Camdas: An automated conformational analysis system using molecular dynamics

We present an automated conformational analysis program, CAMDAS (Conformational Analyzer with Molecular Dynamics And Sampling). CAMDAS performs molecular dynamics (MD) calculations for a target molecule and samples conformers from the trajectory of the MD. The program then evaluates the similarities between each of the sampled conformers in terms of the root- mean-square deviations of the atomic positions, clusters similar conformers, and finally prints out the clustered conformers. This MD-based conformational analysis is a broadly used method, and CAMDAS is intended to provide a convenient framework for the method. CAMDAS has the ability to find the representative conformers automatically from an arbitrarily given structure of the molecule. The accuracy of the program was examined using N- acetylalanine-N-methylamide, and the obtained result was consistent with that of the systematic search method. In the test calculation of cyclodecane, CAMDAS could identify most of the known conformers and their conformational enantiomers by examining only 5000 conformers. In addition, the potential-scaled method, which we have developed previously as an accelerating technique for MD, could find two additional conformers of cyclodecane that have not been reported. CAMDAS presents a convenient way to find the energetically possible conformers of a molecule, which is needed especially in the early stage of drug design.     

Growth Mechanism of Large Monodispersed Silica Particles Prepared from Tetraethoxysilane in the Presence of Sodium Dodecyl Sulfate

Monodispersed silica particles up to ca. 1.2 μm in diameter were prepared by hydrolysis of tetraethoxysilane in the presence of sodium dodecyl sulfate (SDS). The particle size was increased with an increase of SDS added. The geometrical standard deviation of the particles was decreased with an increase of SDS. In the earlier reaction stage, double spherical particles by the coalescence of the particles were frequently observed when large amounts of SDS were added. Particle size was gradually increased after the coalescence occurred and spherical particles were finally obtained. The results of Nielsen’s chronomal analysis suggest that the polynuclear layer growth took place after the coalescence of the particles in the presence of larger amount of SDS.     

Molecular interactions between lipid bilayers and a water-soluble polymer

Molecular interactions between lipid bilayers (liposomes) and chondroitin sulfate C (CS), a water soluble polymer, have been investigated in terms of zeta-potential, particle size, microscopic-viscosity, microscopic-polarity of liposomes and permeability of calcein. Microscopic morphology is dramatically changed by the addition of CS to the positively charged liposomes (Pos.L), while it is not changed by the addition to uncharged liposomes (Unc.L) or negatively charged liposomes (Neg.L). The absolute value of the particle size of Pos.L increases with the addition of CS, while the zeta- potential of Pos.L decreases. Permeability of Pos.L decreases with an increase in the concentration of CS. Phase transition temperature of Pos.L is changed after the addition of CS. These values, however, are not changed for the other liposomes by the addition of CS. The results of gel filtration chromatography show that CS is absorbed on the Pos.L surface. Microscopic viscosity is also increased by the addition of CS to Pos.L due to the adsorption of CS.     

Triethylborane-mediated hydrogallation and hydroindation: novel access to organogalliums and organoindiums

Hydrogallation of carbon[bond]carbon multiple bonds proceeds in the presence of triethylborane as a radical initiator. Several functionalities do not interfere with this reaction. Resulting alkenyl- and alkylgallium species can be trapped by several electrophiles. Highly regioselective radical addition of an indium hydride reagent to alkynes is also achieved. Various functionalities are tolerant under the reaction conditions. The reaction proceeds with complete anti stereoselectivity. Alkenylindiums obtained via hydroindation can be employed for the following cross-coupling reaction with aryl halides in one pot.     

An indication of magnetic-field-induced superconductivity in a bifunctional layered organic conductor,kappa-(BETS)(2)FeBr(4)

Hybrid systems consisting of the conducting layers of organic donor molecules and the magnetic layers of inorganic anions have been focused on as possible bifunctional materials, whose conducting properties can be tuned by controlling the magnetic state of the anion layers on an application of magnetic field. Here we report the magnetoresistance of the antiferromagnetic organic superconductor, kappa-(BETS)2FeBr4 [BETS = bis(ethylenedithio)tetraselenafulvalene], consisting of the two-dimensional superconducting layers of the BETS semications and the insulating layers of the FeBr4- anions. Due to the metamagnetic nature of the Fe3+ spin system, characteristic resistivity decrease was observed just below the antiferromagnetic superconductor-to-ferromagnetic metal transition at 1.6 T. Furthermore, an indication of the onsets of the magnetic-field-induced superconductivity was discovered around 12.5 T.     

