Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile

FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The C-13 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with experimental results. Standard thermodynamic functions have been obtained and changes in thermodynamic properties on going from monomer to tetramer have been presented. (C) 2013 Elsevier B.V. All rights reserved.

Nestmate discrimination in the social wasp Ropalidia marginata: chemical cues and chemosensory mechanism

Nestmate discrimination plays an important role in preserving the integrity of social insect colonies. It is known to occur in the primitively eusocial wasp Ropalidia marginata in which non-nestmate conspecifics are not allowed to come near a nest. However, newly eclosed females are accepted in foreign colonies, suggesting that such individuals may not express the cues that permit differentiation between nestmates and non-nestmates. As cuticular hydrocarbons (CHCs) have been implicated as chemosensory cues used in nestmate recognition in other species, we investigated, using bioassays and chemical analyses, whether CHCs can play a role in nestmate recognition in R. marginata. We found that individuals can be differentiated according to colony membership using their CHC profiles, suggesting a role of CHCs in nestmate discrimination. Non-nestmate CHCs of adult females received more aggression than nestmate CHCs, thereby showing that CHCs are used as cues for nestmate recognition. Contrarily, and as expected, CHCs of newly eclosed females were not discriminated against when presented to a foreign colony. Behavioural sequence analysis revealed the behavioural mechanism involved in sensing nestmate recognition cues. We also found that newly eclosed females had a different CHC profile from that of adult females, thereby providing an explanation for why young females are accepted in foreign colonies. (C) 2013 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Size Control and Magnetic Property Trends in Cobalt Ferrite Nanoparticles Synthesized Using an Aqueous Chemical Route

Cobalt ferrite (CoFe2O4) is an engineering material which is used for applications such as magnetic cores, magnetic switches, hyperthermia based tumor treatment, and as contrast agents for magnetic resonance imaging. Utility of ferrites nanoparticles hinges on its size, dispersibility in solutions, and synthetic control over its coercivity. In this work, we establish correlations between room temperature co-precipitation conditions, and these crucial materials parameters. Furthermore, post-synthesis annealing conditions are correlated with morphology, changes in crystal structure and magnetic properties. We disclose the synthesis and process conditions helpful in obtaining easily sinterable CoFe2O4 nanoparticles with coercive magnetic flux density (H-c) in the range 5.5-31.9 kA/m and M-s in the range 47.9-84.9 A.m(2)Kg(-1). At a grain size of similar to 54 +/- 2 nm (corresponding to 1073 K sintering temperature), multi-domain behavior sets in, which is indicated by a decrease in H-c. In addition, we observe an increase in lattice constant with respect to grain size, which is the inverse of what is expected of in ferrites. Our results suggest that oxygen deficiency plays a crucial role in explaining this inverse trend. We expect the method disclosed here to be a viable and scalable alternative to thermal decomposition based CoFe2O4 synthesis. The magnetic trends reported will aid in the optimization of functional CoFe2O4 nanoparticles

Titanium nitride thin film anode: chemical and microstructural evaluation during electrochemical studies

TIN thin films with (200) fibre texture are deposited on Cu substrate at room temperature using reactive magnetron sputtering. They exhibit a discharge capacity of 172 mu Ah cm(-2) mu m(-1) (300 mAh g(-1)) in a non-aqueous electrolyte containing a Li salt. There is a graded decrease in discharge capacity when cycled between 0.01 and 3.0 V. Electron microscopy investigations indicate significant changes in surface morphology of the cycled TiN electrodes in comparison with the as deposited TiN films. From XPS depth profile analysis, it is inferred that Li intercalated TIN films consist of lithium compounds, hydroxyl groups, titanium sub oxides and TiN. Lithium diffusivity and reactivity decrease with increase in depth and the major reaction with lithium takes place at film surface and grain boundaries. (C) 2014 Elsevier Ltd. All rights reserved.

