Structure, dynamics and thermodynamics of single-file water under confinement: effects of polarizability of water molecules

Various structural, dynamic and thermodynamic properties of water molecules confined in single-wall carbon nanotubes (CNTs) are investigated using both polarizable and non-polarizable water models. The inclusion of polarizability quantitatively affects the nature of hydrogen bonding, which governs many properties of confined water molecules. Polarizable water leads to tighter hydrogen bonding and makes the distance between neighboring water molecules shorter than that for non-polarizable water. Stronger hydrogen bonding also decreases the rotational entropy and makes the diffusion constant smaller than in TIP3P and TIP3PM water models. The reorientational dynamics of the water molecules is governed by a jump mechanism, the barrier for the jump being highest for the polarizable water model. Our results highlight the role of polarizability in governing the dynamics of confined water and demonstrate that the inclusion of polarizability is necessary to obtain agreement with the results of ab initio simulations for the distributions of waiting and jump times. The SPC/E water model is found to predict various water properties in close agreement with the results of polarizable water models with much lower computational costs.

Identifying functionally important cis-peptide containing segments in proteins and their utility in molecular function annotation

Cis-peptide embedded segments are rare in proteins but often highlight their important role in molecular function when they do occur. The high evolutionary conservation of these segments illustrates this observation almost universally, although no attempt has been made to systematically use this information for the purpose of function annotation. In the present study, we demonstrate how geometric clustering and level-specific Gene Ontology molecular-function terms (also known as annotations) can be used in a statistically significant manner to identify cis-embedded segments in a protein linked to its molecular function. The present study identifies novel cis-peptide fragments, which are subsequently used for fragment-based function annotation. Annotation recall benchmarks interpreted using the receiver-operator characteristic plot returned an area-under-curve >0.9, corroborating the utility of the annotation method. In addition, we identified cis-peptide fragments occurring in conjunction with functionally important trans-peptide fragments, providing additional insights into molecular function. We further illustrate the applicability of our method in function annotation where homology-based annotation transfer is not possible. The findings of the present study add to the repertoire of function annotation approaches and also facilitate engineering, design and allied studies around the cis-peptide neighborhood of proteins.

Layer-by-Layer Assembly of Nafion on Surlyn with Ultrahigh Water Vapor Barrier

A layer-by-layer approach was used for the fabrication of multilayer films for ultra high gas barrier applications. The ultra high gas barrier material was designed by incorporating Nafion layer in between bilayers of poly(ethylene imine) and poly(acrylic acid) on a Surlyn substrate. When the barrier film with self-assembled Nafion is exposed to the moist environment, Nafion absorbs and desorbs water molecules simultaneously, thereby reducing the ingress of moisture in to the film. In order to study the effect of Nafion, the fabricated barrier materials with and without the presence of Nafion were tested for water vapor barrier properties. The barrier films were further used for encapsulating organic photovoltaic devices and were evaluated for their potential use in barrier applications. The devices encapsulated with the films containing Nafion exhibited better performance when subjected to accelerated aging conditions. Therefore, this study demonstrates the effectiveness of self-assembled Nafion in reducing the water vapor permeability by nearly five orders of magnitude and in increasing the lifetimes of organic devices by similar to 22 times under accelerated weathering conditions.

Solution processable diketopyrrolopyrrole (DPP) cored small molecules with BODIPY end groups as novel donors for organic solar cells

Two novel triads based on a diketopyrrolopyrrole (DPP) central core and two 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) units attached by thiophene rings have been synthesised having high molar extinction coefficients. These triads were characterised and used as donor materials in small molecule, solution processable organic solar cells. Both triads were blended with PC71BM as an acceptor in different ratios by wt% and their photovoltaic properties were studied. For both the triads a modest photovoltaic performance was observed, having an efficiency of 0.65%. Moreover, in order to understand the ground and excited state properties and vertical absorption profile of DPP and BODIPY units within the triads, theoretical DFT and TDDFT calculations were performed.

