The configurational dependence of binding free energies: A Poisson–Boltzmann study of Neuraminidase inhibitors

The linear finite difference Poisson-Boltzmann (FDPB) equation is applied to the calculation of the electrostatic binding free energies of a group of inhibitors to the Neuraminidase enzyme. An ensemble of enzyme-inhibitor complex conformations was generated using Monte Carlo simulations and the electrostatic binding free energies of subtly different configurations of the enzyme-inhibitor complexes were calculated. It was seen that the binding free energies calculated using FDPB depend strongly on the configuration of the complex taken from the ensemble. This configurational dependence was investigated in detail in the electrostatic hydration free energies of the inhibitors. Differences in hydration energies of up to 7 kcal mol^–1 were obtained for root mean square (RMS) structural deviations of only 0.5 Å. To verify the result, the grid size and parameter dependence of the calculated hydration free energies were systematically investigated. This showed that the absolute hydration free energies calculated using the FDPB equation were very sensitive to the values of key parameters, but that the configurational dependence of the free energies was independent of the parameters chosen. Thus just as molecular mechanics energies are very sensitive to configuration, and single-structure values are not typically used to score binding free energies, single FDPB energies should be treated with the same caution.     

Studies on the catalytic decomposition of N2O over the solid solution La2CuxZn1?xO4 (0

U. Kameswari  J. Christopher  C. S. Swamy 《Reaction Kinetics and Catalysis Letters》1990,41(2):381-388

Free radical rearrangements of organocobaloximes: alkynyl to cycloalkylidene and hexenyl to cyclopentylmethyl

Under irradiation by tungsten light in pyridine solution, several substituted alkylcobaloximes undergo rearrangement to more stable substituted alkyl- or alkenyl-cobaloximes. When the same reactions are carried out in the presence of carbon tetrachloride or chloroform, no rearranged organocobaloximes are obtained, but a variety of organic products are obtained derived from the interception of transient organic radicals by the halogenated solvent. The rearrangements are rationalised in terms of a reversible homolysis of the carbon-cobalt bond, rearrangement of the organic radical and recapture by the cobalt(II) fragment to give complexes that are more stable to irradiation than their precursors.     

Use of an automated image processing program to quantify recombinant adenovirus particles.

Electron microscopy has a pivotal role as an analytical tool in pharmaceutical research. However, digital image data have proven to be too large for efficient quantitative analysis. We describe here the development and application of an automated image processing (AIP) program that rapidly quantifies shape measurements of recombinant adenovirus (rAd) obtained from digitized field emission scanning electron microscope (FESEM) images. The program was written using the macro-recording features within Image-Pro Plus software. The macro program, which is linked to a Microsoft Excel spreadsheet, consists of a series of subroutines designed to automatically measure rAd vector objects from the FESEM images. The application and utility of this macro program has enabled us to rapidly and efficiently analyze very large data sets of rAd samples while minimizing operator time.     

Characterisation of poly(neutral red) modified carbon film electrodes; application as a redox mediator for biosensors

The polymer redox mediator, poly(neutral red) (PNR), has been synthesised and characterised electrochemically to investigate the best electropolymerisation and mediation conditions for application in enzyme biosensors and to clarify the mechanism of action. Neutral red was electropolymerised by potential cycling on carbon film electrode substrates by allowing the monomer to be oxidised during the full 20 cycles of polymerisation or reducing the positive limit of the potential window after the first 2 cycles to impede monomer oxidation with a view to obtaining longer polymer chains and a lesser degree of branching. Comparison was made with glassy carbon substrates. The PNR films on carbon film electrodes were characterised using cyclic voltammetry and electrochemical impedance spectroscopy, as well as in glucose biosensors prepared with PNR. Glucose oxidase enzyme was immobilised by encapsulation in silica sol-gel and compared with that obtained by cross-linking with glutaraldehyde. The biosensors were evaluated by chronoamperometry in 0.1 M phosphate buffer saline solution, pH 7.0, and showed evidence of electron transfer between the enzyme cofactor flavin adenine dinucleotide and PNR dissolved in the enzyme layer competing with PNR-mediated electrochemical degradation of H₂O₂ formed during the enzymatic process. This paper is dedicated to Professor Dr. Algirdas Vaskelis on the occasion of his 70th birthday.     

