Stereochemical recognition of doubly functional aminotransferase in 2-deoxystreptamine biosynthesis

The doubly functional aminotransferase BtrS in the 2-deoxystreptamine (DOS) biosynthesis, in which two transaminations are involved, was characterized by a genetic as well as a chemical approach with the heterologously expressed enzyme. The gene disruption study clearly showed that BtrS is involved, in addition to the previously confirmed first transamination, in the second transamination as well. This dual function of BtrS for the DOS biosynthesis was further confirmed by the structural determination of the reverse reaction product from DOS. Enantiospecific formation of the reverse reaction product from DOS clearly showed that BtrS distinguishes the enantiotopic amino groups of DOS, but in contrast, both enantiomers of 2-deoxy-scyllo-inosose (DOI) were efficiently accepted by BtrS to give a racemic product. This unique stereochemical recognition of DOI chirality and DOS prochirality by BtrS is mechanistically explained by a specific hydrogen-bond donating force in the enzyme active site as a particular feature of this doubly functional enzyme.     

Water-assisted oxo mechanism for heme metabolism

A mechanism of heme metabolism by heme oxygenase (HO) is discussed from B3LYP density functional theory calculations. The concerted OH group attack to the alpha-carbon by the iron-hydroperoxo species is investigated using a model with full protoporphyrin IX to confirm our previous conclusion that this species does not have sufficient oxidizing power for heme oxidation (J. Am. Chem. Soc. 2004, 126, 3672). Calculated activation energies and structures of the intermediates and transition state for this process remain unchanged from those for a small model with porphine in the previous study, which shows that the inclusion of the side chain of the porphyrin ring is not essential in describing the OH group transfer. The activation barrier for a direct oxo attack to the alpha-carbon by an iron-oxo model is calculated to be 49.8 kcal/mol, the barrier height of which looks very high for the enzymatic reaction under physiological conditions. This large activation energy is due to a highly bent porphyrin structure in the transition state. However, a bridging water molecule plays an important role in reducing the porphyrin distortion in the transition state, resulting in a remarkable decrease of the activation barrier to 13.9 kcal/mol. A whole-enzyme model with about 4000 atoms is constructed to elucidate functions of the protein environment in this enzymatic reaction using QM/MM calculations. The key water molecule is fixed in the protein environment to ensure the low-barrier and regioselective heme oxidation. A water-assisted oxo mechanism of heme oxidation by heme oxygenase is proposed from these calculational results.     

Metallic Ni nanoparticles confined in hexagonally ordered mesoporous silica material

Single nanometer-sized metallic Ni particles have been successfully deposited inside a hexagonally ordered mesoporous silica material by using a liquid-phase reductive deposition method.     

Interpolation of contour intervals in Moire topography by phase modulation

A trial has been performed with respect to the interpolation of contour intervals in Moiré topography by making use of phase modulation. A simple mechanical system can bring improved results for the precise measurements of shape of a specimen.     

Attractivity in non-autonomous systems

We discuss some sufficient conditions for attractivity of a closed set by using Liapunov functions and show how to apply our results to the study of asymptotic behaviors of solutions in nonautonomous systems. We also discuss the convergence of solutions by the same idea. These results are extendable to functional differential equations.     

Control of molecular interactions by the hollow of coordination cages

Coordination self-assembly entities have been demonstrated to be useful and powerful alternatives for the construction of predefined and well-organized architectures. Self-assembled coordination cages, which possess an inner hydrophobic cavity, can be utilized to move substrates closer by encapsulation so enabling their interaction with each other and exhibiting of non-classical physical properties.     

Tribochemical reaction dynamics of phosphoric ester lubricant additive by using a hybrid tight-binding quantum chemical molecular dynamics method

To study the atomistic behavior of the phosphoric ester molecule on the nascent Fe surface under boundary lubrication conditions, we adopted a hybrid tight-binding quantum chemical molecular dynamics method. First, we investigated chemical interactions between phosphoric ester and the nascent Fe surface. Phosphoric ester was shown to interact with the nascent Fe surface, forming both covalent and ionic bonds. Formation and dissociation dynamics of covalent bonds during tribochemical reaction was clearly observed during the simulation. The effect of friction condition on the tribochemical reaction dynamics was then studied, and it was indicated that friction would influence the formation and the dissociation of covalent bonds. By using a hybrid tight-binding quantum chemical molecular dynamics method, we obtained insights on initial tribochemical reaction processes for the formation of tribofilm from the phosphoric ester molecule on the nascent Fe surface.     

Electroabsorption spectroscopy of 6-hydroxyquinoline doped in polymer films: Stark shifts and orientational effects

Stark absorption spectroscopy was applied to 6-hydroxyquinoline (6-HQ) doped in polymer films of poly(methyl methacrylate) (PMMA) and poly(vinyl alcohol) (PVA) at temperatures of 50-300 K. The electroabsorption (E-A) spectrum of 6-HQ markedly depends on temperature in a PMMA film. The polarization dependence as well as the temperature dependence of the E-A spectra reveals that 6-HQ is oriented along the direction of the applied electric field at room temperature in a PMMA film. As the temperature becomes lower, the field-induced orientation of 6-HQ is restricted, and only the Stark shift induced by a change in electric dipole moment and in molecular polarizability is observed. On the other hand, E-A spectra of 6-HQ doped in a PVA film are essentially independent of temperature, suggesting that 6-HQ is not oriented along the electric field even at room temperature in PVA. These results show that the molecular motion of 6-HQ in a polymer film is very sensitive to the microenvironment of the surrounding matrix.