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.

Reactions of polyaromatic molecules in crystals under electron beam of the transmission electron microscope.

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 (e 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 e 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 e 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 e 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.

Stabilization of Polyoxometalate Charge Carriers via Redox-Driven Nanoconfinement in Single-Walled Carbon Nanotubes.

We describe the preparation of hybrid redox materials based on polyoxomolybdates encapsulated within single-walled carbon nanotubes (SWNTs). Polyoxomolybdates readily oxidize SWNTs under ambient conditions in solution, and here we study their charge-transfer interactions with SWNTs to provide detailed mechanistic insights into the redox-driven encapsulation of these and similar nanoclusters. We are able to correlate the relative redox potentials of the encapsulated clusters with the level of SWNT oxidation in the resultant hybrid materials and use this to show that precise redox tuning is a necessary requirement for successful encapsulation. The host-guest redox materials described here exhibit exceptional electrochemical stability, retaining up to 86 % of their charge capacity over 1000 oxidation/reduction cycles, despite the typical lability and solution-phase electrochemical instability of the polyoxomolybdates we have explored. Our findings illustrate the broad applicability of the redox-driven encapsulation approach to the design and fabrication of tunable, highly conductive, ultra-stable nanoconfined energy materials.

Counting molecules in nano test tubes: a method for determining the activation parameters of thermally driven reactions through direct imaging.

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.

Single-molecule imaging and kinetic analysis of intermolecular polyoxometalate reactions.

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.

Bond Dissociation and Reactivity of HF and H2O in a Nano Test Tube.

Molecular motion and bond dissociation are two of the most fundamental phenomena underpinning the properties of molecular materials. We entrapped HF and H2O molecules within the fullerene C60 cage, encapsulated within a single-walled carbon nanotube (X@C60)@SWNT, where X = HF or H2O. (X@C60)@SWNT represents a class of molecular nanomaterial composed of a guest within a molecular host within a nanoscale host, enabling investigations of the interactions of isolated single di- or triatomic molecules with the electron beam. The use of the electron beam simultaneously as a stimulus of chemical reactions in molecules and as a sub-angstrom resolution imaging probe allows investigations of the molecular dynamics and reactivity in real time and at the atomic scale, which are probed directly by chromatic and spherical aberration-corrected high-resolution transmission electron microscopy imaging, or indirectly by vibrational electron energy loss spectroscopy in situ during scanning transmission electron microscopy experiments. Experimental measurements indicate that the electron beam triggers homolytic dissociation of the H-F or H-O bonds, respectively, causing the expulsion of the hydrogen atoms from the fullerene cage, leaving fluorine or oxygen behind. Because of a difference in the mechanisms of penetration through the carbon lattice available for F or O atoms, atomic fluorine inside the fullerene cage appears to be more stable than the atomic oxygen under the same conditions. The use of (X@C60)@SWNT, where each molecule X is "packaged" separately from each other, in combination with the electron microscopy methods and density functional theory modeling in this work, enable bond dynamics and reactivity of individual atoms to be probed directly at the single-molecule level.