Doping effect of Ag+, Mn2+ ions on Structural and Optical Properties of ZnO nanoparticles

Pure ZnO and co-doped (Mn, Ag) ZnO nanoparticles have been successfully prepared by chemical co-precipitation method without using a capping agent. X-ray diffraction (XRD) studies confirms the presence of wurtzite (hexagonal) crystal structure similar to undoped ZnO, suggesting that doped Mn, Ag ions are substituted to the regular Zn sites. The morphology of the samples were studied by scanning electron microscopy (SEM). The chemical composition of pure and co-doped ZnO nanoparticles were characterized by energy dispersive X-ray analysis spectroscopy (EDAX). Optical absorption properties were determined by UV-vis Diffuse Reflectance Spectrophotometer. The incorporation of Ag+, Mn2+ in the place of Zn2+ provoked to decrease the size of nanocrystals as compared to pure ZnO. Optical absorption measurements indicates blue shift in the absorption band edge upon Ag, Mn ions doped ZnO nanoparticles.

Structural characterization of folded and extended conformations in peptides containing gamma amino acids with proteinogenic side chains: crystal structures of gamma(n), (alpha gamma)(n) and gamma gamma delta gamma sequences

The crystal structures of nine peptides containing gamma(4)Val and gamma(4)Leu are described. The short sequences Boc-gamma(4)(R)Val](2)-OMe 1, Boc-gamma(4)(R)Val](3)-NHMe 2 and Boc-gamma(4)(S)Val-gamma(4)(R)Val-OMe 3 adopt extended apolar, sheet like structures. The tetrapeptide Boc-gamma(4)(R)Val](4)-OMe 4 adopts an extended conformation, in contrast to the folded C-14 helical structure determined previously for Boc-gamma(4)(R)Leu](4)-OMe. The hybrid alpha gamma sequence Boc-Ala-gamma(4)(R)Leu](2)-OMe 5 adopts an S-shaped structure devoid of intramolecular hydrogen bonds, with both alpha residues adopting local helical conformations. In sharp contrast, the tetrapeptides Boc-Aib-gamma(4)(S)Leu](2)-OMe 6 and Boc-Leu-gamma(4)(R)Leu](2)-OMe 7 adopt folded structures stabilized by two successive C-12 hydrogen bonds. gamma(4)Val residues have also been incorporated into the strand segments of a crystalline octapeptide, Boc-Leu-gamma(4)(R)Val-Val-(D)Pro-Gly-Leu-gamma(4)(R)Val-Val-OMe 8. The gamma gamma delta gamma tetrapeptide containing gamma(4)Val and delta(5)Leu residues adopts an extended sheet like structure. The hydrogen bonding pattern at gamma residues corresponds to an apolar sheet, while a polar sheet is observed at the lone delta residue. The transition between folded and extended structures at gamma residues involves a change of the torsion angle from the gauche to the trans conformation about the C-beta-C-alpha bond.

Spatial modulation of the composition of a binary liquid near a repulsive wall

When a binary liquid is confined by a strongly repulsive wall, the local density is depleted near the wall and an interface similar to that between the liquid and its vapor is formed. This analogy suggests that the composition of the binary liquid near this interface should exhibit spatial modulation similar to that near a liquid-vapor interface even if the interactions of the wall with the two components of the liquid are the same. The Guggenheim adsorption relation quantifies the concentrations of two components of a binary mixture near a liquid-vapor interface and qualitatively states that the majority (minority) component enriches the interface for negative (positive) mixing energy if the surface tensions of the two components are not very different. From molecular dynamics simulations of binary mixtures with different compositions and interactions we find that the Guggenheim relation is qualitatively satisfied at wall-induced interfaces for systems with negative mixing energy at all state points considered. For systems with positive mixing energy, this relation is found to be qualitatively valid at low densities, while it is violated at state points with high density where correlations in the liquid are strong. This observation is validated by a calculation of the density profiles of the two components of the mixture using density functional theory with the Ramakrishnan-Yussouff free-energy functional. Possible reasons for the violation of the Guggenheim relation are discussed.

