompanying UV/visible and fluorescence spectra, as well as H and 3 C NMR spectra are provided. Finally, the details of the DFT calculations and the simulated AFM images are presented. Contents Additional scanning tunnelling and atomic force microscopy results 2 General methods of synthesis 3 3 Experimental details of synthesis 3 3. Synthesis of bistriflate 9... 3 3.2 Synthesis of triflates 0 and... 3 3.3 Synthesis of triflate 2... 3 3.4 Synthesis of naphtho[,2,3,4-ghi]perylene (NP, 4)... 4 3.5 Synthesis of 0-iodonaphtho[,2,3,4- ghi]perylene (INP, 5)... 4 3.6 Synthesis of 0,-diiodonaphtho- [,2,3,4-ghi]perylene (DINP, )... 4 4 UV/Vis and fluorescence spectra 6 5 H and 3 C NMR spectra 7 6 DFT calculations and simulated AFM images dissociation process. The DFT-calculated isosurface plots of the LUMO of DINP are given in Figs. e,f for comparison to the voltage-dependent images. Figure g presents height profiles of both molecules extracted from the data shown in Fig. d which are essentially identical. Figure 2 presents an additional sequence of aryne generation. This sequence demonstrates that molecules can be displaced during dissociation events by up to 20 Å, and that I atoms are not always found symmetrically around the aryne molecule. Complementary STM and AFM experiments on 0- iodonaphtho[,2,3,4-ghi]perylene (INP, 5) molecules are shown in Fig. 3. The observation that repulsive contributions decrease from top to bottom in the AFM image (Fig. 3d) suggests a tilted adsorption geometry with respect to the short axis of the molecules. That is, the halogenated part is further away from the underlying NaCl surface than the hydrogenated part. Finally, Fig. 4 shows imaging of NP molecules on Cu(). Additional scanning tunnelling and atomic force microscopy results Further STM images on NaCl(2ML)/Cu() and DFT-calculated orbital densities of DINP molecules are presented in Fig.. Note that the image shown in Fig. d was recorded after a dissociation-and-healing process discussed in the main text, while Figs. a-c were taken before. The molecule at the bottom left was dissociated and healed, which is the reason for it appearing displaced in Fig. d. The molecule was displaced towards the bottom of the image during the NATURE CHEMISTRY www.nature.com/naturechemistry

