PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules

A program package for molecular simulations of biological molecules was developed. The package, "PEACH version 4 with ABINIT-MP version 20021029," was constructed by incorporating ABINIT-MP, a program for the fragment molecular orbital (FMO) method [Chem.Phys. Lett. 313 (1999) 701], into PEACH, a program package for classical molecular dynamics simulations (MD). A few capabilities of the package were demonstrated. First, high parallel efficiency of FMO was demonstrated in a single point calculation of a protein. Second,FMO-MD simulations [Chem. Phys. Lett. 372 (2003) 342] of a peptide were performed with and without explicit solvent, and the simulations showed the influence of the solvent on the electronic state of the peptide.     

Large-scale synthesis of thiolated Au25 clusters via ligand exchange reactions of phosphine-stabilized Au11 clusters

Phosphine-stabilized Au11 clusters in chloroform were reacted with glutathione (GSH) in water under a nitrogen atmosphere. The resulting Au:SG clusters exhibit an optical absorption spectrum similar to that of Au25(SG)18, which was isolated as one of the major products from chemically prepared Au:SG clusters (Negishi, Y. et al. J. Am. Chem. Soc. 2005, 127, 5261). Rigorous characterization by optical spectroscopy, electrospray ionization mass spectrometry, and polyacrylamide gel electrophoresis confirms that the Au25(SG)18 clusters were selectively obtained on the sub-100 mg scale by ligand exchange reaction under aerobic conditions. The ligand exchange strategy offers a practical and convenient method of synthesizing thiolated Au25 clusters on a large scale.     

Preparation of agglomeration-free hematite particles coated with silica and their reduction behavior in hydrogen

To prepare silica-coated hematite particles without agglomeration, the effects of solid fraction, ion content in solution, and designed layer thickness on agglomeration and dispersion behavior after silica coating were examined. Since the ion concentration remained high in suspension after the hematite particles were prepared, these particles formed aggregates by the compression of an electric double layer on the hematite and silica layer produced a solid bridge between primary hematite particles. Silica bridge formation and agglomeration were almost completely prevented by decreasing the ion concentration and solid fraction of the hematite particles. Furthermore, the effects of the silica-layer thickness and structure on the reduction of hematite to iron under hydrogen gas flow and the iron core stability under air were discussed. When the solid fraction was low in suspension to prevent agglomeration during coating, a densely packed structure of nanoparticles formed by heterogeneous nucleation was observed on the silica-layer surface. Since this structure could not completely prevent oxide diffusion, the layer thickness was increased to 40 nm to obtain a stable iron core under air. Although a dense uniform layer was produced at a high solid fraction during coating, its thickness was reduced to 20 nm to completely reduce hematite to iron.     

Physicochemical properties of dimethylzinc,dimethylcadmium and diethylzinc

Physicochemical properties of dimethylzinc, dimethylcadmium and diethylzinc have been investigated by means of vapor pressure measurement, mass spectroscopy and gas chromatography. The saturated vapor pressure-temperature dependence of these alkyl organometallics was determined to be as follows The temperature ranges for vapor phase decomposition for deposition of each metal were clarified, and vapor-phase species released in the decompositions were investigated. These investigations on the organometallics are to provide basic material data for the establishment of organometallic chemical vapor deposition techniques for Group IIB-VI compounds.     

Synthesis of stimuli‐responsive macroazoinitiators and their use as an inistab toward hairy polymer latex particles

Stimuli‐responsive macroazoinitiators with central azo unit have been synthesized by atom transfer radical polymerization (ATRP) of 2‐(dimethylamino)ethyl methacrylate or 2‐(diethylamino)ethyl methacrylate in 2‐propanol at 25 °C. The mean degree of polymerization of the polymer chains besides the azo group was fixed between 25 and 60. ¹H NMR, gel permeation chromatography, UV‐Vis spectrophotometer, and surface tensiometer were used to characterize the stimuli‐responsive macroazoinitiators in terms of their chemical structure, molecular weight, polydispersity, and pH‐responsive behavior, respectively. Eventually, dispersion polymerization of styrene using the poly[2‐(diethylamino)ethyl methacrylate] (PDEA) macroazoinitiator as an inistab (initiator + stabilizer) in 2‐propanol medium was conducted. Near‐monodisperse 98 nm polystyrene (PS) latex particles with pH‐responsive PDEA hair were successfully synthesized. The PS latex particles with the PDEA hair can be dispersed in acidic aqueous media where the PDEA hair was protonated and was solvated, and can be flocculated in basic aqueous media where the PDEA hair was deprotonated and was precipitated. This dispersion‐flocculation cycle was reversible. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 3431–3443, 2009     

Observation of oscillation in bacterial luminescence.

Oscillation in the bioluminescent intensity from a luminous bacteria suspension was observed. The time course of the luminescence intensity from a suspension containing luminous bacteria was measured. The oscillation mode changed with the liquid broth component. The optical density and dissolved oxygen (DO) concentration were measured simultaneously with the luminescence intensity, and a possibility was indicated that both diauxic growth and oxygen reaction-consumption resulted with oscillation.