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.     

The nonexistence of projective planes of order 12 with a collineation group of order 8

In this article, we prove that there does not exist a symmetric transversal design which admits an automorphism group of order 4 acting semiregularly on the point set and the block set. We use an orbit theorem for symmetric transversal designs to prove our result. As a corollary of the result, we prove that there is no projective plane of order 12 admitting a collineation group of order 8. © 2007 Wiley Periodicals, Inc. J Combin Designs 16: 411–430, 2008     

Acid-catalyzed deprotection mechanism of tert-butyloxycarbonyloxy polymers in chemically amplified resists

A mechanism of acid-catalyzed deprotection of poly(4-tert-butyloxycarbonyloxy-styrene), PBOCST, in chemically amplified resists has been elucidated in terms of elementary processes by means of semiempirical molecular orbital calculations. It is concluded that the overall deprotection of tert-butyloxycarbonyl (t-BOC) group proceeds stepwise; i.e., (a) the first products are an acid carbonate and a tert-butyl cation; (b) a phenolic compound is the secondary and final product from the acid carbonate, which is realized by assistance with a counter anion accompanied by acid; (c) the counter anion also assists acid regeneration from the tert-butyl cation to produce isobutylene. The yield rate of the phenol is proportional to the product of concentrations of the polymer, the catalytic acid, and the counter anion. The activation energy (21 kcal/mol) calculated for the rate-determining step (a) is in good agreement with an experiment. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: 1035–1042, 1998     

A novel condition for capillary electrophoretic analysis of reductively aminated saccharides without removal of excess reagents

We have identified novel CE conditions for the separation of 7‐amino‐4‐methylcoumarin‐labeled monosaccharides and oligosaccharides from glycoproteins. Using a neutrally coated capillary and alkaline borate buffer containing hydroxypropylcellulose and ACN, saccharide derivatives form anionic borate complexes, which move from the cathode to the anode in an electric field and are detected near the anodic end. Excess labeling reagents and other fluorescent products remain at the cathodic end. Fluorimetric detection using an LED as a light source enables determination of monosaccharide derivatives with good linearity between at least 0.4 and 400 μM, may correspond to 140 amol to 140 fmol. The lower LOD (S/N = 5) is only 80 nM in the sample solution (ca. 28 amol). The results were comparable to reported values using fluorometric detection LC. The method was also applied to the analysis of oligosaccharides that were enzymatically released from glycoproteins. Fine resolution enables profiling of glycans in glycoproteins. The applicability of the method was examined by applying it to other derivatives labeled with nonacidic tags such as ethyl p‐aminobenzoate‐ and 2‐aminoacridone‐labeled saccharides.     

Development of ultra-short pulse VUV laser system for nanoscale processing

We have developed intense vacuum ultraviolet (VUV) radiation sources for advanced material processing, such as photochemical surface reactions and precise processing on a nanometer scale. We have constructed a new VUV laser system to generate sub-picosecond pulses at the wavelength of 126 nm. A seed VUV pulse was generated in Xe as the 7th harmonic of a 882-nm Ti:sapphire laser. The optimum conversion was achieved at the pressure of 1.2 Torr. The seed pulse will be amplified by the Ar₂^*\mathrm{Ar}_{2}^{*} media generated by an optical-field-induced ionization Ar plasma produced by the Ti:sapphire laser. We have obtained a gain coefficient of g=0.16 cm⁻¹. Our developing system will provide VUV ultra-short pulses with sub-μJ energy at a repetition rate of 1 kHz.     

Polarization in heavy-ion reactions

A series of experiments is described in which beta-ray asymmetry has been used to determine polarization of heavy-ion reaction products¹²B and the present status of the studies of polarization phenomena in heavy-ion reactions is reviewed. A large amount of angular momentum sustained by the two colliding nuclei gives rise to polarization phenomena of reaction products. Coupling between the degrees of freedom accompanying the intrinsic and the relative motions is investigated from the systematic behaviour of polarization of reaction products disclosed by the experiments.     

