Heat capacty, relative enthalpy, and calorimetric entropy of silicate minerals: an empirical method of prediction.

USGS Publications Warehouse

Robinson, G.R.; Haas, J.L.

1983-01-01

Through the evaluation of experimental calorimetric data and estimates of the molar isobaric heat capacities, relative enthalpies and entropies of constituent oxides, a procedure for predicting the thermodynamic properties of silicates is developed. Estimates of the accuracy and precision of the technique and examples of its application are also presented. -J.A.Z.

FLUID: A numerical interpolation procedure for obtaining thermodynamic and transport properties of fluids

NASA Technical Reports Server (NTRS)

Fessler, T. E.

1977-01-01

A computer program subroutine, FLUID, was developed to calculate thermodynamic and transport properties of pure fluid substances. It provides for determining the thermodynamic state from assigned values for temperature-density, pressure-density, temperature-pressure, pressure-entropy, or pressure-enthalpy. Liquid or two-phase (liquid-gas) conditions are considered as well as the gas phase. A van der Waals model is used to obtain approximate state values; these values are then corrected for real gas effects by model-correction factors obtained from tables based on experimental data. Saturation conditions, specific heat, entropy, and enthalpy data are included in the tables for each gas. Since these tables are external to the FLUID subroutine itself, FLUID can implement any gas for which a set of tables has been generated. (A setup phase is used to establish pointers dynamically to the tables for a specific gas.) Data-table preparation is described. FLUID is available in both SFTRAN and FORTRAN

Interaction of Antitumor Agent Mitoxantrone with Double Helical Synthetic Polyribonucleotides Poly(G)ṡPoly(C) and Poly(I)ṡPoly(C)

NASA Astrophysics Data System (ADS)

Babayan, Yuri S.; Hakobyan, Sergey N.; Ghazaryan, Rusanna S.; Shahinyan, Mariam A.

The interaction of antitumor drug mitoxantrone (MTX) with double-stranded synthetic RNA homopolymers has been studied by means of spectroscopic (UV-Visible absorption, circular dichroism) techniques. The results show a base specificity in this interaction: the association constant with poly(G)ṡpoly(C) is higher than with poly(I)ṡpoly(C). Values of changes of the system enthalpy and entropy due to complex-formation were determined through the temperature dependence of the binding constant. Calculations show that due to the intercalation interaction of MTX, the values of changes of the system entropy and enthalpy differ from those obtained at ehtidium bromide interaction with synthetic polyribonucleotides, which shows that the intercalation interaction of MTX with double-stranded RNA significantly differs from that of ethidium bromide with RNA.

Altered Enthalpy-Entropy Compensation in Picomolar Transition State Analogues of Human Purine Nucleoside Phosphorylase†

PubMed Central

Edwards, Achelle A.; Mason, Jennifer M.; Clinch, Keith; Tyler, Peter C.; Evans, Gary B.; Schramm, Vern L.

2009-01-01

Human purine nucleoside phosphorylase (PNP) belongs to the trimeric class of PNPs and is essential for catabolism of deoxyguanosine. Genetic deficiency of PNP in humans causes a specific T-cell immune deficiency and transition state analogue inhibitors of PNP are in development for treatment of T-cell cancers and autoimmune disorders. Four generations of Immucillins have been developed, each of which contains inhibitors binding with picomolar affinity to human PNP. Full inhibition of PNP occurs upon binding to the first of three subunits and binding to subsequent sites occurs with negative cooperativity. In contrast, substrate analogue and product bind without cooperativity. Titrations of human PNP using isothermal calorimetery indicate that binding of a structurally rigid first-generation Immucillin (K d = 56 pM) is driven by large negative enthalpy values (ΔH = −21.2 kcal/mol) with a substantial entropic (-TΔS) penalty. The tightest-binding inhibitors (K d = 5 to 9 pM) have increased conformational flexibility. Despite their conformational freedom in solution, flexible inhibitors bind with high affinity because of reduced entropic penalties. Entropic penalties are proposed to arise from conformational freezing of the PNP·inhibitor complex with the entropy term dominated by protein dynamics. The conformationally flexible Immucillins reduce the system entropic penalty. Disrupting the ribosyl 5’-hydroxyl interaction of transition state analogues with PNP causes favorable entropy of binding. Tight binding of the seventeen Immucillins is characterized by large enthalpic contributions, emphasizing their similarity to the transition state. By introducing flexibility into the inhibitor structure, the enthalpy-entropy compensation pattern is altered to permit tighter binding. PMID:19425594

Beyond Atomic Sizes and Hume-Rothery Rules: Understanding and Predicting High-Entropy Alloys

DOE PAGES

Troparevsky, M. Claudia; Morris, James R.; Daene, Markus; ...

2015-09-03

High-entropy alloys constitute a new class of materials that provide an excellent combination of strength, ductility, thermal stability, and oxidation resistance. Although they have attracted extensive attention due to their potential applications, little is known about why these compounds are stable or how to predict which combination of elements will form a single phase. Here, we present a review of the latest research done on these alloys focusing on the theoretical models devised during the last decade. We discuss semiempirical methods based on the Hume-Rothery rules and stability criteria based on enthalpies of mixing and size mismatch. To provide insightsmore » into the electronic and magnetic properties of high-entropy alloys, we show the results of first-principles calculations of the electronic structure of the disordered solid-solution phase based on both Korringa Kohn Rostoker coherent potential approximation and large supercell models of example face-centered cubic and body-centered cubic systems. Furthermore, we discuss in detail a model based on enthalpy considerations that can predict which elemental combinations are most likely to form a single-phase high-entropy alloy. The enthalpies are evaluated via first-principles high-throughput density functional theory calculations of the energies of formation of binary compounds, and therefore it requires no experimental or empirically derived input. Finally, the model correctly accounts for the specific combinations of metallic elements that are known to form single-phase alloys while rejecting similar combinations that have been tried and shown not to be single phase.« less

Entropy–enthalpy transduction caused by conformational shifts can obscure the forces driving protein–ligand binding

PubMed Central

Fenley, Andrew T.; Muddana, Hari S.; Gilson, Michael K.

2012-01-01

Molecular dynamics simulations of unprecedented duration now can provide new insights into biomolecular mechanisms. Analysis of a 1-ms molecular dynamics simulation of the small protein bovine pancreatic trypsin inhibitor reveals that its main conformations have different thermodynamic profiles and that perturbation of a single geometric variable, such as a torsion angle or interresidue distance, can select for occupancy of one or another conformational state. These results establish the basis for a mechanism that we term entropy–enthalpy transduction (EET), in which the thermodynamic character of a local perturbation, such as enthalpic binding of a small molecule, is camouflaged by the thermodynamics of a global conformational change induced by the perturbation, such as a switch into a high-entropy conformational state. It is noted that EET could occur in many systems, making measured entropies and enthalpies of folding and binding unreliable indicators of actual thermodynamic driving forces. The same mechanism might also account for the high experimental variance of measured enthalpies and entropies relative to free energies in some calorimetric studies. Finally, EET may be the physical mechanism underlying many cases of entropy–enthalpy compensation. PMID:23150595

Theory of competitive solvation of polymers by two solvents and entropy-enthalpy compensation in the solvation free energy upon dilution with the second solvent.

PubMed

Dudowicz, Jacek; Freed, Karl F; Douglas, Jack F

2015-06-07

We develop a statistical mechanical lattice theory for polymer solvation by a pair of relatively low molar mass solvents that compete for binding to the polymer backbone. A theory for the equilibrium mixture of solvated polymer clusters {AiBCj} and free unassociated molecules A, B, and C is formulated in the spirit of Flory-Huggins mean-field approximation. This theoretical framework enables us to derive expressions for the boundaries for phase stability (spinodals) and other basic properties of these polymer solutions: the internal energy U, entropy S, specific heat CV, extent of solvation Φsolv, average degree of solvation 〈Nsolv〉, and second osmotic virial coefficient B2 as functions of temperature and the composition of the mixture. Our theory predicts many new phenomena, but the current paper applies the theory to describe the entropy-enthalpy compensation in the free energy of polymer solvation, a phenomenon observed for many years without theoretical explanation and with significant relevance to liquid chromatography and other polymer separation methods.

Glass transition memorized by the enthalpy-entropy compensation in the shear thinning of supercooled metallic liquids.

PubMed

Zhang, Meng; Liu, Lin

2018-05-03

To unravel the true nature of glass transition, broader insights into glass forming have been gained by examining the stress-driven glassy systems, where strong shear thinning, i.e., a reduced viscosity under increasing shear rate, is encountered. It is argued that arbitrarily small stress-driven shear rates would "melt" the glass and erase any memory of its thermal history. In this work, we report a glass transition memorized by the enthalpy-entropy compensation in strongly shear-thinned supercooled metallic liquids, which coincides with the thermal glass transition in both the transition temperature and the activation Gibbs free energy. Our findings provide distinctive insights into both glass forming and shear thinning, and enrich current knowledge on the ubiquitous enthalpy-entropy compensation empirical law in condensed matter physics. © 2018 IOP Publishing Ltd.

The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition.

PubMed

Fox, Jerome M; Zhao, Mengxia; Fink, Michael J; Kang, Kyungtae; Whitesides, George M

2018-05-20

Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding and no net change in affinities. This phenomenon-termed enthalpy/entropy (H/S) compensation-hinders efforts in biomolecular design, and its incidence-often a surprise to experimentalists-makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/ S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting-and, perhaps, avoiding or exploiting-this phenomenon in biophysical systems.

Glass transition memorized by the enthalpy-entropy compensation in the shear thinning of supercooled metallic liquids

NASA Astrophysics Data System (ADS)

Zhang, Meng; Liu, Lin

2018-06-01

To unravel the true nature of glass transition, broader insights into glass forming have been gained by examining the stress-driven glassy systems, where strong shear thinning, i.e. a reduced viscosity under increasing shear rate, is encountered. It is argued that arbitrarily small stress-driven shear rates would ‘melt’ the glass and erase any memory of its thermal history. In this work, we report a glass transition memorized by the enthalpy-entropy compensation in strongly shear-thinned supercooled metallic liquids, which coincides with the thermal glass transition in both the transition temperature and the activation Gibbs free energy. Our findings provide distinctive insights into both glass forming and shear thinning, and enrich current knowledge on the ubiquitous enthalpy-entropy compensation empirical law in condensed matter physics.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, David L.; Schoof, Justin C.; Hobbs, Michael L.

This report presents plots of specific heat, enthalpy, entropy, and Gibbs free energy for 1439 species in the JCZS2i database. Included in this set of species are 496 condensed-phase species and 943 gas-phase species. The gas phase species contain 80 anions and 112 cations for a total of 192 ions. The JCZS2i database is used in conjunction with the TIGER thermochemical code to predict thermodynamic states from ambient conditions to high temperatures and pressures. Predictions from the TIGER code using the JCZS2i database can be used in shock physics codes where temperatures may be as high as 20,000 K andmore » ions may be present. Such high temperatures were not considered in the original JCZS database, and extrapolations made for these temperatures were unrealistic. For example, specific heat would sometimes go negative at high temperatures which fails the definition of specific heat. The JCZS2i database is a new version of the JCZS database that is being created to address these inaccuracies. The purpose of the current report is to visualize the high temperature extrapolations to insure that the specific heat, enthalpy, entropy, and Gibbs free energy predictions are reasonable up to 20,000 K.« less

Entropy-enthalpy compensation at the single protein level: pH sensing in the bacterial channel OmpF.

PubMed

Alcaraz, Antonio; Queralt-Martín, María; Verdiá-Báguena, Carmina; Aguilella, Vicente M; Mafé, Salvador

2014-12-21

The pH sensing mechanism of the OmpF channel operates via ligand modification: increasing acidity induces the replacement of cations with protons in critical binding sites decreasing the channel conductance. Aside from the change in enthalpy associated with the binding, there is also a change in the microscopic arrangements of ligands, receptors and the surrounding solvent. We show that the pH-modulation of the single channel conduction involves small free energy changes because large enthalpic and entropic contributions change in opposite ways, demonstrating an approximate enthalpy-entropy compensation for different salts and concentrations.

Computer program for obtaining thermodynamic and transport properties of air and products of combustion of ASTM-A-1 fuel and air

NASA Technical Reports Server (NTRS)

Hippensteele, S. A.; Colladay, R. S.

1978-01-01

A computer program for determining desired thermodynamic and transport property values by means of a three-dimensional (pressure, fuel-air ratio, and either enthalpy or temperature) interpolation routine was developed. The program calculates temperature (or enthalpy), molecular weight, viscosity, specific heat at constant pressure, thermal conductivity, isentropic exponent (equal to the specific heat ratio at conditions where gases do not react), Prandtl number, and entropy for air and a combustion gas mixture of ASTM-A-1 fuel and air over fuel-air ratios from zero to stoichiometric, pressures from 1 to 40 atm, and temperatures from 250 to 2800 K.

Sorption isotherms, thermodynamic properties and glass transition temperature of mucilage extracted from chia seeds (Salvia hispanica L.).

PubMed

Velázquez-Gutiérrez, Sandra Karina; Figueira, Ana Cristina; Rodríguez-Huezo, María Eva; Román-Guerrero, Angélica; Carrillo-Navas, Hector; Pérez-Alonso, César

2015-05-05

Freeze-dried chia mucilage adsorption isotherms were determined at 25, 35 and 40°C and fitted with the Guggenheim-Anderson-de Boer model. The integral thermodynamic properties (enthalpy and entropy) were estimated with the Clausius-Clapeyron equation. Pore radius of the mucilage, calculated with the Kelvin equation, varied from 0.87 to 6.44 nm in the temperature range studied. The point of maximum stability (minimum integral entropy) ranged between 7.56 and 7.63kg H2O per 100 kg of dry solids (d.s.) (water activity of 0.34-0.53). Enthalpy-entropy compensation for the mucilage showed two isokinetic temperatures: (i) one occurring at low moisture contents (0-7.56 kg H2O per 100 kg d.s.), controlled by changes in water entropy; and (ii) another happening in the moisture interval of 7.56-24 kg H2O per 100 kg d.s. and was enthalpy driven. The glass transition temperature Tg of the mucilage fluctuated between 42.93 and 57.93°C. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dominant Alcohol-Protein Interaction via Hydration-Enabled Enthalpy-Driven Binding Mechanism

PubMed Central

Chong, Yuan; Kleinhammes, Alfred; Tang, Pei; Xu, Yan; Wu, Yue

2015-01-01

Water plays an important role in weak associations of small drug molecules with proteins. Intense focus has been on binding-induced structural changes in the water network surrounding protein binding sites, especially their contributions to binding thermodynamics. However, water is also tightly coupled to protein conformations and dynamics, and so far little is known about the influence of water-protein interactions on ligand binding. Alcohols are a type of low-affinity drugs, and it remains unclear how water affects alcohol-protein interactions. Here, we present alcohol adsorption isotherms under controlled protein hydration using in-situ NMR detection. As functions of hydration level, Gibbs free energy, enthalpy, and entropy of binding were determined from the temperature dependence of isotherms. Two types of alcohol binding were found. The dominant type is low-affinity nonspecific binding, which is strongly dependent on temperature and the level of hydration. At low hydration levels, this nonspecific binding only occurs above a threshold of alcohol vapor pressure. An increased hydration level reduces this threshold, with it finally disappearing at a hydration level of h~0.2 (g water/g protein), gradually shifting alcohol binding from an entropy-driven to an enthalpy-driven process. Water at charged and polar groups on the protein surface was found to be particularly important in enabling this binding. Although further increase in hydration has smaller effects on the changes of binding enthalpy and entropy, it results in significant negative change in Gibbs free energy due to unmatched enthalpy-entropy compensation. These results show the crucial role of water-protein interplay in alcohol binding. PMID:25856773

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stratz, S. Adam; Jones, Steven J.; Mullen, Austin D.

Newly-established adsorption enthalpy and entropy values of 12 lanthanide hexafluoroacetylacetonates, denoted Ln[hfac] 4, along with the experimental and theoretical methodology used to obtain these values, are presented for the first time. The results of this work can be used in conjunction with theoretical modeling techniques to optimize a large-scale gas-phase separation experiment using isothermal chromatography. The results to date indicate average adsorption enthalpy and entropy values of the 12 Ln[hfac] 4 complexes ranging from -33 to -139 kJ/mol K and -299 to -557 J/mol, respectively.

On the Enthalpy and Entropy of Point Defect Formation in Crystals

NASA Astrophysics Data System (ADS)

Kobelev, N. P.; Khonik, V. A.

2018-03-01

A standard way to determine the formation enthalpy H and entropy S of point defect formation in crystals consists in the application of the Arrhenius equation for the defect concentration. In this work, we show that a formal use of this method actually gives the effective (apparent) values of these quantities, which appear to be significantly overestimated. The underlying physical reason lies in temperature-dependent formation enthalpy of the defects, which is controlled by temperature dependence of the elastic moduli. We present an evaluation of the "true" H- and S-values for aluminum, which are derived on the basis of experimental data by taking into account temperature dependence of the formation enthalpy related to temperature dependence of the elastic moduli. The knowledge of the "true" activation parameters is needed for a correct calculation of the defect concentration constituting thus an issue of major importance for different fundamental and application issues of condensed matter physics and chemistry.

Estimating the melting point, entropy of fusion, and enthalpy of fusion of organic compounds via SPARC

EPA Science Inventory

The entropies of fusion, enthalies of fusion, and melting points of organic compounds can be estimated through three models developed using the SPARC (SPARC Performs Automated Reasoning in Chemistry) platform. The entropy of fusion is modeled through a combination of interaction ...

Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field.

PubMed

Bell, David R; Qi, Rui; Jing, Zhifeng; Xiang, Jin Yu; Mejias, Christopher; Schnieders, Michael J; Ponder, Jay W; Ren, Pengyu

2016-11-09

Molecular recognition is of paramount interest in many applications. Here we investigate a series of host-guest systems previously used in the SAMPL4 blind challenge by using molecular simulations and the AMOEBA polarizable force field. The free energy results computed by Bennett's acceptance ratio (BAR) method using the AMOEBA polarizable force field ranked favorably among the entries submitted to the SAMPL4 host-guest competition [Muddana, et al., J. Comput.-Aided Mol. Des., 2014, 28, 305-317]. In this work we conduct an in-depth analysis of the AMOEBA force field host-guest binding thermodynamics by using both BAR and the orthogonal space random walk (OSRW) methods. The binding entropy-enthalpy contributions are analyzed for each host-guest system. For systems of inordinate binding entropy-enthalpy values, we further examine the hydrogen bonding patterns and configurational entropy contribution. The binding mechanism of this series of host-guest systems varies from ligand to ligand, driven by enthalpy and/or entropy changes. Convergence of BAR and OSRW binding free energy methods is discussed. Ultimately, this work illustrates the value of molecular modelling and advanced force fields for the exploration and interpretation of binding thermodynamics.

WASP: A flexible FORTRAN 4 computer code for calculating water and steam properties

NASA Technical Reports Server (NTRS)

Hendricks, R. C.; Peller, I. C.; Baron, A. K.

1973-01-01

A FORTRAN 4 subprogram, WASP, was developed to calculate the thermodynamic and transport properties of water and steam. The temperature range is from the triple point to 1750 K, and the pressure range is from 0.1 to 100 MN/m2 (1 to 1000 bars) for the thermodynamic properties and to 50 MN/m2 (500 bars) for thermal conductivity and to 80 MN/m2 (800 bars) for viscosity. WASP accepts any two of pressure, temperature, and density as input conditions. In addition, pressure and either entropy or enthalpy are also allowable input variables. This flexibility is especially useful in cycle analysis. The properties available in any combination as output include temperature, density, pressure, entropy, enthalpy, specific heats, sonic velocity, viscosity, thermal conductivity, surface tension, and the Laplace constant. The subroutine structure is modular so that the user can choose only those subroutines necessary to his calculations. Metastable calculations can also be made by using WASP.

Isothermal titration calorimetric studies on the interaction of the major bovine seminal plasma protein, PDC-109 with phospholipid membranes.

PubMed

Anbazhagan, V; Sankhala, Rajeshwer S; Singh, Bhanu Pratap; Swamy, Musti J

2011-01-01

The interaction of the major bovine seminal plasma protein, PDC-109 with lipid membranes was investigated by isothermal titration calorimetry. Binding of the protein to model membranes made up of diacyl phospholipids was found to be endothermic, with positive values of binding enthalpy and entropy, and could be analyzed in terms of a single type of binding sites on the protein. Enthalpies and entropies for binding to diacylphosphatidylcholine membranes increased with increase in temperature, although a clear-cut linear dependence was not observed. The entropically driven binding process indicates that hydrophobic interactions play a major role in the overall binding process. Binding of PDC-109 with dimyristoylphosphatidylcholine membranes containing 25 mol% cholesterol showed an initial increase in the association constant as well as enthalpy and entropy of binding with increase in temperature, whereas the values decreased with further increase in temperature. The affinity of PDC-109 for phosphatidylcholine increased at higher pH, which is physiologically relevant in view of the basic nature of the seminal plasma. Binding of PDC-109 to Lyso-PC could be best analysed in terms of two types of binding interactions, a high affinity interaction with Lyso-PC micelles and a low-affinity interaction with the monomeric lipid. Enthalpy-entropy compensation was observed for the interaction of PDC-109 with phospholipid membranes, suggesting that water structure plays an important role in the binding process.

Isothermal Titration Calorimetric Studies on the Interaction of the Major Bovine Seminal Plasma Protein, PDC-109 with Phospholipid Membranes

PubMed Central

Anbazhagan, V.; Sankhala, Rajeshwer S.; Singh, Bhanu Pratap; Swamy, Musti J.

2011-01-01

The interaction of the major bovine seminal plasma protein, PDC-109 with lipid membranes was investigated by isothermal titration calorimetry. Binding of the protein to model membranes made up of diacyl phospholipids was found to be endothermic, with positive values of binding enthalpy and entropy, and could be analyzed in terms of a single type of binding sites on the protein. Enthalpies and entropies for binding to diacylphosphatidylcholine membranes increased with increase in temperature, although a clear-cut linear dependence was not observed. The entropically driven binding process indicates that hydrophobic interactions play a major role in the overall binding process. Binding of PDC-109 with dimyristoylphosphatidylcholine membranes containing 25 mol% cholesterol showed an initial increase in the association constant as well as enthalpy and entropy of binding with increase in temperature, whereas the values decreased with further increase in temperature. The affinity of PDC-109 for phosphatidylcholine increased at higher pH, which is physiologically relevant in view of the basic nature of the seminal plasma. Binding of PDC-109 to Lyso-PC could be best analysed in terms of two types of binding interactions, a high affinity interaction with Lyso-PC micelles and a low-affinity interaction with the monomeric lipid. Enthalpy-entropy compensation was observed for the interaction of PDC-109 with phospholipid membranes, suggesting that water structure plays an important role in the binding process. PMID:22022488

Extreme Entropy-Enthalpy Compensation in a Drug Resistant Variant of HIV-1 Protease

PubMed Central

King, Nancy M.; Prabu-Jeyabalan, Moses; Bandaranayake, Rajintha M.; Nalam, Madhavi N. L.; Nalivaika, Ellen A.; Özen, Ayşegül; Haliloglu, Türkan; Yılmaz, Neşe Kurt; Schiffer, Celia A.

2012-01-01

The development of HIV-1 protease inhibitors has been the historic paradigm of rational structure-based drug design, where structural and thermodynamic analyses have assisted in the discovery of novel inhibitors. While the total enthalpy and entropy change upon binding determine the affinity, often the thermodynamics are considered in terms of inhibitor properties only. In the current study, profound changes are observed in the binding thermodynamics of a drug resistant variant compared to wild-type HIV-1 protease, irrespective of the inhibitor bound. This variant (Flap+) has a combination of flap and active site mutations and exhibits extremely large entropy-enthalpy compensation compared to wild-type protease, 5–15 kcal/mol, while losing only 1–3 kcal/mol in total binding free energy for any of six FDA approved inhibitors. Although entropy-enthalpy compensation has been previously observed for a variety of systems, never have changes of this magnitude been reported. The co-crystal structures of Flap+ protease with four of the inhibitors were determined and compared with complexes of both the wildtype protease and another drug resistant variant that does not exhibit this energetic compensation. Structural changes conserved across the Flap+ complexes, which are more pronounced for the flaps covering the active site, likely contribute to the thermodynamic compensation. The finding that drug resistant mutations can profoundly modulate the relative thermodynamic properties of a therapeutic target independent of the inhibitor presents a new challenge for rational drug design. PMID:22712830

Gas chemical adsorption characterization of lanthanide hexafluoroacetylacetonates

DOE PAGES

Stratz, S. Adam; Jones, Steven J.; Mullen, Austin D.; ...

2017-03-21

Newly-established adsorption enthalpy and entropy values of 12 lanthanide hexafluoroacetylacetonates, denoted Ln[hfac] 4, along with the experimental and theoretical methodology used to obtain these values, are presented for the first time. The results of this work can be used in conjunction with theoretical modeling techniques to optimize a large-scale gas-phase separation experiment using isothermal chromatography. The results to date indicate average adsorption enthalpy and entropy values of the 12 Ln[hfac] 4 complexes ranging from -33 to -139 kJ/mol K and -299 to -557 J/mol, respectively.

Behavior of the Enthalpy of Adsorption in Nanoporous Materials Close to Saturation Conditions

PubMed Central

2017-01-01

Many important industrial separation processes based on adsorption operate close to saturation. In this regime, the underlying adsorption processes are mostly driven by entropic forces. At equilibrium, the entropy of adsorption is closely related to the enthalpy of adsorption. Thus, studying the behavior of the enthalpy of adsorption as a function of loading is fundamental to understanding separation processes. Unfortunately, close to saturation, the enthalpy of adsorption is hard to measure experimentally and hard to compute in simulations. In simulations, the enthalpy of adsorption is usually obtained from energy/particle fluctuations in the grand-canonical ensemble, but this methodology is hampered by vanishing insertions/deletions at high loading. To investigate the fundamental behavior of the enthalpy and entropy of adsorption at high loading, we develop a simplistic model of adsorption in a channel and show that at saturation the enthalpy of adsorption diverges to large positive values due to repulsive intermolecular interactions. However, there are many systems that can avoid repulsive intermolecular interactions and hence do not show this drastic increase in enthalpy of adsorption close to saturation. We find that the conventional grand-canonical Monte Carlo method is incapable of determining the enthalpy of adsorption from energy/particle fluctuations at high loading. Here, we show that by using the continuous fractional component Monte Carlo, the enthalpy of adsorption close to saturation conditions can be reliably obtained from the energy/particle fluctuations in the grand-canonical ensemble. The best method to study properties at saturation is the NVT energy (local-) slope methodology. PMID:28521093

Computer program for calculation of real gas turbulent boundary layers with variable edge entropy

NASA Technical Reports Server (NTRS)

Boney, L. R.

