Electron Microscopic Observation of Selective Excitation of Conformational Change of a Single Organic Molecule

Covalent functionalization of 1D and 2D sp2-carbon nanoallotropes - twelve years of progress (2011-2023)

Carbon nanoallotropes have attracted significant attention in the field of materials science due to their unique combination of physicochemical and biological properties, with numerous applications. One-dimensional (1D) and two-dimensional (2D) sp2-carbon nanoallotropes, such as carbon nanohorns (CNHs), carbon nanotubes (CNTs), and graphene, have emerged as prominent candidates for a variety of technological advancements. To fully exploit their exceptional characteristics, the covalent functionalization of these nanostructures may alleviate the problems with the processing and final performance. This route of the carbon nanoallotrope functionalization is based on a covalent attachment of functional groups or molecules (via linkers of various strengths) to their surfaces, enabling precise control over physical, chemical, biological, and electronic properties. Such an approach opens up new avenues for tailoring the nanoallotrope characteristics, such as solubility/dispersibility, reactivity, and interactions with other materials. Over more than the last decade, significant progress has been made in the covalent functionalization of both 1D and 2D sp2-carbon nanoallotropes, paving the way for diverse applications in the nanoelectronics, energy storage, sensing, and biomedical fields. In this comprehensive review, we provide state-of-the-art advancements and achievements in the covalent functionalization of 1D and 2D sp2-carbon nanoallotropes during the past dozen years. We aim to highlight the key strategies, methodologies, and breakthroughs that have significantly contributed to this field. Eventually, we discuss the implications of those advancements and explore the opportunities for future research and applications.

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.

Single-Site Carbon-Supported Metal-Oxo Complexes in Heterogeneous Catalysis: Structure, Reactivity, and Mechanism

When early transition metal complexes are molecularly grafted onto catalyst supports, well-defined, surface-bound species are created, which are highly active and selective single-site heterogeneous catalysts (SSHCs) for diverse chemical transformations. In this minireview, we analyze and summarize a less conventional type of SSHC in which molybdenum dioxo species are grafted onto unusual carbon-unsaturated scaffolds, such as activated carbon, reduced graphene oxide, and carbon nanohorns. The choice of earth-abundant, low-toxicity, versatile metal constituents, and various carbon supports illustrates "catalyst by design" principles and yields insights into new catalytic systems of both academic and technological interest. Here, we summarize experimental and computational investigations of the bonding, electronic structure, reaction scope, and mechanistic pathways of these unusual catalysts.

Cinematographic Recording of a Metastable Floating Island in Two- and Three-Dimensional Crystal Growth

Many chemical reactions go through a cascade of events in which a series of metastable intermediates appear, and crystal nucleation is no exception. Although the consensus on the energetics of nucleation suggests the formation of metastable states preceding the crystal growth, little experimental evidence has been reported for their dynamics at an atomistic level. Operando imaging of two-dimensional nucleation on a defect-free NaCl nanocrystal in carbon nanotubes using a millisecond angstrom-resolution transmission electron microscope revealed the formation of a metastable "floating island" (FI) that migrates thermally on the (100) facet of NaCl as the first intermediate of epitaxy. The speed of the migration at 298 K is estimated to be larger than 0.3 nm ms^-1. When a crystal tumbles in a container, a space repeatedly forms between the crystal and the container wall that hosts the FI. Tumbling changes the surface energy repeatedly and promotes the conversion of the FI into a new epitaxial layer. We anticipate that this surface catalysis mechanism found on the nanoscale also operates in bulk heterogeneous nucleation where agitation and attrition accelerate crystallization.

Synergistically Activated Pd Atom in Polymer-Stabilized Au23Pd1 Cluster

Single Pd atom doped Au₂₃Pd₁ clusters stabilized by polyvinylpyrrolidone (Au₂₃Pd₁:PVP) were selectively synthesized by kinetically controlled coreduction of the Au and Pd precursor ions. The geometric structure of Au₂₃Pd₁:PVP was investigated by density functional theory calculation, aberration-corrected transmission electron microscopy, extended X-ray absorption fine structure analysis, Fourier transform infrared spectroscopy of adsorbed CO, and hydrogenation catalysis. These results showed that Au₂₃Pd₁:PVP takes polydisperse but the same atomic arrangements as undoped Au₂₄:PVP while exposing all the atoms including the Pd atom on the surface. Au₂₃Pd₁:PVP exhibited a significantly higher catalytic activity than Au₂₄:PVP for the aerobic oxidation of p-substituted benzyl alcohols. The kinetic studies showed that the rate-determining step was the hydride abstraction from the α-carbon of the alkoxides for both systems. The activation energy for hydride abstraction by Au₂₃Pd₁:PVP was lower than that by Au₂₄:PVP, indicating that the doped Pd atom acts as the active center.

