Thermodynamic and kinetic studies on the mechanism of binding of methylumbelliferyl glycosides to jacalin

The binding of Artocarpus integrifolia lectin (jacalin) to 4-methylumbelliferyl (Meumb)-glycosides, Gal alpha Meumb, Gal beta Meumb, GalNAc alpha Meumb, GalNAc beta-Meumb, and Gal beta 3GalNAc beta Meumb was examined by extrinsic fluorescence quenching titration and stopped flow spectrofluorimetry. The binding was characterized by 100% quenching of fluorescence of Meumb-glycosides. Their association constants range from 2.0 x 10(4) to 1.58 x 10(6) M-1 at 15 degrees C. Entropic contribution is the major stabilizing force for avid binding of Meumb-glycosides indicating the existence of a hydrophobic site that is complementary to their methylumbelliferyl group. The second order association rate constants for interaction of these sugars with lectin at 15 degrees C vary from 8.8 x 10(5) to 3.24 x 10(6) M-1 S-1, at pH 7.2. The first order dissociation rate constants range from 2.30 to 43.0 S-1 at 15 degrees C. Despite the differences in their association rate constants, the overall values of association constants for these saccharides are determined by their dissociation rate constants. The second order rate constant for the association of Meumb-glycosides follows a pattern consistent with the magnitude of the activation energies involved therin. Activation parameters for association of all ligands illustrate that the origin of the barrier between binding of jacalin to Meumb-glycosides is entropic, and the enthalpic contribution is small. A correlation between these parameters and the structure of the ligands on the association rates underscores the importance of steric factors in determining protein saccharide recognitions.

Theory of laminar flame propagation with non-normal diffusion.

A study has been made of the problem of steady, one-dimensional, laminar flame propagation in premixed gases, with the Lewis number differing from (and equal to) unity. Analytical solutions, using the method of matched asymptotic expansions, have been obtained for large activation energies. Numerical solutions have been obtained for a wide range of the reduced activation temperature parameter (n {geometrically equal to} E/RTb), and the Lewis number δ. The studies reveal that the flame speed eigenvalue is linear in Lewis number for first order and quadratic in Lewis number for second order reactions. For a quick determination of flame speeds, with reasonable accuracy, a simple rule, expressing the flame speed eigenvalue as a function of the Lewis number and the centroid of the reaction rate function, is proposed. Comparisons have been made with some of the earlier works, for both first and second order reactions.

Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

Background: Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various comparative studies at genomic, protein sequence and structure levels, and experimental works highlight the different factors and dominant interacting forces contributing to this increased stability. Methods: In this comparative structure based study, we have used interaction energies between amino acids, to generate structure networks called as Protein Energy Networks (PENs). These PENs are used to compute network, sub-graph, and node specific parameters. These parameters are then compared between the thermophile-mesophile homologues. Results: The results show an increased number of clusters and low energy cliques in thermophiles as the main contributing factors for their enhanced stability. Further more, we see an increase in the number of hubs in thermophiles. We also observe no community of electrostatic cliques forming in PENs. Conclusion: In this study we were able to take an energy based network approach, to identify the factors responsible for enhanced stability of thermophiles, by comparative analysis. We were able to point out that the sub-graph parameters are the prominent contributing factors. The thermophiles have a better-packed hydrophobic core. We have also discussed how thermophiles, although increasing stability through higher connectivity retains conformational flexibility, from a cliques and communities perspective.

Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

Background: Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various comparative studies at genomic, protein sequence and structure levels, and experimental works highlight the different factors and dominant interacting forces contributing to this increased stability. Methods: In this comparative structure based study, we have used interaction energies between amino acids, to generate structure networks called as Protein Energy Networks (PENs). These PENs are used to compute network, sub-graph, and node specific parameters. These parameters are then compared between the thermophile-mesophile homologues. Results: The results show an increased number of clusters and low energy cliques in thermophiles as the main contributing factors for their enhanced stability. Further more, we see an increase in the number of hubs in thermophiles. We also observe no community of electrostatic cliques forming in PENs. Conclusion: In this study we were able to take an energy based network approach, to identify the factors responsible for enhanced stability of thermophiles, by comparative analysis. We were able to point out that the sub-graph parameters are the prominent contributing factors. The thermophiles have a better-packed hydrophobic core. We have also discussed how thermophiles, although increasing stability through higher connectivity retains conformational flexibility, from a cliques and communities perspective.