Group behaviour in physical, chemical and biological systems

Groups exhibit properties that either are not perceived to exist, or perhaps cannot exist, at the individual level. Such `emergent' properties depend on how individuals interact, both among themselves and with their surroundings. The world of everyday objects consists of material entities. These are, ultimately, groups of elementary particles that organize themselves into atoms and molecules, occupy space, and so on. It turns out that an explanation of even the most commonplace features of this world requires relativistic quantum field theory and the fact that Planck's constant is discrete, not zero. Groups of molecules in solution, in particular polymers ('sols'), can form viscous clusters that behave like elastic solids ('gels'). Sol-gel transitions are examples of cooperative phenomena. Their occurrence is explained by modelling the statistics of inter-unit interactions: the likelihood of either state varies sharply as a critical parameter crosses a threshold value. Group behaviour among cells or organisms is often heritable and therefore can evolve. This permits an additional, typically biological, explanation for it in terms of reproductive advantage, whether of the individual or of the group. There is no general agreement on the appropriate explanatory framework for understanding group-level phenomena in biology.

Three-dimensional profiling using a still shot

A method to reliably extract object profiles even with surface discontinuities that leads to 2n pi phase jumps is proposed. The proposed method uses an amplitude-modulated Ronchi grating, which allows one to extract phase and unwrap the same with a single image. Ronchi equivalent image can be derived from modified grating image, which aids in extracting wrapped phase using Fourier transform profilometry. The amplitude of the modified grating aids in phase unwrapping. As we only need a projector that projects an amplitude-modulated grating, the proposed method allows one to extract three-dimensional profile without using full video projectors. This article also deals with noise reduction algorithms for fringe projection techniques. (C) 2014 Society of Photo-Optical Instrumentation Engineers (SPIE)

Microscopic description of the evolution of the local structure and an evaluation of the chemical pressure concept in a solid solution

Extended x-ray absorption fine-structure studies have been performed at the Zn K and Cd K edges for a series of solid solutions of wurtzite Zn1-xCdxS samples with x = 0.0, 0.1, 0.25, 0.5, 0.75, and 1.0, where the lattice parameter as a function of x evolves according to the well-known Vegard's law. In conjunction with extensive, large-scale first-principles electronic structure calculations with full geometry optimizations, these results establish that the percentage variation in the nearest-neighbor bond distances are lower by nearly an order of magnitude compared to what would be expected on the basis of lattice parameter variation, seriously undermining the chemical pressure concept. With experimental results that allow us to probe up to the third coordination shell distances, we provide a direct description of how the local structure, apparently inconsistent with the global structure, evolves very rapidly with interatomic distances to become consistent with it. We show that the basic features of this structural evolution with the composition can be visualized with nearly invariant Zn-S-4 and Cd-S-4 tetrahedral units retaining their structural integrity, while the tilts between these tetrahedral building blocks change with composition to conform to the changing lattice parameters according to the Vegard's law within a relatively short length scale. These results underline the limits of applicability of the chemical pressure concept that has been a favored tool of experimentalists to control physical properties of a large variety of condensed matter systems.

A Stochastic Chemical Dynamic Approach to Correlate Autoimmunity and Optimal Vitamin-D Range

Motivated by several recent experimental observations that vitamin-D could interact with antigen presenting cells (APCs) and T-lymphocyte cells (T-cells) to promote and to regulate different stages of immune response, we developed a coarse grained but general kinetic model in an attempt to capture the role of vitamin-D in immunomodulatory responses. Our kinetic model, developed using the ideas of chemical network theory, leads to a system of nine coupled equations that we solve both by direct and by stochastic (Gillespie) methods. Both the analyses consistently provide detail information on the dependence of immune response to the variation of critical rate parameters. We find that although vitamin-D plays a negligible role in the initial immune response, it exerts a profound influence in the long term, especially in helping the system to achieve a new, stable steady state. The study explores the role of vitamin-D in preserving an observed bistability in the phase diagram (spanned by system parameters) of immune regulation, thus allowing the response to tolerate a wide range of pathogenic stimulation which could help in resisting autoimmune diseases. We also study how vitamin-D affects the time dependent population of dendritic cells that connect between innate and adaptive immune responses. Variations in dose dependent response of anti-inflammatory and pro-inflammatory T-cell populations to vitamin-D correlate well with recent experimental results. Our kinetic model allows for an estimation of the range of optimum level of vitamin-D required for smooth functioning of the immune system and for control of both hyper-regulation and inflammation. Most importantly, the present study reveals that an overdose or toxic level of vitamin-D or any steroid analogue could give rise to too large a tolerant response, leading to an inefficacy in adaptive immune function.

