DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight < 1.5 KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew's correlation coefficient of similar to 0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.

Nanotubes of the disulfides of groups 4 and 5 metals

The layered chalcogenides, having structures analogous to graphite, are known to be unstable toward bending and show high propensity to form curved structures, thus eliminating dangling bonds at the edges. Since the discovery of fullerene and nanotube structures of WS2 and MoS2 by Tenne et al. [1-3], there have been attempts to prepare and characterize nanotubes of other layered dichalcogenides with structures analogous to MoS2. Nanotubes of MoS2 and WS2 were prepared by Tenne et al. by reducing the corresponding oxides to the suboxides followed by heating in an atmosphere of forming gas (5 % H-2 + 95 % N-2) and H2S at 700-900 degreesC [1-3]. Alternative methods of synthesis of MoS2 and WS2 nanotubes have since been proposed by employing the decomposition of the ammonium thiometallates or the corresponding trisulfide precursors. This alternative procedure was based on the observation that the trisulfide seems to be formed as an intermediate in the synthesis of the MoS2 and WS2 nanotubes [4]. Accordingly, the decomposition of the trisulfides of MoS2 and W in a reducing atmosphere directly yielded nanotubes of the disulfides MoS2 and WS2 [5]. In this article, we describe the synthesis, structure, and characterization of a few novel nanotubes of the disulfides of groups 4 and 5 metals. These include nanotubes of NbS2, TaS2, ZrS2, and HfS2. The study enlarges the scope of the inorganic nanotubes significantly and promises other interesting possibilities, including the synthesis of the diselenide nanotubes of these metals.

The production of AlN-rich matrix composites by the reactive infiltration of Al alloys in nitrogen

Aluminium nitride (AlN)-Al matrices reinforced with Al2O3 particulate have been fabricated by reactive infiltration of Al-2% Mg alloy into Al2O3 preforms in N-2 in the temperature range of 900-1075 degreesC. The growth of composites of useful thickness was facilitated by the presence of a Mg-rich external getter, in the absence of which composite growth is self-limiting and terminates prematurely. Successful growth of composites has been attributed to the reduction in residual oxygen partial pressure brought about by the reaction with oxygen of highly volatile Mg in the getter alloy. The microstructure of the matrix consists of AlN-rich regions contiguous with the particulate with metal-rich channels in-between, thereby suggesting that nitridation initiates by preferential wicking of alloy along the particle surfaces. The increase in nitride content of the matrix with temperature is consistent with hardness values that vary between similar to3 and 10 GPa. (C) 2002 Acta Materialia Inc. Published by Elsevier Science Ltd. All rights reserved.

The thermodynamics and phase behaviour of Tb2Pd2O5 and Er2Pd2O5

Isothermal sections of the phase diagrams for the systems Ln-Pd-O (with Ln = Tb or Er) have been established by equilibration of samples at T = 1223 K, and phase identification after quenching by optical and scanning electron microscopy (OM, SEM), energy dispersive spectroscopy (EDS), and X-ray powder diffraction (XRPD). Two oxide phases were stable along the binary Tb-O: Tb2O3+x, a phase of variable composition, and Tb7O12 at T = 1223K. The oxide PdO was not stable at this temperature. Only one ternary oxide Tb2Pd2O5 was identified in the Tb-Pd-O system. No ternary compound was found in the system Er-Pd-O at T = 1223K. However, the compound Er2Pd2O5 could be synthesized at T = 1075 K by the hydrothermal route. In both systems, the alloys and inter-metallic compounds were all found to be in equilibrium with the lanthanide sesquioxide Ln(2)O(3) (where Ln is either Tb or Er). Two solid-state cells, each incorporating a buffer electrode, were designed to measure the Gibbs energy of formation of the ternary oxides, using yttria-stabilized zirconia as the solid electrolyte and pure oxygen gas as the reference electrode. Electromotive force measurements were conducted in the temperature range (900-1275) K for Th-Pd-O system, and at temperatures from (900-1075) K for the system Er-Pd-O. The standard Gibbs energy of formation Delta(f)G(m)degrees,, of the inter-oxide compounds from their component binary oxides Ln(2)O(3) and PdO are represented by equations linear in temperature. Isothermal chemical potential diagrams for the systems Ln-Pd-O (with Ln = Tb or Er) are developed based on the thermodynamic information. (C) 2002 Elsevier Science Ltd. All rights reserved.

