Zinc oxide based photocatalysis: tailoring surface-bulk structure and related interfacial charge carrier dynamics for better environmental applications

As an alternative to the gold standard TiO2 photocatalyst, the use of zinc oxide (ZnO) as a robust candidate for wastewater treatment is widespread due to its similarity in charge carrier dynamics upon bandgap excitation and the generation of reactive oxygen species in aqueous suspensions with TiO2. However, the large bandgap of ZnO, the massive charge carrier recombination, and the photoinduced corrosion-dissolution at extreme pH conditions, together with the formation of inert Zn(OH)(2) during photocatalytic reactions act as barriers for its extensive applicability. To this end, research has been intensified to improve the performance of ZnO by tailoring its surface-bulk structure and by altering its photogenerated charge transfer pathways with an intention to inhibit the surface-bulk charge carrier recombination. For the first time, the several strategies, such as tailoring the intrinsic defects, surface modification with organic compounds, doping with foreign ions, noble metal deposition, heterostructuring with other semiconductors and modification with carbon nanostructures, which have been successfully employed to improve the photoactivity and stability of ZnO are critically reviewed. Such modifications enhance the charge separation and facilitate the generation of reactive oxygenated free radicals, and also the interaction with the pollutant molecules. The synthetic route to obtain hierarchical nanostructured morphologies and study their impact on the photocatalytic performance is explained by considering the morphological influence and the defect-rich chemistry of ZnO. Finally, the crystal facet engineering of polar and non-polar facets and their relevance in photocatalysis is outlined. It is with this intention that the present review directs the further design, tailoring and tuning of the physico-chemical and optoelectronic properties of ZnO for better applications, ranging from photocatalysis to photovoltaics.

Chemical specificity and conformational flexibility in proteinase-inhibitor interaction: Scaffolds for promiscuous binding

One of the most important roles of proteins in cellular milieu is recognition of other biomolecules including other proteins. Protein protein complexes are involved in many essential cellular processes. Interfaces of protein protein complexes are traditionally known to be conserved in evolution and less flexible than other solvent interacting tertiary structural surface. But many examples are emerging where these features do not hold good. An understanding of inter-play between flexibility and sequence conservation is emerging, providing a fresh dimension to the paradigm of sequence structure function relationship. The functional manifestation of the inter-relation between sequence conservation and flexibility of interface is exemplified in this review using proteinase inhibitor protein complexes. (C) 2014 Elsevier Ltd. All rights reserved.

Why is the influence of soil macrofauna on soil structure only considered by soil ecologists?

These last twenty years have seen the development of an abundant literature on the influence of soil macrofauna on soil structure. Amongst these organisms, earthworms, termites and ants are considered to play a key role in regulating the physical, chemical and microbiological properties of soils. Due to these influential impacts, soil ecologists consider these soil macro-invertebrates as `soil engineers' and their diversity and abundance are nowadays considered as relevant bioindicators of soil quality by many scientists and policy makers. Despite this abundant literature, the soil engineering concept remains a `preach to the choir' and bioturbation only perceived as important for soil ecologists. We discussed in this article the main mechanisms by which soil engineers impact soil structure and proposed to classify soil engineers with respect to their capacity to produce biostructures and modify them. We underlined the lack of studies considering biostructure dynamics and presented recent techniques in this purpose. We discussed why soil engineering concept is mainly considered by soil ecologists and call for a better collaboration between soil ecologists and soil physicists. Finally, we summarized main challenges and questions that need to be answered to integrate soil engineers activities in soil structure studies. (C) 2014 Elsevier B.V. All rights reserved.