a 30 Å I tip - z (Å).8 c [00] - z (Å) 3 [00] I tip b - z (Å) 2.2 d I tip -.3 z (Å) 4.2 I tip 30 Å 30 Å 30 Å e f g 4 z (Å) 0 0 distance (Å) Supplementary Figure : Voltage-dependent STM imaging of two DINP molecules on NaCl(2ML)/Cu(). a, Imaging at low voltages (0.2 V, in-gap) corresponds to co-tunnelling in the double-barrier tunnelling junction. b-d, LUMO imaging at different voltages (.6 V,.7 V, and.8 V, respectively). While the lowest voltage corresponds to the tail of the Gaussian-broadened peak, electrons at higher voltages resonantly tunnel into the LUMO. The tunnelling current was I =2pA. DINP molecules adsorb along nonpolar directions on NaCl. Blue depressions are co-adsorbed CO molecules. e,f, DFT-calculated isosurface plots of the LUMO of DINP for high and small values of electron density, respectively. The LUMO is delocalized over the aromatic core with small contributions at the iodine atoms. A model of the molecular structure is overlaid as a guide to the eye. g, Height profiles along the long axes of the dissociated-and-healed (violet) and unchanged (green) molecule, respectively, have been extracted from and are indicated in panel d. 30 a I tip CO 5 3 20 Å b c CO tip d -0.8I tip z (Å).2 CO tip Supplementary Figure 3: STM and AFM imaging of INP molecules on NaCl(2ML)/Cu(). a, STM overview image of an INP (5) and an aryne molecule (3) acquired with an I tip (I =2pA, V = 0.2 V). b, Structure of INP (5). c, STM image of a single INP molecule acquired with a CO tip (I =2pA, V = 0.2 V). d, Corresponding constant-height AFM image ( z =.3 Å). a 4 I H 5 Å 5 Å 5 0 z (Å) 2-8 df (Hz) -0.5 a b 3 & Iodines 5Å.5 CO tip 5Å Cu tip c 5 Å 3 & Iodine Cu tip d 3 z (Å) -0.2 z (Å).4 b 4-0.5 I tip 5Å I tip 5Å Supplementary Figure 2: Additional aryne generation sequence on NaCl(2ML)/Cu(). a, Initial STM image of an DINP molecule. Circle indicates tip position for dehalogenation. b, Image of same frame after iodine dissociation. Inset shows Laplace-filtered image to facilitate identification of individual I atoms. c, One of the I atoms has been picked up. d, Both I atoms have been picked up, and frame has been centered around molecule. (a-c: I =2pA, V = 0.2 V, d: I =5pA, V = 0.06 V.) 5Å -8 df (Hz) -3.4 Supplementary Figure 4: STM and AFM imaging of an NP molecule on Cu(). a, STM image of a single NP molecule adsorbed on Cu() (I =2pA, V = 0.2 V). b, Corresponding constant-height AFM image ( z = 2. Å). NATURE CHEMISTRY www.nature.com/naturechemistry 2