1974-01-01

A user's manual for a computer program which calculates real gas turbulent boundary layers with variable edge entropy on a blunt cone or flat plate at zero angle of attack is presented. An integral method is used. The method includes the effect of real gas in thermodynamic equilibrium and variable edge entropy. A modified Crocco enthalpy velocity relationship is used for the enthalpy profiles and an empirical correlation of the N-power law profile is used for the velocity profile. The skin-friction-coefficient expressions of Spalding and Chi and Van Driest are used in the solution of the momentum equation and in the heat-transfer predictions that use several modified forms of Reynolds analogy.

Bacterial protease uses distinct thermodynamic signatures for substrate recognition.

PubMed

Bezerra, Gustavo Arruda; Ohara-Nemoto, Yuko; Cornaciu, Irina; Fedosyuk, Sofiya; Hoffmann, Guillaume; Round, Adam; Márquez, José A; Nemoto, Takayuki K; Djinović-Carugo, Kristina

2017-06-06

Porphyromonas gingivalis and Porphyromonas endodontalis are important bacteria related to periodontitis, the most common chronic inflammatory disease in humans worldwide. Its comorbidity with systemic diseases, such as type 2 diabetes, oral cancers and cardiovascular diseases, continues to generate considerable interest. Surprisingly, these two microorganisms do not ferment carbohydrates; rather they use proteinaceous substrates as carbon and energy sources. However, the underlying biochemical mechanisms of their energy metabolism remain unknown. Here, we show that dipeptidyl peptidase 11 (DPP11), a central metabolic enzyme in these bacteria, undergoes a conformational change upon peptide binding to distinguish substrates from end products. It binds substrates through an entropy-driven process and end products in an enthalpy-driven fashion. We show that increase in protein conformational entropy is the main-driving force for substrate binding via the unfolding of specific regions of the enzyme ("entropy reservoirs"). The relationship between our structural and thermodynamics data yields a distinct model for protein-protein interactions where protein conformational entropy modulates the binding free-energy. Further, our findings provide a framework for the structure-based design of specific DPP11 inhibitors.

Extrapolation of thermophysical properties data for oxygen to high pressures (5000 to 10,000 psia) at low temperatures (100-600 R)

NASA Technical Reports Server (NTRS)

Weber, L. A.

1971-01-01

Thermophysical properties data for oxygen at pressures below 5000 psia have been extrapolated to higher pressures (5,000-10,000 psia) in the temperature range 100-600 R. The tables include density, entropy, enthalpy, internal energy, speed of sound, specific heat, thermal conductivity, viscosity, thermal diffusivity, Prandtl number, and dielectric constant.

Thermodynamic Origins of Monovalent Facilitated RNA Folding

PubMed Central

Holmstrom, Erik D.; Fiore, Julie L.; Nesbitt, David J.

2012-01-01

Cations have long been associated with formation of native RNA structure and are commonly thought to stabilize the formation of tertiary contacts by favorably interacting with the electrostatic potential of the RNA, giving rise to an “ion atmosphere”. A significant amount of information regarding the thermodynamics of structural transitions in the presence of an ion atmosphere has accumulated and suggests stabilization is dominated by entropic terms. This work provides an analysis of how RNA–cation interactions affect the entropy and enthalpy associated with an RNA tertiary transition. Specifically, temperature-dependent single-molecule fluorescence resonance energy transfer studies have been exploited to determine the free energy (ΔG°), enthalpy (ΔH°), and entropy (ΔS°) of folding for an isolated tetraloop–receptor tertiary interaction as a function of Na+ concentration. Somewhat unexpectedly, increasing the Na+ concentration changes the folding enthalpy from a strongly exothermic process [e.g., ΔH° = −26(2) kcal/mol at 180 mM] to a weakly exothermic process [e.g., ΔH° = −4(1) kcal/mol at 630 mM]. As a direct corollary, it is the strong increase in folding entropy [Δ(ΔS°) > 0] that compensates for this loss of exothermicity for the achievement of more favorable folding [Δ(ΔG°) < 0] at higher Na+ concentrations. In conjunction with corresponding measurements of the thermodynamics of the transition state barrier, these data provide a detailed description of the folding pathway associated with the GAAA tetraloop–receptor interaction as a function of Na+ concentration. The results support a potentially universal mechanism for monovalent facilitated RNA folding, whereby an increasing monovalent concentration stabilizes tertiary structure by reducing the entropic penalty for folding. PMID:22448852

Thermodynamics for the interaction of epsilon-dinitrophenyl-L-lysine and bovine colostral anti-dinitrophenyl immunoglobulin G2.

PubMed Central

Mukkur, T K

1978-01-01

The effect of varying the temperature over a wide range (4--60 degrees C) on the binding of epsilon-dinitrophenyl-L-lysine to bovine colostral anti-dinitrophenyl immunoglobulin G2 yielded a non-linear van't Hoff plot. The extent of curvature was indicative of a large positive heat-capacity change, and the thermodynamic parameters, calculated by using a non-linear least squares computer procedure, revealed an enthalpy--entropy-compensation mechanism for hapten-antibody binding. The enthalpy factor was found to be the primary contributor for the complex-formation at low temperatures, but at increasing temperatures the entropy factor assumed greater importance. At physiological temperature (39 degrees C), the entropy factor was the major contributor to the free energy of reaction. PMID:687378

Is there a link between selectivity and binding thermodynamics profiles?

PubMed

Tarcsay, Ákos; Keserű, György M

2015-01-01

Thermodynamics of ligand binding is influenced by the interplay between enthalpy and entropy contributions of the binding event. The impact of these binding free energy components, however, is not limited to the primary target only. Here, we investigate the relationship between binding thermodynamics and selectivity profiles by combining publicly available data from broad off-target assay profiling and the corresponding thermodynamics measurements. Our analysis indicates that compounds binding their primary targets with higher entropy contributions tend to hit more off-targets compared with those ligands that demonstrated enthalpy-driven binding. Copyright © 2014 Elsevier Ltd. All rights reserved.

Thermodynamics of antagonist binding to rat muscarinic M2 receptors: antimuscarinics of the pridinol, sila-pridinol, diphenidol and sila-diphenidol type.

PubMed Central

Waelbroeck, M.; Camus, J.; Tastenoy, M.; Lambrecht, G.; Mutschler, E.; Kropfgans, M.; Sperlich, J.; Wiesenberger, F.; Tacke, R.; Christophe, J.

1993-01-01

1. We studied the effect of temperature on the binding to rat heart M2 muscarinic receptors of antagonists related to the carbon/silicon pairs pridinol/sila-pridinol and diphenidol/sila-diphenidol (including three germanium compounds) and six structurally related pairs of enantiomers [(R)- and (S)-procyclidine, (R)- and (S)-trihexyphenidyl, (R)- and (S)-tricyclamol, (R)- and (S)-trihexyphenidyl methiodide, (R)- and (S)-hexahydro-diphenidol and (R)- and (S)-hexbutinol]. Binding affinities were determined in competition experiments using [3H]-N-methyl-scopolamine chloride as radioligand. The reference drugs were scopolamine and N-methyl-scopolamine bromide. 2. The affinity of the antagonists either increased or decreased with temperature. van't Hoff plots were linear in the 278-310 degrees K temperature range. Binding of all antagonists was entropy driven. Enthalpy changes varied from large negative values (down to -29 kJ mol-1) to large positive values (up to +30 kJ mol-1). 3. (R)-configurated drugs had a 10 to 100 fold greater affinity for M2 receptors than the corresponding (S)-enantiomers. Enthalpy and entropy changes of the respective enantiomers were different but no consistent pattern was observed. 4. When silanols (R3SiOH) were compared to carbinols (R3COH), the affinity increase caused by C/Si exchange varied between 3 and 10 fold for achiral drugs but was negligible in the case of chiral drugs. Silanols induced more favourable enthalpy and less favourable entropy changes than the corresponding carbinols when binding. Organogermanium compounds (R4Ge) when compared to their silicon counterparts (R4Si) showed no significant difference in affinity as well as in enthalpy and entropy changes. 5. Exchange of a cyclohexyl by a phenyl moiety was associated with an increase or a decrease in drug affinity (depending on the absolute configuration in the case of chiral drugs) and generally also with a more favourable enthalpy change and a less favourable entropy change of drug binding. 6. Replacement of a pyrrolidino by a piperidino group and increasing the length of the alkylene chain bridging the amino group and the central carbon or silicon atom were associated with either an increase or a decrease of entropy and enthalpy changes of drug binding. However, there was no clear correlation between these structural variations and the thermodynamic effects. 7. Taken together, these results suggest that hydrogen bond-forming OH groups and, to a lesser extent, polarizable phenyl groups contribute significantly to the thermodynamics of interactions between these classes of muscarinic antagonists and M2 muscarinic receptors. PMID:8102927

Thermodynamic parameters for adsorption equilibrium of heavy metals and dyes from wastewaters: Research updated.

PubMed

Chang, Yingju; Lai, Juin-Yih; Lee, Duu-Jong

2016-12-01

The standard Gibbs free energy, enthalpy and entropy change data for adsorption equilibrium reported in biosorption literature during January 2013-May2016 were listed. Since the studied biosorption systems are all near-equilibrium processes, the enthalpy and entropy change data evaluated by fitting temperature-dependent free energy data using van Hoff's equation reveal a compensation artifact. Additional confusion is introduced with arbitrarily chosen adsorbate concentration unit in bulk solution that added free energy change of mixing into the reported free energy and enthalpy change data. Different standard states may be chosen for properly describing biosorption processes; however, this makes the general comparison between data from different systems inappropriate. No conclusion should be drawn based on unjustified thermodynamic parameters reported in biosorption studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Adsorption of Organic Molecules to van der Waals Materials: Comparison of Fluorographene and Fluorographite with Graphene and Graphite

PubMed Central

2017-01-01

Understanding strength and nature of noncovalent binding to surfaces imposes significant challenge both for computations and experiments. We explored the adsorption of five small nonpolar organic molecules (acetone, acetonitrile, dichloromethane, ethanol, ethyl acetate) to fluorographene and fluorographite using inverse gas chromatography and theoretical calculations, providing new insights into the strength and nature of adsorption of small organic molecules on these surfaces. The measured adsorption enthalpies on fluorographite range from −7 to −13 kcal/mol and are by 1–2 kcal/mol lower than those measured on graphene/graphite, which indicates higher affinity of organic adsorbates to fluorographene than to graphene. The dispersion-corrected functionals performed well, and the nonlocal vdW DFT functionals (particularly optB86b-vdW) achieved the best agreement with the experimental data. Computations show that the adsorption enthalpies are controlled by the interaction energy, which is dominated by London dispersion forces (∼70%). The calculations also show that bonding to structural features, like edges and steps, as well as defects does not significantly increase the adsorption enthalpies, which explains a low sensitivity of measured adsorption enthalpies to coverage. The adopted Langmuir model for fitting experimental data enabled determination of adsorption entropies. The adsorption on the fluorographene/fluorographite surface resulted in an entropy loss equal to approximately 40% of the gas phase entropy. PMID:28145699

Moderate point: Balanced entropy and enthalpy contributions in soft matter

NASA Astrophysics Data System (ADS)

He, Baoji; Wang, Yanting

2017-03-01

Various soft materials share some common features, such as significant entropic effect, large fluctuations, sensitivity to thermodynamic conditions, and mesoscopic characteristic spatial and temporal scales. However, no quantitative definitions have yet been provided for soft matter, and the intrinsic mechanisms leading to their common features are unclear. In this work, from the viewpoint of statistical mechanics, we show that soft matter works in the vicinity of a specific thermodynamic state named moderate point, at which entropy and enthalpy contributions among substates along a certain order parameter are well balanced or have a minimal difference. Around the moderate point, the order parameter fluctuation, the associated response function, and the spatial correlation length maximize, which explains the large fluctuation, the sensitivity to thermodynamic conditions, and mesoscopic spatial and temporal scales of soft matter, respectively. Possible applications to switching chemical bonds or allosteric biomachines determining their best working temperatures are also briefly discussed. Project supported by the National Basic Research Program of China (Grant No. 2013CB932804) and the National Natural Science Foundation of China (Grant Nos. 11274319 and 11421063).

Human serum albumin binding of certain antimalarials

NASA Astrophysics Data System (ADS)

Marković, Olivera S.; Cvijetić, Ilija N.; Zlatović, Mario V.; Opsenica, Igor M.; Konstantinović, Jelena M.; Terzić Jovanović, Nataša V.; Šolaja, Bogdan A.; Verbić, Tatjana Ž.

2018-03-01

Interactions between eight in-house synthesized aminoquinolines, along with well-known chloroquine, and human serum albumin (HSA) have been studied by fluorescence spectroscopy. The synthesized aminoquinolines, despite being structurally diverse, were found to be very potent antimalarials. Fluorescence measurements indicate that three compounds having additional thiophene or benzothiophene substructure bind more strongly to HSA than other studied compounds. Competitive binding experiments indicate that these three compounds bind significantly stronger to warfarin compared to diazepam binding site. Fluorescence quenching at three temperatures (20, 25, and 37 °C) was analyzed using classical Stern-Volmer equation, and a static quenching mechanism was proposed. The enthalpy and entropy changes upon sulphur-containing compound-HSA interactions were calculated using Van't Hoff equation. Positive values of enthalpy and entropy changes indicate that non-specific, hydrophobic interactions are the main contributors to HSA-compound interaction. Molecular docking and calculated lipophilicity descriptors indicate the same, pointing out that the increased lipophilicity of sulphur-containing compounds might be a reason for their better binding to HSA. Obtained results might contribute to design of novel derivatives with improved pharmacokinetic properties and drug efficacy.

DNA interaction studies of sesamol (3,4-methylenedioxyphenol) food additive.

PubMed

Kashanian, Soheila; Tahmasian Ghobadi, Ameneh; Roshanfekr, Hamideh; Shariati, Zohreh

2013-02-01

The interaction of native calf thymus DNA (CT-DNA) with sesamol (3,4-methylenedioxyphenol) in Tris-HCl buffer at neutral pH 7.4 was monitored by absorption spectrophotometry, viscometry and spectrofluorometry. It is found that sesamol molecules could interact with DNA outside and/or groove binding modes, as are evidenced by: hyperchromism in UV absorption band, very slow decrease in specific viscosity of DNA, and small increase in the fluorescence of methylene blue (MB)-DNA solutions in the presence of increasing amounts of sesamol, which indicates that it is able to partially release the bound MB. Furthermore, the enthalpy and entropy of the reaction between sesamol and CT-DNA showed that the reaction is enthalpy-favored and entropy-disfavored (ΔH = -174.08 kJ mol(-1); ΔS = -532.92 J mol(-1) K(-1)). The binding constant was determined using absorption measurement and found to be 2.7 × 10(4) M(-1); its magnitude suggests that sesamol interacts to DNA with a high affinity.

Borate-polyol complexes in aqueous solution: determination of enthalpies by thermometric titrimetry.

PubMed

Aruga, R

1985-06-01

Enthalpies for the reaction of borate with 1,2-ethanediol, 1,2-propanediol, 1,2,3-propanetriol and d-mannitol have been determined by thermometric titrimetry. From these enthalpies and equilibrium constants taken from the literature, corresponding entropies have been calculated. The data refer to aqueous solutions at 25 degrees and I = 1.0M (NaNO(3)). The results indicate reasons for the differences in the stabilities of the complexes.

The effect of stereochemistry on the thermodynamic characteristics of the binding of fenoterol stereoisomers to the β2-adrenoceptor

PubMed Central

Jozwiak, Krzysztof; Toll, Lawrence; Jimenez, Lucita; Woo, Anthony Yiu-Ho; Xiao, Rui-Ping; Wainer, Irving W.

2010-01-01

The binding thermodynamics of the stereoisomers of fenoterol, (R,R')-, (S,S')- , (R,S')-, and (S,R')-fenoterol, to the β2-adrenergic receptor (β2-AR) have been determined. The experiments utilized membranes obtained from HEK cells stably transfected with cDNA encoding human β2-AR. Competitive displacement studies using [3H]CGP-12177 as the marker ligand were conducted at 4°, 15°, 25°, 30° and 37°C, the binding affinities calculated and the standard enthalpic (ΔH°) and standard entropic (ΔS°) contribution to the standard free energy change (ΔG°) associated with the binding process determined through the construction of van't Hoff plots. The results indicate that the binding of (S,S')- and (S,R')-fenoterol were predominately enthalpy-driven processes while the binding of (R,R')- and (R,S')-fenoterol were entropy-driven. All of the fenoterol stereoisomers are full agonists of the β2-AR, and, therefore, the results of this study are inconsistent with the previously described “thermodynamic agonist-antagonist discrimination”, in which the binding of an agonist to the β-AR is entropy-driven and the binding of an antagonist is enthalpy driven. In addition, the data demonstrate that the chirality of the carbon atom containing the β-hydroxyl group of the fenoterol molecule (the β-OH carbon) is a key factor in the determination of whether the binding process will be enthalpy-driven or entropy-driven. When the configuration at the β-OH carbon is S the binding process is enthalpy-driven while the R configuration produces an entropy-driven process. PMID:20144591

The effect of stereochemistry on the thermodynamic characteristics of the binding of fenoterol stereoisomers to the beta(2)-adrenoceptor.

PubMed

Jozwiak, Krzysztof; Toll, Lawrence; Jimenez, Lucita; Woo, Anthony Yiu-Ho; Xiao, Rui-Ping; Wainer, Irving W

2010-06-01

The binding thermodynamics of the stereoisomers of fenoterol, (R,R')-, (S,S')-, (R,S')-, and (S,R')-fenoterol, to the beta(2)-adrenergic receptor (beta(2)-AR) have been determined. The experiments utilized membranes obtained from HEK cells stably transfected with cDNA encoding human beta(2)-AR. Competitive displacement studies using [(3)H]CGP-12177 as the marker ligand were conducted at 4, 15, 25, 30 and 37 degrees C, the binding affinities calculated and the standard enthalpic (DeltaH degrees ) and standard entropic (DeltaS degrees ) contribution to the standard free energy change (DeltaG degrees ) associated with the binding process determined through the construction of van't Hoff plots. The results indicate that the binding of (S,S')- and (S,R')-fenoterol were predominately enthalpy-driven processes while the binding of (R,R')- and (R,S')-fenoterol were entropy-driven. All of the fenoterol stereoisomers are full agonists of the beta(2)-AR, and, therefore, the results of this study are inconsistent with the previously described "thermodynamic agonist-antagonist discrimination", in which the binding of an agonist to the beta-AR is entropy-driven and the binding of an antagonist is enthalpy-driven. In addition, the data demonstrate that the chirality of the carbon atom containing the beta-hydroxyl group of the fenoterol molecule (the beta-OH carbon) is a key factor in the determination of whether the binding process will be enthalpy-driven or entropy-driven. When the configuration at the beta-OH carbon is S the binding process is enthalpy-driven while the R configuration produces an entropy-driven process. Published by Elsevier Inc.

Binding of the Biogenic Polyamines to Deoxyribonucleic Acids of Varying Base Composition: Base Specificity and the Associated Energetics of the Interaction

PubMed Central

Kabir, Ayesha; Suresh Kumar, Gopinatha

2013-01-01

Background The thermodynamics of the base pair specificity of the binding of the polyamines spermine, spermidine, putrescine, and cadaverine with three genomic DNAs Clostridium perfringens, 27% GC, Escherichia coli, 50% GC and Micrococcus lysodeikticus, 72% GC have been studied using titration calorimetry and the data supplemented with melting studies, ethidium displacement and circular dichroism spectroscopy results. Methodology/Principal Findings Isothermal titration calorimetry, differential scanning calorimetry, optical melting studies, ethidium displacement, circular dichroism spectroscopy are the various techniques employed to characterize the interaction of four polyamines, spermine, spermidine, putersine and cadaverine with the DNAs. Polyamines bound stronger with AT rich DNA compared to the GC rich DNA and the binding varied depending on the charge on the polyamine as spermine>spermidine >putrescine>cadaverine. Thermodynamics of the interaction revealed that the binding was entropy driven with small enthalpy contribution. The binding was influenced by salt concentration suggesting the contribution from electrostatic forces to the Gibbs energy of binding to be the dominant contributor. Each system studied exhibited enthalpy-entropy compensation. The negative heat capacity changes suggested a role for hydrophobic interactions which may arise due to the non polar interactions between DNA and polyamines. Conclusion/Significance From a thermodynamic analysis, the AT base specificity of polyamines to DNAs has been elucidated for the first time and supplemented by structural studies. PMID:23894663

Hidden disorder in the α '→δ transformation of Pu-1.9 at.% Ga

DOE PAGES

Jeffries, J. R.; Manley, M. E.; Wall, M. A.; ...

2012-06-06

Enthalpy and entropy are thermodynamic quantities critical to determining how and at what temperature a phase transition occurs. At a phase transition, the enthalpy and temperature-weighted entropy differences between two phases are equal (ΔH=TΔS), but there are materials where this balance has not been experimentally or theoretically realized, leading to the idea of hidden order and disorder. In a Pu-1.9 at. % Ga alloy, the δ phase is retained as a metastable state at room temperature, but at low temperatures, the δ phase yields to a mixed-phase microstructure of δ- and α'-Pu. The previously measured sources of entropy associated withmore » the α'→δ transformation fail to sum to the entropy predicted theoretically. We report an experimental measurement of the entropy of the α'→δ transformation that corroborates the theoretical prediction, and implies that only about 65% of the entropy stabilizing the δ phase is accounted for, leaving a missing entropy of about 0.5 k B/atom. Some previously proposed mechanisms for generating entropy are discussed, but none seem capable of providing the necessary disorder to stabilize the δ phase. This hidden disorder represents multiple accessible states per atom within the δ phase of Pu that may not be included in our current understanding of the properties and phase stability of δ-Pu.« less

Reference States and Relative Values of Internal Energy, Enthalpy, and Entropy.

ERIC Educational Resources Information Center

Fredrickson, A. G.

1983-01-01

Discusses two reference states (pure chemical compounds and pure elements at specified condition of temperature and pressure) and the relation between these reference states for internal energy and enthalpy. Problem 5.11 from Modell and Reid's "Thermodynamics and its Applications" (p. 141) is used to apply the ideas discussed. (JN)

Communication: Hydrogen bonding interactions in water-alcohol mixtures from X-ray absorption spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lam, Royce K.; Smith, Jacob W.; Saykally, Richard J., E-mail: saykally@berkeley.edu

While methanol and ethanol are macroscopically miscible with water, their mixtures exhibit negative excess entropies of mixing. Despite considerable effort in both experiment and theory, there remains significant disagreement regarding the origin of this effect. Different models for the liquid mixture structure have been proposed to address this behavior, including the enhancement of the water hydrogen bonding network around the alcohol hydrophobic groups and microscopic immiscibility or clustering. We have investigated mixtures of methanol, ethanol, and isopropanol with water by liquid microjet X-ray absorption spectroscopy on the oxygen K-edge, an atom-specific probe providing details of both inter- and intra-molecular structure.more » The measured spectra evidence a significant enhancement of hydrogen bonding originating from the methanol and ethanol hydroxyl groups upon the addition of water. These additional hydrogen bonding interactions would strengthen the liquid-liquid interactions, resulting in additional ordering in the liquid structures and leading to a reduction in entropy and a negative enthalpy of mixing, consistent with existing thermodynamic data. In contrast, the spectra of the isopropanol-water mixtures exhibit an increase in the number of broken alcohol hydrogen bonds for mixtures containing up to 0.5 water mole fraction, an observation consistent with existing enthalpy of mixing data, suggesting that the measured negative excess entropy is a result of clustering or micro-immiscibility.« less

Thermodynamics of nuclear track chemical etching

NASA Astrophysics Data System (ADS)

Rana, Mukhtar Ahmed

2018-05-01

This is a brief paper with new and useful scientific information on nuclear track chemical etching. Nuclear track etching is described here by using basic concepts of thermodynamics. Enthalpy, entropy and free energy parameters are considered for the nuclear track etching. The free energy of etching is determined using etching experiments of fission fragment tracks in CR-39. Relationship between the free energy and the etching temperature is explored and is found to be approximately linear. The above relationship is discussed. A simple enthalpy-entropy model of chemical etching is presented. Experimental and computational results presented here are of fundamental interest in nuclear track detection methodology.

[Thermodynamic analysis of water adsorption and desorption process of Chinese herbal decoction pieces].

PubMed

Cheng, Lin; Luo, Xiao-Jian; Han, Xiu-Lin; Wang, Wen-Kai; Rao, Xiao-Yong; Xu, Shao-Zhong; He, Yan

2016-09-01

Based on the basic theory of thermodynamics, the thermodynamic parameters and related equations in the process of water adsorption and desorption of Chinese herbal decoction pieces were established, and their water absorption and desorption characteristics were analyzed. The physical significance of the thermodynamic parameters, such as differential adsorption enthalpy, differential adsorption entropy, integral adsorption enthalpy, integral adsorption entropy and the free energy of adsorption, were discussed in this paper to provide theoretical basis for the research on the water adsorption and desorption mechanism, optimum drying process parameters, storage conditions and packaging methods of Chinese herbal decoction pieces. Copyright© by the Chinese Pharmaceutical Association.

Hydration of dimethyldodecylamine-N-oxide: enthalpy and entropy driven processes.

PubMed

Kocherbitov, Vitaly; Söderman, Olle

2006-07-13

Dimethyldodecylamine-N-oxide (DDAO) has only one polar atom that is able to interact with water. Still, this surfactant shows very hydrophilic properties: in mixtures with water, it forms normal liquid crystalline phases and micelles. Moreover, there is data in the literature indicating that the hydration of this surfactant is driven by enthalpy while other studies show that hydration of surfactants and lipids typically is driven by entropy. Sorption calorimetry allows resolving enthalpic and entropic contributions to the free energy of hydration at constant temperature and thus directly determines the driving forces of hydration. The results of the present sorption calorimetric study show that the hydration of liquid crystalline phases of DDAO is driven by entropy, except for the hydration of the liquid crystalline lamellar phase which is co-driven by enthalpy. The exothermic heat effect of the hydration of the lamellar phase arises from formation of strong hydrogen bonds between DDAO and water. Another issue is the driving forces of the phase transitions caused by the hydration. The sorption calorimetric results show that the transitions from the lamellar to cubic and from the cubic to the hexagonal phase are driven by enthalpy. Transitions from solid phases to the liquid crystalline lamellar phase are entropically driven, while the formation of the monohydrate from the dry surfactant is driven by enthalpy. The driving forces of the transition from the hexagonal phase to the isotropic solution are close to zero. These sorption calorimetric results are in good agreement with the analysis of the binary phase diagram based on the van der Waals differential equation. The phase diagram of the DDAO-water system determined using DSC and sorption calorimetry is presented.

