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

Temperature-dependence of beam-driven dynamics in graphene-fullerene sandwiches

C60 fullerenes encapsulated between graphene sheets were investigated by aberration-corrected high-resolution transmission electron microscopy at different temperatures, namely about 93 K, 293 K and 733 K, and by molecular dynamics simulations. We studied beam-induced dynamics of the C60 fullerenes and the encapsulating graphene, measured the critical doses for the initial damage to the fullerenes and followed the beam-induced polymerization. We find that, while the doses for the initial damage do not strongly depend on temperature, the clusters formed by the subsequent polymerization are more tubular at lower temperatures, while sheet-like structures are generated at higher temperatures. The experimental findings are supported by the results of first-principles and analytical potential molecular dynamics simulations. The merging of curved carbon sheets is clearly promoted at higher temperatures and proceeds at once over few-nm segments.

In-situ imaging of heat-induced phase transition in a two-dimensional conjugated metal-organic framework

Atomically-resolved in-situ high-resolution transmission electron microscopy (HRTEM) imaging of the structural dynamics in organic materials remains a major challenge. This difficulty persists even with aberration-corrected instruments, as HRTEM images necessitate a high electron dose that is generally intolerable for organic materials. In this study, we report the in-situ HRTEM imaging of heat-induced structural dynamics in a benzenehexathiol-based two-dimensional conjugated metal-organic framework (2D c-MOF, i.e., Cu3(BHT)). Leveraging its hydrogen-free structure and high electrical conductivity, Cu3(BHT) exhibits high electron beam resistance. We demonstrate atomic resolution imaging at an 80 kV electron accelerating voltage using our Cc/Cs-corrected SALVE instrument. However, continuous electron irradiation eventually leads to its amorphization. Intriguingly, under heating in a MEMS holder, the Cu3(BHT) undergoes a phase transition to a new crystalline phase and its phase transition, occurring within the temperature range of 480 °C to 620 °C in dependence on the electron beam illumination. Using HRTEM and energy-dispersive X-ray mapping, we identify this new phase as CuS. Our findings provide insights into the mechanisms governing structural transitions in purposefully engineered structures, potentially pivotal for future endeavours involving the production of metal oxide/sulfide nanoparticles from MOF precursors.

Cinematographic study of stochastic chemical events at atomic resolution

The advent of single-molecule atomic-resolution time-resolved electron microscopy (SMART-EM) has created a new field of 'cinematic chemistry,' allowing for the cinematographic recording of dynamic behaviors of organic and inorganic molecules and their assembly. However, the limited electron dose per frame of video images presents a major challenge in SMART-EM. Recent advances in direct electron counting cameras and techniques to enhance image quality through the implementation of a denoising algorithm have enabled the tracking of stochastic molecular motions and chemical reactions with sub-millisecond temporal resolution and sub-angstrom localization precision. This review showcases the development of dynamic molecular imaging using the SMART-EM technique, highlighting insights into nanomechanical behavior during molecular shuttle motion, pathways of multistep chemical reactions, and elucidation of crystallization processes at the atomic level.

Atomic-Scale Imaging of Clay Mineral Nanosheets and Their Supramolecular Complexes through Electron Microscopy: A Supramolecular Chemist's Perspective

Recent advancements in electron microscopy techniques have revolutionized the ability to directly visualize and understand the intricate world of supramolecular chemistry. This paper provides a concise overview of a study delving into the atomic-scale imaging of monolayer clay mineral nanosheets and their associated supramolecular complexes. The imaging is conducted by harnessing the power of aberration-corrected scanning transmission electron microscopy (STEM). Clay mineral nanosheets, with their anionic charge and ultrathin thickness (of 1 nm), serve as a stable Coulombic host material for cationic guest molecules through electrostatic interactions, facilitating exceptional stability and control during observation. By incorporation of heavy-metal atom markers coordinated within the target molecules, high-angle annular dark field STEM enables a clear visualization of these supramolecular complexes. This approach helps to overcome the limitations of graphene-based systems and expands the possibilities of atomic-scale imaging of nonperiodic molecular assemblies formed by weak supramolecular interactions. The fusion of electron microscopy techniques with the principles of supramolecular and material chemistry offers exciting opportunities for studying the structure, behavior, and properties of complex supramolecular systems. It sheds light on the intricate molecular architectures and design principles governing these systems. This study showcases the immense potential of electron microscopy in supramolecular chemistry and invites researchers from various disciplines to explore the transformative possibilities of atomic-scale imaging in the field.