2 General methods of synthesis All reactions were carried out under argon using ovendried glassware. TLC was performed on Merck silica gel 60 F 254 ; chromatograms were visualized with UV light (254 and 360 nm). Flash column chromatography was performed on Merck silica gel 60 (ASTM 230 400 mesh). H and 3 C NMR spectra were recorded at 500 and 25 MHz (Bruker DPX-500 instrument), or 300 and 75 MHz (Varian Mercury-300 instrument), respectively. Low-resolution electron impact mass spectra were determined at 70 ev on a HP-5988A instrument. High-resolution mass spectra (HRMS) were obtained on a Micromass Autospec spectrometer. UV/Vis spectra were obtained on a Varian Cary 00 Bio or a Jasco V-530 spectrophotometers. Fluorescence spectra were obtained on a Fluoromax-2 spectrometer. Melting points were determined on a Büchi melting point B-540. n-buli was used in solution in hexane (2.5 M). Commercial reagents and anhydrous solvents were purchased from ABCR GmbH or Aldrich Chemical Co., and were used without further purification. Benzyne precursor 6 was prepared following a published procedure 2. Results of mass spectrometry of all compounds are summarized in Tab.. 3 Experimental details of synthesis 3. Synthesis of bistriflate 9 This bisbenzyne precursor was prepared by a modification of a published procedure 3. (8.3 ml, 20.7 mmol) and Tf 2 O(3.5 ml, 20.7 mmol). Then, a saturated aqueous solution of NaHCO 3 was added, and the resulting mixture was extracted with Et 2 O. The combined organic layers were dried over Na 2 SO 4, filtered and concentrated under reduced pressure. The residue was purified by column chromatography (SiO 2 ; hexane) to obtain the bistriflate 9 (5.7 g, 59%) as a white solid. NMR data H NMR (298 K, 300 MHz, CDCl 3 ): δ 7.45 (s, 2H), 0.38 (s, 8H) ppm. 3.2 Synthesis of triflates 0 and A mixture of bistriflate 9 (500 mg, 0.965 mmol), KI (92 mg,.57 mmol) and CsF ( 76 mg,.58 mmol) in THF/CH 3 CN (:, 9.6 ml) was stirred at room temperature for 6 h. After evaporation of the solvents under reduced pressure, the residue was purified by column chromatography (SiO 2 ; hexane) to obtain a mixture of triflates 0 and (74.8 mg, 43%, :3.5) as a colorless oil. NMR data for compound 0 H NMR (298 K, 300 MHz, CDCl 3 ): δ 7.68 (dd, J = 7.7,.4 Hz, H), 7.66 (d, J =.3 Hz, H), 7.24 (d, J = 7.7 Hz, H), 0.35 (s, 9H) ppm. 3 C NMR (298 K, 75 MHz, CDCl 3 ): δ 54.53 (C), 37.4 (CH), 36.83 (CH), 32.45 (C), 28.7 (CH), 8.58 (c, J = 320. Hz, CF 3 ). 95.42 (C), -0.86 (CH 3 ) ppm. NMR data for compound A mixture of 2,5-dibromohydroquinone (7, 5.0 g, 8.8 mmol) and hexamethyldisilazane (HMDS, 8.6 ml, 39.5 mmol) in THF (8.5 ml) was refluxed for 2h. The solvent was evaporated under reduced pressure and the residue was subjected to vacuum to remove unreacted HMDS. The crude compound 8 was dissolved in THF (34 ml), the solution cooled to 00 C, and n-buli (8.3 ml, 20.7 mmol) was added dropwise. Stirring was kept up for 20 min while the temperature reached 80 C. The mixture was again cooled to 00 C, Tf 2 O(3.5 ml, 20.7 mmol) was added dropwise, and stirring was again kept up for 20 min while the temperature returned to 80 C. This procedure was repeated with the addition of extra n-buli H NMR (298 K, 300 MHz, CDCl 3 ): δ 7.79 (d, J = 2.3 Hz, H), 7.74 (dd, J = 8.6, 2.3 Hz, H), 7.09 (d, J = 8.7 Hz, H), 0.36 (d, J = 0.5 Hz, 9H) ppm. 3 C NMR (298 K, 75 MHz, CDCl 3 ): δ 54.82 (C), 45.02 (CH), 40.7 (CH), 36.26 (C), 2.68 (CH), 8.58 (c, J = 320. Hz, CF 3 ), 93.59 (C), -0.86 (CH 3 ) ppm. 3.3 Synthesis of triflate 2 A mixture of bistriflate 9 (300 mg, 0.579 mmol), I 2 (294 mg,.58 mmol) and CsF (76 mg,.58 mmol) in THF/CH 3 CN (:2, 6 ml) was stirred at 60 C for NATURE CHEMISTRY www.nature.com/naturechemistry 3