Time-Resolved Atomistic Imaging and Statistical Analysis of Daptomycin Oligomers with and without Calcium Ions

Daptomycin (DP) is effective against multiple drug-resistant Gram-positive pathogens because of its distinct mechanism of action. An accepted mechanism includes Ca²⁺-triggered aggregation of the DP molecule to form oligomers. DP and its oligomers have so far defied structural analysis at a molecular level. We studied the ability of DP molecule to aggregate by itself in water, the effects of Ca²⁺ ions to promote the aggregation, and the connectivity of the DP molecules in the oligomers by the combined use of dynamic light scattering in water and atomic-resolution cinematographic imaging of DP molecules captured on a carbon nanotube on which the DP molecule is installed as a fishhook. We found that the DP molecule aggregates weakly into dimers, trimers, and tetramers in water, and strongly in the presence of calcium ions, and that the tetramer is the largest oligomer in homogeneous aqueous solution. The dimer remains as the major species, and we propose a face-to-face stacked structure based on dynamic imaging using millisecond and angstrom resolution transmission electron microscopy. The tetramer in its cyclic form is the largest oligomer observed, while the trimer forms in its linear form. The study has shown that the DP molecule has an intrinsic property of forming tetramers in water, which is enhanced by the presence of calcium ions. Such experimental structural information will serve as a platform for future drug design. The data also illustrate the utility of cinematographic recording for the study of self-organization processes.

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.

Meta-Analysis of Children's Acute Psychological Stress and Action Stress on Immune Function under Microscope Images

The immune system is a complex system, mainly including immune cells and immune organs. When the human body is invaded by foreign substances, the immune system will play a role in resisting the attack of harmful substances and pure necrotic cells, which is the defense structure of the body. The purpose of this study was to analyze children's acute psychological stress and action stress, and judge the adverse effects on immune function. Through the stress experiment of rats, three experimental groups were set up, which were placebo control group, placebo stress group, and drug stress group. The experiments include material-level test, sugar preference test, body weight test, and lymphocyte test. The experimental data show that stress reaction not only causes negative emotions, but also reduces weight gain by about 5%, and sugar preference decreases by about 40% compared with the normal group. There was no significant difference in the number of granulocytes and intermediate cells in the blood, but the number of lymphocytes increased from 2.49 × 109/L to 5.03 × 109/L. It shows that acute psychological stress has an inhibitory effect on the immune function of the body; not only suitable load exercise can improve the immune function of the body but also the mechanism may be that moderate load exercise makes the rat axis has better adaptability, and improves hormones, cytokines, and cytokines. The secretion of neurotransmitters can maintain the stability of the body's immune function.

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.

New Magic Au24 Cluster Stabilized by PVP: Selective Formation, Atomic Structure, and Oxidation Catalysis

An unprecedented magic number cluster, Au24Cl x (x = 0-3), was selectively synthesized by the kinetically controlled reduction of the Au precursor ions in a microfluidic mixer in the presence of a large excess of poly(N-vinyl-2-pyrrolidone) (PVP). The atomic structure of the PVP-stabilized Au24Cl x was investigated by means of aberration-corrected transmission electron microscopy (ACTEM) and density functional theory (DFT) calculations. ACTEM video imaging revealed that the Au24Cl x clusters were stable against dissociation but fluctuated during the observation period. Some of the high-resolution ACTEM snapshots were explained by DFT-optimized isomeric structures in which all the constituent atoms were located on the surface. This observation suggests that the featureless optical spectrum of Au24Cl x is associated with the coexistence of distinctive isomers. X-ray photoelectron spectroscopy and Fourier-transform infrared spectroscopy of CO adsorbates revealed the electron-rich nature of Au24Cl x clusters due to the interaction with PVP. The Au24Cl x :PVP clusters catalyzed the aerobic oxidation of benzyl alcohol derivatives without degradation. Hammett analysis and the kinetic isotope effect indicated that the hydride elimination by Au24Cl x was the rate-limiting step with an apparent activation energy of 56 ± 3 kJ/mol, whereas the oxygen pressure dependence of the reaction kinetics suggested the involvement of hydrogen abstraction by coadsorbed O2 as a faster process.

