Novel stereoselective entry to 2'-beta-carbon-substituted 2'-deoxy-4'-thionucleosides from 4-thiofuranoid glycals

2'-Beta-methyl- and 2'-beta-hydroxymethyl-2'-deoxy-4'-thionucleosides have been synthesized through PhSeCl-mediated electrophilic glycosidation using 4-thiofuranoid glycals having carbon substituents at the C2-position as a glycosyl donor. Preparation of these glycals were carried out by means of the C2 lithiation of 1-chloro-4-thiofuranoid glycal with LTMP followed by the Birch reduction of the chlorine atom. [reaction: see text]     

An improved large scale synthesis of 1,4-anhydro-4-thio-d-ribitol

An improved large scale synthesis of 1,4-anhydro-4-thio-d-ribitol (4) from d-ribose has been accomplished by combining the O-allyl and O-p-methoxybenzyl protecting groups. Compound 4 was obtained in 31% yield in eight steps with three chromatographic separations.     

Adsorbed water for the electro-oxidation of methanol at Pt-Ru alloy

Adsorbed water molecules which promote the methanol oxidation reaction (MOR) at Pt-Ru alloy electrode are clearly detected by in-situ FTIR spectroscopy with the attenuated total reflection configuration, which directly supports the "bi-functional mechanism" for the MOR.     

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.     

Syntheses and properties of emissive iridium(III) complexes with tridentate benzimidazole derivatives

A series of novel emissive Ir(III) complexes having the coordination environments of [Ir(N--N--N)2]3+, [Ir(N--N--N)(N--N)Cl]2+, and [Ir(N--N--N)(N--C--N)]2+ with 2,6-bis(1-methyl-benzimidazol-2-yl)pyridine (L1, N--N--N), 1,3-bis(1-methyl-benzimidazol-2-yl)benzene (L2H, N--C--N), 4'-(4-methylphenyl)-2,2':6',2' '-terpyridine (ttpy, N--N--N), and 2,2'-bipyridine (bpy, N--N) have been synthesized and their photophysical and electrochemical properties studied. The Ir(III) complexes exhibited phosphorescent emissions in the 500-600 nm region, with lifetimes ranging from approximately 1-10 micros at 295 K. Analysis of the 0-0 energies and the redox potentials indicated that the lowest excited state of [Ir(L1)(L2)]2+ possessed the highest contribution of 3MLCT (MLCT = metal-to-ligand charge transfer) among the Ir(III) complexes, reflecting the sigma-donating ability of the tridentate ligand, ttpy < L1 < L2. The emission quantum yields (phi) of the Ir(III) complexes ranged from 0.037 to 0.19, and the highest phi value (0.19) was obtained for [Ir(L1)(bpy)Cl]2+. Radiative rate constants (k(r)) were 1.2 x 10(4) s(-1) for [Ir(ttpy)2]3+, 3.7 x 10(4) s(-1) for [Ir(L1)(bpy)Cl]2+, 3.8 x 10(4) s(-1) for [Ir(ttpy)(bpy)Cl]2+, 3.9 x 10(4) s(-1) for [Ir(L1)2]3+, and 6.6 x 10(4) s(-1) for [Ir(L1)(L2)]2+. The highest radiative rate for [Ir(L1)(L2)]2+ with the highest contribution of 3MLCT could be explained in terms of the singlet-triplet mixing induced by spin-orbit coupling of 5d electrons in the MLCT electronic configurations.     

Electric conductivities of 1:1 electrolytes in liquid methanol along the liquid-vapor coexistence curve up to the critical temperature. I. NaCl, KCl, and CsCl solutions

The molar conductivities Lambda of NaCl, KCl, and CsCl in liquid methanol were measured in the concentration range of (0.3-2.0) x 10(-3) mol dm(-3) and the temperature range of 60-240 degrees C along the liquid-vapor coexistence curve. The temperature range corresponds to the solvent density range of (2.78-1.55)rhoc, where rhoc = 0.2756 g cm(-3) is the critical density of methanol. The concentration dependence of Lambda at each temperature and density (pressure) has been analyzed by the Fuoss-Chen-Justice equation to obtain the limiting molar conductivity Lambda0 and the molar association constant KA. For all the electrolytes studied, Lambda0 increased almost linearly with decreasing density at densities above 2.0rhoc, while the opposite tendency was observed at lower densities. The relative contribution of the nonhydrodynamic effect on the translational friction coefficient zeta was estimated in terms of Deltazeta/zeta, where the residual friction coefficient Deltazeta is the difference between zeta and the Stokes friction coefficient zetaS. At densities above 2.0rhoc, Deltazeta/zeta increased with decreasing density though zeta and Deltazeta decrease, and the tendencies are common for all the ions studied. The density dependences of zeta and Deltazeta/zeta were explained well by the Hubbard-Onsager (HO) dielectric friction theory based on the sphere-in-continuum model. At densities below 2.0rhoc, however, the experimental results cannot be explained by the HO theory.     