Multi-Scale Low-Entropy Method for Optimizing the Processing Parameters during Automated Fiber Placement.

PubMed

Han, Zhenyu; Sun, Shouzheng; Fu, Hongya; Fu, Yunzhong

2017-09-03

Automated fiber placement (AFP) process includes a variety of energy forms and multi-scale effects. This contribution proposes a novel multi-scale low-entropy method aiming at optimizing processing parameters in an AFP process, where multi-scale effect, energy consumption, energy utilization efficiency and mechanical properties of micro-system could be taken into account synthetically. Taking a carbon fiber/epoxy prepreg as an example, mechanical properties of macro-meso-scale are obtained by Finite Element Method (FEM). A multi-scale energy transfer model is then established to input the macroscopic results into the microscopic system as its boundary condition, which can communicate with different scales. Furthermore, microscopic characteristics, mainly micro-scale adsorption energy, diffusion coefficient entropy-enthalpy values, are calculated under different processing parameters based on molecular dynamics method. Low-entropy region is then obtained in terms of the interrelation among entropy-enthalpy values, microscopic mechanical properties (interface adsorbability and matrix fluidity) and processing parameters to guarantee better fluidity, stronger adsorption, lower energy consumption and higher energy quality collaboratively. Finally, nine groups of experiments are carried out to verify the validity of the simulation results. The results show that the low-entropy optimization method can reduce void content effectively, and further improve the mechanical properties of laminates.

Discussion of enthalpy, entropy and free energy of formation of GaN

NASA Astrophysics Data System (ADS)

Jacob, K. T.; Rajitha, G.

2009-07-01

Presented in this letter is a critical discussion of a recent paper on experimental investigation of the enthalpy, entropy and free energy of formation of gallium nitride (GaN) published in this journal [T.J. Peshek, J.C. Angus, K. Kash, J. Cryst. Growth 311 (2008) 185-189]. It is shown that the experimental technique employed detects neither the equilibrium partial pressure of N 2 corresponding to the equilibrium between Ga and GaN at fixed temperatures nor the equilibrium temperature at constant pressure of N 2. The results of Peshek et al. are discussed in the light of other information on the Gibbs energy of formation available in the literature. Entropy of GaN is derived from heat-capacity measurements. Based on a critical analysis of all thermodynamic information now available, a set of optimized parameters is identified and a table of thermodynamic data for GaN developed from 298.15 to 1400 K.

Chemical equilibrium. [maximizing entropy of gas system to derive relations between thermodynamic variables

NASA Technical Reports Server (NTRS)

1976-01-01

The entropy of a gas system with the number of particles subject to external control is maximized to derive relations between the thermodynamic variables that obtain at equilibrium. These relations are described in terms of the chemical potential, defined as equivalent partial derivatives of entropy, energy, enthalpy, free energy, or free enthalpy. At equilibrium, the change in total chemical potential must vanish. This fact is used to derive the equilibrium constants for chemical reactions in terms of the partition functions of the species involved in the reaction. Thus the equilibrium constants can be determined accurately, just as other thermodynamic properties, from a knowledge of the energy levels and degeneracies for the gas species involved. These equilibrium constants permit one to calculate the equilibrium concentrations or partial pressures of chemically reacting species that occur in gas mixtures at any given condition of pressure and temperature or volume and temperature.

Thermodynamics of the Si-O-H System

NASA Technical Reports Server (NTRS)

Jacobson, Nathan S.; Opila, Elizabeth J.; Myers, Dwight; Copland, Evan

2004-01-01

Thermodynamic functions for Si(OH)4(g) and SiO(OH)2(g) have been measured using the transpiration method. A second law enthalpy of formation and entropy and a third law enthalpy of formation has been calculated for Si(OH)4. The results are in very good agreement with previous experimental measurements, ab-initio calculations, and estimates.

Kinetics and thermochemistry of 2,5-dimethyltetrahydrofuran and related oxolanes: next next-generation biofuels.

PubMed

Simmie, John M

2012-05-10

The enthalpies of formation, entropies, specific heats at constant pressure, enthalpy functions, and all carbon-hydrogen and carbon-methyl bond dissociation energies have been computed using high-level methods for the cyclic ethers (oxolanes) tetrahydrofuran, 2-methyltetrahydrofuran, and 2,5-dimethyltetrahydrofuran. Barrier heights for hydrogen-abstraction reactions by hydrogen atoms and the methyl radical are also computed and shown to correlate with reaction energy change. The results show a pleasing consistency and considerably expands the available data for these important compounds. Abstraction by ȮH is accompanied by formation of both pre- and postreaction weakly bound complexes. The resulting radicals formed after abstraction undergo ring-opening reactions leading to readily recognizable intermediates, while competitive H-elimination reactions result in formation of dihydrofurans. Formation enthalpies of all 2,3- and 2,5-dihydrofurans and associated radicals are also reported. It is probable that the compounds at the center of this study will be relatively clean-burning biofuels, although formation of intermediate aldehydes might be problematic.

Thermodynamics of Interaction between Some Cellulose Ethers and SDS by Titration Microcalorimetry.

PubMed

Singh; Nilsson

1999-05-01

The interaction between certain nonionic cellulose ethers (ethyl hydroxyethyl cellulose and hydroxypropyl methyl cellulose) and sodium dodecyl sulphate (SDS) has been investigated using isothermal titration microcalorimetry at temperatures between 25-50 degrees C. The observed heat flow curves have been interpreted in terms of a plausible mechanism of the interaction of the substituent groups with SDS monomers and clusters. The data have been related to changes occuring in the system at the macro- and microscopic levels with the addition of surfactants and with temperature. The process consists predominantly of polymer-surfactant interactions initially and surfactant-surfactant interactions at the later stages. A phenomenological model of the cooperative interaction (adsorption) process has been derived, and earlier published equilibrium binding data have been used to recover binding constants and Gibbs energy changes for this process. The adsorption enthalpies and entropies have been recovered along with the heat capacity change. The enthalpic cost of confining the nonpolar regions of the polymers in surfactant clusters is high, but the entropy gain from release of hydration shell water molecules as well as increased freedom of movement of these nonpolar regions in the clusters gives the process a strong entropic driving force. The process is entropy-driven initially and converts to being both enthalpy and entropy-driven at high SDS concentrations. An enthalpy-entropy compensation behavior is seen. Strongly negative heat capacity changes have been obtained resulting from the transfer of nonpolar groups from aqueous into nonpolar environments, as well as a reduction of conformational domains that the chains can populate. Changes in these two components cause the heat capacity change to become less negative at the higher binding levels. The system can be classified as exhibiting nonclassical hydrophobic binding at the later stages of binding. Copyright 1999 Academic Press.

Enthalpy versus entropy: What drives hard-particle ordering in condensed phases?

DOE PAGES

Anthamatten, Mitchell; Ou, Jane J.; Weinfeld, Jeffrey A.; ...

2016-07-27

In support of mesoscopic-scale materials processing, spontaneous hard-particle ordering has been actively pursued for over a half-century. The generally accepted view that entropy alone can drive hard particle ordering is evaluated. Furthermore, a thermodynamic analysis of hard particle ordering was conducted and shown to agree with existing computations and experiments. Conclusions are that (i) hard particle ordering transitions between states in equilibrium are forbidden at constant volume but are allowed at constant pressure; (ii) spontaneous ordering transitions at constant pressure are driven by enthalpy, and (iii) ordering under constant volume necessarily involves a non-equilibrium initial state which has yet tomore » be rigorously defined.« less

A New Thermodynamic Parameter to Predict Formation of Solid Solution or Intermetallic Phases in High Entropy Alloys (Postprint)

DTIC Science & Technology

2015-11-02

George , Relative effects of enthalpy and entropy on the phase stability of equiatomic high-entropy alloys, Acta Mater. 61 (2013) 2628e2638. [4] B... Cantor , I.T.H. Chang, P. Knight, A.J.B. Vincent, Microstructural development in equiatomic multicomponent alloys, Mater. Sci. Eng. A 375e377 (2004...an Al0.5CoCrCuFeNi high entropy alloy, In- termetallics 31 (2012) 165e172. [24] Z. Wu, H. Bei, F. Otto, G.M. Pharr, E.P. George , Recovery

A look at ligand binding thermodynamics in drug discovery.

PubMed

Claveria-Gimeno, Rafael; Vega, Sonia; Abian, Olga; Velazquez-Campoy, Adrian

2017-04-01

Drug discovery is a challenging endeavor requiring the interplay of many different research areas. Gathering information on ligand binding thermodynamics may help considerably in reducing the risk within a high uncertainty scenario, allowing early rejection of flawed compounds and pushing forward optimal candidates. In particular, the free energy, the enthalpy, and the entropy of binding provide fundamental information on the intermolecular forces driving such interaction. Areas covered: The authors review the current status and recent developments in the application of ligand binding thermodynamics in drug discovery. The thermodynamic binding profile (Gibbs energy, enthalpy, and entropy of binding) can be used for lead selection and optimization (binding enthalpy, selectivity, and adaptability). Expert opinion: Binding thermodynamics provides fundamental information on the forces driving the formation of the drug-target complex. It has been widely accepted that binding thermodynamics may be used as a decision criterion along the ligand optimization process in drug discovery and development. In particular, the binding enthalpy may be used as a guide when selecting and optimizing compounds over a set of potential candidates. However, this has been recently called into question by arguing certain difficulties and in the light of certain experimental examples.

The energetic basis of the DNA double helix: a combined microcalorimetric approach

PubMed Central

Vaitiekunas, Paulius; Crane-Robinson, Colyn; Privalov, Peter L.

2015-01-01

Microcalorimetric studies of DNA duplexes and their component single strands showed that association enthalpies of unfolded complementary strands into completely folded duplexes increase linearly with temperature and do not depend on salt concentration, i.e. duplex formation results in a constant heat capacity decrement, identical for CG and AT pairs. Although duplex thermostability increases with CG content, the enthalpic and entropic contributions of an AT pair to duplex formation exceed that of a CG pair when compared at the same temperature. The reduced contribution of AT pairs to duplex stabilization comes not from their lower enthalpy, as previously supposed, but from their larger entropy contribution. This larger enthalpy and particularly the greater entropy results from water fixed by the AT pair in the minor groove. As the increased entropy of an AT pair exceeds that of melting ice, the water molecule fixed by this pair must affect those of its neighbors. Water in the minor groove is, thus, orchestrated by the arrangement of AT groups, i.e. is context dependent. In contrast, water hydrating exposed nonpolar surfaces of bases is responsible for the heat capacity increment on dissociation and, therefore, for the temperature dependence of all thermodynamic characteristics of the double helix. PMID:26304541

Thermodynamic parameters of bonds in glassy materials from viscosity-temperature relationships.

PubMed

Ojovan, Michael I; Travis, Karl P; Hand, Russell J

2007-10-17

Doremus's model of viscosity assumes that viscous flow in amorphous materials is mediated by broken bonds (configurons). The resulting equation contains four coefficients, which are directly related to the entropies and enthalpies of formation and motion of the configurons. Thus by fitting this viscosity equation to experimental viscosity data these enthalpy and entropy terms can be obtained. The non-linear nature of the equation obtained means that the fitting process is non-trivial. A genetic algorithm based approach has been developed to fit the equation to experimental viscosity data for a number of glassy materials, including SiO 2 , GeO 2 , B 2 O 3 , anorthite, diopside, xNa 2 O-(1-x)SiO 2 , xPbO-(1-x)SiO 2 , soda-lime-silica glasses, salol, and α-phenyl-o-cresol. Excellent fits of the equation to the viscosity data were obtained over the entire temperature range. The fitting parameters were used to quantitatively determine the enthalpies and entropies of formation and motion of configurons in the analysed systems and the activation energies for flow at high and low temperatures as well as fragility ratios using the Doremus criterion for fragility. A direct anti-correlation between fragility ratio and configuron percolation threshold, which determines the glass transition temperature in the analysed materials, was found.

Kinetics and Thermodynamics of DNA Processing by Wild Type DNA-Glycosylase Endo III and Its Catalytically Inactive Mutant Forms.

PubMed

Kladova, Olga A; Krasnoperov, Lev N; Kuznetsov, Nikita A; Fedorova, Olga S

2018-03-30

Endonuclease III (Endo III or Nth) is one of the key enzymes responsible for initiating the base excision repair of oxidized or reduced pyrimidine bases in DNA. In this study, a thermodynamic analysis of structural rearrangements of the specific and nonspecific DNA-duplexes during their interaction with Endo III is performed based on stopped-flow kinetic data. 1,3-diaza-2-oxophenoxazine (tC O ), a fluorescent analog of the natural nucleobase cytosine, is used to record multistep DNA binding and lesion recognition within a temperature range (5-37 °C). Standard Gibbs energy, enthalpy, and entropy of the specific steps are derived from kinetic data using Van't Hoff plots. The data suggest that enthalpy-driven exothermic 5,6-dihydrouracil (DHU) recognition and desolvation-accompanied entropy-driven adjustment of the enzyme-substrate complex into a catalytically active state play equally important parts in the overall process. The roles of catalytically significant amino acids Lys120 and Asp138 in the DNA lesion recognition and catalysis are identified. Lys120 participates not only in the catalytic steps but also in the processes of local duplex distortion, whereas substitution Asp138Ala leads to a complete loss of the ability of Endo III to distort a DNA double chain during enzyme-DNA complex formation.

The Elimination of Corrosion . . . is Nanotechnology the Answer to the USAF’s #1 Aging Aircraft Dilemma

DTIC Science & Technology

2009-04-01

mathematically by the expression, G = H – TS, where H is enthalpy, T is absolute temperature, and S is the entropy of the system. 27 Appendix C...given system’s relative stability at a constant pressure and temperature, and is defined by the equation: TSHG  where H is the enthalpy, T is the...thermodynamic properties. AU/ACSC/AVRAM/AY09 37 Table 4 Thermodynamic Values at Standard State (298K)107 Species Name Enthalpy "∆ H o " (kJ

Thermodynamic tabulations for selected phases in the system CaO-Al2O3-SiO2-H2 at 101.325 kPa (1 atm) between 273.15 and 1800 K

USGS Publications Warehouse

Haas, John L.; Robinson, Glipin R.; Hemingway, Bruch S.

1981-01-01

The standard thermodynamic properties of phases in the lime‐alumina‐silica‐ water system between 273.15 and 1800 K at 101.325 kPa (1 atm) were evalated from published experimental data. Phases included in the compilation are boehmite, diaspore, gibbsite, kaolinite, dickite, halloysite, andalusite, kyanite, sillimanite, Ca‐Al cliniopyroxene, anorthite, gehlenite, grossular, prehnite, zoisite, margarite, wollastonite, cyclowollastonite ( = pseudowollastonite), larnite, Ca olivine, hatrurite, and rankinite. The properties include heat capacity, entropy, relative enthalpy, and the Gibbs energy function of the phases and the enthalpies, Gibbs energies, and equilibrium constants for formation both from the elements and the oxides. Tabulated values are given at 50 K intervals with the 2‐sigma confidence limit at 250 K intervals. Summaries for each phase give the temperature‐ dependent functions for heat capacity, entropy, and relative enthalpy and the experimental data used in the final evaluation.

Thermodynamic analysis of the interaction of partially hydrophobic cationic polyelectrolytes with sodium halide salts in water

NASA Astrophysics Data System (ADS)

Bončina, Matjaž; Lukšič, Miha; Seručnik, Mojca; Vlachy, Vojko

2014-05-01

Isothermal titration calorimetry was used to determine the temperature and concentration dependence of the enthalpy of mixing of 3,3- and 6,6-ionene fluorides, bromides, and iodides with low molecular weight salts (NaF, NaCl, NaBr, and NaI) in water. The magnitudes of the enthalpies, measured in the temperature range from 273 to 318 K, depended on the number of methylene groups on the ionene polyion (hydrophobicity), and on the anion of the added salt (ion-specificity). All enthalpies of mixing of 3,3- and 6,6-ionene fluorides with low molecular weight salts (NaCl, NaBr, and NaI) were negative, which is in contrast to the predictions of standard theories of polyelectrolyte solutions. This fact was interpreted in the light of the ion-water short-range interactions that are not accounted for in those theories. In contrast, the enthalpies of mixing of 3,3- and 6,6-ionene bromides and iodides with NaF were positive, being in accord with theory. Using the calorimetric data, we performed a model thermodynamic analysis of the polyelectrolyte-salt mixing process to obtain changes in the apparent standard Gibbs free energy, enthalpy, entropy, and heat capacity relative to the pure ionene fluorides in water. The results prove that halide ions replace fluoride counterions with a strength increasing in the order chloride < bromide < iodide. The process is enthalpy governed, accompanied by a positive change in the heat capacity.

Entropy and the driving force for the filling of carbon nanotubes with water.

PubMed

Pascal, Tod A; Goddard, William A; Jung, Yousung

2011-07-19

The spontaneous filling of hydrophobic carbon nanotubes (CNTs) by water observed both experimentally and from simulations is counterintuitive because confinement is generally expected to decrease both entropy and bonding, and remains largely unexplained. Here we report the entropy, enthalpy, and free energy extracted from molecular dynamics simulations of water confined in CNTs from 0.8 to 2.7-nm diameters. We find for all sizes that water inside the CNTs is more stable than in the bulk, but the nature of the favorable confinement of water changes dramatically with CNT diameter. Thus we find (i) an entropy (both rotational and translational) stabilized, vapor-like phase of water for small CNTs (0.8-1.0 nm), (ii) an enthalpy stabilized, ice-like phase for medium-sized CNTs (1.1-1.2 nm), and (iii) a bulk-like liquid phase for tubes larger than 1.4 nm, stabilized by the increased translational entropy as the waters sample a larger configurational space. Simulations with structureless coarse-grained water models further reveal that the observed free energies and sequence of transitions arise from the tetrahedral structure of liquid water. These results offer a broad theoretical basis for understanding water transport through CNTs and other nanostructures important in nanofluidics, nanofiltrations, and desalination.

Entropy and the driving force for the filling of carbon nanotubes with water

PubMed Central

Pascal, Tod A.; Goddard, William A.; Jung, Yousung

2011-01-01

The spontaneous filling of hydrophobic carbon nanotubes (CNTs) by water observed both experimentally and from simulations is counterintuitive because confinement is generally expected to decrease both entropy and bonding, and remains largely unexplained. Here we report the entropy, enthalpy, and free energy extracted from molecular dynamics simulations of water confined in CNTs from 0.8 to 2.7-nm diameters. We find for all sizes that water inside the CNTs is more stable than in the bulk, but the nature of the favorable confinement of water changes dramatically with CNT diameter. Thus we find (i) an entropy (both rotational and translational) stabilized, vapor-like phase of water for small CNTs (0.8–1.0 nm), (ii) an enthalpy stabilized, ice-like phase for medium-sized CNTs (1.1–1.2 nm), and (iii) a bulk-like liquid phase for tubes larger than 1.4 nm, stabilized by the increased translational entropy as the waters sample a larger configurational space. Simulations with structureless coarse-grained water models further reveal that the observed free energies and sequence of transitions arise from the tetrahedral structure of liquid water. These results offer a broad theoretical basis for understanding water transport through CNTs and other nanostructures important in nanofluidics, nanofiltrations, and desalination. PMID:21709268

Thermodynamic and transport properties of gaseous tetrafluoromethane in chemical equilibrium

NASA Technical Reports Server (NTRS)

Hunt, J. L.; Boney, L. R.

1973-01-01

Equations and in computer code are presented for the thermodynamic and transport properties of gaseous, undissociated tetrafluoromethane (CF4) in chemical equilibrium. The computer code calculates the thermodynamic and transport properties of CF4 when given any two of five thermodynamic variables (entropy, temperature, volume, pressure, and enthalpy). Equilibrium thermodynamic and transport property data are tabulated and pressure-enthalpy diagrams are presented.

Cation symmetry effect on the volatility of ionic liquids.

PubMed

Rocha, Marisa A A; Coutinho, João A P; Santos, Luís M N B F

2012-09-06

This work reports the first data for the vapor pressures at several temperatures of the ionic liquids, [C(N/2)C(N/2)im][NTf(2)] (N = 4, 6, 8, 10, 12) measured using a Knudsen effusion apparatus combined with a quartz crystal microbalance. The morphology and the thermodynamic parameters of vaporization derived from the vapor pressures, are compared with those for the 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide series, [C(N-1)C(1)im][NTf(2)] (N = 3 - 9, 11, and 13). It was found that the volatility of [C(N/2)C(N/2)im][NTf(2)] series is significantly higher than the asymmetric cation ILs with the same total number of carbons in the alkyl side chains, [C(N-1)C(1)im][NTf(2)]. The observed higher volatility is related with the lower enthalpy of vaporization. The symmetric cation, [C(N/2)C(N/2)im][NTf(2)], presents lower entropies of vaporization compared with the asymmetric [C(N-1)C(1)im][NTf(2)], indicating an increase of the absolute liquid entropy in the symmetric cation ILs, being a reflection of a change of the ion dynamics in the IL liquid phase. Moreover both the enthalpy and entropy of vaporization of the [C(N/2)C(N/2)im][NTf(2)] ILs, present a clear odd-even effect with higher enthalpies/entropies of vaporization for the odd number of carbons in each alkyl chain ([C(3)C(3)im][NTf(2)] and [C(5)C(5)im][NTf(2)]).

High-Temperature Specific Heat of the TmBiGeO5 and YbBiGeO5 Compounds

NASA Astrophysics Data System (ADS)

Denisova, L. T.; Belousova, N. V.; Galiakhmetova, N. A.; Denisov, V. M.; Golubeva, E. O.

2018-02-01

The TmBiGeO5 and YbBiGeO5 compounds have been synthesized from Tm2O3 (Yb2O3), Bi2O3, and GeO2 oxides by the solid-state synthesis with successive burning at 1003, 1073, 1123, 1143, 1173, and 1223 K. High-temperature specific heat of the oxide compounds has been measured by differential scanning calorimetry. Basing on the experimental dependences C p = f( T), the thermodynamic properties of the oxide compounds, i.e., the enthalpy and entropy variations, have been calculated.

Spectroscopic investigation of the effect of salt on binding of tartrazine with two homologous serum albumins: quantification by use of the Debye-Hückel limiting law and observation of enthalpy-entropy compensation.

PubMed

Bolel, Priyanka; Datta, Shubhashis; Mahapatra, Niharendu; Halder, Mintu

2012-08-30

Formation of ion pair between charged molecule and protein can lead to interesting biochemical phenomena. We report the evolution of thermodynamics of the binding of tartrazine, a negatively charged azo colorant, and serum albumins with salt. The dye binds predominantly electrostatically in low buffer strengths; however, on increasing salt concentration, affinity decreases considerably. The calculated thermodynamic parameters in high salt indicate manifestation of nonelectrostatic interactions, namely, van der Waals force and hydrogen bonding. Site-marker competitive binding studies and docking simulations indicate that the dye binds with HSA in the warfarin site and with BSA at the interface of warfarin and ibuprofen binding sites. The docked poses indicate nearby amino acid positive side chains, which are possibly responsible for electrostatic interaction. Using the Debye-Hückel interionic attraction theory for binding equilibria, it is shown that, for electrostatic binding the calculated free energy change increases linearly with square root of ionic strength. Also UV-vis, fluorescence, CD data indicate a decrease of interaction with salt concentration. This study quantitatively relates how ionic strength modulates the strength of the protein-ligand electrostatic interaction. The binding enthalpy and entropy have been found to compensate one another. The enthalpy-entropy compensation (EEC), general property of weak intermolecular interactions, has been discussed.

Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding

PubMed Central

Smirnov, Alexey; Zubrienė, Asta; Manakova, Elena; Gražulis, Saulius

2018-01-01

The structure-thermodynamics correlation analysis was performed for a series of fluorine- and chlorine-substituted benzenesulfonamide inhibitors binding to several human carbonic anhydrase (CA) isoforms. The total of 24 crystal structures of 16 inhibitors bound to isoforms CA I, CA II, CA XII, and CA XIII provided the structural information of selective recognition between a compound and CA isoform. The binding thermodynamics of all structures was determined by the analysis of binding-linked protonation events, yielding the intrinsic parameters, i.e., the enthalpy, entropy, and Gibbs energy of binding. Inhibitor binding was compared within structurally similar pairs that differ by para- or meta-substituents enabling to obtain the contributing energies of ligand fragments. The pairs were divided into two groups. First, similar binders—the pairs that keep the same orientation of the benzene ring exhibited classical hydrophobic effect, a less exothermic enthalpy and a more favorable entropy upon addition of the hydrophobic fragments. Second, dissimilar binders—the pairs of binders that demonstrated altered positions of the benzene rings exhibited the non-classical hydrophobic effect, a more favorable enthalpy and variable entropy contribution. A deeper understanding of the energies contributing to the protein-ligand recognition should lead toward the eventual goal of rational drug design where chemical structures of ligands could be designed based on the target protein structure. PMID:29503769

[Mathematic modeling and experimental validation of macrostate quality expression for multicomponent in Chinese materia medica].

PubMed

He, Fuyuan; Deng, Kaiwen; Shi, Jilian; Liu, Wenlong; Pi, Fengjuan

2011-11-01

To establish the unitive multicomponent quality system bridged macrostate mathematic model parameters of material quality and microstate component concentration for Chinese materia medica (CMM). According to law of biologic laws of thermodynamics, the state functions of macrostate qulity of the CMM were established. The validation test was carried out as modeling drug as alcohol extract of Radix Rhozome (AERR), their enthalpy of combustion was determined, and entropy and the capability of information by chromatographic fingerprint were assayed, and then the biologic apparent macrostate parameters were calculated. The biologic macrostate mathematic models, for the CMM quality controll, were established as parameters as the apparent equilibrium constant, biologic enthalpy, Gibbs free energy and biologic entropy etc. The total molarity for the 10 batchs of AERR were 0.153 4 mmol x g(-1) with 28.26% of RSD, with the average of apparent equilibrium constants, biologic enthalpy, Gibbs free energy and biologic entropy were 0.039 65, 8 005 J x mol(-1), -2.408 x 10(7) J x mol(-1) and - 8.078 x 10(4) J x K(-1) with RSD as 6.020%, 1.860%, 42.32% and 42.31%, respectively. The macrostate quality models for CMM can represent their intrinsic quality for multicomponent dynamic system such as the CMM, to manifest out as if the forest away from or tree near from to see it.

