Quantitative structure-property relationships for octanol-air partition coefficients of polychlorinated biphenyls

Based on nine quantum chemical descriptors computed by PM3 Hamiltonian, using partial least squares analysis, a significant quantitative structure-property relationship for the logarithm of octanol-air partition coefficients (log K-OA) of polychlorinated biphenyls (PCBs) was obtained. The cross-validated Q(cum)(2) value of the model is 0.962, indicating a good predictive ability. The intermolecular dispersive interactions and thus the size of the PCB molecules play a key role in governing log K-OA. The greater the size of PCB molecules, the greater the log K-OA values. Increasing E-LUMO (the energy of the lowest unoccupied molecular orbital) values of the PCBs leads to decreasing log K-OA values, indicating possible interactions between PCB and octanol molecules. Increasing Q(Cl)(+) (the most positive net atomic charges on a chlorine atom) and Q(C)(-) (the largest negative net atomic charge on a carbon atom) values of PCBs results in decreasing log K-OA values, implying possible intermolecular electrostatic interactions between octanol and PCB molecules. (C) 2002 Elsevier Science Ltd. All rights reserved.

Application of static charge transfer within an ionic-liquid force field and its effect on structure and dynamics

The effects of linear scaling of the atomic charges of a reference potential on the structure, dynamics, and energetics of the ionic liquid 1,3-dimethylimidazolium chloride are investigated. Diffusion coefficients that span over four orders of magnitude are observed between the original model and a scaled model in which the ionic charges are +/- 0.5 e. While the three-dimensional structure of the liquid is less affected, the partial radial distribution functions change markedly-with the positive result that for ionic charges of +/- 0.7 e, an excellent agreement is observed with ab initio molecular dynamics data. Cohesive energy densities calculated from these partial-charge models are also in better agreement with those calculated from the ab initio data. We postulate that ionic-liquid models in which the ionic charges are assumed to be +/- 1 e overestimate the intermolecular attractions between ions, which results in overstructuring, slow dynamics, and increased cohesive energy densities. The use of scaled-charge sets may be of benefit in the simulation of these systems-especially when looking at properties beyond liquid structure-thus providing on alternative to computationally expensive polarisable force fields.

Critical analysis and extension of the Hirshfeld atoms in molecules

The computational approach to the Hirshfeld [Theor. Chim. Acta 44, 129 (1977)] atom in a molecule is critically investigated, and several difficulties are highlighted. It is shown that these difficulties are mitigated by an alternative, iterative version, of the Hirshfeld partitioning procedure. The iterative scheme ensures that the Hirshfeld definition represents a mathematically proper information entropy, allows the Hirshfeld approach to be used for charged molecules, eliminates arbitrariness in the choice of the promolecule, and increases the magnitudes of the charges. The resulting "Hirshfeld-I charges" correlate well with electrostatic potential derived atomic charges

Relacions estructura-propietat per un conjunt d'hidrocarburs a partir de nous descriptors tridimensionals derivats de la semblança molecular quàntica

En aquest article es defineixen uns nous índexs tridimensionals per a la descripció de les molècules a partir de paràmetres derivats de la Teoria de la Semblança Molecular i de les distàncies euclidianes entre els àtoms i les càrregues atòmiques efectives. Aquests indexs, anomenats 3D, s'han aplicat a l'estudi de les relacions estructura-propietat d'una família d'hidrocarburs, i han demostrat una capacitat de descripció de tres propietats de la família (temperatura d'ebullició, temperatura de fusió i densitat) molt més acurada que quan s'utilitzen els indexs 2D clàssics

Synthesis, mechanism of formation, and molecular orbital calculations of arylamidoximes

A simple and easy synthesis of ten arylamidoximes from arylnitriles and hydroxylamine is described. The formation of the arylamides has been observed to a much lesser extent in the present work. A new mechanism for the formation of arylamidoximes, as well as arylamides, from arylnitriles and hydroxylamine is suggested. Quantum mechanical calculations have been carried out to support this mechanism. The enthalpy of formation in conjunction with atomic charges of the reactants and intermediates helped to understand more about the generation of the products.

A neural networks study of quinone compounds with trypanocidal activity

This work investigates neural network models for predicting the trypanocidal activity of 28 quinone compounds. Artificial neural networks (ANN), such as multilayer perceptrons (MLP) and Kohonen models, were employed with the aim of modeling the nonlinear relationship between quantum and molecular descriptors and trypanocidal activity. The calculated descriptors and the principal components were used as input to train neural network models to verify the behavior of the nets. The best model for both network models (MLP and Kohonen) was obtained with four descriptors as input. The descriptors were T(5) (torsion angle), QTS1 (sum of absolute values of the atomic charges), VOLS2 (volume of the substituent at region B) and HOMO-1 (energy of the molecular orbital below HOMO). These descriptors provide information on the kind of interaction that occurs between the compounds and the biological receptor. Both neural network models used here can predict the trypanocidal activity of the quinone compounds with good agreement, with low errors in the testing set and a high correctness rate. Thanks to the nonlinear model obtained from the neural network models, we can conclude that electronic and structural properties are important factors in the interaction between quinone compounds that exhibit trypanocidal activity and their biological receptors. The final ANN models should be useful in the design of novel trypanocidal quinones having improved potency.

