Stop-Frame Filming and Discovery of Reactions at the Single-Molecule Level by Transmission Electron Microscopy

Abstract

We report an approach, named chemTEM, to follow chemical transformations at the single-molecule level with the electron beam of a transmission electron microscope (TEM) applied as both a tunable source of energy and a sub-angstrom imaging probe. Deposited on graphene, disk-shaped perchlorocoronene molecules are precluded from intermolecular interactions. This allows monomolecular transformations to be studied at the single-molecule level in real time and reveals chlorine elimination and reactive aryne formation as a key initial stage of multistep reactions initiated by the 80 keV e-beam. Under the same conditions, perchlorocoronene confined within a nanotube cavity, where the molecules are situated in very close proximity to each other, enables imaging of intermolecular reactions, starting with the Diels–Alder cycloaddition of a generated aryne, followed by rearrangement of the angular adduct to a planar polyaromatic structure and the formation of a perchlorinated zigzag nanoribbon of graphene as the final product. ChemTEM enables the entire process of polycondensation, including the formation of metastable intermediates, to be captured in a one-shot “movie”. A molecule with a similar size and shape but with a different chemical composition, octathio[8]circulene, under the same conditions undergoes another type of polycondensation via thiyl biradical generation and subsequent reaction leading to polythiophene nanoribbons with irregular edges incorporating bridging sulfur atoms. Graphene or carbon nanotubes supporting the individual molecules during chemTEM studies ensure that the elastic interactions of the molecules with the e-beam are the dominant forces that initiate and drive the reactions we image. Our ab initio DFT calculations explicitly incorporating the e-beam in the theoretical model correlate with the chemTEM observations and give a mechanism for direct control not only of the type of the reaction but also of the reaction rate. Selection of the appropriate e-beam energy and control of the dose rate in chemTEM enabled imaging of reactions on a time frame commensurate with TEM image capture rates, revealing atomistic mechanisms of previously unknown processes.

Mechanistic Insights into Surface-Supported Chemical Reactions

“…Based on data gained through images showing the transition of perchlorocoronene from a face-on orientation to an edge-on orientation on graphene. This reaction is triggered by the 80 keV electron beam and has been recorded in situ [3]. b Reaction scheme derived from the experimental data and additional DFT calculations shows cleavage of C-Cl bonds by the electron beam and subsequent Diels-Alder cycloaddition of the formed aryne to the graphene substrate [3].…”

“…Recently, progress has been made in the visualization of intermolecular reactions by aberration corrected transmission electron microscopy in real space [3,[5][6][7][8][9]. Reactions can be induced via the electron beam and followed in situ.…”

“…The rather high energy of the electron beam imposes requirements on the stability of the chemical species to be investigated, as well as on the support. In a recent study, hetero-atoms (such as Cl and S) have been introduced for enhanced contrast for single-molecule imaging and higher stability under the electron beam [3] (Fig. 1a, b).…”

“…This reaction is triggered by the 80 keV electron beam and has been recorded in situ [3]. b Reaction scheme derived from the experimental data and additional DFT calculations shows cleavage of C-Cl bonds by the electron beam and subsequent Diels-Alder cycloaddition of the formed aryne to the graphene substrate [3]. c STM and d AFM images along with e the derived chemical structure models show the thermally induced cyclization of 1,2-bis (2-ethynylphenyl)ethyne on Au(111) towards an (E)-1,1′-bi(indenylidene) diradical, which then reacts towards poly-(E)-1,1′-bi-(indenylidene) chains via radical step growth [4].…”

Single-atom fabrication with electron and ion beams: From surfaces and two-dimensional materials toward three-dimensional atom-by-atom assembly

“…49,55,[59][60][61][62][63][64][65][66][67][68][69] Some of these are further illustrated in Figure 3. 62,[70][71][72][73][74][75][76] What is remarkable is that these changes often involve one atom or small groups of atoms, and can be monitored in real time with atomic resolution. Further examples of controllable electron-beam-induced phenomena are discussed throughout this issue.…”