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.

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.

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.

Chemical Reactions of Molecules Promoted and Simultaneously Imaged by the Electron Beam in Transmission Electron Microscopy.

The main objective of this Account is to assess the challenges of transmission electron microscopy (TEM) of molecules, based on over 15 years of our work in this field, and to outline the opportunities in studying chemical reactions under the electron beam (e-beam). During TEM imaging of an individual molecule adsorbed on an atomically thin substrate, such as graphene or a carbon nanotube, the e-beam transfers kinetic energy to atoms of the molecule, displacing them from equilibrium positions. Impact of the e-beam triggers bond dissociation and various chemical reactions which can be imaged concurrently with their activation by the e-beam and can be presented as stop-frame movies. This experimental approach, which we term ChemTEM, harnesses energy transferred from the e-beam to the molecule via direct interactions with the atomic nuclei, enabling accurate predictions of bond dissociation events and control of the type and rate of chemical reactions. Elemental composition and structure of the reactant molecules as well as the operating conditions of TEM (particularly the energy of the e-beam) determine the product formed in ChemTEM processes, while the e-beam dose rate controls the reaction rate. Because the e-beam of TEM acts simultaneously as a source of energy for the reaction and as an imaging tool monitoring the same reaction, ChemTEM reveals atomic-level chemical information, such as pathways of reactions imaged for individual molecules, step-by-step and in real time; structures of illusive reaction intermediates; and direct comparison of catalytic activity of different transition metals filmed with atomic resolution. Chemical transformations in ChemTEM often lead to previously unforeseen products, demonstrating the potential of this method to become not only an analytical tool for studying reactions, but also a powerful instrument for discovery of materials that can be synthesized on preparative scale.

Energetics of atomic scale structure changes in graphene.

The presence of defects in graphene has an essential influence on its physical and chemical properties. The formation, behaviour and healing of defects are determined by energetic characteristics of atomic scale structure changes. In this article, we review recent studies devoted to atomic scale reactions during thermally activated and irradiation-induced processes in graphene. The formation energies of vacancies, adatoms and topological defects are discussed. Defect formation, healing and migration are quantified in terms of activation energies (barriers) for thermally activated processes and by threshold energies for processes occurring under electron irradiation. The energetics of defects in the graphene interior and at the edge is analysed. The effects of applied strain and a close proximity of the edge on the energetics of atomic scale reactions are overviewed. Particular attention is given to problems where further studies are required.

Isotope substitution extends the lifetime of organic molecules in transmission electron microscopy.

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.

Subnanometer-Wide Indium Selenide Nanoribbons.

Indium selenides (InxSey) have been shown to retain several desirable properties, such as ferroelectricity, tunable photoluminescence through temperature-controlled phase changes, and high electron mobility when confined to two dimensions (2D). In this work we synthesize single-layer, ultrathin, subnanometer-wide InxSey by templated growth inside single-walled carbon nanotubes (SWCNTs). Despite the complex polymorphism of InxSey we show that the phase of the encapsulated material can be identified through comparison of experimental aberration-corrected transmission electron microscopy (AC-TEM) images and AC-TEM simulations of known structures of InxSey. We show that, by altering synthesis conditions, one of two different stoichiometries of sub-nm InxSey, namely InSe or ß-In2Se3, can be prepared. Additionally, in situ AC-TEM heating experiments reveal that encapsulated ß-In2Se3 undergoes a phase change to γ-In2Se3 above 400 °C. Further analysis of the encapsulated species is performed using X-ray photoelectron spectroscopy (XPS), thermogravimetric analysis (TGA), energy dispersive X-ray analysis (EDX), and Raman spectroscopy, corroborating the identities of the encapsulated species. These materials could provide a platform for ultrathin, subnanometer-wide phase-change nanoribbons with applications as nanoelectronic components.

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.

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.

Atomic mechanism of metal crystal nucleus formation in a single-walled carbon nanotube.

Knowing how crystals nucleate at the atomic scale is crucial for understanding, and in turn controlling, the structure and properties of a wide variety of materials. However, because of the scale and highly dynamic nature of nuclei, the formation and early growth of nuclei are very difficult to observe. Here, we have employed single-walled carbon nanotubes as test tubes, and an 'atomic injector' coupled with aberration-corrected transmission electron microscopy, to enable in situ imaging of the initial steps of nucleation at the atomic scale. With three different metals we observed three main processes prior to heterogeneous nucleation: formation of crystal nuclei directly from an atomic seed (Fe), from a pre-existing amorphous nanocluster (Au) or by coalescence of two separate amorphous sub-nanometre clusters (Re). We demonstrate the roles of the amorphous precursors and the existence of an energy barrier before nuclei formation. In all three cases, crystal nucleus formation occurred through a two-step nucleation mechanism.

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.

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.

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.

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

We report an approach, named chemTEM, to follow chemical transformations at the single-molecule level with the electron beam of a transmission electron microscope (TEM) applied as both a tunable source of energy and a sub-angstrom imaging probe. Deposited on graphene, disk-shaped perchlorocoronene molecules are precluded from intermolecular interactions. This allows monomolecular transformations to be studied at the single-molecule level in real time and reveals chlorine elimination and reactive aryne formation as a key initial stage of multistep reactions initiated by the 80 keV e-beam. Under the same conditions, perchlorocoronene confined within a nanotube cavity, where the molecules are situated in very close proximity to each other, enables imaging of intermolecular reactions, starting with the Diels-Alder cycloaddition of a generated aryne, followed by rearrangement of the angular adduct to a planar polyaromatic structure and the formation of a perchlorinated zigzag nanoribbon of graphene as the final product. ChemTEM enables the entire process of polycondensation, including the formation of metastable intermediates, to be captured in a one-shot "movie". A molecule with a similar size and shape but with a different chemical composition, octathio[8]circulene, under the same conditions undergoes another type of polycondensation via thiyl biradical generation and subsequent reaction leading to polythiophene nanoribbons with irregular edges incorporating bridging sulfur atoms. Graphene or carbon nanotubes supporting the individual molecules during chemTEM studies ensure that the elastic interactions of the molecules with the e-beam are the dominant forces that initiate and drive the reactions we image. Our ab initio DFT calculations explicitly incorporating the e-beam in the theoretical model correlate with the chemTEM observations and give a mechanism for direct control not only of the type of the reaction but also of the reaction rate. Selection of the appropriate e-beam energy and control of the dose rate in chemTEM enabled imaging of reactions on a time frame commensurate with TEM image capture rates, revealing atomistic mechanisms of previously unknown processes.

Approaches to modelling irradiation-induced processes in transmission electron microscopy.

The recent progress in high-resolution transmission electron microscopy (HRTEM) has given rise to the possibility of in situ observations of nanostructure transformations and chemical reactions induced by electron irradiation. In this article we briefly summarise experimental observations and discuss in detail atomistic modelling of irradiation-induced processes in HRTEM, as well as mechanisms of such processes recognised due to modelling. Accurate molecular dynamics (MD) techniques based on first principles or tight-binding models are employed in the analysis of single irradiation-induced events, and classical MD simulations are combined with a kinetic Monte Carlo algorithm to simulate continuous irradiation of nanomaterials. It has been shown that sulphur-terminated graphene nanoribbons are formed inside carbon nanotubes as a result of an irradiation-selective chemical reaction. The process of fullerene formation in HRTEM during continuous electron irradiation of a small graphene flake has been simulated, and mechanisms driving this transformation analysed.