Profiling of Luteal Transcriptome during Prostaglandin F2-Alpha Treatment in Buffalo Cows: Analysis of Signaling Pathways Associated with Luteolysis

In several species including the buffalo cow, prostaglandin (PG) F-2 alpha is the key molecule responsible for regression of corpus luteum (CL). Experiments were carried out to characterize gene expression changes in the CL tissue at various time points after administration of luteolytic dose of PGF(2 alpha) in buffalo cows. Circulating progesterone levels decreased within 1 h of PGF(2 alpha) treatment and evidence of apoptosis was demonstrable at 18 h post treatment. Microarray analysis indicated expression changes in several of immediate early genes and transcription factors within 3 h of treatment. Also, changes in expression of genes associated with cell to cell signaling, cytokine signaling, steroidogenesis, PG synthesis and apoptosis were observed. Analysis of various components of LH/CGR signaling in CL tissues indicated decreased LH/CGR protein expression, pCREB levels and PKA activity post PGF(2 alpha) treatment. The novel finding of this study is the down regulation of CYP19A1 gene expression accompanied by decrease in expression of E-2 receptors and circulating and intra luteal E-2 post PGF(2 alpha) treatment. Mining of microarray data revealed several differentially expressed E-2 responsive genes. Since CYP19A1 gene expression is low in the bovine CL, mining of microarray data of PGF(2 alpha)-treated macaques, the species with high luteal CYP19A1 expression, showed good correlation between differentially expressed E-2 responsive genes between both the species. Taken together, the results of this study suggest that PGF(2 alpha) interferes with luteotrophic signaling, impairs intraluteal E-2 levels and regulates various signaling pathways before the effects on structural luteolysis are manifest.

Carbon nanotubes and graphene-based chemical sensors

The chemical sensing behaviour of the carbon nano-tube and graphene-based sensors for detecting various chemical analytes is presented in this article. A focus on detection mechanisms has been provided to assess their relative potential under different environmental conditions. The performance of these two carbon allotropes is compared based on their sensitivity towards various types of electron donating and accepting molecules. Although these carbon materials still have to meet crucial challenges in fabrication and optimization, continued progress in this field may lead to a sensor with superior sensitivity for a wide range of applications.

Influence of source concentration on structural and optical properties of SnO2 nanoparticles prepared by chemical precipitation method

In present work, a systematic study has been carried out to understand the influence of source concentration on structural and optical properties of the SnO2 nanoparticles. SnO2 nanoparticles have been prepared by using chemical precipitation method at room temperature with aqueous ammonia as a stabilizing agent. X-ray diffraction analysis reveals that SnO2 nanoparticles exhibit tetragonal structure and the particle size is in range of 4.9-7.6 nm. High resolution transmission electron microscopic image shows that all the particles are nearly spherical in nature and particle size lies in range of 4.6-7 nm. Compositional analysis indicates the presence of Sn and O in samples. Blue shift has been observed in optical absorption spectra due to quantum confinement and the bandgap is in range of 4-4.16 eV. The origin of photoluminescence in SnO2 is found to be due to recombination of electrons in singly occupied oxygen vacancies with photo-excited holes in valance band.