Low temperature synthesis of ferromagnetic (LaK)MnO3 from KCl, KBr and KI fluxes

Potassium doped lanthanum manganites have been synthesized from KCl, KBr and KI fluxes at 900, 850 and 750 °C respectively. While all the flux-grown oxides are ferromagnetic metals (Tc=290–330 K), the oxides grown from KCl and KBr fluxes crystallize in the rhombohedral structure and that synthesized from KI flux adopts the cubic structure. The enhancement in Tc correlates with the increasing tendency of the flux to get oxidized and decreasing melting points of the flux. Nearly stoichiometric (LaK)MnO3 with 33 % of Mn4+ concentration could be prepared at temperature as low as 750 °C. Composition of all the phases have been obtained from the chemical analysis of the elements present.

Reduction of oxygen impurity at GaN/beta-Si(3)N(4)/Si interface via SiO(2) to Ga(2)O conversion by exposing of Si surface under Ga flux

The removal of native oxide from Si (1 1 1) surfaces was investigated by X-ray photoelectron spectroscopy (XPS) and secondary ion mass spectra (SIMS) depth profiles. Two different oxide removal methods, performed under ultrahigh-vacuum (UHV) conditions, were carried out and compared. The first cleaning method is thermal desorption of oxide at 900 degrees C. The second method is the deposition of metallic gallium followed by redesorption. A significant decrease in oxygen was achieved by thermal desorption at 900 degrees C under UHV conditions. By applying a subsequent Ga deposition/redesorption, a further reduction in oxygen could be achieved. We examine the merits of an alternative oxide desorption method via conversion of the stable SiO(2) surface oxide into a volatile Ca(2)O oxide by a supply of Ga metals. Furthermore, ultra thin films of pure silicon nitride buffer layer were grown on a Si (1 1 1) surface by exposing the surface to radio-frequency (RF) nitrogen plasma followed by GaN growth. The SIMS depth profile shows that the oxygen impurity can be reduced at GaN/beta-Si(3)N(4)/Si interfaces by applying a subsequent Ga deposition/redesorption. (C) 2011 Elsevier B.V. All rights reserved.

Seismic Hazard and Microzonation Studies using Geographic Information System - A Case Study of Bangalore city

Seismic hazard and microzonation of cities enable to characterize the potential seismic areas that need to be taken into account when designing new structures or retrofitting the existing ones. Study of seismic hazard and preparation of geotechnical microzonation maps has been attempted using Geographical Information System (GIS). GIS will provide an effective solution for integrating different layers of information thus providing a useful input for city planning and in particular input to earthquake resistant design of structures in an area. Seismic hazard is the study of expected earthquake ground motions at any point on the earth. Microzonation is the process of sub division of region in to number of zones based on the earthquake effects in the local scale. Seismic microzonation is the process of estimating response of soil layers under earthquake excitation and thus the variation of ground motion characteristic on the ground surface. For the seismic microzonation, geotechnical site characterization need to be assessed at local scale (micro level), which is further used to assess of the site response and liquefaction susceptibility of the sites. Seismotectonic atlas of the area having a radius of 350km around Bangalore has been prepared with all the seismogenic sources and historic earthquake events (a catalogue of about 1400 events since 1906). We have attempted to carryout the site characterization of Bangalore by collating conventional geotechnical boreholes data (about 900 borehole data with depth) and integrated in GIS. 3-D subsurface model of Bangalore prepared using GIS is shown in Figure 1.Further, Shear wave velocity survey based on geophysical method at about 60 locations in the city has been carried out in 220 square Kms area. Site response and local site effects have been evaluated using 1-dimensional ground response analysis. Spatial variability of soil overburden depths, ground surface Peak Ground Acceleration’s(PGA), spectral acceleration for different frequencies, liquefaction susceptibility have been mapped in the 220 sq km area using GIS.ArcInfo software has been used for this purpose. These maps can be used for the city planning and risk & vulnerability studies. Figure 2 shows a map of peak ground acceleration at rock level for Bangalore city. Microtremor experiments were jointly carried out with NGRI scientists at about 55 locations in the city and the predominant frequency of the overburden soil columns were evaluated.

