Atomic-Number (Z)-Correlated Atomic Sizes for Deciphering Electron Microscopic Molecular Images

With the advent of atomic-resolution transmission electron microscopy (AR-TEM) achieving sub-{\AA}ngstrom image resolution and submillisecond time resolution, an era of visual 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 here 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 (ZCHN) and low-noise (ZCLN) conditions. The new molecular models will stimulate the imaginations of chemists planning to use AR-TEM for their research.Comment: 27 pages, 6 figure

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.journal articl

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.11Nsciescopu

Excited state modulation of C70 dimerization in a carbon nanotube under a variable electron acceleration voltage

Cinematographic recording of chemical reactions with transmission electron microscopy provides information unavailable by any other analytical methods. Studies have thus far remained mostly phenomenological, lacking information on the reactive species involved. To gain insight into the nature of the reactive species, we need to obtain kinetic information under various temperatures and variable acceleration voltages, i.e., electronic energy supply. We studied the mechanism of [2 + 2] dimerization of [70] fullerene in a carbon nanotube as an example. We describe herein a statistical analysis of individual reaction events of the dimerization that revealed dose-dependent first-order kinetics and voltage-dependent crossover from a singlet to a triplet mechanism, as highlighted by the pre-exponential factor (the frequency of excitation) that is a million times larger for the singlet reaction than for the triplet one. Comparison with the results of a recent study of [60] fullerene dimerization lets us propose that electron-impact excitation of the carbon nanotube is the first step, followed by energy transfer to fullerene molecules and their dimerization via an excited state. The results show that a variable-voltage kinetic study is indispensable for discussing the mechanism of chemical transformations under electron microscopic observation.11Nsciescopu

Free-energy function for discriminating the native fold of a protein from misfolded decoys.

In this study, free-energy function (FEF) for discriminating the native fold of a protein from misfolded decoys was investigated. It is a physics-based function using an all-atom model, which comprises the hydration entropy (HE) and the total dehydration penalty (TDP). The HE is calculated using a hybrid of a statistical-mechanical theory applied to a molecular model for water and the morphometric approach. The energetic component is suitably taken into account in a simple manner as the TDP. On the basis of the results from a careful test of the FEF, which have been performed for 118 proteins in representative decoy sets, we show that its performance is distinctly superior to that of any other function. The FEF varies largely from model to model for the candidate models for the native structure (NS) obtained from nuclear magnetic resonance experiments, but we can find models or a model for which the FEF becomes lower than for any of the decoy structures. A decoy set is not suited to the test of a free-energy or potential function in cases where a protein isolated from a protein complex is considered and the structure in the complex is used as the model NS of the isolated protein without any change or where portions of the terminus sides of a protein are removed and the percentage of the secondary structures lost due to the removal is significantly high. As these findings are made possible, we can assume that our FEF precisely captures the features of the true NS

Hierarchical Assembly of siRNA with Tetraamino Fullerene in Physiological Conditions for Efficient Internalization into Cells and Knockdown

Delivery of siRNA is a key technique in alternative gene therapy, where the siRNA cargo must be effectively loaded onto a tailor-designed carrier molecule and smoothly unloaded precisely upon arrival at the target cells or organs. Any toxicity issues also need to be mitigated by suitable choice of the carrier molecule. A water-soluble cationic fullerene, tetra­(piperazino)[60]­fullerene epoxide (TPFE), was previously shown to be nontoxic and effective for lung-targeted in vivo siRNA delivery by way of agglutination-induced accumulation. We found in this in vitro study that hierarchical reversible assembly of micrometer-sized TPFE–siRNA–serum protein ternary complexes is the key element for effective loading and release, and stabilization of otherwise highly unstable siRNA under the physiological conditions. The amphiphilic TPFE molecule forms a sub-10 nm-sized stable micelle because of strong cohesion between fullerene molecules, and this fullerene aggregate protects siRNA and induces the hierarchical assembly. Unlike popularly used polyamine carriers, TPFE is not toxic at the dose used for the siRNA delivery