Influence of the solvent representation on vibrational entropy calculations: Generalized born versus distance‐dependent dielectric model

The harmonic model is the most popular approximation for estimating the “configurational” entropy of a solute in molecular mechanics/Poisson‐Boltzmann solvent accessible surface area (MM/PBSA)‐type binding free energy calculations. Here, we investigate the influence of the solvent representation in the harmonic model by comparing estimates of changes in the vibrational entropies for 30 trypsin/ligand complexes on ligand binding. Second derivatives of Amber generalized Born (GB) solvation models are available in the nucleic acid builder code. They allow one to use these models for the calculation of vibrational entropies instead of using a simpler solvation model based on a distance‐dependent dielectric (DDD) constant. Estimates of changes in the vibrational entropies obtained with a DDD model are systematically and significantly larger, by on average, 6 kcal mol^?1 (at T = 300 K), than estimates obtained with a GB model and so are more favorable for complex formation. The difference becomes larger the more the vibrational entropy contribution disfavors complex formation, that is, the larger the ligand is (for the complexes considered here). A structural decomposition of the estimates into per‐residue contributions reveals polar interactions between the ligand and the surrounding protein, in particular involving charged nitrogens, as a main source of the differences. Snapshots minimized with the DDD model showed a structural deviation from snapshots minimized in explicit water that is larger by, on average, 0.5 Å RMSD compared to snapshots that were minimized with GB^HCT. As experimental vibrational entropies of biomacromolecules are elusive, there is no direct way to establish a solvent model's superiority. Thus, we can only recommend using the GB harmonic model for vibrational entropy calculations based on the reasoning that smaller structural deviations should point to the implicit solvent model that closer approximates the energy landscape of the solute in explicit solvent. © 2012 Wiley Periodicals, Inc.     

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.     

The solubilisation behaviour of some dichloroalkanes in aqueous solutions of PEO-PPO-PEO triblock copolymers: a dynamic light scattering, fluorescence spectroscopy, and SANS study

The aggregation behaviour of PEO-PPO-PEO triblock copolymers in water and in water + chlorinated additive mixtures was studied by means of fluorescence spectroscopy, dynamic light scattering (DLS), and small-angle neutron scattering (SANS). The copolymers were chosen such as to investigate the effects of molecular architecture (L35 and 10R5) and molecular weight by keeping constant the hydrophilic/hydrophobic balance (F88 and F108). 1,2-Dichloroethane was used as a prototype of water basins contaminants. The hydrodynamic radius of the block copolymer aggregates (R(h,M)) and the intensity ratio of pyrene of the first and the third vibrational band (I(1)/I(3)) were determined as a function of temperature (10-45 degrees C) and concentration. The copolymer architecture essentially does not affect R(h,M) in the entire range of temperature and concentration investigated. At a given temperature, increasing macromolecular size leads to a decrease of R(h,M). With rising temperature R(h,M) also decreases. According to the DLS results, the I(1)/I(3) change with temperature clearly detects the aggregation only for F88 and F108. The presence of 1,2-dichloroethane, at concentrations close to its solubility in water, does not lead to changes in the distribution of hydrodynamic radii for L35 and 10R5. Larger quantities of additive induce the formation of quite polydisperse mixed aggregates for L35 and of networks for 10R5. In the case of F88 and F108, low concentrations of additive lead to formation of mixed aggregates with smaller R(h,M). The SANS results corroborate the DLS and fluorescence findings proving enhancement of the copolymer aggregation through the presence of 1,2-dichloroethane. The DLS findings combined with those from the fluorescence spectroscopy provide some insight into the site of solubilisation of the additive in the aggregates.     

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.     

Dispersions of nanosilica in biocompatible copolymers

Dispersions of nanosilica in matrices of biocompatible copolymers were prepared by melt blending. Copolymers with variable molecular size at fixed hydrophilic/hydrophobic ratio and nanosilicas with different interfacial areas were studied. For comparison, a nanoclay was also investigated. The interfacial area played a relevant role in conferring peculiar properties on the nanohybrids. Amazingly, the macromolecule adsorbed on the nanosilica surface maintains some crystallinity which was quantitatively evaluated. In contrast, all the macromolecule anchored to the nanoclay surface is amorphous. The change of the crystalline state was reflected in the dielectric and the electrical conductivity properties. The micro-morphology revealed grape-like structures the size of which decreases with the silica content. These agglomerates were invoked to be responsible for the drastic change of the macromolecule thermal degradation. The copolymer/nanoclay showed a rather compact microstructure and a thermal degradation similar to that of pure macromolecule.     

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.