Understanding the Electron Beam Resilience of Two-Dimensional Conjugated Metal-Organic Frameworks

Knowledge of the atomic structure of layer-stacked two-dimensional conjugated metal-organic frameworks (2D c-MOFs) is an essential prerequisite for establishing their structure-property correlation. For this, atomic resolution imaging is often the method of choice. In this paper, we gain a better understanding of the main properties contributing to the electron beam resilience and the achievable resolution in the high-resolution TEM images of 2D c-MOFs, which include chemical composition, density, and conductivity of the c-MOF structures. As a result, sub-angstrom resolution of 0.95 Å has been achieved for the most stable 2D c-MOF of the considered structures, Cu3(BHT) (BHT = benzenehexathiol), at an accelerating voltage of 80 kV in a spherical and chromatic aberration-corrected TEM. Complex damage mechanisms induced in Cu3(BHT) by the elastic interactions with the e-beam have been explained using detailed ab initio molecular dynamics calculations. Experimental and calculated knock-on damage thresholds are in good agreement.

Electron beam-induced demetallation of Fe, Co, Ni, Cu, Zn, Pd, and Pt metalloporphyrins: insights in e-beam chemistry and metal cluster formations

Electron beams are versatile tools for nanoscale fabrication processes, however, the underlying e-beam chemistry remains in its infancy. Through operando transmission electron microscopy investigations, we elucidate a redox-driven cargo release of individual metal atoms triggered by electron beams. The chosen organic delivery molecule, tetraphenylporphyrin (TPP), proves highly versatile, forming complexes with nearly all metals from the periodic table and being easily processed in solution. A comprehensive cinematographic analysis of the dynamics of single metal atoms confirms the nearly instantaneous ejection of complexed metal atoms under an 80 kV electron beam, underscoring the system's broad versatility. Providing mechanistic insights, we employ density functional theory to support the proposed reductive demetallation pathway facilitated by secondary electrons, contributing novel perspectives to electron beam-mediated chemical reaction mechanisms. Lastly, our findings demonstrate that all seven metals investigated form nanoclusters once ejected from TPP, highlighting the method's potential for studying and developing sustainable single-atom and nanocluster catalysts.

Characterization of emerging 2D materials after chemical functionalization

The chemical modification of 2D materials has proven a powerful tool to fine tune their properties. With this motivation, the development of new reactions has moved extremely fast. The need for speed, together with the intrinsic heterogeneity of the samples, has sometimes led to permissiveness in the purification and characterization protocols. In this review, we present the main tools available for the chemical characterization of functionalized 2D materials, and the information that can be derived from each of them. We then describe examples of chemical modification of 2D materials other than graphene, focusing on the chemical description of the products. We have intentionally selected examples where an above-average characterization effort has been carried out, yet we find some cases where further information would have been welcome. Our aim is to bring together the toolbox of techniques and practical examples on how to use them, to serve as guidelines for the full characterization of covalently modified 2D materials.

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.

