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

アゾール類から生成するジアゾ中間体を利用する新反応

京都大学0048新制・課程博士博士(工学)甲第21126号工博第4490号新制||工||1698(附属図書館)京都大学大学院工学研究科合成・生物化学専攻(主査)教授 村上 正浩, 教授 杉野目 道紀, 教授 松田 建児学位規則第4条第1項該当Doctor of Philosophy (Engineering)Kyoto UniversityDGA

The stereoselective synthesis of α-amino aldols starting from terminal alkynes.

Accepted 18 Jul 2014.A new procedure for the stereoselective synthesis of syn α-amino β-oxy ketones is reported. It consists of two steps; in the first step, α-amino silyl enol ethers having a (Z) geometry are prepared from 1-alkynes via 1-sulfonyl-1, 2, 3-triazoles. In the second step, the silyl enol ethers undergo the TiCl4-mediated Mukaiyama aldol reaction with aldehydes to produce α-amino β-oxy ketones with excellent syn-selectivity

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

Time-resolved Atomistic Imaging and Statistical Analysis of Daptomycin Oligomers with and without Calcium Ion

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, and we studied the process 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 a homogeneous aqueous solution. The dimer remains as the major species under a variety of conditions, and we propose a face-to-face stacked structure based on dynamic imaging using millisecond and angstrom resolution transmission electron microscopy. The tetramer is the largest oligomer observed both in the absence and in the presence of a large excess of calcium ions. Taken together with statistical data, the microscopic structural information obtained at a single-molecule level favors a cyclic form of the dimer and the tetramer over a linear or stacked form. Such experimental structural information is new and will serve as a platform for future drug design. The data also illustrate the utility of cinematographic recording of dynamic motions of molecules for the study of self-organization processes

Precision synthesis and atomistic analysis of deep blue cubic quantum dots made via self-organization

As a crystal approaches a few nm in size, atoms become nonequivalent, bonds vibrate, and quantum effects emerge. To study quantum dots (QDs) with structural control common in molecular science, we need atomic precision synthesis and analysis. We describe here the synthesis of QDs of lead bromide perovskite via self-organization of a lead malate chelate complex and PbBr3– under ambient conditions. Millisecond and angstrom resolution electron microscopic analysis revealed the structure and the dynamic behavior of individual QDs—structurally uniform cubes made of 64 lead atoms, where eight malate molecules are located on the eight corners of the cubes, and oleylamonium cations lipophilize and stabilize the edges and faces. Lacking translational symmetry, the cube is to be viewed as a molecule rather than a nanocrystal. The QD exhibits quantitative photoluminescence and stable electroluminescence at 460 nm with a narrow half-maximum linewidth of 15 nm, reflecting minimum structural defects. This controlled synthesis and precise analysis demonstrate the potential of cinematic chemistry for the characterization of nanomaterials beyond the conventional limit

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

SignificanceThe destruction of specimen molecules by an electron beam (e-beam) is either beneficial, as in mass spectrometry capitalizing on ion formation, or deleterious, as in electron microscopy. In the latter application, the e-beam not only produces the specimen image, but also causes information loss upon prolonged irradiation. However, the atomistic mechanism of such loss has been unclear. Performing single-molecule kinetic analysis of C60 dimerization in a carbon nanotube (CNT) under variable-temperature/voltage conditions, we identified three reactive species-that is, radical cation, singlet, and triplet excited states-reacting competitively as the voltage and the properties of the CNT were changed. The key enabler was in situ continuous recording of the whole reaction process, suggesting an upcoming new era of "cinematic chemistry."11Nsciescopu