Cobalt-catalyzed Heck-type reaction of alkyl halides with styrenes

A cobalt complex, CoCl2[1,6-bis(diphenylphosphino)hexane], catalyzes an alkylation reaction of styrenes in the presence of Me3SiCH2MgCl in ether to yield beta-alkylstyrenes. A variety of alkyl halides including alkyl chlorides can be employed as an alkyl source. A radical mechanism is strongly suggested for this alkylation reaction.     

Reactivity of hydroperoxide bound to a mononuclear non-heme iron site

The first isolation and spectroscopic characterization of the mononuclear hydroperoxo-iron(III) complex [Fe(H(2)bppa)(OOH)](2+) (2) and the stoichiometric oxidation of substrates by the mononuclear iron-oxo intermediate generated by its decomposition have been described. The purple species 2 obtained from reaction of [Fe(H(2)bppa)(HCOO)](ClO(4))(2) with H(2)O(2) in acetone at -50 degrees C gave characteristic UV-vis (lambda(max) = 568 nm, epsilon = 1200 M(-1) cm(-1)), ESR (g = 7.54, 5.78, and 4.25, S = (5)/(2)), and ESI mass spectra (m/z 288.5 corresponding to the ion, [Fe(bppa)(OOH)](2+)), which revealed that 2 is a high-spin mononuclear iron(III) complex with a hydroperoxide in an end-on fashion. The resonance Raman spectrum of 2 in d(6)-acetone revealed two intense bands at 621 and 830 cm(-1), which shifted to 599 and 813 cm(-1), respectively, when reacted with (18)O-labeled H(2)O(2). Reactions of the isolated (bppa)Fe(III)-OOH (2) with various substrates (single turnover oxidations) exhibited that the iron-oxo intermediate generated by decomposition of 2 is a nucleophilic species formulated as [(H(2)bppa)Fe(III)-O*].     

Injectable Polypeptide Hydrogel Depot System for Assessment of the Immune Response–Inducing Efficacy of Sustained Antigen Release Alone

Vaccines typically contain an antigen, delivery system (vehicle), and adjuvant, all of which contribute to inducing a potent immune response. Consequently, design of new vaccines is difficult, because the contributions and interactions of these components are difficult to distinguish. Here, it is aimed to develop an easy‐to‐use, non‐immunogenic, injectable depot system for sustained antigen release that will be suitable for assessing the efficacy of prolonged antigen exposure per se for inducing an immune response. This should mimic real‐life infections. Recombinant elastin‐like polypeptides with periodic cysteine residues (cELPs) are selected, which reportedly show little or no immunogenicity, as carriers and tetanus toxoid (Ttd) as an antigen. After subcutaneous injection of the mixture, cELP rapidly forms a disulfide cross‐linked hydrogel in situ, within which Ttd is physically incorporated, affording a biodegradable antigen depot. A series of Ttd‐containing hydrogels is examined. A single injection induces high levels of tetanus antibody with high avidity for at least 20 weeks in mice. The chain length of cELP proves critical, whereas differences in hydrophobicity has little effect, although hydrophilic cELPs are more rapidly biodegraded. This system's ability to distinguish the contribution of sustained antigen release to antibody induction should be helpful for rational design of next‐generation vaccines.     

Photoredox‐Catalyzed Alkenylation of Benzylsulfonium Salts

Visible light‐mediated radical alkenylation of benzylsulfonium salts was achieved by means of fac‐Ir(ppy)₃ as a photocatalyst, giving allylbenzenes as products. A variety of functional groups, such as halogen, ester, and cyano, were well tolerated in this transformation. Starting benzylsulfonium salts could be readily prepared from benzyl alcohols by an acid‐mediated substitution, increasing the synthetic utility of this transformation.     

Structural disorder and diffusional pathway of oxide ions in a doped Pr2NiO4-based mixed conductor

MEM nuclear density analysis from neutron diffraction data measured in situ at 1015.6 degrees C has indicated the two-dimensional network of curved O2-O3-O2 oxide-ion diffusion paths on the (Pr,La)-O layer in a K2NiF4-type structured oxide-ionic and electronic mixed conductor (Pr0.9La0.1)2(Ni0.74Cu0.21Ga0.05)O4+delta.