Irradiation induced reactions in carbon nanomaterials in transmission electron microscopy

Aberration corrected transmission electron microscopy is a powerful tool for the structural characterisation of materials at the atomic scale, but the passage of high velocity electrons through the material can often induce structural changes via the transfer of large amounts of energy from the beam. The work in this thesis theoretically considers the nature of this transfer of energy and its impact upon the material being studied. The computational modelling of molecular species encapsulated inside carbon nanotubes and their response to electron irradiation is compared to results from TEM experiments, and used to explain the experimental observations. The high rate of destruction of C-H bonds under the beam is quantified, and its implications for TEM studies of organic materials considered. An effective solution for mitigating this rate of destruction is found, applied to a model system, and then confirmed experimentally. Using the considerations of stability under the beam, two experimentally witnessed reactions are investigated in detail, and careful comparison to intermediate structures observed in TEM allows full reaction mechanisms to be proposed. The dynamic motion of atomic defects in irradiated graphene is considered with the aid of a large library of experimental TEM images. A novel defect structure is observed, and is seen to undergo structural rearrangements on a quicker time-scale than accessible to TEM imaging. This species enables the very quick migration of defect structures across the graphene lattice, and is attributed to a trivacancy structure. The rates of beam induced reactions are considered in the framework of chemical kinetics, and a method for extracting kinetic parameters of a reaction from the statistics of a large number of TEM observations of it occurring is developed. This is used to obtain the first cross-sections for the formation and healing of the irradiation induced Stone-Wales bond rotation, and the first experimental activation energy for its healing. The latter agrees well with a theoretically predicted mechanism of catalysis, while the former demonstrates that the widely assumed process of direct knock-on damage cannot be responsible for the beam induced reaction. An alternative mechanism is proposed, resulting from the electronic excitation of the defect

The effects of encapsulation on damage to molecules by electron radiation

Encapsulation of materials imaged by high resolution transmission electron microscopy presents a promising route to the reduction of sample degradation, both independently and in combination with other traditional solutions to controlling radiation damage. In bulk crystals, the main effect of encapsulation (or coating) is the elimination of diffusion routes of beam-induced radical species, enhancing recombination rates and acting to limit overall damage. Moving from bulk to low dimensional materials has significant effects on the nature of damage under the electron beam. We consider the major changes in mechanisms of damage of low dimensional materials by separating the effects of dimensional reduction from the effects of encapsulation. An effect of confinement is discussed using a model example of coronene molecules encapsulated inside single walled carbon nanotubes as determined from molecular dynamics simulations calculating the threshold energy required for hydrogen atom dissociation. The same model system is used to estimate the rate at which the nanotube can dissipate excess thermal energy above room temperature by acting as a thermal sink

Imaging an unsupported metal–metal bond in dirhenium molecules at the atomic scale

Metallic bonds remain one of the most important and least understood of the chemical bonds. In this study, we generated Re2 molecules in which the Re–Re core is unsupported by ligands. Real-time imaging of the atomic-scale dynamics of Re2 adsorbed on a graphitic lattice allows direct measurement of Re–Re bond lengths for individual molecules that changes in discrete steps correlating with bond order from one to four. Direct imaging of the Re–Re bond breaking process reveals a new bonding state with the bond order less than one and a high-amplitude vibrational stretch, preceding the bond dissociation. The methodology, based on aberration-corrected transmission electron microscopy imaging, is shown to be a powerful analytical tool for the investigation of dynamics of metallic bonding at the atomic level

Accurate EELS background subtraction – an adaptable method in MATLAB

Electron energy-loss spectroscopy (EELS) is a technique that can give useful information on elemental composition and bonding environments. However in practice, the complexity of the background contributions, which can arise from multiple sources, can hamper the interpretation of the spectra. As a result, background removal is both an essential and difficult part of EELS analysis, especially during quantification of elemental composition. Typically, a power law is used to fit the background but this is often not suitable for many spectra such as in the low-loss region (< 50 eV) and when there are overlapping EELS edges. In this article, we present a series of scripts written in MATLAB v. R2019b that aims to provide statistical information on the model used to fit the background, allowing the user to determine the accuracy of background subtraction. The scripts were written for background subtraction of vibrational EELS in the ultralow-loss region near the zero-loss peak but can also be applied to other kinds of EEL spectra. The scripts can use a range of models for fitting, provided by the Curve Fitting Toolbox of MATLAB, and the user is able to precisely define the window for fitting as well as for edge integration. We demonstrate the advantages of using these scripts by comparing their background subtraction of example spectra to the most commonly used software, Gatan Microscopy Suite 3. The example spectra include those containing multiple scattering, multiple overlapping peaks, as well as vibrational EELS. Additionally, a comprehensive guide to using the scripts has been included in the Supplementary Information

