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

SignificanceAtomic 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.

Ionization and electron excitation of C60 in a carbon nanotube: A variable temperature/voltage transmission electron microscopic study.

There is increasing attention to chemical applications of transmission electron microscopy, which is often plagued by radiation damage. The damage in organic matter predominantly occurs via radiolysis. Although radiolysis is highly important, previous studies on radiolysis have largely been descriptive and qualitative, lacking in such fundamental information as the product structure, the influence of the energy of the electrons, and the reaction kinetics. We need a chemically well-defined system to obtain such data and have chosen as a model a variable-temperature and variable-voltage (VT/VV) study of the [2 + 2] dimerization of a van der Waals dimer [60]fullerene (C60) to C120 in a carbon nanotube (CNT), as studied for several hundred individual reaction events at atomic resolution. We report here the identification of five reaction pathways that serve as mechanistic models of radiolysis damage. Two of them occur via a radical cation of the specimen generated by specimen ionization, and three involve singlet or triplet excited states of the specimen, as initiated by electron excitation of the CNT, followed by energy transfer to the specimen. The [2 + 2] product was identified by measuring the distance between the two C60 moieties, and the mechanisms were distinguished by the pre-exponential factor and the Arrhenius activation energy­the standard protocol of chemical kinetic studies. The results illustrate the importance of VT/VV kinetic analysis in the studies of radiation damage and show that chemical ionization and electron excitation are inseparable, but different, mechanisms of radiation damage, which has so far been classified loosely under the single term "ionization."

Blue Shift of Localized Surface Plasmon Resonance of Gold Ultrathin Nanorod by Forming a Single Atomic Silver Shell via Antigalvanic Process.

Gold ultrathin nanorods (Au UNRs) are anisotropic nanostructures constructed by attaching gold nanoclusters in one dimension. Au UNRs exhibit localized surface plasmon resonance (LSPR) only in the longitudinal direction because their diameter is smaller than the Fermi wavelength of an electron (<2 nm). In this study, we found that the LSPR wavelength of oleylamine-stabilized Au UNRs is blue-shifted simply by mixing with Ag(I). High-resolution elemental mapping and X-ray photoelectron spectroscopy of the resulting UNRs indicate that a Ag monatomic layer is formed on the Au UNR surface by the antigalvanic reduction of Ag(I). This process allowed us to synthesize a series of Au@Ag core-shell UNRs with LSPR wavelengths in the range of 1.2-2.0 µm.

RhRu Bimetallic Oxide Cluster Catalysts for Cross-Dehydrogenative Coupling of Arenes and Carboxylic Acids.

Noble-metal-based bimetallic oxide clusters are promising novel catalysts. In this study, we developed carbon-supported RhRu bimetallic oxide clusters (RhRuOx/C) with a mean diameter of 1.2 nm, which showed remarkable catalytic activity for the cross-dehydrogenative coupling (CDC) of arenes and carboxylic acids with O2 as the sole oxidant. RhRu bimetallic oxide cluster formation was confirmed by aberration-corrected high-angle annular dark-field scanning transmission electron microscopy with energy-dispersive X-ray spectroscopy and synchrotron X-ray absorption spectroscopy. Kinetic isotope and substituent effects indicated that arene C-H bond cleavage was the rate-determining step and proceeded via electrophilic concerted metalation-deprotonation mechanism, with a carboxylate as an internal base. Density functional theory calculations supported the proposed mechanism and indicated that the active center for C-H bond activation was Rh(V) rather than Rh(III), while Ru enhanced the electrophilicity of the Rh(V) site by decreasing the negative charge of the surrounding oxygen atoms. Electron-rich arenes showed relatively high reactivity for the RhRuOx/C-catalyzed CDC reaction, and both aliphatic and aromatic carboxylic acids were applicable to the reaction. The RhRuOx/C catalyst is promising for the CDC reaction of arenes and carboxylic acids to produce aryl esters. This work promotes the development of noble-metal-based bimetallic oxide clusters for C-H bond activation reactions.

Grinding-Induced Water Solubility Exhibited by Mechanochromic Luminescent Supramolecular Fibers.

