Binding of BIS like and other ligands with the GSK-3 beta kinase: a combined docking and MM-PBSA study

Binding of several bisindolylmaleimide (BIS) like (BIS-3, BIS-8 and UCN1) and other ligands (H89, SB203580 and Y27632) with the glycogen synthase kinase-3 (GSK-3 beta) has been studied using combined docking, molecular dynamics and Poisson-Boltzmann surface area analysis approaches. The study generated novel binding modes of these ligands that can rationalize why some ligands inhibit GSK-3 beta while others do not. The relative binding free energies associated with these binding modes are in agreement with the corresponding measured specificities. This study further provides useful insight regarding possible existence of multiple conformations of some ligands like H89 and BIS-8. It is also found that binding modes of BIS-3, BIS-8 and UCN1 with GSK-3 beta and PDK1 kinases are similar. These new insights are expected to be useful for future rational design of novel, more potent GSK-3 beta-specific inhibitors as promising therapeutics.

Towards sustainability: a new, solid-state synthetic route for supported metal nanocatalysts

Noble metal ions like Pt(IV) and Pd(II) were impregnated on gamma-alumina and aerosol 300 silica surfaces. Reduction of these ions using ammonia borane in the solid state resulted in the formation of the respective metal nanoparticles embedded in BNHx polymer which is dispersed on the oxide support. Removal of the BNH polymer was accomplished by washing the samples repeatedly with methanol. In this process the polymer undergoes solvolysis to release H-2 accompanied by the formation of ammonium methoxy borate salt, which has been removed by repeated methanol washings. As a result, metal nanoparticles well dispersed on gamma-alumina and aerosol 300 silica were obtained. These samples have been characterized by a combination of techniques, including electron microscopy, powder X-ray diffraction, NMR spectroscopy and surface area analyser.

Effect of convection and viscoelasticity on spinodal decomposition in fluids

Current analytical work on the effect of convection and viscoelasticity on the early and late stages of spinodal decomposition is briefly described. In the early stages, the effect of viscoelastic stresses was analysed using a simple Maxwell model for the stress, which was incorporated in the Langevin equation for the momentum field. The viscoelastic stresses are found to enhance the rate of decomposition. In the late stages, the pattern formed depends on the relative composition of the two species. Droplet spinodal decomposition occurs when the concentration of one of the species is small. Convective transport does not have a significant effect on the growth of a single droplet, but it does result in an attractive interaction between non - Brownian droplets which could lead to coalescence. The effect of convective transport for the growth of random interfaces in a near symmetric quench was analysed using an 'area distribution function', which gives the distribution of surface area of the interface in curvature space. It was found that the curvature of the interface decreases proportional to t in the late stages of spinodal decomposition, and the surface area also decreases proportional to t.

Geotechnical properties of some Indian fly ashes

To reduce the cost of disposal of large quantities of fly ash generated and environmental problems associated with it, efforts are made to utilize fly ash for geotechnical applications. Geotechnical properties of fly ash play a key role in enhancing their application. Physical properties and chemical composition control the index properties arid engineering behaviour. The paper brings out the rob of surface area, surface characteristics, reactive silica and lime content of fly ashes on index, compaction, consolidation and strength properties of fly ashes.

Esterification of stearic acid with p-cresol over modified Indian bentonite clay catalysts

The esterification of stearic acid with p-cresol using modified Indian bentonite clay catalysts has been reported. The reaction was studied over exchanged clays, acid activated clays, exchanged acid activated clays, aluminium pillared clay, aluminium pillared acid activated clay, molecular sieve Al-MCM-41, zeolite H beta, ZrO2, S-ZrO2, p-TSA, montmorillonite K10, and montmorillonite KSF in o-xylene for 6 h. The catalysts were characterized by X-ray diffraction and surface area measurements. The acidity was determined by n-butylamine back-titration method and DRIFTS after pyridine adsorption. Acid activated Indian bentonite (AAIB) was found to be a better catalyst compared to other catalysts in the esterification of stearic acid with p-cresol.

Spontaneous self-assembly of designed cyclic dipeptide (Phg-Phg) into two-dimensional nano- and mesosheets

In this study, we present the spontaneous self-assembly of designed simplest aromatic cyclic dipeptides of (L-Phg-L-Phg) and (D-Phg-L-Phg) to form highly stable two-dimensional (2D) nano- and mesosheets with large lateral surface area. Various microscopy data revealed that the morphology of 2D mesosheets resembles the hierarchical natural materials with layered structure. Solution and solid-state NMR studies on cyclo(L-Phg-L-Phg) revealed the presence of strong (N-H-O) hydrogen-bonded molecular chains supported by aromatic pi-pi interactions to form 2D mesosheets. Interestingly, cyclo(D-Phg-L-Phg) self-assembles to form single-crystalline as well as non-crystalline 2D rhomboid sheets with large lateral dimension. X-ray diffraction analysis revealed the stacking of (N-H-O) hydrogen-bonded molecular layers along c-axis supported by aromatic pi-pi interactions. The thermogravimetric analysis shows two transitions with overall high thermal stability attributed to layered hierarchy found in 2D mesosheets.