Functional characterization of heat-shock protein 90 from Oryza sativa and crystal structure of its N-terminal domain

Heat-shock protein 90 (Hsp90) is an ATP-dependent molecular chaperone that is essential for the normal functioning of eukaryotic cells. It plays crucial roles in cell signalling, cell-cycle control and in maintaining proteome integrity and protein homeostasis. In plants, Hsp90s are required for normal plant growth and development. Hsp90s are observed to be upregulated in response to various abiotic and biotic stresses and are also involved in immune responses in plants. Although there are several studies elucidating the physiological role of Hsp90s in plants, their molecular mechanism of action is still unclear. In this study, biochemical characterization of an Hsp90 protein from rice (Oryza sativa; OsHsp90) has been performed and the crystal structure of its N-terminal domain (OsHsp90-NTD) was determined. The binding of OsHsp90 to its substrate ATP and the inhibitor 17-AAG was studied by fluorescence spectroscopy. The protein also exhibited a weak ATPase activity. The crystal structure of OsHsp90-NTD was solved in complex with the nonhydrolyzable ATP analogue AMPPCP at 3.1 angstrom resolution. The domain was crystallized by cross-seeding with crystals of the N-terminal domain of Hsp90 from Dictyostelium discoideum, which shares 70% sequence identity with OsHsp90-NTD. This is the second reported structure of a domain of Hsp90 from a plant source.

Building upon Supramolecular Synthons: Some Aspects of Crystal Engineering

It has been 20 years since the concept of supramolecular synthon was introduced with the purpose of rational supramolecular synthesis. While this concept has been greatly successful in employing a retrosynthetic approach in crystal engineering, the past few years have seen a continuous evolution of supramolecular synthons from being a synthetic subunit to a basic unit for understanding the dynamics of crystallization. This review attempts to give a glimpse of such developments.

The crystal structure of a lectin from Butea monosperma: Insight into its glycosylation and binding of ligands

Crystal structure of a lectin purified from Butea monosperma seeds was determined by Molecular Replacement method. Its primary structure was determined by Tandem Mass Spectroscopy and electron density maps from X-ray diffraction data. Its quaternary structure was tetrameric, formed of two monomers, alpha and beta, beta appearing as truncated alpha. The occurrence of two tetramers in the asymmetric unit of the crystal might be a consequence of asymmetric contacts due to difference in glycosylation and variable loops structures, to form an `octamer-structure'. The crystal structure showed binding pockets for gamma Abu, having a proposed role in plant defense, at the interface of canonical dimer-partners. Hemagglutination studies, enzyme kinetics, isothermal titration calorimetry and molecular dynamics showed that the lectin is specific to N-acetyl D-galactosamine, galactose and lactose in decreasing order, and alpha-amylase inhibitor. (C) 2014 Elsevier B.V. All rights reserved.

Variation of Electrical Resistivity with High Pressure in Ge-Te-Sn Glasses: A Composition Dependent Study

The variation of normalized electrical resistivity in the system of glasses Ge15Te85-xSnx with (1 <= x <= 5) has been studied as a function of high pressure for pressures up to 9.5 GPa. It is found that with the increase in pressure, the resistivity decreases initially and shows an abrupt fall at a particular pressure, indicating the phase transition from semiconductor to near metallic at these pressures, which lie in the range 1.5-2.5 GPa, and then continues being metallic up to 9.5 GPa. This transition pressure is seen to decrease with the increase in the percentage content of tin due to increasing metallicity of tin. The semiconductor to near metallic transition is exactly reversible and may have its origin in a reduction of the band gap due to high pressure.

Crystal landscape in the orcinol:4,4 `-bipyridine system: synthon modularity, polymorphism and transferability of multipole charge density parameters

Polymorphism in the orcinol: 4,4'-bipyridine cocrystal system is analyzed in terms of a robust convergent modular phenol...pyridine supramolecular synthon. Employing the Synthon Based Fragments Approach (SBFA) to transfer the multipole charge density parameters, it is demonstrated that the crystal landscape can be quantified in terms of intermolecular interaction energies in the five crystal forms so far isolated in this complex system. There are five crystal forms. The first has an open, divergent O-H...N based structure with alternating orcinol and bipyridine molecules. The other four polymorphs have different three-dimensional packing but all of them are similar at an interaction level, and are based on a modular O-H...N mediated supramolecular synthon that consists of two orcinol and two bipyridine molecules in a closed, convergent structure. The SBFA method, which depends on the modularity of synthons, provides good agreement between experiment and theory because it takes into account the supramolecular contribution to charge density. The existence of five crystal forms in this system shows that polymorphism in cocrystals need not be considered to be an unusual phenomenon. Studies of the crystal landscape could lead to an understanding of the kinetic pathways that control the crystallization processes, in other words the valleys in the landscape. These pathways are traditionally not considered in exercises pertaining to computational crystal structure prediction, which rather monitors the thermodynamics of the various stable forms in the system, in other words the peaks in the landscape.

