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

Disproportionation chemistry in K2PtCl4 visualized at atomic resolution using scanning transmission electron microscopy

The direct observation of a solid-state chemical reaction can reveal otherwise hidden mechanisms that control the reaction kinetics. However, probing the chemical bond breaking and formation at the molecular level remains challenging because of the insufficient spatial-temporal resolution and composition analysis of available characterization methods. Using atomic-resolution differential phase-contrast imaging in scanning transmission electron microscopy, we have visualized the decomposition chemistry of K2PtCl4 to identify its transient intermediate phases and their interfaces that characterize the chemical reduction process. The crystalline structure of K2PtCl4 is found to undergo a disproportionation reaction to form K2PtCl6, followed by gradual reduction to crystalline Pt metal and KCl. By directly imaging different Pt─Cl bond configurations and comparing them to models predicted via density functional theory calculations, a causal connection between the initial and final states of a chemical reaction is established, showcasing new opportunities to resolve reaction pathways through atomistic experimental visualization.

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 σ_obs 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 (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.

Molecular Encapsulation from the Liquid Phase and Graphene Nanoribbon Growth in Carbon Nanotubes

Growing graphene nanoribbons from small organic molecules encapsulated in carbon nanotubes can result in products with uniform width and chirality. We propose a method based on encapsulation of 1,2,4-trichlorobenzene from the liquid phase and subsequent annealing. This procedure results in graphene nanoribbons several tens of nanometers long. The presence of nanoribbons was proven by Raman spectra both on macroscopic samples and on the nanoscale by tip-enhanced Raman scattering and high-resolution transmission electron microscopic images.

Giant Carbon Nano-Test Tubes as Versatile Imaging Vessels for High-Resolution and In Situ Observation of Proteins

Cryogenic electron microscopy is one of the fastest and most robust methods for capturing high-resolution images of proteins, but stringent sample preparation, imaging conditions, and in situ radiation damage inflicted during data acquisition directly affect the resolution and ability to capture dynamic details, thereby limiting its broader utilization and adoption for protein studies. We addressed these drawbacks by introducing synthesized giant carbon nano-test tubes (GCNTTs) as radiation-insulating materials that lessen the irradiation impact on the protein during data acquisition, physical molecular concentrators that localize the proteins within a nanoscale field of view, and vessels that create a microenvironment for solution-phase imaging. High-resolution electron microscopy images of single and aggregated hemoglobin molecules within GCNTTs in both solid and solution states were acquired. Subsequent scanning transmission electron microscopy, small-angle neutron scattering, and fluorescence studies demonstrated that the GCNTT vessel protected the hemoglobin molecules from electron irradiation-, light-, or heat-induced denaturation. To demonstrate the robustness of GCNTT as an imaging platform that could potentially augment the study of proteins, we demonstrated the robustness of the GCNTT technique to image an alternative protein, d-fructose dehydrogenase, after cyclic voltammetry experiments to review encapsulation and binding insights. Given the simplicity of the material synthesis, sample preparation, and imaging technique, GCNTT is a promising imaging companion for high-resolution, single, and dynamic protein studies under electron microscopy.

Atomic-Resolution Imaging of Small Organic Molecules on Graphene

Here, we demonstrate atomic-resolution scanning transmission electron microscopy (STEM) imaging of light elements in small organic molecules on graphene. We use low-dose, room-temperature, aberration-corrected STEM to image 2D monolayer and bilayer molecular crystals, followed by advanced image processing methods to create high-quality composite images from ∼10²-10⁴ individual molecules. In metalated porphyrin and phthalocyanine derivatives, these images contain an elementally sensitive contrast with up to 1.3 Å resolution─sufficient to distinguish individual carbon and nitrogen atoms. Importantly, our methods can be applied to molecules with low masses (∼0.6 kDa) and nanocrystalline domains containing just a few hundred molecules, making it possible to study systems for which large crystals cannot easily be grown. Our approach is enabled by low-background graphene substrates, which we show increase the molecules' critical dose by 2-7×. These results indicate a new route for low-dose, atomic-resolution electron microscopy imaging to solve the structures of small organic molecules.

