Relaxation mode analysis of a peptide system: comparison with principal component analysis

This article reports the first attempt to apply the relaxation mode analysis method to a simulation of a biomolecular system. In biomolecular systems, the principal component analysis is a well-known method for analyzing the static properties of fluctuations of structures obtained by a simulation and classifying the structures into some groups. On the other hand, the relaxation mode analysis has been used to analyze the dynamic properties of homopolymer systems. In this article, a long Monte Carlo simulation of Met-enkephalin in gas phase has been performed. The results are analyzed by the principal component analysis and relaxation mode analysis methods. We compare the results of both methods and show the effectiveness of the relaxation mode analysis.     

Control of shell thickness in silica-coating of Au nanoparticles and their X-ray imaging properties

This paper describes a performance of precise control of shell thickness in silica-coating of Au nanoparticles based on a sol-gel process, and an investigation into X-ray imaging properties for the silica-coated Au (Au/SiO(2)) particles. The Au nanoparticles with a size of 16.9±1.2 nm prepared through a conventional citrate reduction method were used as core particles. The Au nanoparticles were silica-coated with a sol-gel reaction using tetraethylorthosilicate (TEOS) as a silica source, sodium hydroxide (NaOH) as a catalyst, and (3-aminopropyl) trimethoxysilane (APMS) as a silane coupling agent. An increase in TEOS concentration resulted in an increase in shell thickness. Under certain concentrations of Au, H(2)O, NaOH, and APMS, the Au/SiO(2) particles with silica shell thickness of 6.0-61.0 nm were produced with varying TEOS concentration. Absorption peak wavelength of surface plasmon resonance of the Au/SiO(2) colloid solution depended on silica shell thickness, which agreed approximately with the predictions by Mie theory. The as-prepared colloid solution could be concentrated up to an Au concentration of 0.19 M with salting-out and centrifugation. The concentrated colloid solution showed an X-ray image with high contrast, and a computed tomography value for the colloid solution with an Au concentration of 0.129 M was achieved 1329.7±52.7 HU.     

Sol–gel and transfer technique for fabricating dual ceramic thin film patterns on plastics

A technique that realizes alternating, two kinds of ceramic ribbons on plastics is proposed. An Si(100) plate with periodic trenches coated with a polyimide (PI)-polyvinylpyrrolidone (PVP) mixture layer was used as the mother substrate. An indium–tin–oxide (ITO) thin film was deposited on the mother substrate by the sol–gel method with a firing process, followed by transferring it to a polycarbonate (PC) substrate by melting the PC surface in contact with the ITO thin film. This resulted in patterned ITO ribbons on the PC substrate where the ridges of PC were formed between the ribbons. A ZnO thin film was prepared on a flat Si(100) substrate coated with a PI-PVP mixture layer, followed by firing, and then was transferred on the PC ridges in the same manner, resulting in alternating ITO and ZnO ribbons on the PC substrate. The technique proposed here allows dense, alternating ceramic ribbons to be fabricated on plastics irrespective of the combinations of ceramics and plastics.     

Polysilazane as the source of silica: the formation of dense silica coatings at room temperature and the new route to organic–inorganic hybrids

Xylene solutions of perhydropolysilazane (PHPS) were used as the coating solutions for preparing silica coatings at room temperature. The PHPS-to-silica conversion was achieved by exposing the spin-on coatings to the vapor from aqueous ammonia. In order to examine the significance of the mechanical properties of the PHPS-derived silica coatings, the pencil hardness was measured, which was compared with that of tetraethoxysilane (TEOS)-derived silica coatings. The pencil hardness was over 9H at a load of 1 kg, which was much higher than that of the TEOS-derived silica gel films, and was comparable to that of the TEOS-derived films heat treated at 300 °C. Second, poly(methyl methacrylate) (PMMA)–silica hybrid coatings were prepared from xylene solutions of PMMA and PHPS via exposure to the vapor from aqueous ammonia. Crack-free, optically transparent PMMA–silica hybrid coatings could be prepared, where PHPS-to-silica conversion was confirmed by infrared absorption spectroscopy. The refractive index was around 1.42–1.50, and the contact angle with water increased from 35 to 70° with increasing PMMA content. The pencil hardness greatly increased during the PHPS-to-silica conversion, and was much higher than that of the non-heat treated TEOS-derived hybrid coatings. The durability in tetrahydrofuran (THF) was also evaluated by measuring the reduction in thickness occurring during soaking in THF. The durability decreased with increasing PMMA content, but was much higher than that of the non-heat treated TEOS-derived hybrid coatings. Both the hardness and the durability were comparable to those of the TEOS-derived coatings heated at 300 °C. The hybrid coatings could also be deposited on poly(ethylene terephthalate) substrates, where no cracks were observed at high PMMA contents even when the substrate was bent.     