Dimethyl sulfoxide induced structural transformations and non-monotonic concentration dependence of conformational fluctuation around active site of lysozyme

Experimental studies have observed significant changes in both structure and function of lysozyme (and other proteins) on addition of a small amount of dimethyl sulfoxide (DMSO) in aqueous solution. Our atomistic molecular dynamic simulations of lysozyme in water-DMSO reveal the following sequence of changes on increasing DMSO concentration. (i) At the initial stage (around 5% DMSO concentration) protein's conformational flexibility gets markedly suppressed. From study of radial distribution functions, we attribute this to the preferential solvation of exposed protein hydrophobic residues by the methyl groups of DMSO. (ii) In the next stage (10-15% DMSO concentration range), lysozome partially unfolds accompanied by an increase both in fluctuation and in exposed protein surface area. (iii) Between 15-20% concentration ranges, both conformational fluctuation and solvent accessible protein surface area suddenly decrease again indicating the formation of an intermediate collapse state. These results are in good agreement with near-UV circular dichroism (CD) and fluorescence studies. We explain this apparently surprising behavior in terms of a structural transformation which involves clustering among the methyl groups of DMSO. (iv) Beyond 20% concentration of DMSO, the protein starts its final sojourn towards the unfolding state with further increase in conformational fluctuation and loss in native contacts. Most importantly, analysis of contact map and fluctuation near the active site reveal that both partial unfolding and conformational fluctuations are centered mostly on the hydrophobic core of active site of lysozyme. Our results could offer a general explanation and universal picture of the anomalous behavior of protein structure-function observed in the presence of cosolvents (DMSO, ethanol, tertiary butyl alcohol, dioxane) at their low concentrations. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3694268]

Dielectric Barrier Discharge Cascaded with Red Mud Waste to Enhance NOX Removal from Diesel Engine Exhaust

Red mud is a waste by-product generated during the processing of bauxite, the most common ore of aluminium. With the presence of ferric oxide, high surface area, resistance to poisoning and low cost, red mud made itself a good alternative to the existing commercial automobile catalyst. The cascading of dielectric barrier discharge plasma with red mud improved the NOX removal from diesel engine exhaust significantly. The DeNO(X) efficiency with discharge plasma was 74% and that with red mud was 31%. The efficiency increased to 92% when plasma was cascaded with red mud catalyst operating at a temperature of 400 degrees C. The NOX removal was dominated by NO2 removal. The studies were conducted at different temperatures and the results were discussed.

Synthesis and characterization of carbon-covered alumina (CCA) supported TiO2 nanocatalysts with enhanced visible light photodegradation of Rhodamine B

The anatase phase of titania (TiO2) nano-photocatalysts was prepared using a modified sol gel process and thereafter embedded on carbon-covered alumina supports. The carbon-covered alumina (CCA) supports were prepared via the adsorption of toluene 2,4-diisocyanate (TDI) on the surface of the alumina. TDI was used as the carbon source for the first time for the carbon-covered alumina support system. The adsorption of TDI on alumina is irreversible; hence, the resulting organic moiety can undergo pyrolysis at high temperatures resulting in the formation of a carbon coating on the surface of the alumina. The TiO2 catalysts were impregnated on the CCA supports. X-ray diffraction analysis indicated that the carbon deposited on the alumina was not crystalline and also showed the successful impregnation of TiO2 on the CCA supports. In the Raman spectra, it could be deduced that the carbon was rather a conjugated olefinic or polycyclic hydrocarbons which can be considered as molecular units of a graphitic plane. The Raman analysis of the catalysed CCAs showed the presence of both the anatase titania and D and G band associated with the carbon of the CCAs. The scanning electron microscope micrographs indicated that the alumina was coated by a carbon layer and the energy dispersive X-ray spectra showed the presence of Al, O and C in the CCA samples, with the addition of Ti for the catalyst impregnated supports. The Brunauer Emmet and Teller surface area analysis showed that the incorporating of carbon on the alumina surface resulted in an increase in surface area, while the impregnation with TiO2 resulted in a further increase in surface area. However, a decrease in the pore volume and diameter was observed. The photocatalytic activity of the nanocatalysts was studied for the degradation of Rhodamine B dye. The CCA-TiO2 nanocatalysts were found to be more photocatalytically active under both visible and UV light irradiation compared to the free TIO2 nanocatalysts.

Transition metal oxide loaded MCM catalysts for photocatalytic degradation of dyes

Transition metal oxide (TiO2, Pe(2)O(3), CoO) loaded MCM-41 and MCM-48 were synthesized by a two-step surfactant-based process. Nanoporous, high surface area compounds were obtained after calcination of the compounds. The catalysts were characterized by SEM, XRD, XPS, UV-vis and BET surface area analysis. The catalysts showed high activity for the photocatalytic degradation of both anionic and cationic dyes. The degradation of the dyes was described using Langmuir-Hinshelwood kinetics and the associated rate parameters were determined.