Magnetic nanoribbons with embedded cobalt grown inside single-walled carbon nanotubes

Molecular magnetism and specifically magnetic molecules have recently gained plenty of attention as key elements for quantum technologies, information processing, and spintronics. Transition to the nanoscale and implementation of ordered structures with defined parameters is crucial for advanced applications. Single-walled carbon nanotubes (SWCNTs) provide natural one-dimensional confinement that can be implemented for encapsulation, nanosynthesis, and polymerization of molecules into nanoribbons. Recently, the formation of atomically precise graphene nanoribbons inside SWCNTs has been reported. However, there have been only a limited amount of approaches to form ordered magnetic structures inside the nanotube channels and the creation of magnetic nanoribbons is still lacking. In this work we synthesize and reveal the properties of cobalt-phthalocyanine based nanoribbons (CoPcNRs) encapsulated in SWCNTs. Raman spectroscopy, transmission electron microscopy, absorption spectroscopy, and density functional theory calculations allowed us to confirm the encapsulation and to reveal the specific fingerprints of CoPcNRs. The magnetic properties were studied by transverse magnetooptical Kerr effect measurements, which indicated a strong difference in comparison with the pristine unfilled SWCNTs due to the impact of Co incorporated atoms. We anticipate that this approach of polymerization of encapsulated magnetic molecules inside SWCNTs will result in a diverse class of protected low-dimensional ordered magnetic materials for various applications.

Quasi-two-dimensional NaCl crystals encapsulated between graphene sheets and their decomposition under an electron beam

Quasi-two-dimensional (2D) sodium chloride (NaCl) crystals of various lateral sizes between graphene sheets were manufactured via supersaturation from a saline solution. Aberration-corrected transmission electron microscopy was used for systematic in situ investigations of the crystals and their decomposition under an 80 kV electron beam. Counterintuitively, bigger clusters were found to disintegrate faster under electron irradiation, but in general no correlation between crystal sizes and electron doses at which the crystals decompose was found. As for the destruction process, an abrupt decomposition of the crystals was observed, which can be described by a logistic decay function. Density-functional theory molecular dynamics simulations provide insights into the destruction mechanism, and indicate that even without account for ionization and electron excitations, free-standing NaCl crystals must quickly disintegrate due to the ballistic displacement of atoms from their surface and edges during imaging. However, graphene sheets mitigate damage development by stopping the displaced atoms and enable the immediate recombination of defects at the surface of the crystal. At the same time, once a hole in graphene appears, the displaced atoms escape, giving rise to the quick destruction of the crystal. Our results provide quantitative data on the stability of encapsulated quasi 2D NaCl crystals under electron irradiation and allow the conclusion that only high-quality graphene is suitable for protecting ionic crystals from beam damage in electron microscopy studies.

Low-Energy Electron Irradiation Damage in Few-Monolayer Pentacene Films

Crystalline films of pentacene molecules, two to four monolayers in thickness, are grown via in situ sublimation on silicon substrates in the ultrahigh vacuum chamber of a low-energy electron microscope. It is observed that the diffraction pattern of the pentacene layers fades upon irradiation with low-energy electrons. The damage cross section is found to increase by more than an order of magnitude for electron energies from 0 to 10 eV and by another order of magnitude from 10 to 40 eV. Close to 0 eV, damage is virtually nil. Creation of chemically reactive atomic centers after electron attachment or impact ionization is thought to trigger chemical reactions between neighboring molecules that gradually transform the layer into a disordered carbon nanomembrane. Additionally, diminishing spectroscopic features related to the unoccupied band structure of the layers, accompanied by loss of definition in real-space images, and an increase in the background intensity of diffraction images during irradiation point to chemical changes and formation of a disordered layer.

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.