Theoretical study of the structure and stability of NbxOy, and NbxOy+ (x = 1-3; y = 2-5, 7, 8) clusters

Geometric, thermodynamic and electronic properties of cluster neutrals NbxOy and cations NbxOy+ (x = 1-3; y = 2-5, 7, 8) have been characterized theoretically. A DFT calculation using a hybrid combination of B3LYP with contracted Huzinaga basis sets. Numerical results of the relative stabilities, ionization potentials and band gaps of different clusters are in agreement with experiment. Analysis of dissociation channels supports the more stable building blocks as formed by NbO2, NbO2+ NbO3 and NbO3+ stoichiometries. The net atomic charges suggest that oxygen donor molecules can interact more favorably on central niobium atoms of cluster cations, while the interaction with oxygen acceptor molecules is more favorable on the terminal oxygen atoms of neutral clusters. A topological analysis of the electron localization function gradient field indicates that the clusters may be described as having a strong ionic interaction between Nb and O atoms. Published by Elsevier B.V. B.V.

An ab initio study of oxygen vacancies and doping process of Nb and Cr atoms on TiO2 (110) surface models

We theoretically investigated how the formation of oxygen vacancies and the addition of niobium and chromium atoms as dopants modify the varistor properties of TiO2. The calculations were carried out at the HF level using a contracted basis set, developed by Huzinaga et al.. to represent the atomic centers on the (110) surface for the large (TiO2)(15) cluster model. The change of the values for the net atomic charges and band gap after oxygen vacancy formation and the presence of dopants in the lattice are analyzed and discussed. It is shown that the formation of oxygen vacancies decreases the band gap while an opposite effect is found when dopants are located in the reduced surface. The theoretical results are compared with available experimental data. A plausible explanation of the varistor behavior of this system is proposed. (C) 1997 John Wiley & Sons, Inc.

A structure-activity relationship study of quinone compounds with trypanocidal activity

A set of 25 quinone compounds with anti-trypanocidal activity was studied by using the density functional theory (DFT) method in order to calculate atomic and molecular properties to be correlated with the biological activity. The chemometric methods principal component analysis (PCA), hierarchical cluster analysis (HCA), stepwise discriminant analysis (SDA), Kth nearest neighbor (KNN) and soft independent modeling of class analogy (SIMCA) were used to obtain possible relationships between the calculated descriptors and the biological activity studied and to predict the anti-trypanocidal activity of new quinone compounds from a prediction set. Four descriptors were responsible for the separation between the active and inactive compounds: T-5 (torsion angle), QTS1 (sum of absolute values of the atomic charges), VOLS2 (volume of the substituent at region B) and HOMO-1 (energy of the molecular orbital below HOMO). These descriptors give information on the kind of interaction that occurs between the compounds and the biological receptor. The prediction study was done with a set of three new compounds by using the PCA, HCA, SDA, KNN and SIMCA methods and two of them were predicted as active against the Trypanosoma cruzi. (c) 2005 Elsevier SAS. All rights reserved.

Gas-phase reactivity of protonated 2-oxazoline derivatives: mass spectrometry and computational studies

RATIONALE: Oxazolines have attracted the attention of researchers worldwide due to their versatility as carboxylic acid protecting groups, chiral auxiliaries, and ligands for asymmetric catalysis. Electrospray ionization tandem mass spectrometric (ESI-MS/MS) analysis of five 2-oxazoline derivatives has been conducted, in order to understand the influence of the side chain on the gas-phase dissociation of these protonated compounds under collision-induced dissociation (CID) conditions. METHODS: Mass spectrometric analyses were conducted in a quadrupole time-of-flight (Q-TOF) spectrometer fitted with electrospray ionization source. Protonation sites have been proposed on the basis of the gas-phase basicity, proton affinity, atomic charges, and a molecular electrostatic potential map obtained on the basis of the quantum chemistry calculations at the B3LYP/6-31 + G(d, p) and G2(MP2) levels. RESULTS: Analysis of the atomic charges, gas-phase basicity and proton affinities values indicates that the nitrogen atom is a possible proton acceptor site. On the basis of these results, two main fragmentation processes have been suggested: one taking place via neutral elimination of the oxazoline moiety (99 u) and another occurring by sequential elimination of neutral fragments with 72 u and 27 u. These processes should lead to formation of R+. CONCLUSIONS: The ESI-MS/MS experiments have shown that the side chain could affect the dissociation mechanism of protonated 2-oxazoline derivatives. For the compound that exhibits a hydroxyl at the lateral chain, water loss has been suggested to happen through an E2-type elimination, in an exothermic step. Copyright (C) 2012 John Wiley & Sons, Ltd.