Atomic-Scale Time-Resolved Imaging of Krypton Dimers, Chains and Transition to a One-Dimensional Gas

Single-atom dynamics of noble-gas elements have been investigated using time-resolved transmission electron microscopy (TEM), with direct observation providing for a deeper understanding of chemical bonding, reactivity, and states of matter at the nanoscale. We report on a nanoscale system consisting of endohedral fullerenes encapsulated within single-walled carbon nanotubes ((Kr@C60)@SWCNT), capable of the delivery and release of krypton atoms on-demand, via coalescence of host fullerene cages under the action of the electron beam (in situ) or heat (ex situ). The state and dynamics of Kr atoms were investigated by energy dispersive X-ray spectroscopy (EDS), electron energy loss spectroscopy (EELS), and X-ray photoelectron spectroscopy (XPS). Kr atom positions were measured precisely using aberration-corrected high-resolution TEM (AC-HRTEM), aberration-corrected scanning TEM (AC-STEM), and single-atom spectroscopic imaging (STEM-EELS). The electron beam drove the formation of 2Kr@C120 capsules, in which van der Waals Kr2 and transient covalent [Kr2]+ bonding states were identified. Thermal coalescence led to the formation of longer coalesced nested nanotubes containing more loosely bound Krn chains (n = 3-6). In some instances, delocalization of Kr atomic positions was confirmed by STEM analysis as the transition to a one-dimensional (1D) gas, as Kr atoms were constrained to only one degree of translational freedom within long, well-annealed, nested nanotubes. Such nested nanotube structures were investigated by Raman spectroscopy. This material represents a highly compressed and dimensionally constrained 1D gas stable under ambient conditions. Direct atomic-scale imaging has revealed elusive bonding states and a previously unseen 1D gaseous state of matter of this noble gas element, demonstrating TEM to be a powerful tool in the discovery of chemistry at the single-atom level.

Electron-beam-promoted fullerene dimerization in nanotubes: insights from DFT computations

Fullerene dimerization inside a peapod is analyzed at DFT level by characterizing the stationary points and deriving the energy profile of the initial and reversible process named phase 1. We find that the barriers for the radical cation mechanism are significantly lower than those found for the neutral pathway. The peapod is mainly providing one-dimensional confinement for the reaction to take place in a more efficient way. Car-Parrinello metadynamics simulations provide hints on structures for the initial steps of the irreversible phase 2 where bond formation and breaking lead to important structural reorganizations within the coalescence process.

Revolutionizing the structural design and determination of covalent-organic frameworks: principles, methods, and techniques

Covalent organic frameworks (COFs) represent an important class of crystalline porous materials with designable structures and functions. The interconnected organic monomers, featuring pre-designed symmetries and connectivities, dictate the structures of COFs, endowing them with high thermal and chemical stability, large surface area, and tunable micropores. Furthermore, by utilizing pre-functionalization or post-synthetic functionalization strategies, COFs can acquire multifunctionalities, leading to their versatile applications in gas separation/storage, catalysis, and optoelectronic devices. Our review provides a comprehensive account of the latest advancements in the principles, methods, and techniques for structural design and determination of COFs. These cutting-edge approaches enable the rational design and precise elucidation of COF structures, addressing fundamental physicochemical challenges associated with host-guest interactions, topological transformations, network interpenetration, and defect-mediated catalysis.

Formation of carbon propeller-like molecules from starphenes under electron irradiation

Formation of carbon propeller-like molecules (CPLMs) from starphenes on a graphene substrate under electron irradiation with about 100% yield is observed in molecular dynamics simulations using the REBO-1990EVC_CH potential and CompuTEM algorithm. A CPLM consists of three carbon atomic chains connected to the central hexagon and is formed as a result of the spontaneous breaking of bonds between zigzag atomic rows in starphene arms after hydrogen removal by electron impacts. In the absence of the substrate, the CPLM yield is slightly decreased due to sticking between forming chains, while the formation time is increased threefold. The increase of the kinetic electron energy from 45 to 80 keV has no effect on the CPLM formation. Density functional theory (DFT) calculations performed show the stability of CPLMs with respect to the formation of new bonds between carbon atoms in the chains. DFT calculations using the accurate hybrid B3LYP functional provide an insight into the electronic structure of these new molecules.