The effect of annealing on the proton conductivity of Mg-doped α-Al2O3

In order to evaluate the effect of annealing treatment on the proton conductivity of ??-alumina, the electrical conductivity of Mg-doped polycrystalline ??-alumina kept at 1,873?K under various conditions of the surrounding atmosphere and then cooled in the furnace was measured in the temperature range 1,173?C1,473?K. The H⁺/D⁺ isotope effect on the electrical conductivity was also examined under a hydrogen atmosphere at 1,273?K. The protonic conductivity measured at 1,273?K increased with the increase in the activity of oxygen and water vapor in the annealing atmosphere at 1,873?K. It is considered that the solubility limit of magnesium ions in ??-alumina in equilibrium with the small amount of the spinel phase increased with the increase in the activity of oxygen and water vapor at 1,873?K. This enhanced amount of magnesium ions is frozen in a non-equilibrium state to 1,273?K and works as the enriched acceptor dopant for the incorporation of protons.     

A family of translation planes of order q 2m+1 with two orbits of length 2 and q 2m+1−1 on l ∞

A class of translation planes of order q ^2m+1, where q is an odd prime power and m1, is constructed. If m=1, then this class is contained in the class of order q ³ constructed by Hiramine [5]. These planes of order q ^2m+1 are of dimension 2m+1 over their kernels. If q ^2m+13³, then the linear translation complements of these planes have two orbits of length 2 and q ^2m+1–1 on l and this class contains many planes which are not generalized André planes. If q ^2m+1= 3³, then each plane of this class is isomorphic to the Hering plane of order 27.Dedicated to Professor Tuyosi Oyama on his 60th birthday     

Syntheses, structures, and coordination chemistry of phosphole-containing hybrid calixphyrins: promising macrocyclic P,N2,X-mixed donor ligands for designing reactive transition-metal complexes

The syntheses, structures, and coordination chemistry of phosphole-containing hybrid calixphyrins (P,N2,X-hybrid calixphyrins) and the catalytic activities of their transition-metal complexes are reported. The 5,10-porphodimethene type 14pi-P,(NH)2,X- and 16pi-P,N2,X-hybrid calixphyrins (X = O, S, NH) are prepared via acid-promoted dehydrative condensation between a sigma4-phosphatripyrrane and the corresponding 2,5-bis[hydroxy(phenyl)methyl]heteroles followed by DDQ oxidation. Both spectroscopic and crystallographic data of the hybrid calixphyrins have revealed that the conformation and size of the macrocyclic platforms as well as the oxidation state of the -conjugated pyrrole-heterole-pyrrole (N-X-N) units vary considerably depending on the combination of heteroles. The sigma3-P,(NH)2,S- and sigma3-P,N2,S-hybrids react with Pd(OAc)2 and Pd(dba)2, respectively, to afford the same Pd(II)-P,N2,S-hybrid complex, in which the calixphyrin platform is regarded as a dianionic ligand. In the complexation with [RhCl(CO)2]2 in dichloromethane, the sigma3-P,N2,S-hybrid behaves as a neutral ligand to afford an ionic Rh(I)-P,N2,S-hybrid complex, whereas the sigma3-P,N2,NH-hybrid behaves as an anionic ligand to produce Rh(III)-P,N3-hybrid complexes. In the latter reaction, it is likely that a neutral Rh(I)-P,N3-hybrid complex, generated as a highly nucleophilic intermediate, undergoes C-Cl bond activation of the solvent. The complexation of AuCl(SMe2) with the sigma3-P,N2,X-hybrids (X = S, NH) leads to the formation of the corresponding Au(I)-monophosphine complexes. The spectral data and crystal structures of these metal complexes exhibit the hemilabile nature of the phosphole-containing hybrid calixphyrin platforms derived from the flexible phosphole unit and the redox active N-X-N units. The hybrid calixphyrin-palladium and -rhodium complexes catalyze the Heck reaction and hydrosilylations, respectively, implying that the metal center in the core is capable of activating the substrates under appropriate reaction conditions. The present results demonstrate the potential utility of the phosphole-containing hybrid calixphyrins as a new class of macrocyclic P,N2,X-mixed donor ligands for designing highly reactive transition-metal complexes.