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.

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.

De Novo Synthesis of Free-Standing Flexible 2D Intercalated Nanofilm Uniform over Tens of cm2.

Of a variety of intercalated materials, 2D intercalated systems have attracted much attention both as materials per se, and as a platform to study atoms and molecules confined among nanometric layers. High-precision fabrication of such structures has, however, been a difficult task using the conventional top-down and bottom-up approaches. The de novo synthesis of a 3-nm-thick nanofilm intercalating a hydrogen-bonded network between two layers of fullerene molecules is reported here. The two-layered film can be further laminated into a multiply film either in situ or by sequential lamination. The 3 nm film forms uniformly over an area of several tens of cm2 at an air/water interface and can be transferred to either flat or perforated substrates. A free-standing film in air prepared by transfer to a gold comb electrode shows proton conductivity up to 1.4 × 10-4 S cm-1 . Electron-dose-dependent reversible bending of a free-standing 6-nm-thick nanofilm hung in a vacuum is observed under electron beam irradiation.