Time-resolved imaging and analysis of the electron beam-induced formation of an open-cage metallo-azafullerene

The visualization of single-molecule reactions provides crucial insights into chemical processes, and the ability to do so has grown with the advances in high-resolution transmission electron microscopy. There is currently a limited mechanistic understanding of chemical reactions under the electron beam. However, such reactions may enable synthetic methodologies that cannot be accessed by traditional organic chemistry methods. Here we demonstrate the synthetic use of the electron beam, by in-depth single-molecule, atomic-resolution, time-resolved transmission electron microscopy studies, in inducing the formation of a doubly holed fullerene-porphyrin cage structure from a well-defined benzoporphyrin precursor deposited on graphene. Through real-time imaging, we analyse the hybrid's ability to host up to two Pb atoms, and subsequently probe the dynamics of the Pb-Pb binding motif in this exotic metallo-organic cage structure. Through simulation, we conclude that the secondary electrons, which accumulate in the periphery of the irradiated area, can also initiate chemical reactions. Consequently, designing advanced carbon nanostructures by electron-beam lithography will depend on the understanding and limitations of molecular radiation chemistry.

An Unusual Microdomain Factor Controls Interaction of Organic Halides with the Palladium Phase and Influences Catalytic Activity in the Mizoroki-Heck Reaction

In this work, using a combination of scanning and transmission electron microscopy (SEM and TEM), the transformations of palladium-containing species in imidazolium ionic liquids in reaction mixtures of the Mizoroki-Heck reaction and in related organic media are studied to understand a challenging question of the relative reactivity of organic halides as key substrates in modern catalytic technologies. The microscopy technique detects the formation of a stable nanosized palladium phase under the action of an aryl (Ar) halide capable of forming microcompartments in an ionic liquid. For the first time, the correlation between the reactivity of the aryl halide and the microdomain structure is observed: Ar-I (well-developed microdomains) > Ar-Br (microphase present) > Ar-Cl (minor amount of microphase). Previously, it is assumed that molecular level factors, namely, carbon-halogen bond strength and the ease of bond breakage, are the sole factors determining the reactivity of aryl halides in catalytic transformations. The present work reports a new factor connected with the nature of the organic substrates used and their ability to form a microdomain structure and concentrate metallic species, highlighting the importance of considering both the molecular and microscale properties of the reaction mixtures.

Bimetallic Nanoalloy Catalysts for Green Energy Production: Advances in Synthesis Routes and Characterization Techniques

Bimetallic Nanoalloy catalysts have diverse uses in clean energy, sensing, catalysis, biomedicine, and energy storage, with some supported and unsupported catalysts. Conventional synthetic methods for producing bimetallic alloy nanoparticles often produce unalloyed and bulky particles that do not exhibit desired characteristics. Alloys, when prepared with advanced nanoscale methods, give higher surface area, activity, and selectivity than individual metals due to changes in their electronic properties and reduced size. This review demonstrates the synthesis methods and principles to produce and characterize highly dispersed, well-alloyed bimetallic nanoalloy particles in relatively simple, effective, and generalized approaches and the overall existence of conventional synthetic methods with modifications to prepare bimetallic alloy catalysts. The basic concepts and mechanistic understanding are represented with purposely selected examples. Herein, the enthralling properties with widespread applications of nanoalloy catalysts in heterogeneous catalysis are also presented, especially for Hydrogen Evolution Reaction (HER), Oxidation Reduction Reaction (ORR), Oxygen Evolution Reaction (OER), and alcohol oxidation with a particular focus on Pt and Pd-based bimetallic nanoalloys and their numerous fields of applications. The high entropy alloy is described as a complicated subject with an emphasis on laser-based green synthesis of nanoparticles and, in conclusion, the forecasts and contemporary challenges for the controlled synthesis of nanoalloys are addressed.

