Study of structures, energies and vibrational frequencies of (O-2)(n)(+) (n=2-5) clusters by GGA and meta-GGA density functional methods

Using Generalized Gradient Approximation (GGA) and meta-GGA density functional methods, structures, binding energies and harmonic vibrational frequencies for the clusters O-4(+), O-6(+), O-8(+) and O-10(+) have been calculated. The stable structures of O-4(+), O-6(+), O-8(+) and O-10(+) have point groups D-2h, D-3h, D-4h, and D-5h optimized on the quartet, sextet, octet and dectet potential energy surfaces, respectively. Rectangular (D-2h) O-4(+) has been found to be more stable compared to trans-planar (C-2h) on the quartet potential energy surface. Cyclic structure (D-3h) of CA cluster ion has been calculated to be more stable than other structures. Binding energy (B.E.) of the cyclic O-6(+) is in good agreement with experimental measurement. The zero-point corrected B.E. of O-8(+) with D4h symmetry on the octet potential energy surface and zero-point corrected B.E. of O-10(+) with D-5h symmetry on the dectet potential energy surface are also in good agreement with experimental values. The B.E. value for O-4(+) is close to the experimental value when single point energy is calculated by Brueckner coupled-cluster method, BD(T). (C) 2014 Elsevier B.V. All rights reserved.

CHARACTERIZATION AND MICROHARDNESS OF ELECTRODEPOSITED Ni-W COATINGS OBTAINED FROM GLUCONATE BATH

Ni-W alloy coatings are electrodeposited with direct and pulse current using gluconate bath at pH5. Effects of direct current (DC) and pulse current (PC) on structural characteristics of the coatings have been investigated by energy dispersive X-ray spectroscopy (EDXS), X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), atomic force microscopy (AFM), differential scanning calorimetry (DSC) and X-ray photoelectron spectroscopy (XPS). EDXS shows that W contents are 13.3 and 12.6 at.% in DC and PC (10:40) Ni-W coatings, respectively. FESEM analysis exhibits the homogeneous coarse nodular morphology in DC plated deposits. DSC studies reveal that Ni-W coatings are thermally stable up to 400 degrees C. XPS studies demonstrate that DC plated coating has significant amount of Ni and W in elemental form along with their respective oxidized species. In contrast, mainly oxidized metals are present in the as-deposited coatings prepared with PC plating. The microhardness of pulse current (100:400) deposited Ni-W coating is about 750HK that is much higher than DC plated coating (635 HK). Heat treatment of the deposits carried out at different temperatures show a significant increase in microhardness which can be comparable with hard chromium coatings.

Structural and functional analysis of two universal stress proteins YdaA and YnaF from Salmonella typhimurium: possible roles in microbial stress tolerance

In many organisms ``Universal Stress Proteins'' CUSPS) are induced in response to a variety of environmental stresses. Here we report the structures of two USPs, YnaF and YdaA from Salmonella typhimurium determined at 1.8 angstrom and 2.4 angstrom resolutions, respectively. YnaF consists of a single USP domain and forms a tetrameric organization stabilized by interactions mediated through chloride ions. YdaA is a larger protein consisting of two tandem USP domains. Two protomers of YdaA associate to form a structure similar to the YnaF tetramer. YdaA showed ATPase activity and an ATP binding motif G-2X-G-9X-G(S/T/N) was found in its C-terminal domain. The residues corresponding to this motif were not conserved in YnaF although YnaF could bind ATP. However, unlike YdaA, YnaF did not hydrolyse ATP in vitro. Disruption of interactions mediated through chloride ions by selected mutations converted YnaF into an ATPase. Residues that might be important for ATP hydrolysis could be identified by comparing the active sites of native and mutant structures. Only the C-terminal domain of YdaA appears to be involved in ATP hydrolysis. The structurally similar N-terminal domain was found to bind a zinc ion near the segment equivalent to the phosphate binding loop of the C-terminal domain. Mass spectrometric analysis showed that YdaA might bind a ligand of approximate molecular weight 800 daltons. Structural comparisons suggest that the ligand, probably related to an intermediate in lipid A biosynthesis, might bind at a site close to the zinc ion. Therefore, the N-terminal domain of YdaA binds zinc and might play a role in lipid metabolism. Thus, USPs appear to perform several distinct functions such as ATP hydrolysis, altering membrane properties and chloride sensing. (C) 2015 Elsevier Inc. All rights reserved.