Studies on the conformation of amino acids XII. Energy calculations on prolyl residue

The favoured conformations of the prolyl residue have been obtained by calculating their potential energies arising from bond-angle strain, torsion-angle strain, non-bonded and electrostatic interatomic energies. In addition to the five membered ring, the peptide unit at the amino end (with ω = 180°) and the C′ atom at the carboxyl end have been taken into account. It is found that there are two local minima in the configurational space of the parameters defining the conformation, as is actually observed-one (denoted by B) with Cγ displaced on the same side as C′, which is lower in energy than the other (denoted by A) with Cγ displaced on the opposite side of C′. The other four atoms Cδ, N, Cα, Cβ are nearly in a plane. The conformations of minimum energy (for both A and B) have bond angles very close to the mean observed values while the torsion angles are well within the range observed in various structures for each type. Taking into account the fact that the influence of neighbouring molecules in a crystal structure may make the conformation of a molecule different from the minimal one, the ranges of the conformational parameters for which the energy is within 0.6 kcal/mole above the minimum value (called the "most probable range") and within 1.2 kcal/mole (called the "probable range") have been determined. The ranges thus obtained, agree well with observation, and most of the observed data lie within the most probable ranges, although differing appreciably from the conformation of minimum energy. The study has been extended, in a limited way, to the conformation of the ring in the amino acid proline. Since the nitrogen is tetrahedral in this (as contrasted with being planar in the prolyl residue), it is found that any one of the five atoms can be out of plane (either way), with the other four lying nearly in a plane. These correspond to low energy conformations (up to 1.2 kcal/mole above the minimum). One such example, in which the Cα atom is out of plane is known for dl-proline · HCl. It is also shown that in these calculations energies due to bond length distortions can be neglected to a good degree of approximation, provided the 'best' values of the bond lengths for the particular compound are used in the theoretical calculations.

Main chain and segmental dynamics of semi interpenetrating based on polyisoprene and poly(methyl methacrylate)

Main chain and segmental dynamics of polyisoprene (PI) and poly(methyl methacrylate)(PMMA) chains in semi IPNs were systematically studied over a wide range of temperatures (above and below T-g of both polymers) as a function of composition, crosslink density, and molecular weight. The immiscible polymers retained most of its characteristic molecular motion; however, the semi IPN synthesis resulted in dramatic changes in the motional behavior of both polymers due to the molecular level interpenetration between two polymer chains. ESR spin probe method was found to be sensitive to the concentration changes of PMMA in semi IPNs. Low temperature spectra showed the characteristics of rigid limit spectra, and in the range of 293-373 K.complex spectra were obtained with the slow component mostly arisingout of the PMMA rich regions and fast component from the PI phase. We found that the rigid PMMA chains closely interpenetrated into thehighly mobile PI network imparts motional restriction in nearby PI chains, and the highly mobile PI chains induce some degree of flexibility in highly rigid PMMA chains. Molecular level interchain mixing was found to be more efficient at a PMMA concentration of 35 wt.%. Moreover, the strong interphase formed in the above mentionedsemi IPN contributed to the large slow component in the ESR spectra at higher temperature. The shape of the spectra along with the data obtained from the simulations of spectra was correlated to the morphology of the semi IPNs. The correlation time measurement detected the motional region associated with the glass transition of PI and PMMA, and these regions were found to follow the same pattern of shifts in a-relaxation of PI and PMMA observed in DMA analysis. Activation energies associated with the T-g regions were also calculated. T-50G was found to correlate with the T-g of PMMA, and the volume of polymer segments undergoing glass transitional motion was calculated to be 1.7 nm(3).C-13 T-1 rho measurements of PMMA carbons indicate that the molecular level interactions were strong in semi IPN irrespective of the immiscible nature of polymers. The motional characteristics of H atoms attached to carbon atoms in both polymers were analyzed using 2D WISE NMR. Main relaxations of both components shifted inward, and both SEM and TEM analysis showed the development of a nanometer sized morphology in the case of highly crosslinked semi IPN. (C) 2010 Elsevier Ltd. All rights reserved.

Mechanism of the addition of alcohols to substituted phenylisothiocyanates : Electrical effects of the substituents on the reaction

The addition reaction of alcohols to substituted phenylisothiocyanates is found to be a second-order reaction. The reaction is catalysed by triethylamine. First-order rate constants of the addition reaction have been determined in excess of ethanol, for a number of substituted phenylisothiocyanates and the rate data give a satisfactory linear correlation with Hammett σ constants of groups. While the energies of activation vary randomly with substitution, the entropies of activation bear a linear relationship to the energies of activation. Infra-red spectra indicate that the thiourethanes which are the products of the addition reaction exist in the thioamide form. The most prominent resonance form which can satisfactorily explain both the kinetic and infrared data, has been suggested.