Synthesis of mixed glycosyl disulfides/selenenylsulfides using benzyltriethylammonium tetrathiomolybdate as a sulfur transfer reagent

An easy and mild method has been developed for the synthesis of mixed glycosyl disulfides/selenenylsulfides from glycosyl halides and diaryl/dialkyl dichalcogenides in the presence of benzyltriethylammonium tetrathiomolybdate (BnEt3N)(2)MoS4]. The salient feature of this method is the sulfur transfer from BnEt3N](2)MoS4 to form glycosyl disulfides which with excess tetrathiomolybdate further undergo exchange reaction with other dichalcogenides in a one-pot operation. (C) 2014 Elsevier Ltd. All rights reserved.

Inhibition of ERK and proliferation in NK cell lines by soluble HLA-E released from Japanese encephalitis virus infected cells

Productive infection of human endothelial cells with Japanese encephalitis virus (JEV), a single stranded RNA virus induces shedding of sHLA-E. We show here that sHLA-E that is released upon infection with this flavivirus can inhibit IL-2 and PMA mediated ERK 1/2 phosphorylation in two NK cell lines, Nishi and NKL. Virus infected or IFN-gamma treated cell culture supernatants containing sHLA-E were found to partially inhibit IL-2 mediated induction of CD25 molecules on NKL cells. It was also found that sHLA-E could inhibit IL-2 induced H-3]-thymidine incorporation suggesting that, similar to cell surface expressed HLA-E, sHLA-E could also inhibit NK cell responses. Hence JEV-induced shedding of sHLA-E needs further investigation to better understand immune responses in JEV infections since it may have a role in viral evasion of NK cell responses. (C) 2014 Elsevier B.V. All rights reserved.

Molecules support morphology: species status of South Indian populations of the widely distributed Hanuman langur

The taxonomy of the Hanuman langur (Semnopithecus spp.), a widely distributed Asian colobine monkey, has been in a flux for a long time due to much disagreement between various classification schemes. However, results from a recent field-based morphological study were consistent with Hill's (Ceylon J Sci 21:277-305, 1939) species level classification scheme. Here we tested the validity of S. hypoleucos and S. priam, the two South Indian species recognized by Hill. To this end, one mitochondrial and four nuclear markers were sequenced from over 72 non-invasive samples of Hanuman langurs and S. johnii collected from across India. The molecular data were subjected to various tree building methods. The nuclear data was also used in a Bayesian structure analysis and to determine the genealogical sorting index of each hypothesized species. Results from nuclear data suggest that the South Indian population of Hanuman langur consists of two units that correspond to the species recognized by Hill. However in the mitochondrial tree S. johnii and S. priam were polyphyletic probably due to retention of ancestral polymorphism and/or low levels of hybridization. Implications of these results on conservation of Hanuman langurs are also discussed.

Differential Cocrystallization Behavior of Isomeric Pyridine Carboxamides toward Antitubercular Drug Pyrazinoic Acid

Pyrazinoic acid, the active form of the antitubercular pro-drug Pyrazinamide, is an amphiprotic molecule containing carboxylic acid and pyridine groups and therefore can form both salts and cocrystals with relevant partner molecules. Cocrystallization of pyrazinoic acid with isomeric pyridine carboxamide series resulted in a dimorphic mixed-ionic complex with isonicotinamide and in eutectics with nicotinamide and picolinamide, respectively. It is observed that with alteration of the carboxamide position, steric and electrostatic compatibility issues between molecules of the combination emerge and affect intermolecular interactions and supramolecular growth, thus leading to either cocrystal or eutectic for different pyrazinoic acid-pyridine carboxamide combinations. Intermolecular interaction energy calculations have been performed to understand the role of underlying energetics on the formation of cocrystal/eutectic in different combinations. On the other hand, two molecular salts with piperazine and cytosine and a gallic acid cocrystal of the drug were obtained, and their X-ray crystal structures were also determined in this work.

Effect of grain boundary engineering on the microstructure and mechanical properties of copper containing austenitic stainless steel

The present investigation deals with grain boundary engineering of a modified austenitic stainless steel to obtain a material with enhanced properties. Three types of processing that are generally in agreement with the principles of grain boundary engineering were carried out. The parameters for each of the processing routes were fine-tuned and optimized. The as-processed samples were characterized for microstructure and texture. The influence of processing on properties was estimated by evaluating the room temperature mechanical properties through micro-tensile tests. It was possible to obtain remarkably high fractions of CSL boundaries in certain samples. The results of the micro-tensile tests indicate that the grain boundary engineered samples exhibited higher ductility than the conventionally processed samples. The investigation provides a detailed account of the approach to be adopted for GBE processing of this grade of steel. (C) 2014 Elsevier B.V. All rights reserved.

