In this work, some vinylpyranoanthocyanin-phenolic pigments were studied using both theoretical and experimental approaches. Detailed conformational analysis carried out both at classical and quantum levels strongly suggested a conformational flexibility. The vinylic group was associated with a putative formation of four conformer populations with implication in the physicochemical properties of the molecules in study. The theoretical results obtained are consistent with the appropriate NMR experiments carried out for these compounds.

Substantial progress in our understanding of interfacial structure and dynamics has stemmed from the recent development of algorithms that allow for an intrinsic analysis of fluid interfaces. These work by identifying the instantaneous location of the interface, at the atomic level, for each molecular configuration and then computing properties relative to this location. Such a procedure eliminates the broadening of the interface caused by capillary waves and reveals the underlying features of the system. However, a precise definition of which molecules actually belong to the interfacial layer is difficult to achieve in practice. Furthermore, it is not known if the different intrinsic analysis methods are consistent with each other and yield similar results for the interfacial properties. In this paper, we carry out a systematic and detailed comparison of the available methods for intrinsic analysis of fluid interfaces, based on a molecular dynamics simulation of the interface between liquid water and carbon tetrachloride. We critically assess the advantages and shortcomings of each method, based on reliability, robustness, and speed of computation, and establish consistent criteria for determining which molecules belong to the surface layer. We believe this will significantly contribute to make intrinsic analysis methods widely and routinely applicable to interfacial systems.

Anthocyanins are natural pigments that present a characteristic red color at low pH (<2). Anthocyanin-pyruvic acid adducts, commonly referred to as vitisins, are anthocyanin derivatives usually found in red wines. Looking at the two-dimensional structures, vitisins apparently have a greater conjugation system than anthocyanins. Following the common conjugation rules, making the chromophore more conjugated increases the value of lambda(max), and vitisins should have a longer lambda(max) than anthocyanins. However, they have a surprising lower lambda(max), presenting an orange color, under the same pH conditions. Another class of anthocyanin-derived pigments, portisins have the expected relative behaviour with a longer lambda(max) than anthocyanins. In this work, a quantum study on molecular models of pigment models was carried out. The results obtained enabled to present a putative explanation of the color change in these series.

Chemically reactive, alpha, beta-unsaturated carbonyl compounds are common environmental pollutants able to produce a wide range of adverse effects, including, e.g. mutagenicity. This toxic property can often be related to chemical structure, in particular to specific molecular substructures or fragments (alerts), which can then be used in specialized software or expert systems for predictive purposes. In the past, there have been many attempts to predict the mutagenicity of alpha, beta-unsaturated carbonyl compounds through quantitative structure activity relationships (QSAR) but considering only one exclusive endpoint: the Ames test. Besides, even though those studies give a comprehensive understanding of the phenomenon, they do not provide substructural information that could be useful forward improving expert systems based on structural alerts (SAs). This work reports an evaluation of classification models to probe the mutagenic activity of alpha, beta-unsaturated carbonyl compounds over two endpoints - the Ames and mammalian cell gene mutation tests - based on linear discriminant analysis along with the topological Substructure molecular design (TOPS-MODE) approach. The obtained results showed the better ability of the TOPS-MODE approach in flagging structural alerts for the mutagenicity of these compounds compared to the expert system TOXTREE. Thus, the application of the present QSAR models can aid toxicologists in risk assessment and in prioritizing testing, as well as in the improvement of expert systems, such as the TOXTREE software, where SAs are implemented.

Disulfide bonds provide an inexhaustible source of information on molecular evolution and biological specificity. In this work, we described the amino acid composition around disulfide bonds in a set of disulfide-rich proteins using appropriate descriptors, based on ANOVA (for all twenty natural amino acids or classes of amino acids clustered according to their chemical similarities) and Scheffe (for the disulfide-rich proteins superfamilies) statistics. We found that weakly hydrophilic and aromatic amino acids are quite abundant in the regions around disulfide bonds, contrary to aliphatic and hydrophobic amino acids. The density distributions (as a function of the distance to the center of the disulfide bonds) for all defined entities presented an overall unimodal behavior: the densities are null at short distances, have maxima at intermediate distances and decrease for long distances. In the end, the amino acid environment around the disulfide bonds was found to be different for different superfamilies, allowing the clustering of proteins in a biologically relevant way, suggesting that this type of chemical information might be used as a tool to assess the relationship between very divergent sets of disulfide-rich proteins.

A linear least-squares methodology was used to determine the vibrational scaling factors for the X3LYP density functional. Uncertainties for these scaling factors were calculated according to the method devised by Irikura [J. Phys. Chem. A 109, 8430 (2005)]. The calibration set was systematically partitioned according to several of its descriptors and the scaling factors for X3LYP were recalculated for each subset. The results show that the scaling factors are only significant up to the second digit, irrespective of the calibration set used. Furthermore, multivariate statistical analysis allowed us to conclude that the scaling factors and the associated uncertainties are independent of the size of the calibration set and strongly suggest the practical impossibility of obtaining vibrational scaling factors with more than two significant digits. (c) 2010 American Institute of Physics. [doi:10.1063/1.3493630]

Adsorption of hydroxyl on the Au(1 1 0), Au(1 00). and Au(1 1 1) surfaces has been investigated by means of density functional based methods and cluster models and periodic slabs. According to the cluster models, the optimized results indicate that the use of different functional has an indistinct effect on the equilibrium geometry, but adsorption energies computed by different exchange-correlation functionals may differ up to 0.8 eV. At the B3LYP level, the final structures of adsorbed OH are upright and the preferred modes for its adsorption onto the Au(1 1 0), Au(1 00), and Au(1 1 1) surfaces are the short-bridge site with an adsorption energy of -1.96 eV, the bridge site (-1.79 eV), and the hollow hcp site (-1.25 eV), respectively. According to the periodic calculations, the final (OH)(ads) Structures are in a few cases more tilted as compared to the cluster model data, as well as giving a different preferred adsorption site for the Au(1 1 1) surface (i.e.: the bridge site). Furthermore, the stability order of adsorption gathered on the three surfaces, i.e.: Au(1 1 0) > Au(1 0 0) > Au(1 11), is in accord with experimental reports and in concordance with the decreasing of the coordination number of the gold atoms in each surface. Finally, periodic calculations carried out for the stepped Au(3 2 1) surface reveal that adsorption of OH is more favorable on the bridge between the Au(1 1 1) and Au(1 0 0) microfacets, and its adsorption energy is higher than on the low-index surfaces.