Quantification of the Particle Size and Stability of Graphene Oxide in a Variety of Solvents

The exceptional solution processing potential of graphene oxide (GO) is always one of its main advantages over graphene in terms of its industrial relevance in coatings, electronics, and energy storage. However, the presence of a variety of functional groups on the basal plane and edges of GO makes understanding suspension behavior in aqueous and organic solvents, a major challenge. Acoustic spectroscopy can also measure zeta potential to provide unique insight into flocculating, meta-stable, and stable suspensions of GO in deionized water and a variety of organic solvents (including ethanol, ethylene glycol, and mineral oil). As expected, a match between solvent polarity and the polar functional groups on the GO surface favors stable colloidal suspensions accompanied by a smaller aggregate size tending toward disperse individual flakes of GO. This work is significant since it describes the characteristics of GO in solution and its ability to act as a precursor for graphene-based materials.

Electrochemical behavior of Zn-graphene composite coatings

A Zn-graphene composite coating was electrodeposited on mild steel. The graphene was synthesized by electrochemical exfoliation of graphite. Electron microscopy, energy-dispersive X-ray spectroscopy and X-ray diffraction techniques were used to characterize the coatings. Compared to a pure Zn coating, the Zn-graphene coating exhibited reduced grain size, reduced surface defects, hillock structures over the coating surface and an altered texture. The corrosion behavior of the coatings was examined by Tafel polarization and electrochemical impedance spectroscopic methods. A significant improvement in the corrosion resistance in terms of reduction in corrosion current and corrosion rate and increase in polarization resistance was noted in the case of the Zn coating containing graphene.

Metallophosphoesterases: structural fidelity with functional promiscuity

Calcineurin-like metallophosphoesterases (MPEs) form a large superfamily of binuclear metal-ion-centre-containing enzymes that hydrolyse phosphomono-, phosphodi-or phosphotri-esters in a metal-dependent manner. The MPE domain is found in Mre11/SbcD DNA-repair enzymes, mammalian phosphoprotein phosphatases, acid sphingomyelinases, purple acid phosphatases, nucleotidases and bacterial cyclic nucleotide phosphodiesterases. Despite this functional diversity, MPEs show a remarkably similar structural fold and active-site architecture. In the present review, we summarize the available structural, biochemical and functional information on these proteins. We also describe how diversification and specialization of the core MPE fold in various MPEs is achieved by amino acid substitution in their active sites, metal ions and regulatory effects of accessory domains. Finally, we discuss emerging roles of these proteins as non-catalytic protein-interaction scaffolds. Thus we view the MPE superfamily as a set of proteins with a highly conserved structural core that allows embellishment to result in dramatic and niche-specific diversification of function.

Synthesis and electrochemical behaviour of NiFeCr nanoparticle coatings

NiFeCr nanoparticles with a Ni-rich composition were synthesized using a wet chemical synthesis technique. As-synthesized nanoparticles were crystalline with an average size of 6.8 +/- 2.5 nm. For electrochemical analysis, as-synthesized nanoparticles were mixed with epoxy and coated over a mild steel substrate. Electrochemical measurements exhibited a very high polarization resistance and very low corrosion current for the nanoparticle-epoxy coated sample illustrating high resistance of the NiFeCr nanoparticle-epoxy coating towards highly corrosive media.

