A computational study of the effect of an external electric field on the geometry of selected donor–acceptor complexes

To understand the effect of Au and thiol atoms in octane molecule, a structural and charge density analysis has been carried out by high level ab initio quantum chemical calculations using MP2 and B3PW91 methods with the basis sets 6-311G(d,p) and LANL2DZ. The optimized geometries, specifically, the geometry obtained from both levels reveal the effect of S- and Au-atoms in octane molecule. An introduction of sulfur atom in octane molecule lengthen its backbone C–C bond distances, and further adding of Au-atom at the terminals of octane dithiolate stabilizes these distances. The bond densities of the C–C bonds of octane are 1.6 eÅ⁻³, these values are decreased significantly and the charges are largely depleted, when thiol and Au-atoms added in the octane molecule. The presence of negative Laplacian ²ρ(r) at bond critical points of C–C and C–H bonds, indicate, the charges are concentrated in these bonds, confirm that these bonds exhibit an open shell type interaction. The moderate values of density and the negative Laplacian of S–C bonds confirm the covalent character. The positive ²ρ(r) value of Au–S bonds, characterize, the bonding interaction is a closed shell interaction. The combined observed low value of electron density and the positive Laplacian of Au–S bond comprises, the gold and S interaction is not a covalent interaction, but it is a very weak coordination bond interaction. The small positive value of total energy density in Au–S bond indicates, the charges in these bonds are highly depleted and this is further confirmed by the Laplacian of bond characterization.     

Effects of electric fields on proton transport through water chains

Molecular dynamics simulations on quantum energy surfaces are carried out to study the effects of perturbing electric fields on proton transport (PT) in protonated water chains. As an idealized model of a hydrophobic cavity in the interior of a protein the water molecules are confined into a carbon nanotube (CNT). The water chain connects a hydrated hydronium ion (H3O+) at one end of the CNT and an imidazole molecule at the other end. Without perturbing electric fields PT from the hydronium proton donor to the imidazole acceptor occurs on a picosecond time scale. External perturbations to PT are created by electric fields of varying intensities, normal to the CNT axis, generated by a neutral pair of charges on the nanotube wall. For fields above approximately 0.5 VA, the hydronium ion is effectively trapped at the CNT center, and PT blocked. Fields of comparable strength are generated inside proteins by nearby polar/charged amino acids. At lower fields the system displays a rich dynamic behavior, where the excess charge shuttles back and forth along the water chain before reaching the acceptor group on the picosecond time scale. The effects of the perturbing field on the proton movement are analyzed in terms of structural and dynamic properties of the water chain. The implications of these observations on PT in biomolecular systems and its control by external perturbing fields are discussed.     

Comparison of different separation technologies for proteome analyses: isoform resolution as a prerequisite for the definition of protein biomarkers on the level of posttranslational modifications

In this article we evaluate methods used to reveal the molecular complexity, which is generated in biological samples by posttranslational modifications (PTM) of proteins. We show how distinct molecular differences on the level of phosphorylation sites in a single protein (ovalbumin) can be resolved with different success using 1D and 2D gel-electrophoresis and reversed-phase liquid chromatography (LC) with monolithic polystyrol-divinylbenzol (PS-DVB) columns for protein separation, and matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS) for protein identification. Phosphorylation site analysis was performed using enzymatic dephosphorylation in combination with differential peptide mass mapping. Liquid chromatography-MALDI-TOF MS coupling with subsequent on-target tryptic protein digestion turned out to be the fastest method tested but yielded low resolution for the analysis of PTM, whereas 2D gel-electrophoresis, due to its unique capability of resolving highly complex isoform pattern, turned out to be the most suitable method for this purpose. The evaluated methods complement one another and in connection with efficient technologies for differential and quantitative analysis, these approaches have the potential to reveal novel molecular details of protein biomarkers.     