Vegetation impact on stream chemical fluxes: Mule Hole watershed (South India)

The proportion of chemical elements passing through vegetation prior to being exported in a stream was quantified for a forested tropical watershed(Mule Hole, South India) using an extensive hydrological and geochemical monitoring at several scales. First, a solute annual mass balance was established at the scale of the soil-plant profile for assessing the contribution of canopy interaction and litter decay to the solute fluxes of soil inputs (overland flow) and soil outputs (pore water flow as seepages). Second, based on the respective contributions of overland flow and seepages to the stream flow as estimated by a hydrological lumped model, we assigned the proportion of chemical elements in the stream that transited through the vegetation at both flood event (End Member Mixing Analysis) and seasonal scales. At the scale of the 1D soil-plant profile, leaching from the canopy constituted the main source of K above the ground surface. Litter decay was the main source of Si, whereas alkalinity, Ca and Mg originated in the same proportions from both sources. The contribution of vegetation was negligible for Na. Within the soil, all elements but Na were removed from the pore water in proportions varying from 20% for Cl to 95% for K: The soil output fluxes corresponded to a residual fraction of the infiltration fluxes. The behavior of K, Cl, Ca and Mg in the soil-plant profile can be explained by internal cycling, as their soil output fluxes were similar to the atmospheric inputs. Na was released from soils as a result of Na-plagioclase weathering and accompanied by additional release of Si. Concentration of soil pore water by evapotranspiration might limit the chemical weathering in the soil. Overall, the solute K, Ca, Mg, alkalinity and Si fluxes associated with the vegetation turnover within the small experimental watershed represented 10-15 times the solute fluxes exported by the stream, of which 83-97% transited through the vegetation. One important finding is that alkalinity and Si fluxes at the outlet were not linked to the ``current weathering'' of silicates in this watershed. These results highlight the dual effect of the vegetation cover on the solute fluxes exported from the watershed: On one hand the runoff was limited by evapotranspiration and represented only 10% of the annual rainfall, while on the other hand, 80-90% of the overall solute flux exported by the stream transited through the vegetation. The approach combining geochemical monitoring and accurate knowledge of the watershed hydrological budget provided detailed understanding of several effects of vegetation on stream fluxes: (1) evapotranspiration (limiting), (2) vertical transfer through vegetation from vadose zone to ground surface (enhancing) and (3) redistribution by throughfalls and litter decay. It provides a good basis for calibrating geochemical models and more precisely assessing the role of vegetation on soil processes. (C) 2014 Elsevier Ltd. All rights reserved.

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.

Genome-wide methylation profiling identifies an essential role of reactive oxygen species in pediatric glioblastoma multiforme and validates a methylome specific for H3 histone family 3A with absence of G-CIMP/isocitrate dehydrogenase 1 mutation

Background. Pediatric glioblastoma multiforme (GBM) is rare, and there is a single study, a seminal discovery showing association of histone H3.3 and isocitrate dehydrogenase (IDH) 1 mutation with a DNA methylation signature. The present study aims to validate these findings in an independent cohort of pediatric GBM, compare it with adult GBM, and evaluate the involvement of important functionally altered pathways. Methods. Genome-wide methylation profiling of 21 pediatric GBM cases was done and compared with adult GBM data (GSE22867). We performed gene mutation analysis of IDH1 and H3 histone family 3A (H3F3A), status evaluation of glioma cytosine-phosphate-guanine island methylator phenotype (G-CIMP), and Gene Ontology analysis. Experimental evaluation of reactive oxygen species (ROS) association was also done. Results. Distinct differences were noted between methylomes of pediatric and adult GBM. Pediatric GBM was characterized by 94 hypermethylated and 1206 hypomethylated cytosine-phosphate-guanine (CpG) islands, with 3 distinct clusters, having a trend to prognostic correlation. Interestingly, none of the pediatric GBM cases showed G-CIMP/IDH1 mutation. Gene Ontology analysis identified ROS association in pediatric GBM, which was experimentally validated. H3F3A mutants (36.4%; all K27M) harbored distinct methylomes and showed enrichment of processes related to neuronal development, differentiation, and cell-fate commitment. Conclusions. Our study confirms that pediatric GBM has a distinct methylome compared with that of adults. Presence of distinct clusters and an H3F3A mutation-specific methylome indicate existence of epigenetic subgroups within pediatric GBM. Absence of IDH1/G-CIMP status further indicates that findings in adult GBM cannot be simply extrapolated to pediatric GBM and that there is a strong need for identification of separate prognostic markers. A possible role of ROS in pediatric GBM pathogenesis is demonstrated for the first time and needs further evaluation.