Molecular and Functional Characterization of RecD, a Novel Member of the SF1 Family of Helicases, from Mycobacterium tuberculosis

Background: The heterotrimeric M. tuberculosis RecBCD complex, or each of its individual subunits, remains uncharacterized. Results: MtRecD exists as a homodimer in solution, catalyzes ssDNA-dependent ATP hydrolysis, unwinding of DNA replication/recombination intermediates, and interacts with RecA. Conclusion: MtRecD possesses strong 5 3- and weak 3 5-helicase activities. Significance: These findings provide insights into the mechanism underlying DSB repair and homologous recombination in mycobacteria. The annotated whole-genome sequence of Mycobacterium tuberculosis revealed the presence of a putative recD gene; however, the biochemical characteristics of its encoded protein product (MtRecD) remain largely unknown. Here, we show that MtRecD exists in solution as a stable homodimer. Protein-DNA binding assays revealed that MtRecD binds efficiently to single-stranded DNA and linear duplexes containing 5 overhangs relative to the 3 overhangs but not to blunt-ended duplex. Furthermore, MtRecD bound more robustly to a variety of Y-shaped DNA structures having 18-nucleotide overhangs but not to a similar substrate containing 5-nucleotide overhangs. MtRecD formed more salt-tolerant complexes with Y-shaped structures compared with linear duplex having 3 overhangs. The intrinsic ATPase activity of MtRecD was stimulated by single-stranded DNA. Site-specific mutagenesis of Lys-179 in motif I abolished the ATPase activity of MtRecD. Interestingly, although MtRecD-catalyzed unwinding showed a markedly higher preference for duplex substrates with 5 overhangs, it could also catalyze significant unwinding of substrates containing 3 overhangs. These results support the notion that MtRecD is a bipolar helicase with strong 5 3 and weak 3 5 unwinding activities. The extent of unwinding of Y-shaped DNA structures was approximate to 3-fold lower compared with duplexes with 5 overhangs. Notably, direct interaction between MtRecD and its cognate RecA led to inhibition of DNA strand exchange promoted by RecA. Altogether, these studies provide the first detailed characterization of MtRecD and present important insights into the type of DNA structure the enzyme is likely to act upon during the processes of DNA repair or homologous recombination.

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.

Damage mechanisms in stainless steel and chromium carbide coatings under controlled environment fretting conditions

Fretting is of a serious concern in many industrial components, specifically, in nuclear industry for the safe and reliable operation of various component and/or system. Under fretting condition small amplitude oscillations induce surface degradation in the form of surface cracks and/or surface wear. Comprehensive experimental studies have been carried out simulating different fretting regimes under ambient and vacuum (10(-9) MPa) conditions and, temperature up to 400 degrees C. Studies have been carried out with stainless steel spheres on stainless steel flats, and stainless steel spheres against chromium carbide, with 25% nickel chrome binder coatings. Mechanical responses are correlated with the damage observed. It has been observed that adhesion plays a vital role in material degradation process, and its effectiveness depends on mechanical variables such as normal load, interfacial tangential displacement, characteristics of the contacting bodies and most importantly on the environment conditions. Material degradation mechanism for ductile materials involved severe plastic deformation, which results in the initiation or nucleation of cracks. Ratcheting has been observed as the governing damage mode for crack nucleation under cyclic tangential loading condition. Further, propagation of the cracks has been observed under fatigue and their orientation has been observed to be governed by the contact conditions prevailing at the contact interface. Coated surfaces show damage in the form of brittle fracture and spalling of the coatings. Existence of stick slip has been observed under high normal load and low displacement amplitude. It has also been observed that adhesion at the contact interface and instantaneous cohesive strength of the contacting bodies dictates the occurrence of material transfer. The paper discusses the mechanics and mechanisms involved in fretting damage under controlled environment conditions. (C) 2015 Elsevier B.V. All rights reserved.

Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications

17 independent crystal structures of family I uracil-DNA glycosylase from Mycobacterium tuberculosis (MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic parameters of binding in the complexes have been measured using isothermal titration calorimetry. The two-domain protein exhibits open and closed conformations, suggesting that the closure of the domain on DNA binding involves conformational selection. Segmental mobility in the enzyme molecule is confined to a 32-residue stretch which plays a major role in DNA binding. Uracil and its derivatives can bind to the protein in two possible orientations. Only one of them is possible when there is a bulky substituent at the 50 position. The crystal structures of the complexes provide a reasonable rationale for the observed thermodynamic parameters. In addition to providing fresh insights into the structure, plasticity and interactions of the protein molecule, the results of the present investigation provide a platform for structure-based inhibitor design.

