A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation

For applying to a number of theoretical methodologies based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics method connecting AMBER9 with GAUSSIAN03, we have developed an AMBER-GAUSSIAN interface (AG-IF), which can be one of the simplest architectures. In the AG-IF, only a few subroutines addition is necessary to retrieve the QM/MM energy and forces, obtained by GAUSSIAN, for solving a set of Newtonian equations of motion in AMBER. It is, therefore, easy to be modified for individual applications since AG-IF utilizes most of those functions originally equipped not only in AMBER but also in GAUSSIAN. In the present minimal implementation, only AMBER is modified, whereas GAUSSIAN is left unchanged. Moreover, a different method of calculating electrostatic forces of MM atoms interacting with QM region is proposed. Using the AG-IF, we also demonstrate three examples of application: (i) the QM versus MM comparison in the radial distribution function, (ii) the free energy gradient method, and (iii) the charge from interaction energy and forces.     

Preparation and evaluation of magnetic carbonaceous materials for pesticide and metal removal

When diluted solutions of giant micelles are under turbulent flow, large attenuations of the turbulence can be observed due to the action of the micelles on the dissipative vortices formed within the flow. This particular property is rapidly lost when the solution is heated due breakup of the giant micelles. Based on this property, we present a thermal-flow study of a mixed giant micelle formed by the combination of two surfactants and sodium salicylate. One of the surfactants, cetyltrimethylammonium bromide (C(16)TAB) was kept fixed, and the others were dodecyltrimethylammonium bromide (C(12)TAB), tetradecyltrimethylammonium bromide (C(14)TAB), octadecyltrimethylammonium bromide (C(18)TAB), polyoxyethylene (10) oleyl ether (Brij 97) or sodium dodecyl sulfate (SDS). Thermal diagrams for the combinations of the surfactants reveal deviations of the ideality. For the cationic surfactants, a synergistic effect was only observed when C(16)TAB was combined with the shorter surfactants.     

An efficient synthesis of cyclopropyl silyl ketones

The reaction of silylcyclopropyl bromides with dichloromethyl methyl ether in the presence of n-butyllithium is investigated. Under basic reaction conditions, the corresponding cyclopropylidene derivatives are exclusively obtained. The resulting cyclopropylidene compounds are subjected to protonolysis or trapping with electrophiles in a one-pot to give the cyclopropyl silyl ketone derivatives in good yields. Acidic treatment of derived cyclopropyl silyl ketone allows isomerization to give the thermodynamically favorable trans form exclusively.     

Scanning laser microscope for imaging nanostructured superconductors

The nanofabrication of superconductors yields various interesting features in superconducting properties. A variety of different imaging techniques have been developed for probing the local superconducting profiles. A scanning pulsed laser microscope has been developed by the combination of the XYZ piezo-driven stages and an optical fiber with an aspheric focusing lens. The scanning laser microscope is used to understand the position-dependent properties of a superconducting MgB₂ stripline of length 100 μm and width of 3 μm under constant bias current. Our results show that the superconducting stripline can clearly be seen in the contour image of the scanning laser microscope on the signal voltage. It is suggested from the observed image that the inhomogeneity is relevant in specifying the operating conditions such as detection efficiency of the sensor.     

Highly stereospecific protonation of stereoregular living PMMA anions with several alcohols

Living and highly isotactic poly(methyl methacrylate) (PMMA) anion (M̄n = 2.5 × 10³) prepared with t-C₄H₉MgBr as an initiator was protonated with phenol in toluene at −78°C. The reaction was stereospecific toward meso addition, and the meso/racemo ratio at the chain-end of the resultant polymer was 89/11. Addition of 1,4-dioxane to the living isotactic PMMA anion in toluene at −78°C remarkably reduced the viscosity of the system, and protonation of the PMMA anion with phenol in the presence of 1,4-dioxane enhanced the meso-specificity to 94%. On the other hand, the protonation reaction of the living syndiotactic PMMA anion (M̄n = 2.5 × 10³), which was generated by t-C₄H₉Li/(n-C₄H₉)₃Al in toluene at −93°C, with t-butanol was found to be 97% racemo-specific. These highly stereospecific protonation reactions of the stereoregular PMMA anions were in contrast to the protonation of the anions with methanol or benzyl alcohol which was almost non-stereospecific.