Dependency of ligand free energy landscapes on charge parameters and solvent models

We performed replica-exchange molecular dynamics (REMD) simulations of six ligands to examine the dependency of their free energy landscapes on charge parameters and solvent models. Six different charge parameter sets for each ligand were first generated by RESP and AM1-BCC methods using three different conformations independently. RESP charges showed some conformational dependency. On the other hand, AM1-BCC charges did not show conformational dependency and well reproduced the overall trend of RESP charges. The free energy landscapes obtained from the REMD simulations of ligands in vacuum, Generalized-Born (GB), and TIP3P solutions were then analyzed. We found that even small charge differences can produce qualitatively different landscapes in vacuum condition, but the differences tend to be much smaller under GB and TIP3P conditions. The simulations in the GB model well reproduced the landscapes in the TIP3P model using only a fraction of the computational cost. The protein-bound ligand conformations were rarely the global minimum states, but similar conformations were found to exist in aqueous solution without proteins in regions close to the global minimum, local minimum or intermediate states.     

Copper-Free Sonogashira coupling in water with an amphiphilic resin-supported palladium complex

The palladium-catalyzed coupling reaction of aryl halides with terminal alkynes, the Sonogashira coupling, took place in water under copper-free conditions by use of an amphiphilic polystyrene-poly(ethylene glycol) (PS-PEG) resin-supported palladium-phosphine complex to give the corresponding aryl-substituted alkynes in high yields. The PS-PEG resin-supported palladium catalyst was recovered by simple filtration and reused four times without any loss of catalytic activity.     

Rubber friction: Comparison of theory with experiment

We have measured the friction force acting on a rubber block slid on a concrete surface. We used both unfilled and filled (with carbon black) styrene butadiene (SB) rubber and have varied the temperature from −10 °C to 100 °C and the sliding velocity from 1 μm/s to 1000 μm/s. We find that the experimental data at different temperatures can be shifted into a smooth master-curve, using the temperature-frequency shifting factors obtained from measurements of the bulk viscoelastic modulus. The experimental data has been analyzed using a theory which takes into account the contributions to the friction from both the substrate asperity-induced viscoelastic deformations of the rubber, and from shearing the area of real contact. For filled SB rubber the frictional shear stress σ_f in the area of real contact results mainly from the energy dissipation at the opening crack on the exit side of the rubber-asperity contact regions. For unfilled rubber we instead attribute σ_f to shearing of a thin rubber smear film, which is deposited on the concrete surface during run in. We observe very different rubber wear processes for filled and unfilled SB rubber, which is consistent with the different frictional processes. Thus, the wear of filled SB rubber results in micrometer-sized rubber particles which accumulate as dry dust, which is easily removed by blowing air on the concrete surface. This wear process seams to occur at a steady rate. For unfilled rubber a smear film forms on the concrete surface, which cannot be removed even using a high-pressure air stream. In this case the wear rate appears to slow down after some run in time period.     

Influence of ordering change on the optical and thermal properties of inflation polyethylene films

Changes of thermal diffusivity inside femtosecond laser-structured volumes as small as few percent were reliably determined (with standard deviation less than 1%) with miniaturized sensors. An increase of thermal diffusivity of a crystalline high-density polyethylene (HDPE) inflation films by 10-20% from the measured (1.16 ± 0.01) × 10⁻⁷ m² s⁻¹ value in regions not structured by femtosecond laser pulses is considerably larger than that of non-crystalline polymers, 0-3%. The origin of the change of thermal diffusivity are interplay between the laser induced disordering, voids’ formation, compaction, and changes in molecular orientation. It is shown that laser structuring can be used to modify thermal and optical properties. The birefringence and infrared spectroscopy with thermal imaging of CH₂ vibrations are confirming inter-relation between structural, optical, and thermal properties of the laser-structured crystalline HDPE inflation films. Birefringence modulation as high as Δn ∼ ± 1 × 10⁻³ is achieved with grating structures.     

Syntheses and characterizations of 4-(3,17beta-dihydroxyestra-1,3,5(10)-trien-6alpha- and 6beta-yl)amino-7-nitro-2,1,3-benzoxadiazoles as fluorescent probes.

4-(3,17Beta-dihydroxyestra-1,3,5(10)-trien-6alpha- and 6beta-yl)amino-7-nitro-2,1,3-benzoxadiazoles have been synthesized and characterized as fluorescent probes for use in a receptor assay and/or a homogeneous immunoassay for estradiol. The fluorescence intensities are strongly dependent upon the solvent polarity used. The intensities in water were reduced to less than 1% of those in ethyl acetate, and a blue shift was also observed in polar solvents. The quenched fluorescence in aqueous solution was recovered by adding bovine serum albumin or an anti-estradiol antibody. Adding intact estradiol inhibited the fluorescence recovered by the antibody.     

Baseline noise and measurement uncertainty in liquid chromatography.

The stochastic properties of baseline noise in HPLC systems with a UV photo-diode array, photo-multiplier and gamma-ray detector were examined by dividing the noise into auto-correlated random process (Markov process) and an independent process (white noise). The present work focused on the effect of the stochastic noise properties on a theoretical estimation of the standard deviation (SD) of area measurements in instrumental analyses. An estimation theory, called FUMI theory (Function of Mutual Information), was taken as an example. A computer simulation of noise was also used. It was shown that the reliability (confidence intervals) of theoretical SD estimates mainly depends on the following factors: the ratio of the white noise and Markov process occurring in the baselines; the number of data points used for the estimation; the width of a target peak for which the SD is estimated.     

Weak and Strong Convergence Theorems for a Nonexpansive Mapping and an Equilibrium Problem

In this paper, we introduce two iterative sequences for finding a common element of the set of fixed points of a nonexpansive mapping and the set of solutions of an equilibrium problem in a Hilbert space. Then, we show that one of the sequences converges strongly and the other converges weakly.