Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

Topological study of intramolecular hydrogen bonding in beta-hydroxyethylperoxy radical and beta-hydroxyethoxy radical along its dissociation pathway

The presence of intramolecular hydrogen bond (IHB) in beta-hydroxyethylperoxy and beta-hydroxyethoxy radicals was investigated using the QTAIM topological study on UB3LYP/6-311++G(2d,2p) charge densities. Only one of the two conformers of beta-hydroxyethylperoxy radical which were previously considered to present IHB displays a bond critical point (BCP) associated to an IHB. Furthermore, the atomic energies and electron populations indicate no evidence of IHB in the second conformer. Nevertheless, very small differences in molecular energies were obtained using several one-step and multi-step methods (G3, G3B3) between both conformers. No BCP is found between the hydroxyl hydrogen and the oxygen in the most stable conformer or in the transition state for the dissociation path of beta-hydroxyethoxy radical. However, a BCP is formed in the last steps of this path, thereby yielding H-bonded products.     

Efficient chiral discrimination by 77Se NMR

[reaction: see text] Several (77)Se NMR experiments were performed by titrating a sample of selenides with the chiral shift reagent methylbenzylamine (MBA), followed by acquisition of (77)Se NMR spectra. Eventually, we observed the appearance of two anisochronous resonances, with a relatively large separation, from 37 to 56 Hz, corresponding to the formation of the diastereomeric complexes. This methodology avoids derivatization processes, and the studied compound can be easily recovered from the NMR tube.     

Use of modified rice husks as a natural solid adsorbent of trace metals: characterisation and development of an on-line preconcentration system for cadmium and lead determination by FAAS

The use of rice husks as an alternative adsorbent in an on-line preconcentration system for Cd (II) and Pb (II) determination by flame atomic absorption spectrometry (FAAS) is described. The potential of rice husks as a natural adsorbent was evaluated as a material modified with 0.75 mol l⁻¹ NaOH solution and in the unmodified form. For this task, several techniques such as spectroscopy and thermogravimetry were used for elucidation of possible functional groups responsible for the uptake of Cd (II) and Pb (II). Furthermore, based on adsorption studies and adsorption isotherms applied to the Langmüir model, it was possible to verify that modified rice husks present a higher adsorption capacity for both metals. After establishing this material as a promising natural adsorbent, it was used for on-line preconcentration of Cd (II) and Pb (II) metals. The multivariate optimisation of chemical and flow variables was performed by using a full factorial design (2⁴) including the following factors: preconcentration time, preconcentration flow rate, concentration and volume of eluent. The optimum pH values used for on-line preconcentration were taken from prior univariate experiments. Under optimised conditions for Cd (II) determination (4 min of preconcentration at a 6 ml min⁻¹ preconcentration flow rate, in which comprises 24 ml of preconcentration volume, 200 μl elution volume and 1.0 mol l⁻¹ HNO₃ solution as eluent), the system achieved a detection limit of 1.14 μg l⁻¹ and an enrichment factor of 72.4. Similar conditions were used for Pb (II) determination (4 min of preconcentration, 6 ml min⁻¹ preconcentration flow rate, 300 μl elution volume and 1.0 mol l⁻¹ HNO₃ solution as eluent) from which a detection limit of 14.1 μg l⁻¹ and enrichment factor of 46.0 were achieved. Also, rice husks have been shown to be a homogeneous and stable adsorbent in which more than 100 preconcentration/elution cycles provide a relative standard deviation (RSD) of less than 6.0% on the analytical signal. The satisfactory accuracy of the method developed was obtained by using spiked water samples (mineral water and lake water) and spiked red wine samples. These values were confirmed by electrothermal atomic absorption spectrometry (ETAAS). The certified reference material [pig kidney (CRM 186)] and the reference material [beech leaves (CRM 100)] were also used.     