Direct visualization of carbon black aggregates in nitrile butadiene rubber by THz near-field microscope

The use of filling agents for rubber reinforcement is beneficial in various industrial applications, and several experimental methods have been used to study the effect of fillers on rubber. However, due to the lack of a suitable imaging technique, filler dispersion and distribution in rubber cannot be easily displayed. Thus, we utilize the THz near-field microscope (THz-NFM) to directly visualize the distribution of carbon black (CB) aggregates in nitrile butadiene rubber (NBR). The THz time-domain spectroscopy (THz-TDS) was used to evaluate the optical properties of the NBR specimens. Results revealed significant indices contrast between CB and NBR at the THz regime, which was attributed to the variation in electrical conductivities. The micrographs of NBR in the THz-NFM revealed the distribution of CB aggregates. The area fraction (AF) of the CB aggregates was calculated using a binary thresholding algorithm to compare with the transmission electron microscope method. Both methods yielded comparable AF values, suggesting, for the first time, that CB can be detected in the NBR without preprocessing the specimens.

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.

An Organic Molecular Nanobarrel that Hosts and Solubilizes C60

Organic cages have gained increasing attention in recent years as molecular hosts and porous materials. Among these, barrel-shaped cages or molecular nanobarrels are promising systems to encapsulate large hosts as they possess windows of the same size as their internal cavity. However, these systems have received little attention and remain practically unexplored despite their potential. Herein, we report the design and synthesis of a new trigonal prismatic organic nanobarrel with two large triangular windows with a diameter of 12.7 Å optimal for the encapsulation of C₆₀ . Remarkably, this organic nanobarrel shows a high affinity for C₆₀ in solvents in which C₆₀ is virtually insoluble, providing stable solutions of C₆₀ .

Host-Guest Chemistry in Boron Nitride Nanotubes: Interactions with Polyoxometalates and Mechanism of Encapsulation

Boron nitride nanotubes (BNNTs) are an emerging class of molecular container offering new functionalities and possibilities for studying molecules at the nanoscale. Herein, BNNTs are demonstrated as highly effective nanocontainers for polyoxometalate (POM) molecules. The encapsulation of POMs within BNNTs occurs spontaneously at room temperature from an aqueous solution, leading to the self-assembly of a POM@BNNT host-guest system. Analysis of the interactions between the host-nanotube and guest-molecule indicate that Lewis acid-base interactions between W═O groups of the POM (base) and B-atoms of the BNNT lattice (acid) likely play a major role in driving POM encapsulation, with photoactivated electron transfer from BNNTs to POMs in solution also contributing to the process. The transparent nature of the BNNT nanocontainer allows extensive investigation of the guest-molecules by photoluminescence, Raman, UV-vis absorption, and EPR spectroscopies. These studies revealed considerable energy and electron transfer processes between BNNTs and POMs, likely mediated via defect energy states of the BNNTs and resulting in the quenching of BNNT photoluminescence at room temperature, the emergence of new photoluminescence emissions at cryogenic temperatures (<100 K), a photochromic response, and paramagnetic signals from guest-POMs. These phenomena offer a fresh perspective on host-guest interactions at the nanoscale and open pathways for harvesting the functional properties of these hybrid systems.

Single‐Walled Carbon Nanotubes Encapsulated within Metallacycles

Mechanically interlocked derivatives of carbon nanotubes (MINTs) are interesting nanotube products since they show high stability without altering the carbon nanotube structure. So far, MINTs have been synthesized using ring‐closing metathesis, disulfide exchange reaction, H‐bonding or direct threading with macrocycles. Here, we describe the encapsulation of single‐walled carbon nanotubes within a palladium‐based metallosquare. The formation of MINTs was confirmed by a variety of techniques, including high‐resolution transmission electron microscopy. We find the making of these MINTs is remarkably sensitive to structural variations of the metallo‐assemblies. When a metallosquare with a cavity of appropriate shape and size is used, the formation of the MINT proceeds successfully by both templated clipping and direct threading. Our studies also show indications on how supramolecular coordination complexes can help expand the potential applications of MINTs.