How Much Binding Affinity Can be Gained by Filling a Cavity?

PubMed Central

Kawasaki, Yuko; Chufan, Eduardo E.; Lafont, Virginie; Hidaka, Koushi; Kiso, Yoshiaki; Amzel, L. Mario; Freire, Ernesto

2011-01-01

Binding affinity optimization is critical during drug development. Here we evaluate the thermodynamic consequences of filling a binding cavity with functionalities of increasing van der Waals radii (-H, -F, -Cl and CH3) that improve the geometric fit without participating in hydrogen bonding or other specific interactions. We observe a binding affinity increase of two orders of magnitude. There appears to be three phases in the process. The first phase is associated with the formation of stable van der Waals interactions. This phase is characterized by a gain in binding enthalpy and a loss in binding entropy, attributed to a loss of conformational degrees of freedom. For the specific case presented in this paper, the enthalpy gain amounts to −1.5 kcal/mol while the entropic losses amount to +0.9 kcal/mol resulting in a net 3.5-fold affinity gain. The second phase is characterized by simultaneous enthalpic and entropic gains. This phase improves the binding affinity 25-fold. The third phase represents the collapse of the trend and is triggered by the introduction of chemical functionalities larger than the binding cavity itself (CH(CH3)2). It is characterized by large enthalpy and affinity losses. The thermodynamic signatures associated with each phase provide guidelines for lead optimization. PMID:20028396

Tested Demonstrations.

ERIC Educational Resources Information Center

Gilbert, George L., Ed.

1990-01-01

Presented are two demonstrations; "Heat of Solution and Colligative Properties: An Illustration of Enthalpy and Entropy," and "A Vapor Pressure Demonstration." Included are lists of materials and experimental procedures. Apparatus needed are illustrated. (CW)

DNA Nanostructures as Models for Evaluating the Role of Enthalpy and Entropy in Polyvalent Binding

PubMed Central

Nangreave, Jeanette; Yan, Hao; Liu, Yan

2011-01-01

DNA nanotechnology allows the design and construction of nano-scale objects that have finely tuned dimensions, orientation, and structure with remarkable ease and convenience. Synthetic DNA nanostructures can be precisely engineered to model a variety of molecules and systems, providing the opportunity to probe very subtle biophysical phenomena. In this study, several such synthetic DNA nanostructures were designed to serve as models to study the binding behavior of polyvalent molecules and gain insight into how small changes to the ligand/receptor scaffolds, intended to vary their conformational flexibility, will affect their association equilibrium. This approach has yielded a quantitative identification of the roles of enthalpy and entropy in the affinity of polyvalent DNA nanostructure interactions, which exhibit an intriguing compensating effect. PMID:21381740

Retention behavior of neutral solutes in pressurized flow-driven capillary electrochromatography using an ODS column.

PubMed

Nakagawa, Hiroyuki; Kitagawa, Shinya; Araki, Shuki; Ohtani, Hajime

2006-02-01

Several alkyl benzenes are separated by pressurized flow-driven capillary electrochromatography using a temperature-controlled capillary column packed with octadecyl siloxane-modified silica gel, and the effect of applied voltage on the retention is investigated. The van't Hoff plot shows good linearity at the column temperature between 305 and 330 K under applications from -6 to +6 kV. The applied voltage causes a relatively large variation in the enthalpy and the entropy of transfer of the solute from the mobile phase to the stationary phase (> 20%). However, the direction of variation in the enthalpy is almost opposite to that in the entropy, both of which might compensate each other. Therefore, the retention factor is not significantly varied (< 4%) by the application of voltage.

Bizarre behavior of heat capacity in crystals due to interplay between two types of anharmonicities.

PubMed

Yurchenko, Stanislav O; Komarov, Kirill A; Kryuchkov, Nikita P; Zaytsev, Kirill I; Brazhkin, Vadim V

2018-04-07

The heat capacity of classical crystals is determined by the Dulong-Petit value C V ≃ D (where D is the spatial dimension) for softly interacting particles and has the gas-like value C V ≃ D/2 in the hard-sphere limit, while deviations are governed by the effects of anharmonicity. Soft- and hard-sphere interactions, which are associated with the enthalpy and entropy of crystals, are specifically anharmonic owing to violation of a linear relation between particle displacements and corresponding restoring forces. Here, we show that the interplay between these two types of anharmonicities unexpectedly induces two possible types of heat capacity anomalies. We studied thermodynamics, pair correlations, and collective excitations in 2D and 3D crystals of particles with a limited range of soft repulsions to prove the effect of interplay between the enthalpy and entropy types of anharmonicities. The observed anomalies are triggered by the density of the crystal, changing the interaction regime in the zero-temperature limit, and can provide about 10% excess of the heat capacity above the Dulong-Petit value. Our results facilitate understanding effects of complex anharmonicity in molecular and complex crystals and demonstrate the possibility of new effects due to the interplay between different types of anharmonicities.

Bizarre behavior of heat capacity in crystals due to interplay between two types of anharmonicities

NASA Astrophysics Data System (ADS)

Yurchenko, Stanislav O.; Komarov, Kirill A.; Kryuchkov, Nikita P.; Zaytsev, Kirill I.; Brazhkin, Vadim V.

2018-04-01

The heat capacity of classical crystals is determined by the Dulong-Petit value CV ≃ D (where D is the spatial dimension) for softly interacting particles and has the gas-like value CV ≃ D/2 in the hard-sphere limit, while deviations are governed by the effects of anharmonicity. Soft- and hard-sphere interactions, which are associated with the enthalpy and entropy of crystals, are specifically anharmonic owing to violation of a linear relation between particle displacements and corresponding restoring forces. Here, we show that the interplay between these two types of anharmonicities unexpectedly induces two possible types of heat capacity anomalies. We studied thermodynamics, pair correlations, and collective excitations in 2D and 3D crystals of particles with a limited range of soft repulsions to prove the effect of interplay between the enthalpy and entropy types of anharmonicities. The observed anomalies are triggered by the density of the crystal, changing the interaction regime in the zero-temperature limit, and can provide about 10% excess of the heat capacity above the Dulong-Petit value. Our results facilitate understanding effects of complex anharmonicity in molecular and complex crystals and demonstrate the possibility of new effects due to the interplay between different types of anharmonicities.

Gas-phase acidities of cysteine-polyalanine peptides I: A(3,4)CSH and HSCA(3,4).

PubMed

Ren, Jianhua; Tan, John P; Harper, Robert T

2009-10-15

The gas-phase acidities of four cysteine-polyalanine peptides, A(3,4)CSH and HSCA(3,4), were determined using the extended Cooks kinetic method with full entropy analysis. A triple-quadrupole mass spectrometer with an electrospray interface was employed for the experimental study. The ion activation was achieved via collision-induced dissociation (CID) experiments. The deprotonation enthalpies (Delta(acid)H) of the peptides were determined to be 332.2 +/- 2.0 kcal/mol (A(3)CSH), 325.9 +/- 2.0 kcal/mol (A(4)CSH), 319.3 +/- 3.0 kcal/mol (HSCA(3)), and 319.2 +/- 4.0 kcal/mol (HSCA(4)). The deprotonation entropies (Delta(acid)S) of the peptides were estimated based on the entropy term (Delta(DeltaS)) and the deprotonation entropies of the reference acids. By using the deprotonation enthalpies and entropies, the gas-phase acidities (Delta(acid)G) of the peptides were derived: 325.0 +/- 2.0 kcal/mol (A(3)CSH), 320.2 +/- 2.0 kcal/mol (A(4)CSH), 316.3 +/- 3.0 kcal/mol (HSCA(3)), and 315.4 +/- 4.0 kcal/mol (HSCA(4)). Conformations and energetic information of the peptides were calculated through simulated annealing (Tripos), geometry optimization (AM1), and single-point energy calculations (B3LYP/6-31+G(d)), respectively. The calculated theoretical deprotonation enthalpies (Delta(acid)H) of 334.2 kcal/mol (A(3)CSH), 327.7 kcal/mol (A(4)CSH), 320.6 kcal/mol (HSCA(3)), and 318.6 kcal/mol (HSCA(4)) are in good agreement with the experimentally determined values. Both the experimental and computational studies suggest that the two N-terminal cysteine peptides, HSCA(3,4), are significantly more acidic than the corresponding C-terminal ones, A(3,4)CSH. The high acidities of the former are likely due to the helical conformational effects for which the thiolate anion may be strongly stabilized by the interaction with the helix macrodipole.

A thermodynamic study of Abeta(16-21) dissociation from a fibril using computer simulations

NASA Astrophysics Data System (ADS)

Dias, Cristiano; Mahmoudinobar, Farbod; Su, Zhaoqian

Here, I will discuss recent all-atom molecular dynamics simulations with explicit water in which we studied the thermodynamic properties of Abeta(16-21) dissociation from an amyloid fibril. Changes in thermodynamics quantities, e.g., entropy, enthalpy, and volume, are computed from the temperature dependence of the free-energy computed using the umbrella sampling method. We find similarities and differences between the thermodynamics of peptide dissociation and protein unfolding. Similarly to protein unfolding, Abeta(16-21) dissociation is characterized by an unfavorable change in enthalpy, a favorable change in the entropic energy, and an increase in the heat capacity. A main difference is that peptide dissociation is characterized by a weak enthalpy-entropy compensation. We characterize dock and lock states of the peptide based on the solvent accessible surface area. The Lennard-Jones energy of the system is observed to increase continuously in lock and dock states as the peptide dissociates. The electrostatic energy increases in the lock state and it decreases in the dock state as the peptide dissociates. These results will be discussed as well as their implication for fibril growth.

A Rigidifying Salt-Bridge Favors the Activity of Thermophilic Enzyme at High Temperatures at the Expense of Low-Temperature Activity

PubMed Central

Lam, Sonia Y.; Yeung, Rachel C. Y.; Yu, Tsz-Ha; Sze, Kong-Hung; Wong, Kam-Bo

2011-01-01

Background Thermophilic enzymes are often less active than their mesophilic homologues at low temperatures. One hypothesis to explain this observation is that the extra stabilizing interactions increase the rigidity of thermophilic enzymes and hence reduce their activity. Here we employed a thermophilic acylphosphatase from Pyrococcus horikoshii and its homologous mesophilic acylphosphatase from human as a model to study how local rigidity of an active-site residue affects the enzymatic activity. Methods and Findings Acylphosphatases have a unique structural feature that its conserved active-site arginine residue forms a salt-bridge with the C-terminal carboxyl group only in thermophilic acylphosphatases, but not in mesophilic acylphosphatases. We perturbed the local rigidity of this active-site residue by removing the salt-bridge in the thermophilic acylphosphatase and by introducing the salt-bridge in the mesophilic homologue. The mutagenesis design was confirmed by x-ray crystallography. Removing the salt-bridge in the thermophilic enzyme lowered the activation energy that decreased the activation enthalpy and entropy. Conversely, the introduction of the salt-bridge to the mesophilic homologue increased the activation energy and resulted in increases in both activation enthalpy and entropy. Revealed by molecular dynamics simulations, the unrestrained arginine residue can populate more rotamer conformations, and the loss of this conformational freedom upon the formation of transition state justified the observed reduction in activation entropy. Conclusions Our results support the conclusion that restricting the active-site flexibility entropically favors the enzymatic activity at high temperatures. However, the accompanying enthalpy-entropy compensation leads to a stronger temperature-dependency of the enzymatic activity, which explains the less active nature of the thermophilic enzymes at low temperatures. PMID:21423654

A rigidifying salt-bridge favors the activity of thermophilic enzyme at high temperatures at the expense of low-temperature activity.

PubMed

Lam, Sonia Y; Yeung, Rachel C Y; Yu, Tsz-Ha; Sze, Kong-Hung; Wong, Kam-Bo

2011-03-01

Thermophilic enzymes are often less active than their mesophilic homologues at low temperatures. One hypothesis to explain this observation is that the extra stabilizing interactions increase the rigidity of thermophilic enzymes and hence reduce their activity. Here we employed a thermophilic acylphosphatase from Pyrococcus horikoshii and its homologous mesophilic acylphosphatase from human as a model to study how local rigidity of an active-site residue affects the enzymatic activity. Acylphosphatases have a unique structural feature that its conserved active-site arginine residue forms a salt-bridge with the C-terminal carboxyl group only in thermophilic acylphosphatases, but not in mesophilic acylphosphatases. We perturbed the local rigidity of this active-site residue by removing the salt-bridge in the thermophilic acylphosphatase and by introducing the salt-bridge in the mesophilic homologue. The mutagenesis design was confirmed by x-ray crystallography. Removing the salt-bridge in the thermophilic enzyme lowered the activation energy that decreased the activation enthalpy and entropy. Conversely, the introduction of the salt-bridge to the mesophilic homologue increased the activation energy and resulted in increases in both activation enthalpy and entropy. Revealed by molecular dynamics simulations, the unrestrained arginine residue can populate more rotamer conformations, and the loss of this conformational freedom upon the formation of transition state justified the observed reduction in activation entropy. Our results support the conclusion that restricting the active-site flexibility entropically favors the enzymatic activity at high temperatures. However, the accompanying enthalpy-entropy compensation leads to a stronger temperature-dependency of the enzymatic activity, which explains the less active nature of the thermophilic enzymes at low temperatures.

Enthalpy of formation of Fe 3Al 2Si 3O 12 (almandine) by high temperature alkali borate solution calorimetry

NASA Astrophysics Data System (ADS)

Chatillon-Colinet, C.; Kleppa, O. J.; Newton, R. C.; Perkins, D., III

1983-03-01

A high-temperature solution calorimetric method suitable for thermochemical studies of anhydrous minerals containing Fe 2+ ions has been developed. The method is based on an oxide melt solvent with 52 wt% LiBO 2 and 48 wt% NaBO 2 maintained at a temperature of 750°C. In a first application of this method the enthalpies of solution of synthetic almandine, fayalite, a mixture of fayalite plus quartz on FeSiO 3 composition, and natural quartz were measured. For the reaction: ? the enthalpy change at 1023 K is -3.82 ± 0.87 kcal, based on fayalite, quartz, corundum and almandine, and -5.96 ± 0.90 kcal based on the fayalite plus quartz mixture, corundum, and almandine. These values lead to standard molar enthalpies of formation of almandine from the oxides at 1023 K of -14.10 ± 1.22 kcal and -16.24 ± 1.74 kcal, respectively. The measured enthalpy of formation of almandine is less negative by several kilocalories than values derived from analysis of the phase equilibrium work of HSU (1968), but in closer agreement with the phase equilibrium study of O'NEILL and WOOD (1979) and similar to the phase equilibrium deduction of FROESE (1973). The agreement of the present almandine enthalpy of formation with O'NEILL and WOOD (1979) and FROESE (1973) suggests that almandine entropies at 298 K to be obtained from their studies, in the range 79-81 cal/K, are more nearly correct than the several estimates based on oxide sum and volume-entropy systematics, most of which are much lower.

Thermodynamic studies of aqueous solutions of 2,2,2-cryptand at 298.15 K: enthalpy-entropy compensation, partial entropies, and complexation with K+ ions.

PubMed

Shaikh, Vasim R; Terdale, Santosh S; Ahamad, Abdul; Gupta, Gaurav R; Dagade, Dilip H; Hundiwale, Dilip G; Patil, Kesharsingh J

2013-12-19

The osmotic coefficient measurements for binary aqueous solutions of 2,2,2-cryptand (4,7,13,16,21,24-hexaoxa-1,10-diazabicyclo[8.8.8] hexacosane) in the concentration range of ~0.009 to ~0.24 mol·kg(-1) and in ternary aqueous solutions containing a fixed concentration of 2,2,2-cryptand of ~0.1 mol·kg(-1) with varying concentration of KBr (~0.06 to ~0.16 mol·kg(-1)) have been reported at 298.15 K. The diamine gets hydrolyzed in aqueous solutions and needs proper approach to obtain meaningful thermodynamic properties. The measured osmotic coefficient values are corrected for hydrolysis and are used to determine the solvent activity and mean ionic activity coefficients of solute as a function of concentration. Strong ion-pair formation is observed, and the ion-pair dissociation constant for the species [CrptH](+)[OH(-)] is reported. The excess and mixing thermodynamic properties (Gibbs free energy, enthalpy, and entropy changes) have been obtained using the activity data from this study and the heat data reported in the literature. Further, the data are utilized to compute the partial molal entropies of solvent and solute at finite as well as infinite dilution of 2,2,2-cryptand in water. The concentration dependent non-linear enthalpy-entropy compensation effect has been observed for the studied system, and the compensation temperature along with entropic parameter are reported. Using solute activity coefficient data in ternary solutions, the transfer Gibbs free energies for transfer of the cryptand from water to aqueous KBr as well as transfer of KBr from water to aqueous cryptand were obtained and utilized to obtain the salting constant (ks) and thermodynamic equilibrium constant (log K) values for the complex (2,2,2-cryptand:K(+)) at 298.15 K. The value of log K = 5.8 ± 0.1 obtained in this work is found to be in good agreement with that reported by Lehn and Sauvage. The standard molar entropy for complexation is also estimated for the 2,2,2-cryptand-KBr complex in aqueous medium.

The thermodynamic parameters of solution of L-phenylalanine in water

NASA Astrophysics Data System (ADS)

Kustov, A. V.; Korolev, V. P.

2007-02-01

The heat effects of solution of L-phenylalanine in water were measured over wide concentration and temperature ranges. The enthalpies of solution of L-phenylalanine were found to be independent of the content of the amino acid in solution over the concentration range studied. The standard enthalpies, heat capacities, and entropies of solution of the amino acid and the solubility of L-phenylalanine over the temperature range studied were calculated.

Chemical Reaction Equilibrium in Nanoporous Materials: NO Dimerization Reaction in Carbon Slit Nanopores

DTIC Science & Technology

2006-09-01

hi 0T − Tsi 0T , 10 where the molar enthalpy, hi 0T, and the molar entropy, si 0T, may be expressed as hi 0T = Hfi Tr + Tr T cpi 0...TdT , 11 si 0T = si 0Tr + Tr T cpi 0 T T dT . 12 In Eqs. 11 and 12, Hfi Tr is the enthalpy of formation of species i at the

Enthalpy-Entropy Compensation in the Binding of Modulators at Ionotropic Glutamate Receptor GluA2.

PubMed

Krintel, Christian; Francotte, Pierre; Pickering, Darryl S; Juknaitė, Lina; Pøhlsgaard, Jacob; Olsen, Lars; Frydenvang, Karla; Goffin, Eric; Pirotte, Bernard; Kastrup, Jette S

2016-06-07

The 1,2,4-benzothiadiazine 1,1-dioxide type of positive allosteric modulators of the ionotropic glutamate receptor A2 (GluA2) are promising lead compounds for the treatment of cognitive disorders, e.g., Alzheimer's disease. The modulators bind in a cleft formed by the interface of two neighboring ligand binding domains and act by stabilizing the agonist-bound open-channel conformation. The driving forces behind the binding of these modulators can be significantly altered with only minor substitutions to the parent molecules. In this study, we show that changing the 7-fluorine substituent of modulators BPAM97 (2) and BPAM344 (3) into a hydroxyl group (BPAM557 (4) and BPAM521 (5), respectively), leads to a more favorable binding enthalpy (ΔH, kcal/mol) from -4.9 (2) and -7.5 (3) to -6.2 (4) and -14.5 (5), but also a less favorable binding entropy (-TΔS, kcal/mol) from -2.3 (2) and -1.3 (3) to -0.5 (4) and 4.8 (5). Thus, the dissociation constants (Kd, μM) of 4 (11.2) and 5 (0.16) are similar to those of 2 (5.6) and 3 (0.35). Functionally, 4 and 5 potentiated responses of 10 μM L-glutamate at homomeric rat GluA2(Q)i receptors with EC50 values of 67.3 and 2.45 μM, respectively. The binding mode of 5 was examined with x-ray crystallography, showing that the only change compared to that of earlier compounds was the orientation of Ser-497 pointing toward the hydroxyl group of 5. The favorable enthalpy can be explained by the formation of a hydrogen bond from the side-chain hydroxyl group of Ser-497 to the hydroxyl group of 5, whereas the unfavorable entropy might be due to desolvation effects combined with a conformational restriction of Ser-497 and 5. In summary, this study shows a remarkable example of enthalpy-entropy compensation in drug development accompanied with a likely explanation of the underlying structural mechanism. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The high-temperature heat capacity of the (Th,U)O 2 and (U,Pu)O 2 solid solutions

DOE PAGES

Valu, S. O.; Benes, O.; Manara, D.; ...

2016-11-09

The enthalpy increment data for the (Th,U)O 2 and (U,Pu)O 2 solid solutions are reviewed and complemented with new experimental data (400–1773 K) and many-body potential model simulations. The results of the review show that from room temperature up to about 2000 K the enthalpy data are in agreement with the additivity rule (Neumann-Kopp) in the whole composition range. Above 2000 K the effect of Oxygen Frenkel Pair (OFP) formation leads to an excess enthalpy (heat capacity) that is modeled using the enthalpy and entropy of OFP formation from the end-members. Here, a good agreement with existing experimental work ismore » observed, and a reasonable agreement with the results of the many-body potential model, which indicate the presence of the diffuse Bredig (superionic) transition that is not found in the experimental enthalpy increment data.« less

A General Method for Automatic Computation of Equilibrium Compositions and Theoretical Rocket Performance of Propellants

NASA Technical Reports Server (NTRS)

Gordon, Sanford; Zeleznik, Frank J.; Huff, Vearl N.

1959-01-01

A general computer program for chemical equilibrium and rocket performance calculations was written for the IBM 650 computer with 2000 words of drum storage, 60 words of high-speed core storage, indexing registers, and floating point attachments. The program is capable of carrying out combustion and isentropic expansion calculations on a chemical system that may include as many as 10 different chemical elements, 30 reaction products, and 25 pressure ratios. In addition to the equilibrium composition, temperature, and pressure, the program calculates specific impulse, specific impulse in vacuum, characteristic velocity, thrust coefficient, area ratio, molecular weight, Mach number, specific heat, isentropic exponent, enthalpy, entropy, and several thermodynamic first derivatives.

Quantum chemical study of small AlnBm clusters: Structure and physical properties

NASA Astrophysics Data System (ADS)

Loukhovitski, Boris I.; Sharipov, Alexander S.; Starik, Alexander M.

2017-08-01

The structure and physical properties, including rotational constants, characteristic vibrational temperatures, collision diameter, dipole moment, static polarizability, the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), and formation enthalpy of the different isomeric forms of AlnBm clusters with n + m ⩽ 7 are studied using density functional theory. The search of the structure of isomers has been carried employing multistep hierarchical algorithm. Temperature dependencies of thermodynamic functions, such as enthalpy, entropy, and specific heat capacity, have been determined both for the individual isomers and for the ensembles with equilibrium and frozen compositions for the each class of clusters taking into account the anharmonicity of cluster vibrations and the contribution of their excited electronic states. The prospects of the application of small AlnBm clusters as the components of energetic materials are also considered.

Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration

PubMed Central

2013-01-01

Here we present a novel, end-point method using the dead-end-elimination and A* algorithms to efficiently and accurately calculate the change in free energy, enthalpy, and configurational entropy of binding for ligand–receptor association reactions. We apply the new approach to the binding of a series of human immunodeficiency virus (HIV-1) protease inhibitors to examine the effect ensemble reranking has on relative accuracy as well as to evaluate the role of the absolute and relative ligand configurational entropy losses upon binding in affinity differences for structurally related inhibitors. Our results suggest that most thermodynamic parameters can be estimated using only a small fraction of the full configurational space, and we see significant improvement in relative accuracy when using an ensemble versus single-conformer approach to ligand ranking. We also find that using approximate metrics based on the single-conformation enthalpy differences between the global minimum energy configuration in the bound as well as unbound states also correlates well with experiment. Using a novel, additive entropy expansion based on conditional mutual information, we also analyze the source of ligand configurational entropy loss upon binding in terms of both uncoupled per degree of freedom losses as well as changes in coupling between inhibitor degrees of freedom. We estimate entropic free energy losses of approximately +24 kcal/mol, 12 kcal/mol of which stems from loss of translational and rotational entropy. Coupling effects contribute only a small fraction to the overall entropy change (1–2 kcal/mol) but suggest differences in how inhibitor dihedral angles couple to each other in the bound versus unbound states. The importance of accounting for flexibility in drug optimization and design is also discussed. PMID:24250277

Energetics of phosphate binding to ammonium and guanidinium containing metallo-receptors in water.

PubMed

Tobey, Suzanne L; Anslyn, Eric V

2003-12-03

The design and synthesis of receptors containing a Cu(II) binding site with appended ammonium groups (1) and guanidinium groups (2), along with thermodynamics analyses of anion binding, are reported. Both receptors 1 and 2 show high affinities (10(4) M(-1)) and selectivities for phosphate over other anions in 98:2 water:methanol at biological pH. The binding of the host-guest pairs is proposed to proceed through ion-pairing interactions between the charged functional groups on both the host and the guest. The affinities and selectivities for oxyanions were determined using UV/vis titration techniques. Additionally, thermodynamic investigations indicate that the 1:phosphate complex is primarily entropy driven, while the 2:phosphate complex displays both favorable enthalpy and entropy changes. The thermodynamic data for binding provide a picture of the roles of the host, guest, counterions, and solvent. The difference in the entropy and enthalpy driving forces for the ammonium and guanidinium containing hosts are postulated to derive primarily from differences in the solvation shell of these two groups.

Thermodynamic studies for adsorption of ionizable pharmaceuticals onto soil.

