Isotope Substitution Extends the Lifetime of Organic Molecules in Transmission Electron Microscopy

Abstract

Structural characterisation of individual molecules by high‐resolution transmission electron microscopy (HRTEM) is fundamentally limited by the element and electron energy‐specific interactions of the material with the high energy electron beam. Here, the key mechanisms controlling the interactions between the e‐beam and C–H bonds, present in all organic molecules, are examined, and the low atomic weight of hydrogen—resulting in its facile atomic displacement by the e‐beam—is identified as the principal cause of the instability of individual organic molecules. It is demonstrated theoretically and proven experimentally that exchanging all hydrogen atoms within molecules with the deuterium isotope, and therefore doubling the atomic weight of the lightest atoms in the structure, leads to a more than two‐fold increase in the stability of organic molecules in the e‐beam. Substitution of H for D significantly reduces the amount of kinetic energy transferred from the e‐beam to the atom (main factor contributing to stability) and also increases the barrier for bond dissociation, primarily due to the changes in the zero‐point energy of the C–D vibration (minor factor). The extended lifetime of coronene‐d12, used as a model molecule, enables more precise analysis of the inter‐molecular spacing and more accurate measurement of the molecular orientations.

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

“…Having higher atomic numbers than carbon, Cl or S can provide a sufficient and clear contrast for single-molecule imaging, and the fact that Cl and S atoms are significantly heavier than carbon ensures higher stability of PCC and OTC under the e-beam as compared, for example, to the analogous hydrogen-containing molecules. 25 We employ single-layer graphene and SWNTs as substrates to support the molecules during their reaction because the low contrast of the atomically thin carbon structures enables virtually unobscured observation of individual molecules, while the extremely high thermal and electrical conductivities of graphene and SWNT effectively mitigate any ionization and heating effects of the e-beam on the molecules during chemTEM experiments. Our previous experimental and theoretical analyses of the behavior of molecules under the e-beam clearly indicate that it is elastic (knock-on) interactions with the e-beam that transfer the energy T to the molecules which are dominant when a single molecule is adsorbed on graphene 27,28 or in a carbon nanotube, 25,29 which is different to complex radiolysis reactions previously documented for molecules in a crystal or in thick films under high energy e-beams (as in electron beam lithography), or to ionization processes taking place in molecular monolayers under a low energy e-beam.…”

“…3−9,21−23 Moreover, at different energies (accessible values range between 20–300 keV), the e-beam can trigger qualitatively different chemical processes in the same material, 24 while tuning the e-beam dose rate may potentially control the rates of reactions. 25 Therefore, our chemTEM methodology lends itself well to the recording of continuous “movies” of chemical reactions by acquiring a time series of AC-HRTEM images for a single molecule, where the reaction is taking place simultaneously with the imaging process.…”

“…Provided that the sample is very thin ( i.e ., a single molecule or a chain of molecules within a single-walled carbon nanotube (SWNT) or on a monolayer of graphene), it is the direct interactions of the e-beam with atomic nuclei that are the dominant forces, such that during AC-HRTEM imaging, the kinetic energy of fast electrons, controlled by the accelerating voltage of the microscope, is transferred directly to the atoms in ballistic collisions, with the maximum amount of energy received by a stationary atom in a collision being determined by the formula:where E is the energy of incident electrons (80 keV in our case), m e is the mass of an electron, c is the speed of light and, most importantly, T is inversely proportional to the atomic weight of the element ( M ), so that under the same TEM imaging conditions, lighter elements receive significantly more energy from the e-beam. 25 If the value of T exceeds the energy threshold for atom displacement from the molecule ( E d ), there is a nonzero likelihood for the molecule to become reactive as described by the cross section function σ d , the value which determines the rate of a given chemical transformation ( k ) under the e-beam:where n is the number of bonds of this type in the molecule, and j is the dose rate of the e-beam in units of e – /nm 2 ·s. 26 The latter parameter is precisely determined and readily controlled by TEM operating conditions which gives direct control of the rate of the observed reaction in chemTEM experiments: The greater the rate of the collisions between the fast electrons and the molecule, the faster the observed reaction.…”

Carbon Nanotubes as Electrically Active Nanoreactors for Multi-Step Inorganic Synthesis: Sequential Transformations of Molecules to Nanoclusters and Nanoclusters to Nanoribbons

“…Because the  1 -I atoms are not expected to form any directional interactions with sp 2 -carbon atoms of the SWNT, the energy difference between dissimilar orientations of [M6I14] 2-is not expected to be sufficiently high to hinder the tumbling motion of the nanoclusters observed in time-series HRTEM imaging (Supporting Videos 1 and 2). The EDX spectra of the metal iodide nanoclusters in nanotubes clearly distinguish W and Mo in n·[W6I14] 2-@SWNT 2n+ (Fig 2g) and n·[Mo6I14] 2-@SWNT 2n+ (Fig 3i) [19,20,33]. Generally, if the amount of transferred energy from the e-beam to an atom exceeds the threshold of displacement of the atom and dissociation of the chemical bonds, the atom is knocked out of the molecule [34] and a chain of chemical transformations is triggered by the e-beam.…”

Chemical reactions at the graphitic step-edge: changes in product distribution of catalytic reactions as a tool to explore the environment within carbon nanoreactors

“…For instance, the transformation of coronene molecules axially stacked inside SWNT into graphene nanoribbons can be directly observed in TEM highlighting the unique templating role of SWNT nanoreactor. [ 17 ] Although very powerful, utilisation of TEM is however limited to a small number of molecular or nanoparticulate structures which have sufficient stability under the ebeam. Whereas the majority of organic molecules and molecular catalysts used in traditional synthetic chemistry become rapidly damaged by electron beam irradiation, [ 17 ] and therefore hinder the investigation of the precise inner reaction environment.…”