Most mechanochromic luminescent compounds are crystalline and highly hydrophobic; however, mechanochromic luminescent molecular assemblies comprising amphiphilic molecules have rarely been explored. This study investigated mechanochromic luminescent supramolecular fibers composed of dumbbell-shaped 9,10-bis(phenylethynyl)anthracene-based amphiphiles without any tetraethylene glycol (TEG) substituents or with two TEG substituents. Both amphiphiles formed water-insoluble supramolecular fibers via linear hydrogen bond formation. Both compounds acquired water solubility when solid samples composed of supramolecular fibers are ground. Grinding induces the conversion of 1D supramolecular fibers into micellar assemblies where fluorophores can form excimers, thereby resulting in a large redshift in the fluorescence spectra. Excimer emission from the ground amphiphile without TEG chains is retained after dissolution in water. The micelles are stable in water because hydrophilic dendrons surround the hydrophobic luminophores. By contrast, when water is added to a ground amphiphile having TEG substituents, fragmented supramolecular fibers with the same molecular arrangement as the initial supramolecular fibers are observed, because fragmented fibers are thermodynamically preferable to micelles as the hydrophobic arrays of fluorophores are covered with hydrophilic TEG chains. This leads to the recovery of the initial fluorescent properties for the latter amphiphile. These supramolecular fibers can be used as practical mechanosensors to detect forces at the mesoscale.

Structures, fundamental properties, and potential applications of low-dimensional C60 polymers and other nanocarbons: a review.

Since carbon (C) atom has a variety of chemical bonds via hybridization between s and p atomic orbitals, it is well known that there are robust carbon materials. In particular, discovery of C60 has been an epoch making to cultivate nanocarbon fields. Since then, nanocarbon materials such as nanotube and graphene have been reported. It is interesting to note that C60 is soluble and volatile unlike nanotube and graphene. This indicates that C60 film is easy to be produced on any kinds of substrates, which is advantage for device fabrication. In particular, electron-/photo-induced C60 polymerization finally results in formation of one-dimensional (1D) metallic peanut-shaped and 2D dumbbell-shaped semiconducting C60 polymers, respectively. This enables us to control the physicochemical properties of C60 films using electron-/photo-lithography techniques. In this review, we focused on the structures, fundamental properties, and potential applications of the low-dimensional C60 polymers and other nanocarbons such as C60 peapods, wavy-structured graphene, and penta-nanotubes with topological defects. We hope this review will provide new insights for producing new novel nanocarbon materials and inspire broad readers to cultivate new further research in carbon materials.

We review the structures, fundamental properties, and applications of low-dimensional C₆₀ polymers and other related nanocarbons such as C₆₀ peapods, wavy-structured graphene, and penta-nanotubes from a standpoint of topological defects.

Reduction-Induced Self-Propelled Oscillatory Motion of Perylenediimides on Water.

The emergence of macroscopic self-propelled oscillatory motion based on molecular design has attracted continual attention in relation to autonomous systems in living organisms. Herein, a series of perylenediimides (PDIs) with various imide side chains was prepared to explore the impact of molecular design and alignment on the self-propelled motion at the air-water interface. When placed on an aqueous solution containing a reductant, a solid disk of neutral PDI was reduced to form the water-soluble, surface-active PDI dianion species, which induces a surface tension gradient in the vicinity of the disk for self-propelled motion. We found that centimeter-scale oscillatory motion could be elicited by controlling the supply rate of PDI dianion species through the reductant concentration and the structure of the imide side chains. Furthermore, we found that the onset and speed of the self-propelled motion could be changed by the crystallinity of PDI at the water surface. This design principle using π-conjugated molecules and their self-assemblies could advance self-propelled, non-equilibrium systems powered by chemical energy.

Ion-Pairing Chromonic Liquid Crystals via Alternately Stacked Assembly of Amphiphilic Charged π-Electronic Systems.

