Crystal structure of the new FeSe(1-x) superconductor

The newly discovered superconductor FeSe(1-x) (x approximately 0.08, T(c)(onset) approximately 13.5 K at ambient pressure rising to 27 K at 1.48 GPa) exhibits a structural phase transition from tetragonal to orthorhombic below 70 K at ambient pressure-the crystal structure in the superconducting state shows remarkable similarities to that of the REFeAsO(1-x)F(x) (RE = rare earth) superconductors.     

Structure activity relationships of quinoxalin-2-one derivatives as platelet-derived growth factor-beta receptor (PDGFbeta R) inhibitors, derived from molecular modeling

We previously reported a quinoxalin-2-one compound (Compound 1) that had inhibitory activity equivalent to existing platelet-derived growth factor-beta receptor (PDGFbeta R) inhibitors. Lead optimization of Compound 1 to increase its activity and selectivity, using structural information regarding PDGFbeta R-ligand interactions, is urgently needed. Here we present models of the PDGFbeta R kinase domain complexed with quinoxalin-2-one derivatives. The models were constructed using comparative modeling, molecular dynamics (MD) and ligand docking. In particular, conformations derived from MD, and ligand binding site information presented by alpha-spheres in the pre-docking processing, allowed us to identify optimal protein structures for docking of target ligands. By carrying out molecular modeling and MD of PDGFbeta R in its inactive state, we obtained two structural models having good Compound 1 binding potentials. In order to distinguish the optimal candidate, we evaluated the structural activity relationships (SAR) between the ligand-binding free energies and inhibitory activity values (IC50 values) for available quinoxalin-2-one derivatives. Consequently, a final model with a high SAR was identified. This model included a molecular interaction between the hydrophobic pocket behind the ATP binding site and the substitution region of the quinoxalin-2-one derivatives. These findings should prove useful in lead optimization of quinoxalin-2-one derivatives as PDGFb R inhibitors.     

Implementation of pi-pi interactions in molecular dynamics simulation

No explicit pi-pi interaction term has been incorporated in the conventional molecular dynamics (MD) simulation programs in spite of its significant role in the folding of biomolecules and the clustering of organic chemicals. In this article, we propose a technique to emphasize the effect of pi-pi interactions using a function of energy and implement it into an MD simulation program. Several trial calculations show that the pi-pi incorporated program gives improved results consistent with experimental data on atom geometry and has no unfavorable interference with the conventional computational framework. This indicates an importance of the explicit consideration of pi-pi interactions in MD simulation.     

Chameleon reactivity of the allene bond of 4-vinylidene-2-oxazolidinone: novel through-space conjugative nucleophilic addition of electron-rich alkenes and hetero-nucleophiles

The Calpha==Cbeta double bond of allene carbamates 1 serves as an electron acceptor similar to the double bond of conjugated enones by means of a through-space interaction with the N--SO2 bond; the carbamate double bond is thus subject to nucleophilic addition for a wide variety of nucleophiles, which proceeds under mild conditions by heating at 70-100 degrees C. Depending on the kind of nucleophiles, 1 displays three different reaction modes: 1) Typically enol ethers and allylsilanes promote 1,3-sulfonyl migration of 1 and undergo the inverse electron demand Diels-Alder reaction with the 1-aza-1,3-butadiene intermediates II thus formed to furnish bicyclic 2-alkoxy-5-sulfonyltetrahydropyridines 2 and 2-silylmethyl-5-sulfonyltetrahydropyridines 3, respectively, with high regio- and stereoselectivity and retention of configuration of the double bonds of these electron-rich alkenes; 2) silanes (RnSiH4-n, n=1-3) and thiols deliver the hydride and the thiolate at the Cbeta carbon and promote the 1,3-sulfonyl migration, followed by protonation of the thus-formed carbamate anion (Z)-III to provide, for example, (Z)-4 a and (Z)-4 j, respectively; 3) alcohols simply add to the Calpha==Cbeta double bond and provide (E)-6. Usually, the reaction with alcohols is accompanied by the second pathway, giving rise to, for example, (Z)-4 b in addition to (E)-6 b. Phenol engages in the third pathway and provides (E)-6 g exclusively. Heteroaromatics, such as furans and benzofurans follow the first pathway, however, in a different regioselectivity from enol ethers and allylsilanes, delivering the oxygen atom at the 3-position of 5-sulfonyltetrahydropyridines (2 g and 2 h). Indoles, on the other hand, show a dichotomy, equally enjoying the first and the third pathways and provide mixtures of (E)-7 and (E)-8, respectively.     

Pyridylazulenes: synthesis, color changes, and structure of the colored product

A facile method for the synthesis of 1- and 2-pyridylazulenes, and of 1,3-dipyridylazulenes, is described. Color and spectral changes of these pyridylazulenes upon the addition of either acid or metal ions were investigated in detail. The color changed from blue to red upon the addition of trifluoroacetic acid or soft metal ions, depending on the substitution patterns of the pyridyl group on the azulene skeleton. The structures of the protonated or coordinated products were examined on the basis of the spectral data. It was found that the protonation or coordination of metal ions occurred on the nitrogen atom of the pyridine ring, but not on the carbon atom of azulene ring. The transition intervals of several pyridylazulenes for use as pH indicators were also determined.     

Shape Estimation of Anisometric Particles Using Size Measurement Techniques

This study was conducted to establish a simple method for evaluating the morphology of fine anisometric particles using size measurement techniques. The size distributions of mica particles and carbon fibers classified into narrower size ranges were measured by gravitational sedimentation and laser diffraction techniques. The ratio of mean diameters determined for flaky particles strongly depended on the aspect ratio, i.e. flatness. The relationship between particle shape and diameter is discussed theoretically. The experimental results were similar to those predicted. The flatness of fine particles can be evaluated by the ratio of the median diameter determined by laser diffraction to that determined by sedimentation.     

Observation of 18O/16O isotope effects at the cathode of a polymer electrolyte membrane fuel cell

¹⁸O/¹⁶O isotope effects were observed at the cathode of a polymer electrolyte membrane fuel cell at 25 and 35°C. Results of experiments in which the ¹⁸O/¹⁶O isotope ratios of the oxygen gases supplied to and exhausted from the cell were measured revealed that the lighter isotope ¹⁶O reacted more preferentially to form water molecules at the cathode than the heavier one, ¹⁸O. The value of the oxygen isotope separation factor, S₁, defined as the ratio of the ¹⁸O/¹⁶O isotope ratios of the oxygen gases supplied to and exhausted from the cell, ranged from 1.0030 to 1.0139, and tended to decrease with decreasing rate of oxygen utilisation (θ) and with increasing flow rate of the feed oxygen gas (D_F). The value of another separation factor, S₂, defined as the ratio of the ¹⁸O/¹⁶O isotope ratios of the exhausted oxygen gas and oxygen having reacted to form water molecules at the cathode, ranged from 1.0049 to 1.0304. The S₂ value was much less affected by the change in θ and D_F than the S₁ value with the majority of the S₂ value being in the range of 1.0240–1.0304.