Nanotube-Based 1D Heterostructures Coupled by van der Waals Forces

1D van der Waals heterostructures based on carbon nanotube templates are raising a lot of excitement due to the possibility of creating new optical and electronic properties, by either confining molecules inside their hollow core or by adding layers on the outside of the nanotube. In contrast to their 2D analogs, where the number of layers, atomic type and relative orientation of the constituting layers are the main parameters defining physical properties, 1D heterostructures provide an additional degree of freedom, i.e., their specific diameter and chiral structure, for engineering their characteristics. The current state-of-the-art in synthesizing 1D heterostructures are discussed here, in particular focusing on their resulting optical properties, and details the vast parameter space that can be used to design heterostructures with custom-built properties that can be integrated into a large variety of applications. First, the effects of van der Waals coupling on the properties of the simplest and best-studied 1D heterostructure, namely a double-walled carbon nanotube, are described, and then heterostructures built from the inside and the outside are considered, which all use a nanotube as a template, and, finally, an outlook is provided for the future of this research field.

A Singular Molecule-to-Molecule Transformation on Video: The Bottom-Up Synthesis of Fullerene C60 from Truxene Derivative C60H30

Singular reaction events of small molecules and their dynamics remain a hardly understood territory in chemical sciences since spectroscopy relies on ensemble-averaged data, and microscopic scanning probe techniques show snapshots of frozen scenes. Herein, we report on continuous high-resolution transmission electron microscopic video imaging of the electron-beam-induced bottom-up synthesis of fullerene C₆₀ through cyclodehydrogenation of tailor-made truxene derivative 1 (C₆₀H₃₀), which was deposited on graphene as substrate. During the reaction, C₆₀H₃₀ transformed in a multistep process to fullerene C₆₀. Hereby, the precursor, metastable intermediates, and the product were identified by correlations with electron dose-corrected molecular simulations and single-molecule statistical analysis, which were substantiated with extensive density functional theory calculations. Our observations revealed that the initial cyclodehydrogenation pathway leads to thermodynamically favored intermediates through seemingly classical organic reaction mechanisms. However, dynamic interactions of the intermediates with the substrate render graphene as a non-innocent participant in the dehydrogenation process, which leads to a deviation from the classical reaction pathway. Our precise visual comprehension of the dynamic transformation implies that the outcome of electron-beam-initiated reactions can be controlled with careful molecular precursor design, which is important for the development and design of materials by electron beam lithography.

Deep neural network analysis of nanoparticle ordering to identify defects in layered carbon materials

Smoothness/defectiveness of the carbon material surface is a key issue for many applications, spanning from electronics to reinforced materials, adsorbents and catalysis. Several surface defects cannot be observed with conventional analytic techniques, thus requiring the development of a new imaging approach. Here, we evaluate a convenient method for mapping such "hidden" defects on the surface of carbon materials using 1-5 nm metal nanoparticles as markers. A direct relationship between the presence of defects and the ordering of nanoparticles was studied experimentally and modeled using quantum chemistry calculations and Monte Carlo simulations. An automated pipeline for analyzing microscopic images is described: the degree of smoothness of experimental images was determined by a classification neural network, and then the images were searched for specific types of defects using a segmentation neural network. An informative set of features was generated from both networks: high-dimensional embeddings of image patches and statics of defect distribution.

Disentangling Rotational Dynamics and Ordering Transitions in a System of Self-Organizing Protein Nanorods via Rotationally Invariant Latent Representations

The dynamics of complex ordering systems with active rotational degrees of freedom exemplified by protein self-assembly is explored using a machine learning workflow that combines deep learning-based semantic segmentation and rotationally invariant variational autoencoder-based analysis of orientation and shape evolution. The latter allows for disentanglement of the particle orientation from other degrees of freedom and compensates for lateral shifts. The disentangled representations in the latent space encode the rich spectrum of local transitions that can now be visualized and explored via continuous variables. The time dependence of ensemble averages allows insight into the time dynamics of the system and, in particular, illustrates the presence of the potential ordering transition. Finally, analysis of the latent variables along the single-particle trajectory allows tracing these parameters on a single-particle level. The proposed approach is expected to be universally applicable for the description of the imaging data in optical, scanning probe, and electron microscopy seeking to understand the dynamics of complex systems where rotations are a significant part of the process.

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.

