Cooperative motions of protein and hydration water molecules: molecular dynamics study of scytalone dehydratase

Two molecular dynamics (MD) simulations totaling 25 ns of simulation time of monomeric scytalone dehydratase (SD) were performed. The enzyme has a ligand-binding pocket containing a cone-shaped alpha+beta barrel, and the C-terminal region covers the binding pocket. Our simulations clarified the difference in protein dynamics and conformation between the liganded protein and the unliganded protein. The liganded protein held the ligand molecule tightly and the initial structure was maintained during the simulation. The unliganded protein, on the other hand, fluctuated dynamically and its structure changed largely from the initial structure. In the equilibrium state, the binding pocket was fully solvated by opening of the C-terminal region, and the protein dynamics was connected with hydration water molecules entry into and release from the binding pocket. In addition, the cooperative motions of the unliganded protein and the hydration water molecules produced the path through the protein interior for ligand binding.     

Polyether-bridged sexithiophene as a complexation-gated molecular wire for intramolecular photoinduced electron transfer

The porphyrin-sexithiophene-fullerene triad 2, where the two central thiophene units of the sexithiophene spacer are bridged with a crown-ether-like polyether chain, undergoes efficient intramolecular electron transfer from the photoexcited porphyrin moiety to the fullerene through the sexithiophene. However, complexation with a sodium cation in the crown ether ring causes complete suppression of electron transfer as a result of a drastic conformational change of the sexithiophene backbone. Furthermore, decomplexation resumes the photoinduced electron transfer. This on/off switching phenomenon indicates that the polyether-bridged sexithiophene can function as a complexation-gated molecular wire.     

1,6-dihydro-3(2H)-pyridinones as synthetic intermediates. Total synthesis of (±)-tecomanine

The first and stereoselective total synthesis of (±)-tecomanine ($\text{1}$) has been achieved from ethyl 1,6-dihydro-3(2H)-pyridinone-1-carboxylate ($\text{2}$) as a synthon.     

Synthesis and structure of 1-zirconacyclopent-3-yne complexes without substituents adjacent to the triple bond

Five-membered metallacyclic alkynes that have no substituents adjacent to the triple bond have been synthesized, isolated, and structurally characterized. Zirconocene dichlorides, Cp'2ZrCl2 (Cp' = C5H5, C5H4-t-Bu), reacted with 1,4-dichlorobut-2-yne in the presence of magnesium to give 1-zirconacyclopent-3-yne compounds (5 (a) Cp' = C5H5, (b) Cp' = C5H4-t-Bu) that have a -CH2CCCH2- moiety in good yields. They are stable enough to be isolated in a pure form, despite the absence of substituents. 5a reacted with an equimolar amount of Cp2Zr(but-1-ene)(PMe3) to produce a bimetallic complex in which the zirconacyclopentyne coordinates to the other zirconocene moiety as an alkyne.     

Effect of Electrode Pattern on the Column Structure and Yield Stress of Electrorheological Fluids

For electrorheological (ER) suspensions, the aggregate structures of particles were observed in electric fields by the use of transparent cells with different electrode patterns. Although the suspension is dispersed to noninteracting particles without electric fields, many aggregates are formed on the electrode surface in electric fields. Since the dipole–dipole interactions cause chain structures of particles and equilibrium conformations of chains are always aligned with electric field, the aggregates indicate the presence of columns spanning the electrode gap. The particle concentration in columns which are developed between parallel-plate electrodes is about 22 vol %. In striped electrodes, the particles construct striped aggregates along the electrodes and no particles remain in the insulating region. The particle concentration in striped aggregates is about 35 vol %. The nonuniformity of electric field is responsible for the high particle concentration. The increase in particle concentration of column lead to the high yield stress of electrified suspension. Therefore, the ER performance of suspension as an overall response can be improved by the electrode design.     

New lariat ether carboxylic and hydroxamic acids: Synthesis and lanthanide ion complexation

Twenty-six new lariat ether carboxylic and hydroxamic acids based upon dibenzo-13-crown-4, dibenzo-14-crown-4, dibenzo-16-crown-5 and dibenzo-19-crown-6 ring systems are synthesized and the solid-state structure for a dibenzo-19-crown-6 lariat ether hydroxamic acid is determined. The efficiency and selectivity for lanthanide ion extraction into chloroform by these proton-ionizable lariat ethers is strongly influenced by the crown ether ring size, lipophilic group attachment site and identity of the acidic function. In general, the lariat ether hydroxamic acids were more efficient and selective lanthanide ion extractants than the corresponding lariat ether carboxylic acids. The ¹H nmr and ir binding studies indicate that both the macrocyclic polyether unit and the proton-ionizable group are involved in lanthanide ion complexation.     

Biodegradable Polyurethanes from Plant Components

Abstract

Polyurethane (PU) sheets and foams having plant components in their network were prepared by using the following procedure. Polyethylene glycol (PEG) was mixed with one of the following; molasses, lignin, woodmeal, or coffee grounds. The mixture obtained was reacted with diphenylmethane diisocyanate (MDI) at room temperature, and precured PUs were prepared. The precured PUs were heat-pressed and PU sheets were obtained. In order to make PU foam, the above mixture was reacted with MDI after the addition of plasticizer, surfactant (silicone oil), catalyst (di-n-butyltin dilaurate), and droplets of water under vigorous stirring. The glass transition temperature, tensile and compression strengths, and Young's modulus of the PU sheets and foams increased with an increasing amount of plant components. This suggests that saccharide and lignin residues act as hard segments in PUs. It was found that the PUs obtained were biodegradable in soil. The rate of biodegradation of the PUs derived from molasses and coffee grounds was between that of cryptomeria (Cryptomeria japonica) and beech (Fagus sieboldi).     

3,4-Thienylene-ethynylene Oligomers

Several well-defined 3,4-thienylene-ethynylene oligomers with different chain lengths have been synthesized and characterized. X-Ray crystallographic analyses proved their unique, totally helical conformations.     

Pyrolysis of Dibenzyl Selenides to Bibenzyls

The formation of carbon-carbon bond by sulfur extrusion such as pyrolysis of cyclic sulfones is well known as an important synthetic method, especially for the synthesis of cyclophane framework.¹⁾ Little is known about selenium extrusion as the counterpart, though organoseleniums have been properly appreciated as a useful tool for manipulating a functional group.²⁾ Lardon reported that the thermal decomposition of dibenzyl diselenide led to a mixture of dibenzyl selenide and polyselenides.³⁾ In contrast, recent reports showed that at 210°C, heating bis(diphenylmethyl) diselenide resulted in ready selenium extrusion to 1,1,2,2-tetraphenylethane⁴⁾, and dianthrylmethyl mono- and diselenides to 1,2-dianthrylethane.⁵⁾ Therefore,- it is worthwhile to study the thermal behavior of dibenzyl selenide itself.     

Synthesis of Optically Active Aromatic Ether Ketone Macrocycles Containing 2,2′-Dimethoxy-1,1′-binaphthyl-6,6′-diyl Moieties

Optically active aromatic ether ketone macrocycles containing 2,2′-dimethoxy-1,1′-binaphthyl-6,6′-diyl moieties were synthesized through electrophilic aromatic substitution reaction and stepwise nucleophilic aromatic substitution reactions. Structures of the resulting macrocycles were confirmed by NMR and matrix assisted laser desorption/ionization time of flight (MALDI-TOF) mass measurements.