Studies on a chitooligosaccharide-specific lectin from Coccinia indica. Thermodynamics and kinetics of umbelliferyl glycoside binding.

Coccinia indica agglutinin (CIA) is a chitooligosaccharide-specific lectin with two binding sites/homodimer of M(r) 32,000. Quenching studies implied tryptophan involvement in binding activity, which was confirmed by chemical modification experiments (A. R. Sanadi and A. Surolia, submitted for publication). Binding of 4-methylumbelliferyl chitooligosaccharides has been carried out to study their binding by CIA. Reversal experiments confirm the validity of the data previously obtained (A. R. Sanadi and A. Surolia, submitted for publication) from intrinsic fluorescence studies. Surprisingly, unlike wheat germ agglutinin, there is no consistent thermodynamic effect of the chromophoric label on binding activities as compared with the native sugars. From the changes in the optical properties of the chromophoric group upon binding to CIA, it has been possible to confirm that the tryptophan located in the binding site is closest to the fourth subsite. Thermodynamic analysis shows that the binding of the labeled tetrasaccharide is very strongly entropically driven, with the terminal, nonreducing sugar residue protruding from the binding pocket. The results of stopped-flow kinetic studies on the binding of the chromophoric trisaccharide by CIA show that the mechanism of binding is a one-step process.

Preparation, characterization and thermal decomposition of praseodymium, terbium and neodymium carbonates

The preparation of three different types of carbonates of praseodymium, neodymium and terbium has been described. The carbonates have been characterized by potentiometry, chemical analysis, X-ray crystallography, infra-red spectroscopy and by their thermal behaviour. The thermal decomposition of several carbonates has been studied exhaustively under a variety of conditions and the stoicheiometry, thermodynamics and energetics of the reactions at various stages of decomposition have been examined. The stoicheiometry of the oxides obtained as final products of decomposition has been examined.

The thermodynamics and phase behaviour of Tb2Pd2O5 and Er2Pd2O5

Isothermal sections of the phase diagrams for the systems Ln-Pd-O (with Ln = Tb or Er) have been established by equilibration of samples at T = 1223 K, and phase identification after quenching by optical and scanning electron microscopy (OM, SEM), energy dispersive spectroscopy (EDS), and X-ray powder diffraction (XRPD). Two oxide phases were stable along the binary Tb-O: Tb2O3+x, a phase of variable composition, and Tb7O12 at T = 1223K. The oxide PdO was not stable at this temperature. Only one ternary oxide Tb2Pd2O5 was identified in the Tb-Pd-O system. No ternary compound was found in the system Er-Pd-O at T = 1223K. However, the compound Er2Pd2O5 could be synthesized at T = 1075 K by the hydrothermal route. In both systems, the alloys and inter-metallic compounds were all found to be in equilibrium with the lanthanide sesquioxide Ln(2)O(3) (where Ln is either Tb or Er). Two solid-state cells, each incorporating a buffer electrode, were designed to measure the Gibbs energy of formation of the ternary oxides, using yttria-stabilized zirconia as the solid electrolyte and pure oxygen gas as the reference electrode. Electromotive force measurements were conducted in the temperature range (900-1275) K for Th-Pd-O system, and at temperatures from (900-1075) K for the system Er-Pd-O. The standard Gibbs energy of formation Delta(f)G(m)degrees,, of the inter-oxide compounds from their component binary oxides Ln(2)O(3) and PdO are represented by equations linear in temperature. Isothermal chemical potential diagrams for the systems Ln-Pd-O (with Ln = Tb or Er) are developed based on the thermodynamic information. (C) 2002 Elsevier Science Ltd. All rights reserved.

System Gd-Rh-O: Thermodynamics and phase relations

Thermodynamic properties of GdRhO3 are investigated in the temperature range from 900 to 1300 K by employing a solid-state electrochemical cell, incorporating calcia-stabilized zirconia as the electrolyte. The standard Gibbs free energy of formation of GdRhO3 from component binary oxide Gd2O3 with C-rare earth structure and Rh2O3 with orthorhombic structure can be expressed as; Delta G(f(ox))(o)(+/- 60)/J mol(-1) = -56603 + 3.78(T/K) Based on the thermodynamic information on GdRhO3 from experiment and auxiliary data for binary oxides from the literature and estimated properties of Gd-Rh alloys, phase relations are computed for the system Gd-Rh-O at 1273 K. Gibbs free energies for intermetallic phases in the binary Gd-Rh are evaluated using calorimetric data available in the literature for two compositions and Miedema's model, consistent with the binary phase diagram. Isothermal section of the ternary phase diagram, oxygen potential-composition diagram and a 3-D chemical potential diagram for the system Gd-Rh-O at 1273 K are developed. Phase relations in the ternary Gd-Rh-O are also computed as a function of temperature at constant oxygen partial pressures. The ternary oxide, GdRhO3 decomposes to Gd2O3 with B-rare earth structure, metallic Rh and O-2 at 1759(+/- 2) K in pure O-2 and 1649(+/- 2) K in air at a total pressure P-0 -0.1 MPa. (c) 2012 Elsevier B.V. All rights reserved.

