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.     

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     

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.     

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,...     

Gradient-norm-based histogram equalization taking account of HSV color space distribution

In the present paper, we propose an image contrast enhancement method that can enhance the contrast of a color image naturally by taking account of a color space shape. The proposed method realizes the natural enhancement based on two kinds of intensity histograms: a gradient-norm-based histogram and an ideal histogram derived from the shape of a color space. The former histogram is used to suppress over-enhancement in the flat regions of an image and the latter histogram is used to prevent the whole image from being darken. Concretely, the aforementioned intensity histograms are appropriately mixed into a histogram with a weight based on the average intensity of the input image. The contrast enhancement of the input image is realized using the cumulative histogram of the mixed histogram as an intensity transform function. To verify the validity of the proposed method, in experiments, the proposed method is applied to a variety of images and experimental results are evaluated qualitatively and quantitatively.     

Masking mechanisms of bitter taste of drugs studied with ion selective electrodes

The masking mechanisms of the bitter taste of propantheline bromide (PB) and oxyphenonium (OB) bromide by native and modified cyclodextrins, saccharides, surfactants, organic acids, nonionic and anionic polymers, and other compounds were investigated with ion selective electrodes. The intensity of the bitter taste for a mixed solution of cyclodextrin with PB or OB was quantitatively explained from the observed electromotive force with the following assumptions: the complex and the masking agent do not have any tastes and the bitter taste is independent of other tastes. Sodium dodecyl sulfate reduced the bitter taste remarkably, and this reduction was also explicable on the basis of the same mechanism. Sodium taurodeoxycholate enhanced the bitter taste, because of its strong bitterness, although it formed 1 : 1 complexes with PB and OB. The masking mechanism of saccharides was ascribed to overcoming the weak bitterness of the drug by the strong sweetness. Lambda-carrageenan suppressed the bitter taste remarkably. This suppression was ascribed to the binding of PB and OB to lambda-carrageenan, the effect of the solution viscosity on the bitter taste, and the covering of the bitter taste receptor by lambda-carrageenan. It was suggested that the moderate masking by other polymers was attributable to the effect of the solution viscosity or the receptor covering. Native and modified beta-cyclodextrins, sodium dodecyl sulfate, lambda-carrageenan, Tween 20, and sodium carboxymethyl cellulose are good masking agents for the bitter tastes of PB and OB. The drug ion selective electrode is a useful tool for understanding of the masking mechanism of the bitter taste, screening of masking agents, and estimation of appropriate concentrations of the masking agents.     

Total synthesis and structural elucidation of azaspiracid-1. Synthesis-based analysis of originally proposed structures and indication of their non-identity to the natural product

The key building blocks (6, 7, and 8) for the intended construction of the originally proposed structures of azaspiracid-1, a potent marine-derived neurotoxin, were coupled and the products elaborated to the targeted compounds (1a,b) and their C-20 epimers (2 and 3). The assembly of the three intermediates was accomplished by a dithiane-based coupling reaction that united the C(1)-C(20) (7) and C(21)-C(27) (8) fragments, followed by a Stille-type coupling which allowed the incorporation of the C(28)-C(40) fragment (6) into the growing substrate. Neither of the final products (1a,b) matched the natural substance by TLC or (1)H NMR spectroscopic analysis, suggesting one or more errors in the originally proposed structure for this notorious biotoxin.