Long-term observation of fluorescence of free single molecules to explore protein-folding energy landscapes

A method was developed to detect fluorescence intensity signals from single molecules diffusing freely in a capillary cell. A unique optical system based on a spherical mirror was designed to enable quantitative detection of the fluorescence intensity. Furthermore, "flow-and-stop" control of the sample can extend the observation time of single molecules to several seconds, which is more than 1000 times longer than the observation time available using a typical confocal method. We used this method to scrutinize the fluorescence time series of the labeled cytochrome c in the unfolded state. Time series analyses of the trajectories based on local equilibrium state analysis revealed dynamically differing substates on a millisecond time scale. This system presents a new avenue for experimental characterization of the protein-folding energy landscape.     

A working hypothesis for broadening framework types of zeolites in seed-assisted synthesis without organic structure-directing agent

Recent research has demonstrated a new synthesis route to useful zeolites such as beta, RUB-13, and ZSM-12 via seed-assisted, organic structure-directing agent (OSDA)-free synthesis, although it had been believed that these zeolites could be essentially synthesized with OSDAs. These zeolites are obtained by adding seeds to the gels that otherwise yield other zeolites; however, the underlying crystallization mechanism has not been fully understood yet. Without any strategy, it is unavoidable to employ a trial-and-error procedure for broadening zeolite types by using this synthesis method. In this study, the effect of zeolite seeds with different framework structures is investigated to understand the crystallization mechanism of zeolites obtained by the seed-assisted, OSDA-free synthesis method. It has been found that the key factor in the successful synthesis of zeolites in the absence of OSDA is the common composite building unit contained both in the seeds and in the zeolite obtained from the gel after heating without seeds. A new working hypothesis for broadening zeolite types by the seed-assisted synthesis without OSDA is proposed on the basis of the findings of the common composite building units in zeolites. This hypothesis enables us to design the synthesis condition of target zeolites. The validity of the hypothesis is experimentally tested and verified by synthesizing several zeolites including ECR-18 in K-aluminosilicate system.     

High-yield diastereoselective synthesis of planar chiral [2]- and [3]rotaxanes constructed from per-ethylated pillar[5]arene and pyridinium derivatives

Planar chiral [2]- and [3]rotaxanes constructed from pillar[5]arenes as wheels and pyridinium derivatives as axles were obtained in high yield using click reactions. The process of rotaxane formation was diastereoselective; the obtained [2]rotaxane was a racemic mixture consisting of (pS, pS, pS, pS, pS) and (pR, pR, pR, pR, pR) forms of the per-ethylated pillar[5]arene (C2) wheel, and other possible types of the [2]rotaxane did not form. Isolation of the enantiopure [2]rotaxanes with one axle through (pS, pS, pS, pS, pS)-C2 or (pR, pR, pR, pR, pR)-C2 wheels was accomplished. Furthermore, pillar[5]arene-based [3]rotaxane was successfully synthesized by attachment of two pseudo [2]rotaxanes onto a bifunctional linker. [3]Rotaxane formed in a 1:2:1 mixture with one axle threaded through two (pS, pS, pS, pS, pS)-C2, one (pS, pS, pS, pS, pS)-C2 and one (pR, pR, pR, pR, pR)-C2 (meso form), or two (pR, pR, pR, pR, pR)-C2 wheels. The [3]rotaxane enantiomers and the meso form were successfully isolated using appropriate chiral HPLC column chromatography. The procedure developed in this study is the starting point for the creation of pillar[5]arene-based interlocked molecules.     

Cooperative catalytic reactions using distinct transition-metal catalysts: ruthenium- and copper-catalyzed enantioselective propargylic alkylation

The enantioselective propargylic alkylation of propargylic alcohols with β-ketoesters in the presence of a thiolate-bridged diruthenium complex and a copper complex as co-catalyst affords the corresponding propargylic alkylated products in excellent yields as a mixture of two diastereoisomers with high enantioselectivity (up to 95% enantiomeric excess (ee)). The findings reported herein not only open up a new type of enantioselective propargylic substitution reaction, but also a new aspect of cooperative catalytic reactions using distinct transition metals to realize a useful transformation that cannot be achieved by a single catalyst.     