Low-energy electron irradiation induced synthesis of molecular nanosheets: influence of the electron beam energy

Aromatic self-assembled monolayers (SAMs) can be cross-linked into molecular nanosheets - carbon nanomembranes (CNMs) -via low-energy electron irradiation. Due to their favorable mechanical stability and tunable functional properties, they possess a high potential for various applications including nanosensors and separation membranes for osmosis or energy conversion devices. Despite this potential, the mechanistic details of the electron irradiation induced cross-linking process still need to be understood in more detail. Here, we studied the cross-linking of 4'-nitro-1,1'-biphenyl-4-thiol SAM on gold. The SAM samples were irradiated with different electron energies ranging from 2.5 to 100 eV in ultra-high vacuum and subsequently analysed by complementary techniques. We present results obtained via spectroscopy and microscopy characterization by high-resolution X-ray photoelectron spectroscopy (XPS), low-energy electron diffraction with micrometre sized electron beams (μLEED) and low-energy electron microscopy (LEEM). To demonstrate the formation of CNMs, the formed two-dimensional molecular materials were transferred onto grids and oxidized wafer and analyzed by optical, scanning electron microscopy (SEM) and atomic force microscopy (AFM). We found a strong energy dependence for the cross section for the cross-linking process, the rate of which decreases exponentially towards lower electron energies by about four orders of magnitude. We conduct a comparative analysis of the cross sections for the C-H bond scission via electron impact ionization and dissociative electron attachment and find that these different ionization mechanisms are responsible for the variation of the cross-linking cross section with electron energy.

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.

Direct Visualization of Crystalline Domains in Carboxylated Nanocellulose Fibers

Direct visualization of soft organic molecules like cellulose is extremely challenging under a high-energy electron beam. Herein, we adopt two ionization damage extenuation strategies to visualize the lattice arrangements of the β-(1→4)-d-glucan chains in carboxylated nanocellulose fibers (C-NCFs) having cellulose II crystalline phase using high-resolution transmission electron microscopy. Direct imaging of individual nanocellulose fibrils with high-resolution and least damage under high-energy electron beam is achieved by employing reduced graphene oxide, a conducting material with high electron transmittance and Ag⁺ ions, with high electron density, eliminating the use of sample-specific, toxic staining agents, or other advanced add-on techniques. Furthermore, the imaging of cellulose lattices in a C-NCF/TiO₂ nanohybrid system is accomplished in the presence of Ag⁺ ions in a medium revealing the mode of association of C-NCFs in the system, which validates the feasibility of the presented strategy. The methods adopted here can provide further understanding of the fine structures of carboxylated nanocellulose fibrils for studying their structure-property relationship for various applications.

Substrate-Selective Morphology of Cesium Iodide Clusters on Graphene

Formation and characterization of low-dimensional nanostructures is crucial for controlling the properties of two-dimensional (2D) materials such as graphene. Here, we study the structure of low-dimensional adsorbates of cesium iodide (CsI) on free-standing graphene using aberration-corrected transmission electron microscopy at atomic resolution. CsI is deposited onto graphene as charged clusters by electrospray ion-beam deposition. The interaction with the electron beam forms two-dimensional CsI crystals only on bilayer graphene, while CsI clusters consisting of 4, 6, 7, and 8 ions are exclusively observed on single-layer graphene. Chemical characterization by electron energy-loss spectroscopy imaging and precise structural measurements evidence the possible influence of charge transfer on the structure formation of the CsI clusters and layers, leading to different distances of the Cs and I to the graphene.

Effect of Temperature on the Nucleation and Growth of Precious Metal Nanocrystals

Understanding the effect of physical parameters (e.g., temperature) on crystallisation dynamics is of paramount importance for the synthesis of nanocrystals of well-defined sizes and geometries. However, imaging nucleation and growth is an experimental challenge owing to the resolution required and the kinetics involved. Here, by using an aberration-corrected transmission electron microscope, we report the fabrication of precious metal nanocrystals from nuclei and the identification of the dynamics of their nucleation at three different temperatures (20, 50, and 100 °C). A fast, and apparently linear, acceleration of the growth rate is observed against increasing temperature (78.8, 117.7, and 176.5 pm min^-1 , respectively). This work appears to be the first direct observation of the effect of temperature on the nucleation and growth of metal nanocrystals.

