ASEDock-docking based on alpha spheres and excluded volumes

ASEDock is a novel docking program based on a shape similarity assessment between a concave portion (i.e., concavity) on a protein and the ligand. We have introduced two novel concepts into ASEDock. One is an ASE model, which is defined by the combination of alpha spheres generated at a concavity in a protein and the excluded volumes around the concavity. The other is an ASE score, which evaluates the shape similarity between the ligand and the ASE model. The ASE score selects and refines the initial pose by maximizing the overlap between the alpha spheres and the ligand, and minimizing the overlap between the excluded volume and the ligand. Because the ASE score makes good use of the Gaussian-type function for evaluating and optimizing the overlap between the ligand and the site model, it can pose a ligand onto the docking site relatively faster and more effectively than using potential energy functions. The posing stage through the use of the ASE score is followed by full atomistic energy minimization. Because the posing algorithm of ASEDock is free from any bias except for shape, it is a very robust docking method. A validation study using 59 high-quality X-ray structures of the complexes between drug-like molecules and the target proteins has demonstrated that ASEDock can faithfully reproduce experimentally determined docking modes of various druglike molecules in their target proteins. Almost 80% of the structures were reconstructed within the estimated experimental error. The success rate of approximately 98% was attained based on the docking criterion of the root-mean-square deviation (RMSD) of non-hydrogen atoms (< or = 2.0 A). The markedly high success of ASEDock in redocking experiments clearly indicates that the most important factor governing the docking process is shape complementarity.     

A practical approach to non-natural or N-unsubstituted α-arylglycine derivatives: Hf(OTf)4-doped Me3SiCl system-catalyzed aminomethylation of electron-rich arenes with a new type of N,O-acetal

The authors have demonstrated the Hf(OTf)₄-doped Me₃SiCl system-catalyzed aminomethylation of electron-rich aromatic compounds, such as indoles and anilines, with new types of N,O-acetals having a variety of functional groups, such as cyano, ester, bis(trimethylsilyl)amino, diallylamino, and cyclic amino moieties, for the preparation of non-natural aromatic amino acid derivatives. Aminomethylation using an N,O-acetal with a bis(trimethylsilyl)amino group was particularly successful in the direct preparation of an N-unsubstituted α-indolylglycine derivative, which required only a standard aqueous workup.     

Convectional,sedimentation, and drying dissipative patterns of colloidal crystals of poly (methyl methacrylate) spheres on a cover glass

Direct observation of the convectional dissipative patterns was successful during the course of dryness of colloidal crystals of poly (methyl methacrylate) spheres on a cover glass. Formation processes of the convectional patterns of spoke-like lines were observed as a function of sphere size and also sphere concentration. During dryness of the suspensions, the brilliant iridescent colors changed beautifully. Macro- and microscopic drying patterns and thickness profiles of the dried film were observed. Sharp broad rings were observed especially at low sphere concentrations. The water evaporation accompanied with the convectional flow of water and the colloidal spheres played an important role for these dissipative structure formation.     

Existing condition and migration property of ions in lithium electrolytes with ionic liquid solvent

Ionization conditions of each ionic species in lithium ionic liquid electrolytes, LiTFSI/BMI-TFSI and LiTFSI/BDMI-TFSI, were confirmed based on the diffusion coefficients of the species measured by the pulsed gradient spin-echo (PGSE) NMR technique. We found that the diffusion coefficient ratios of the cation and anion species D(Li)(obs)/D(F)(obs) of the lithium salt and D(H)(obs)/D(F)(obs) of the ionic liquid solvent were effective guides to evaluate the ionization condition responsible for their mobility. Lithium ions were found to be stabilized, forming the solvated species as Li(TFSI)3(2-). TFSI- anion coordination could be relaxed by the dispersion of silica to form a gel electrolyte, LiTFSI/BDMI-TFSI/silica. It is expected that the oxygen sites on the silica directly attract Li+, releasing the TFSI- coordination. The lithium species, loosing TFSI- anions, kept a random walk feature in the gel without the diffusion restriction attributed from the strong chemical and morphological effect as that in the gel with the polymer. We can conclude that the silica dispersion is a significant approach to provide the appropriate lithium ion condition as a charge-transporting species in the ionic liquid electrolytes.     

