All scanning tunneling microscopy (STM) experiments were performed at room temperature (20°C - 22°C) using a PicoLE (Keysight) instrument in constant current mode. STM tips were manually cut from a Pt/Ir wire (80% Pt / 20% Ir, diameter 0.25 mm) that was bought from Advent Research Materials. Prior to imaging, a saturated solution of pentacosadiynoic acid (PCDA) in 1-phenyloctane was dropcasted on the surface of freshly cleaved or covalently modified highly oriented pyrolytic graphite (CM-HOPG). PCDA (≥ 97%) and 1-phenyloctane (98%) were purchased from Sigma-Aldrich and used without further purification. ZYB grade HOPG was obtained from Advanced Ceramics Inc., Cleveland, OH, USA. All STM images were processed using the Scanning Probe Imaging Processor (SPIP) software (Image Metrology ApS). To correct for thermal drift, the STM images in Figure 2 of the main text are calibrated using recorded graphite images. Graphite was imaged at Vs = –0.001 V and It = 200 pA (Figure 2A), or at Vs = –0.001 V and It = 600 pA (Figure 2C). Nanoshaving of corrals in the CM-HOPG was performed using the Keysight PicoLITH 2.1 software. For polydiacetylene formation electrical pulses were applied to the STM tip with a magnitude of -3.8 V and a duration of 10 – 110 µs. For every pulse the STM tip was momentarily withdrawn from the surface by 1 nm. Imaging parameters for the STM images are indicated in the figure captions and denoted by Vs for sample bias and It for tunneling current.
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S2. Self-assembly of PCDA on HOPG open terraces
Figure S1. (a & b) STM topography images showing self-assembly of PCDA on open HOPG terraces. Domain sizes range from 100 nm2 up to 10,000 nm2. PCDA is dropcasted from a saturated 1-phenyloctane solution. Imaging parameters: (a) Vs = -0.7 V, It = 70 pA; (b) Vs = -0.8 V, It = 500 pA.
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S3. Polymerization of PCDA on HOPG open terraces
Figure S2. STM topography image demonstrating the domain boundary limitations of polydiacetylene growth. A pulse of -3.8 V was applied for 10 µs at the location indicated by the green arrow. Imaging parameters: Vs = -0.7 V, It = 70 pA.
Figure S3. (a, b, & c) Consecutive STM topography images showing the formation and desorption of polydiacetylene chains. The scan direction in which the images were acquired is displayed in the top right corner of each image. (a) A single voltage pulse of -3.8 V was applied for 10 µs at the location indicated by the green arrow, resulting in three divergent polydiacetylene chains. (b) During imaging the polymer to the left desorbed at the position marked by the red dashed line. Also the upper polymer (red circle) is desorbed upon imaging. (c) Only one polymer strand remains on the surface. Imaging parameters: (a-c) Vs = -0.8 V, It = 500 pA.
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Figure S4. STM topography images illustrating polymer cutting upon prolonged scanning. (a) PCDA self-assembly within a nanocorral on HOPG. (b) A polydiacetylene molecule created upon applying an electrical pulse (-3.8 V for 10 µs) at the position indicated by the green arrow. (c) The polydiacetylene molecule from (b) is cut in two at the location marked by the red arrow. Imaging parameters: (a-c) Vs = -0.8 V, It = 60 pA.
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S4. Covalent Modification of HOPG using Cyclic Voltammetry
Covalent modification of HOPG is carried out using cyclic voltammetry in aqueous solutions of 3,5-bis-tert-butylbenzenediazonium (3,5-TBD). 3,5-TBD is unstable and was therefore generated in situ by diazotization of the corresponding aniline precursor. Hereto, a 5 mL solution of 3,5-bis-tert-butylaniline (≥3 mM) in aqueous HCl (50 mM) is prepared, and 100 µL of aqueous NaNO2 (0.1 M) is added to initiate the diazotization reaction. The solution was gently shaken for 1.5 min in order for the reaction to proceed and then added to the electrochemical cell. CV was performed using an Autolab PGSTAT101 potentiostat (Metrohm_Autolab BV, The Netherlands) and a lab-built single-compartment three-electrode cell, with a working electrode area of 50.3 mm2, Pt wire counter, and Ag/AgCl/3.0 M NaCl reference electrode. Every CV experiment consisted of 3 voltage sweeps run from +0.6 V to -0.35 V, giving a typical current-voltage diagram as shown in Figure S5. Prior to each experiment, the HOPG working electrode was cleaved using Scotch tape in order to create a pristine surface. After covalent modification of the HOPG surface, the sample was rinsed with Milli-Q water to wash away potential physisorbed material from the surface. 3,5-Bis-tert-butylaniline (98%) and analytical grade hydrochloric acid were purchased from Sigma-Aldrich and used without further purification. High-purity water (Milli-Q, Millipore, 18.2 MΩ cm, TOC < 3 ppb) was used for preparation of the aqueous solution.
Figure S5. Cyclic voltammogram recorded in an aqueous solution of 2 mM 3,5-TBD with freshly cleaved HOPG as the working electrode. An irreversible reduction peak is observed at -0.23 V vs. Ag/AgCl which is assigned to the reduction of the diazonium.
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S5. Polymers inside circular corral
Figure S6. STM topography image showing polydiacetylene chains formed inside a circular nanocorral. The slow nanoshaving direction for formation of the corral was carefully chosen to run orthogonal a major symmetry axes of graphite (red arrow). After corral formation, multiple voltage pulses of -3.8 V were applied for 110 µs at the top of the circular corral and each polymer propagated to the opposite end. Imaging parameters: Vs = -0.8 V, It = 60 pA.