Structure, chemistry, and energetics of organic and inorganic adsorbates on Ga-rich GaAs and GaP(001) surfaces

The work described in this dissertation includes fundamental investigations into three surface processes, namely inorganic film growth, water-induced oxidation, and organic functionalization/passivation, on the GaP and GaAs(001) surfaces. The techniques used to carry out this work include scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations. Atomic structure, electronic structure, reaction mechanisms, and energetics related to these surface processes are discussed at atomic or molecular levels.

First, we investigate epitaxial Zn₃P₂ films grown on the Ga-rich GaAs(001)(6×6) surface. The film growth mechanism, electronic properties, and atomic structure of the Zn₃P₂/GaAs(001) system are discussed based on experimental and theoretical observations. We discover that a P-rich amorphous layer covers the crystalline Zn3P2 film during and after growth. We also propose more accurate picture of the GaP interfacial layer between Zn₃P₂ and GaAs, based on the atomic structure, chemical bonding, band diagram, and P-replacement energetics, than was previously anticipated.

Second, DFT calculations are carried out in order to understand water-induced oxidation mechanisms on the Ga-rich GaP(001)(2×4) surface. Structural and energetic information of every step in the gaseous water-induced GaP oxidation reactions are elucidated at the atomic level in great detail. We explore all reasonable ground states involved in most of the possible adsorption and decomposition pathways. We also investigate structures and energies of the transition states in the first hydrogen dissociation of a water molecule on the (2×4) surface.

Finally, adsorption structures and thermal decomposition reactions of 1-propanethiol on the Ga-rich GaP(001)(2×4) surface are investigated using high resolution STM, XPS, and DFT simulations. We elucidate adsorption locations and their associated atomic structures of a single 1-propanethiol molecule on the (2×4) surface as a function of annealing temperature. DFT calculations are carried out to optimize ground state structures and search transition states. XPS is used to investigate variations of the chemical bonding nature and coverage of the adsorbate species.

Comparison of the thermodynamics and base-pair dynamics of a full LNA:DNA duplex and of the isosequential DNA:DNA duplex

Locked nucleic acids (LNA), conformationally restricted nucleotide analogues, are known to enhance pairing stability and selectivity toward complementary strands. With the aim to contribute to a better understanding of the origin of these effects, the structure, thermal stability, hybridization thermodynamics, and base-pair dynamics of a full-LNA:DNA heteroduplex and of its isosequential DNA:DNA homoduplex were monitored and compared. CD measurements highlight differences in the duplex structures: the homoduplex and heteroduplex present B-type and A-type helical conformations, respectively. The pairing of the hybrid duplex is characterized, at all temperatures monitored (between 15 and 37 degrees C), by a larger stability constant but a less favorable enthalpic term. A major contribution to this thermodynamic profile emanates from the presence of a hairpin structure in the LNA single strand which contributes favorably to the entropy of interaction but leads to an enthalpy penalty upon duplex formation. The base-pair opening dynamics of both systems was monitored by NMR spectroscopy via imino protons exchange measurements. The measurements highlight that hybrid G-C base-pairs present a longer base-pair lifetime and higher stability than natural G-C base-pairs, but that an LNA substitution in an A-T base-pair does not have a favorable effect on the stability. The thermodynamic and dynamic data confirm a more favorable stacking of the bases in the hybrid duplex. This study emphasizes the complementarities between dynamic and thermodynamical studies for the elucidation of the relevant factors in binding events.

Methane transformation to carbon and hydrogen on Pd(100): Pathways and energetics from density functional theory calculations

Density functional theory with gradient corrections has been employed to study the reaction pathways and the reaction energetics for the transformations of CH4 to C and H on a Pd(100) surface. On examination of transition state structures identified in each elementary reaction, a clear relationship between the valencies of the CHx fragments and the locations of the transition states emerges. The higher the valency of the CHx fragment, the higher the coordination number of the CHx with the surface atoms. The calculated reaction energetics are in good agreement with the experiments. In addition, calculation results are also used to illustrate an interesting issue concerning the CH3 stability on Pd surfaces. (C) 2002 American Institute of Physics.