Nanocrystalline graphene at high temperatures: insight into nanoscale processes

During high temperature pyrolysis of polymer thin films, nanocrystalline graphene with a high defect density, active edges and various nanostructures is formed. The catalyst-free synthesis is based on the temperature assisted transformation of a polymer precursor. The processing conditions have a strong influence on the final thin film properties. However, the precise elemental processes that govern the polymer pyrolysis at high temperatures are unknown. By means of time resolved in situ transmission electron microscopy investigations we reveal that the reactivity of defects and unsaturated edges plays an integral role in the structural dynamics. Both mobile and stationary structures with varying size, shape and dynamics have been observed. During high temperature experiments, small graphene fragments (nanoflakes) are highly unstable and tend to lose atoms or small groups of atoms, while adjacent larger domains grow by addition of atoms, indicating an Ostwald-like ripening in these 2D materials, besides the mechanism of lateral merging of nanoflakes with edges. These processes are also observed in low-dose experiments with negligible electron beam influence. Based on energy barrier calculations, we propose several inherent temperature-driven mechanisms of atom rearrangement, partially involving catalyzing unsaturated sites. Our results show that the fundamentally different high temperature behavior and stability of nanocrystalline graphene in contrast to pristine graphene is caused by its reactive nature. The detailed analysis of the observed dynamics provides a pioneering overview of the relevant processes during ncg heating.

New Frontiers in Electron Beam-Driven Chemistry in and around Graphene

Modern aberration corrected transmission electron microscopes offer the potential for electron beam sensitive materials, such as graphene, to be examined with low energy electrons to minimize, and even avoid, damage while still affording atomic resolution, and thus providing excellent characterization. Here in this review, the exploits in which the electron beam interactions, which are often considered negative, are explored to usefully drive a wealth of chemistry in and around graphene, importantly, with no other external stimuli. After introducing the technique, this review covers carbon phase reactions between amorphous carbon, graphene, fullerenes, carbon chains, and carbon nanotubes. It then explores different studies with clusters and nanoparticles, followed by coverage of single atom and molecule interactions with graphene, and finally concludes and highlights the anticipated exciting future for electron beam driving chemistry in and around graphene.

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.

Direct Imaging of Photoswitching Molecular Conformations Using Individual Metal Atom Markers

Photoswitching behavior of individual organic molecules was imaged by annular dark-field scanning transmission electron microscopy (ADF-STEM) using a highly electron beam transparent graphene support. Photoswitching azobenzene derivatives with ligands at each end containing single transition-metal atoms (Pt) were designed (Pt-complex), and the distance between the strong ADF-STEM contrast from the two Pt atoms in each Pt-complex is used to track molecular length changes. UV irradiation was used to induce photoswitching of the Pt complex on graphene, and we show that the measured Pt-Pt distances within isolated molecules decrease from ∼2.1 nm to ∼1.4 nm, indicative of a trans-to- cis isomerization. Light illumination of the Pt-complex on the graphene support also caused their diffusion out from initial clusters to the surrounding area of graphene, indicating that the light-activated mobilization overcomes the intermolecular van der Waals interactions. This approach shows how individual isolated heavy metal atoms can be included as markers into complex molecules to track their structural changes using ADF-STEM on graphene supports, providing an effective method to study a diverse range of complex organic materials at the single molecule level.

Direct Correlation of Carbon Nanotube Nucleation and Growth with the Atomic Structure of Rhenium Nanocatalysts Stimulated and Imaged by the Electron Beam

Subnanometer Re clusters confined in a single-walled carbon nanotube are activated by the 80 keV electron beam to promote the catalytic growth of a new carbon nanotube. Transmission electron microscopy images the entire process step-by-step, with atomic resolution in real time, revealing details of the initial nucleation followed by a two-stage growth. The atomic dynamics of the Re cluster correlate strongly with the nanotube formation process, with the growth accelerating when the catalyst becomes more ordered. In addition to the nanotube growth catalyzed by Re nanoclusters, individual atoms of Re released from the nanocluster play a role in the nanotube formation.

