Solvent Sensitivity of Protein Unfolding: Dynamical Study of Chicken Villin Headpiece Subdomain in Water Ethanol Binary Mixture

We carry out a series of long atomistic molecular dynamics simulations to study the unfolding of a small protein, chicken villin headpiece (HP-36), in water-ethanol (EtOH) binary mixture. The prime objective of this work is to explore the sensitivity of protein unfolding dynamics toward increasing concentration of the cosolvent and unravel essential features of intermediates formed in search of a dynamical pathway toward unfolding. In water ethanol binary mixtures, HP-36 is found to unfold partially, under ambient conditions, that otherwise requires temperature as high as similar to 600 K to denature in pure aqueous solvent. However, an interesting course of pathway is observed to be followed in the process, guided by the formation of unique intermediates. The first step of unfolding is essentially the separation of the cluster formed by three hydrophobic (phenylalanine) residues, namely, Phe-7, Phe-11, and Phe-18, which constitute the hydrophobic core, thereby initiating melting of helix-2 of the protein. The initial steps are similar to temperature-induced unfolding as well as chemical unfolding using DMSO as cosolvent. Subsequent unfolding steps follow a unique path. As water-ethanol shows composition-dependent anomalies, so do the details of unfolding dynamics. With an increase in cosolvent concentration, different partially unfolded intermediates are found to be formed. This is reflected in a remarkable nonmonotonic composition dependence of several order parameters, including fraction of native contacts and protein-solvent interaction energy. The emergence of such partially unfolded states can be attributed to the preferential solvation of the hydrophobic residues by the ethyl groups of ethanol. We further quantify the local dynamics of unfolding by using a Marcus-type theory.

Remarkable role of positional isomers in the design of sensors for the ratiometric detection of copper and mercury ions in water

Cation sensing properties of the three positional isomers of rhodamine based sensors (1-3) are studied in water. The sensors differ only in the position of pyridine's nitrogen. The chemosensor 1, with pyridine nitrogen at ortho-position, showed a selective colorimetric detection of Cu(II) ions in water, at physiological pH 7.4 and also in medium containing BSA (bovine serum albumin) and blood serum. Notably the compound 2 and 3, with pyridine end located at meta-and para-positions did not show any color change with Cu(II) ions, although both the compounds showed turn-on change both in color and fluorescence with Hg(II) ions specifically. All the probes showed ratiometric changes with the specific metal ions. The changing position of nitrogen also changed the complexation pattern of the sensors with the metal ions. Probe 1 showed 2 : 1 complexation with Cu(II), whereas 2 and 3 showed 1 : 1 complexation with Hg(II) ions. The mechanism investigation showed that the change in color upon addition of metal ions is due to the ring-opening of the spirolactam ring of the probes. Cu(II) interacted with ligand 1 through a three-point interaction mode comprising carbonyl oxygen, amido nitrogen and pyridine nitrogen end. But in case of 2 and 3, Hg2+ only interacted through pyridine nitrogen ends. Quantitative estimation of Cu2+ and Hg2+ in complex biological media such as bovine albumin protein (BSA) and human blood serum were performed using these sensors. Rapid on-site detection as well as discrimination of these toxic ions was demonstrated using easily prepared portable test-strips.

Effect of TiN particulate reinforcement on corrosive behaviour of aluminium 6061 composites in chloride medium

In the present investigation, the corrosive behaviour of Al 6061-TiN particulate composites prepared by liquid metallurgy has been studied in chloride medium using electroanalytical techniques such as Tafel, cyclic polarization and electrochemical impedance spectroscopy (EIS). Surface morphology of the sample electrodes was examined using scanning electron micrography and energy dispersive X-ray methods. X-ray diffraction technique was used to confirm inclusion of TiN particulates in the matrix alloy and identify the alloying elements and intermetallic compounds in the Al 6061 composites. Polarization studies indicate an increase in the corrosion resistance in composites compared to the matrix alloy. EIS study reveals that the polarization resistance (R (p)) increases with increase in TiN content in composites, thus confirming improved corrosion resistance in composites. The observed decrease in corrosion rate in the case of composites is due to decoupling between TiN particles and Al 6061 alloy. It is understood that after the initiation of corrosion, interfacial corrosion products may have decoupled the conducting ceramic TiN from Al 6061 matrix alloy thus eliminating the galvanic effect between them.

