Theory of docking scores and its application to a customizable scoring function

In general, the docking scoring tends to have a size dependence related to the ranking of compounds. In this paper, we describe a novel method of parameter optimization for docking scores which reduce the size dependence and can efficiently discriminate active compounds from chemical databases. This method is based on a simplified theoretical model of docking scores which enables us to utilize large amounts of data of known active and inactive compounds for a particular target without requiring large computational resources or a complicated procedure. This method is useful for making scoring functions for the identification of novel scaffolds using the knowledge of active compounds for a particular target or a customized scoring function for an interesting family of drug targets.     

Synthetic Approach to 4a-Methyltetrahydrofluorene-Type Diterpenoids via an Aromatic Oxidation of Phenol Derivatives

An intramolecular aromatic oxidation of a phenolic compound with a hypervalent iodine reagent afforded the coupling product, in which the coupling took place at the para-position of the methoxy goup of the starting material instead of the desired para-position of the isopropenyl group, unfortunately.      

X-ray characterisation of local molecular orientation in the electroclinic effect of surface-stabilised SmA liquid crystals

The local molecular orientation in the electroclinic effect of the chiral smectic A phase in a surface-stabilised cell has been determined using a time-resolved synchrotron X-ray microbeam diffraction technique. Space- and time-resolved X-ray wide-angle halo scattering under an electric field reveals the static and dynamic intralayer molecular orientation. The molecular orientation varies spatially in accordance with the stripe texture and is dependent on the applied voltage. It has been found that the deviation of the molecular orientation from the rubbing direction depends strongly on the sample history. The relation between the apparent molecular orientation and the layer structure is discussed.     

Determination of zinc in marine/lacustrine sediments by graphite furnace atomic absorption spectrometry using Pd/Mg chemical modifier and slurry sampling

Effectiveness of Pd/Mg chemical modifier for the accurate direct determination of zinc in marine/lacustrine sediments by graphite furnace atomic absorption spectrometry (GF-AAS) using slurry samples was evaluated. A calibration curve prepared by aqueous zinc standard solution with addition of Pd/Mg chemical modifier is used to determine the zinc concentration in the sediment. The accuracy of the proposed method was confirmed using Certified Reference Materials, NMIJ CRM 7303-a (lacustrine sediment) from National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology, Japan, and MESS-3 (marine sediment) and PACS-2 (marine sediment) from National Research Council, Canada. The analytical results obtained by employing Pd/Mg modifier are in good agreement with the certified values of all the reference sediment materials. Although for NRC MESS-3 an accurate determination of zinc is achieved even without the chemical modifier, the use of Pd/Mg chemical modifier is recommended as it leads to establishment of a reliable and accurate direct analytical method. One quantitative analysis takes less than 15 minutes after we obtain dried sediment samples, which is several tens of times faster than conventional analytical methods using acid digested sample solutions. The detection limits are 0.13?µg?g^?1 (213.9?nm) and 16?µg?g^?1 (307.6?nm), respectively, in sediment samples, when 40?mg of dried powdered samples are suspended in 20?mL of 0.1?mol?L^?1 nitric acid and a 10?µl portion of the slurry sample is measured. The precision of the proposed method is 8–15% (RSD).     

Synthesis and photophysical properties of 2,2′-binaphthalene-based receptor bearing trimethylsilyl groups to improve the solubility

Two trimethylsilyl groups were introduced at 5- and 5′-positions of 2,2′-binaphthalene to improve the solubility of 2,2′-binaphthalene-based receptors. The X-ray crystallographic analysis revealed the twisted structure of 2 in the solid state. The solubility of 2 was moderately improved by 3.1-fold comparing with mother skeleton 1. As a practical example of 2, receptor 8 bearing two aza-15-crown-5 moieties was prepared and the selective binding of 8 with Ba²⁺ can be observed by the formation of sandwich-like complex, which shows no prevention of binding ability of the receptor by introduction of the bulky substituents.     

Conformation and Atropisomeric Properties of Indometacin Derivatives

The stereochemistry around the N‐benzoylated indole moiety of indometacin was studied by restricting the rotation about the N? C7′ and/or C7′? C1′ bond. In the 2′,6′‐disubstituted ones, an atropisomeric property was found and the atropoisomers were separated and isolated as stable forms. Their biological abilities to inhibit cyclooxygenase‐1 (COX‐1) and cyclooxygenase‐2 (COX‐2) were examined. Only the aR‐isomer showed specific inhibition of COX‐1, and COX‐2 was not inhibited by either atropisomer. Conformational analysis in NMR studies and X‐ray crystallography, and CD spectra in combination with calculations were utilized to elucidate the bioactive conformations.     

Design of a reaction field using a linear‐combination‐based isotropic periodic sum method

In our previous study (Takahashi et al., J. Chem. Theory Comput. 2012, 8, 4503), we developed the linear‐combination‐based isotropic periodic sum (LIPS) method. The LIPS method is based on the extended isotropic periodic sum theory that produces a ubiquitous interaction potential function to estimate homogeneous and heterogeneous systems. The LIPS theory also provides the procedure to design a periodic reaction field. To demonstrate this, in the present work, a novel reaction field of the LIPS method was developed. The novel reaction field was labeled LIPS‐SW, because it provides an interaction potential function with a shape that resembles that of the switch function method. To evaluate the ability of the LIPS‐SW method to describe in homogeneous and heterogeneous systems, we carried out molecular dynamics (MD) simulations of bulk water and water–vapor interfacial systems using the LIPS‐SW method. The results of these simulations show that the LIPS‐SW method gives higher accuracy than the conventional interaction potential function of the LIPS method. The accuracy of simulating water–vapor interfacial systems was greatly improved, while that of bulk water systems was maintained using the LIPS‐SW method. We conclude that the LIPS‐SW method shows great potential for high‐accuracy, high‐performance computing to allow large scale MD simulations. © 2014 Wiley Periodicals, Inc.     

Labile Base-Stabilized Silyliumylidene Ions. Non-Metallic Species Capable of Activating Multiple Small Molecules

Several base-stabilized silyliumylidene ions ( 2 and 3 ) with different ligands were synthesized. Their behaviour appeared strongly dependent on the nature of ligand. Indeed, in contrast to the poorly reactive silyliumylidene ions 3 c,d stabilized by strongly donating ligands (DMAP, NHC), the silylene- and sulfide-supported one ( 2-H and 3 a ) exhibits higher reactivity toward various small molecules. Furthermore, their capability to successively activate multiple small molecules was clearly demonstrated by processes involving successive reactions with silane/formamide, CO₂ and H₂. Moreover, HBPin adduct of 3 a ( 8-C ) catalyzes the hydroboration of pyridine. Of particular interest, silylene-supported silyliumylidene complex 2-H is one of the rare species able to activate two H₂ molecules.     

Supercurrent pumping in Josephson junctions with a half-metallic ferromagnet

A Josephson current through a half-metallic ferromagnet between two conventional superconductors is theoretically studied. The spin dynamics such as magnon excitation plays a crucial role not only for the conversion between spin-singlet and spin-triplet pairs but also for the formation of the composite state of a triplet Cooper pair and magnon, by which the Josephson current flows between the superconductors. We propose the supercurrent pumping driven by the coherent precession of the magnetization by tuning the microwave frequency to the ferromagnetic resonance frequency in a ferromagnetic Josephson junction.