Time-Resolved Imaging of Stochastic Cascade Reactions over a Submillisecond to Second Time Range at the Angstrom Level

Many chemical reactions, such as multistep catalytic cycles, are cascade reactions in which a series of transient intermediates appear and disappear stochastically over an extended period. The mechanisms of such reactions are challenging to study, even in ultrafast pump-probe experiments. The dimerization of a van der Waals dimer of [60]fullerene producing a short carbon nanotube is a typical cascade reaction and is probably the most frequently studied in carbon materials chemistry. As many as 23 intermediates were predicted by theory, but only the first stable one has been verified experimentally. With the aid of fast electron microscopy, we obtained cinematographic recordings of individual molecules at a maximum frame rate of 1600 frames per second. Using Chambolle total variation algorithm processing and automated cross-correlation image matching analysis, we report on the identification of several metastable intermediates by their shape and size. Although the reaction events occurred stochastically, varying the lifetime of each intermediate accordingly, the average lifetime for each intermediate structure could be obtained from statistical analysis of many cinematographic images for the cascade reaction. Among the shortest-living intermediates, we detected one that lasted less than 3 ms in three independent cascade reactions. We anticipate that the rapid technological development of microscopy and image processing will soon initiate an era of cinematographic studies of chemical reactions and cinematic chemistry.

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.

Nanodelivery of nucleic acids

There is growing need for a safe, efficient, specific and non-pathogenic means for delivery of gene therapy materials. Nanomaterials for nucleic acid delivery offer an unprecedented opportunity to overcome these drawbacks; owing to their tunability with diverse physico-chemical properties, they can readily be functionalized with any type of biomolecules/moieties for selective targeting. Nucleic acid therapeutics such as antisense DNA, mRNA, small interfering RNA (siRNA) or microRNA (miRNA) have been widely explored to modulate DNA or RNA expression Strikingly, gene therapies combined with nanoscale delivery systems have broadened the therapeutic and biomedical applications of these molecules, such as bioanalysis, gene silencing, protein replacement and vaccines. Here, we overview how to design smart nucleic acid delivery methods, which provide functionality and efficacy in the layout of molecular diagnostics and therapeutic systems. It is crucial to outline some of the general design considerations of nucleic acid delivery nanoparticles, their extraordinary properties and the structure-function relationships of these nanomaterials with biological systems and diseased cells and tissues.

Atomic-number (Z)-correlated atomic sizes for deciphering electron microscopic molecular images

Atomic resolution transmission electron microscopy (TEM) has opened up a new era of molecular science by providing atomic video images of dynamic motions of single organic and inorganic molecules. However, the images often look different from the images of molecular models, because these models are designed to visualize the electronic properties of the molecule instead of nuclear electrostatic potentials that are felt by the e-beam in TEM imaging. Here, we propose a molecular model that reproduces TEM images using atomic radii correlated to atomic number (Z). The model serves to provide a priori a useful idea of how a single molecule, molecular assemblies, and thin crystals of organic or inorganic materials look in TEM.

With the advent of atomic resolution transmission electron microscopy (AR-TEM) achieving sub-Ångstrom image resolution and submillisecond time resolution, an era of cinematic molecular science where chemists can visually study the time evolution of molecular motions and reactions at atomistic precision has arrived. However, the appearance of experimental TEM images often differs greatly from that of conventional molecular models, and the images are difficult to decipher unless we know in advance the structure of the specimen molecules. The difference arises from the fundamental design of the molecular models that represent atomic connectivity and/or the electronic properties of molecules rather than the nuclear charge of atoms and electrostatic potentials that are felt by the e-beam in TEM imaging. We found a good correlation between the atomic number (Z) and the atomic size seen in TEM images when we consider shot noise in digital images. We propose Z-correlated (ZC) atomic radii for modeling AR-TEM images of single molecules and ultrathin crystals with which we can develop a good estimate of the molecular structure from the TEM image much more easily than with conventional molecular models. Two parameter sets were developed for TEM images recorded under high-noise (ZC_HN) and low-noise (ZC_LN) conditions. The molecular models will stimulate the imaginations of chemists planning to use AR-TEM for their research.