Clustering phenomena in Al-4.4 at. % Zn alloy with 0.03 and 0.08 at. % Ag additions

The influence of 0.03 and 0.08 at. % Ag additions on the clustering of Zn atoms in an Al-4.4 at. % Zn alloy has been studied by resistometry. The effect of quenching and ageing temperatures shows that the ageing-ratio method of calculating the vacancy-solute atom binding energy is not applicable to these alloys. Zone-formation in Al-Zn is unaffected by Ag additions, but the zone-reversion process seems to be influenced. Apparent vacancy-formation energies in the binary and ternary alloys have been used to evaluate the v-Ag atom binding energy as 0.21 eV. It is proposed that, Ag and Zn being similar in size, the relative vacancy binding results from valency effects, and that in Al-Zn-Ag alloys clusters of Zn and Ag may form simultaneously, unaffected by the presence of each other. © 1970 Chapman and Hall Ltd.

Space-charge limited conduction in doped polypyrrole devices

Doping dependent current-voltage (I-V) and capacitance-voltage (C-V) measurements were carried out on polypyrrole devices in metal-polymer-metal sandwich structure. Temperature dependent I-V measurements infer that space-charge limited conduction (SCLC) with exponential trap distribution is appropriate for the moderately doped samples, whereas trap-free SCLC is observed in lightly doped samples. Trap densities and energies are estimated, the effective mobility is calculated using the Poole-Frenkel model, and the mobility exhibits thermally activated behavior. Frequency dependent capacitance-voltage characteristics show a peak near zero bias voltage, which implies that these devices are symmetric with a negligible barrier height at the metal-polymer interface. Low frequency capacitance measurements have revealed a negative capacitance at higher voltages due to the processes associated with the injection and redistribution of space-charges. (C) 2010 American Institute of Physics.

Room-temperature equal channel angular extrusion of pure magnesium

In this paper, we demonstrate a way to impart severe plastic deformation to magnesium at room temperature to produce ultrafine grain size of similar to 250 nm through equal channel angular extrusion (ECAE). The strategy to deform magnesium at lower temperature or to achieve such grain sizes has been proposed as: (i) to obtain a suitable initial orientation with high Schmid factor for basal slip and low Schmid factor for pyramidal/prismatic slip; (ii) to take advantage of low stacking fault energy of basal and high stacking fault energies of prismatic/pyramidal planes in order to relatively work-harden the basal plane with respect to the pyramidal/prismatic plane; and (iii) to lower the temperature of deformation in steps, leading to continual refinement of grains, resulting in finer grain size. The experimental as well as simulated texture of ECAE-processed samples indicate that the deformation mechanism leading to ultrafine grain size is slip-dominated. The recrystallization mechanism during ECAE has been found to be orientation-dependent. (C) 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Free-to-bound and bound exciton transitions at isoelectronic impurities: GaP(Zn,O)

We show, for sufficiently high temperatures and sufficiently weak majority-carrier binding energies, that the dominant radiative transition at an isoelectronic acceptor (donor) in p-type (n-type) material consists of the recombination of singly trapped minority carriers (bound by central-cell forces) with free majority carriers attracted by a Coulomb interaction. There are two reasons why the radiative recombination rate of the free-to-bound process is greater than the bound exciton process, which dominates at lower temperatures: (i) The population of free majority-carrier states greatly exceeds that of exciton states at higher temperatures, and (ii) the oscillator strength of the free-to-bound transition is greatly enhanced by the Coulomb attraction between the free carrier and the charged isoelectronic impurity. This enhancement is important for isoelectronic centers and is easily calculable from existing exciton models. We show that the free carrier attracted by a Coulomb interaction can be viewed as a continuum excited state of the bound exciton. When we apply the results of our calculations to the GaP(Zn, O) system, we find that the major part of the room-temperature luminescence from nearest-neighbor isoelectronic Zn-O complexes results from free-to-bound recombination and not exciton recombination as has been thought previously. Recent experiments on impulse excitation of luminescence in GaP(Zn, O) are reevaluated in the light of our calculations and are shown to be consistent with a strong free-to-bound transition. For deep isoelectronic centers with weakly bound majority carriers, we predict an overwhelming dominance of the free-to-bound process at 300°K.