Network properties of protein-decoy structures

Convergence of the vast sequence space of proteins into a highly restricted fold/conformational space suggests a simple yet unique underlying mechanism of protein folding that has been the subject of much debate in the last several decades. One of the major challenges related to the understanding of protein folding or in silico protein structure prediction is the discrimination of non-native structures/decoys from the native structure. Applications of knowledge-based potentials to attain this goal have been extensively reported in the literature. Also, scoring functions based on accessible surface area and amino acid neighbourhood considerations were used in discriminating the decoys from native structures. In this article, we have explored the potential of protein structure network (PSN) parameters to validate the native proteins against a large number of decoy structures generated by diverse methods. We are guided by two principles: (a) the PSNs capture the local properties from a global perspective and (b) inclusion of non-covalent interactions, at all-atom level, including the side-chain atoms, in the network construction accommodates the sequence dependent features. Several network parameters such as the size of the largest cluster, community size, clustering coefficient are evaluated and scored on the basis of the rank of the native structures and the Z-scores. The network analysis of decoy structures highlights the importance of the global properties contributing to the uniqueness of native structures. The analysis also exhibits that the network parameters can be used as metrics to identify the native structures and filter out non-native structures/decoys in a large number of data-sets; thus also has a potential to be used in the protein `structure prediction' problem.

Transition metal oxide loaded MCM catalysts for photocatalytic degradation of dyes

Transition metal oxide (TiO2, Pe(2)O(3), CoO) loaded MCM-41 and MCM-48 were synthesized by a two-step surfactant-based process. Nanoporous, high surface area compounds were obtained after calcination of the compounds. The catalysts were characterized by SEM, XRD, XPS, UV-vis and BET surface area analysis. The catalysts showed high activity for the photocatalytic degradation of both anionic and cationic dyes. The degradation of the dyes was described using Langmuir-Hinshelwood kinetics and the associated rate parameters were determined.

Dilithium phthalocyanine as a catalyst for oxygen reduction in non-aqueous Li-O-2 cells

The electrochemical performance of Li-O-2 cells depends mainly on the kinetics of the cathode reaction, namely, oxygen reduction reaction in non-aqueous electrolytes. The catalyst plays an important role on the kinetics of the reaction. In the present work, dilithium phthalocyanine is used as the catalyst in the cathode of Li-O-2 cells. Dual-layer O-2 electrodes are fabricated employing a high surface area microporous carbon with Ni gauge current collector present between the two layers. Discharge capacity of Li-O-2 cell measured at 0.2 mA.cm(-2) is about 30 mAh.cm(-2). Phthalocyanine ring is considered to interact with O-2 producing Li2Pc+delta - O-2(-delta) as a reaction intermediate, which facilitates the electron-transfer reaction.

Influence of Bottom Bubbling Rate on Formation of Metal Emulsion in Al-Cu Alloy and Molten Salt System

In steel refining process, an increase of interfacial area between the metal and slag through the metal droplets emulsified into the slag, so-called ``metal emulsion'', is one prevailing view for improving the reaction rate. The formation of metal emulsion was experimentally evaluated using Al-Cu alloy as metal phase and chloride salt as slag phase under the bottom bubbling condition. Samples were collected from the center of the salt phase in the container. Large number of metal droplets were separated from the salt by dissolving it into water. The number, surface area, and weight of the droplets increased with the gas flow rate and have local maximum values. The formation and sedimentation rates of metal droplets were estimated using a mathematical model. The formation rate increased with the gas flow rate and has a local maximum value as a function of gas flow rate, while the sedimentation rate is independent of the gas flow rate under the bottom bubbling condition. Three types of formation mode of metal emulsion, which occurred by the rupture of metal film around the bubble, were observed using high speed camera. During the process, an elongated column covered with metal film was observed with the increasing gas flow rate. This elongated column sometimes reached to the top surface of the salt phase. In this case, it is considered that fine droplets were not formed and in consequence, the weight of metal emulsion decreased at higher gas flow rate.

Rapid sonochemical synthesis of mesoporous MnO2 for supercapacitor applications

Mesoporous MnO2 samples with average pore-size in the range of 2-20 nm are synthesized in sonochemical method from KMnO4 by using a tri-block copolymer, namely, poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol) (P123) as a soft template as well as a reducing agent. The MnO2 samples are found to be poorly crystalline. On increasing the amplitude of sonication, a change in the morphology of MnO2 from nanoparticles to nanorods and also change in porosity are observed. A high BET surface area of 245 m(2) g(-1) is achieved for MnO2 sample. The MnO2 samples are subjected to electrochemical capacitance studies by cyclic voltammetry (CV) and galvanostatic charge-discharge cycling in 0.1 M aqueous Ca(NO3)(2) electrolyte. A maximum specific capacitance (SC) of 265 Fg(-1) is obtained for the MnO2 sample synthesized in sonochemical method using an amplitude of 30 mu m. The MnO2 samples also possess good electrochemical stability due to their favourable porous structure and high surface area. (C) 2012 Elsevier B.V. All rights reserved.