Soft crystals, which exhibit unique mechanical properties due to weak external stimuli, are expected as next-generation of new industrial materials, in particular, their application to nanomechanical devices using technology of microelectromechanical system is already attracting a lot of attention. Therefore, it is important to evaluate the mechanical properties of molecular crystals with as high accuracy as possible with limited computational resources. In this paper, we will introduce a method for optimizing the crystal structure to analyze the mechanical properties and polymorphic transition mechanism of soft crystals when an external stress is applied, using our molecular crystal calculation method.
About 40 years ago, the basic concept of cryo-electron microscopy was introduced, where biological specimens were kept close to nature state by being embedded in vitreous ice and observed directly with electron microscope. Since then, technology and equipment have improved significantly, making it now possible to determine the atomic coordinates of many biomolecules. Here, we will introduce the latest structural study of biomolecules using single particle cryo-electron microscopy.
Recent marked development called “Resolution revolution” has made cryo-electron microscopy （Cryo-EM） the third method of structure determination at atomic resolution next to X-ray crystallography and NMR. In this review, actual situation surrounding Cryo-EM including an outline about the workflow from sample preparation to image analysis and differences between Cryo-EM analysis and X-ray crystallography is introduced. We hope that this review is useful for researchers particularly who will start Cryo-EM analysis.
The metalloenzyme ‘hydrogenase’ catalyzes the reversible oxidation of dihydrogen. Crystallographic structures of［NiFe］hydrogenases from sulfate-reducing bacteria have been determined and give detailed insight into pathways for the transfer of electrons, protons and hydrogen molecules.［NiFe］hydrogenases contain one nickel and one iron in the active site, the latter carries non-protein diatomic ligands, one CO and two CN－s. A possible catalytic mechanism of the oxygen-sensitive［NiFe］hydrogenases for the heterolytic dihydrogen splitting is proposed.
Oxygen is needed to produce energy for aerobic organism. Oxygen molecule exhibits high reactivity, thereby constantly leading to super-reactive molecules called reaction oxygen species. My research has focused on the system involved in the cellular redox control including the O2-sensing, H2O2-scavenging and protecting the cells, and have revealed their molecular mechanisms by means of the structural, biochemical and spectroscopic analyses.
In the protein crystallography, antibodies are frequently used as ‘crystallization chaperones’, where their binding facilitates production of high-quality diffracting crystals of complex macromolecules that are otherwise resistant to crystallization. To develop an ideal antibody fragment, we have designed a novel antibody fragment format, called ‘Fv-clasp’, that is a fusion of an anti-parallel coiled-coil structure derived from the hMst1 SARAH domain to the Fv fragment of an antibody. We have demonstrated that Fv-clasp has superior properties over conventional antibody fragments including Fab and single-chain Fv（scFv）in terms of producibility, stability, and crystallizability.
High-resolution X-ray powder diffraction measurement system with temporal resolution of sub-second under controlled gas and vapor atmospheres at BL02B2 of SPring-8 was developed to study structural change processes in gas storage and reaction materials. The measurement system mainly consists of a six one-dimensional solid-state detectors, a sample changer, a gas cell for a capillary sample, and a remote gas handling system. This system is not only capable of fast powder diffraction measurement, but also of automatic measurement even at extremely low gas pressures. The acquisition of powder diffraction data can be synchronized with the control of the pressure with a high frame rate of up to 100 Hz. Using this developed system, structural transition of nanoporous Cu coordination polymer under various gas adsorption processes were be observed on the sub-second time scale.
We demonstrate that quasielastic neutron scattering is effective for analyzing transport dynamics of chemically-bound hydrogen cations within crystal structures of minerals. In this report, our recent results of its application for hydrogen in brucite Mg（OH）2 are described. We observed two types of hydrogen transport dynamics, which included（i）jump within a single two-dimensional layer of hydrogen lattice, and（ii）jump from a layer into the next-nearest layer. The former observed at ≥ 230 K is ascribed to surface diffusion within basal planes of brucite grains, while the latter observed at 430 K is ascribed to proton conduction through the interior of the grains. These transport dynamics observed in the prototypical two-dimensional structure of brucite will have implication for understanding of hydrogen transport mechanisms occurring within various types of mineral structures.
Convergent-beam electron diffraction （CBED） is one of the powerful tools for nano-meter scale structural analysis. From its specific futures such as nano-meter probe, dynamical scattering, and direct determination of electrostatic potential, CBED can be applied for space group determination, observation of orbital-ordered state, and local structure analysis. In this paper, some examples for recent results obtained by CBED method are described.
Fundamental concepts of Bragg coherent diffraction imaging （BCDI） are briefly reviewed. BCDI is increasingly popular for imaging crystalline nanoparticles under in-situ conditions. In contrast to the conventional coherent diffraction imaging （CDI） that measures a forward coherent scattering in a small angle region, BCDI is based on coherent Bragg diffraction from a crystalline sample for imaging, enabling us to observe the 3D minute displacement field of the lattice planes as well as the electron density of the particle, which provides new insight into the relationship between physical properties and lattice strain/defects.
Experimental methods of Bragg coherent diffraction imaging （BCDI） are briefly reviewed. BCDI has become an essential visualization technique that images the 3D displacement and strain field in the crystalline materials in situ. Nevertheless, the BCDI experiment is still not as common as the other conventional X-ray diffraction techniques presumably because of particular instrumentation utilizing delicate coherent X-ray optics and goniometer, which further requires a combination with the data reduction that reconstructs measured particle images during the experiment. Here, we briefly review the experimental methods of BCDI and its application to the alloy nanoparticles. We also discuss the advantages and challenges of BCDI as an analysis method and future perspectives.