D-A-D-structured conducting polymer-modified electrodes for detection of lead(II) ions in water

Donor-acceptor-donor-structured thiophene derivative-based conducting polymer poly(7,9-dithiophene-2yl-8H-cyclopentaa]acenaphthalene-8-one) was chemically synthesized. This polymer was used to modify both glassy-carbon and carbon-paste electrode, which was used to detect lead(II) ions present in water in the range of 1 mM to 0.1 mu M. Cyclic voltammetry confirms the formation of the co-ordination complex between the soft segment of polymer and the dissolved lead ion. Anodic stripping voltammetry was carried out by the modified electrode to determine the lower limit of detection of dissolved lead(II) species in the solution. Differential adsorptive stripping and impedance measurements were also conducted to find the lowest possible response of the as-synthesized polymer to lead(II) ion in water. The electrochemical performance of the modified electrodes at different pH (4, 7 and 9) environments was carried out by stripping voltammetry, to get optimum sensitivity and stability under these conditions. Finally, interference analysis was carried out to detect the modified electrode's sensitivity towards lead ion affinity in water.

Rapid determination of main constituents of packed juices by reverse phase-high performance liquid chromatography: an insight in to commercial fruit drinks

The present work reports the compositional analysis of thirteen different packed fruit juices using high performance liquid chromatography (HPLC). Vitamin C, organic acids (citric and malic) and sugars (fructose, glucose and sucrose) were separated, analyzed and quantified using different reverse phase methods. A new rapid reverse phase HPLC method was developed for routine analysis of vitamin C in fruit juices. The precision results of the methods showed that the relative standard deviations of the repeatability and reproducibility were < 0.05 and < 0.1 respectively. Correlation coefficient of the calibration models developed was found to be higher than 0.99 in each case. It has been found that the content of Vitamin C was less variable amongst different varieties involved in the study. It is also observed that in comparison to fresh juices, the packed juices contain lesser amounts of vitamin C. Citric acid was found as the major organic acids present in packed juices while maximum portion of sugars was of sucrose. Comparison of the amount of vitamin C, organic acids and sugars in same fruit juice of different commercial brands is also reported.

Fluctuating micro-heterogeneity in water-tert-butyl alcohol mixtures and lambda-type divergence of the mean cluster size with phase transition-like multiple anomalies

Water-tert-butyl alcohol (TBA) binary mixture exhibits a large number of thermodynamic and dynamic anomalies. These anomalies are observed at surprisingly low TBA mole fraction, with x(TBA) approximate to 0.03-0.07. We demonstrate here that the origin of the anomalies lies in the local structural changes that occur due to self-aggregation of TBA molecules. We observe a percolation transition of the TBA molecules at x(TBA) approximate to 0.05. We note that ``islands'' of TBA clusters form even below this mole fraction, while a large spanning cluster emerges above that mole fraction. At this percolation threshold, we observe a lambda-type divergence in the fluctuation of the size of the largest TBA cluster, reminiscent of a critical point. Alongside, the structure of water is also perturbed, albeit weakly, by the aggregation of TBA molecules. There is a monotonic decrease in the tetrahedral order parameter of water, while the dipole moment correlation shows a weak nonlinearity. Interestingly, water molecules themselves exhibit a reverse percolation transition at higher TBA concentration, x(TBA) approximate to 0.45, where large spanning water clusters now break-up into small clusters. This is accompanied by significant divergence of the fluctuations in the size of largest water cluster. This second transition gives rise to another set of anomalies around. Both the percolation transitions can be regarded as manifestations of Janus effect at small molecular level. (C) 2014 AIP Publishing LLC.

Modeling of Bubble-Size Distribution in Water and Freon Co-Blown Free Rise Polyurethane Foams

A model has been developed to simulate the foam characteristics obtained, when chemical (water) and physical (Freon) blowing agents are used together for the formation of polyurethane foams. The model considers the rate of reaction, the consequent rise in temperature of the reaction mixture, nucleation of bubbles, and mass transfer of CO2 and Freon to them till the time of gelation. The model is able to explain the experimental results available in literature. It further predicts that the nucleation period gets reduced with increase in water (at constant Freon content), whereas with increase in Freon (at constant water) concentration nucleation period decreases marginally leading to narrower bubble-size distribution. By the use of uniform sized nuclei added initially, the model predicts that the bubble-size distribution can be made independent of the rate of homogeneous nucleation and can, thus, offer an extra parameter for its control. (C) 2014 Wiley Periodicals, Inc.