Dynamic assembly of porphyrin wires trapped on a highly oriented pyrolitic graphite surface

Carefully designed porphyrin building blocks assemble through selective imidazole binding in various solvents to form linear multiporphyrin objects. From a dynamic mixture of monomers, dimers, and oligomers, linear objects were observed on a highly oriented pyrolitic graphite (HOPG) surface. On the surface, the objects' morphology clearly depended on the solvent used for deposition and was modified upon heating.     

Fluorescence imaging of potassium ions in living cells using a fluorescent probe based on a thrombin binding aptamer-peptide conjugate

When a biotinylated FRET probe based on a peptide-thrombin binding aptamer conjugate was introduced together with streptavidin and biotinylated nuclear export signal peptide into HeLa cells, the resulting ternary complex enabled visualization of K(+) concentration changes in the cell.     

A modified method using static head-space gas chromatography for determining the stability constants of 1-alkanol/alpha-cyclodextrin complexation

A modification of the conventional static head-space gas chromatography method (SHSGC method) to determine stability constants for 1-alkanol/alpha-CD inclusion complexes was investigated. The 1 : 1 stability constants determined by this modified SHSGC method are in reasonable agreement with the corresponding values reported previously. The modified SHSGC method precludes the necessity of the calibration curve by the use of Henry's law constant of guest. Consequently, the modified SHSGC method is more advantageous than the conventional SHSGC method because the experimental time required for determination of the stability constant is markedly reduced.     

A long-range-corrected time-dependent density functional theory

We apply the long-range correction (LC) scheme for exchange functionals of density functional theory to time-dependent density functional theory (TDDFT) and examine its efficiency in dealing with the serious problems of TDDFT, i.e., the underestimations of Rydberg excitation energies, oscillator strengths, and charge-transfer excitation energies. By calculating vertical excitation energies of typical molecules, it was found that LC-TDDFT gives accurate excitation energies, within an error of 0.5 eV, and reasonable oscillator strengths, while TDDFT employing a pure functional provides 1.5 eV lower excitation energies and two orders of magnitude lower oscillator strengths for the Rydberg excitations. It was also found that LC-TDDFT clearly reproduces the correct asymptotic behavior of the charge-transfer excitation energy of ethylene-tetrafluoroethylene dimer for the long intramolecular distance, unlike a conventional far-nucleus asymptotic correction scheme. It is, therefore, presumed that poor TDDFT results for pure functionals may be due to their lack of a long-range orbital-orbital interaction.     

Temperature dependence of formation of nanorods and dots of iodine compounds on an H-terminated Si(111) surface in a concentrated HI solution

Immersion of atomically flat, H-terminated Si(111) surfaces in 7.6 M HI for 0.5 - 4 h caused spontaneous formation of nanosized clusters at the Si surface. X-ray photoelectron spectroscopy analysis suggested that the clusters were composed of silicon iodides (such as SiHxI4-x), produced most probably by Si etching with HI. Atomic force microscopy inspection revealed that the immersion at a low temperature below about 30 degrees C led to the formation of long rod-shaped clusters, oriented in the (112) direction or equivalents, whereas the immersion at a high temperature above 30 degrees C led to the formation of circular dot clusters, their size and shape changing abruptly at about 70 degrees C. It is shown experimentally that the formation of dot clusters at a high immersion temperature is explained on the basis of thermodynamics, whereas that of oriented rod clusters at a low temperature is explained by a kinetics-controlled mechanism.     

Rational synthesis of Pt spheres with hollow interior and nanosponge shell using silica particles as template

Here we report a facile and efficient method to prepare Pt spheres with hollow interior and nanosponge shell with high surface area. Such a unique Pt nanostructure can effectively improve the electrocatalytic performance of Pt catalysts by facilitating the access of electroactive species to the full-extent Pt surface.