Phase behavior of a symmetrical binary fluid mixture

We have investigated the phase behavior of a symmetrical binary fluid mixture for the situation where the chemical potentials mu(1) and mu(2) of the two species differ. Attention is focused on the set of interparticle interaction strengths for which, when mu(1)=mu(2), the phase diagram exhibits both a liquid-vapor critical point and a tricritical point. The corresponding phase behavior for the case mu(1) not equalmu(2) is investigated via integral-equation theory calculations within the mean spherical approximation and grand canonical Monte Carlo (GCMC) simulations. We find that two possible subtypes of phase behavior can occur, these being distinguished by the relationship between the triple lines in the full phase diagram in the space of temperature, density, and concentration. We present the detailed form of the phase diagram for both subtypes and compare with the results from GCMC simulations, finding good overall agreement. The scenario via which one subtype evolves into the other is also studied, revealing interesting features.     

Contributions of the different water sources to the Elqui river runoff (northern Chile) evaluated by H/O isotopes

We present the results of an isotope (2H and 18O) and hydrogeochemical study in order to constrain the origin, recharge, and evolution of the surface and groundwater in the arid Andean realm of the Elqui watershed. The results of 2H and18O analyses of water samples obtained during our summer and winter campaigns indicate a generally meteoric origin of the river and spring waters of the watershed. The isotope signature of water of the Elqui river and its tributaries as well as that of groundwater in the coastal region fits the 2H-18O relation of delta2H =7.61delta18O+6.1. A relatively fast discharge and a quasi-closed catchment area can be asserted for water along the river flow path. The tributaries from the more arid coastal area, north of the Elqui river, differ in their isotopic signature due to evaporation and hydrochemically due to interactions with the strongly altered and fractured volcanic rocks of the basement. In the Andean zone, the18O-enriched hydrothermal spring of Ba?os del Toro exhibits the influence of water-rock interaction processes. The chemistry of the river water changes from sulphate- to chloride-rich along the river course from the high Andean mountains to the coast. The sulphate-rich character of these Andean waters reflects their passage through sulphide-rich rock massifs that were subjected to strong oxidation processes in the near superficial environment. This sulphate signature is enforced by past and present mining of precious metal epithermal deposits (e.g. those of El Indio-Tambo Au-Cu-As district), in which mineralised zones were developed during a series of Miocene magmatic-hydrothermal episodes in the Andean realm. Owing to the proximity of the lower Elqui river waters and its tributaries to the Pacific coast, the chloride character may be induced by agricultural and marine (sea spray, fog) sources. Generally, the main source of the Elqui river water is mainly attributed to surface runoff and less to contributions from the basement fractured aquifer.     

Sulphur and oxygen isotopic characters of dissolved sulphate in groundwater from the Pleistocene aquifer in the southern Jordan Valley (Jericho area, Palestine)

Sulphate and chloride concentrations in the shallow Pleistocene aquifer systems in the lower Jordan valley area indicate a general trend of increasing salinity eastward and southward. This study was conducted in one of the important sub-basins feeding the Pleo-Pleistocene aquifer in the Jericho area in the southern part of the valley using S and O isotopes of dissolved sulphate. The results show that sulphate has mainly two contributions to the groundwater. One is the surface seepage, which is present as a salty leachate form with the positive delta34Ssulphate values of primary gypsum in Lisan and Samara formations, and the second is the upwelling saline water which was in contact with a deep secondary gypsum, aragonites and salty rocks and rose up under heavy abstraction with depleted 34S in sulphate and relatively high sulphate and chloride content. The latest was clearly shown in the Arab Project wells to the east that is undergoing a continuous heavy abstraction. The isotopic signatures of S and O in these wells to the east show that this depleted 34S and highly concentrated sulphate might also indicate a dissolved sulphate originating from pyrite oxidation that results from the interaction with a pyrite-rich aquifer, which can well up with salty water under heavy abstraction and is oxidised in the upper aerobic shallow aquifer.     

Soil-structure interaction of tunnel-structures under consideration of far- and near-field effects

The response of a tunnel structure under a moving and oscillating dynamic load can be calculated by means of a hybrid Integral–Transformation–Method–FEM approach. In the ITM approach analytical solutions of ideal geometries of the infinite continuum are superposed such that the wave–number impedance and transfer–function at the interior of a circular tunnel can be calculated efficiently. By this means the infinite continuum can be coupled to an arbitrary tunnel structure which is modelled by the FEM with corresponding form–functions. In order to reduce the effort for the coupling, the characteristics of the analytically given transfer–functions which can be split into near– and far–fields is taken into account. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)