Arching a bay area of triphenyleno[1,12-bcd]thiophene with group 14 functionalities: Synthesis of the first triphenylene derivatives having thiophene and metallafluorene moieties

Arching a bay area of triphenyleno[1,12-bcd]thiophene with group 14 functionalities gave the first triphenylene derivatives whose two pairs of bay carbons are connected by two different heteroatom functionalities. Triphenyleno[1,12-bcd:4,5-b′c′d′]dithiophene, which had been only accessible through the very severe reaction conditions, was synthesized under the mild reaction conditions. Photophysical properties of newly-obtained heterolotriphenylene derivatives are discussed with theoretical calculations.     

Degradation of liposome cluster caused by the interaction with endocrine disrupting chemicals (EDCs)

The interaction between endocrine disrupting chemicals (EDCs) and liposome clusters was investigated using UV-vis spectroscopy and observed by microscope. Since liposome clusters are composed of small unilamellar liposomes and membrane proteins, they are regarded as a model of plasma membranes. The size of each cluster was 10microm in diameter. UV-vis spectroscopy of liposome clusters showed an apparent absorption at 300nm which was affected by the interaction with EDCs. Four EDCs caused an alteration in absorption in a concentration-dependence manner between 0.1 and 10ppm (i.e. 0.1-10mg/l). Microscopic observation showed that the effect was caused by the degradation of liposome clusters while degradation was induced by the interaction; liposome was broken down by EDCs. This report suggests that the liposome cluster can be applied for universal detection of EDCs based on the interaction between a plasma membrane model and EDCs.     

Synthesis, structures and optical properties of trisilasumanene and its related compounds

Novel trisilasumanenes that have no substituents on the exo carbon atoms, silicon analogues of sumanene, were prepared via repetitive lithiations of triphenylene followed by introduction of silicon functionalities. The optical properties of these trisilasumanenes and their related compounds were investigated by UV-vis and fluorescence spectroscopy.     

Molecular dynamics and residual entropy in the soft crystal, SmE phase, of 4-butyl-4'-isothiocyano-1,1'-biphenyl

Molecular dynamics and resulting disorder in the soft crystal, smectic E (SmE) phase, were studied in detail for the title compound, 4-butyl-4'-isothiocyano-1,1'-biphenyl (4TCB), by (1)H NMR spectroscopy and adiabatic calorimetry. The ordered crystal phase of 4TCB was realized for the first time under ambient pressure after long two-step annealing and used as the reference state in the analysis of the experimental results. Four motional modes were identified in the SmE phase through the analysis of the (1)H NMR T(1). The residual entropy was determined as ca. 6 J K(-1) mol(-1). This magnitude implies that most of the disorder in the SmE phase at high temperatures is removed on cooling except for the head-to-tail disorder of the rod-shaped 4TCB molecule. Standard thermodynamic functions are tabulated below 375 K.     

A novel quantum mechanical/molecular mechanical approach to the free energy calculation for isomerization of glycine in aqueous solution

The free energy change associated with the isomerization reaction of glycine in water solution has been studied by a hybrid quantum mechanical/molecular mechanical (QM/MM) approach combined with the theory of energy representation (QM/MM-ER) recently developed. The solvation free energies for both neutral and zwitterionic form of glycine have been determined by means of the QM/MM-ER simulation. The contributions of the electronic polarization and the fluctuation of the QM solute to the solvation free energy have been investigated. It has been found that the contribution of the density fluctuation of the zwitterionic solute is estimated as -4.2 kcal/mol in the total solvation free energy of -46.1 kcal/mol, while that of the neutral form is computed as -3.0 kcal/mol in the solvation free energy of -15.6 kcal/mol. The resultant free energy change associated with the isomerization of glycine in water has been obtained as -7.8 kcal/mol, in excellent agreement with the experimental data of -7.3 or -7.7 kcal/mol, implying the accuracy of the QM/MM-ER approach. The results have also been compared with those computed by other methodologies such as the polarizable continuum model and the classical molecular simulation. The efficiency and advantage of the QM/MM-ER method has been discussed.     

Template-directed photoreversible ligation of DNA via 7-carboxyvinyl-7-deaza-2′-deoxyadenosine

An efficient template-directed photoligation of oligodeoxynucleotide (ODN) using 7-deaza-2′-deoxyadenosine derivative ^VZA is described. When ODN containing ^VZA at the 5′ end was photoirradiated with ODNs containing a pyrimidine base at the 3′ end in the presence of template ODN, rapid and efficient ligation (cycloaddition reaction) was observed without any byproduct formation. ODNs containing ^VZA showed an extremely high reactivity as compared with those reported in previous photoligations.     

Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles

The authors propose explicit symplectic integrators of molecular dynamics (MD) algorithms for rigid-body molecules in the canonical and isobaric-isothermal ensembles. They also present a symplectic algorithm in the constant normal pressure and lateral surface area ensemble and that combined with the Parrinello-Rahman algorithm. Employing the symplectic integrators for MD algorithms, there is a conserved quantity which is close to Hamiltonian. Therefore, they can perform a MD simulation more stably than by conventional nonsymplectic algorithms. They applied this algorithm to a TIP3P pure water system at 300 K and compared the time evolution of the Hamiltonian with those by the nonsymplectic algorithms. They found that the Hamiltonian was conserved well by the symplectic algorithm even for a time step of 4 fs. This time step is longer than typical values of 0.5-2 fs which are used by the conventional nonsymplectic algorithms.     

Hyperfine resolved spectrum of the bromomethyl radical, CH2Br, by Fourier transform microwave spectroscopy

Pure rotational spectra of the bromomethyl radical, CH(2)Br, were measured by using a Fourier transform microwave (FT-MW) spectrometer in order to fully resolve hyperfine structures arising from both the bromine and hydrogen nuclei. We detected a total of 124 lines for the (79)Br and (81)Br isotopomers, including K(a)=0 (ortho species) and K(a)=1 (para species). No hyperfine splitting due to the hydrogen nuclei was observed for the para species, directly confirming the planarity of the radical. We conducted a global analysis of our present FT-MW results and previous measurements in the millimeter-wave region and obtained an exhaustive list of molecular constants. The sign of the Fermi constant of the bromine nucleus was unambiguously determined to be positive, which is opposite to that found in previous work in the millimeter-wave region and in electron spin resonance experiment on this radical. The present study permitted a systematic comparison to be made of the hyperfine coupling constants of both the halogen and hydrogen nuclei for CH(2)X-type compounds, where X=F, Cl, and Br.     

Measurement and correlation of liquid–liquid equilibria for acetonitrile + n-alkane systems

The reduction of sulfur content in gasoline and diesel fuel is a great environmental concern to reduce the motor vehicle emissions. Oxidative desulfurization using acetonitrile biphasic system has received much attention in recent years. The oxidative desulfurization can be oxidized the unreactive sulfur contents in the hydrodesulfurization and removed effectively. For the oxidative desulfurization process design and development, liquid–liquid equilibria (LLE) for acetonitrile biphasic systems are needed as fundamental information. In our previous work, LLE for acetonitrile + n-octane and + n-decane systems have been reported. In this work, therefore, LLE for acetonitrile + n-hexadecane system was measured. Furthermore, NRTL equation was applied to correlate the LLE for these three acetonitrile + n-alkane systems.