Exploring the Crystal Structure Landscape with a Heterosynthon Module: Fluorobenzoic Acid:1,2-Bis(4-pyridyl)ethylene 2:1 Cocrystals

The crystal structure landscape of the 2:1 benzoic acid:dipyridylethylene cocrystal (BA:DPE-I) is explored experimentally with fluoro-substituted benzoic acids and extended with studies employing the Cambridge Structural Database (CSD). The interpretation of the cocrystal landscape is facilitated by considering the kinetically favored and robust acidpyridine heterosynthon as a modular unit. Information based on high-throughput crystallography shows that polymorphs and pseudopolymorphs may belong to the same landscape but arise from different crystallization pathways because of complex and different kinetic features, and secondary synthon preferences. Using the CSD as a guide, the coformer was changed from 1,2-bis(4-pyridyl)ethylene (DPE-I) to 1,2-bis(4-pyridyl)ethane (DPE-II) and this provides an extended interpretation of the BA:DPE-I cocrystal landscape, also highlighting the complexity of the kineticthermodynamic dichotomy during the molecule-to-crystal progression.

Metal-organic chemical vapor-deposited cobalt oxide films as negative electrodes for thin film Li-ion battery

In this study, thin films of cobalt oxide (Co3O4) have been grown by the metal-organic chemical vapor deposition (MOCVD) technique on stainless steel substrate at two preferred temperatures (450 degrees C and 500 degrees C), using cobalt acetylacetonate dihydrate as precursor. Spherical as well as columnar microstructures of Co3O4 have been observed under controlled growth conditions. Further investigations reveal these films are phase-pure, well crystallized and carbon-free. High-resolution TEM analysis confirms that each columnar structure is a continuous stack of minute crystals. Comparative study between these Co3O4 films grown at 450 degrees C and 500 degrees C has been carried out for their application as negative electrodes in Li-ion batteries. Our method of electrode fabrication leads to a coating of active material directly on current collector without any use of external additives. A high specific capacity of 1168 micro Ah cm(-2) mu m(-1) has been measured reproducibly for the film deposited at 500 degrees C with columnar morphology. Further, high rate capability is observed when cycled at different current densities. The Co3O4 electrode with columnar structure has a specific capacity 38% higher than the electrode with spherical microstructure (grown at 450 degrees C). Impedance measurements on the Co3O4 electrode grown at 500 degrees C also carried out to study the kinetics of the electrode process. (C) 2014 Published by Elsevier B.V.

Antimicrobial Peptides with Potential for Biofilm Eradication: Synthesis and Structure Activity Relationship Studies of Battacin Peptides

We report on the first chemical syntheses and structureactivity analyses of the cyclic lipopeptide battacin which revealed that conjugation of a shorter fatty acid, 4-methyl-hexanoic acid, and linearization of the peptide sequence improves antibacterial activity and reduces hemolysis of mouse blood cells. This surprising finding of higher potency in linear lipopeptides than their cyclic counterparts is economically beneficial. This novel lipopeptide was membrane lytic and exhibited antibiofilm activity against Pseudomonas aeruginosa, Staphylococcus aureus, and, for the first time, Pseudomonas syringe pv. actinidiae. The peptide was unstructured in aqueous buffer and dimyristoylphosphatidylcholine-polymerized diacetylene vesicles, with 12% helicity induced in 50% v/v of trifluoroethanol. Our results indicate that a well-defined secondary structure is not essential for the observed antibacterial activity of this novel lipopeptide. A truncated pentapeptide conjugated to 4-methyl hexanoic acid, having similar potency against Gram negative and Gram positive pathogens was identified through alanine scanning.

Electronic Structure of CH3NH3PbX3 Perovskites: Dependence on the Halide Moiety

A combination of measurements using photoelectron spectroscopy and calculations using density functional theory (DFT) was applied to compare the detailed electronic structure of the organolead halide perovskites CH3NH3PbI3 and CH3NH3PbBr3. These perovskite materials are used to absorb light in mesoscopic and planar heterojunction solar cells. The Pb 4f core level is investigated to get insight into the chemistry of the two materials. Valence level measurments are also included showing a shift of the valence band edges where there is a higher binding energy of the edge for the CH3NH3PbBr3 perovskite. These changes are supported by the theoretical calculations which indicate that the differences in electronic structure are mainly caused by the nature of the halide ion rather than structural differences. The combination of photoelectron spectroscopy measurements and electronic structure calculations is essential to disentangle how the valence band edge in organolead halide perovskites is governed by the intrinsic difference in energy levels of the halide ions from the influence of chemical bonding.

