Time operators for quantum walks

Letters in Mathematical Physics - We study time operators for discrete-time quantum systems. Quantum walks are typical examples. We construct time operators for one-dimensional homogeneous quantum...     

Regioselective protection of sugars catalyzed by dimethyltin dichloride

The first catalytic process for protection of hydroxyl groups in sugars has been developed. Highly regioselective protection was accomplished along with high chemical yield. The regioselectivity of the benzoylation was realized as an intrinsic character of sugars based on a stereorelationship among their hydroxyl groups. Furthermore, complete protection of alpha-methyl glucoside and beta-methyl xyloside was accomplished.     

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.     

Chemocavity: specific concavity in protein reserved for the binding of biologically functional small molecules

The idea that there should be a specific site on a protein for a particular functional small molecule is widespread. It is, however, usually not so easy to understand what characteristics of the site determine the binding ability of the functional small molecule. We have focused on the concurrence rate of the 20 standard amino acids at such binding sites. In order to correlate the concurrence rate and the specific binding site, we have analyzed high-quality X-ray structures of complexes between proteins and small molecules. A novel index characterizing the binding site based on the concurrency rate has been introduced. Using this index we have identified that there is a specific concavity designated as a chemocavity where a specific group of small molecules, i.e., canonical molecular group, is highly inclined to be bound. This study has demonstrated that a chemocavity is reserved for a specific canonical molecular group, and the prevalent idea has been confirmed.     

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.     

Approaches toward High‐Mannose‐Type Glycan Libraries

Asparagine‐linked (N‐linked) sugar chains are widely found in the rough endoplasmic reticulum (ER), which has attracted renewed attention because of its participation in the glycoprotein quality control process. In the ER, newly formed glycoproteins are properly folded to higher‐order structures by the action of a variety of lectin chaperones and processing enzymes and are transported into the Golgi, while terminally misfolded glycoproteins are carried into the cytosol for degradation. A group of proteins related to this system are known to recognize subtle differences in the high‐mannose‐type oligosaccharide structures of glycoproteins; however, their molecular foundations are still unclear. In order to gain a more precise understanding, our group has established a strategy for the systematic synthesis of high‐mannose‐type glycans. More recently, we have developed “top‐down” chemoenzymatic approaches that allow expeditious access to theoretically all types of high‐mannose glycans. This strategy comprehensively delivered 37 high‐mannose‐type glycans, including G1M9–M3 glycans, and opened up the possibility of the elucidation of structure–function relationships with a series of high‐mannose‐type glycans.     

Rates of electronic excitation hopping in anisotropic ionic crystals of [Ru(2,2'-bipyridine)3]X2 (X = ClO4-, PF6-, SbF6-); Monte Carlo simulation of single- and multi-exponential emission decays

Emission decays of triplet metal-to-ligand charge transfer states in anisotropic crystals of [Ru(1 - x)Os(x)(bpy)(3)]X(2) (bpy = 2,2'-bipyridine, X = PF(6)-, ClO(4)-, SbF(6)-, and 0.115 > x > 0.001) at approximately 300 K were measured by means of time-correlated single-photon counting. Rates of excitation hopping calculated on the basis of an interaction between transition dipoles of a donor cation and an acceptor cation are insufficient to simulate the single-exponential decays (x = 0.0099) and the multiexponential decays (x = 0.060 and 0.115) of the PF(6)- salt crystals. A limiting rate of excitation hopping to an imaginary cation at the van der Waals distance via a super-exchange interaction between d orbitals through the bpy ligands was determined to be 0.83 x 10(10) s(-1) on average by means of a step-by-step Monte Carlo simulation, assuming an distance-attenuation factor, beta, of the exchange interaction of 10 nm-1. The total rate of excitation hopping via both a dipole-dipole mechanism and a super-exchange mechanism to the neighboring sites of the cation was calculated to be 5.4 x 10(9) s(-1) for the PF(6)- crystal. Anisotropic diffusion constants estimated from the hopping rates and lengths in the PF(6)- crystal are 9.3 x 10(-6), 9.1 x 10(-6), and 1.4 x 10(-6) cm(2)s(-1) along the a axis, the b axis, and the c axis, respectively, which are compared with an isotropic diffusion constant, 1.3 x 10(-6) cm(2) s(-1), estimated from the pseudo-bimolecular rate constant of excitation transfer to [Os(bpy)(3)](2+), using an isotropic Smoluchowski equation. A multiexponential emission decay of [Ru(0.885)Os(0.115)(bpy)(3)](PF(6))(2) was also simulated to determined the limiting rate of excitation transfer to [Os(bpy)(3)](2+) at the van der Waals distance (2.6 x 10(11) s(-1)). The magnitude of beta determined is 6.5 and 11.5 nm(-1) for the ClO(4)- and the SbF(6)- salt crystals, respectively, on reference to that of beta (10 nm(-1)) for the PF(6)- salt crystal.     

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     

Hue-preserving image enhancement in CIELAB color space considering color gamut

Optical Review - In this paper, we propose a color image enhancement method that uses the CIELAB color space to improve the quality of degraded images for human visual perception. In our method,...