Regioselective Synthesis of Nitrofuran Containing Novel Spiropyrrolidine Library through 1,3-Dipolar Cycloaddition Reactions

A novel series of nitrofuran containing spiropyrrolidines has been synthesized with high regioselectivity in moderate to excellent yields via 1,3-dipolar cycloaddition reaction of azomethine ylides with various substituted chalcones.

Effects of hydrogen bonding on amide-proton chemical shift anisotropy in a proline-containing model peptide

Longitudinal relaxation due to cross-correlation between dipolar ((HN-1H alpha)-H-1) and amide-proton chemical shift anisotropy (H-1(N) CSA) has been measured in a model tripeptide Piv-(L)Pro-(L)Pro-(L)Phe-OMe. The peptide bond across diproline segment is known to undergo cis/trans isomerization and only in the cis form does the lone Phe amide-proton become involved in intramolecular hydrogen bonding. The strength of the cross correlated relaxation interference is found to be significantly different between cis and trans forms, and this difference is shown as an influence of intramolecular hydrogen bonding on the amide-proton CSA. (C) 2015 Elsevier B.V. All rights reserved.

Electron-Rich Triphenylamine-Based Sensors for Picric Acid Detection

This paper demonstrates the role of solvent in selectivity and sensitivity of a series of electron-rich compounds for the detection of trace amounts of picric acid. Two new electron-rich fluorescent esters (6, 7) containing a triphenylamine backbone as well as their analogous carboxylic acids (8, 9) have been synthesized and characterized. Fluorescent triphenylamine coupled with an ethynyl moiety constitutes p-electron-rich selective and sensitive probes for electron-deficient picric acid (PA). In solution, the high sensitivity of all the sensors toward PA can be attributed to a combined effect of the ground-state charge-transfer complex formation and resonance energy transfer between the sensor and analyte. The acids 8 and 9 also showed enhanced sensitivity for nitroaromatics in the solid state, and their enhanced sensitivity could be attributed to exciton migration due to close proximity of the neighboring acid molecules, as evident from the X-ray diffraction study. The compounds were found to be quite sensitive for the detection of trace amount of nitroaromatics in solution, solid, and contact mode.

Porous membranes designed from bi-phasic polymeric blends containing silver decorated reduced graphene oxide synthesized via a facile one-pot approach

In this work, porous membranes were designed by selectively etching the PEO phase, by water, from a melt-mixed PE/PEO blend. The pure water flux and the resistance across the membrane were systematically evaluated by employing an indigenously developed cross flow membrane setup. Both the phase morphology and the cross sectional morphology of the membranes was assessed by scanning electron microscopy and an attempt was made to correlate the observed morphology with the membrane performance. In order to design antibacterial membranes for water purification, partially reduced graphene oxide (rGO), silver nanoparticles (Ag) and silver nanoparticles decorated with rGO (rGO-Ag) were synthesized and incorporated directly into the blends during melt mixing. The loss of viability of bacterial cells was determined by the colony counting method using E. coli as a model bacterium. SEM images display that the direct contact with the rGO-Ag nanoparticles disrupts the cell membrane. In addition, the rGO-Ag nanoparticles exhibited a synergistic effect with respect to bacterial cell viability in comparison to both rGO and Ag nanoparticles. The possible mechanism associated with the antibacterial activity in the membranes was discussed. This study opens new avenues in designing antibacterial membranes for water purification.

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.

Coherent (photon) vs incoherent (current) detection of multidimensional optical signals from single molecules in open junctions

The nonlinear optical response of a current-carrying single molecule coupled to two metal leads and driven by a sequence of impulsive optical pulses with controllable phases and time delays is calculated. Coherent (stimulated, heterodyne) detection of photons and incoherent detection of the optically induced current are compared. Using a diagrammatic Liouville space superoperator formalism, the signals are recast in terms of molecular correlation functions which are then expanded in the many-body molecular states. Two dimensional signals in benzene-1,4-dithiol molecule show cross peaks involving charged states. The correlation between optical and charge current signal is also observed. (C) 2015 AIP Publishing LLC.