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Instruments / Technical Area	Publication Details	Published
E02-JEM ARM 300CF	Direct measurement of single-molecule dynamics and reaction kinetics in confinement using time-resolved transmission electron microscopy Kayleigh L. Y. Fung , Stephen T. Skowron , Ruth Hayter , Stephen E. Mason , Benjamin L. Weare , Quentin M. Ramasse , Christopher S. Allen , Andrei N. Khlobystov Physical Chemistry Chemical Physics DOI: 10.1039/D2CP05183D Diamond Proposal Number(s): [22887, 23260, 25251] Open Access Show Abstract ▼ Abstract: 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. A period of molecular movement was found to precede the intermolecular addition of perchlorocoronene (PCC) in carbon nanotubes, with a stronger dependence on the nanotube diameter controlling the local environments around molecules than the reaction temperature (-175, 23 or 400 oC). 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 images. Polymerisation was shown to proceed from a single point, with molecules reacting sequentially in a domino effect. The reaction mechanism was corroborated by correlating TEM measurements, where the reaction is triggered by the 80 keV electron beam, with the same reaction triggered by UV irradiation using mass spectrometry, detecting molecular species matching TEM observations.	Feb 2023
I19-Small Molecule Single Crystal Diffraction	Reactions of polyaromatic molecules in crystals under electron beam of the transmission electron microscope Kayleigh L. Y. Fung , Benjamin L. Weare , Michael W. Fay , Stephen P. Argent , Andrei N. Khlobystov Micron 7 DOI: 10.1016/j.micron.2022.103395 Show Abstract ▼ Abstract: Reactivity of a series of related molecules under the 80 keV electron beam have been investigated and correlated with their structures and chemical composition. Hydrogenated and halogenated derivatives of hexaazatrinaphthylene, coronene, and phthalocyanine were prepared by sublimation in vacuum to form solventless crystals then deposited onto transmission electron microscopy (TEM) grids. The transformation of the molecules in the microcrystals were triggered by an 80 keV electron beam in the TEM and studied using correlated selected area electron diffraction, conventional bright field imaging, and energy dispersive X-ray spectroscopy. The critical fluence (ē nm-2) required to cause a disappearance of the diffraction pattern was recorded and used as a measure of the reactivity of the molecules. The same electron flux (102 ē nm-2 s-1) was used throughout. Fully halogenated molecules were found to be the most stable and did not change significantly under our experimental conditions, followed by fully hydrogenated molecules with critical fluences of 104 ē nm-2. Surprisingly, semi-halogenated molecules that contained an equal number of hydrogen and halogen atoms were found to be the least stable, with critical fluences an order of magnitude lower at 103 ē nm-2. This is attributed to elimination of H-X (where X = F or Cl), followed by polymerisation of aryne / aryl radicals within the crystal. The critical fluence for the semi-fluorinated hexaazatrinaphthylene is the lowest as the presence of water molecules in its crystal lattice significantly decreased the stability of the organic molecules under the electron beam. Semi-halogenation reduces the beam stability of organic molecules compared to the parent hydrogenated molecule, thus providing the chemical guidance for design of electron beam stable materials. Understanding of molecular reactivity in the electron beam is necessary for advancement of molecular imaging and analysis methods by the TEM, molecular materials processing, and electron beam-driven synthesis of novel materials.	Dec 2022
E02-JEM ARM 300CF	Counting molecules in nano test tubes: a method for determining the activation parameters of thermally driven reactions through direct imaging Kayleigh L. Y. Fung , Stephen T. Skowron , Christopher S. Allen , Andrei N. Khlobystov Chemical Communications 38 DOI: 10.1039/D1CC03827C Diamond Proposal Number(s): [22887, 23260, 25251] Show Abstract ▼ Abstract: A methodology for measuring activation parameters of a thermally driven chemical reaction by direct imaging and counting reactant molecules has been developed. The method combines the use of single walled carbon nanotubes (SWNTs) as a nano test tube, transmission electron microscopy (TEM) as an imaging tool, and a heating protocol that decouples the effect of the electron beam from the thermal activation. Polycyclic aromatic perchlorocoronene molecules are stable within SWNTs at room temperature, allowing imaging of individual molecules before and after each heating cycle between 500–600 °C. Polymerisation reaction rates can be determined at different temperatures simply by counting the number of molecules, resulting in an enthalpy of activation of 104 kJ mol−1 and very large entropic contributions to the Gibbs free energy of activation. This experimental methodology provides a link between reactions at the single-molecule level and macroscopic chemical kinetics parameters, through filming the chemical reaction in direct space.	Sep 2021
E02-JEM ARM 300CF	Single-molecule imaging and kinetic analysis of intermolecular polyoxometalate reactions Jack W. Jordan , Kayleigh L. Y. Fung , Stephen T. Skowron , Christopher Allen , Johannes Biskupek , Graham N. Newton , Ute Kaiser , Andrei N. Khlobystov Chemical Science 126 DOI: 10.1039/D1SC01874D Diamond Proposal Number(s): [23260] Open Access Show Abstract ▼ Abstract: We induce and study reactions of polyoxometalate (POM) molecules, [PW12O40]3− (Keggin) and [P2W18O62]6− (Wells–Dawson), at the single-molecule level. Several identical carbon nanotubes aligned side by side within a bundle provided a platform for spatiotemporally resolved imaging of ca. 100 molecules encapsulated within the nanotubes by transmission electron microscopy (TEM). Due to the entrapment of POM molecules their proximity to one another is effectively controlled, limiting molecular motion in two dimensions but leaving the third dimension available for intermolecular reactions between pairs of neighbouring molecules. By coupling the information gained from high resolution structural and kinetics experiments via the variation of key imaging parameters in the TEM, we shed light on the reaction mechanism. The dissociation of W–O bonds, a key initial step of POM reactions, is revealed to be reversible by the kinetic analysis, followed by an irreversible bonding of POM molecules to their nearest neighbours, leading to a continuous tungsten oxide nanowire, which subsequently transforms into amorphous tungsten-rich clusters due to progressive loss of oxygen atoms. The overall intermolecular reaction can therefore be described as a step-wise reductive polycondensation of POM molecules, via an intermediate state of an oxide nanowire. Kinetic analysis enabled by controlled variation of the electron flux in TEM revealed the reaction to be highly flux-dependent, which leads to reaction rates too fast to follow under the standard TEM imaging conditions. Although this presents a challenge for traditional structural characterisation of POM molecules, we harness this effect by controlling the conditions around the molecules and tuning the imaging parameters in TEM, which combined with theoretical modelling and image simulation, can shed light on the atomistic mechanisms of the reactions of POMs. This approach, based on the direct space and real time chemical reaction analysis by TEM, adds a new method to the arsenal of single-molecule kinetics techniques.	Apr 2021

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