Gas-phase reactivity of 2-hydroxy-1,4-naphthoquinones: a computational and mass spectrometry study of lapachol congeners

In order to understand the influence of alkyl side chains on the gas-phase reactivity of 1,4-naphthoquinone derivatives, some 2-hydroxy-1,4-naphthoquinone derivatives have been prepared and studied by electrospray ionization tandem mass spectrometry in combination with computational quantum chemistry calculations. Protonation and deprotonation sites were suggested on the basis of gas-phase basicity, proton affinity, gas-phase acidity (?Gacid), atomic charges and frontier orbital analyses. The nature of the intramolecular interaction as well as of the hydrogen bond in the systems was investigated by the atoms-in-molecules theory and the natural bond orbital analysis. The results were compared with data published for lapachol (2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinone). For the protonated molecules, water elimination was verified to occur at lower proportion when compared with side chain elimination, as evidenced in earlier studies on lapachol. The side chain at position C(3) was found to play important roles in the fragmentation mechanisms of these compounds. Copyright (c) 2012 John Wiley & Sons, Ltd.

(Table 1) Age determination of basalts from DSDP Hole 30-289

The Pacific plate has undergone a substantial northward displacement during the late Mesozoic and the Cainozoic. Here we give additional documentation for such motion based on palaeomagnetic measurements of a sequence of sedimentary and basalt samples collected from middle Oligocene to Aptian sections of Deep Sea Drilling Project (DSDP) site 289 (Andrews, 1975; 00° 29.92'S, 158° 30.69'E) drilled on the Ontong Java Plateau.

Major element and mineral composition of gabbroic xenoliths and megacrysts from Jeju Island, South Korea

Gabbroic xenoliths and diverse megacrysts (e.g., clinopyroxenes, amphiboles and plagioclases), which correspond to the lithology ranging from gabbro-norite to gabbro, occur in the Pleisto-Holocene alkali basalts from Jeju Island, South Korea. The gabbroic xenoliths consist primarily of moderate-K2O plagioclase, Ti-Al-rich clinopyroxene and CaO-rich orthopyroxene; additionally, TiO2-rich amphibole (kaersutite) and Ti-Fe oxides might or might not be present. The plagioclase is the most dominant phase (approx. 60-70 vol.%). The xenoliths and megacrysts provide evidence for the modal metasomatism of the lower continental crust by the mafic magmas during the Pleistocene. The coarse grain size (up to 5 mm), moderate Mg# [=100xMg/(Mg+Fe(total)) atomic ratio] of pyroxenes (70-77) and textural features (e.g., poikilitic) indicate that the gabbroic xenoliths are consistent with a cumulus origin. The clinopyroxenes from these xenoliths are enriched in REE with smooth convex-upward MREE patterns, which are expected for cumulus minerals formed from a melt enriched in incompatible trace elements. The strikingly similar major and trace element variations and the patterns of constituent minerals clearly indicate a genetic link between the gabbroic xenoliths (plus megacrysts) and the host basalt, indicating that the xenoliths belong to the Jeju Pleisto-Holocene magma system. On the basis of the textural features, the mineral equilibria and the major and trace element variations, the xenoliths appear to have crystallized from basaltic melts at the reservoir-roof environment within the lower crust (4-7 kbars) above the present Moho estimates beneath Jeju Island, where the xenoliths represent wall rocks. Following the consolidation of the xenolith lithologies, volatile- and incompatible element-enriched melt/fluid, as metasomatic agents, infiltrated through the grain boundaries and/or cracks and reacted with the preexisting anhydrous phases, which produced the metasomatic amphiboles. This volatile-enriched melt/fluid could have evolved from the initially anhydrous compositions to the volatile-saturated compositions by the active fractional crystallization in the Jeju Pleisto-Holocene magma system. This process was significant in that it was a relatively young event and played an important role in the formation of the hydrous minerals and the metasomatization of the lower continental crust, which is a plume-impacted area along the Asian continental margin. The major and trace element analyses of the mineral phases from the xenoliths were performed to define the principal geochemical characteristics of the crustal lithosphere segment represented by the studied xenoliths.

Petrology, geochemistry, and geodynamics at DSDP Hole 66-493

At Site 493, DSDP Leg 66, dioritic basement was reached below lower Miocene (NN1 Zone, 22-24 Ma) terrigenous sediments. Petrographical, mineralogical (including microprobe analyses), and chemical features of the dioritic rocks reveal their magmatic affinity with the calc-alkaline series. Furthermore, their radiometric age (35.3 m.y.) links the basement to the Sierra Madre Occidental in Mexico and to mid-Tertiary volcanic arcs in Central America. The presence of Oligocene diorite 50 km from the trench axis confirms the truncation of the south Mexico margin, which we explain as the result of a 650 to 800 km left-lateral displacement of Central America relative to North America. Truncation must have occurred in the late Miocene, after the diorite intrusion and prior to the present subduction.