In this study, a new assembly strategy for lyotropic chromonic liquid crystals (LCLCs) is proposed using iπ-iπ interactions, mainly comprising electrostatic and dispersion forces, between charged π-electronic systems to form stacking structures supported by the hydration of triethylene glycol (TEG) units.  Meso-TEG-aryl-substituted porphyrin AuIII complex, an amphiphilic π-electronic cation, showed diverse states and assembly modes in ion pairs depending on the coexisting counteranions.  The PCCp- ion pair formed a hexagonal columnar (Colh) LC phase based on a charge-by-charge assembly, suggesting the formation of an ordered arrangement of charged p-electronic systems through iπ-iπ interactions, with reduced interactions between the TEG chains.  Furthermore, in the presence of water, LCLC behaviors in the Colh and nematic columnar phases according to the amount of water were observed for the PCCp- ion pair via iπ-iπ interactions.  Magnetic-field-induced orientation of the charge-by-charge columnar structures upon dehydration was observed.  Furthermore, single-stranded charge-by-charge columnar structures, as components of the LCLCs, were observed using transmission electron microscopy (TEM).

Diphosphine-Protected IrAu12 Superatom with Open Site(s): Synthesis and Programmed Stepwise Assembly.

One or two phenylacetylide (PA) ligand(s) were successfully removed from the IrAu12 superatomic core of [IrAu12(dppe)5(PA)2]+ (dppe=1,2-bis(diphenylphosphino)ethane) by reaction with controlled amounts of tetrafluoroboric acid. Optical and nuclear magnetic resonance spectroscopies and density functional theory calculations revealed the formation of open Au site(s) on the IrAu12 core of [IrAu12(dppe)5(PA)1]2+ and [IrAu12(dppe)5]3+ with the remaining structure intact. Isocyanide was efficiently trapped at the open electrophilic site on [IrAu12(dppe)5(PA)1]2+, whereas a dimer or trimer of the IrAu12 superatoms was formed using diisocyanide as a linker. These results open the door to designed assembly of chemically modified metal superatoms.

Pentagon-Rich Caged Carbon Catalyst for the Oxygen Reduction Reaction in Acidic Electrolytes.

The interaction between electron spin and oxygen molecules in non-platinum catalysts, particularly carbon catalysts, significantly influences the catalytic performance of the oxygen reduction reaction (ORR). A promising approach to developing high-performance catalysts involves introducing five-membered ring structures with spin into graphitic carbons. In this study, we present the successful synthesis of cage-like cubic carbon catalysts enriched with pentagon structures using pentagon ring-containing C60 and a NaCl template. The number of pentagons contained in the structure was increased by doping with nitrogen and annealing, and the number of electron spins also increased, thereby improving catalytic activity. The prepared catalyst exhibits remarkable activity in ORR under acidic electrolytes. Furthermore, we elucidate the correlation between the pentagon structure, the number of spin, and catalytic activity, demonstrating that enhanced activity is contingent upon the presence of spin. Density functional theory (DFT) calculations support the role of spin in improving activity. The concept of spin and the introduction of pentagon structures provide new design principles for carbon catalysts.

Wavy Graphene-Like Network Forming during Pyrolysis of Polyacrylonitrile into Carbon Fiber.

Carbon fiber (CF) obtained by pyrolysis of polyacrylonitrile (PAN-CF) surpasses metals in properties suitable for diverse applications such as aircraft manufacture and power turbine blades. PAN-CF obtained by pyrolysis at 1200-1400 °C shows a remarkably high tensile strength of 7 GPa, much higher than pitch-based CF (pb-CF) consisting of piles of pure graphene networks. However, little information has been available on the atomistic structure of PAN-CF and on how it forms during pyrolysis. We pyrolyzed an acrylonitrile 9-mer in a carbon nanotube, monitored the course of the reaction using atomic-resolution electron microscopy and Raman spectroscopy, and found that this oligomer forms a thermally reactive wavy graphene-like network (WGN) at 1200-1400 °C during slow graphitization taking place between 900 and 1800 °C. Ptychographic microscopic analysis indicated that such material consists of 5-, 6-, and larger-membered rings; hence, it is not flat but wavy. The experimental data suggest that, during PAN-CF manufacturing, many layers of WGN hierarchically pile up to form a chemically and physically interdigitated noncrystalline phase that resists fracture and increases the tensile strength─the properties expected for high-entropy materials. pb-CF using nearly pure carbon starting material, on the other hand, forms a crystalline graphene network and is brittle.

Saturated Linkers in Two-Dimensional Covalent Organic Frameworks Boost Their Luminescence.