Heteroaryl-substituted C3-bridged oligopyrroles: potential building subunits of anion-responsive pi-conjugated oligomers

Acyclic anion receptors (BF 2 complexes of dipyrrolyldiketones) with heteroaryl moieties synthesized by using cross-coupling reactions have unique electronic states, as observed in UV/vis absorption spectra. Among heteroaryl-substituted derivatives, a pyrrolyl-substituted receptor exhibits an extremely high affinity for anions in solution.     

Asymmetric induction in the preparation of helical receptor-anion complexes: ion-pair formation with chiral cations

Asymmetry through ion pairing: Upon addition of chloride and bromide ions, as chiral ammonium salts, to solutions of pyrrole-based π-conjugated linear oligomers, helical structures form with asymmetric induction, which is guided by the formation of diastereomeric ion pairs with chiral counter cations. These ions pairs exhibit circular dichroism (CD) and strong circularly polarized luminescence (CPL) with g(lum) values of greater than 0.1.     

Energetics of dopant atoms in subsurface positions of diamond semiconductor

We present a set of ab initio energetics for a substitutional boron (B) impurity atom in subsurface positions, from the topmost to the fifth atomic layer, of both C(001)-2×1:H and C(111)-1×1:H. We compare the calculated surface-B binding energies with those obtained for P [T. Miyazaki, H. Kato, H. Okushi, S. Yamasaki, e-J. Surf. Sci. Nanotech. 4 (2006) 124]. The surface-P binding energies become larger as the position of P is closer to the two surfaces. They are up to 4 eV for C(001)-2×1:H and 2.6 eV for C(111)-1×1:H, respectively. For B, in contrast, the binding energies are within 0.5 eV for both surfaces. An implication of our finding in the context of a mechanism for P and B doping in diamond is discussed.     

First asymmetric total syntheses of (-)-subincanadines a and B, skeletally rearranged pentacyclic monoterpenoid indole alkaloids in aspidospermasubincanum

We achieved the first asymmetric total syntheses of novel Aspidosperma indole alkaloids, (-)-subincanadines A and B, which involve an intramolecular diastereoselective Pictet-Spengler cyclization and an intramolecular Nozaki-Hiyama-Kishi reaction as key steps in the total syntheses.     

New synthesis of (+/-)-isonucleosides

[Structure: see text] A novel method for synthesizing isonucleosides, a new class of anti-HIV nucleosides, is described. 2,2-Dimethyl-1,3-dioxan-5-one was converted into a dioxabicyclohexane derivative in six steps. After cleaving the epoxide group with thiophenol, the resulting product was subjected to the Mitsunobu reaction in the presence of a nucleobase to give the desired isonucleoside derivative via migration of the thiophenyl group. Removal of the thiophenyl group under radical conditions followed by deprotection led to the 4'-substituted 2',3'-dideoxyisonucleosides as a racemic mixture.     

Study on the intermolecular interaction of C60 and simulations on the orientational properties of C60 in crystals

We developed the new intermolecular interaction model of C(60) with the quantitative accuracy for the molecular orientational properties in crystals. The energy difference (DeltaE) and the activation barrier (E(barrier)) between the two stable orientations (P and H orientations) in crystals are in the values of +14.7 and +260 meV in our model, respectively; these values are in fairly good agreement with the experimental values (DeltaE approximately +11 meV, E(barrier)=+235-+290 meV in experiments). The relaxation calculation for C(60) crystals using our model revealed that there is the reversal of the stable orientations between the P and H orientations under the high H-orientation occupancy (p(H)) in crystals, when p(H)>0.83, DeltaE<0. From the molecular dynamics calculations for C(60) crystals using our model, it is found that the phase transition is induced at T(C)=200-260 K, which is consistent with the experimental value of 260 K. Immediately below T(C), we found a great variety of molecular rotational jumps involving that between the P and H orientations every about 10(-9) s due to the thermal activation. In the high temperature phase (>T(C)), all molecules rotate irregularly like in Brownian motion involving the rotational "slumber" for approximately 10(-12)-10(-11) s.