PubMed

Maszkowska, Joanna; Wagil, Marta; Mioduszewska, Katarzyna; Kumirska, Jolanta; Stepnowski, Piotr; Białk-Bielińska, Anna

2014-09-01

Although pharmaceutical compounds (PCs) are being used more and more widely, and studies have been carried out to assess their presence in the environment, knowledge of their fate and behavior, especially under different environmental conditions, is still limited. The principle objective of the present work, therefore, is to evaluate the adsorption behavior of three ionizable, polar compounds occurring in different forms: cationic (propranolol - PRO), anionic (sulfisoxazole - SSX) and neutral (sulfaguanidine - SGD) onto soil under various temperature conditions. The adsorption thermodynamics of these researched compounds were extensively investigated using parameters such as enthalpy change (ΔH°), Gibbs free energy change (ΔG°) as well as entropy change (ΔS°). These calculations reveal that sorption of PRO is exothermic, spontaneous and enthalpy driven, sorption of SGD is endothermic, spontaneous and entropy driven whereas sorption of SSX is endothermic, spontaneous only above the temperature of 303.15K and entropy driven. Furthermore, we submit that the calculated values yield valuable information regarding the sorption mechanism of PRO, SGD and SSX onto soils. Copyright © 2014 Elsevier Ltd. All rights reserved.

Thermodynamics of open networks: Ordering and entropy in NaAlSiO4 glass, liquid, and polymorphs

USGS Publications Warehouse

Richet, P.; Robie, R.A.; Rogez, J.; Hemingway, B.S.; Courtial, P.; Tequi, C.

1990-01-01

The thermodynamic properties of carnegieite and NaAlSiO4 glass and liquid have been investigated through Cp determinations from 10 to 1800 K and solution-calorimetry measurements. The relative entropies S298-S0 of carnegieite and NaAlSiO4 glass are 118.7 and 124.8 J/mol K, respectively. The low-high carnegieite transition has been observed at 966 K with an enthalpy of transition of 8.1??0.3 kJ/mol, and the enthalpy of fusion of carnegieite at the congruent melting point of 1799 K is 21.7??3 kJ/mol. These results are consistent with the reported temperature of the nepheline-carnegieite transition and available thermodynamic data for nepheline. The entropy of quenched NaAlSiO4 glass at 0 K is 9.7??2 J/mol K and indicates considerable ordering among AlO4 and SiO4 tetrahedra. In the liquid state, progressive, temperature-induced Si, Al disordering could account for the high configurational heat capacity. Finally, the differences between the entropies and heat capacities of nepheline and carnegieite do not seem to conform to current polyhedral modeling of these properties ?? 1990 Springer-Verlag.

Multi-Scale Low-Entropy Method for Optimizing the Processing Parameters during Automated Fiber Placement

PubMed Central

Han, Zhenyu; Sun, Shouzheng; Fu, Hongya; Fu, Yunzhong

2017-01-01

Automated fiber placement (AFP) process includes a variety of energy forms and multi-scale effects. This contribution proposes a novel multi-scale low-entropy method aiming at optimizing processing parameters in an AFP process, where multi-scale effect, energy consumption, energy utilization efficiency and mechanical properties of micro-system could be taken into account synthetically. Taking a carbon fiber/epoxy prepreg as an example, mechanical properties of macro–meso–scale are obtained by Finite Element Method (FEM). A multi-scale energy transfer model is then established to input the macroscopic results into the microscopic system as its boundary condition, which can communicate with different scales. Furthermore, microscopic characteristics, mainly micro-scale adsorption energy, diffusion coefficient entropy–enthalpy values, are calculated under different processing parameters based on molecular dynamics method. Low-entropy region is then obtained in terms of the interrelation among entropy–enthalpy values, microscopic mechanical properties (interface adsorbability and matrix fluidity) and processing parameters to guarantee better fluidity, stronger adsorption, lower energy consumption and higher energy quality collaboratively. Finally, nine groups of experiments are carried out to verify the validity of the simulation results. The results show that the low-entropy optimization method can reduce void content effectively, and further improve the mechanical properties of laminates. PMID:28869520

Protein flexibility and conformational entropy in ligand design targeting the carbohydrate recognition domain of galectin-3.

PubMed

Diehl, Carl; Engström, Olof; Delaine, Tamara; Håkansson, Maria; Genheden, Samuel; Modig, Kristofer; Leffler, Hakon; Ryde, Ulf; Nilsson, Ulf J; Akke, Mikael

2010-10-20

Rational drug design is predicated on knowledge of the three-dimensional structure of the protein-ligand complex and the thermodynamics of ligand binding. Despite the fundamental importance of both enthalpy and entropy in driving ligand binding, the role of conformational entropy is rarely addressed in drug design. In this work, we have probed the conformational entropy and its relative contribution to the free energy of ligand binding to the carbohydrate recognition domain of galectin-3. Using a combination of NMR spectroscopy, isothermal titration calorimetry, and X-ray crystallography, we characterized the binding of three ligands with dissociation constants ranging over 2 orders of magnitude. (15)N and (2)H spin relaxation measurements showed that the protein backbone and side chains respond to ligand binding by increased conformational fluctuations, on average, that differ among the three ligand-bound states. Variability in the response to ligand binding is prominent in the hydrophobic core, where a distal cluster of methyl groups becomes more rigid, whereas methyl groups closer to the binding site become more flexible. The results reveal an intricate interplay between structure and conformational fluctuations in the different complexes that fine-tunes the affinity. The estimated change in conformational entropy is comparable in magnitude to the binding enthalpy, demonstrating that it contributes favorably and significantly to ligand binding. We speculate that the relatively weak inherent protein-carbohydrate interactions and limited hydrophobic effect associated with oligosaccharide binding might have exerted evolutionary pressure on carbohydrate-binding proteins to increase the affinity by means of conformational entropy.

Tailoring nanoscopic confines to maximize catalytic activity of hydronium ions

NASA Astrophysics Data System (ADS)

Shi, Hui; Eckstein, Sebastian; Vjunov, Aleksei; Camaioni, Donald M.; Lercher, Johannes A.

2017-05-01

Acid catalysis by hydronium ions is ubiquitous in aqueous-phase organic reactions. Here we show that hydronium ion catalysis, exemplified by intramolecular dehydration of cyclohexanol, is markedly influenced by steric constraints, yielding turnover rates that increase by up to two orders of magnitude in tight confines relative to an aqueous solution of a Brønsted acid. The higher activities in zeolites BEA and FAU than in water are caused by more positive activation entropies that more than offset higher activation enthalpies. The higher activity in zeolite MFI with pores smaller than BEA and FAU is caused by a lower activation enthalpy in the tighter confines that more than offsets a less positive activation entropy. Molecularly sized pores significantly enhance the association between hydronium ions and alcohols in a steric environment resembling the constraints in pockets of enzymes stabilizing active sites.

Hydrogen absorption properties of Mg-Ni alloys prepared by bulk mechanical alloying

NASA Astrophysics Data System (ADS)

Kuji, Toshiro

2001-04-01

The thermodynamic properties of the hydrides of Mg2-xNi (x=0-0.5) alloys produced by bulk mechanical alloying (BMA) were determined from pressure-composition (PC) isotherms for absorption over temperatures from 623 to 423 K. The vant Hoff plot for the plateau pressures of isotherms clearly indicated the existence of high and low temperature hydrides with different entropy and enthalpy for hydride formation. It was found that both the entropy and enthalpy values for the high temperature hydride were more negative than for the low temperature hydride. The phase transition temperature was 525 K for Mg2.0Ni and decreased while increasing the value of x. This allotropic transformation was well confirmed by in-situ XRD observations from RT to 673 K under hydrogen atmosphere or in vacuum.

Unsteady specific work and isentropic efficiency of a radial turbine driven by pulsed detonations

NASA Astrophysics Data System (ADS)

Rouser, Kurt P.

There has been longstanding government and industry interest in pressure-gain combustion for use in Brayton cycle based engines. Theoretically, pressure-gain combustion allows heat addition with reduced entropy loss. The pulsed detonation combustor (PDC) is a device that can provide such pressure-gain combustion and possibly replace typical steady deflagration combustors. The PDC is inherently unsteady, however, and comparisons with conventional steady deflagration combustors must be based upon time-integrated performance variables. In this study, the radial turbine of a Garrett automotive turbocharger was coupled directly to and driven, full admission, by a PDC in experiments fueled by hydrogen or ethylene. Data included pulsed cycle time histories of turbine inlet and exit temperature, pressure, velocity, mass flow, and enthalpy. The unsteady inlet flowfield showed momentary reverse flow, and thus unsteady accumulation and expulsion of mass and enthalpy within the device. The coupled turbine-driven compressor provided a time-resolved measure of turbine power. Peak power increased with PDC fill fraction, and duty cycle increased with PDC frequency. Cycle-averaged unsteady specific work increased with fill fraction and frequency. An unsteady turbine efficiency formulation is proposed, including heat transfer effects, enthalpy flux-weighted total pressure ratio, and ensemble averaging over multiple cycles. Turbine efficiency increased with frequency but was lower than the manufacturer reported conventional steady turbine efficiency.

An Improved Mnemonic Diagram for Thermodynamic Relationships.

ERIC Educational Resources Information Center

Rodriguez, Joaquin; Brainard, Alan J.

1989-01-01

Considers pressure, volume, entropy, temperature, Helmholtz free energy, Gibbs free energy, enthalpy, and internal energy. Suggests the mnemonic diagram is for use with simple systems that are defined as macroscopically homogeneous, isotropic, uncharged, and chemically inert. (MVL)

Exergie /4th revised and enlarged edition/

NASA Astrophysics Data System (ADS)

Baloh, T.; Wittwer, E.

The theoretical concept of exergy is explained and its practical applications are discussed. Equilibrium and thermal equilibrium are reviewed as background, and exergy is considered as a reference point for solid-liquid, liquid-liquid, and liquid-gas systems. Exergetic calculations and their graphic depictions are covered. The concepts of enthalpy and entropy are reviewed in detail, including their applications to gas mixtures, solutions, and isolated substances. The exergy of gas mixtures, solutions, and isolated substances is discussed, including moist air, liquid water in water vapor, dry air, and saturation-limited solutions. Mollier exergy-enthalpy-entropy diagrams are presented for two-component systems, and exergy losses for throttling, isobaric mixing, and heat transfer are addressed. The relationship of exergy to various processes is covered, including chemical processes, combustion, and nuclear reactions. The optimization of evaporation plants through exergy is discussed. Calculative examples are presented for energy production and heating, industrial chemical processes, separation of liquid air, nuclear reactors, and others.

Effect of Temperature on the Physico-Chemical Properties of a Room Temperature Ionic Liquid (1-Methyl-3-pentylimidazolium Hexafluorophosphate) with Polyethylene Glycol Oligomer

PubMed Central

Wu, Tzi-Yi; Chen, Bor-Kuan; Hao, Lin; Peng, Yu-Chun; Sun, I-Wen

2011-01-01

A systematic study of the effect of composition on the thermo-physical properties of the binary mixtures of 1-methyl-3-pentyl imidazolium hexafluorophosphate [MPI][PF6] with poly(ethylene glycol) (PEG) [Mw = 400] is presented. The excess molar volume, refractive index deviation, viscosity deviation, and surface tension deviation values were calculated from these experimental density, ρ, refractive index, n, viscosity, η, and surface tension, γ, over the whole concentration range, respectively. The excess molar volumes are negative and continue to become increasingly negative with increasing temperature; whereas the viscosity and surface tension deviation are negative and become less negative with increasing temperature. The surface thermodynamic functions, such as surface entropy, enthalpy, as well as standard molar entropy, Parachor, and molar enthalpy of vaporization for pure ionic liquid, have been derived from the temperature dependence of the surface tension values. PMID:21731460

Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations.

PubMed

Piaggi, Pablo M; Valsson, Omar; Parrinello, Michele

2017-07-07

Crystallization is a process of great practical relevance in which rare but crucial fluctuations lead to the formation of a solid phase starting from the liquid. As in all first order first transitions, there is an interplay between enthalpy and entropy. Based on this idea, in order to drive crystallization in molecular simulations, we introduce two collective variables, one enthalpic and the other entropic. Defined in this way, these collective variables do not prejudge the structure into which the system is going to crystallize. We show the usefulness of this approach by studying the cases of sodium and aluminum that crystallize in the bcc and fcc crystalline structures, respectively. Using these two generic collective variables, we perform variationally enhanced sampling and well tempered metadynamics simulations and find that the systems transform spontaneously and reversibly between the liquid and the solid phases.

A comparative study of the adsorption equilibrium of progesterone by a carbon black and a commercial activated carbon

NASA Astrophysics Data System (ADS)

Valenzuela-Calahorro, Cristóbal; Navarrete-Guijosa, Antonio; Stitou, Mostafa; Cuerda-Correa, Eduardo M.

2007-04-01

In this paper the adsorption process of a natural steroid hormone (progesterone) by a carbon black and a commercial activated carbon has been studied. The corresponding equilibrium isotherms have been analyzed according to a previously proposed model which establishes a kinetic law satisfactorily fitting the C versus t isotherms. The analysis of the experimental data points out the existence of two well-defined sections in the equilibrium isotherms. A general equation including these two processes has been proposed, the global adsorption process being fitted to such equation. From the values of the kinetic equilibrium constant so obtained, values of standard average adsorption enthalpy ( ΔH°) and entropy ( ΔS°) have been calculated. Finally, information related to variations of differential adsorption enthalpy ( ΔH) and entropy ( ΔS) with the surface coverage fraction ( θ) was obtained by using the corresponding Clausius-Clapeyron equations.

Phase Transition Enthalpy Measurements of Organic and Organometallic Compounds and Ionic Liquids. Sublimation, Vaporization, and Fusion Enthalpies from 1880 to 2015. Part 2. C11-C192

NASA Astrophysics Data System (ADS)

Acree, William; Chickos, James S.

2017-03-01

The second part of this compendium concludes with a collection of phase change enthalpies of organic molecules inclusive of C11-C192 reported over the period 1880-2015. Also included are phase change enthalpies including fusion, vaporization, and sublimation enthalpies for organometallic, ionic liquids, and a few inorganic compounds. Paper I of this compendium, published separately, includes organic compounds from C1 to C10 and describes a group additivity method for evaluating solid, liquid, and gas phase heat capacities as well as temperature adjustments of phase changes. Paper II of this compendium also includes an updated version of a group additivity method for evaluating total phase change entropies which together with the fusion temperature can be useful in estimating total phase change enthalpies. Other uses include application in identifying potential substances that either form liquid or plastic crystals or exhibit additional phase changes such as undetected solid-solid transitions or behave anisotropically in the liquid state.

Temperature Dependence of Uranium and Vanadium Adsorption on Amidoxime-Based Adsorbents in Natural Seawater

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuo, Li-Jung; Gill, Gary A.; Tsouris, Costas

Recent advances in the development of amidoxime-based adsorbents have made it highly promising for seawater uranium extraction. However, there is a great need to understand the influence of temperature on the uranium sequestration performance of the adsorbents in natural seawater. Here in this work, the apparent enthalpy and entropy of the sorption of uranium (VI) and vanadium (V) with amidoxime-based adsorbents were determined in natural seawater tests at 8, 20, and 31 °C that cover a broad range of ambient seawater temperature. The sorption of U was highly endothermic, producing apparent enthalpies of 57 ± 6.0 and 59 ± 11more » kJ mol -1 and apparent entropies of 314 ± 21 and 320 ± 36 J K-1 mol -1, respectively, for two adsorbent formulations. In contrast, the sorption of V showed a much smaller temperature sensitivity, producing apparent enthalpies of 6.1 ± 5.9 and -11 ± 5.7 kJ mol -1 and apparent entropies of 164 ± 20 and 103 ± 19 J K -1 mol -1, respectively. This new thermodynamic information suggests that amidoxime-based adsorbents will deliver significantly increased U adsorption capacities and improved selectivity in warmer waters. A separate field study of seawater uranium adsorption conducted in a warm seawater site (Miami, FL, USA) confirm the observed strong temperature effect on seawater uranium mining. Lastly, this strong temperature dependence demonstrates that the warmer the seawater where the amidoxime-based adsorbents are deployed the greater the yield for seawater uranium extraction.« less

Temperature Dependence of Uranium and Vanadium Adsorption on Amidoxime-Based Adsorbents in Natural Seawater

DOE PAGES

Kuo, Li-Jung; Gill, Gary A.; Tsouris, Costas; ...

2018-01-16

Recent advances in the development of amidoxime-based adsorbents have made it highly promising for seawater uranium extraction. However, there is a great need to understand the influence of temperature on the uranium sequestration performance of the adsorbents in natural seawater. Here in this work, the apparent enthalpy and entropy of the sorption of uranium (VI) and vanadium (V) with amidoxime-based adsorbents were determined in natural seawater tests at 8, 20, and 31 °C that cover a broad range of ambient seawater temperature. The sorption of U was highly endothermic, producing apparent enthalpies of 57 ± 6.0 and 59 ± 11more » kJ mol -1 and apparent entropies of 314 ± 21 and 320 ± 36 J K-1 mol -1, respectively, for two adsorbent formulations. In contrast, the sorption of V showed a much smaller temperature sensitivity, producing apparent enthalpies of 6.1 ± 5.9 and -11 ± 5.7 kJ mol -1 and apparent entropies of 164 ± 20 and 103 ± 19 J K -1 mol -1, respectively. This new thermodynamic information suggests that amidoxime-based adsorbents will deliver significantly increased U adsorption capacities and improved selectivity in warmer waters. A separate field study of seawater uranium adsorption conducted in a warm seawater site (Miami, FL, USA) confirm the observed strong temperature effect on seawater uranium mining. Lastly, this strong temperature dependence demonstrates that the warmer the seawater where the amidoxime-based adsorbents are deployed the greater the yield for seawater uranium extraction.« less

Solvation thermodynamics of amino acid side chains on a short peptide backbone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hajari, Timir; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de

The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvationmore » free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side chain cavities in bulk water, in agreement with earlier work in the literature on analysis of cavity fluctuations at nonpolar molecular surfaces. The cavity and dispersion interaction contributions correlate quite well with the solvent accessible surface area of the nonpolar side chains attached to the backbone. This correlation however is weak for the overall solvation free energies owing to the fact that the cavity and dispersion free energy contributions are almost exactly cancelling each other.« less

Solvation thermodynamics of amino acid side chains on a short peptide backbone

NASA Astrophysics Data System (ADS)

Hajari, Timir; van der Vegt, Nico F. A.

2015-04-01

The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvation free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side chain cavities in bulk water, in agreement with earlier work in the literature on analysis of cavity fluctuations at nonpolar molecular surfaces. The cavity and dispersion interaction contributions correlate quite well with the solvent accessible surface area of the nonpolar side chains attached to the backbone. This correlation however is weak for the overall solvation free energies owing to the fact that the cavity and dispersion free energy contributions are almost exactly cancelling each other.

The role of ligands on the equilibria between functional states of a G protein-coupled receptor.

PubMed

Kim, Tae Hun; Chung, Ka Young; Manglik, Aashish; Hansen, Alexandar L; Dror, Ron O; Mildorf, Thomas J; Shaw, David E; Kobilka, Brian K; Prosser, R Scott

2013-06-26

G protein-coupled receptors exhibit a wide variety of signaling behaviors in response to different ligands. When a small label was incorporated on the cytosolic interface of transmembrane helix 6 (Cys-265), (19)F NMR spectra of the β2 adrenergic receptor (β2AR) reconstituted in maltose/neopentyl glycol detergent micelles revealed two distinct inactive states, an activation intermediate state en route to activation, and, in the presence of a G protein mimic, a predominant active state. Analysis of the spectra as a function of temperature revealed that for all ligands, the activation intermediate is entropically favored and enthalpically disfavored. β2AR enthalpy changes toward activation are notably lower than those observed with rhodopsin, a likely consequence of basal activity and the fact that the ionic lock and other interactions stabilizing the inactive state of β2AR are weaker. Positive entropy changes toward activation likely reflect greater mobility (configurational entropy) in the cytoplasmic domain, as confirmed through an order parameter analysis. Ligands greatly influence the overall changes in enthalpy and entropy of the system and the corresponding changes in population and amplitude of motion of given states, suggesting a complex landscape of states and substates.

Thermodynamic and related properties of parahydrogen from the triple point to 300 K at pressures to 1000 bar

NASA Technical Reports Server (NTRS)

Weber, L. A.

1975-01-01

Compressibility measurements and thermodynamic properties data for parahydrogen were extended to higher temperatures and pressures. Results of an experimental program are presented in the form of new pressure, volume and temperature data in the temperature range 23 to 300 K at pressures up to 800 bar. Also given are tables of thermodynamic properties on isobars to 1000 bar including density, internal energy, enthalpy, entropy, specific heats at constant volume and constant pressure, velocity of sound, and surface derivatives. The accuracy of the data is discussed and comparisons are made with previous data.

The Observed Properties of Liquid Helium at the Saturated Vapor Pressure

NASA Astrophysics Data System (ADS)

Donnelly, Russell J.; Barenghi, Carlo F.

1998-11-01

The equilibrium and transport properties of liquid 4He are deduced from experimental observations at the saturated vapor pressure. In each case, the bibliography lists all known measurements. Quantities reported here include density, thermal expansion coefficient, dielectric constant, superfluid and normal fluid densities, first, second, third, and fourth sound velocities, specific heat, enthalpy, entropy, surface tension, ion mobilities, mutual friction, viscosity and kinematic viscosity, dispersion curve, structure factor, thermal conductivity, latent heat, saturated vapor pressure, thermal diffusivity and Prandtl number of helium I, and displacement length and vortex core parameter in helium II.

Thermophysical properties of parahydrogen from the freezing liquid line to 5000 R for pressures to 10000 psia

NASA Technical Reports Server (NTRS)

Mccarty, R. D.; Weber, L. A.

1972-01-01

The tables include entropy, enthalpy, internal energy, density, volume, speed of sound, specific heat, thermal conductivity, viscosity, thermal diffusivity, Prandtl number, and the dielectric constant for 65 isobars. Quantities of special utility in heat transfer and thermodynamic calculations are also included in the isobaric tables. In addition to the isobaric tables, tables for the saturated vapor and liquid are given, which include all of the above properties, plus the surface tension. Tables for the P-T of the freezing liquid, index of refraction, and the derived Joule-Thomson inversion curve are also presented.

Thermophysical properties of Helium-4 from 0.8 to 1500 K with pressures to 2000 MPa

NASA Technical Reports Server (NTRS)

Arp, Vincent D.; Mccarty, Robert D.

1989-01-01

Tabular summary data of the thermophysical properties of fluid helium are given for temperatures from 0.8 to 1500 K, with pressures to 2000 MPa between 75 and 300 K, or to 100 MPa outside of this temperature band. Properties include density, specific heats, enthalpy, entropy, internal energy, sound velocity, expansivity, compressibility, thermal conductivity, and viscosity. The data are calculated from a computer program which is available from the National Institute of Standards and Technology. The computer program is based on carefully fitted state equations for both normal and superfluid helium.

Thermodynamic data for modeling acid mine drainage problems: compilation and estimation of data for selected soluble iron-sulfate minerals

USGS Publications Warehouse

Hemingway, Bruch S.; Seal, Robert R.; Chou, I-Ming

2002-01-01

Enthalpy of formation, Gibbs energy of formation, and entropy values have been compiled from the literature for the hydrated ferrous sulfate minerals melanterite, rozenite, and szomolnokite, and a variety of other hydrated sulfate compounds. On the basis of this compilation, it appears that there is no evidence for an excess enthalpy of mixing for sulfate-H2O systems, except for the first H2O molecule of crystallization. The enthalpy and Gibbs energy of formation of each H2O molecule of crystallization, except the first, in the iron(II) sulfate - H2O system is -295.15 and -238.0 kJ?mol-1, respectively. The absence of an excess enthalpy of mixing is used as the basis for estimating thermodynamic values for a variety of ferrous, ferric, and mixed-valence sulfate salts of relevance to acid-mine drainage systems.

The Contribution of the Activation Entropy to the Gas-Phase Stability of Modified Nucleic Acid Duplexes

NASA Astrophysics Data System (ADS)

Hari, Yvonne; Dugovič, Branislav; Istrate, Alena; Fignolé, Annabel; Leumann, Christian J.; Schürch, Stefan

2016-07-01

Tricyclo-DNA (tcDNA) is a sugar-modified analogue of DNA currently tested for the treatment of Duchenne muscular dystrophy in an antisense approach. Tandem mass spectrometry plays a key role in modern medical diagnostics and has become a widespread technique for the structure elucidation and quantification of antisense oligonucleotides. Herein, mechanistic aspects of the fragmentation of tcDNA are discussed, which lay the basis for reliable sequencing and quantification of the antisense oligonucleotide. Excellent selectivity of tcDNA for complementary RNA is demonstrated in direct competition experiments. Moreover, the kinetic stability and fragmentation pattern of matched and mismatched tcDNA heteroduplexes were investigated and compared with non-modified DNA and RNA duplexes. Although the separation of the constituting strands is the entropy-favored fragmentation pathway of all nucleic acid duplexes, it was found to be only a minor pathway of tcDNA duplexes. The modified hybrid duplexes preferentially undergo neutral base loss and backbone cleavage. This difference is due to the low activation entropy for the strand dissociation of modified duplexes that arises from the conformational constraint of the tc-sugar-moiety. The low activation entropy results in a relatively high free activation enthalpy for the dissociation comparable to the free activation enthalpy of the alternative reaction pathway, the release of a nucleobase. The gas-phase behavior of tcDNA duplexes illustrates the impact of the activation entropy on the fragmentation kinetics and suggests that tandem mass spectrometric experiments are not suited to determine the relative stability of different types of nucleic acid duplexes.

Computer programs for thermodynamic and transport properties of hydrogen (tabcode-II)

NASA Technical Reports Server (NTRS)

Roder, H. M.; Mccarty, R. D.; Hall, W. J.

1972-01-01

The thermodynamic and transport properties of para and equilibrium hydrogen have been programmed into a series of computer routines. Input variables are the pair's pressure-temperature and pressure-enthalpy. The programs cover the range from 1 to 5000 psia with temperatures from the triple point to 6000 R or enthalpies from minus 130 BTU/lb to 25,000 BTU/lb. Output variables are enthalpy or temperature, density, entropy, thermal conductivity, viscosity, at constant volume, the heat capacity ratio, and a heat transfer parameter. Property values on the liquid and vapor boundaries are conveniently obtained through two small routines. The programs achieve high speed by using linear interpolation in a grid of precomputed points which define the surface of the property returned.

Solubility and dissolution thermodynamics of tetranitroglycoluril in organic solvents at 295-318 K

NASA Astrophysics Data System (ADS)

Zheng, Zhihua; Wang, Jianlong; Hu, Zhiyan; Du, Hongbin

2017-08-01

The solubility data of tetranitroglycoluril in acetone, methanol, ethanol, ethyl acetate, nitromethane and chloroform at temperatures ranging from 295-318 K were measured by gravimetric method. The solubility data of tetranitroglycoluril were fitted with Apelblat semiempirical equation. The dissolution enthalpy, entropy and Gibbs energy of tetranitroglycoluril were calculated using the Van't Hoff and Gibbs equations. The results showed that the Apelblat semiempirical equation was significantly correlated with solubility data. The dissolving process was endothermic, entropy-driven, and nonspontaneous.