Multi-step atomic mechanism of platinum nanocrystals nucleation and growth revealed by in-situ liquid cell STEM

The understanding of crystal growth mechanisms has broadened substantially. One significant advancement is based in the conception that the interaction between particles plays an important role in the growth of nanomaterials. This is in contrast to the classical model, which neglects this process. Direct imaging of such processes at atomic-level in liquid-phase is essential for establishing new theoretical models that encompass the full complexity of realistic scenarios and eventually allow for tailoring nanoparticle growth. Here, we investigate at atomic-scale the exact growth mechanisms of platinum nanocrystals from single atom to final crystals by in-situ liquid phase scanning transmission electron microscopy. We show that, after nucleation, the nanocrystals grow via two main stages: atomic attachment in the first stage, where the particles initially grow by attachment of the atoms until depletion of the surrounding zone. Thereafter, follows the second stage of growth, which is based on particle attachment by different atomic pathways to finally form mature nanoparticles. The atomic mechanisms underlying these growth pathways are distinctly different and have different driving forces and kinetics as evidenced by our experimental observations.

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.

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.

Piecing Together Large Polycyclic Aromatic Hydrocarbons and Fullerenes: A Combined ChemTEM Imaging and MALDI-ToF Mass Spectrometry Approach

Motivated by their importance in chemistry, physics, astronomy and materials science, we investigate routes to the formation of large polycyclic aromatic hydrocarbon (PAH) molecules and the fullerene C₆₀ from specific smaller PAH building blocks. The behaviour of selected PAH molecules under electron (using transmission electron microscopy, TEM) and laser irradiation is examined, where four specific PAHs—anthracene, pyrene, perylene and coronene—are assembling into larger structures and fullerenes. This contrasts with earlier TEM studies in which large graphene flakes were shown to transform into fullerenes via a top-down route. A new combined approach is presented in which spectrometric and microscopic experimental techniques exploit the stabilisation of adsorbed molecules through supramolecular interactions with a graphene substrate and enable the molecules to be characterised and irradiated sequentially. Thereby allowing initiation of transformation and characterisation of the resultant species by both mass spectrometry and direct-space imaging. We investigate the types of large PAH molecule that can form from smaller PAHs, and discuss the potential of a “bottom-up” followed by “top-down” mechanism for forming C₆₀.

Neural Network Analysis of Electron Microscopy Video Data Reveals the Temperature-Driven Microphase Dynamics in the Ions/Water System

Real-time field-emission scanning electron microscopy (FE-SEM) measurements and neural network analysis were successfully merged to observe the temperature-induced behavior of soft liquid microdomains in mixtures of different ionic liquids with water. The combination of liquid FE-SEM and in situ heating techniques revealed temperature-driven solution restructuring for ions/water systems with different water states and their critical point behavior expressed in a rapid switch between thermal expansion and shrinkage of liquid microphases at temperatures of ≈100-130 °C, which was directly recorded on electron microscopy videos. Automation of FE-SEM video analysis by a neural network approach allowed quantification of the morphological changes in ions/water systems during heating on the basis of thousands of images processed with a speed almost equal to the frame rate of original electron microscopy videos. Tracking and evolution of the micro-heterogeneous domains, hypothesized in the Ioliomics concept, was mapped and quantified for the first time. The present study describes the concept for quick acquisition of big data in electron microscopy, develops rapid neural network analysis and shows how to link microscopic data to fundamental molecular properties.

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.

