Further evaluation and development of charge similarity indices for choosing molecular analogues

Two molecular charge similarity index (CSI ) methods are further evaluated for practical application: one method based on a simple CNDO -type approximation to the electron density function and the other based on an ab initio pseudo total charge density function. The test system consists of isosteric analogues of dimethyl ether and methoxy acetic acid. The effects of differences in skeletal structure on the CSI measure of electron density similarity about corresponding atoms is estimated, and two new developments are presented for application of the ab initio-based method: (1) an INDO -type approximation which improves the efficiency of the CSI calculation; and (2) a FOCUS feature which enables comparisons of local molecule regions.     

Production, purification, and biochemical characterization of two beta-glucosidases from Sclerotinia sclerotiorum

The filamentous fungus Sclerotinia sclerotiorum produces beta-glucosidases in liquid culture with a variety of carbon sources, including cellulose (filter paper), xylan, barley straw, oat meal, and xylose. Analysis by native polyacrylamide gel electrophoresis (PAGE) followed by an activity staining with the specific chromogenic substrate, 5-bromo 4-chloro 3-indolyl beta-1,4 glucoside (X-glu) showed that two extracellular beta-glucosidases, designated as beta-glu1 and beta-glu2, were in the filter paper culture filtrate. Only one enzyme designated as beta-glu x was revealed by the same method in the xylose culture filtrate. Beta-glu1 and beta-glu2 were purified to homogeneity. The purification procedure consist of a common step of anion-exchange chromatography on DEAE-Sepharose CL6B, both high-performance liquid chromatography (HPLC) anion-exchange and gel filtration columns for beta-glu1 and only HPLC gel filtration for beta-glu2. Beta-glu1 has a molecular mass of 196 kDa and 96.5 kDa, as estimated by gel filtration and sodium dodecyl sulfate (SDS)-PAGE, respectively, suggesting that the native enzyme may consist of two identical subunits. The same analysis showed that beta-glu2 is a monomeric protein with an apparent molecular mass of about 76.5 kDa. Beta-glu1 and beta-glu2 hydrolyses PNPGlc and cellobiose, with apparent Km values respectively for PNPGlc and cellobiose of 0.1 and 1.9 mM for beta-glu1 and 2.8 and 8 mM for beta-glu2. Both enzymes exhibit the same temperature and pH optima for PNPGlc hydrolysis (60 degrees C and pH 5.0). beta-glu1 was stable over a pH range of 3-8 and kept 50% of its activity after 30 min of heating at 60 degrees C without substrate. It was further characterized by studying the effect of some cations and various reagents on its activity.     

Theoretical study of the magnetic behavior of ferric wheels.

Calculations of exchange coupling constants (J) based on density functional theory for eight complete, nonmodeled ferric wheels have been performed, and a comparison with the values obtained from magnetic susceptibility data is presented. The calculated J values obtained with a generalized-gradient approximation (GGA) functional are in good agreement with the experiment probably because the inclusion of pseudopotentials partially compensates the overestimation of the spin delocalization. The magnetostructural correlation obtained shows a strong dependence of the exchange coupling on both the Fe-O-Fe bond angle and the Fe-O bond distance. This correlation holds for both the ferric wheels and the alkoxo-bridged Fe(III) dinuclear complexes reported in the literature.     

Nature of the Lewis acid sites on molybdenum and ruthenium sulfides: an electrostatic potential study

The energy of formation and the Lewis acid strength of sulfur vacancies or coordinative unsaturated sites on the MoS2 edges were studied using density functional theory for periodic systems and an electrostatic potential-based methodology. The results suggest that the more energetically favorable sites are located on the sulfur edges; however, their Lewis acid strength is considerably smaller than the site acidity at the molybdenum edges. The acid strength for the reported most hydrodesulfurization active site of RuS2 was also determined. In general, the Lewis acid for the site on RuS2 is 100% smaller than the sites on the Mo edges and around 20% larger than the most favorable site on the S edges of MoS2. Binding of the pyridine molecule in the eta1 adsorption configuration on the considered sites has corroborated the trend of Lewis acidity suggested by the electrostatic potential methodology.     

Dynamics or Stochastic Conductance Switching of Phenylene–Ethynylene Oligomers?

Scanning tunneling microscopy (STM) studies of phenylene-ethynylene oligomers inserted in alkanethiolate self assembled monolayers (SAMs) are presented. Spontaneous changes in appearance of bundles of inserted molecules during imaging are observed. The results indicate that the appearance changes are caused by fluctuations of the number of molecules in the bundles, by diffusion and exchange of molecules, in contrast to previous reports which attribute the changes to stochastic conductance switching. The packing density of the SAM around the bundles of inserted molecules influence the fluctuations, as the fluctuations observed at 77 K all take place in bundles inserted at locally less-densely packed SAM areas. At room temperature fluctuations of bundles inserted in well-ordered areas are also observed.     

Typing dinucleotide repeat loci using microplate array diagonal gel electrophoresis: proof of principle

Polymorphic dinucleotide repeat loci ('microsatellite markers') are found in varying abundance throughout the genomes of most organisms. They have been extensively used for genetic studies, but conventional techniques used for their genotyping require sophisticated equipment. Microplate array diagonal gel electrophoresis (MADGE) has previously been extended to economical high-throughput genotyping of trinucleotide and tetranucleotide microsatellite amplicons. However, the capability of this technique to resolve the alleles of dinucleotide repeat loci has not been explored previously. Here we show that a modified microsatellite-MADGE approach can provide sufficient resolution for dinucleotide repeat typing. This enables economical and convenient set up for analysis of single markers in many samples in parallel, suitable, for example, for population association studies.     