A new set of atomic radii for accurate estimation of solvation free energy by Poisson–Boltzmann solvent model

The Poisson–Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations. The presented PB radii were optimized using results from explicit solvent simulations of the large systems. In addition, we discriminated PB radii for N‐ and C‐terminal residues from those for nonterminal residues. The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment. The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules. © 2014 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Masking mechanisms of bitter taste of drugs studied with ion selective electrodes

The masking mechanisms of the bitter taste of propantheline bromide (PB) and oxyphenonium (OB) bromide by native and modified cyclodextrins, saccharides, surfactants, organic acids, nonionic and anionic polymers, and other compounds were investigated with ion selective electrodes. The intensity of the bitter taste for a mixed solution of cyclodextrin with PB or OB was quantitatively explained from the observed electromotive force with the following assumptions: the complex and the masking agent do not have any tastes and the bitter taste is independent of other tastes. Sodium dodecyl sulfate reduced the bitter taste remarkably, and this reduction was also explicable on the basis of the same mechanism. Sodium taurodeoxycholate enhanced the bitter taste, because of its strong bitterness, although it formed 1 : 1 complexes with PB and OB. The masking mechanism of saccharides was ascribed to overcoming the weak bitterness of the drug by the strong sweetness. Lambda-carrageenan suppressed the bitter taste remarkably. This suppression was ascribed to the binding of PB and OB to lambda-carrageenan, the effect of the solution viscosity on the bitter taste, and the covering of the bitter taste receptor by lambda-carrageenan. It was suggested that the moderate masking by other polymers was attributable to the effect of the solution viscosity or the receptor covering. Native and modified beta-cyclodextrins, sodium dodecyl sulfate, lambda-carrageenan, Tween 20, and sodium carboxymethyl cellulose are good masking agents for the bitter tastes of PB and OB. The drug ion selective electrode is a useful tool for understanding of the masking mechanism of the bitter taste, screening of masking agents, and estimation of appropriate concentrations of the masking agents.     

Rates of electronic excitation hopping in anisotropic ionic crystals of [Ru(2,2'-bipyridine)3]X2 (X = ClO4-, PF6-, SbF6-); Monte Carlo simulation of single- and multi-exponential emission decays

Emission decays of triplet metal-to-ligand charge transfer states in anisotropic crystals of [Ru(1 - x)Os(x)(bpy)(3)]X(2) (bpy = 2,2'-bipyridine, X = PF(6)-, ClO(4)-, SbF(6)-, and 0.115 > x > 0.001) at approximately 300 K were measured by means of time-correlated single-photon counting. Rates of excitation hopping calculated on the basis of an interaction between transition dipoles of a donor cation and an acceptor cation are insufficient to simulate the single-exponential decays (x = 0.0099) and the multiexponential decays (x = 0.060 and 0.115) of the PF(6)- salt crystals. A limiting rate of excitation hopping to an imaginary cation at the van der Waals distance via a super-exchange interaction between d orbitals through the bpy ligands was determined to be 0.83 x 10(10) s(-1) on average by means of a step-by-step Monte Carlo simulation, assuming an distance-attenuation factor, beta, of the exchange interaction of 10 nm-1. The total rate of excitation hopping via both a dipole-dipole mechanism and a super-exchange mechanism to the neighboring sites of the cation was calculated to be 5.4 x 10(9) s(-1) for the PF(6)- crystal. Anisotropic diffusion constants estimated from the hopping rates and lengths in the PF(6)- crystal are 9.3 x 10(-6), 9.1 x 10(-6), and 1.4 x 10(-6) cm(2)s(-1) along the a axis, the b axis, and the c axis, respectively, which are compared with an isotropic diffusion constant, 1.3 x 10(-6) cm(2) s(-1), estimated from the pseudo-bimolecular rate constant of excitation transfer to [Os(bpy)(3)](2+), using an isotropic Smoluchowski equation. A multiexponential emission decay of [Ru(0.885)Os(0.115)(bpy)(3)](PF(6))(2) was also simulated to determined the limiting rate of excitation transfer to [Os(bpy)(3)](2+) at the van der Waals distance (2.6 x 10(11) s(-1)). The magnitude of beta determined is 6.5 and 11.5 nm(-1) for the ClO(4)- and the SbF(6)- salt crystals, respectively, on reference to that of beta (10 nm(-1)) for the PF(6)- salt crystal.