Direct Imaging of Atomic Permeation Through a Vacancy Defect in the Carbon Lattice

Porous graphene has shown promise as a new generation of selective membrane for sieving atoms, ions and molecules. However, the atomistic mechanisms of permeation through defects in the graphenic lattice are still unclear and remain unobserved in action, at the atomic level. Here, the direct observation of palladium atoms from a nanoparticle passing through a defect in a single-walled carbon nanotube one-by-one has been achieved with atomic resolution in real time, revealing key stages of the atomic permeation. Bonding between the moving atom and dangling bonds around the orifice, immediately before and after passing through the subnano-pore, plays an important role in the process. Curvature of the graphenic lattice crucially defines the direction of permeation from concave to convex side due to a difference in metal-carbon bonding at the curved surfaces as confirmed by density functional theory calculations, demonstrating the potential of porous carbon nanotubes for atom sieving

Host–Guest Hybrid Redox Materials Self‐Assembled from Polyoxometalates and Single‐Walled Carbon Nanotubes

The development of next‐generation molecular‐electronic, electrocatalytic, and energy‐storage systems depends on the availability of robust materials in which molecular charge‐storage sites and conductive hosts are in intimate contact. It is shown here that electron transfer from single‐walled carbon nanotubes (SWNTs) to polyoxometalate (POM) clusters results in the spontaneous formation of host–guest POM@SWNT redox‐active hybrid materials. The SWNTs can conduct charge to and from the encapsulated guest molecules, allowing electrical access to >90% of the encapsulated redox species. Furthermore, the SWNT hosts provide a physical barrier, protecting the POMs from chemical degradation during charging/discharging and facilitating efficient electron transfer throughout the composite, even in electrolytes that usually destroy POMs

Resonant inelastic X-ray scattering of a Ru photosensitizer: Insights from individual ligands to the electronic structure of the complete molecule

N 1s Resonant Inelastic X-ray Scattering (RIXS) was used to probe the molecular electronic structure of the ruthenium photosensitizer complex cis-bis(isothiocyanato) bis(2,2′-bipyridyl-4,4′-dicarboxylato) ruthenium(II), known as “N3.” In order to interpret these data, crystalline powder samples of the bipyridine-dicarboxylic acid ligand (“bi-isonicotinic acid”) and the single ring analog “isonicotinic acid” were studied separately using the same method. Clear evidence for intermolecular hydrogen bonding is observed for each of these crystalline powders, along with clear vibronic coupling features. For bi-isonicotinic acid, these results are compared to those of a physisorbed multilayer, where no hydrogen bonding is observed. The RIXS of the “N3” dye, again prepared as a bulk powder sample, is interpreted in terms of the orbital contributions of the bi-isonicotinic acid and thiocyanate ligands by considering the two different nitrogen species. This allows direct comparison with the isolated ligand molecules where we highlight the impact of the central Ru atom on the electronic structure of the ligand. Further interpretation is provided through complementary resonant photoemission spectroscopy and density functional theory calculations. This combination of techniques allows us to confirm the localization and relative coupling of the frontier orbitals and associated vibrational losses

Direct measurement of single-molecule dynamics and reaction kinetics in confinement using time-resolved transmission electron microscopy

We report experimental methodologies utilising transmission electron microscopy (TEM) as an imaging tool for reaction kinetics at the single molecule level, in direct space and with spatiotemporal continuity. Using reactions of perchlorocoronene (PCC) in nanotubes of different diameters and at different temperatures, we found a period of molecular movement to precede the intermolecular addition of PCC, with a stronger dependence of the reaction rate on the nanotube diameter, controlling the local environments around molecules, than on the reaction temperature (−175, 23 or 400 °C). Once initiated, polymerisation of PCC follows zero-order reaction kinetics with the observed reaction cross section σobs of 1.13 × 10−9 nm2 (11.3 ± 0.6 barn), determined directly from time-resolved TEM image series acquired with a rate of 100 frames per second. Polymerisation was shown to proceed from a single point, with molecules reacting sequentially, as in a domino effect, due to the strict conformational requirement of the Diels–Alder cycloaddition creating the bottleneck for the reaction. The reaction mechanism was corroborated by correlating structures of reaction intermediates observed in TEM images, with molecular weights measured by using mass spectrometry (MS) when the same reaction was triggered by UV irradiation. The approaches developed in this study bring the imaging of chemical reactions at the single-molecule level closer to traditional concepts of chemistry