Exclusive Detection of Sub-Nanomolar Levels of Palladium(II) in Water: An Excellent Probe for Multiple Applications

A new colorimetric probe has been developed for the detection and estimation of Pd-II at sub-nanomolar concentrations. The probe consisted of rhodamine (signaling unit), which was linked with a bis-picolyl moiety (binding site) through a phenyl ring. Pd-II induced opening of the spirolactam ring of the probe with the generation of a prominent pink color. The excellent selectivity of the probe towards Pd-II over Pd-0 or Rh-II ensured its potential utility for the detection of residual palladium contamination in pharma-ceutical drugs and in Pd-catalyzed reactions. The probe showed a ``turn-on'' (bright yellow) fluorescence upon the addition of Pd-II, which made it suitable for the detection of Pd contaminants in mammalian cells.

Wave propagation of phonon and phason displacement modes in quasicrystals: Determination of wave parameters

The paper presents the study of wave propagation in quasicrystals. Our interest is in the computation of the wavenumber (k(n)) and group speed (c(g)) of the phonon and phason displacement modes of one, two, and three dimensional quasicrystals. These wave parameter expressions are derived and computed using the elasto-hydrodynamic equations for quasicrystals. For the computation of the wavenumber and group speeds, we use Fourier transform approximation of the phonon and the phason displacement modes. The characteristic equations obtained are a polynomial equation of the wavenumber (k(n)), with frequency as a parameter. The corresponding group speeds (c(g)) for different frequencies are then computed from the wavenumber k(n). The variation of wavenumber and group speeds with frequency is plotted for the 1-D quasicrystal, 2-D decagonal Al-Ni-Co quasicrystals, and 3-D icosahedral Al-Pd-Mn and Zn-Mg-Sc quasicrystals. From the wavenumber and group speeds plots, we obtain the cut-off frequencies for different spatial wavenumber eta(m). The results show that for 1-D, 2-D, and 3-D quasicrystals, the phonon displacement modes are non-dispersive for low values of eta(m) and becomes dispersive for increasing values of eta(m). The cut-off frequencies are not observed for very low values of eta(m), whereas the cut-off frequency starts to appear with increasing eta(m). The group speeds of the phason displacement modes are orders of magnitude lower than that of the phonon displacement modes, showing that the phason modes do not propagate, and they are essentially the diffusive modes. The group speeds of the phason modes are also not influenced by eta(m). The group speeds for the 2-D quasicrystal at 35 kHz is also simulated numerically using Galerkin spectral finite element methods in frequency domain and is compared with the results obtained using wave propagation analysis. The effect of the phonon and phason elastic constants on the group speeds is studied using 3-D icosahedral Al-Pd-Mn and Zn-Mg-Sc quasicrystals. It is also shown that the phason elastic constants and the coupling coefficient do not affect the group speeds of the phonon displacement modes. (C) 2015 AIP Publishing LLC.

Evolution of texture and its influence on the failure of components in some aluminium alloys

This paper describes the evolution of crystallographic texture in three of the most important high strength aluminium alloys, viz., AA2219, AA7075 and AFNOR7020 in the cold rolled and artificially aged condition. Bulk texture results were obtained by plotting pole figures from X-ray diffraction results followed by Orientation Distribution Function (ODF) analysis and micro-textures were measured using EBSD. The results indicate that the deformation texture components Cu, Bs and S, which were also present in the starting materials, strengthen with increase in amount of deformation. On the other hand, recrystallization texture components Goss and Cube weaken. The Bs component is stronger in the deformation texture. This is attributed to the shear banding. In-service applications indicate that the as-processed AFNOR7020 alloy fails more frequently compared to the other high strength Al alloys used in the aerospace industry. Detailed study of deformation texture revealed that strong Brass (Bs) component could be associated to shear banding, which in turn could explain the frequent failures in AFNOR7020 alloy. The alloying elements in this alloy that could possibly influence the stacking fault energy of the material could be accounted for the strong Bs component in the texture.