Dynamic and thermodynamic anomalies of water at low temperatures: from bulk water to reverse micelles and DNA hydration layer

Liquid water is known to exhibit remarkable thermodynamic and dynamic anomalies, ranging from solvation properties in supercritical state to an apparent divergence of the linear response functions at a low temperature. Anomalies in various dynamic properties of water have also been observed in the hydration layer of proteins, DNA grooves and inside the nanocavity, such as reverse micelles and nanotubes. Here we report studies on the molecular origin of these anomalies in supercooled water, in the grooves of DNA double helix and reverse micelles. The anomalies have been discussed in terms of growing correlation length and intermittent population fluctuation of 4- and 5-coordinated species. We establish correlation between thermodynamic response functions and mean squared species number fluctuation. Lifetime analysis of 4- and 5-coordinated species reveals interesting differences between the role of the two species in supercooled and constrained water. The nature and manifestations of the apparent and much discussed liquid-liquid transition under confinement are found to be markedly different from that in the bulk. We find an interesting `faster than bulk' relaxation in reverse micelles which we attribute to frustration effects created by competition between the correlations imposed by surface interactions and that imposed by hydrogen bond network of water.

Thermodynamics of oxygen in liquid copper, lead and copper lead alloys

Solid oxide galvanic cells of the type Pt, Ni-NiO I Solid electrolyte ( Ometa,, Cermet. Pt were used to measure the activity coefficient of oxygen in liquid copper at 11 00 and 1 300eC, and in lead at 11 00'C. Similar cells were used to study the activity coefficient of oxygen in the whole range of Cu + Pb alloys at 1100'C and in lead-rich alloys at 900 and 750'C.The results obtained are discussed in terms of proposed solution models. An equation based on the formation of 'species' of the form M,O in solutions of oxygen in binary alloys is shown to fit the experimental data.

Electrochemical determination of activities in Cr2O3 Al2O3 solid solutions

The activity of Cr20~ in Cr20~-A12Oa solid solution has been determined in the temperature range 800~176 from electromotive force measurements on the solid oxide galvanic cell Pt,Cr + Cr2OJY~O~-ThO2/Cr + Cr~A12-xO~,Pt The activities of Cr203 and A120~ in the solid solution show both positive and negative deviations from Raoult's law. The heat and entropy of mixing of the solid Solution obtained from the temperature dependence of the emf can be expressed as AH = XCr203XA1203 [31,700Xcrzo3 -}- 37,470XA1203] J mole -I hS = -- 1.8R [Xcr2o3 In Xcr2o3 + XA12o3 In XAaos]The entropy of mixing is 10% lower than that predicted by the Temkin model.The large positive heat of mixing in the Cr2Os-A12Oa solid solution, however, suggests that this apparent: entropy discrepancy originates with the clustering of positive ions on the cation sublattice. The asymmetric miscibility gap exhibited in the CrzOa-A12Oa system below 900~ is consistent with the thermodynamic data trends recorded at the more elevated temperatures.

Thermodynamic study of Fe2O3 Fe2(SO4)3 equilibrium using an oxyanionic electrolyte (Na2SO4 I)

The emf of the cell, Pt, Ar + O2 + SO2 + SO3/Na2SO4-I/Fe2O2 + Fe2(SO4)3, Pt, has been measured in the temperature range 800 to 1000 K, using a gas mixture of known input composition as the reference electrode. The equilibrium composition of the reference gas at the measuring temperatures was computed using the thermodynamic data on the gaseous species reported in the literature. A mixture of ferric oxide and sulfate was kept in a closed system to ensure establishment of equilibrium partial pressure at the electrode. The cell was designed to avoid physical contact between Fe2(SO4)3 and Na2SO4 electrolyte. Uncertainties arising from the formation of sulfate solid solution were thus eliminated. The Gibbs’ energy of formation of ferric sulfate calculated from the emf is discussed in comparison with data reported in the literature. There is no evidence for the formation of oxysulfates in the Fe-S-0 system. Based on the results obtained in the present study for Fe2(SO4)3 and literature data for other phases, chemical potential diagrams have been constructed for the Fe-S-O system at 900 and 1100 K.