Comparison of atomic scale dynamics for the middle and late transition metal nanocatalysts

Catalysis of chemical reactions by nanosized clusters of transition metals holds the key to the provision of sustainable energy and materials. However, the atomistic behaviour of nanocatalysts still remains largely unknown due to uncertainties associated with the highly labile metal nanoclusters changing their structure during the reaction. In this study, we reveal and explore reactions of nm-sized clusters of 14 technologically important metals in carbon nano test tubes using time-series imaging by atomically-resolved transmission electron microscopy (TEM), employing the electron beam simultaneously as an imaging tool and stimulus of the reactions. Defect formation in nanotubes and growth of new structures promoted by metal nanoclusters enable the ranking of the different metals both in order of their bonding with carbon and their catalytic activity, showing significant variation across the Periodic Table of Elements. Metal nanoclusters exhibit complex dynamics shedding light on atomistic workings of nanocatalysts, with key features mirroring heterogeneous catalysis.

The atomistic behaviour of nanocatalysts still remains largely unknown. Here, the authors reveal and explore reactions of nm-sized clusters of 14 technologically important metals in carbon nano test tubes using time-series imaging by atomically-resolved transmission electron microscopy.

Selective Laser-Assisted Synthesis of Tubular van der Waals Heterostructures of Single-Layered PbI2 within Carbon Nanotubes Exhibiting Carrier Photogeneration

The electronic and optical properties of two-dimensional layered materials allow the miniaturization of nanoelectronic and optoelectronic devices in a competitive manner. Even larger opportunities arise when two or more layers of different materials are combined. Here, we report on an ultrafast energy efficient strategy, using laser irradiation, which allows bulk synthesis of crystalline single-layered lead iodide in the cavities of carbon nanotubes by forming cylindrical van der Waals heterostructures. In contrast to the filling of van der Waals solids into carbon nanotubes by conventional thermal annealing, which favors the formation of inorganic nanowires, the present strategy is highly selective toward the growth of monolayers forming lead iodide nanotubes. The irradiated bulk material bearing the nanotubes reveals a decrease of the resistivity as well as a significant increase in the current flow upon illumination. Both effects are attributed to the presence of single-walled lead iodide nanotubes in the cavities of carbon nanotubes, which dominate the properties of the whole matrix. The present study brings in a simple, ultrafast and energy efficient strategy for the tailored synthesis of rolled-up single-layers of lead iodide (i.e., single-walled PbI₂ nanotubes), which we believe could be expanded to other two-dimensional (2D) van der Waals solids. In fact, initial tests with ZnI₂ already reveal the formation of single-walled ZnI₂ nanotubes, thus proving the versatility of the approach.

Positive and negative regulation of carbon nanotube catalysts through encapsulation within macrocycles

One of the most attractive applications of carbon nanomaterials is as catalysts, due to their extreme surface-to-volume ratio. The substitution of C with heteroatoms (typically B and N as p- and n-dopants) has been explored to enhance their catalytic activity. Here we show that encapsulation within weakly doping macrocycles can be used to modify the catalytic properties of the nanotubes towards the reduction of nitroarenes, either enhancing it (n-doping) or slowing it down (p-doping). This artificial regulation strategy presents a unique combination of features found in the natural regulation of enzymes: binding of the effectors (the macrocycles) is noncovalent, yet stable thanks to the mechanical link, and their effect is remote, but not allosteric, since it does not affect the structure of the active site. By careful design of the macrocycles' structure, we expect that this strategy will contribute to overcome the major hurdles in SWNT-based catalysts: activity, aggregation, and specificity.

Reversible dispersion and release of carbon nanotubes via cooperative clamping interactions with hydrogen-bonded nanorings

Due to their outstanding electronic and mechanical properties, single-walled carbon nanotubes (SWCNTs) are promising nanomaterials for the future generation of optoelectronic devices and composites. However, their scarce solubility limits their application in many technologies that demand solution-processing of high-purity SWCNT samples. Although some non-covalent functionalization approaches have demonstrated their utility in extracting SWCNTs into different media, many of them produce short-lived dispersions or ultimately suffer from contamination by the dispersing agent. Here, we introduce an unprecedented strategy that relies on a cooperative clamping process. When mixing (6,5)SWCNTs with a dinucleoside monomer that is able to self-assemble in nanorings via Watson-Crick base-pairing, a synergistic relationship is established. On one hand, the H-bonded rings are able to associate intimately with SWCNTs by embracing the tube sidewalls, which allows for an efficient SWCNT debundling and for the production of long-lasting SWCNT dispersions of high optical quality along a broad concentration range. On the other, nanoring stability is enhanced in the presence of SWCNTs, which are suitable guests for the ring cavity and contribute to the establishment of multiple cooperative noncovalent interactions. The inhibition of these reversible interactions, by just adding, for instance, a competing solvent for hydrogen-bonding, proved to be a simple and effective method to recover the pristine nanomaterial with no trace of the dispersing agent.