TiO2 microcrystallized glass plate mediated photocatalytic degradation of estrogenic pollutant in water

Photocatalytic degradation of estriol (E3) in an aqueous medium was investigated in the presence of TiO2 microcrystallized glass plates. To begin with, transparent glasses associated with the composition 0.4BaO-0.4TiO(2)-B2O3 (BTBO) were fabricated by the conventional melt-quench technique and subsequently subjected to controlled heat treatment at an appropriate temperature to grow anatase TiO2 microcrystals in the glass matrix. The fabricated samples were subjected to differential scanning calorimetry. X-ray diffraction and scanning electron microscopy to obtain thermal, structural and microstructural details. The photocatalytic activity of glass samples for estriol degradation was monitored by fluorescence spectroscopy. The limit of detection for estriol using fluorescence spectroscopy was analyzed. The results showed that microcrystallized TiO2 glass composites have more photocatalytic activity than as quenched glass. The degradation rate coefficient of microcrystallized TiO2 glass composite (334.54 min(-1) m(-2)) was found to be ten times larger than that of the as-quenched BTBO glasses (37.74 min(-1) m(-2)) implying that the anatase phase of TiO2 in BTBO glasses was responsible for high photocatalytic activity of estriol degradation. (c) 2014 Elsevier B.V. All rights reserved.

The putative role of some conserved water molecules in the structure and function of human transthyretin

Human transthyretin (hTTR) is a multifunctional protein that is involved in several neurodegenerative diseases. Besides the transportation of thyroxin and vitamin A, it is also involved in the proteolysis of apolipoprotein A1 and A beta peptide. Extensive analyses of 32 high-resolution X-ray and neutron diffraction structures of hTTR followed by molecular-dynamics simulation studies using a set of 15 selected structures affirmed the presence of 44 conserved water molecules in its dimeric structure. They are found to play several important roles in the structure and function of the protein. Eight water molecules stabilize the dimeric structure through an extensive hydrogen-bonding network. The absence of some of these water molecules in highly acidic conditions (pH <= 4.0) severely affects the interfacial hydrogen-bond network, which may destabilize the native tetrameric structure, leading to its dissociation. Three pairs of conserved water molecules contribute to maintaining the geometry of the ligand-binding cavities. Some other water molecules control the orientation and dynamics of different structural elements of hTTR. This systematic study of the location, absence, networking and interactions of the conserved water molecules may shed some light on various structural and functional aspects of the protein. The present study may also provide some rational clues about the conserved water-mediated architecture and stability of hTTR.

Vesicular Nanostructure Formation by Self-Assembly of Anisotropic Penta-phenol-Substituted Fullerene in Water

A study on self-assembly of anisotropically substituted penta-aryl fullerenes in water has been reported. The penta-phenol-substituted amphiphilic fullerene derivative C60Ph5(OH)(5)],exhibited self-assembled vesicular nanostructures in water under the experimental conditions. The size of the vesicles Was observed to depend upon the kinetics of self-assembly and could be varied from similar to 300 to similar to 70 nm. Our mechanistic study indicated that the self-assembly of C60Ph5(OH)(5) is driven by extensive intermolecular as well as water-mediated hydrogen :bonding along with fullerene-fullerene hydrophobic interaction in water. The cumulative effect of these interactions is responsible for the stability of vesicular structures even on the removal of solvent. The substitution of phenol with anisole resulted in different packing and interaction of the fullerene derivative, as Indicated in the molecular dynamics studies, thus resulting in different self-assembled nanostructures. The hollow vesicles were further encapsulated with a hydrophobic conjugated polymer and water-soluble dye as guest molecules. Such confinement of pi-conjugated polymers in fullerene has significance in bulk heterojunction devices for efficient exciton diffusion.

An Efficient Tertiary Azidation of 1,3-Dicarbonyl Compounds in Water Catalyzed by Tetrabutylammonium Iodide

An efficient azidation of 1,3-dicarbonyl compounds led to tertiary azides in the presence of tetrabutylammonium iodide (TBAI). TBAI is used as a pre-catalyst along with aq. tert-butyl hydroperoxide (TBHP) as an oxidant in aqueous medium. This operationally simple, practical, mild and green method provides an opportunity to synthesize a variety of azidated -keto esters, amides, and ketones in good yields.