Supplementary Table : Mass spectrometry data for investigated compounds. Compound Molecular formula MS (EI) HRMS (EI) m/z (%) calculated found 0, C 0 H 2 F 3 IO 3 SSi 424 (M +, 2), 423.9273 423.9273 409 (00) 2 C 0 H F 3 I 2 O 3 SSi 550 (M +, 28), 549.8240 549.8260 535 (00) 4 C 26 H 4 326 (M +, 00) 326.096 362.09 5 C 26 H 3 I 452 (M +, 00) 452.0062 452.0069 C 26 H 2 I 2 578 (M +, 00) 577.9028 577.905 a Electron ionization. 6 h. After evaporation of the solvents under reduced pressure, the residue was purified by column chromatography (SiO 2 ; hexane) to obtain triflate 2 (96 mg, 30%) as a white solid. NMR data H NMR (298 K, 500 MHz, CDCl 3 ): δ 7.93 (s, H), 7.76 (s, H), 0.35 (s, 9H) ppm. 3 C NMR (298 K, 25 MHz, CDCl 3 ): δ 53.74 (C), 45.85 (CH), 35.49 (C), 30.5 (CH), 8.5 (c, J = 320.2 Hz, CF 3 ), 09.50 (C), 08. (C), -0.98 (CH 3 ) ppm. 3.4 Synthesis of naphtho[,2,3,4-ghi ]perylene (NP, 4) This compound was prepared by a modification of a published procedure 4. 29.95 (2CH), 29.75 (2CH), 29.55 (2C), 29.36 (2C), 26.8 (2CH), 26.49 (2C), 25.28 (2CH), 23.96 (2CH) ppm. 3.5 Synthesis of 0-iodonaphtho[,2,3,4-ghi ]perylene (INP, 5) A mixture of perylene (3, 50 mg, 0.98 mmol), triflates 0 and (68 mg, 0.396 mmol) and CsF (80 mg,.88 mmol) in THF/CH 3 CN (:, 8 ml) was stirred at 60 C for 6 h. The resulting suspension was filtered to give a residue, which was subsequently washed with H 2 O (2 x 2 ml), CH 3 OH (2 x 2 ml) and Et 2 O (4 x 2 ml) to afford compound 5 (25 mg, 28%) as a yellow solid. Mp: 266 C. NMR data A mixture of perylene (3, 50 mg, 0.98 mmol), triflate 6 (44 µl, 0.594 mmol) and CsF (27 mg,.78 mmol) in THF/CH 3 CN (:, 9.6 ml) was stirred at 60 C for 6 h. The resulting suspension was filtered to give a residue, which was subsequently washed with H 2 O(2x2mL), CH 3 OH (2 x 2 ml) and Et 2 O(4x 2 ml) to afford compound 4 (50.7 mg, 78%) as a yellow solid. Mp: 270 C. H NMR (298 K, 300 MHz, CDCl 3 ): δ 9.38 (d, J =.8 Hz, H), 8.88 (d, J = 7.7 Hz, 3H), 8.82 (d, J = 9.7 Hz, H), 8.75 (d, J = 8.9 Hz, H), 8.2 8. (m, 5H), 7.95 (t, J = 7.8 Hz, 2H) ppm. 3.6 Synthesis of 0,-diiodonaphtho[,2,3,4-ghi ]perylene (DINP, ) NMR data H NMR (323 K, 300 MHz, CDCl 3 ): δ 9.0 (dd, J = 6.4, 3.4 Hz, 2H), 8.99 (d, J = 9. Hz, 2H), 8.89 (dd, J = 7.8,. Hz, 2H), 8.2 (d, J = 9. Hz, 2H), 8.6 (dd, J = 8.0,. Hz, 2H), 7.96 (d, J = 7.9 Hz, 2H), 7.94 7.90 (m, 2H) ppm. 3 C NMR (323 K, 75 MHz, CDCl 3 ): δ 35.60 (2C), 33.80 (2C), 3.52 (2C), 3.06 (2CH), 30.30 (2CH), A mixture of perylene (3, 37 mg, 0.46 mmol), triflate 2 (60 mg, 0.29 mmol) and CsF (33 mg, 0.876 mmol) in THF/CH 3 CN (:, 5.8 ml) was stirred at 60 C for 6 h. The resulting suspension was filtered NATURE CHEMISTRY www.nature.com/naturechemistry 4

