Inclusion of radiation damage dynamics in high-resolution transmission electron microscopy image simulations: The example of graphene

Abstract

Computer image simulations provide a crucial aid to high-resolution transmission electron microscopy (HRTEM) in gaining fundamental understanding of the structure of materials. Interpretation of HRTEM images is, however, complicated due to continuous structure deformation caused by the imaging electron beam. A computational methodology has been implemented that takes into account the effects of the electron beam on deformation of sample structure during observation and imaging in HRTEM. The evolution of the sample structure is described as a sequence of externally initiated discrete damage events with a frequency determined by the cross section, which depends on the energy of the electron beam. A series of images showing structure evolution with time is obtained by coupling molecular dynamics simulations with the image simulation. These simulation parts are linked by two experimental parameters: the energy of the electron beam and the electron dose rate. As the energy of the electron beam also determines resolution and contrast of the obtained HRTEM image, a careful selection of its value is required to achieve a fine balance between reduction of the sample damage caused by the electron beam and the quality of the acquired image. The proposed computational approach is used to simulate the recently observed process of structural transformation of a small graphene flake into a fullerene cage. The simulated series of images showing the evolution of a graphene flake under the 80 keV electron beam closely reproduces experimental HRTEM images with regard to the structure evolution route, evolution rate, and signal-to-noise ratio. We show that under the increased electron beam energy of 200 keV a similar observation will be obscured by high damage rate or low signal-to-noise ratio.

Reaction kinetics of bond rotations in graphene

“…Bookmark not defined. This cross-section is also well known theoretically in both graphene [14] and other carbon nanomaterials such as nanotubes, [15,16] graphene flakes, [17] and graphene nanoribbons. [18] The other major…”

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

“…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. 30 Overall, the kinetic energy of fast electrons in chemTEM experiments which is directly transferred to the atomic displacement within the molecule offers the most direct way of triggering and monitoring a chemical reaction which can be successfully interpreted within the framework of elastic interactions, as shown for the two types of molecules PCC and OTC discussed below.…”

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

“…In practical terms, the value of σ d for the most easily broken chemical bond within a molecule and typical values of the e‐beam dose rate j required for AC‐HRTEM imaging can be used to estimate the time required for ejection of the first atom from the molecule (e.g. in the chemical kinetics terms, the ejection of first atom from coronene is likely to be a rate‐controlling step for the decomposition of molecules within the stacks), t ev , under the e‐beam:where n is the number of bonds of such type in the molecule. Considering that ejection of an atom from the organic molecule leads to highly reactive radical species causing rapid decomposition, t ev gives a good estimate for the observed life‐time of the molecule under the e‐beam.…”