Entropic Description of Gas Hydrate Ice-Liquid Equilibrium via Enhanced Sampling of Coexisting Phases

NASA Astrophysics Data System (ADS)

Małolepsza, Edyta; Kim, Jaegil; Keyes, Tom

2015-05-01

Metastable β ice holds small guest molecules in stable gas hydrates, so its solid-liquid equilibrium is of interest. However, aqueous crystal-liquid transitions are very difficult to simulate. A new molecular dynamics algorithm generates trajectories in a generalized N P T ensemble and equilibrates states of coexisting phases with a selectable enthalpy. With replicas spanning the range between β ice and liquid water, we find the statistical temperature from the enthalpy histograms and characterize the transition by the entropy, introducing a general computational procedure for first-order transitions.

Entropic description of gas hydrate ice/liquid equilibrium via enhanced sampling of coexisting phases

DOE PAGES

Malolepsza, Edyta; Kim, Jaegil; Keyes, Tom

2015-04-28

Metastable β ice holds small guest molecules in stable gas hydrates, so its solid/liquid equilibrium is of interest. However, aqueous crystal/liquid transitions are very difficult to simulate. A new MD algorithm generates trajectories in a generalized NPT ensemble and equilibrates states of coexisting phases with a selectable enthalpy. Furthermore, with replicas spanning the range between β ice and liquid water we find the statistical temperature from the enthalpy histograms and characterize the transition by the entropy, introducing a general computational procedure for first-order transitions.

Study on the interaction of the toxic food additive carmoisine with serum albumins: a microcalorimetric investigation.

PubMed

Basu, Anirban; Kumar, Gopinatha Suresh

2014-05-30

The interaction of the synthetic azo dye and food colorant carmoisine with human and bovine serum albumins was studied by microcalorimetric techniques. A complete thermodynamic profile of the interaction was obtained from isothermal titration calorimetry studies. The equilibrium constant of the complexation process was of the order of 10(6)M(-1) and the binding stoichiometry was found to be 1:1 with both the serum albumins. The binding was driven by negative standard molar enthalpy and positive standard molar entropy contributions. The binding affinity was lower at higher salt concentrations in both cases but the same was dominated by mostly non-electrostatic forces at all salt concentrations. The polyelectrolytic forces contributed only 5-8% of the total standard molar Gibbs energy change. The standard molar enthalpy change enhanced whereas the standard molar entropic contribution decreased with rise in temperature but they compensated each other to keep the standard molar Gibbs energy change almost invariant. The negative standard molar heat capacity values suggested the involvement of a significant hydrophobic contribution in the complexation process. Besides, enthalpy-entropy compensation phenomenon was also observed in both the systems. The thermal stability of the serum proteins was found to be remarkably enhanced on binding to carmoisine. Copyright © 2014 Elsevier B.V. All rights reserved.

Criteria for predicting the formation of single-phase high-entropy alloys

DOE PAGES

Troparevsky, M Claudia; Morris, James R..; Kent, Paul R.; ...

2015-03-15

High entropy alloys constitute a new class of materials whose very existence poses fundamental questions. Originally thought to be stabilized by the large entropy of mixing, these alloys have attracted attention due to their potential applications, yet no model capable of robustly predicting which combinations of elements will form a single-phase currently exists. Here we propose a model that, through the use of high-throughput computation of the enthalpies of formation of binary compounds, is able to confirm all known high-entropy alloys while rejecting similar alloys that are known to form multiple phases. Despite the increasing entropy, our model predicts thatmore » the number of potential single-phase multicomponent alloys decreases with an increasing number of components: out of more than two million possible 7-component alloys considered, fewer than twenty single-phase alloys are likely.« less

Investigating homology between proteins using energetic profiles.

PubMed

Wrabl, James O; Hilser, Vincent J

2010-03-26

Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding) and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved local stability, may provide guidance for a future thermodynamically informed classification of protein homology.

Electrochemistry of the Zinc-Silver Oxide System. Part 1: Thermodynamic Studies Using Commercial Miniature Cells.

ERIC Educational Resources Information Center

Smith, Michael J.; Vincent, Colin A.

1989-01-01

Uses reversible electrochemical cells near equilibrium to study basic thermodynamic concepts such as maximum work and free energy. Selects sealed, miniature, commercial cells to obtain accurate measurement of enthalpy, entropy, and Gibbs free energy. (MVL)

Thermodynamic analysis of Bacillus subtilis endospore protonation using isothermal titration calorimetry

NASA Astrophysics Data System (ADS)

Harrold, Zoë R.; Gorman-Lewis, Drew

2013-05-01

Bacterial proton and metal adsorption reactions have the capacity to affect metal speciation and transport in aqueous environments. We coupled potentiometric titration and isothermal titration calorimetry (ITC) analyses to study Bacillus subtilis spore-proton adsorption. We modeled the potentiometric data using a four and five-site non-electrostatic surface complexation model (NE-SCM). Heats of spore surface protonation from coupled ITC analyses were used to determine site specific enthalpies of protonation based on NE-SCMs. The five-site model resulted in a substantially better model fit for the heats of protonation but did not significantly improve the potentiometric titration model fit. The improvement observed in the five-site protonation heat model suggests the presence of a highly exothermic protonation reaction circa pH 7 that cannot be resolved in the less sensitive potentiometric data. From the log Ks and enthalpies we calculated corresponding site specific entropies. Log Ks and site concentrations describing spore surface protonation are statistically equivalent to B. subtilis cell surface protonation constants. Spore surface protonation enthalpies, however, are more exothermic relative to cell based adsorption suggesting a different bonding environment. The thermodynamic parameters defined in this study provide insight on molecular scale spore-surface protonation reactions. Coupled ITC and potentiometric titrations can reveal highly exothermic, and possibly endothermic, adsorption reactions that are overshadowed in potentiometric models alone. Spore-proton adsorption NE-SCMs derived in this study provide a framework for future metal adsorption studies.

Fragile-to-fragile liquid transition at Tg and stable-glass phase nucleation rate maximum at the Kauzmann temperature TK

NASA Astrophysics Data System (ADS)

Tournier, Robert F.

2014-12-01

An undercooled liquid is unstable. The driving force of the glass transition at Tg is a change of the undercooled-liquid Gibbs free energy. The classical Gibbs free energy change for a crystal formation is completed including an enthalpy saving. The crystal growth critical nucleus is used as a probe to observe the Laplace pressure change Δp accompanying the enthalpy change -Vm×Δp at Tg where Vm is the molar volume. A stable glass-liquid transition model predicts the specific heat jump of fragile liquids at T≤Tg, the Kauzmann temperature TK where the liquid entropy excess with regard to crystal goes to zero, the equilibrium enthalpy between TK and Tg, the maximum nucleation rate at TK of superclusters containing magic atom numbers, and the equilibrium latent heats at Tg and TK. Strong-to-fragile and strong-to-strong liquid transitions at Tg are also described and all their thermodynamic parameters are determined from their specific heat jumps. The existence of fragile liquids quenched in the amorphous state, which do not undergo liquid-liquid transition during heating preceding their crystallization, is predicted. Long ageing times leading to the formation at TK of a stable glass composed of superclusters containing up to 147 atom, touching and interpenetrating, are evaluated from nucleation rates. A fragile-to-fragile liquid transition occurs at Tg without stable-glass formation while a strong glass is stable after transition.

Signatures of Solvation Thermodynamics in Spectra of Intermolecular Vibrations

PubMed Central

2017-01-01

This study explores the thermodynamic and vibrational properties of water in the three-dimensional environment of solvated ions and small molecules using molecular simulations. The spectrum of intermolecular vibrations in liquid solvents provides detailed information on the shape of the local potential energy surface, which in turn determines local thermodynamic properties such as the entropy. Here, we extract this information using a spatially resolved extension of the two-phase thermodynamics method to estimate hydration water entropies based on the local vibrational density of states (3D-2PT). Combined with an analysis of solute–water and water–water interaction energies, this allows us to resolve local contributions to the solvation enthalpy, entropy, and free energy. We use this approach to study effects of ions on their surrounding water hydrogen bond network, its spectrum of intermolecular vibrations, and resulting thermodynamic properties. In the three-dimensional environment of polar and nonpolar functional groups of molecular solutes, we identify distinct hydration water species and classify them by their characteristic vibrational density of states and molecular entropies. In each case, we are able to assign variations in local hydration water entropies to specific changes in the spectrum of intermolecular vibrations. This provides an important link for the thermodynamic interpretation of vibrational spectra that are accessible to far-infrared absorption and Raman spectroscopy experiments. Our analysis provides unique microscopic details regarding the hydration of hydrophobic and hydrophilic functional groups, which enable us to identify interactions and molecular degrees of freedom that determine relevant contributions to the solvation entropy and consequently the free energy. PMID:28783431

Hydration Differences Explain the Large Variations in the Complexation Thermodynamics of Modified γ-Cyclodextrins with Bile Salts.

PubMed

Køhler, Jonatan; Schönbeck, Christian; Westh, Peter; Holm, René

2016-01-28

The structure and thermodynamics of inclusion complexes of seven different γ-cyclodextrins (γCDs) and three biologically relevant bile salts (BS) were investigated in the present study. Natural γCD and six modified γCDs [two methyl-γCDs, one sulfobutyl ether-γCD (SBEγCD), and three 2-hydroxypropyl-γCDs (HPγCD)] and their complexes with BS were investigated by isothermal titration calorimetry, NMR, and molecular dynamics simulations. With the exception of the fully methylated γCD, which did not bind the BSs investigated, all of the γCDs formed 1:1 complexes with the BS, and the structures were similar to those with natural γCD; i.e., the modifications of the γCD had limited structural impact on the formation of complexes. Isothermal titration calorimetry was carried out over in the temperature interval 5-55 °C to enable the calculation of the stability constant (K) and the thermodynamic parameters enthalpy (ΔH°), entropy (ΔS°), and heat capacity (ΔCp°). The stability constants decreased with an increased degree of substitution (DS), with methyl substituents having a lower effect on the stability constant than the sulfobutyl ether and hydroxypropyl substituents on the stability constants. Enthalpy-entropy compensation was observed, since both enthalpy and entropy increased with the degree of substitution, which may reflect dehydration of the hydrophobic surface on both CD and BS. Calculations based on ΔCp° data suggested that each of the substituents dehydrated 10-20 (hydroxypropyl), 22-33 (sulfobutyl ether), and 10-15 Å(2) (methyl) of the BS surface area, in reasonable agreement with estimates from the molecular dynamics simulations. Combined with earlier investigations on modified βCDs, these results indicate general trends of the substituents on the thermodynamics of complex formation.

Adsorption equilibrium and thermodynamics of CO2 and CH4 on carbon molecular sieves

NASA Astrophysics Data System (ADS)

Song, Xue; Wang, Li'ao; Ma, Xu; Zeng, Yunmin

2017-02-01

Carbon molecular sieves (CMS) are widely used in the separation of dioxide carbon and methane. In this research, three commercial CMS were utilized to analyze the pore structure and chemical properties. The adsorption isotherms of CO2 and CH4 were studied at 298 K, 308 K and 318 K over the pressure range of 0-1 MPa by an Intelligent Gravimetric analysis (IGA-100B, UK). Langmuir model was adopted to fit the experimental data. The working capacity and selectivity were employed to evaluate the adsorbents. The adsorption thermodynamics were discussed. The adsorbed amounts of both CO2 and CH4 are found to be highly related with the BET specific surface area and the volume of micropores, and also are interrelated with the total pore volume and micropore surface area. The standard enthalpy change (ΔHΘ), standard Gibbs free energy (ΔGΘ) and standard entropy change (ΔSΘ) at zero surface loading are negative, manifesting the adsorption process is exothermic and spontaneous, and the system tends to be ordered. With the increasing surface coverage, the absolute values of Gibbs free energy (ΔG) decrease whereas the absolute values of enthalpy change (ΔH) and entropy change(ΔS) increase. This indicates that as the adsorbed amount increases, the degree of the spontaneity reduces, the intermolecular forces among the adsorbate molecules increase, the orderliness of the system improves and the adsorbed amount approaches the maximum adsorbed capacity.

GASP - THERMODYNAMIC AND TRANSPORT PROPERTIES OF HELIUM, METHANE, NEON, NITROGEN, CARBON MONOXIDE, CARBON DIOXIDE, OXYGEN, AND ARGON

NASA Technical Reports Server (NTRS)

Hendricks, R. C.

1994-01-01

A computer program, GASP, has been written to calculate the thermodynamic and transport properties of argon, carbon dioxide, carbon monoxide, fluorine, methane, neon, nitrogen, and oxygen. GASP accepts any two of pressure, temperature, or density as input. In addition, entropy and enthalpy are possible inputs. Outputs are temperature, density, pressure, entropy, enthalpy, specific heats, expansion coefficient, sonic velocity, viscosity, thermal conductivity, and surface tension. A special technique is provided to estimate the thermal conductivity near the thermodynamic critical point. GASP is a group of FORTRAN subroutines. The user typically would write a main program that invoked GASP to provide only the described outputs. Subroutines are structured so that the user may call only those subroutines needed for his particular calculations. Allowable pressures range from 0.l atmosphere to 100 to l,000 atmospheres, depending on the fluid. Similarly, allowable pressures range from the triple point of each substance to 300 degrees K to 2000 degrees K, depending on the substance. The GASP package was developed to be used with heat transfer and fluid flow applications. It is particularly useful in applications of cryogenic fluids. Some problems associated with the liquefication, storage, and gasification of liquefied natural gas and liquefied petroleum gas can also be studied using GASP. This program is written in FORTRAN IV for batch execution and is available for implementation on IBM 7000 series computers. GASP was developed in 1971.

Entropy and biological systems: experimentally-investigated entropy-driven stacking of plant photosynthetic membranes.

PubMed

Jia, Husen; Liggins, John R; Chow, Wah Soon

2014-02-24

According to the Second Law of Thermodynamics, an overall increase of entropy contributes to the driving force for any physicochemical process, but entropy has seldom been investigated in biological systems. Here, for the first time, we apply Isothermal Titration Calorimetry (ITC) to investigate the Mg(2+)-induced spontaneous stacking of photosynthetic membranes isolated from spinach leaves. After subtracting a large endothermic interaction of MgCl₂ with membranes, unrelated to stacking, we demonstrate that the enthalpy change (heat change at constant pressure) is zero or marginally positive or negative. This first direct experimental evidence strongly suggests that an entropy increase significantly drives membrane stacking in this ordered biological structure. Possible mechanisms for the entropy increase include: (i) the attraction between discrete oppositely-charged areas, releasing counterions; (ii) the release of loosely-bound water molecules from the inter-membrane gap; (iii) the increased orientational freedom of previously-aligned water dipoles; and (iv) the lateral rearrangement of membrane components.

Entropy and biological systems: Experimentally-investigated entropy-driven stacking of plant photosynthetic membranes

PubMed Central

Jia, Husen; Liggins, John R.; Chow, Wah Soon

2014-01-01

According to the Second Law of Thermodynamics, an overall increase of entropy contributes to the driving force for any physicochemical process, but entropy has seldom been investigated in biological systems. Here, for the first time, we apply Isothermal Titration Calorimetry (ITC) to investigate the Mg2+-induced spontaneous stacking of photosynthetic membranes isolated from spinach leaves. After subtracting a large endothermic interaction of MgCl2 with membranes, unrelated to stacking, we demonstrate that the enthalpy change (heat change at constant pressure) is zero or marginally positive or negative. This first direct experimental evidence strongly suggests that an entropy increase significantly drives membrane stacking in this ordered biological structure. Possible mechanisms for the entropy increase include: (i) the attraction between discrete oppositely-charged areas, releasing counterions; (ii) the release of loosely-bound water molecules from the inter-membrane gap; (iii) the increased orientational freedom of previously-aligned water dipoles; and (iv) the lateral rearrangement of membrane components. PMID:24561561

Calculation of Cyclodextrin Binding Affinities: Energy, Entropy, and Implications for Drug Design

PubMed Central

Chen, Wei; Chang, Chia-En; Gilson, Michael K.

2004-01-01

The second generation Mining Minima method yields binding affinities accurate to within 0.8 kcal/mol for the associations of α-, β-, and γ-cyclodextrin with benzene, resorcinol, flurbiprofen, naproxen, and nabumetone. These calculations require hours to a day on a commodity computer. The calculations also indicate that the changes in configurational entropy upon binding oppose association by as much as 24 kcal/mol and result primarily from a narrowing of energy wells in the bound versus the free state, rather than from a drop in the number of distinct low-energy conformations on binding. Also, the configurational entropy is found to vary substantially among the bound conformations of a given cyclodextrin-guest complex. This result suggests that the configurational entropy must be accounted for to reliably rank docked conformations in both host-guest and ligand-protein complexes. In close analogy with the common experimental observation of entropy-enthalpy compensation, the computed entropy changes show a near-linear relationship with the changes in mean potential plus solvation energy. PMID:15339804

Stabilization of a protein conferred by an increase in folded state entropy.

PubMed

Dagan, Shlomi; Hagai, Tzachi; Gavrilov, Yulian; Kapon, Ruti; Levy, Yaakov; Reich, Ziv

2013-06-25

Entropic stabilization of native protein structures typically relies on strategies that serve to decrease the entropy of the unfolded state. Here we report, using a combination of experimental and computational approaches, on enhanced thermodynamic stability conferred by an increase in the configurational entropy of the folded state. The enhanced stability is observed upon modifications of a loop region in the enzyme acylphosphatase and is achieved despite significant enthalpy losses. The modifications that lead to increased stability, as well as those that result in destabilization, however, strongly compromise enzymatic activity, rationalizing the preservation of the native loop structure even though it does not provide the protein with maximal stability or kinetic foldability.

Thermodynamics--A Practical Subject.

ERIC Educational Resources Information Center

Jones, Hugh G.

1984-01-01

Provides a simplified, synoptic overview of the area of thermodynamics, enumerating and explaining the four basic laws, and introducing the mathematics involved in a stepwise fashion. Discusses such basic tools of thermodynamics as enthalpy, entropy, Helmholtz free energy, and Gibbs free energy, and their uses in problem solving. (JM)

Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning Approach.

PubMed

Ramakrishnan, Raghunathan; Dral, Pavlo O; Rupp, Matthias; von Lilienfeld, O Anatole

2015-05-12

Chemically accurate and comprehensive studies of the virtual space of all possible molecules are severely limited by the computational cost of quantum chemistry. We introduce a composite strategy that adds machine learning corrections to computationally inexpensive approximate legacy quantum methods. After training, highly accurate predictions of enthalpies, free energies, entropies, and electron correlation energies are possible, for significantly larger molecular sets than used for training. For thermochemical properties of up to 16k isomers of C7H10O2 we present numerical evidence that chemical accuracy can be reached. We also predict electron correlation energy in post Hartree-Fock methods, at the computational cost of Hartree-Fock, and we establish a qualitative relationship between molecular entropy and electron correlation. The transferability of our approach is demonstrated, using semiempirical quantum chemistry and machine learning models trained on 1 and 10% of 134k organic molecules, to reproduce enthalpies of all remaining molecules at density functional theory level of accuracy.

Size-Dependent Melting Behavior of Colloidal In, Sn, and Bi Nanocrystals

PubMed Central

Liu, Minglu; Wang, Robert Y.

2015-01-01

Colloidal nanocrystals are a technologically important class of nanostructures whose phase change properties have been largely unexplored. Here we report on the melting behavior of In, Sn, and Bi nanocrystals dispersed in a polymer matrix. This polymer matrix prevents the nanocrystals from coalescing with one another and enables previously unaccessed observations on the melting behavior of colloidal nanocrystals. We measure the melting temperature, melting enthalpy, and melting entropy of colloidal nanocrystals with diameters of approximately 10 to 20 nm. All of these properties decrease as nanocrystal size decreases, although the depression rate for melting temperature is comparatively slower than that of melting enthalpy and melting entropy. We also observe an elevated melting temperature during the initial melt-freeze cycle that we attribute to surface stabilization from the organic ligands on the nanocrystal surface. Broad endothermic melting valleys and very large supercoolings in our calorimetry data suggest that colloidal nanocrystals exhibit a significant amount of surface pre-melting and low heterogeneous nucleation probabilities during freezing. PMID:26573146

Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima

PubMed Central

Yin, Yimeng; Das, Pratyush K; Jolma, Arttu; Zhu, Fangjie; Popov, Alexander; Xu, You; Nilsson, Lennart

2018-01-01

Most transcription factors (TFs) can bind to a population of sequences closely related to a single optimal site. However, some TFs can bind to two distinct sequences that represent two local optima in the Gibbs free energy of binding (ΔG). To determine the molecular mechanism behind this effect, we solved the structures of human HOXB13 and CDX2 bound to their two optimal DNA sequences, CAATAAA and TCGTAAA. Thermodynamic analyses by isothermal titration calorimetry revealed that both sites were bound with similar ΔG. However, the interaction with the CAA sequence was driven by change in enthalpy (ΔH), whereas the TCG site was bound with similar affinity due to smaller loss of entropy (ΔS). This thermodynamic mechanism that leads to at least two local optima likely affects many macromolecular interactions, as ΔG depends on two partially independent variables ΔH and ΔS according to the central equation of thermodynamics, ΔG = ΔH - TΔS. PMID:29638214

Thermodynamic criteria analysis for the use of taro starch spherical aggregates as microencapsulant matrix.

PubMed

Hoyos-Leyva, Javier D; Bello-Pérez, Luis A; Alvarez-Ramirez, J

2018-09-01

Spherical aggregates can be obtained from taro starch by spray-drying without using bonding agents. Accurate information about thermal issues of spherical aggregates can provide valuable information for assessing the application as encapsulant. Spherical aggregates of taro starch were obtained by spray-drying and analyzed using dynamic vapour sorption. The use of the Guggenheim, Anderson and de Boer (GAB) model indicated a Type II isotherm pattern with weaker interactions in the multilayer region. Differential enthalpy and entropy estimates reflected a mesoporous microstructure, implying that energetic mechanisms dominate over transport mechanisms in the sorption process. The limitation by energetic mechanisms was corroborated with enthalpy-entropy compensation estimates. The diffusivity coefficient was of the order of 10 -8  m 2 ·s -1 , which is in line with results obtained for common materials used for encapsulation purposes. The thermodynamic properties and the lack of a bonding agent indicated the viability of spherical aggregates of taro starch for encapsulation of biocompounds. Copyright © 2018 Elsevier Ltd. All rights reserved.

Thermochemistry of the gaseous fluorides of samarium, europium, and thulium

NASA Astrophysics Data System (ADS)

Kleinschmidt, P. D.; Lau, K. H.; Hildenbrand, D. L.

1981-01-01

The gaseous mono-, di-, and trifluorides of the lanthanide metals samarium, europium, and thulium were characterized thermochemically from high temperature equilibrium studies carried out by mass spectrometry. Reaction enthalpies and entropies were derived using second-law analysis throughout, and the results were used to evaluate the enthalpies of formation and bond dissociation energies (BDE) of the gaseous fluorides, and to obtain approximate values for the electronic entropies of the MF and MF2 species. The dissociation energies of the monofluorides D°0(SmF)=134 kcal/mole, D°0(EuF)=129 kcal/mole, and D°0(TmF)=121 kcal/mole, all ±2 kcal/mole, are in good agreement with values predicted by the Rittner electrostatic model, whereas values in the polyatomic fluorides show considerable variation and do not seem to follow any clear trends. Although the BDE values in some instances differ from previous estimates, their sums yield trifluoride heats of atomization that are in close accord with values derived from the vaporization thermodynamics of the solid trifluorides.

Thermodynamic and related properties of oxygen from the triple point to 300 K at pressures to 1000 bar

NASA Technical Reports Server (NTRS)

Weber, L. A.

1977-01-01

The results of an experimental program are presented in the form of PVT data in the temperature range 58 to 300 K at pressures up to 800 bar. Tables of the derived thermodynamic properties on isobars to 1000 bar are given, including density, internal energy, enthalpy, entropy, specific heats at constant volume and constant pressure, velocity of sound, and the surface derivatives (delta P/delta T) sub rho and (delta P/delta Rho) sub T. Auxiliary tables in engineering units are also given. The accuracy of the data is discussed and comparisons are made with previous data.

High-temperature heat capacity of CdO-V2O5 oxides

NASA Astrophysics Data System (ADS)

Denisova, L. T.; Chumilina, L. G.; Belousova, N. V.; Denisov, V. M.; Galiakhmetova, N. A.

2017-12-01

Vanadates Cd2V2O7 and CdV2O6 have been prepared from CdO i V2O5 by three-phase synthesis with subsequent burning at 823-1073 K and 823-853 K, respectively. The molar heat capacity of these oxide compounds has been measured by differential scanning calorimetry. The enthalpy change, the entropy change, and the reduced Gibbs energy are calculated using the experimental dependences C p = f( T). It is shown that there is a correlation between the specific heat capacity and the composition of CdO-V2O5 oxide system.

Determining the main thermodynamic parameters of caffeine melting by means of DSC

NASA Astrophysics Data System (ADS)

Agafonova, E. V.; Moshchenskii, Yu. V.; Tkachenko, M. L.

2012-06-01

The temperature and enthalpy of the melting of caffeine, which are 235.5 ± 0.1°C and 19.6 ± 0.2 kJ/mol, respectively, are determined by DSC. The melting entropy and the cryoscopic constant of caffeine are calculated.

The How and Why of Chemical Reactions

ERIC Educational Resources Information Center

Schubert, Leo

1970-01-01

Presents a discussion of some of the fundamental concepts in thermodynamics and quantum mechanics including entropy, enthalpy, free energy, the partition function, chemical kinetics, transition state theory, the making and breaking of chemical bonds, electronegativity, ion sizes, intermolecular energies and of their role in explaining the nature…

Regeneration of aluminum hydride

DOEpatents

Graetz, Jason Allan; Reilly, James J.

2009-04-21

The present invention provides methods and materials for the formation of hydrogen storage alanes, AlH.sub.x, where x is greater than 0 and less than or equal to 6 at reduced H.sub.2 pressures and temperatures. The methods rely upon reduction of the change in free energy of the reaction between aluminum and molecular H.sub.2. The change in free energy is reduced by lowering the entropy change during the reaction by providing aluminum in a state of high entropy, by increasing the magnitude of the change in enthalpy of the reaction or combinations thereof.