The dynamics of spatiotemporal modulations

The modulational instability of traveling waves is often thought to be a crucial point in the mechanism of transition to space-time disorder and turbulence. The aim of this paper is to study the effect of spatiotemporal modulations on some dynamics u(0)(x,t), which may occur as an instability process when a control parameter varies, for instance. We analyze the properties of the modulated dynamics of the form g(1)(x)g(2)(t)u(0)(x,t) compared to those of the reference dynamics u(0)(x,t), using operator theory. We show that, if the reference dynamics is invariant under some space-time symmetry in the sense of Ref. [J. Nonlinear Sci. 2, 183 (1992)], the modulation has the effect of either deforming this symmetry or breaking it, depending on whether the corresponding operator remains unitary or not. We also demonstrate that the smallest Euclidean space containing the modulated dynamics has a dimension smaller than or equal to the smallest Euclidean space containing u(0)(x,t). The previous results are then applied to the case of modulated uniformly traveling waves. While the spatiotemporal translation invariance of the wave never persists in the presence of a modulation, the existence of a spatiotemporal symmetry depends on the resonance of the Fourier sidebands due to the modulation. In case of nonresonance, a spatiotemporal symmetry exists and is explicitly determined. In this situation, the modulated wave and the carrier wave have the same spectrum (up to a normalization factor), the same entropy, and the spatial (resp., temporal) two-point correlation is deformed only by the spatial (resp., temporal) modulation. (c) 1995 American Institute of Physics.     

Joint QTAIM and Hirshfeld study of the sigma and pi charge distribution and electron delocalization in carbonyl compounds: a comparative study with the resonance model

Atomic charges and delocalization indexes (DIs) for a series of carbonyl compounds comprising dimethyl ketone, acetaldehyde, acetic acid, methyl acetate, acetamide, methyl vinyl ketone, divinyl ketone, and benzoic acid were studied using two different atomic partitionings: the QTAIM and the Hirshfeld (stockholder) scheme. The resonance model, traditionally employed to explain the reactivity of these compounds, is not in line with the total atomic charges and DIs calculated by both methodologies. However, the resonance model is supported to some extent by the pi charges and pi DIs calculated by both schemes, but the calculated values indicate that the pi population delocalizes only to a small degree. Although the absolute values of QTAIM and stockholder atomic charges are significantly different, the pi charges and the values of the DIs show similar trends for all the atoms and molecules of this study; this is especially the case for the pi DIs. A study of the electron density on the level of a single MO performed for CO, H2CO, F2CO, and H2CS reveals that the differences in the atomic sigma charges computed with both partitionings can be traced back to their different treatment of interatomic regions.     

Characterisation of Sugar Cane Combustion Particles in the Araraquara Region, Southeast Brazil

Biomass burning is an important primary and secondary source of aerosol particles. The presence of carbonaceous particles in the respirable size range makes the study of this fraction important in view of possible health and climatic effects. The annual burning of sugar cane plantations causes emission of huge amounts of pyrogenic particles. Aerosol samples were collected in Araraquara city, São Paulo state, Brazil, during the harvest season for fine and coarse particles and bulk; they were analysed by electron-probe microanalysis, including facilities for low-Z element determination (low-Z EPMA) and by energy-dispersive X-ray fluorescence (EDXRF), in order to investigate the elemental composition of individual particles and bulk samples, respectively. Numerical analysis of the EPMA results by hierarchical clustering shows high contributions of carbonaceous particles that can be distinguished mainly in two different types: biogenic and carbon-rich. Additionally, two significant contributions of aluminosilicate particles were identified: as rather pure aluminosilicates or mixed with carbonaceous species. The EDXRF results are compatible with those of aerosol particles in Amazon, which is nowadays one of the main sources of biogenic particles in the world.     

The role of hydrogen bonding in supercooled methanol

The role of hydrogen bonding on the microscopic properties of supercooled methanol has been analyzed by means of molecular dynamics simulations. Thermodynamic, structural, and dynamical properties have been investigated in supercooled methanol. The results have been compared with those of an ideal methanol-like system whose molecules have the same dipole moment as the methanol but lack sites for hydrogen bonding. Upon cooling the methanol samples, translational relaxation times increase more rapidly than reorientational ones. This effect is much more important when hydrogen bonds are suppressed. Suppression of hydrogen bonds also results in lower critical temperatures for diffusion and for several characteristic relaxation time constants. The anisotropy of individual dynamics and the existence of dynamical heterogeneities have also been investigated.     

The Birch reduction-dialkylation reaction. Scope and limitations

The Birch reduction-dialkylation reaction has been studied with different aromatic carboxylic acids and primary and secondary bromides. From these results it can be concluded that it is a reasonably general reaction. However, we found important exceptions with the primary bromides: allyl bromide, β-phenethyl bromide, and 5-bromo-2-methyl-2-pentene. The unusual behavior of allyl bromide is briefly discussed.