Structural, thermal and quantum chemical studies of p-coumaric and caffeic acids

Two hydroxycinnamic acids viz., p-coumaric, and caffeic acids have been extracted and purified from Parthenium hysterophorus, subsequently characterized by elemental analysis, FT-IR, NMR, single crystal X-ray crystallography. The optimized structures of these acids were calculated in terms of density functional theory by Gaussian 09. The validation of experimental and theoretically obtained data for structural parameters such as bond lengths and bond angles has have been carried out to analyze the statistical significance by curve fitting analysis and the values of correlation coefficient found to be 0.985, 0.992, and 0.984, 0.975 in p-coumaric, and caffeic acids, respectively. The calculated HOMO and LUMO energies show the eventual charge transfer interaction within the molecule. Thermal studies were also carried out by thermogravimetry (TG), differential thermogravimetric analysis (DTA), and derivative thermogravimetry (DTG). (C) 2014 Elsevier B.V. All rights reserved.

Synthesis, X-ray structure and in vitro cytotoxicity studies of Cu(I/II) complexes of thiosemicarbazone: special emphasis on their interactions with DNA

4-(p-X-phenyl)thiosemicarbazone of napthaldehyde {where X = Cl (HL1) and X = Br (HL2)}, thiosemicarbazone of quinoline-2-carbaldehyde (HL3) and 4-(p-fluorophenyl) thiosemicarbazone of salicylaldehyde (H2L4) and their copper(I) {Cu(HL1)(PPh3)(2)Br]center dot CH3CN (1) and Cu(HL2)(PPh3)(2)Cl]center dot DMSO (2)} and copper(II) {((Cu2L2Cl)-Cl-3)(2)(mu-Cl)(2)]center dot 2H(2)O (3) and Cu(L-4)(Py)] (4)} complexes are reported herein. The synthesized ligands and their copper complexes were successfully characterized by elemental analysis, cyclic voltammetry, NMR, ESI-MS, IR and UV-Vis spectroscopy. Molecular structures of all the Cu(I) and Cu(II) complexes have been determined by X-ray crystallography. All the complexes (1-4) were tested for their ability to exhibit DNA-binding and - cleavage activity. The complexes effectively interact with CT-DNA possibly by groove binding mode, with binding constants ranging from 10(4) to 10(5) M-1. Among the complexes, 3 shows the highest chemical (60%) as well as photo-induced (80%) DNA cleavage activity against pUC19 DNA. Finally, the in vitro antiproliferative activity of all the complexes was assayed against the HeLa cell line. Some of the complexes have proved to be as active as the clinical referred drugs, and the greater potency of 3 may be correlated with its aqueous solubility and the presence of the quinonoidal group in the thiosemicarbazone ligand coordinated to the metal.

Dynamics of the chemical bond: inter- and intra-molecular hydrogen bond

In this discussion, we show that a static definition of a `bond' is not viable by looking at a few examples for both inter-and intra-molecular hydrogen bonding. This follows from our earlier work (Goswami and Arunan, Phys. Chem. Chem. Phys. 2009, 11, 8974) which showed a practical way to differentiate `hydrogen bonding' from `van der Waals interaction'. We report results from ab initio and atoms in molecules theoretical calculations for a series of Rg center dot center dot center dot HX complexes (Rg = He/Ne/Ar and X = F/Cl/Br) and ethane-1,2-diol. Results for the Rg center dot center dot center dot HX/DX complexes show that Rg center dot center dot center dot DX could have a `deuterium bond' even when Rg center dot center dot center dot HX is not `hydrogen bonded', according to the practical criterion given by Goswami and Arunan. Results for ethane-1,2-diol show that an `intra-molecular hydrogen bond' can appear during a normal mode vibration which is dominated by the O center dot center dot center dot O stretching, though a `bond' is not found in the equilibrium structure. This dynamical `bond' formation may nevertheless be important in ensuring the continuity of electron density across a molecule. In the former case, a vibration `breaks' an existing bond and in the later case, a vibration leads to `bond' formation. In both cases, the molecule/complex stays bound irrespective of what happens to this `hydrogen bond'. Both these cases push the borders on the recent IUPAC recommendation on hydrogen bonding (Arunan et al. Pure. Appl. Chem. 2011, 83 1637) and justify the inclusive nature of the definition.