Molar heat capacity and entropy of calcium metal

USGS Publications Warehouse

Hemingway, B.S.; Robie, R.A.; Chase, M.W.

1997-01-01

The heat capacity of calcium has been measured at 85 mean temperatures between T ??? 8 K and T ??? 369 K using an adiabatically-shielded calorimeter in an intermittent heating mode. At T = 298.15 K, the recommended values for the molar heat capacity, molar entropy, and molar enthalpy increment referred to T = 0 are (25.77 ?? 0.08) J??K-1??mol-1, (42.90 ?? 0.11) J??K-1??mol-1, and (5811 ?? 12) J??mol-1, respectively. The uncertainties are twice the standard deviation of the mean. ?? 1997 Academic Press Limited.

Explanation to the difference in the ketyl radical formation yields of benzophenone and benzil

NASA Astrophysics Data System (ADS)

Okutsu, Tetsuo; Muramatsu, Hidenori; Horiuchi, Hiroaki; Hiratsuka, Hiroshi

2005-03-01

p Ka values of benzophenone ketyl and benzil ketyl radicals were determined as 9.4 and 12.4, respectively. We can successfully explain the difference in quantum yield of the proton transfer between benzophenone ketyl and benzil ketyl radicals by these values. Reaction enthalpies of the proton transfer are the same (-80 kJ mol -1) for these radicals, and the difference in p Ka value can be explained by that reaction entropies. Reaction entropies between two radicals are discussed by the possible structure of the radicals.

Thermodynamics of Activation Gating in Olfactory-Type Cyclic Nucleotide-Gated (CNGA2) Channels

PubMed Central

Nache, Vasilica; Kusch, Jana; Biskup, Christoph; Schulz, Eckhard; Zimmer, Thomas; Hagen, Volker; Benndorf, Klaus

2008-01-01

Olfactory-type cyclic nucleotide-gated (CNG) ion channels open by the binding of cyclic nucleotides to a binding domain in the C-terminus. Employing the Eyring rate theory, we performed a thermodynamic analysis of the activation gating in homotetrameric CNGA2 channels. Lowering the temperature shifted the concentration-response relationship to lower concentrations, resulting in a decrease of both the enthalpy ΔH and entropy ΔS upon channel opening, suggesting that the order of an open CNGA2 channel plus its environment is higher than that of the closed channel. Activation time courses induced by cGMP concentration jumps were used to study thermodynamics of the transition state. The activation enthalpies ΔH‡ were positive at all cGMP concentrations. In contrast, the activation entropy ΔS‡ was positive at low cGMP concentrations and became then negative at increasing cGMP concentrations. The enthalpic and entropic parts of the activation energies approximately balance each other at all cGMP concentrations, leaving the free enthalpy of activation in the range between 19 and 21 kcal/mol. We conclude that channel activation proceeds through different pathways at different cGMP concentrations. Compared to the unliganded channel, low cGMP concentrations generate a transitional state of lower order whereas high cGMP concentrations generate a transitional state of higher order. PMID:18567637

Intrinsic Thermodynamics and Structures of 2,4- and 3,4-Substituted Fluorinated Benzenesulfonamides Binding to Carbonic Anhydrases.

PubMed

Zubrienė, Asta; Smirnov, Alexey; Dudutienė, Virginija; Timm, David D; Matulienė, Jurgita; Michailovienė, Vilma; Zakšauskas, Audrius; Manakova, Elena; Gražulis, Saulius; Matulis, Daumantas

2017-01-20

The goal of rational drug design is to understand structure-thermodynamics correlations in order to predict the chemical structure of a drug that would exhibit excellent affinity and selectivity for a target protein. In this study we explored the contribution of added functionalities of benzenesulfonamide inhibitors to the intrinsic binding affinity, enthalpy, and entropy for recombinant human carbonic anhydrases (CA) CA I, CA II, CA VII, CA IX, CA XII, and CA XIII. The binding enthalpies of compounds possessing similar chemical structures and affinities were found to be very different, spanning a range from -90 to +10 kJ mol -1 , and are compensated by a similar opposing entropy contribution. The intrinsic parameters of binding were determined by subtracting the linked protonation reactions. The sulfonamide group pK a values of the compounds were measured spectrophotometrically, and the protonation enthalpies were measured by isothermal titration calorimetry (ITC). Herein we describe the development of meta- or ortho-substituted fluorinated benzenesulfonamides toward the highly potent compound 10 h, which exhibits an observed dissociation constant value of 43 pm and an intrinsic dissociation constant value of 1.1 pm toward CA IX, an anticancer target that is highly overexpressed in various tumors. Fluorescence thermal shift assays, ITC, and X-ray crystallography were all applied in this work. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

COMPARISON OF SORPTION ENERGTICS FOR HYDROPHOBIC ORGANIC CHEMICALS BY SYNTHETIC AND NATURAL SORBENTS FROM METHANOL/WATER SOLVENT MIXTURES

EPA Science Inventory

Reversed-phase liquid chromatography (RPLC) was used to investigate the thermodynamics and mechanisms of hydrophobic organic chemical (HOC) retention from methanol/water solvent mixtures. The enthalpy-entropy compensation model was used to infer that the hydro- phobic sorptive me...

Thermodynamic properties of zeolites: low-temperature heat capacities and thermodynamic functions for phillipsite and clinoptilolite. Estimates of the thermochemical properties of zeolitic water at low temperature.

USGS Publications Warehouse

Hemingway, B.S.; Robie, R.A.

1984-01-01

Measured heat capacities between 15 and 305 K and calculated heat capacities, entropies, enthalpy functions and Gibbs energy functions are reported and analysed for phillipsite and clinoptilolite. - J.A.Z.

Large entropy derived from low-frequency vibrations and its implications for hydrogen storage

NASA Astrophysics Data System (ADS)

Wang, Xiaoxia; Chen, Hongshan

2018-02-01

Adsorption and desorption are driven by the energy and entropy competition, but the entropy effect is often ignored in hydrogen storage and the optimal adsorption strength for the ambient storage is controversial in the literature. This letter investigated the adsorption states of the H2 molecule on M-B12C6N6 (M = Li, Na, Mg, Ca, and Sc) and analyzed the correlation among the zero point energy (ZPE), the entropy change, and the adsorption energy and their effects on the delivery capacities. The ZPE has large correction to the adsorption energy due to the light mass of hydrogen. The computations show that the potential energies along the spherical surface centered at the alkali metals are very flat and it leads to large entropy (˜70 J/mol.K) of the adsorbed H2 molecules. The entropy change can compensate the enthalpy change effectively, and the ambient storage can be realized with relatively weak adsorption of ΔH = -12 kJ/mol. The results are encouraging and instructive for the design of hydrogen storage materials.

Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method.

PubMed

Du, Bin; Zhang, Zhen; Grubner, Sharon; Yurkovich, James T; Palsson, Bernhard O; Zielinski, Daniel C

2018-06-05

Reaction-equilibrium constants determine the metabolite concentrations necessary to drive flux through metabolic pathways. Group-contribution methods offer a way to estimate reaction-equilibrium constants at wide coverage across the metabolic network. Here, we present an updated group-contribution method with 1) additional curated thermodynamic data used in fitting and 2) capabilities to calculate equilibrium constants as a function of temperature. We first collected and curated aqueous thermodynamic data, including reaction-equilibrium constants, enthalpies of reaction, Gibbs free energies of formation, enthalpies of formation, entropy changes of formation of compounds, and proton- and metal-ion-binding constants. Next, we formulated the calculation of equilibrium constants as a function of temperature and calculated the standard entropy change of formation (Δ f S ∘ ) using a model based on molecular properties. The median absolute error in estimating Δ f S ∘ was 0.013 kJ/K/mol. We also estimated magnesium binding constants for 618 compounds using a linear regression model validated against measured data. We demonstrate the improved performance of the current method (8.17 kJ/mol in median absolute residual) over the current state-of-the-art method (11.47 kJ/mol) in estimating the 185 new reactions added in this work. The efforts here fill in gaps for thermodynamic calculations under various conditions, specifically different temperatures and metal-ion concentrations. These, to our knowledge, new capabilities empower the study of thermodynamic driving forces underlying the metabolic function of organisms living under diverse conditions. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Thermodynamics of T cell receptor – peptide/MHC interactions: progress and opportunities

PubMed Central

Armstrong, Kathryn M.; Insaidoo, Francis K.; Baker, Brian M.

2013-01-01

αβ T cell receptors (TCR) recognize peptide antigens presented by class I or class II major histocompatibility complex molecules (pMHC). Here we review the use of thermodynamic measurements in the study of TCR-pMHC interactions, with attention to the diversity in binding thermodynamics and how this is related to the variation in TCR-pMHC interfaces. We show that there is no enthalpic or entropic signature for TCR binding; rather, enthalpy and entropy changes vary in a compensatory manner that reflects a narrow free energy window for the interactions that have been characterized. Binding enthalpy and entropy changes do not correlate with structural features such as buried surface area or the number of hydrogen bonds within TCR-pMHC interfaces, possibly reflecting the myriad of contributors to binding thermodynamics, but likely also reflecting a reliance on van’t Hoff over calorimetric measurements and the unaccounted influence of equilibria linked to binding. TCR-pMHC binding heat capacity changes likewise vary considerably. In some cases the heat capacity changes are consistent with conformational differences between bound and free receptors, but there is little data indicating these conformational differences represent the need to organize commonly disordered CDR loops. In this regard, we discuss how thermodynamics may provide additional insight into conformational changes occurring upon TCR binding. Finally, we highlight opportunities for the further use of thermodynamic measurements in the study of TCR-pMHC interactions, not only for understanding TCR binding in general, but for understanding specifics of individual interactions and the engineering of T cell receptors with desired molecular recognition properties. PMID:18496839

Vacuum drying of apples (cv. Golden Delicious): drying characteristics, thermodynamic properties, and mass transfer parameters

NASA Astrophysics Data System (ADS)

Nadi, Fatemeh; Tzempelikos, Dimitrios

2018-01-01

In this work, apples of cv. Golden Delicious were cut into slices that were 5 and 7 mm thick and then vacuum dried at 50, 60 and 70 °C and pressure of 0.02 bar. The thin layer model drying kinetics was studied, and mass transfer properties, specifically effective moisture diffusivity and convective mass transfer coefficient, were evaluated using the Fick's equation of diffusion. Also, thermodynamic parameters of the process, i.e. enthalpy (ΔH), entropy (ΔS) and Gibbs free energy (ΔG), were determined. Colour properties were evaluated as one of the important indicators of food quality and marketability. Determination of mass transfer parameters and thermodynamic properties of vacuum dried apple slices has not been discussed much in the literature. In conclusion, the Nadi's model fitted best the observed data that represent the drying process. Thermodynamic properties were determined based on the dependence of the drying constant of the Henderson and Pabis model on temperature, and it was concluded that the variation in drying kinetics depends on the energy contribution of the surrounding environment. The enthalpy and entropy diminished, while the Gibbs free energy increased with the increase of the temperature of drying; therefore, it was possible to verify that variation in the diffusion process in the apple during drying depends on energetic contributions of the environment. The obtained results showed that diffusivity increased for 69%, while the mass transfer coefficient increase was even higher, 75%, at the variation of temperature of 20 °C. The increase in the dimensionless Biot number was 20%.

Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin

PubMed Central

Isaksen, Geir Villy; Åqvist, Johan; Brandsdal, Bjørn Olav

2014-01-01

Life has effectively colonized most of our planet and extremophilic organisms require specialized enzymes to survive under harsh conditions. Cold-loving organisms (psychrophiles) express heat-labile enzymes that possess a high specific activity and catalytic efficiency at low temperatures. A remarkable universal characteristic of cold-active enzymes is that they show a reduction both in activation enthalpy and entropy, compared to mesophilic orthologs, which makes their reaction rates less sensitive to falling temperature. Despite significant efforts since the early 1970s, the important question of the origin of this effect still largely remains unanswered. Here we use cold- and warm-active trypsins as model systems to investigate the temperature dependence of the reaction rates with extensive molecular dynamics free energy simulations. The calculations quantitatively reproduce the catalytic rates of the two enzymes and further yield high-precision Arrhenius plots, which show the characteristic trends in activation enthalpy and entropy. Detailed structural analysis indicates that the relationship between these parameters and the 3D structure is reflected by significantly different internal protein energy changes during the reaction. The origin of this effect is not localized to the active site, but is found in the outer regions of the protein, where the cold-active enzyme has a higher degree of softness. Several structural mechanisms for softening the protein surface are identified, together with key mutations responsible for this effect. Our simulations further show that single point-mutations can significantly affect the thermodynamic activation parameters, indicating how these can be optimized by evolution. PMID:25165981

Vacuum drying of apples (cv. Golden Delicious): drying characteristics, thermodynamic properties, and mass transfer parameters

NASA Astrophysics Data System (ADS)

Nadi, Fatemeh; Tzempelikos, Dimitrios

2018-07-01

In this work, apples of cv. Golden Delicious were cut into slices that were 5 and 7 mm thick and then vacuum dried at 50, 60 and 70 °C and pressure of 0.02 bar. The thin layer model drying kinetics was studied, and mass transfer properties, specifically effective moisture diffusivity and convective mass transfer coefficient, were evaluated using the Fick's equation of diffusion. Also, thermodynamic parameters of the process, i.e. enthalpy ( ΔH), entropy ( ΔS) and Gibbs free energy ( ΔG), were determined. Colour properties were evaluated as one of the important indicators of food quality and marketability. Determination of mass transfer parameters and thermodynamic properties of vacuum dried apple slices has not been discussed much in the literature. In conclusion, the Nadi's model fitted best the observed data that represent the drying process. Thermodynamic properties were determined based on the dependence of the drying constant of the Henderson and Pabis model on temperature, and it was concluded that the variation in drying kinetics depends on the energy contribution of the surrounding environment. The enthalpy and entropy diminished, while the Gibbs free energy increased with the increase of the temperature of drying; therefore, it was possible to verify that variation in the diffusion process in the apple during drying depends on energetic contributions of the environment. The obtained results showed that diffusivity increased for 69%, while the mass transfer coefficient increase was even higher, 75%, at the variation of temperature of 20 °C. The increase in the dimensionless Biot number was 20%.

Translational Entropy and DNA Duplex Stability.

PubMed

Privalov, Peter L; Crane-Robinson, Colyn

2018-01-09

Investigation of folding/unfolding DNA duplexes of various size and composition by superprecise calorimetry has revised several long-held beliefs concerning the forces responsible for the formation of the double helix. It was established that: 1) the enthalpy and the entropy of duplex unfolding are temperature dependent, increasing with temperature rise and having the same heat capacity increment for CG and AT pairs; 2) the enthalpy of AT melting is greater than that of the CG pair, so the stabilizing effect of the CG pair in comparison with AT results not from its larger enthalpic contribution (as expected from its extra hydrogen bond), but from the larger entropic contribution of the AT pair that results from its ability to fix ordered water in the minor groove and release it upon duplex unfolding; 3) the translation entropy, resulting from the appearance of a new kinetic unit on duplex dissociation, determines the dependence of duplex stability on its length and its concentration (it is an order-of-magnitude smaller than predicted from the statistical mechanics of gases and is fully expressed by the stoichiometric correction term); 4) changes in duplex stability on reshuffling the sequence (the "nearest-neighbor effect") result from the immobilized water molecules fixed by AT pairs in the minor groove; and 5) the evaluated thermodynamic components permit a quantitative expression of DNA duplex stability. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Thermochemical study of the system Fe-As-S

USGS Publications Warehouse

Barton, P.B.

1969-01-01

The results of Toulmin and Barton (1964) for the Fe-S system have been combined with a series of new measurements on As-bearing assemblages in the 500??-850??C temperature range to derive data on the free energies, enthalpies, and entropies of formation for arsenopyrite, loellingite, orpiment, realgar, FeAs, and Fe2As. The enthalpies and free energies of formation of orpiment and realgar are only approximately one-half as large as indicated in recent compilations of thermochemical data (Wagman et al., 1965). Data are also presented for the covariation of activity of S2(g) with temperature and composition of the sulfur-arsenic liquid. ?? 1969.

Regeneration of aluminum hydride

DOEpatents

Graetz, Jason Allan; Reilly, James J; Wegrzyn, James E

2012-09-18

The present invention provides methods and materials for the formation of hydrogen storage alanes, AlH.sub.x, where x is greater than 0 and less than or equal to 6 at reduced H.sub.2 pressures and temperatures. The methods rely upon reduction of the change in free energy of the reaction between aluminum and molecular H.sub.2. The change in free energy is reduced by lowering the entropy change during the reaction by providing aluminum in a state of high entropy, and by increasing the magnitude of the change in enthalpy of the reaction or combinations thereof.

On the studies of thermodynamics properties of fast neutron irradiated (LixK1-x)2SO4 crystals

NASA Astrophysics Data System (ADS)

El-Khatib, A. M.; Kassem, M. E.; Gomaa, N. G.; Mahmoud, S. A.

The effect of fast neutron irradiation on the thermodynamic properties of (LixK1-x)2SO4, (x = 0.1, 0.2,˙˙˙˙˙˙˙˙0.5) has been studied. The measurements were carried out in the vicinity of phase transition. The study reveals that as the lithium content decreases the first high temperature phase Tc = 705 K disappears, while the second one is shifted to lower temperature. It is observed also that the specific heat, Cp, decreases sharply with neutron integrated fluence φ and increases once more. Both entropy and enthalpy changes increase with the increase of neutron integrated fluence.

A Critical Evaluation of the Thermophysical Properties of Mercury

NASA Astrophysics Data System (ADS)

Holman, G. J. F.; ten Seldam, C. A.

1994-09-01

For the use of a mercury column for precise pressure measurements—such as the pressurized 30 meter mercury-in-steel column used at the Van der Waals-Zeeman Laboratory for the calibration of piston gauges up to nearly 300 MPa—it is highly important to have accurate knowledge of such properties of mercury as density, isobaric secant and tangent volume thermal expansion coefficients, and isothermal secant and tangent compressibilities as functions of temperature and pressure. In this paper we present a critical assessment of the available information on these properties. Recommended values are given for the properties mentioned and, in addition, for properties derived from theses such as entropy, enthalpy, internal energy, and the specific heat capacities.

Determination of Kinetic and Thermodynamic Parameters that Describe Isothermal Seed Germination: A Student Research Project.

ERIC Educational Resources Information Center

Hageseth, Gaylord T.

1982-01-01

Describes a project for students to collect and fit data to a theoretical mathematical model that describes the rate of isothermal seed germination, including activation energy for substrate and produce and the autocatalytic reaction, and changes in enthalpy, entropy, and the Gibb's free energy. (Author/SK)

Solubility behavior of lamivudine crystal forms in recrystallization solvents.

PubMed

Jozwiakowski, M J; Nguyen, N A; Sisco, J M; Spancake, C W

1996-02-01

Lamivudine can be obtained as acicular crystals (form I, 0.2 hydrate) from water or methanol and as bipyramidal crystals (form II, nonsolvated) from many nonaqueous solvents. Form II is thermodynamically favored in the solid state (higher melting point and greater density than form I) at ambient relative humidities. Solubility measurements on both forms versus solvent and temperature was used to determine whether entropy or enthalpy was the driving force for solubility. Solution calorimetry data indicated that form I is favored (less soluble) in all solvents studied on the basis of enthalpy alone. In higher alcohols and other organic solvents, form I has a larger entropy of solution than form II, which compensates for the enthalpic factors and results in physical stability for form II in these systems. The metastable crystal form solubility at 25 degrees C was estimated to be 1.2-2.3 times as high as the equilibrium solubility of the stable form, depending on the temperature, solvent, and crystal form. Binary solvent studies showed that > 18-20% water must be present in ethanol to convert the excess solid to form I at equilibrium.

Determination of Adsorption Equations for Chloro Derivatives of Aniline on Halloysite Adsorbents Using Inverse Liquid Chromatography.

PubMed

Słomkiewicz, Piotr M; Szczepanik, Beata; Garnuszek, Magdalena; Rogala, Paweł; Witkiewicz, Zygfryd

2017-11-01

Chloro derivatives of aniline are commonly used in the production of dyes, pharmaceuticals, and agricultural agents. They are toxic compounds with a large accumulation ability and low natural biodegradability. Halloysite is known as an efficient adsorbent of toxic compounds, such as phenols or herbicides, from wastewater. Inverse LC was applied to measure the adsorption of aniline and 2-chloroaniline (2-CA), 3-chloroaniline (3-CA), and 4-chloroaniline (4-CA) on halloysite adsorbents. A peak division (PD) method was used to determine a Langmuir equation in accordance with the adsorption measurement results. The values of adsorption equilibrium constants and enthalpy were determined and compared by breakthrough curve and PD methods. The physical sense of the calculated adsorption enthalpy values was checked by applying Boudart's entropy criteria. Of note, adsorption enthalpy values for halloysite adsorbents decreased in the following order: aniline > 4-CA > 2-CA > 3-CA.

NMR Studies of Protein Hydration and Protein-Ligand Interactions

NASA Astrophysics Data System (ADS)

Chong, Yuan

Water on the surface of a protein is called hydration water. Hydration water is known to play a crucial role in a variety of biological processes including protein folding, enzymatic activation, and drug binding. Although the significance of hydration water has been recognized, the underlying mechanism remains far from being understood. This dissertation employs a unique in-situ nuclear magnetic resonance (NMR) technique to study the mechanism of protein hydration and the role of hydration in alcohol-protein interactions. Water isotherms in proteins are measured at different temperatures via the in-situ NMR technique. Water is found to interact differently with hydrophilic and hydrophobic groups on the protein. Water adsorption on hydrophilic groups is hardly affected by the temperature, while water adsorption on hydrophobic groups strongly depends on the temperature around 10 C, below which the adsorption is substantially reduced. This effect is induced by the dramatic decrease in the protein flexibility below 10 C. Furthermore, nanosecond to microsecond protein dynamics and the free energy, enthalpy, and entropy of protein hydration are studied as a function of hydration level and temperature. A crossover at 10 C in protein dynamics and thermodynamics is revealed. The effect of water at hydrophilic groups on protein dynamics and thermodynamics shows little temperature dependence, whereas water at hydrophobic groups has stronger effect above 10 C. In addition, I investigate the role of water in alcohol binding to the protein using the in-situ NMR detection. The isotherms of alcohols are first measured on dry proteins, then on proteins with a series of controlled hydration levels. The free energy, enthalpy, and entropy of alcohol binding are also determined. Two distinct types of alcohol binding are identified. On the one hand, alcohols can directly bind to a few specific sites on the protein. This type of binding is independent of temperature and can be facilitated by hydration. On the other hand, alcohols can bind to many nonspecific sites on the protein. In dry proteins, this type of binding only occurs above a threshold of alcohol vapor pressure. Such a threshold is gradually reduced by increasing the hydration level and can be removed above a critical hydration level. Hydration also shifts the nonspecific alcohol binding from an entropy-driven to an enthalpy-driven process. This dissertation reveals the mechanism of protein hydration and the detailed roles of hydration in ligand binding, with important implications for the understanding of protein functions.

The cancer Warburg effect may be a testable example of the minimum entropy production rate principle

NASA Astrophysics Data System (ADS)

Marín, Dolores; Sabater, Bartolomé

2017-04-01

Cancer cells consume more glucose by glycolytic fermentation to lactate than by respiration, a characteristic known as the Warburg effect. In contrast with the 36 moles of ATP produced by respiration, fermentation produces two moles of ATP per mole of glucose consumed, which poses a puzzle with regard to the function of the Warburg effect. The production of free energy (ΔG), enthalpy (ΔH), and entropy (ΔS) per mole linearly varies with the fraction (x) of glucose consumed by fermentation that is frequently estimated around 0.9. Hence, calculation shows that, in respect to pure respiration, the predominant fermentative metabolism decreases around 10% the production of entropy per mole of glucose consumed in cancer cells. We hypothesize that increased fermentation could allow cancer cells to accomplish the Prigogine theorem of the trend to minimize the rate of production of entropy. According to the theorem, open cellular systems near the steady state could evolve to minimize the rates of entropy production that may be reached by modified replicating cells producing entropy at a low rate. Remarkably, at CO2 concentrations above 930 ppm, glucose respiration produces less entropy than fermentation, which suggests experimental tests to validate the hypothesis of minimization of the rate of entropy production through the Warburg effect.

The cancer Warburg effect may be a testable example of the minimum entropy production rate principle.

PubMed

Marín, Dolores; Sabater, Bartolomé

2017-04-28

Cancer cells consume more glucose by glycolytic fermentation to lactate than by respiration, a characteristic known as the Warburg effect. In contrast with the 36 moles of ATP produced by respiration, fermentation produces two moles of ATP per mole of glucose consumed, which poses a puzzle with regard to the function of the Warburg effect. The production of free energy (ΔG), enthalpy (ΔH), and entropy (ΔS) per mole linearly varies with the fraction (x) of glucose consumed by fermentation that is frequently estimated around 0.9. Hence, calculation shows that, in respect to pure respiration, the predominant fermentative metabolism decreases around 10% the production of entropy per mole of glucose consumed in cancer cells. We hypothesize that increased fermentation could allow cancer cells to accomplish the Prigogine theorem of the trend to minimize the rate of production of entropy. According to the theorem, open cellular systems near the steady state could evolve to minimize the rates of entropy production that may be reached by modified replicating cells producing entropy at a low rate. Remarkably, at CO 2 concentrations above 930 ppm, glucose respiration produces less entropy than fermentation, which suggests experimental tests to validate the hypothesis of minimization of the rate of entropy production through the Warburg effect.

Mass dependence of the activation enthalpy and entropy of unentangled linear alkane chains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeong, Cheol; Douglas, Jack F.