Colloidal crystals of core-shell type spheres with poly(styrene) core and poly(ethylene oxide) shell

Elastic modulus and crystal growth kinetics have been studied for colloidal crystals of core–shell type colloidal spheres (diameter = 160–200 nm) in aqueous suspension. Crystallization properties of three kinds of spheres, which have poly(styrene) core and poly(ethylene oxide) shell with different oxyethylene chain length (n = 50, 80 and 150), were examined by reflection spectroscopy. The suspensions were deionized exhaustively for more than 1 year using mixed bed of ion-exchange resins. The rigidities of the crystals range from 0.11 to 120 Pa and from 0.56 to 76 Pa for the spheres of n = 50 and 80, respectively, and increase sharply as the sphere volume fraction increase. The g factor, parameter for crystal stability, range from 0.029 to 0.13 and from 0.040 to 0.11 for the spheres of n = 50 and 80, respectively. These g values indicate the formation of stable crystals, and the values were decreased as the sphere volume fraction increased. Two components of crystal growth rate coefficients, fast and slow, were observed in the order from 10⁻³ to 10¹ s⁻¹. This is due to the secondary process in the colloidal crystallization mechanism, corresponding to reorientation from metastable crystals formed in the primary process and/or Ostwald-ripening process. There are no distinct differences in the structural, kinetic and elastic properties among the colloidal crystals of the different core–shell size spheres, nor difference between those of core–shell spheres and silica or poly(styrene) spheres. The results are very reasonably interpreted by the fact that colloidal crystals are formed in a closed container owing to long-range repulsive forces and the Brownian movement of colloidal spheres surrounded by extended electrical double layers, and their formation is not influenced by the rigidity and internal structure of the spheres.     

Scattering of a TM plane wave from periodic random surfaces

This paper deals with the scattering of a TM plane wave from conductive periodic random surfaces. By means of the stochastic functional approach, the scattered field is expressed in terms of a harmonic series representation, in which the coefficients are homogeneous random functions and are given by Wiener-Hermite expansions. An approximate solution for the Wiener kernels is obtained up to the second order. Several anomalies appear in the angular distribution of the incoherent scattering because of combinations of scattering due to surface randomness and diffraction due to surface periodicity. These are incoherent Wood's anomalies associated with guided surface waves propagating along the surface, enhanced backscattering and diffracted backscattering enhancement. The physical reasons for these anomalies and numerical results are discussed.     

Peptide free‐energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95

The C96 and AMBER95 force fields were compared with small model peptides Ac‐(Ala)_n‐NMe (Ac = CH₃CO, NMe = NHCH₃, n=2 and 3) in vacuo and in TIP3P water by computing the free‐energy profiles using multicanonical molecular dynamics method. The C96 force field is a modified version of the AMBER95 force field, which was adjusted to reproduce the energy difference between extended β‐ and constrained α‐helical energies for the alanine tetrapeptide, obtained by the high level ab initio MO method. The slight modification resulted in a large difference in the free energy profiles. The C96 force field prefers relatively extended conformers, whereas the AMBER95 force field favors turn conformations. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 748–762, 2000     

Designing an “A‐Ring‐with‐Branches” Polymer Topology by Electrostatic Self‐Assembly and Covalent Fixation with Interiorly Functionalized Telechelics Having Cyclic Ammonium Groups

A novel and unusual polymer topology, i.e. a‐ring‐with‐two‐branches, has been constructed efficiently by making use of an interiorly functionalized poly(tetrahydrofuran) (poly(THF)) having two pyrrolidinium groups. The dicarboxylate counterion, i. e. terephthalate, was then introduced by an ion‐exchange reaction of the interiorly located pyrrolidinium group. Subsequent heat treatment under appropriate dilution caused an efficient polymer cyclization to produce an a‐ring‐with‐two‐branches polymer topology in high yield through the selective and quantitative ring‐opening of the pyrrolidinium groups by the dicarboxylate counterion.     

Benzylic triflates prepared in‐situ: novel initiators for mono‐, bi‐ and trifunctional living poly(THF)s

Mono‐, bis‐, and tris(trifluoromethanesulfonate ester)s ((triflate ester)s) were prepared by the reaction of benzyl alcohol ( 1 ), 1,4‐bis(hydroxymethyl)benzene ( 2 ) and 1,3,5‐tris(hydroxymethyl)benzene ( 3 ) with trifluoromethanesulfonic anhydride in the presence of 2,6‐di‐tert‐butylpyridine. These benzylic triflate esters were applied in‐situ for the living polymerization of tetrahydrofuran (THF). The subsequent end‐capping reaction with a suitable nucleophile proceeded quantitatively to produce mono, bi‐ and, in particular, novel trifunctional telechelic poly(THF)s, respectively.