A Disulfide Stabilized beta-Sandwich Defines the Structure of a New Cysteine Framework M-Superfamily Conotoxin

The structure of a new cysteine framework (-C-CC-C-C-C) ``M''-superfamily conotoxin, Mo3964, shows it to have a beta-sandwich structure that is stabilized by inter-sheet cross disulfide bonds. Mo3964 decreases outward K+ currents in rat dorsal root ganglion neurons and increases the reversal potential of the Na(V)1.2 channels. The structure of Mo3964 (PDB ID: 2MW7) is constructed from the disulfide connectivity pattern, i.e., 1-3, 2-5, and 4-6, that is hitherto undescribed for the ``M''-superfamily conotoxins. The tertiary structural fold has not been described for any of the known conus peptides. NOE (549), dihedral angle (84), and hydrogen bond (28) restraints, obtained by measurement of (h3)J(NC') scalar couplings, were used as input for structure calculation. The ensemble of structures showed a backbone root mean square deviation of 0.68 +/- 0.18 angstrom, with 87% and 13% of the backbone dihedral (phi, psi) angles lying in the most favored and additional allowed regions of the Ramachandran map. The conotoxin Mo3964 represents a new bioactive peptide fold that is stabilized by disulfide bonds and adds to the existing repertoire of scaffolds that can be used to design stable bioactive peptide molecules.

Suspensions of polymer-grafted nanoparticles with added polymers-Structure and effective pair-interactions

We present the results of combined experimental and theoretical (molecular dynamics simulations and integral equation theory) studies of the structure and effective interactions of suspensions of polymer grafted nanoparticles (PGNPs) in the presence of linear polymers. Due to the absence of systematic experimental and theoretical studies of PGNPs, it is widely believed that the structure and effective interactions in such binary mixtures would be very similar to those of an analogous soft colloidal material-star polymers. In our study, polystyrene-grafted gold nanoparticles with functionality f = 70 were mixed with linear polystyrene (PS) of two different molecular weights for obtaining two PGNP: PS size ratios, xi = 0.14 and 2.76 (where, xi = M-g/M-m, M-g and M-m being the molecular weights of grafting and matrix polymers, respectively). The experimental structure factor of PGNPs could be modeled with an effective potential (Model-X), which has been found to be widely applicable for star polymers. Similarly, the structure factor of the blends with xi = 0.14 could be modeled reasonably well, while the structure of blends with xi = 2.76 could not be captured, especially for high density of added polymers. A model (Model-Y) for effective interactions between PGNPs in a melt of matrix polymers also failed to provide good agreement with the experimental data for samples with xi = 2.76 and high density of added polymers. We tentatively attribute this anomaly in modeling the structure factor of blends with xi = 2.76 to the questionable assumption of Model-X in describing the added polymers as star polymers with functionality 2, which gets manifested in both polymer-polymer and polymer-PGNP interactions especially at higher fractions of added polymers. The failure of Model-Y may be due to the neglect of possible many-body interactions among PGNPs mediated by matrix polymers when the fraction of added polymers is high. These observations point to the need for a new framework to understand not only the structural behavior of PGNPs but also possibly their dynamics and thermo-mechanical properties as well. (C) 2015 AIP Publishing LLC.