Potential functions for hydrogen bond interactions - IV. Minimum Energy Conformation of the α-Helical Structure of PoIy-L-Alanine

Making use of the empirical potential functions for peptide NH .. O bonds, developed in this laboratory, the relative stabilities of the rightand left-handed α-helical structures of poly-L-alanine have been investigated, by calculating their conformational energies (V). The value of Vmin of the right-handed helix (αP) is about - 10.4 kcal/mole, and that of the left-handed helix (αM) is about - 9.6 kcal/mole, showing that the former is lower in energy by 0.8 kcal/mole. The helical parameters of the stable conformation of αP are n ∼ 3.6 and h ∼ 1.5 Å. The hydrogen bond of length 2.85 Å and nonlinearity of about 10° adds about 4.0 kcal/ mole to the stabilising energy of the helix in the minimum enregy region. The energy minimum is not sharply defined, but occurs over a long valley, suggesting that a distribution of conformations (φ{symbol}, ψ) of nearly the same energy may occur for the individual residues in a helix. The experimental data of a-helical fibres of poly-L-alanine are in good agreement with the theoretical results for αP. In the case of proteins, the mean values of (φ{symbol}, ψ) for different helices are distributed, but they invariably occur within the contour for V = Vmin + 2 kcal/mole for αP.

The Role of Interface Modification on Thermal Degradation and Crystallization Behavior of Composites from Commingled Polypropylene Fiber and Banana Fiber

The thermal degradation behavior of banana fiber and polypropylene/banana fiber composites has been studied by thermogravimetric analysis. Banana fiber was found to be decomposing in two stages, first one around 320 degrees C and the second one around 450 degrees C. For chemically treated banana fiber, the decomposition process has been at a higher temperature, indicating thermal stability for the treated fiber. Activation energies for thermal degradation were estimated using Coats and Redfern method. Calorific value of the banana fiber was measured using a constant volume isothermal bomb calorimeter. rystallization studies exhibited an increase in the crystallization temperature and crystallinity of polypropylene upon the addition of banana fiber. POLYM. COMPOS., 31:1113-1123, 2010. (C) 2009 Society of Plastics Engineers.

Structure of Ce1-xSnxO2 and its relation to oxygen storage property from first-principles analysis

CeO2-SnO2 solid solution has been reported to possess high oxygen storage/release property which possibly originates from local structural distortion. We have performed first-principles based density functional calculations of Ce1-xSnxO2 structure (x=0, 0.25, 0.5, 1) to understand its structural stability in fluorite in comparison to rutile structure of the other end-member SnO2, and studied the local structural distortion induced by the dopant Sn ion. Analysis of relative energies of fluorite and rutile phases of CeO2, SnO2, and Ce1-xSnxO2 indicates that fluorite structure is the most stable for Ce1-xSnxO2 solid solution. An analysis of local structural distortions reflected in phonon dispersion show that SnO2 in fluorite structure is highly unstable while CeO2 in rutile structure is only weakly unstable. Thus, Sn in Ce1-xSnxO2-fluorite structure is associated with high local structural distortion whereas Ce in Ce1-xSnxO2-rutile structure, if formed, will show only marginal local distortion. Determination of M-O (M=Ce or Sn) bond lengths and analysis of Born effective charges for the optimized structure of Ce1-xSnxO2 show that local coordination of these cations changes from ideal eightfold coordination expected of fluorite lattice to 4+4 coordination, leading to generation of long and short Ce-O and Sn-O bonds in the doped structure. Bond valence analyses for all ions show the presence of oxygen with bond valence similar to 1.84. These weakly bonded oxygen ions are relevant for enhanced oxygen storage/release properties observed in Ce1-xSnxO2 solid solution. (C) 2010 American Institute of Physics.

Resistometric studies of solute-vacancy interactions and clustering kinetics in an FCC matrix [AlZn Alloy with Ag, Ce, Dy, Li, Nb, Pt, Sb, Y, or Yb]

Al-4.4 a/oZn and Al-4.4 a/oZn with Ag, Ce, Dy, Li, Nb, Pt, Y, or Yb, alloys have been investigated by resistometry with a view to study the solute-vacancy interactions and clustering kinetics in these alloys. Solute-vacancy binding energies have been evaluated for all these elements by making use of appropriate methods of evaluation. Ag and Dy additions yield some interesting results and these have been discussed in the thesis. Solute-vacancy binding energy values obtained here have been compared with other available values and discussed. A study of the type of interaction between vacancies and solute atoms indicates that the valency effect is more predominant than the elastic effect.