Halogen bonds in some dihalogenated phenols: applications to crystal engineering

3,4-Dichlorophenol (1) crystallizes in the tetragonal space group I4(1)/a with a short axis of 3.7926 (9) angstrom. The structure is unique in that both type I and type II Cl.....Cl interactions are present, these contact types being distinguished by the angle ranges of the respective C-Cl....Cl angles. The present study shows that these two types of contacts are utterly different. The crystal structures of 4-bromo-3-chlorophenol (2) and 3-bromo-4-chlorophenol (3) have been determined. The crystal structure of (2) is isomorphous to that of (1) with the Br atom in the 4-position participating in a type II interaction. However, the monoclinic P2(1)/c packing of compound (3) is different; while the structure still has O-H....O hydrogen bonds, the tetramer O-H.....O synthon seen in (1) and (2) is not seen. Rather than a type I Br....Br interaction which would have been mandated if (3) were isomorphous to (1) and (2), Br forms a Br....O contact wherein its electrophilic character is clearly evident. Crystal structures of the related compounds 4-chloro-3-iodophenol (4) and 3,5-dibromophenol (5) were also determined. A computational survey of the structural landscape was undertaken for (1), (2) and (3), using a crystal structure prediction protocol in space groups P2(1)/c and I4(1)/a with the COMPASS26 force field. While both tetragonal and monoclinic structures are energetically reasonable for all compounds, the fact that (3) takes the latter structure indicates that Br prefers type II over type I contacts. In order to differentiate further between type I and type II halogen contacts, which being chemically distinct are expected to have different distance fall-off properties, a variable-temperature crystallography study was performed on compounds (1), (2) and (4). Length variations with temperature are greater for type II contacts compared with type I. The type II Br....Br interaction in (2) is stronger than the corresponding type II Cl....Cl interaction in (1), leading to elastic bending of the former upon application of mechanical stress, which contrasts with the plastic deformation of (1). The observation of elastic deformation in (2) is noteworthy; in that it finds an explanation based on the strengths of the respective halogen bonds, it could also be taken as a good starting model for future property design. Cl/Br isostructurality is studied with the Cambridge Structural Database and it is indicated that this isostructurality is based on shape and size similarity of Cl and Br, rather than arising from any chemical resemblance.

Electric field induced short range to long range structural ordering and its influence on the Eu+3 photoluminescence in the lead-free ferroelectric Na1/2Bi1/2TiO3

Eu+3 was incorporated into the lattice of a lead-free ferroelectric Na1/2Bi1/2TiO3 (NBT) as per the nominal formula Na0.5Bi0.5-xEuxTiO3. This system was investigated with regard to the Eu+3 photoluminescence (PL) and structural behaviour as a function of composition and electric field. Electric field was found to irreversibly change the features in the PL spectra and also in the x-ray diffraction patterns below the critical composition x = 0.025. Detailed analysis revealed that below the critical composition, electric field irreversibly suppresses the structural heterogeneity inherent of the host matrix NBT and brings about a long range ferroelectric state with rhombohedral (R3c) distortion. It is shown that the structural disorder on the nano-scale opens a new channel for radiative transition which manifests as a new emission line branching off from the main D-5(0)-> F-7(0) line along with a concomitant change in the relative intensity of the other crystal field induced Stark lines with different J values. The study suggests that Eu+3 luminescence can be used to probe the relative degree of field induced structural ordering in relaxor ferroelectrics and also in high performance piezoelectric alloys where electric field couples very strongly with the lattice and structural degrees of freedom. (C) 2015 AIP Publishing LLC.

Measurement of Large Dipolar Couplings of a Liquid Crystal with Terminal Phenyl Rings and Estimation of the Order Parameters

NMR spectroscopy is a powerful means of studying liquid-crystalline systems at atomic resolutions. Of the many parameters that can provide information on the dynamics and order of the systems, H-1-C-13 dipolar couplings are an important means of obtaining such information. Depending on the details of the molecular structure and the magnitude of the order parameters, the dipolar couplings can vary over a wide range of values. Thus the method employed to estimate the dipolar couplings should be capable of estimating both large and small dipolar couplings at the same time. For this purpose, we consider here a two-dimensional NMR experiment that works similar to the insensitive nuclei enhanced by polarization transfer (INEPT) experiment in solution. With the incorporation of a modification proposed earlier for experiments with low radio frequency power, the scheme is observed to enable a wide range of dipolar couplings to be estimated at the same time. We utilized this approach to obtain dipolar couplings in a liquid crystal with phenyl rings attached to either end of the molecule, and estimated its local order parameters.