The Structure of the Holo-Acyl Carrier Protein of Leishmania major Displays a Remarkably Different Phosphopantetheinyl Transferase Binding Interface

The genome of Leishmania major encodes a type II fatty acid biosynthesis pathway for which no structural or biochemical information exists. Here, for the first time, we have characterized the central player of the pathway, the acyl carrier protein (LmACP), using nuclear magnetic resonance (NMR). Structurally, the LmACP molecule is similar to other type II ACPs, comprising a four-helix bundle, enclosing a hydrophobic core. Dissimilarities in sequence, however, exist in helix II (recognition helix) of the protein. The enzymatic conversion of apo-LmACP into the holo form using type I (Escherichia coli AcpS) and type II (Sfp type) phosphopantetheinyl transferases (PPTs) is relatively slow. Mutagenesis studies underscore the importance of the residues present at the protein protein interaction interface of LmACP in modulating the activity of PPTs. Interestingly, the cognate PPT for this ACP, the L. major 4'-phosphopantetheinyl transferase (LmPPT), does not show any enzymatic activity toward it, though it readily converts other type I and type II ACPs into their holo forms. NMR chemical shift perturbation studies suggest a moderately tight complex between LmACP and its cognate PPT, suggesting inhibition. We surmise that the unique surface of LmACP might have evolved to complement its cognate enzyme (LmPPT), possibly for the purpose of regulation.

Electronic structure origin of conductivity and oxygen reduction activity changes in low-level Cr-substituted (La, Sr)MnO3

The electronic structure of the (La0.8Sr0.2)(0.98)Mn1-xCrxO3 model series (x = 0, 0.05, or 0.1) was measured using soft X-ray synchrotron radiation at room and elevated temperature. O K-edge near-edge X-ray absorption fine structure (NEXAFS) spectra showed that low-level chromium substitution of (La, Sr)MnO3 resulted in lowered hybridisation between O 2p orbitals and M 3d and M 4sp valance orbitals. Mn L-3-edge resonant photoemission spectroscopy measurements indicated lowered Mn 3d-O 2p hybridisation with chromium substitution. Deconvolution of O K-edge NEXAFS spectra took into account the effects of exchange and crystal field splitting and included a novel approach whereby the pre-peak region was described using the nominally filled t(2g) up arrow state. 10% chromium substitution resulted in a 0.17 eV lowering in the energy of the t(2g) up arrow state, which appears to provide an explanation for the 0.15 eV rise in activation energy for the oxygen reduction reaction, while decreased overlap between hybrid O 2p-Mn 3d states was in qualitative agreement with lowered electronic conductivity. An orbital-level understanding of the thermodynamically predicted solid oxide fuel cell cathode poisoning mechanism involving low-level chromium substitution on the B-site of (La, Sr)MnO3 is presented. (C) 2015 AIP Publishing LLC.

Molecular Dynamics Study of the Structure, Flexibility, and Hydrophilicity of PETIM Dendrimers: A Comparison with PAMAM Dendrimers

A new class of dendrimers, the poly(propyl ether imine) (PETIM) dendrimer, has been shown to be a novel hyperbranched polymer having potential applications as a drug delivery vehicle. Structure and dynamics of the amine terminated PETIM dendrimer and their changes with respect to the dendrimer generation are poorly understood. Since most drugs are hydrophobic in nature, the extent of hydrophobicity of the dendrimer core is related to its drug encapsulation and retention efficacy. In this study, we carry out fully atomistic molecular dynamics (MD) simulations to characterize the structure of PETIM (G2-G6) dendrimers in salt solution as a function of dendrimer generation at different protonation levels. Structural properties such as radius of gyration (R-g), radial density distribution, aspect ratio, and asphericity are calculated. In order to assess the hydrophilicity of the dendrimer, we compute the number of bound water molecules in the interior of dendrirner as well as the number of dendrimer-water hydrogen bonds. We conclude that PETIM dendrimers have relatively greater hydrophobicity and flexibility when compared with their extensively investigated PAMAM counterparts. Hence PETIM dendrimers are expected to have stronger interactions with lipid membranes as well as improved drug encapsulation and retention properties when compared with PAMAM dendrimers. We compute the root-mean-square fluctuation of dendrimers as well as their entropy to quantify the flexibility of the dendrimer. Finally we note that structural and solvation properties computed using force field parameters derived based on the CHARMM general purpose force field were in good quantitative agreement with those obtained using the generalized Amber force field (GAFF).