Insights into the Functional Roles of N-Terminal and C-Terminal Domains of Helicobacter pylori DprA

DNA processing protein A (DprA) plays a crucial role in the process of natural transformation. This is accomplished through binding and subsequent protection of incoming foreign DNA during the process of internalization. DprA along with Single stranded DNA binding protein A (SsbA) acts as an accessory factor for RecA mediated DNA strand exchange. H. pylori DprA (HpDprA) is divided into an N-terminal domain and a C-terminal domain. In the present study, individual domains of HpDprA have been characterized for their ability to bind single stranded (ssDNA) and double stranded DNA (dsDNA). Oligomeric studies revealed that HpDprA possesses two sites for dimerization which enables HpDprA to form large and tightly packed complexes with ss and dsDNA. While the N-terminal domain was found to be sufficient for binding with ss or ds DNA, C-terminal domain has an important role in the assembly of poly-nucleoprotein complex. Using site directed mutagenesis approach, we show that a pocket comprising positively charged amino acids in the N-terminal domain has an important role in the binding of ss and dsDNA. Together, a functional cross talk between the two domains of HpDprA facilitating the binding and formation of higher order complex with DNA is discussed.

Solid-state optical absorption from optimally tuned time-dependent range-separated hybrid density functional theory

We present a framework for obtaining reliable solid-state charge and optical excitations and spectra from optimally tuned range-separated hybrid density functional theory. The approach, which is fully couched within the formal framework of generalized Kohn-Sham theory, allows for the accurate prediction of exciton binding energies. We demonstrate our approach through first principles calculations of one- and two-particle excitations in pentacene, a molecular semiconducting crystal, where our work is in excellent agreement with experiments and prior computations. We further show that with one adjustable parameter, set to produce the known band gap, this method accurately predicts band structures and optical spectra of silicon and lithium fluoride, prototypical covalent and ionic solids. Our findings indicate that for a broad range of extended bulk systems, this method may provide a computationally inexpensive alternative to many-body perturbation theory, opening the door to studies of materials of increasing size and complexity.

Morphological and functional characterisation of the burrow systems of six earthworm species (Lumbricidae)

Earthworm burrow systems are generally described based on postulated behaviours associated with the three ecological types. In this study, we used X-ray tomography to obtain 3D information on the burrowing behaviour of six very common anecic (Aporrectodea nocturna and Lumbricus terrestris) and endogeic (Aporrectodea rosea, Allolobophora chlorotica, Aporrectodea caliginosa, Aporrectodea icterica) earthworm species, introduced into repacked soil cores for 6 weeks. A simple water infiltration test, the Beerkan method, was also used to assess some functional properties of these burrow systems. Endogeic worms make larger burrow systems, which are more highly branched, less continuous and of smaller diameter, than those of anecic worms. Among the anecic species, L. terrestris burrow systems are shorter (9.2 vs 21.2 m) with a higher number (14.5 vs 23.5) of less branched burrows (12.2 vs 20.2 branches m(-1)), which are also wider (7.78 vs 5.16 mm) than those of A. nocturna. In comparison, the burrow systems made by endogeic species appeared similar to each other. However, A. rosea burrows were short and narrow, whereas A. icterica had a longer burrow system (15.7 m), more intense bioturbation intensity (refilled macropores or soil lateral compaction around them) and thus a greater number of burrows. Regarding water infiltration, anecic burrow systems were far more efficient due to open burrows linking the top and bottom of the cores. For endogeic species, we observed a linear relationship between burrow length and the water infiltration rate (R (2) = 0.49, p < 0.01). Overall, the three main characteristics significantly influencing water infiltration were burrow length, burrow number and bioturbation volume. This last characteristic highlighted the effect of burrow refilling by casts.