Total publications: 603
433. Response to "Comment on 'Uncertainties in scaling factors for ab initio vibrational zero-point energies' and 'Calibration sets and the accuracy of vibrational scaling factors: A case study with the X3LYP hybrid functional'" [J. Chem. Phys. 134, 167101 (2011)]
in JOURNAL OF CHEMICAL PHYSICS, 2011, ISSN: 0021-9606, Volume: 134,
Editorial Material, Indexed in: crossref, scopus, wos
434. Review of Computer-Aided Models for Predicting Collagen Stability
in Current Computer Aided-Drug Design, 2011, ISSN: 1573-4099, Volume: 7,
Article, Indexed in: crossref
435. Solvation Free Energy Profile of the SCN- Ion across the Water-1,2-Dichloroethane Liquid/Liquid Interface. A Computer Simulation Study
in JOURNAL OF PHYSICAL CHEMISTRY C, 2011, ISSN: 1932-7447, Volume: 115,
Article, Indexed in: crossref, scopus, wos
The solvation free energy profile of a single SCN- ion is calculated across the water-1,2-dichloroethane liquid/liquid interface at 298 K by the constraint force method. The obtained results show that the free energy cost of transferring the ion from the aqueous to the organic phase is about 70 kJ/mol, The free energy profile shows a small but clear well at the aqueous side of the interface, in the subsurface region of the water phase, indicating the ability of the SCN- ion to be adsorbed in the close vicinity of the interface. Upon entrance of the SCN- ion to the organic phase a coextraction of the water molecules of its first hydration shell occurs. Accordingly, when it is located at the boundary of the two phases the SCN- ion prefers orientations in which its bulky S atom is located at the aqueous side, and the small N atom, together with its first hydration shell, at the organic side of the interface.
436. Structural and Thermodynamic Characterization of Polyphenylbenzenes
in JOURNAL OF PHYSICAL CHEMISTRY A, 2011, ISSN: 1089-5639, Volume: 115,
Article, Indexed in: crossref, scopus, wos
The thermodynamic and structural study of a series of polyphenylbenzenes, from benzene, n(Ph) = 0, to hexaphenylbenzene, n(Ph) = 6, is presented. The available literature data for this group of compounds was extended by the determination of the relevant thermodynamic properties for 1,2,4-triphenylbenzene, 1,2,4,5-tetraphenylbenzene, and hexaphenylbenzene, as well as structural determination by X-ray crystallography for some of the studied compounds. Gas phase energetics in this class of compounds was analyzed from the derived standard molar enthalpies of formation in the gaseous phase. The torsional profiles relative to the phenyl-phenyl hindered rotations in some selected polyphenylbenzenes, as well as the gas phase structures and energetics, were derived from quantum chemical calculations. In the ideal gas phase, a significant enthalpic destabilization was observed in hexaphenylbenzene relative to the other polyphenylbenzenes, due to steric crowding between the six phenyl substituents. A relatively low enthalpy of sublimation was observed for hexaphenylbenzene, in agreement with the decreased surface area able to establish intermolecular interactions. The apparently anomalous low entropy of sublimation observed for hexaphenylbenzene is explained by its high molecular symmetry and the six highly hindered phenyl internal rotations. For the series of polyphenylbenzenes considered, it was shown that the differentiation in the entropy of sublimation can be chiefly ascribed to the torsional freedom of the phenyl substituents in the gas phase and the entropy terms related with molecular symmetry.
437. Towards the Discovery of a Novel Class of Monoamine Oxidase Inhibitors: Structure-Property-Activity and Docking Studies on Chromone Amides
in CHEMMEDCHEM, 2011, ISSN: 1860-7179, Volume: 6,
Article, Indexed in: crossref, scopus, wos
438. Two New Parameters Based on Distances in a Receiver Operating Characteristic Chart for the Selection of Classification Models
in JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2011, ISSN: 1549-9596, Volume: 51,
Article, Indexed in: crossref, scopus, wos
There are several indices that provide an indication of different types on the performance of QSAR classification models, being the area under a Receiver Operating Characteristic (ROC) curve still the most powerful test to overall assess such performance. All ROC related parameters can be calculated for both the training and test sets, but, nevertheless, neither of them constitutes an absolute indicator of the classification performance by themselves. Moreover, one of the biggest drawbacks is the computing time needed to obtain the area under the ROC curve, which naturally slows down any calculation algorithm. The present study proposes two new parameters based on distances in a ROC curve for the selection of classification models with an appropriate balance in both training and test sets, namely the following: the ROC graph Euclidean distance (ROCED) and the ROC graph Euclidean distance corrected with Fitness Function (FIT(lambda)) (ROCFIT). The behavior of these indices was observed through the study on the mutagenicity for four genotoxicity end points of a number of nonaromatic halogenated derivatives. It was found that the ROCED parameter gets a better balance between sensitivity and specificity for both the training and prediction sets than other indices such as the Matthews correlation coefficient, the Wilk's lambda, or parameters like the area under the ROC curve. However, when the ROCED parameter was used, the follow-on linear discriminant models showed the lower statistical significance. But the other parameter, ROCFIT, maintains the ROCED capabilities while improving the significance of the models due to the inclusion of FIT(lambda)).
439. What does an ionic liquid surface really look like? Unprecedented details from molecular simulations
in PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2011, ISSN: 1463-9076, Volume: 13,
Article, Indexed in: crossref, scopus, wos
We present the first intrinsic analysis of the surface of the [bmim][PF(6)] room-temperature ionic liquid. Our detailed analysis reveals unprecedented details about the structure of the interface by providing the relative prevalence of different molecular orientations. These results suggest that experimental data should be reinterpreted considering a distribution of molecular arrangements.
440. Yeast Network and Report of New Stochastic-Credibility Cell Cycle Models
in Current Bioinformatics, 2011, ISSN: 1574-8936, Volume: 6,
Article, Indexed in: crossref