Thermodynamics and log–contrast analysis in fluid geochemistry

There are two principal chemical concepts that are important for studying the natural environment. The first one is thermodynamics, which describes whether a system is at equilibrium or can spontaneously change by chemical reactions. The second main concept is how fast chemical reactions (kinetics or rate of chemical change) take place whenever they start. In this work we examine a natural system in which both thermodynamics and kinetic factors are important in determining the abundance of NH+4 , NO−2 and NO−3 in superficial waters. Samples were collected in the Arno Basin (Tuscany, Italy), a system in which natural and antrophic effects both contribute to highly modify the chemical composition of water. Thermodynamical modelling based on the reduction-oxidation reactions involving the passage NH+4 -> NO−2 -> NO−3 in equilibrium conditions has allowed to determine the Eh redox potential values able to characterise the state of each sample and, consequently, of the fluid environment from which it was drawn. Just as pH expresses the concentration of H+ in solution, redox potential is used to express the tendency of an environment to receive or supply electrons. In this context, oxic environments, as those of river systems, are said to have a high redox potential because O2 is available as an electron acceptor. Principles of thermodynamics and chemical kinetics allow to obtain a model that often does not completely describe the reality of natural systems. Chemical reactions may indeed fail to achieve equilibrium because the products escape from the site of the rection or because reactions involving the trasformation are very slow, so that non-equilibrium conditions exist for long periods. Moreover, reaction rates can be sensitive to poorly understood catalytic effects or to surface effects, while variables as concentration (a large number of chemical species can coexist and interact concurrently), temperature and pressure can have large gradients in natural systems. By taking into account this, data of 91 water samples have been modelled by using statistical methodologies for compositional data. The application of log–contrast analysis has allowed to obtain statistical parameters to be correlated with the calculated Eh values. In this way, natural conditions in which chemical equilibrium is hypothesised, as well as underlying fast reactions, are compared with those described by a stochastic approach

Thermodynamics and Lithium Intercalation in CeO(2)-TiO(2) Thin Film

The kinetics and the thermodynamics of electrochemical intercalation of lithium into CeO(2)-TiO(2) films prepared by the sol-gel process were studied by galvanostatic intermittent titration technique (GITT) as function of the depth of lithium intercalation. The open-circuit-potential versus x in Li(x)(CeO(2)-TiO(2)) curve consists of two straight lines with different slopes, one in the range of 0.03 <= x <= 0.09 and the other of 0.09 < x <= 0.15. The standard Gibbs energy for lithium intercalation Delta G(1)(0) was 6kJ/mol for x = 0.09 in Li(x)(CeO(2)-TiO(2)) at room temperature. The chemical diffusion coefficient value, D(Li+), of lithium intercalation into thin film oxide was 2.14.10(-11) cm(2)/s at x = 0.15, and the value of the component diffusion coefficient D(Li+),(k) was about one order of magnitude lower than the coefficient of chemical diffusion.

Structural properties and energetics of diffuse Rb-87 clusters in three-dimension

A correlated two-body basis function is used to describe the three-dimensional bosonic clusters interacting via two-body van der Waals potential. We calculate the ground state and the zero orbital angular momentum excited states for Rb-N clusters with up to N = 40. We solve the many-particle Schrodinger equation by potential harmonics expansion method, which keeps all possible two-body correlations in the calculation and determines the lowest effective many-body potential. We study energetics and structural properties for such diffuse clusters both at dimer and tuned scattering length. The motivation of the present study is to investigate the possibility of formation of N-body clusters interacting through the van der Waals interaction. We also compare the system with the well studied He, Ne, and Ar clusters. We also calculate correlation properties and observe the generalised Tjon line for large cluster. We test the validity of the shape-independent potential in the calculation of the ground state energy of such diffuse cluster. These are the first such calculations reported for Rb clusters. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4730972]

Selected values of chemical thermodynamics properties.

In portfolio.

Application of chemical thermodynamics to the study of alloy formation, progress report for ...

"Work performed under Contract No. AT(30-1)-647"--p.2 of cover.

Chemical thermodynamics.

Corrections sheet inserted.

Ordering induced by chemical, thermal and mechanical constraints at solid interfaces

We know that classical thermodynamics even out of equilibrium always leads to stable situation which means degradation and consequently d sorder. Many experimental evidences in different fields show that gradation and order (symmetry breaking) during time and space evolution may appear when maintaining the system far from equilibrium. Order through fluctuations, stochastic processes which occur around critical points and dissipative structures are the fundamental background of the Prigogine-Glansdorff and Nicolis theory. The thermodynamics of macroscopic fluctuations to stochastic approach as well as the kinetic deterministic laws allow a better understanding of the peculiar fascinating behavior of organized matter. The reason for the occurence of this situation is directly related to intrinsic non linearities of the different mechanisms responsible for the evolution of the system. Moreover, when dealing with interfaces separating two immiscible phases (liquid - gas, liquid -liquid, liquid - solid, solid - solid), the situation is rather more complicated. Indeed coupling terms playing the major role in the conditions of instability arise from the peculiar singular static and dynamic properties of the surface and of its vicinity. In other words, the non linearities are not only intrinsic to classical steps involving feedbacks, but they may be imbedded with the non-autonomous character of the surface properties. In order to illustrate our goal we discuss three examples of ordering in far from equilibrium conditions: i) formation of chemical structures during the oxidation of metals and alloys; ii) formation of mechanical structures during the oxidation of metals iii) formation of patterns at a solid-liquid moving interface due to supercooling condition in a melt of alloy. © 1984, Walter de Gruyter. All rights reserved.