Direct observation of organic single-molecules in their pristine state using transmission electron microscopy (TEM) is a challenging task because the electron irradiation during high-resolution imaging can modify the structure under investigation. However, recent advances in low-voltage aberration-corrected high-resolution transmission electron microscopy (AC-HRTEM) allow atomic resolution even at accelerating voltages as low as 20kV  allowing atomic-resolution imaging even for light-element materials with knock-on damage thresholds below 80kV . However knock-on damage is not the only damaging process. A reduction of the electron beam-induced charging and radiolysis effects can be obtained by dedicated sample preparation such as embedding the sensitive material into a chemically inert, conducting, and one-atom thick container such as a carbon nanotube  or in between two layers of graphene . By combining dedicated low-voltage TEM instrumentation with sophisticated sample preparation, electron irradiation-induced damage mechanisms slow down or can even be completely turned off which even allows imaging of molecules containing hydrogen-carbon bonds .
In this work we apply low voltage AC-HRTEM not only to image but also to trigger a previously unknown chemical reaction – the polycondensation of perchlorocoronene (PCC), which leads to the formation of graphene nanoribbons, an exciting polymeric structure with significant potential for electronic applications. The multi-step mechanism of this reaction was determined by AC-HRTEM and is both complex and difficult to postulate a priori or from macroscopic observations. However our time-series imaging at the single-molecule level reveals the nature of key intermediates and follows the pathways of their transformations, thus providing the most direct experience of chemical reactions and demonstrating the physical reality of the elusive steric factor in real space. Figure 1a shows a time series of PCC molecules stacked in single walled carbon nanotube and their electron beam induced changes over time as a product of the accumulated electron dose. A close examination of the experimental images (Figure 1b) indicates that intermolecular reactions are possible only when a PCC molecule can change its orientations with respect to the neighbouring molecules: two non-parallel molecules are able to join together to form angular species which gradually transform into planar species approximately twice the length of the original PCC molecules.
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[3 ]Meyer JC, Eder F, Kurasch S, Skakalova V, Kotakoski J, Park HJ, Roth S, Chuvilin A, Eyhusen S, Benner G, Krasheninnikov AV, Kaiser U, PRL 108 (2012), 196102
 Algara-Siller G, Kurasch D, Sedighi M, Lehtinen O, Kaiser U, Appl. Phys. Lett. 103 (2013) 203107
 Chamberlain TW, Biskupek J, Skowron ST, Bayliss PA, Bichoutskaia E, Kaiser U, Khlobystov AN, Small 11 (2015) 622-629
We acknowledge the financial support of the German Research Foundation (DFG) and the Ministry of Research, Science and the Arts of Baden-Württemberg within the SALVE project.
To cite this abstract:Johannes Biskupek, Thomas Chamberlain, Stephen Skowron, Elena Besley, Andrei Khlobystov, Ute Kaiser; Imaging of Electron Beam Triggered Phase Transformations and Chemical Reactions of Organic Molecules by Aberration-Corrected Low-Voltage Transmission Electron Microscopy. The 16th European Microscopy Congress, Lyon, France. https://emc-proceedings.com/abstract/imaging-of-electron-beam-triggered-phase-transformations-and-chemical-reactions-of-organic-molecules-by-aberration-corrected-low-voltage-transmission-electron-microscopy/. Accessed: October 29, 2020
EMC Abstracts - https://emc-proceedings.com/abstract/imaging-of-electron-beam-triggered-phase-transformations-and-chemical-reactions-of-organic-molecules-by-aberration-corrected-low-voltage-transmission-electron-microscopy/