Double-layer effects and distance dependence of electron transfer in reduction of nitro aromatic radical anions

The first example of the effect of an electric double layer on the reduction of electrochemically generated radical species is reported. The anion radical of methyl 5-(2,4-dichlorophenoxy)-2-nitrobenzoate (pesticide bifenox) is electrochemically reduced in acetonitrile to a phenylhydroxylamine derivative in a process involving three electrons. This heterogeneous reaction is strongly influenced by the concentration and nature of the cation of the indifferent electrolyte. Depending on the type of tetraalkylammonium cation, the redox potential changes by 0.45 V. The kinetic parameters were obtained for five tetraalkylammonium hexafluorophosphate salts. The Frumkin correction, which assumes that the outer Helmholtz plane coincides with the reaction site, was applied to kinetic data of the radical anion reduction. The correction of the apparent rate accounted for the observed effect only in the case of tetramethylammonium salt. The presence of higher tetraalkylammonium homologues causes deviations from the predicted dependence of the electron-transfer rate on the phi2 potential of the outer Helmholtz plane. Hence, the nature of the cation of the electrolyte exerts a further effect extending beyond the electrostatic repulsion only. The corrected rate of electron transfer decreases exponentially with increasing size of the alkyl chain of the indifferent electrolyte cation in the order methyl > ethyl > propyl > butyl > hexyl. The rate decay is characterized by an exponent beta = 0.83. This confirms that the reaction plane for the reduction of the bifenox radical anion is different for each electrolyte. Due to this fact the Frumkin correction cannot fully account for the observed dependence of the heterogeneous rate on the solution composition. The observed effect is not specific to the bifenox radical. A similar influence of the concentration and nature of the cation of the indifferent electrolyte was observed for other nitro compounds, namely, nitrobenzene, nitrobenzoate, and nitrofen.     

Development and validation of HPLC methods for the analysis of phenethylamine and indoloquinazoline alkaloids in Evodia species

The aim of this study was to evaluate the chromatographic performance of a PEG stationary phase, in comparison with those of C18 columns, for the HPLC analysis of phenethylamine ((+/-)-synephrine) and indoloquinazoline (rutaecarpine and evodiamine) alkaloids in methanolic extracts of fruits of Evodia rutaecarpa (Juss.) Benth. and E. rutaecarpa (Juss.) Benth. var. officinalis (Dode) Huang (i.e., E. officinalis Dode) (Rutaceae family). The method was validated and showed good linearity, precision, accuracy, sensitivity, and specificity. The highest content of both phenethylamine and indoloquinazoline alkaloids was found in methanolic fruit extracts of E. rutaecarpa, and it was closely related to the degree of maturity. E. officinalis fruits displayed low amounts of both types of alkaloids. Furthermore, an enantioselective HPLC method for the enantioseparation of (+/-)-synephrine from Evodia fruits was applied, by using a protein-based chiral stationary phase with cellobiohydrolase (CBH) as the chiral selector (Chiral-CBH). Isolation of synephrine from Evodia aqueous fruit extracts was carried out by strong cation-exchange SPE. The results of the application of the method to the analysis of Evodia samples showed that (-)-synephrine was the main component while (+)-synephrine was present in low concentration.     

Comparison of bovine and porcine beta-lactoglobulin: a mass spectrometric analysis

Nano-electrospray-ionization mass spectrometry (nano-ESI-MS) is applied to comparison of bovine and porcine beta-lactoglobulin (BLG and PLG). The conformational and oligomeric properties of the two proteins under different solvent and experimental conditions are analyzed. The pH-dependence of dimerization is described for the pH range 2-11. The results indicate maximal dimer accumulation at pH 6 for BLG and pH 4 for PLG, as well as a lower stability of the PLG dimer at pH 4 compared to BLG at pH 6. Conformational stability appears to be higher for BLG at acidic pH, but higher for PLG at basic pH. The higher stability of BLG at low pH is revealed by means of either chemical or thermal denaturation. Equilibrium folding intermediates of both proteins are detected. Finally, conditions are found that promote dissociation of the BLG dimer at pH 6 into folded monomers.     