Composition dependent multiple structural transformations of myoglobin in aqueous ethanol solution: A combined experimental and theoretical study

Experimental studies (circular dichroism and ultra-violet (UV) absorption spectra) and large scale atomistic molecular dynamics simulations (accompanied by order parameter analyses) are combined to establish a number of remarkable (and unforeseen) structural transformations of protein myoglobin in aqueous ethanol mixture at various ethanol concentrations. The following results are particularly striking. (1) Two well-defined structural regimes, one at x(EtOH) similar to 0.05 and the other at x(EtOH) similar to 0.25, characterized by formation of distinct partially folded conformations and separated by a unique partially unfolded intermediate state at x(EtOH) similar to 0.15, are identified. (2) Existence of non-monotonic composition dependence of (i) radius of gyration, (ii) long range contact order, (iii) residue specific solvent accessible surface area of tryptophan, and (iv) circular dichroism spectra and UV-absorption peaks are observed. Interestingly at x(EtOH) similar to 0.15, time averaged value of the contact order parameter of the protein reaches a minimum, implying that this conformational state can be identified as a molten globule state. Multiple structural transformations well known in water-ethanol binary mixture appear to have considerably stronger effects on conformation and dynamics of the protein. We compare the present results with studies in water-dimethyl sulfoxide mixture where also distinct structural transformations are observed along with variation of co-solvent composition. (C) 2015 AIP Publishing LLC.

Dependence of ``critical cloud fraction' on aerosol composition

Recent studies, over regions influenced by biomass burning aerosol, have shown that it is possible to define a critical cloud fraction' (CCF) at which the aerosol direct radiative forcing switch from a cooling to a warming effect. Using 4 years of multi-satellite data analysis, we show that CCF varies with aerosol composition and changed from 0.28 to 0.13 from postmonsoon to winter as a result of shift from less absorbing to moderately absorbing aerosol. Our results indicate that we can estimate aerosol absorption from space using independently measured top of the atmosphere (TOA) fluxes Cloud Aerosol Lidar with Orthogonal Polarization-Moderate resolution Imaging Spectroradiometer-Clouds and the Earth's Radiant Energy System (CALIPSO-MODIS-CERES)] combined algorithms for example.

Differences in host species relationships and biogeographic influences produce contrasting patterns of prevalence, community composition and genetic structure in two genera of avian malaria parasites in southern Melanesia

1. Host-parasite interactions have the potential to influence broadscale ecological and evolutionary processes, levels of endemism, divergence patterns and distributions in host populations. Understanding the mechanisms involved requires identification of the factors that shape parasite distribution and prevalence. 2. A lack of comparative information on community-level host-parasite associations limits our understanding of the role of parasites in host population divergence processes. Avian malaria (haemosporidian) parasites in bird communities offer a tractable model system to examine the potential for pathogens to influence evolutionary processes in natural host populations. 3. Using cytochrome b variation, we characterized phylogenetic diversity and prevalence of two genera of avian haemosporidian parasites, Plasmodium and Haemoproteus, and analysed biogeographic patterns of lineages across islands and avian hosts, in southern Melanesian bird communities to identify factors that explain patterns of infection. 4. Plasmodium spp. displayed isolation-by-distance effects, a significant amount of genetic variation distributed among islands but insignificant amounts among host species and families, and strong local island effects with respect to prevalence. Haemoproteus spp. did not display isolation-by-distance patterns, showed marked structuring of genetic variation among avian host species and families, and significant host species prevalence patterns. 5. These differences suggest that Plasmodium spp. infection patterns were shaped by geography and the abiotic environment, whereas Haemoproteus spp. infection patterns were shaped predominantly by host associations. Heterogeneity in the complement and prevalence of parasite lineages infecting local bird communities likely exposes host species to a mosaic of spatially divergent disease selection pressures across their naturally fragmented distributions in southern Melanesia. Host associations for Haemoproteus spp. indicate a capacity for the formation of locally co-adapted host-parasite relationships, a feature that may limit intraspecific gene flow or range expansions of closely related host species.