to give a residue, which was subsequently washed with H 2 O(2x2 ml), CH 3 OH (2 x 2 ml), Et 2 O (2 x 2 ml) and CHCl 3 (30 x 0.5 ml) to afford compound (7. mg, 20%) as a yellow solid. Mp: 295 C (dec). NMR data H NMR (333 K, 300 MHz, CDCl 3 ): δ 9.53 (s, 2H), 8.90 (d, J = 7.8 Hz, 2H), 8.79 (d, J = 9.0 Hz, 2H), 8.20 (d, J = 9.2 Hz, 2H), 8.6 (d, J = 8. Hz, 2H), 7.97 (t, J = 7.8 Hz, 2H) ppm. NATURE CHEMISTRY www.nature.com/naturechemistry 5

4 UV/Vis and fluorescence spectra Supplementary Figure 5: Absorption (solid line) and emission (dashed line) spectra of compound 4 in CH 2Cl 2. Supplementary Figure 6: Absorption (solid line) and emission (dashed line) spectra of compound 5 in CH 2Cl 2. Supplementary Figure 7: Absorption (solid line) and emission (dashed line) spectra of compound in CH 2Cl 2. NATURE CHEMISTRY www.nature.com/naturechemistry 6

5 H and 3 C NMR spectra Supplementary Figure 8: H (top) and 3 C (bottom) NMR spectra of compounds 0 and. NATURE CHEMISTRY www.nature.com/naturechemistry 7

Supplementary Figure 9: H (top) and 3 C (bottom) NMR spectra of compound 2. NATURE CHEMISTRY www.nature.com/naturechemistry 8

Supplementary Figure 0: H (top) and 3 C (bottom) NMR spectra of compound 4. NATURE CHEMISTRY www.nature.com/naturechemistry 9

Supplementary Figure : H NMR spectra of compound 5. Supplementary Figure 2: H NMR spectra of compound. NATURE CHEMISTRY www.nature.com/naturechemistry 0

6 DFT calculations and simulated AFM images The geometry of free aryne and NP molecules were calculated with density functional theory (DFT) 5. A code with numerical atomic orbitals as basis functions 6 and the Perdew-Burke-Ernzerhof exchange-correlation functional (PBE) 7 was applied. We have validated the results of our calculations by comparing simulated AFM images with the experimental data shown in Fig. 4 of the main text. To this end we calculated the total energy of a molecule interacting with a small tip assembly. The tip has been modelled by a vertical Cu-dimer terminated with a single CO molecule 8. We used the Cu-dimer as the metallic part of the tip in our calculations, since it is spherical symmetric, and the small number of atoms reduces the computational costs. Here, the Cu-Cu distance has been fixed to 2.75 Å, while the other atoms were relaxed for the isolated tip, leading to a very small intrinsic spring constant of 0.03 N/m. The vertical attractive forces will however lead to an additional spring constant of approximately 0.26 N/m 9. To obtain the frequency shift we took the second derivative with respect to the z-direction. The three points in z-direction required to obtain the second derivative correspond to distances of 4.775 Å, 4.8 Å and 4.825 Å between the C atom of the tip and the molecular plane. The lateral spacing of the grid (in x- and y-direction) was 0.2 Å. First, we considered a fixed CO at the tip. All four tip atoms are confined along a line perpendicular to the sample surface. The frequency shift images of aryne and NP are shown in Figs. 3a and 3b, respectively. The image resembles the charge density very closely. The main difference between the molecules is that the outer ring of aryne appears curved in contrast to the one of NP. Next, the influence of the relaxation of the CO is examined. We calculated the frequency shift keeping the Cu-dimer tip fixed while relaxing the CO until the forces were smaller than 0.8 pn. The frequency shift images in Figs. 3c and 3d including relaxations of the CO show some distinct differences to the images using a fixed CO. Tilting of the CO enlarges the apparent sizes of the outer rings when comparing with the results with a fixed tip. In addition, the bonds appear sharper, but less pronounced in frequency shift differences. Finally, Fig. 3e shows the relative energy for aryne molecules (3) as a function of the outermost carboncarbon bond length. The optimized value is between the lengths of a double and a triple bond. Values for the single, double and triple bond have been obtained by DFT calculations of free ethane, ethene (ethylene), and ethyne (acetylene) molecules, respectively. non-relaxed relaxed a c 5 Å aryne, 3 NP, 4 b -4 Δf (Hz) 4 e 3 energy (ev) 2 triple bond double bond d single bond 0..2.3.4.5.6 C-C distance (Å) Supplementary Figure 3: Results of DFT calculations. a,b, Simulated AFM images of aryne and NP, respectively, with the CO molecule at the tip fixed. c,d, As above, but the CO molecule at the tip was allowed to relax. This results in image distortions due to the tilting of the molecule. The molecular structures are overlaid as a guide to the eye. e, Energy as a function of the outermost (leftmost in panels a- d) carbon-carbon distance. Dashed lines indicate values for single, double and triple bonds as calculated from free ethane, ethene, and ethyne molecules, respectively. NATURE CHEMISTRY www.nature.com/naturechemistry

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