Crystal structure of the trigonal form of isotactic polypropylene as an example of density-driven polymer structure

Propene-hexene copolymers crystallize in a new polymorphic form of isotactic polypropylene when the concentration of hexene is higher than nearly 10-15 mol %. The hexene units are included in the crystals, inducing an increase of density that allows crystallization of 3-fold helical chains in a trigonal unit cell according to the space group R3c or Rc, where the helical symmetry of the chains is maintained in the crystal lattice. The structure of this new form is similar to those of isotactic polybutene and polystyrene and does not crystallize in polypropylene homopolymer because it would have too low density. The crystal structure of isotactic polypropylene is therefore no longer an exception to the principles of polymer crystallography, but the new structure represents the fulfillment of these principles and indicates that the packing of polymer molecules is mainly driven by density.     

Measurement of PAHs in environmental matrices: results from an interlaboratory comparison on the different steps of the measurement procedure

Proficiency testing (PT) is becoming a feature of laboratory accreditation and the PT results are used to assess the technical competence of the participating laboratories. ISPRA (former APAT) plays an important role in supporting the Italian laboratories belonging to the network of the Regional Environmental Agencies to improve the quality of their analytical measurements. As a consequence, ISPRA organized an interlaboratory comparison to assess the performance of the laboratories on PAH measurement procedure. The interlaboratory comparison was drawn separating the different steps of the measurement (from the extraction to the instrumental measurement). Two matrix reference materials: (1) a polluted soil and (2) an extract reference material of the same polluted soil and a “blind” PAH mixture standard stock solution were distributed to 59 Italian laboratories. The results of interlaboratory comparison showed a significant dispersion of the PAH measurements that masks the effects of the different extraction and cleanup procedures used, but it is consistent with the results of other European interlaboratory comparisons.     

Regularization and preconditioning of KKT systems arising in nonnegative least‐squares problems

A regularized Newton‐like method for solving nonnegative least‐squares problems is proposed and analysed in this paper. A preconditioner for KKT systems arising in the method is introduced and spectral properties of the preconditioned matrix are analysed. A bound on the condition number of the preconditioned matrix is provided. The bound does not depend on the interior‐point scaling matrix. Preliminary computational results confirm the effectiveness of the preconditioner and fast convergence of the iterative method established by the analysis performed in this paper. Copyright © 2008 John Wiley & Sons, Ltd.     

Reversible and irreversible denaturation processes in globular proteins: from collective to molecular spectroscopic analysis

Different spectroscopic techniques were applied for studying the structural properties of lysozyme in salt‐free aqueous solutions. The results of vibrational and Brillouin scattering measurements were compared to obtain both single‐molecule and collective properties of the solutions. The characterization of the protein system, from the conformation of the polypeptide chain to the exposure of side chains to the solvent and the arrangement of the solution network, was then achieved in the range 25–85 °C. Through the analysis of the indole breathing mode, a different environment for the six tryptophan residues of an unfolded lysozyme could be evidenced. Short and long exposures to high temperatures were used to modulate the competition between the thermally induced reversible and irreversible denaturation processes. These different thermal treatments were applied to distinguish between the effects of global unfolding of the single molecule from those of self‐aggregation and gel formation. It has been observed that clusterization occurs at melting temperatures with slow kinetics; also, aggregates evolve from the completely unfolded state of the protein and lead to a sensitive increase in viscosity. This effect probably hinders any further conformational rearrangement of the molecules in the aggregate; thus as a consequence, the disordered structure of clusters does not change to give the β‐sheet organization, characteristic of filaments or fibrils. Copyright © 2011 John Wiley & Sons, Ltd.     

