The main objective of this Account is to assess the challenges of transmission electron microscopy (TEM) of molecules, based on over 15 years of our work in this field, and to outline the opportunities in studying chemical reactions under the electron beam (e-beam). During TEM imaging of an individual molecule adsorbed on an atomically thin substrate, such as graphene or a carbon nanotube, the e-beam transfers kinetic energy to atoms of the molecule, displacing them from equilibrium positions. Impact of the e-beam triggers bond dissociation and various chemical reactions which can be imaged concurrently with their activation by the e-beam and can be presented as stop-frame movies. This experimental approach, which we term ChemTEM, harnesses energy transferred from the e-beam to the molecule via direct interactions with the atomic nuclei, enabling accurate predictions of bond dissociation events and control of the type and rate of chemical reactions. Elemental composition and structure of the reactant molecules as well as the operating conditions of TEM (particularly the energy of the e-beam) determine the product formed in ChemTEM processes, while the e-beam dose rate controls the reaction rate. Because the e-beam of TEM acts simultaneously as a source of energy for the reaction and as an imaging tool monitoring the same reaction, ChemTEM reveals atomic-level chemical information, such as pathways of reactions imaged for individual molecules, step-by-step and in real time; structures of illusive reaction intermediates; and direct comparison of catalytic activity of different transition metals filmed with atomic resolution. Chemical transformations in ChemTEM often lead to previously unforeseen products, demonstrating the potential of this method to become not only an analytical tool for studying reactions, but also a powerful instrument for discovery of materials that can be synthesized on preparative scale.

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Incorporating heteroatoms into the graphene lattice may be used to tailor its electronic, mechanical and chemical properties, although directly observed substitutions have thus far been limited to incidental Si impurities and P, N and B dopants introduced using low-energy ion implantation. We present here the heaviest impurity to date, namely Ge ions implanted into monolayer graphene. Although sample contamination remains an issue, atomic resolution scanning transmission electron microscopy imaging and quantitative image simulations show that Ge can either directly substitute single atoms, bonding to three carbon neighbors in a buckled out-of-plane configuration, or occupy an in-plane position in a divacancy. First-principles molecular dynamics provides further atomistic insight into the implantation process, revealing a strong chemical effect that enables implantation below the graphene displacement threshold energy. Our results demonstrate that heavy atoms can be implanted into the graphene lattice, pointing a way toward advanced applications such as single-atom catalysis with graphene as the template.

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.

Theory is developed to address a significant problem of how two charged dielectric particles interact in the presence of a polarizable medium that is a dilute solution of a strong electrolyte. The electrostatic force is defined by characteristic parameters for the interacting particles (charge, radius, and dielectric constant) and for the medium (permittivity and Debye length), and is expressed in the form of a converging infinite series. The limiting case of weak screening and large inter-particle separation is considered, which corresponds to small (macro)ions that carry constant charge. The theory yields a solution in the limit of monopole and dipole terms that agrees exactly with existing analytical expressions, which are generally used to describe ion-ion and ion-molecular interactions in a medium. Results from the theory are compared with DLVO theory and with experimental measurements for the electrostatic force between two PMMA particles contained in a nonpolar solvent (hexadecane) with an added charge control agent.