Oxygen, sulfur and selenium terminated single-walled heterocyclic carbon nanobelts (SWHNBs) as potential 3D organic semiconductors

Carbon nanomaterials such as polyaromatic hydrocarbons (PAHs), graphene, fullerenes and nanotubes are on the frontline of materials research due to their excellent physical properties, which in recent years, have started to compete with conventional inorganic materials in charge transfer based applications. Recently, a variety of new structures such as single-walled carbon nanobelts (SWCNBs) have been conceived, however, to date only one 'all-phenyl' example has been synthesised, due to problems with their stability and the challenging synthetic methodologies required. This study introduces a new class of phenacene-based SWCNBs and their chalcogenide derivatives, forming the new sub-class of single-walled heterocyclic carbon nanobelts (SWHNBs) which are expected to be both more stable and easier to synthesise than the all carbon analogues. Subsequent theoretical examination of the structure-property relationships found that unlike the small-molecule acene homologues (tetracene, pentacene etc.) which become more reactive with addition of oxygen, an increase in the molecular size of the SWCNBs actually stabilises the HOMO energy level, in correlation with the increasingly negative nuclear independent chemical shift (NICS) calculations of their cylindrical aromaticities. The FMO energies of the phenacene SWCNBs are similar to that of the nanobelt reported by Itami and co-workers, but those of the SWHNBs are deeper and thus more stable. The sulfur derivative of one SWHNB was found to give hole-charge transfer mobilities as high as 1.12 cm2 V-1 s-1, which is three orders of magnitude larger than the corresponding unsubstituted SWCNB (3 × 10-3 cm2 V-1 s-1). These findings suggest the candidates are air-stable and potentially high-performing organic semiconductors for organic thin film transistor (OTFT) devices, while the structure-property relationships uncovered here will aid the design and synthesis of future three-dimensional organic nanomaterials.

Entanglement and decoherence in electron microscopy

Interaction of the probe with the specimen in an electron microscope inevitably leads to entanglement between the probe and the scatterer. In spite of the importance of entanglement in many areas of modern physics, this subject has not been touched in the literature. Here, we develop some ideas about entanglement in electron microscopy for a number of scattering mechanisms. The relationship between entropy, density matrices, and coherence is discussed. In addition, we explore the questions "Why is Bragg scattering coherent and energy loss incoherent?" and "When does decoherence play a role?" It seems to be possible to measure decoherence on extremely short timescales of ∼10^-8s. This is especially important in view of recent developments in ultrafast electron microscopy.

Band gap modification and photoluminescence enhancement of graphene nanoribbon filled single-walled carbon nanotubes

Molecule encapsulation inside the single-walled carbon nanotube (SWCNT) core has been demonstrated to be a successful route for the modification of nanotube properties. SWCNT diameter-dependent filling results in band gap modification together with the enhancement of photoluminescence quantum yield. However, the interaction between the inner structure and the outer shell is complex. It depends on the orientation of the molecules inside, the geometry of the host nanotube and on several other mechanisms determining the resulting properties of the hybrid nanosystem. In this work we study the influence of encapsulated graphene nanoribbons on the optical properties of the host single-walled carbon nanotubes. The interplay of strain and dielectric screening caused by the internal environment of the nanotube affects its band gap. The photoluminescence of the filled nanotubes becomes enhanced when the graphene nanoribbons are polymerized inside the SWCNTs at low temperatures. We show a gradual photoluminescence quenching together with a selective signal enhancement for exact nanotube geometries, specifically (14,6) and (13,8) species. A precise adjustment of the optical properties and an enhancement of the photoluminescence quantum yield upon filling for nanotubes with specific diameters were assigned to optimal organization of the inner structures.

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.