KNApSAcK-3D: a three-dimensional structure database of plant metabolites.

Studies on plant metabolites have attracted significant attention in recent years. Over the past 8 years, we have constructed a unique metabolite database, called KNApSAcK, that contains information on the relationships between metabolites and their expressing organism(s). In the present paper, we introduce KNApSAcK-3D, which contains the three-dimensional (3D) structures of all of the metabolic compounds included in the original KNApSAcK database. The 3D structure for each compound was optimized using the Merck Molecular Force Field (MMFF94), and a multiobjective genetic algorithm was used to search extensively for possible conformations and locate the global minimum. The resulting set of structures may be used for docking studies to identify new and potentially unexpected binding sites for target proteins. The 3D structures may also be utilized for more qualitative studies, such as the estimation of biological activities using 3D-QSAR. The database can be accessed via a link from the KNApSAcK Family website (http://kanaya.naist.jp/KNApSAcK_Family/) or directory at http://kanaya.naist.jp/knapsack3d/.

Mesoporous silica spherical particles.

This review highlights the current status on the synthesis and applications of mesoporous silica spherical particles. Mesoporous silica spherical particles are expected to be applied in various fields and the properties depend on the size and size distribution. Many researchers have been working on the synthesis of mesoporous silica spherical particles by means of several approaches and a variety of synthetic parameters have been correlated to the nature of the products. The synthetic approaches are categorized into following four; emulsion based approach, formation from a homogeneous solution, aerosol and morphology template. In this review, the preparation and the potential applications of mesoporous silica spherical particles are summarized.

Preparation of hexagonal platy particles of nanoporous silica using hydrotalcite as morphology template.

Hexagonal platy composite particles with a hydrotalcite core and a nanoporous silica shell with a thickness of ca. 100 nm were synthesized by the reaction of a Mg-Al hydrotalcite with a homogeneous aqueous solution containing tetraethoxysilane, hexadecyltrimethylammonium chloride, ammonia and methanol at 3 degrees C. The calcination of the products at 500 degrees C in air led to the composite particle with a Mg/Al mixed oxide core and a nanoporous silica shell. Hexagonal platy particles of nanoporous silica with a pore diameter of 2.3 nm and BET surface area of 700 m(2) (g of silica)(-1) were obtained by removing the Mg/Al mixed oxide core.

Deposition of thin mesoporous silica films on glass substrates from basic solution.

Transparent thin (ca. 100 nm) films of silica-surfactant mesostructured materials were deposited on borosilicate glass plates and soda-lime glass tubes from aqueous solutions containing tetraethoxysilane, alkyltrimethylammonium chloride, ammonia, and methanol. By calcination in air, the films became mesoporous (BET surface area of 700-900 m2 g-1) with pore diameter 2.0-2.8 nm.

Resolving 45-pm-separated Si-Si atomic columns with an aberration-corrected STEM.

Si-Si atomic columns separated by 45 pm were successfully resolved with a 300-kV aberration-corrected scanning transmission electron microscope (STEM) equipped with a cold-field emission gun. Using a sufficiently small Gaussian effective source size and a 0.4-eV energy spread at 300 kV, the focused electron probe on the specimen was simulated to be sub-50 pm. Image simulation showed that the present probe condition was sufficient to resolve 45 pm Si-Si dumbbells. A silicon crystalline specimen was observed from the [114] direction with a high-angle annular dark field STEM and the intensity profile showed 45 pm separation. A spot corresponding to (45 pm)(-1) was confirmed in the power spectrum of the Fourier transform.