Ultra-Fast Electron Microscopic Imaging of Single Molecules With a Direct Electron Detection Camera and Noise Reduction

Time-resolved imaging of molecules and materials made of light elements is an emerging field of transmission electron microscopy (TEM), and the recent development of direct electron detection cameras, capable of taking as many as 1,600 fps, has potentially broadened the scope of the time-resolved TEM imaging in chemistry and nanotechnology. However, such a high frame rate reduces electron dose per frame, lowers the signal-to-noise ratio (SNR), and renders the molecular images practically invisible. Here, we examined image noise reduction to take the best advantage of fast cameras and concluded that the Chambolle total variation denoising algorithm is the method of choice, as illustrated for imaging of a molecule in the 1D hollow space of a carbon nanotube with ~1 ms time resolution. Through the systematic comparison of the performance of multiple denoising algorithms, we found that the Chambolle algorithm improves the SNR by more than an order of magnitude when applied to TEM images taken at a low electron dose as required for imaging at around 1,000 fps. Open-source code and a standalone application to apply Chambolle denoising to TEM images and video frames are available for download.

Stereochemistry of Simple Molecules inside Nanotubes and Fullerenes: Unusual Behavior of Usual Systems

Over the past three decades, carbon nanotubes and fullerenes have become remarkable objects for starting the implementation of new models and technologies in different branches of science. To a great extent, this is defined by the unique electronic and spatial properties of nanocavities due to the ramified π-electron systems. This provides an opportunity for the formation of endohedral complexes containing non-covalently bonded atoms or molecules inside fullerenes and nanotubes. The guest species are exposed to the force field of the nanocavity, which can be described as a combination of electronic and steric requirements. Its action significantly changes conformational properties of even relatively simple molecules, including ethane and its analogs, as well as compounds with C-O, C-S, B-B, B-O, B-N, N-N, Al-Al, Si-Si and Ge-Ge bonds. Besides that, the cavity of the host molecule dramatically alters the stereochemical characteristics of cyclic and heterocyclic systems, affects the energy of pyramidal nitrogen inversion in amines, changes the relative stability of cis and trans isomers and, in the case of chiral nanotubes, strongly influences the properties of R- and S- enantiomers. The present review aims at primary compilation of such unusual stereochemical effects and initial evaluation of the nature of the force field inside nanotubes and fullerenes.

Nanoparticle Characterization: What to Measure?

What to measure? is a key question in nanoscience, and it is not straightforward to address as different physicochemical properties define a nanoparticle sample. Most prominent among these properties are size, shape, surface charge, and porosity. Today researchers have an unprecedented variety of measurement techniques at their disposal to assign precise numerical values to those parameters. However, methods based on different physical principles probe different aspects, not only of the particles themselves, but also of their preparation history and their environment at the time of measurement. Understanding these connections can be of great value for interpreting characterization results and ultimately controlling the nanoparticle structure-function relationship. Here, the current techniques that enable the precise measurement of these fundamental nanoparticle properties are presented and their practical advantages and disadvantages are discussed. Some recommendations of how the physicochemical parameters of nanoparticles should be investigated and how to fully characterize these properties in different environments according to the intended nanoparticle use are proposed. The intention is to improve comparability of nanoparticle properties and performance to ensure the successful transfer of scientific knowledge to industrial real-world applications.

Chemical kinetics study through observation of individual reaction events with atomic-resolution electron microscopy

Single-molecule atomic-resolution real-time electron microscopic movie imaging is an emerging new tool for obtaining dynamic structural information on molecules and molecular assemblies. This method provides a hitherto inaccessible possibility to in situ observe the time evolution of chemical events at various temperatures from the beginning till the end, as demonstrated for the kinetics study of [2 + 2] cycloaddition of [60]fullerene molecules, which was found to occur via an excited state or via radical cation depending on the temperature. One unique feature of this methodology is that, by observing directly the reaction events, one can obtain information on the frequency of events unperturbed by molecular diffusion. With the obtained experimental data set, we provided the first experimental proof of what the quantum mechanical transition state theory predicted, in that isolated molecules behave as if all their accessible states were occupied in a random order. We also found that, under the 1-D reaction conditions, molecular-level information on a few hundred molecules suffices to deduce statistically meaningful kinetics data that match with those obtained by bulk experiments.

Direct Microscopic Analysis of Individual C60 Dimerization Events: Kinetics and Mechanisms

Modern transition state theory states that the statistical behavior of a chemical reaction is the sum of individual chemical events that occur randomly. Statistical analysis of each event for individual molecules in a three-dimensional space however is practically impossible. We report here that kinetics and mechanisms of chemical reactions can be investigated by using a one-dimensional system where reaction events can be observed in situ and counted one by one using variable-temperature (VT) atomic-resolution transmission electron microscopy (TEM). We thereby provide direct proof that the ensemble behavior of random events conforms to the Rice-Ramsperger-Kassel-Marcus theory, as illustrated for [2 + 2] cycloaddition of C₆₀ molecules in carbon nanotubes (CNTs). This method gives kinetic and structural information for different types of reactions occurring simultaneously in the microscopic view field, suggesting that the VT-TEM opens a new dimension of chemical kinetics research on molecules and their assemblies in their excited and ionized states. The study carried out at 393-493 K showed that pristine CNT primarily acts as a singlet sensitizer of the cycloaddition reaction that takes place with an activation energy of 33.5 ± 6.8 kJ/mol. On the other hand, CNT suffers electron damage of the conjugated system at 103-203 K and promotes a reactive radical cation path that takes place with an activation energy of only 1.9 ± 0.7 kJ/mol. The pre-exponential factor of the Arrhenius plot gave us further mechanistic insights.