The development of highly luminescent two-dimensional covalent organic frameworks (COFs) for sensing applications remains challenging. To suppress commonly observed photoluminescence quenching of COFs, we propose a strategy involving interrupting the intralayer conjugation and interlayer interactions using cyclohexane as the linker unit. By variation of the building block structures, imine-bonded COFs with various topologies and porosities are obtained. Experimental and theoretical analyses of these COFs disclose high crystallinity and large interlayer distances, demonstrating enhanced emission with record-high photoluminescence quantum yields of up to 57% in the solid state. The resulting cyclohexane-linked COF also exhibits excellent sensing performance for the trace recognition of Fe3+ ions, explosive and toxic picric acid, and phenyl glyoxylic acid as metabolites. These findings inspire a facile and general strategy to develop highly emissive imine-bonded COFs for detecting various molecules.

Supramolecular Polymer Polymorphism: Spontaneous Helix-Helicoid Transition through Dislocation of Hydrogen-Bonded π-Rosettes.

Polymorphism, a phenomenon whereby disparate self-assembled products can be formed from identical molecules, has incited interest in the field of supramolecular polymers. Conventionally, the monomers that constitute supramolecular polymers are engineered to facilitate one-dimensional aggregation and, consequently, their polymorphism surfaces primarily when the states of assembly differ significantly. This engenders polymorphs of divergent dimensionalities such as one- and two-dimensional aggregates. Notwithstanding, realizing supramolecular polymer polymorphism, wherein polymorphs maintain one-dimensional aggregation, persists as a daunting challenge. In this work, we expound upon the manifestation of two supramolecular polymer polymorphs formed from a large discotic supramolecular monomer (rosette), which consists of six hydrogen-bonded molecules with an extended π-conjugated core. These polymorphs are generated in mixtures of chloroform and methylcyclohexane, attributable to distinctly different disc stacking arrangements. The face-to-face (minimal displacement) and offset (large displacement) stacking arrangements can be predicated on their distinctive photophysical properties. The face-to-face stacking results in a twisted helix structure. Conversely, the offset stacking induces inherent curvature in the supramolecular fiber, thereby culminating in a hollow helical coil (helicoid). While both polymorphs exhibit bistability in nonpolar solvent compositions, the face-to-face stacking attains stability purely in a kinetic sense within a polar solvent composition and undergoes conversion into offset stacking through a dislocation of stacked rosettes. This occurs without the dissociation and nucleation of monomers, leading to unprecedented helicoidal folding of supramolecular polymers. Our findings augment our understanding of supramolecular polymer polymorphism, but they also highlight a distinctive method for achieving helicoidal folding in supramolecular polymers.

Fast electron damage mechanism of epoxy resin studied by electron energy loss spectroscopy and electron diffraction.

The damage mechanism and exposure tolerance of epoxy resins to fast electrons remain unclear. We quantitatively investigated the effects of electron irradiation on a common epoxy resin by dose-dependent electron energy loss spectroscopy. The results show that sp3 states of nitrogen, oxygen, and their adjacent carbon atoms were converted to sp2 states, forming imine (C=N) and carbonyl (C=O) as the total electron dose increased. The sp3 to sp2 conversion mechanism was proposed. The epoxy resin was very sensitive to fast electrons and the original electronic states were maintained up to a total dose of ∼103e- nm-2 at a low temperature of 103 K. Dose-dependent electron diffraction revealed that the intra- and intermolecular geometries changed below and around the total dose of ∼103e- nm-2.

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.

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.

Rim Binding of Cyclodextrins in Size-Sensitive Guest Recognition.

Cyclodextrins (CDs) are doughnut-shaped cyclic oligosaccharides having a cavity and two rims. Inclusion binding in the cavity has long served as a classic model of molecular recognition, and rim binding has been neglected. We found that CDs recognize guests by size-sensitive binding using the two rims in addition to the cavity, using single-molecule electron microscopy and a library of graphitic cones as a solid-state substrate for complexation. For example, with its cavity and rim binding ability combined, γ-CD can recognize a guest of radius between 4 and 9 Å with a size-recognition precision of better than 1 Å, as shown by structural analysis of thousands of individual specimens and statistical analysis of the data thereof. A 2.5 ms resolution electron microscopic video provided direct evidence of the process of size recognition. The data suggest the occurrence of the rim binding mode for guests larger than the size of the CD cavity and illustrate a unique application of dynamic molecular electron microscopy for deciphering the spatiotemporal details of supramolecular events.