Production, purification, and biochemical characterization of two β-glucosidases from Sclerotinia sclerotiorum

The filamentous fungus Sclerotinia sclerotiorum prudces ß-glucosidases in liquid culture with a variety of carbon sources, including cellulose (filter paper), xylan, barley straw, oat meal, and xylose. Analysis by native polyacrylamide gel electrophoresis (PAGE) followed by an activity staining with the specific chromogenic substrate, 5-bromo 4-chloro 3-indolyl ß-1,4 glucoside (X-glu) showed that two extracellular β-glucosidases, designated as ß-glul1 and \-glu2, were in the filter paper culture filtrate. Only one enzyme designated as ß-glus was revealed by the same method in the xylose culture filtrate. ß-glu1 and ß-glu2 were purified to homogeneity. The purification procedure consist of a common step of anion-exchange chromatography on DEAE-Sepharose CL6B, both high-performance liquid chromatography (HPLC) anion-exchange and gel filtration columns for ß-glu1 and only HPLC gel filtration for ß-glu2. ß-glu1 has a molecular mass of 196 kDa and 96.5 kDa, as estimated by gel filtration and sodium dodecyl sulfate (SDS)-PAGE, respectively, suggesting that the native enzyme may consist of two identical subunits. The same analysis showed that ß-glu2 is a monomeric protein with an apparent molecular mass of about 76.5 kDa. ß-glu1 and ß-glu2 hydrolyses PNPG1c and cellobiose, with apparent K _m values respectively for PNPGlc and cellobiose of 0.1 and 1.9 mM for ß-glu1 and 2.8 and 8 mM for ß-glu2. Both enzymes exhibit the same temperature and pH optima for PNPG1c hydrolysis (60°C and pH 5.0). ß-glu1 was stable over a pH range of 3–8 and kept 50% of its activity after 30 min of heating at 60°C without substrate. It was further characterized by studying the effect of some cations and various reagents on its activity.     

Mechanism of 1,3-migration in allylperoxyl radicals: computational evidence for the formation of a loosely bound radical-dioxygen complex

The three pathways postulated for 1,3-migration of the peroxyl group in the allylperoxyl radical (1a), a key reaction involved in the spontaneous autoxidation of unsaturated lipids of biological importance, have been investigated by means of quantum mechanical electronic structure calculations. According to the barrier heights calculated from RCCSD(T)/6-311+G(3df,2p) energies with optimized molecular geometries and harmonic vibrational frequencies determined at the UMP2/6-311+G(3df,2p) level, the allylperoxyl rearrangement proceeds by fragmentation of 1a through a transition structure (TS1) with a calculated DeltaH++(298 K) of 21.7 kcal/mol to give an allyl radical-triplet dioxygen loosely bound complex (CX). In a subsequent step, the triplet dioxygen moiety of CX recombines at either end of the allyl radical moiety to convert the complex to the rearranged peroxyl radical (1a') or to revert to the starting peroxyl radical 1a. CX shows an electron charge transfer of 0.026 e in the direction allyl --> O(2). The dominant attractive interactions holding in association the allyl radical-triplet dioxygen pair in CX are due chiefly to dispersion forces. The DeltaH(298 K) for dissociation of CX in its isolated partners, allyl radical and triplet dioxygen, is predicted to be at least 1 kcal/mol. The formation of CX prevents the diffusion of its partners and maintains the stereocontrol along the fragmentation-recombination processes. The concerted 1,3-migration in allylperoxyl radical is predicted to take place through a five-membered ring peroxide transition structure (TS2) showing two long C-O bonds. The DeltaH++(298 K) calculated for this pathway is less favorable than the fragmentation-recombination pathway by 1.9 kcal/mol. The cyclization of 1a to give a dioxolanyl radical intermediate (2a) is found to proceed through a five-membered ring transition structure (TS3) with a calculated DeltaH++(298 K) of 33.9 kcal/mol. Thus, the sequence of ring closure 1a --> 2a and ring opening 2a --> 1a' is unlikely to play any significant role in allylperoxyl rearrangement 1a --> 1a'. In the three pathways investigated, the energy of the transition structure is predicted to be somewhat lower in either heptane or aqueous solution than in the gas phase. Although the energy lowering calculated for TS1 is smaller than the calculated for TS2 and TS3, it is very unlikely that the solvent effects may reverse the predicted preference of the fragmentation-recombination pathway over the concerted and stepwise ring closure-ring opening mechanisms.     

Relative formation of ground- and excited-state NO−2 in collisions of fast metastable atoms and molecules (Ar*, H*, D*, H*2, D*2) with NO2

Collisions ot fast metastable beams of Ar, H, and D atoms, and H₂ and D₂ molecules with NO₂ producing positive ions and NO^?₂ were studied. The ratio of the ³B₁-¹A₁ NO^?₂ cross sections is a linear function of the projectile velocity. This finding is tentatively interpreted in the framework of a Landau-Zener model Earlier results on O^?₂ are re-examined.