Near-atomic-scale observation of grain boundaries in a layer-stacked two-dimensional polymer

Two-dimensional (2D) polymers hold great promise in the rational materials design tailored for next-generation applications. However, little is known about the grain boundaries in 2D polymers, not to mention their formation mechanisms and potential influences on the material's functionalities. Using aberration-corrected high-resolution transmission electron microscopy, we present a direct observation of the grain boundaries in a layer-stacked 2D polyimine with a resolution of 2.3 Å, shedding light on their formation mechanisms. We found that the polyimine growth followed a "birth-and-spread" mechanism. Antiphase boundaries implemented a self-correction to the missing-linker and missing-node defects, and tilt boundaries were formed via grain coalescence. Notably, we identified grain boundary reconstructions featuring closed rings at tilt boundaries. Quantum mechanical calculations revealed that boundary reconstruction is energetically allowed and can be generalized into different 2D polymer systems. We envisage that these results may open up the opportunity for future investigations on defect-property correlations in 2D polymers.

Confinement of Dyes inside Boron Nitride Nanotubes: Photostable and Shifted Fluorescence down to the Near Infrared

Fluorescence is ubiquitous in life science and used in many fields of research ranging from ecology to medicine. Among the most common fluorogenic compounds, dyes are being exploited in bioimaging for their outstanding optical properties from UV down to the near IR (NIR). However, dye molecules are often toxic to living organisms and photodegradable, which limits the time window for in vivo experiments. Here, it is demonstrated that organic dye molecules are passivated and photostable when they are encapsulated inside a boron nitride nanotube (dyes@BNNT). The results show that the BNNTs drive an aggregation of the encapsulated dyes, which induces a redshifted fluorescence from visible to NIR-II. The fluorescence remains strong and stable, exempt of bleaching and blinking, over a time scale longer than that of free dyes by more than 10⁴ . This passivation also reduces the toxicity of the dyes and induces exceptional chemical robustness, even in harsh conditions. These properties are highlighted in bioimaging where the dyes@BNNT nanohybrids are used as fluorescent nanoprobes for in vivo monitoring of Daphnia Pulex microorganisms and for diffusion tracking on human hepatoblastoma cells with two-photon imaging.

Atomic-Scale Imaging of a Free-Standing Monolayer Clay Mineral Nanosheet Using Scanning Transmission Electron Microscopy

Although aberration-corrected scanning transmission electron microscope (STEM) enables the atomic-scale visualization of ultrathin 2D materials such as graphene, imaging of electron-beam sensitive 2D materials with structural complexity is an intricate problem. We here report the first atomic-scale imaging of a free-standing monolayer clay mineral nanosheet via the annular dark field (ADF) STEM. The monolayer clay nanosheet was stably observed under optimal conditions, and we confirmed that the hexagonal contrast pattern with a pore of ∼4 Å corresponds to the atomic structure of clay mineral that consisted of adjacent Si, Al, Mg, and O atoms by comparison with simulations. The findings offer the usefulness of ADF-STEM techniques for the atomic scale imaging of clay minerals and various 2D materials having electron-beam sensitivity and structural complexity than few-atom-thick graphene analogues.

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.

Real-Time Visualization of Solid-Phase Ion Migration Kinetics on Nanowire Monolayer

Ion migration has been recognized as a critical step in determining the performance of numerous devices in chemistry, biology, and material science. However, direct visualization and quantitative investigation of solid-phase ion migration among anisotropic nanostructures have been a challenging task. Here, we report an in-situ ChemTEM method to quantitatively investigate the solid-phase ion migration process among coassembled nanowires (NWs). This complicated process was tracked within a NW and between NWs with an obvious nanogap, which was revealed by both phase field simulation and ab initio modeling theoretical evaluation. A migration "bridge" between neighboring NWs was observed. Furthermore, these new observations could be applied to migration of other metal ions on semiconductor NWs. These findings provide critical insights into the solid-phase ion migration kinetics occurring in nanoscale systems with generality and offer an efficient tool to explore other ion migration processes, which will facilitate fabrication of customized and new heteronanostructures in the future.

Distinctive stability of a free-standing monolayer clay mineral nanosheet via transmission electron microscopy

The distinctive stability of the monolayer clay mineral demonstrated by electron diffraction.

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.

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.