Capturing the Moment of Emergence of Crystal Nucleus from Disorder.

Crystallization is the process of atoms or molecules forming an organized solid via nucleation and growth. Being intrinsically stochastic, the research at an atomistic level has been a huge experimental challenge. We report herein in situ detection of a crystal nucleus forming during nucleation/growth of a NaCl nanocrystal, as video recorded in the interior of a vibrating conical carbon nanotube at 20-40 ms frame-1 with localization precision of <0.1 nm. We saw NaCl units assembled to form a cluster fluctuating between featureless and semiordered states, which suddenly formed a crystal. Subsequent crystal growth at 298 K and shrinkage at 473 K took place also in a stochastic manner. Productive contributions of the graphitic surface and its mechanical vibration have been experimentally indicated.

Nano- and Microspheres Containing Inorganic and Biological Nanoparticles: Self-Assembly and Electron Tomographic Analysis.

Organofullerene amphiphiles show diverse behaviors in water, forming vesicles, micelles, Langmuir-Blodgett films, and anisotropic nanostructures. We found that gradual in situ protonation of an organic solution of (4-heptylphenyl)5C60-K+ by water or buffer generates the corresponding protonated molecule, (4-heptylphenyl)5C60H, which self-assembles to form nano- and microspheres of organofullerene (fullerspheres) with uniform diameters ranging from 30 nm to 2.5 µm that are controlled by the preparation or pH of the buffer. By using an aqueous solution of an organic dye, inorganic nanoparticle, protein, and virus, we encapsulated these entities in the fullersphere. This approach via self-assembly is distinct from other preparations of organic core-shell particles that generally require polymerization for the construction of a robust shell. The sphere is entirely amorphous, thermally stable up to 300 °C under vacuum, and resistant to electron irradiation, and we found the unconventional utility of the sphere for electron tomographic imaging of nanoparticles and biomaterials.

Interfacial Chemistry of Conical Fullerene Amphiphiles in Water.

Amphiphiles are used for a variety of applications in our daily life and in industrial processes. They typically possess hydrophobic and hydrophilic moieties within the molecule, thereby performing a myriad of functions through the formation of two- and three-dimensional assemblies in water, such as Gibbs monolayers and micelles. However, these functions are often inseparable because they emerge from the same structural feature of the molecule, and are difficult to control because the structural diversity is limited to either long-chain hydrocarbons bearing a polar end group(s) or polymers bearing polar groups exposed to the exterior surface. In this Account, we describe the chemistry of a new class of amphiphiles, conical fullerene amphiphiles (CFAs), utilizing a superhydrophobic [60]fullerene group as a nonpolar apex with added structural features to make it soluble in water. By selective functionalization of only one side of the fullerene molecule, the CFA molecules spontaneously assemble in water through strong hydrophobic interactions among the fullerene apexes and exhibit unusual supramolecular and interfacial behavior. They form unilamellar micelles and vesicles at a critical aggregation concentration as low as micromolar, not showing any air-water and oil-water interfacial activity. The strong preference for self-assembly in water over monolayer formation at an air-water interface makes CFAs unique among conventional nonpolymeric surfactants. The CFA assemblies are often so mechanically robust that they can be transferred to the surface of a solid substrate and analyzed by high-resolution microscopy. Because of this rigid conical structure of a few nanometers in size, CFA molecules aggregate readily in water to form a hierarchical assembly with biomolecules and nanomaterials while maintaining the structural integrity of the CFA aggregate to form multicomponent agglomerates of controllable structural features. For instance, tissue-selective in vivo transport of DNA and siRNA has been achieved. Hybridization of a CFA vesicle with a transition metal catalyst enables the construction of a structurally defined nanospace and an interface for precise control of the nanoscale morphology of polymers. Solubilization of hydrophobic nanocarbons and nanoparticles is also achieved through hemimicelle formation on solid surfaces. The examples reported here illustrate the potential of the conical fullerene motif for the design of amphiphiles as well as supramolecular structures at molecular and tens of nanometers scale.