Covalent Reversible Inhibitors of Cysteine Proteases Containing the Nitrile Warhead: Recent Advancement in the Field of Viral and Parasitic Diseases

In the field of drug discovery, the nitrile group is well represented among drugs and biologically active compounds. It can form both non-covalent and covalent interactions with diverse biological targets, and it is amenable as an electrophilic warhead for covalent inhibition. The main advantage of the nitrile group as a warhead is mainly due to its milder electrophilic character relative to other more reactive groups (e.g., -CHO), reducing the possibility of unwanted reactions that would hinder the development of safe drugs, coupled to the ease of installation through different synthetic approaches. The covalent inhibition is a well-assessed design approach for serine, threonine, and cysteine protease inhibitors. The mechanism of hydrolysis of these enzymes involves the formation of a covalent acyl intermediate, and this mechanism can be exploited by introducing electrophilic warheads in order to mimic this covalent intermediate. Due to the relevant role played by the cysteine protease in the survival and replication of infective agents, spanning from viruses to protozoan parasites, we will review the most relevant and recent examples of protease inhibitors presenting a nitrile group that have been introduced to form or to facilitate the formation of a covalent bond with the catalytic cysteine active site residue.     

Quantification of Protein “Biomarkers” in Wheat-Based Food Systems: Dealing with Process-Related Issues

Selected food proteins may represent suitable markers for assessing either the presence/absence of specific food ingredients or the type and intensity of food processes. A fundamental step in the quantification of any protein marker is choosing a proper protocol for solubilizing the protein of interest. This step is particularly critical in the case of solid foods and when the protein analyte is prone to undergo intermolecular disulfide exchange reactions with itself or with other protein components in the system as a consequence of process-induced unfolding. In this frame, gluten-based systems represent matrices where a protein network is present and the biomarker proteins may be either linked to other components of the network or trapped into the network itself. The protein biomarkers considered here were wheat gluten toxic sequences for coeliac (QQPFP, R5), wheat germ agglutinin (WGA), and chicken egg ovalbumin (OVA). These proteins were considered here in the frame of three different cases dealing with processes different in nature and severity. Results from individual cases are commented as for: (1) the molecular basis of the observed behavior of the protein; (2) the design of procedure aimed at improving the recovery of the protein biomarker in a form suitable for reliable identification and quantification; (3) a critical analysis of the difficulties associated with the plain transfer of an analytical protocol from one product/process to another. Proper respect for the indications provided by the studies exemplified in this study may prevent coarse errors in assays and vane attempts at estimating the efficacy of a given treatment under a given set of conditions. The cases presented here also indicate that recovery of a protein analyte often does not depend in a linear fashion on the intensity of the applied treatment, so that caution must be exerted when attributing predictive value to the results of a particular study.     

Repositioning of Quinazolinedione-Based Compounds on Soluble Epoxide Hydrolase (sEH) through 3D Structure-Based Pharmacophore Model-Driven Investigation

The development of new bioactive compounds represents one of the main purposes of the drug discovery process. Various tools can be employed to identify new drug candidates against pharmacologically relevant biological targets, and the search for new approaches and methodologies often represents a critical issue. In this context, in silico drug repositioning procedures are required even more in order to re-evaluate compounds that already showed poor biological results against a specific biological target. 3D structure-based pharmacophoric models, usually built for specific targets to accelerate the identification of new promising compounds, can be employed for drug repositioning campaigns as well. In this work, an in-house library of 190 synthesized compounds was re-evaluated using a 3D structure-based pharmacophoric model developed on soluble epoxide hydrolase (sEH). Among the analyzed compounds, a small set of quinazolinedione-based molecules, originally selected from a virtual combinatorial library and showing poor results when preliminarily investigated against heat shock protein 90 (Hsp90), was successfully repositioned against sEH, accounting the related built 3D structure-based pharmacophoric model. The promising results here obtained highlight the reliability of this computational workflow for accelerating the drug discovery/repositioning processes.