Identification of diethylene glycol monobutyl ether as a source of contamination in an ion trap mass spectrometer

Tandem liquid chromatography-mass spectrometry coupled to online radioactive material detection (LC/RAM/MS/MS) is a technique that is used routinely for in vivo and in vitro drug metabolism studies and allows for a simultaneous correlation between radiochemical peaks and mass spectral data. The compound diethylene glycol monobutyl ether (DGBE), a component of a commercially available scintillation cocktail for RAM analysis, was identified as a source of overwhelming chemical noise in a mass spectrometer which was used in an LC/RAM/MS/MS configuration. In this report, we describe the identification of DGBE as the source of the chemical noise and the methods that were used to minimize the exposure of the mass spectrometer to volatile components of the scintillation cocktail.     

Photolithographic Patterning and Doping of Silica Xerogel Films

This study shows that conventional photolithography can be applied for patterning native or organic dye-doped silica films (0.5 m thick) obtained via a base-catalyzed sol-gel process. Photoresist was spin-coated onto high optical quality xerogel films, soft-baked, exposed to UV irradiation through a photomask, and developed with a commercial photoresist developing solution. Etching away of the photoresist-unprotected areas of the silica films was carried out with a dilute HF solution, while the remaining unexposed photoresist was removed with acetone. Interdigitated array patterns with features as small as 0.5 mm show a smooth surface and extremely sharp interfaces. Densification of the films at 550°C for 2 h decreases the film thickness by 11%, increases the refractive index from 1.420 to 1.456, and allows for well-defined patterning down to length scales of 10 m. Since the densification conditions are incompatible with organic dopants, it is demonstrated that sol-gel films can be doped after pattering (post-doping) by adsorption of cationic dyes from solution. Scanning electron microscopy reveals that the microstructure of patterned sol-gel films is similar to that of bulk monoliths, indicating that the photolithographic procedure is not harmful to the film quality. All patterned films demonstrate highly regular light diffraction patterns.     

Moisture absorption and absorption kinetics in polyelectrolyte films: influence of film thickness

Specular X-ray reflectivity (XR) and quartz crystal microbalance (QCM) measurements were used to determine the absorption of water into thin poly(4-ammonium styrenesulfonic acid) films from saturated vapor at 25 degrees C. The effect of film thickness on the absorption kinetics and overall absorption was investigated in the range of thickness from (3 to 200) nm. The equilibrium swelling of all the films irrespective of film thickness was (0.57+/-0.03) volume fraction. Although the equilibrium absorption is independent ofthickness, the absorption rate substantially decreases for film thickness < 100 nm. For the thinnest film (3 nm), there is a 5 orders of magnitude decrease in the diffusion coefficient for water.     

Meso-tetraaryl cofacial bisporphyrins delivered by Suzuki cross-coupling

The Suzuki cross-coupling methodology provides a facile synthetic approach for the modular preparation of meso-tetraaryl cofacial bisporphyrins anchored by xanthene and dibenzofuran. This synthetic method furnishes cofacial bisporphyrin templates with enhanced steric and electronic protection from mu-oxo formation and oxidative degradation. The ability of these platforms to support multielectron oxidation chemistry mediated by proton-coupled electron transfer (PCET) is demonstrated by their reactivity for the catalytic disproportionation of hydrogen peroxide to oxygen and water.     

Intramolecular C-H activation by inferred terminal cobalt imido intermediates

Reaction of TpR,MeCo(I) dinitrogen complexes (R = iPr, tBu) with trimethylsilyl azide yields structurally characterized compounds that imply the formation of reactive intermediates of the type TpR,MeCo=NSiMe3. These cobalt imido species apparently abstract hydrogen from the 3-substituent of the Tp-ligand, leading to the formation of amido complexes accompanied by either Co-C bond formation (R = tBu) or C-C bond formation (R = iPr).