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

Abstract

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 ...

Nanoparticle Characterization: What to Measure?

“…The power of LC TEM has been demonstrated by studying several aspects of synthesis and use of gold nanoparticles, namely their nucleation rates, and the dynamics and assembly between bare and functionalized particles (Figure b) . Finally, atomic‐resolution transmission electron microscopy (AR‐TEM) enables the study of dynamic processes and provides real‐time observation of changes at the molecular level with atomic sensitivity . The first study in 2007 reported AR‐TEM movies of conformational changes of a single hydrocarbon molecule .…”

A Thermodynamic Description of Turbulence as a Source of Stochastic Kinetic Energy for 3D Self‐Assembly

“…In situ transmission electron microscopy reveals selfassembly events rather than the entire self-assembly process itself and its underlying dynamics. [50,51] Moreover, it is impossible to avoid the influence of the electron beam on the physical and chemical properties of the particles as well as on the resolution of the footage. It is likely that a change in the properties of the particle can lead to altered particle interactions and therewith an altered self-assembly.…”

“…We cannot see how the structure formed or which pathways were taken. In situ transmission electron microscopy reveals self‐assembly events rather than the entire self‐assembly process itself and its underlying dynamics . Moreover, it is impossible to avoid the influence of the electron beam on the physical and chemical properties of the particles as well as on the resolution of the footage.…”

Toward Precision Measurement and Manipulation of Single‐Molecule Reactions by a Confined Space

“…In other words, it is indeed elementary reactions from the perspective of that specific mole‐cule, and all kinds of chemical processes can be broken down into a set of SMRs. Direct observations of SMRs effectively mitigate the static and dynamic heterogeneity of real‐world molecular systems, facilitating the detection of short‐lived reaction intermediates, and offering unparalleled insight on complex reaction mechanisms and structure–activity relationship . The ability to analyze SMR is not only crucial for synthetic chemistry, but also chemical biology as well, especially to uncover the hidden “personalities” of biomolecules .…”

“…A future perspective regarding the promises and challenges to develop SMR measurement approaching the space‐time limit, as well as the possibility to realize precision single‐molecule synthesis is also given at the end of this review. Since a huge amount of other intriguing approaches, e.g., electron microscopy has been developed for SMR research as well, it is unlikely to include all of them here due to the limit of space, and therefore the selection of papers mainly reflects the authors' own research interest. It is also highly recommended that the readers can refer to some other comprehensive reviews for additional information on each specific single‐molecule technique that is covered in this review, e.g., fluorescence, Raman, scanning probe, electric conductance, force, etc.…”