Kinetics of Sulphation of Nickel and Cobalt Ferrites with Na$O, Melt Containing F'e3+ Ions

It has been experimentally established that nickel and cobalt can be extracted from their ferrites with sodium sulphate melt containing femc ions. The kinetics of extraction from synthetic ferrites using a melt of sodium and ferric sulphates of eutectic composition has been studied as a function of the particle size of the ferrite and temperature in the range 900 to 1073 K. The divalent ions in the ferrite exchange with the ferric ion in the melt, leaving a residue of hematite.The rate of reaction conforms to the Crank-Ginstling-Brounshtein diffusion model. The reaction rate is governed by the counter-diffusion of ~ e an~d ~+i ' +(or co2+) ions in the hematite lattice. Analytical expressions for the rate constants have been derived from the experimental data as a function of particle size and temperature. The activation energy for the extraction of nickel from nickel ferrite is 154(+10) kJ mol-' and the corresponding value for cobalt is 142(+10)kJ mol;'. In sulphation roasting of minerals containing nickel, the yield of nickel is generally limited to 75% due to the formation of insoluble ferrites. The use of melts based on sodium sulphate provides a possible route for enhancing the recovery of nickel to approximately 98%.

Gibbs energy of formation of CuCrO4 and phase relations in the system Cu-Cr-O below 735 K

A solid state galvanic cell incorporating yttria-stabilized zirconia electrolyte and ruthenium(IV) oxide electrodes has been used to measure the equilibrium chemical potential of oxygen corresponding to the decomposition of CuCrO4 in the range 590–760 K. For the reaction CuO(tenorite) + CuCr2O4(spinel) + 1.5O2(g)→2CuCrO4(orth), ΔGXXX = −183540 + 249.6T(±900) J mol−1. The decomposition temperature of CuCrO4 in pure oxygen at a pressure of 1.01 × 105 Pa is 735(±1) K. By combining the results obtained in this study with data on the Gibbs energy of formation of CuCr2O4 and CuCrO2 reported earlier, the standard Gibbs energy of formation of CuCrO4 and the phase relations in the system Cu-Cr-O at temperatures below 735 K have been deduced. Electron microscopic studies have indicated that the decomposition of CuCrO4 to CuCr2O4 is topotactic.

Electrochemical determination of the Gibbs energy of formation of MgAl2O4

The standard Gibbs energy of formation of the spinel MgAl2O4 from component oxides, MgO and α-Al2O3, has been determined in the temperature range 900 to 1250 K using a solid-state cell incorporating single-crystal CaF2 as the solid electrolyte. The cell can be represented as—Pt,O2,MgO+MgF2|CaF2|MgF2+MgAl2O4+α-Al2O3,O2,Pt—The standard Gibbs energy of formation from binary oxides, computed from the reversible emf, can be represented by the expression—capdeltaG°f,ox=−23600 − 5.91T(±150) J/mol—The ‘second-law’ enthalpy of formation of MgAl2O4 obtained in this study is in good agreement with high-temperature solution calorimetric studies reported in the literature.

System Cu-Rh-O: Phase diagram and thermodynamic properties of ternary oxides CuRhO2 and CuRh204

An isothermal section of the phase diagram for the system Cu-Rh-O at 1273 K has been established by equilibration of samples representing eighteen different compositions, and phase identification after quenching by optical and scanning electron microscopy (SEM), X-ray diffraction (XRD), and energy dispersive analysis of X-rays (EDX). In addition to the binary oxides Cu2O, CuO, and Rh2O3, two ternary oxides CuRhO2 and CuRh2O4 were identified. Both the ternary oxides were in equilibrium with metallic Rh. There was no evidence of the oxide Cu2Rh2O5 reported in the literature. Solid alloys were found to be in equilibrium with Cu2O. Based on the phase relations, two solid-state cells were designed to measure the Gibbs energies of formation of the two ternary oxides. Yttria-stabilized zirconia was used as the solid electrolyte, and an equimolar mixture of Rh+Rh2O3 as the reference electrode. The reference electrode was selected to generate a small electromotive force (emf), and thus minimize polarization of the three-phase electrode. When the driving force for oxygen transport through the solid electrolyte is small, electrochemical flux of oxygen from the high oxygen potential electrode to the low potential electrode is negligible. The measurements were conducted in the temperature range from 900 to 1300 K. The thermodynamic data can be represented by the following equations: {fx741-1} where Δf(ox) G o is the standard Gibbs energy of formation of the interoxide compounds from their component binary oxides. Based on the thermodynamic information, chemical potential diagrams for the system Cu-Rh-O were developed.