Atomic-Resolution Transmission Electron Microscopic Movies for Study of Organic Molecules, Assemblies, and Reactions: The First 10 Years of Development

A molecule is a quantum mechanical entity. "Watching motions and reactions of a molecule with our eyes" has therefore been a dream of chemists for a century. This dream has come true with the aid of the movies of atomic-resolution transmission electron microscopic (AR-TEM) molecular images through real-time observation of dynamic motions of single organic molecules (denoted hereafter as single-molecule atomic-resolution real-time (SMART) TEM imaging). Since 2007, we have reported movies of a variety of single organic molecules, organometallic molecules, and their assemblies, which are rotating, stretching, and reacting. Like movies in the theater, the atomic-resolution molecular movies provide us information on the 3-D structures of the molecules and also their time evolution. The success of the SMART-TEM imaging crucially depends on the development of "chemical fishhooks" with which fish (organic molecules) in solution can be captured on a single-walled carbon nanotube (CNT, serving as a "fishing rod"). The captured molecules are connected to a slowly vibrating CNT, and their motions are displayed on a monitor in real time. A "fishing line" connecting the fish and the rod may be a σ-bond, a van der Waals force, or other weak connections. Here, the molecule/CNT system behaves as a coupled oscillator, where the low-frequency anisotropic vibration of the CNT is transmitted to the molecules via the weak chemical connections that act as an energy filter. Interpretation of the observed motions of the molecules at atomic resolution needs us to consider the quantum mechanical nature of electrons as well as bond rotation, letting us deviate from the conventional statistical world of chemistry. What new horizons can we explore? We have so far carried out conformational studies of individual molecules, assigning anti or gauche conformations to each C-C bond in conformers that we saw. We can also determine the structures of van der Waals assemblies of organic molecules, thereby providing mechanistic insights into crystal formation-phenomena of general significance in science, engineering, and our daily life. Whereas many of the single organic molecules in a vacuum seen by SMART-TEM are sufficiently long-lived for detailed studies, molecules with low ionization potentials (<6 eV) were found to undergo chemical reactions, for example, [60]fullerene and organometallic compounds possibly via a hole catalysis mechanism, where a radical cation of CNT generated under electron irradiation catalyzes the transformation via an electron transfer mechanism. Common organic molecules whose ionization potentials are much higher (>8 eV) than that of CNT (5 eV) remain stable for a time long enough for observation at 60-120 kV acceleration voltage, as they are not oxidized by the CNT radical cation. Alternatively, the reaction may have taken place via an excited state of a molecule produced by energy transfer from CNT possessing excess energy provided by the electron beam. SMART-TEM imaging is a simple approach to the study of the structures and reactions of molecules and their assemblies and will serve as a gateway to the research and education of the science connecting the quantum mechanical world and the real world.

Selective Imaging of Discrete Polyoxometalate Ions on Graphene Oxide under Variable Voltage Conditions

Monosubstituted lacunary Keggin [CoSiW11O39](6-) ions on graphene oxide (GO) were used in a comparative imaging study using aberration corrected transmission electron microscopy at two different acceleration voltages, 80 and 200 kV. By performing a set of static and dynamical studies, together with image simulations, we show how the use of lower voltages results in better stability and resolution of the underlying GO support while the use of higher voltages permits better resolution of the individual tungsten atoms and leads to less kinetic motion of the cluster, thus leading to a more accurate identification of cluster orientation and better stability under dynamical imaging conditions. Applying different voltages also influences the visibility of both GO and the lighter Co at lower or higher voltages, respectively.

Covalently Binding Atomically Designed Au9 Clusters to Chemically Modified Graphene

Atomic-resolution transmission electron microscopy was used to identify individual Au₉ clusters on a sulfur-functionalized graphene surface. The clusters were preformed in solution and covalently attached to the surface without any dispersion or aggregation. Comparison of the experimental images with simulations allowed the rotational motion, without lateral displacement, of individual clusters to be discerned, thereby demonstrating a robust covalent attachment of intact clusters to the graphene surface.