2015-10-14

The mass scaling of the self-diffusion coefficient D of polymers in the liquid state, D ∼ M{sup β}, is one of the most basic characteristics of these complex fluids. Although traditional theories such as the Rouse and reptation models of unentangled and entangled polymer melts, respectively, predict that β is constant, this exponent for alkanes has been estimated experimentally to vary from −1.8 to −2.7 upon cooling. Significantly, β changes with temperature T under conditions where the chains are not entangled and at temperatures far above the glass transition temperature T{sub g} where dynamic heterogeneity does not complicate the descriptionmore » of the liquid dynamics. Based on atomistic molecular dynamics simulations on unentangled linear alkanes in the melt, we find that the variation of β with T can be directly attributed to the dependence of the enthalpy ΔH{sub a} and entropy ΔS{sub a} of activation on the number of alkane backbone carbon atoms, n. In addition, we find a sharp change in the melt dynamics near a “critical” chain length, n ≈ 17. A close examination of this phenomenon indicates that a “buckling transition” from rod-like to coiled chain configurations occurs at this characteristic chain length and distinct entropy-enthalpy compensation relations, ΔS{sub a} ∝ ΔH{sub a}, hold on either side of this polymer conformational transition. We conclude that the activation free energy parameters exert a significant influence on the dynamics of polymer melts that is not anticipated by either the Rouse and reptation models. In addition to changes of ΔH{sub a} and ΔS{sub a} with M, we expect changes in these free energy parameters to be crucial for understanding the dynamics of polymer blends, nanocomposites, and confined polymers because of changes of the fluid free energy by interfacial interactions and geometrical confinement.« less

Modeling the gas-phase thermochemistry of organosulfur compounds.

PubMed

Vandeputte, Aäron G; Sabbe, Maarten K; Reyniers, Marie-Françoise; Marin, Guy B

2011-06-27

Key to understanding the involvement of organosulfur compounds in a variety of radical chemistries, such as atmospheric chemistry, polymerization, pyrolysis, and so forth, is knowledge of their thermochemical properties. For organosulfur compounds and radicals, thermochemical data are, however, much less well documented than for hydrocarbons. The traditional recourse to the Benson group additivity method offers no solace since only a very limited number of group additivity values (GAVs) is available. In this work, CBS-QB3 calculations augmented with 1D hindered rotor corrections for 122 organosulfur compounds and 45 organosulfur radicals were used to derive 93 Benson group additivity values, 18 ring-strain corrections, 2 non-nearest-neighbor interactions, and 3 resonance corrections for standard enthalpies of formation, standard molar entropies, and heat capacities for organosulfur compounds and organosulfur radicals. The reported GAVs are consistent with previously reported GAVs for hydrocarbons and hydrocarbon radicals and include 77 contributions, among which 26 radical contributions, which, to the best of our knowledge, have not been reported before. The GAVs allow one to estimate the standard enthalpies of formation at 298 K, the standard entropies at 298 K, and standard heat capacities in the temperature range 300-1500 K for a large set of organosulfur compounds, that is, thiols, thioketons, polysulfides, alkylsulfides, thials, dithioates, and cyclic sulfur compounds. For a validation set of 26 organosulfur compounds, the mean absolute deviation between experimental and group additively modeled enthalpies of formation amounts to 1.9  kJ  mol(-1). For an additional set of 14 organosulfur compounds, it was shown that the mean absolute deviations between calculated and group additively modeled standard entropies and heat capacities are restricted to 4 and 2 J  mol(-1)  K(-1), respectively. As an alternative to Benson GAVs, 26 new hydrogen-bond increments are reported, which can also be useful for the prediction of radical thermochemistry. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Adsorption Thermodynamics and Intrinsic Activation Parameters for Monomolecular Cracking of n -Alkanes on Brønsted Acid Sites in Zeolites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Janda, Amber; Vlaisavljevich, Bess; Lin, Li-Chiang

Experimental measurements of the rate coefficient (kapp) and apparent enthalpies and entropies of activation (ΔHapp and ΔSapp) for alkane cracking catalyzed by acidic zeolites can be used to characterize the effects of zeolite structure and alkane size on the intrinsic enthalpy and entropy of activation, ΔHint‡ and ΔSint‡. To determine ΔHint‡ and ΔSint‡, enthalpies and entropies of adsorption, ΔHads-H+ and ΔSads-H+, must be determined for alkane molecules moving from the gas phase to Brønsted acid sites at reaction temperatures (>673 K). Experimental values of ΔHapp and ΔSapp must also be properly defined in terms of ΔHads-H+ and ΔSads-H+. We reportmore » here a method for determining ΔHads-H+ and ΔSads-H+ in which the adsorption site is represented by a fixed volume that includes the proton. Values of ΔHads-H+ and ΔSads-H+ obtained from Monte Carlo simulations are in good agreement with values obtained from experimental data measured at 300–400 K. An important feature of the simulations, however, is their ability to account for the redistribution of alkane adsorbed at protons in different locations with increasing temperature. Values of ΔHint‡ and ΔSint‡ for the cracking of propane through n-hexane, determined from measured values of kapp and ΔHapp and simulated values of ΔHads-H+ and ΔSads-H+, agree well with values obtained independently from quantum mechanics/molecular mechanics calculations. Application of our method of analysis reveals that the observed increase in kapp with increasing n-alkane size is due primarily to a decrease in ΔHint‡ with increasing chain length and that ΔSint‡ is independent of chain length.« less

Thermochemistry of C7H16 to C10H22 alkane isomers: primary, secondary, and tertiary C-H bond dissociation energies and effects of branching.

PubMed

Hudzik, Jason M; Bozzelli, Joseph W; Simmie, John M

2014-10-09

Standard enthalpies of formation (ΔH°f 298) of methyl, ethyl, primary and secondary propyl, and n-butyl radicals are evaluated and used in work reactions to determine internal consistency. They are then used to calculate the enthalpy of formation for the tert-butyl radical. Other thermochemical properties including standard entropies (S°(T)), heat capacities (Cp(T)), and carbon-hydrogen bond dissociation energies (C-H BDEs) are reported for n-pentane, n-heptane, 2-methylhexane, 2,3-dimethylpentane, and several branched higher carbon number alkanes and their radicals. ΔH°f 298 and C-H BDEs are calculated using isodesmic work reactions at the B3LYP (6-31G(d,p) and 6-311G(2d,2p) basis sets), CBS-QB3, CBS-APNO, and G3MP2B3 levels of theory. Structures, moments of inertia, vibrational frequencies, and internal rotor potentials are calculated at the B3LYP/6-31G(d,p) level for contributions to entropy and heat capacities. Enthalpy calculations for these hydrocarbon radical species are shown to have consistency with the CBS-QB3 and CBS-APNO methods using all work reactions. Our recommended ideal gas phase ΔH°f 298 values are from the average of all CBS-QB3, CBS-APNO, and for G3MP2B3, only where the reference and target radical are identical types, and are compared with literature values. Calculated values show agreement between the composite calculation methods and the different work reactions. Secondary and tertiary C-H bonds in the more highly branched alkanes are shown to have bond energies that are several kcal mol(-1) lower than the BDEs in corresponding smaller molecules often used as reference species. Entropies and heat capacities are calculated and compared to literature values (when available) when all internal rotors are considered.

Extra-thermodynamic study on surface diffusion in reversed-phase liquid chromatography using silica gels bonded with alkyl ligands of different chain lengths

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miyabe, Kanji; Guiochon, Georges A

2005-06-01

Surface diffusion on adsorbents made of silica gels bonded to C{sub 1}, C{sub 4}, C{sub 8}, and C{sub 18} alkyl ligands was studied in reversed-phase liquid chromatography (RPLC) from the viewpoints of two extrathermodynamic relationships: enthalpy-entropy compensation (EEC) and linear free-energy relationship (LFER). First, the values of the surface diffusion coefficient (D{sub s}), normalized by the density of the alkyl ligands, were analyzed with the modified Arrhenius equation, following the four approaches proposed in earlier research. This showed that an actual EEC resulting from substantial physicochemical effects occurs for surface diffusion and suggested a mechanistic similarity of molecular migration bymore » surface diffusion, irrespective of the alkyl chain length. Second, a new model based on EEC was derived to explain the LFER between the logarithms of D{sub s} measured under different RPLC conditions. This showed that the changes of free energy, enthalpy, and entropy of surface diffusion are linearly correlated with the carbon number in the alkyl ligands of the bonded phases and that the contribution of the C{sub 18} ligand to the changes of the thermodynamic parameters corresponds to that of the C{sub 10} ligand. The new LFER model correlates the slope and intercept of the LFER to the compensation temperatures derived from the EEC analyses and to several parameters characterizing the molecular contributions to the changes in enthalpy and entropy. Finally, the new model was used to estimate D{sub s} under various RPLC conditions. The values of D{sub s} that were estimated from only two original experimental D{sub s} data were in agreement with corresponding experimental D{sub s} values, with relative errors of {approx}20%, irrespective of some RPLC conditions.« less

Intrinsic thermodynamics of inhibitor binding to human carbonic anhydrase IX.

PubMed

Linkuvienė, Vaida; Matulienė, Jurgita; Juozapaitienė, Vaida; Michailovienė, Vilma; Jachno, Jelena; Matulis, Daumantas

2016-04-01

Human carbonic anhydrase 9th isoform (CA IX) is an important marker of numerous cancers and is increasingly interesting as a potential anticancer drug target. Various synthetic aromatic sulfonamide-bearing compounds are being designed as potent inhibitors of CA IX. However, sulfonamide compound binding to CA IX is linked to several reactions, the deprotonation of the sulfonamide amino group and the protonation of the CA active site Zn(II)-bound hydroxide. These linked reactions significantly affect the affinities and other thermodynamic parameters such as enthalpies and entropies of binding. The observed and intrinsic affinities of compound binding to CA IX were determined by the fluorescent thermal shift assay. The enthalpies and entropies of binding were determined by the isothermal titration calorimetry. The pKa of CA IX was determined to be 6.8 and the enthalpy of CA IX-Zn(II)-bound hydroxide protonation was -24 kJ/mol. These values enabled the analysis of intrinsic thermodynamics of a library of compounds binding to CA IX. The most strongly binding compounds exhibited the intrinsic affinity of 0.01 nM and the observed affinity of 2 nM. The intrinsic thermodynamic parameters of compound binding to CA IX helped to draw the compound structure to thermodynamics relationship. It is important to distinguish the intrinsic from observed parameters of any disease target protein interaction with its inhibitors as drug candidates when drawing detailed compound structure to thermodynamics correlations. Copyright © 2016 Elsevier B.V. All rights reserved.

NMR structure and dynamics of the engineered fluorescein-binding lipocalin FluA reveal rigidification of beta-barrel and variable loops upon enthalpy-driven ligand binding.

PubMed

Mills, Jeffrey L; Liu, Gaohua; Skerra, Arne; Szyperski, Thomas

2009-08-11

The NMR structure of the 21 kDa lipocalin FluA, which was previously obtained by combinatorial design, elucidates a reshaped binding site specific for the dye fluorescein resulting from 21 side chain replacements with respect to the parental lipocalin, the naturally occurring bilin-binding protein (BBP). As expected, FluA exhibits the lipocalin fold of BBP, comprising eight antiparallel beta-strands forming a beta-barrel with an alpha-helix attached to its side. Comparison of the NMR structure of free FluA with the X-ray structures of BBP.biliverdin IX(gamma) and FluA.fluorescein complexes revealed significant conformational changes in the binding pocket, which is formed by four loops at the open end of the beta-barrel as well as adjoining beta-strand segments. An "induced fit" became apparent for the side chain conformations of Arg 88 and Phe 99, which contact the bound fluorescein in the complex and undergo concerted rearrangement upon ligand binding. Moreover, slower internal motional modes of the polypeptide backbone were identified by measuring transverse (15)N backbone spin relaxation times in the rotating frame for free FluA and also for the FluA.fluorescein complex. A reduction in the level of such motions was detected upon complex formation, indicating rigidification of the protein structure and loss of conformational entropy. This hypothesis was confirmed by isothermal titration calorimetry, showing that ligand binding is enthalpy-driven, thus overcompensating for the negative entropy associated with both ligand binding per se and rigidification of the protein. Our investigation of the solution structure and dynamics as well as thermodynamics of lipocalin-ligand interaction not only provides insight into the general mechanism of small molecule accommodation in the deep and narrow cavity of this abundant class of proteins but also supports the future design of corresponding binding proteins with novel specificities, so-called "anticalins".

The H[subscript 3]PO[subscript 4] Acid Ionization Reactions: A Capstone Multiconcept Thermodynamics General Chemistry Laboratory Exercise

ERIC Educational Resources Information Center

Nyasulu, Frazier; Barlag, Rebecca; Wise, Lindy; McMills, Lauren

2013-01-01

The thermodynamic properties of weak acid ionization reactions are determined. The thermodynamic properties are corresponding values of the absolute temperature (T), the weak acid equilibrium constant (K[subscript a]), the enthalpy of ionization (delta[subscript i]H[degrees]), and the entropy of ionization (delta[subscript i]S[degrees]). The…

Introduction of Differential Scanning Calorimetry in a General Chemistry Laboratory Course: Determination of Thermal Properties of Organic Hydrocarbons

ERIC Educational Resources Information Center

D'Amelia, Ronald; Franks, Thomas; Nirode, William F.

2007-01-01

In first-year general chemistry undergraduate courses, thermodynamics and thermal properties such as melting points and changes in enthalpy ([Delta]H) and entropy ([Delta]S) of phase changes are frequently discussed. Typically, classical calorimetric methods of analysis are used to determine [Delta]H of reactions. Differential scanning calorimetry…

Thermodynamic criteria for estimating the kinetic parameters of catalytic reactions

NASA Astrophysics Data System (ADS)

Mitrichev, I. I.; Zhensa, A. V.; Kol'tsova, E. M.

2017-01-01

Kinetic parameters are estimated using two criteria in addition to the traditional criterion that considers the consistency between experimental and modeled conversion data: thermodynamic consistency and the consistency with entropy production (i.e., the absolute rate of the change in entropy due to exchange with the environment is consistent with the rate of entropy production in the steady state). A special procedure is developed and executed on a computer to achieve the thermodynamic consistency of a set of kinetic parameters with respect to both the standard entropy of a reaction and the standard enthalpy of a reaction. A problem of multi-criterion optimization, reduced to a single-criterion problem by summing weighted values of the three criteria listed above, is solved. Using the reaction of NO reduction with CO on a platinum catalyst as an example, it is shown that the set of parameters proposed by D.B. Mantri and P. Aghalayam gives much worse agreement with experimental values than the set obtained on the basis of three criteria: the sum of the squares of deviations for conversion, the thermodynamic consistency, and the consistency with entropy production.

Thermodynamic study of quercetin and rutin mixtures with alcohols

NASA Astrophysics Data System (ADS)

Szymczyk, Katarzyna; Taraba, Anna

2018-04-01

The paper presents interactions between quercetin (3,3‧,4‧,5,7-pentahydroxyflavone) and its glycoside, rutin with short chain alcohols, methanol, ethanol and 1-propanol studied by the surface tension measurements. An attempt was made to investigate the effect of flavonoid and alcohol concentrations as well as temperature on the thermodynamic parameters of alcohols adsorption at the water-air interface that is the standard free enthalpy, enthalpy and entropy of adsorption as well as the infinite dilution activity coefficient. The obtained results show that the mixtures of quercetin with methanol and rutin with ethanol are characterized by the best adsorption properties but all studied systems become less structured after adsorption.

Partially purified Carica papaya lipase: a versatile biocatalyst for the hydrolytic resolution of (R,S)-2-arylpropionic thioesters in water-saturated organic solvents.

PubMed

Ng, I-Son; Tsai, Shau-Wei

2005-07-05

With the hydrolytic resolution of (R,S)-naproxen 2,2,2-trifluoroethyl thioesters in water-saturated isooctane as a model system, improvements of the specific lipase activity and thermal stability were found when a crude Carica papaya lipase (CPL) was partially purified and employed as the biocatalyst. The partially purified Carica papaya lipase (PCPL) was furthermore explored as an effective enantioselective biocatalyst for the hydrolytic resolution of (R,S)-profen thioesters in water-saturated organic solvents. The kinetic analysis in water-saturated isooctane indicated that both acyl donor and acyl acceptor have profound influences on the lipase activity, E-value, and enantioselectivity. Inversion of the enantioselectivity from (S)- to (R)-thioester was found for (R,S)-fenoprofen and (R,S)-ketoprofen thioesters that contained a bulky substituent at the meta-position of 2-phenyl moiety of the acyl part. Kinetic constants for the acylation step were furthermore estimated for elucidating the kinetic data and postulating an active site model. The thermodynamic analysis indicated that the enantiomer discrimination was driven by the difference of activation enthalpy (DeltaDeltaH) and that of activation entropy (DeltaDeltaS), yet the latter was dominated for most of the reacting systems. The postulated active site model was supported from the variation of DeltaDeltaH and DeltaDeltaS with the acyl moiety, in which a good linear enthalpy-entropy compensation relationship was also illustrated. A comparison of the performances between Candida rugosa lipase (CRL) and PCPL indicated that PCPL was superior to CRL in terms of the better thermal stability, similar or better lipase activity for the fast-reacting substrate, time-course-stability, and lower enzyme cost.

Why Does the Human Body Maintain a Constant 37-Degree Temperature?: Thermodynamic Switch Controls Chemical Equilibrium in Biological Systems

NASA Astrophysics Data System (ADS)

Chun, Paul W.

2005-01-01

Applying the Planck-Benzinger methodology to biological systems, we have established that the negative Gibbs free energy minimum at a well-defined stable temperature, langTSrang, where the bound unavailable energy TΔS° = 0, has its origin in the sequence-specific hydrophobic interactions. Each such system we have examined confirms the existence of a thermodynamic molecular switch wherein a change of sign in [ΔCp°]reaction leads to a true negative minimum in the Gibbs free energy change of reaction, and hence a maximum in the related equilibrium constant, Keq. At this temperature, langTSrang, where ΔH°(TS)(-) = ΔG°(TS)(-)min, the maximum work can be accomplished in transpiration, digestion, reproduction or locomotion. In the human body, this temperature is 37°C. The langTSrang values may vary from one living organism to another, but the fact that the value of TΔS°(T) = 0 will not. There is a lower cutoff point, langThrang, where enthalpy is unfavorable but entropy is favorable, i.e. ΔH°(Th)(+) = TΔS°(Th)(+), and an upper limit, langTmrang, above which enthalpy is favorable but entropy is unfavorable, i.e. ΔH°(Tm)(-) = TΔS°(Tm)(-). Only between these two temperature limits, where ΔG°(T) = 0, is the net chemical driving force favorable for such biological processes as protein folding, protein-protein, protein-nucleic acid or protein-membrane interactions, and protein self-assembly. All interacting biological systems examined using the Planck-Benzinger methodology have shown such a thermodynamic switch at the molecular level, suggesting that its existence may be universal.

Combined effect of dopant and electron beam-irradiation on phase transition in lithium potassium sulphate

NASA Astrophysics Data System (ADS)

Kassem, M. E.; Gaafar, M.; Abdel Gawad, M. M. H.; El-Muraikhi, M.; Ragab, I. M.

2004-02-01

Thermodynamic studies of polycrystalline ruthenium (Ru) doped LiKSO 4 have been made for different concentrations of Ru in the range 0%, 0.1%, 0.2%, 0.5%, 1%, 2%, 3% by weight. The thermal behaviour has been investigated using a differential scanning calorimeter in the vicinity of high temperature phases. From this, the effect of electron beam-irradiation on the thermal properties of these polycrystalline samples has been studied. The results showed a change in the transition temperature Tc, as well as the value of specific heat CPmax at the transition temperature due to the change in Ru content and irradiation energies. The change of enthalpy and entropy of the polycrystalline have been estimated numerically.

Specific heat and related thermophysical properties of liquid Fe-Cu-Mo alloy

NASA Astrophysics Data System (ADS)

Wang, Haipeng; Luo, Bingchi; Chang, Jian; Wei, Bingbo

2007-08-01

The specific heat and related thermophysical properties of liquid Fe77.5Cu13Mo9.5 monotectic alloy were investigated by an electromagnetic levitation drop calorimeter over a wide temperature range from 1482 to 1818 K. A maximum undercooling of 221 K (0.13 T m) was achieved and the specific heat was determined as 44.71 J·mol-1·K-1. The excess specific heat, enthalpy change, entropy change and Gibbs free energy difference of this alloy were calculated on the basis of experimental results. It was found that the calculated results by traditional estimating methods can only describe the solidification process under low undercooling conditions. Only the experimental results can reflect the reality under high undercooling conditions. Meanwhile, the thermal diffusivity, thermal conductivity, and sound speed were derived from the present experimental results. Furthermore, the solidified microstructural morphology was examined, which consists of (Fe) and (Cu) phases. The calculated interface energy was applied to exploring the correlation between competitive nucleation and solidification microstructure within monotectic alloy.

Thermochemical properties for isooctane and carbon radicals: computational study.

PubMed

Snitsiriwat, Suarwee; Bozzelli, Joseph W

2013-01-17

Thermochemical properties for isooctane, its internal rotation conformers, and radicals with corresponding bond energies are determined by use of computational chemistry. Enthalpies of formation are determined using isodesmic reactions with B3LYP density function theory and composite CBS-QB3 methods. Application of group additivity with comparison to calculated values is illustrated. Entropy and heat capacities are determined using geometric parameters, internal rotor potentials, and frequencies from B3LYP/6-31G(d,p) calculations for the lowest energy conformer. Internal rotor potentials are determined for the isooctane parent and for the primary, secondary, and tertiary radicals in order to identify isomer energies. Intramolecular interactions are shown to have a significant effect on the enthalpy of formation of the isooctane parent and its radicals. The computed standard enthalpy of formation for the lowest energy conformers of isooctane from this study is -54.40 ± 1.60 kcal mol(-1), which is 0.8 kcal mol(-1) lower than the evaluated experimental value -53.54 ± 0.36 kcal mol(-1). The standard enthalpy of formation for the primary radical for a methyl on the quaternary carbon is -5.00 ± 1.69 kcal mol(-1), for the primary radical on the tertiary carbon is -5.18 ± 1.69 kcal mol(-1), for the secondary isooctane radical is -9.03 ± 1.84 kcal mol(-1), and for the tertiary isooctane radical is -12.30 ± 2.02 kcal mol(-1). Bond energy values for the isooctane radicals are 100.64 ± 1.73, 100.46 ± 1.73, 96.41 ± 1.88 and 93.14 ± 2.05 kcal mol(-1) for C3•CCCC2, C3CCCC2•, C3CC•CC2, and C3CCC•C2, respectively. Entropy and heat capacity values are reported for the lowest energy homologues.

Effect of dissociation on thermodynamic properties of pure diatomic gases

NASA Technical Reports Server (NTRS)

Woolley, Harold W

1955-01-01

A graphical method is described by which the enthalpy, entropy, and compressibility factor for the equilibrium mixture of atoms and diatomic molecules for pure gaseous elements may be obtained and shown for any dissociating element for which the necessary data exist. Results are given for hydrogen, oxygen, and nitrogen. The effect of dissociation on the heat capacity is discussed briefly.

Determining the thermodynamic melting parameters of sulfamethoxazole, trimethoprim, urea, nicodin, and their double eutectics by differential scanning calorimetry

NASA Astrophysics Data System (ADS)

Agafonova, E. V.; Moshchenskii, Yu. V.; Tkachenko, M. L.

2013-08-01

The literature data on the thermodynamic melting characteristics of sulfamethoxazole, urea, trimethoprim, and nicodin are analyzed for individual compounds. Their enthalpies and melting points, either individually or in the composition of eutectics, are found by means of DSC. The entropies of fusion and the cryoscopic constants of individual compounds are calculated.

Application of cinchona-sulfonate-based chiral zwitterionic ion exchangers for the separation of proline-containing dipeptide rotamers and determination of on-column isomerization parameters from dynamic elution profiles.

PubMed

Wernisch, Stefanie; Trapp, Oliver; Lindner, Wolfgang

2013-09-17

The interconversion of cis and trans isomers of dipeptides containing C-terminal proline was studied by dynamic chromatography on zwitterionic chiral stationary phases at temperatures ranging from -15°C to +45°C The cis-trans isomers could be separated below 0°C and above 0-10°C plateau formation and peak coalescence phenomena occurred, which is characteristic for a dynamic process at the time-scale of partitioning. At and above room temperature, full coalescence was observed, which allowed separations of enantiomers without interference from interconversion effects. Analysis of the dynamic elution profiles of the interconverting peptides allowed the determination of isomerization rate constants and thermodynamic activation parameters (isomerization enthalpy, entropy and activation energy). In accordance with established results, isomerization rates and thermodynamic parameters were found to depend on the nature of the N-terminal amino acid. Isomerization barriers were only slightly lower than values determined with other methods but significant differences in the relative contributions of the activation enthalpy and entropy as well as isomerization rates pointed toward selector-moderated isomerization dynamics. Copyright © 2013 Elsevier B.V. All rights reserved.

Ratio of entropy to enthalpy in thermal transitions in biological tissues.

PubMed

Jacques, Steven L

2006-01-01

Thermal transitions in biological tissues that have been reported in the literature are summarized in terms of the apparent molar entropy (DeltaS) and molar enthalpy (DeltaH) involved in the transition. A plot of DeltaS versus DeltaH for all the data yields a straight line, consistent with the definition of free energy, DeltaG=DeltaH+TDeltaS. Various bonds may be involved in cooperative bond breakage during thermal transitions; however, for the sake of description, the equivalent number of cooperative hydrogen bonds can be cited. Most of the tissue data behave as if 10 to 20 hydrogen bonds are cooperatively broken during coagulation, with one transition, the expression of heat shock protein, involving 90 cooperative hydrogen bonds. The data are consistent with DeltaS=a+bDeltaH, where a=-327.5 J(mol K) and b=31.47 x 10(-4) K(-1). If each additional hydrogen bond adds 19 x 10(3) Jmol to DeltaH, then each additional bond adds 59.8 J(mol K) to DeltaS. Hence, the dynamics of irreversible thermal transitions can be described in terms of one free parameter, the apparent number of cooperative hydrogen bonds broken during the transition.

Mapping heat exchange in an allosteric protein.

PubMed

Gupta, Shaweta; Auerbach, Anthony

2011-02-16

Nicotinic acetylcholine receptors (AChRs) are synaptic ion channels that spontaneously isomerize (i.e., gate) between resting and active conformations. We used single-molecule electrophysiology to measure the temperature dependencies of mouse neuromuscular AChR gating rate and equilibrium constants. From these we estimated free energy, enthalpy, and entropy changes caused by mutations of amino acids located between the transmitter binding sites and the middle of the membrane domain. The range of equilibrium enthalpy change (13.4 kcal/mol) was larger than for free energy change (5.5 kcal/mol at 25°C). For two residues, the slope of the rate-equilibrium free energy relationship (Φ) was approximately constant with temperature. Mutant cycle analysis showed that both free energies and enthalpies are additive for energetically independent mutations. We hypothesize that changes in energy associated with changes in structure mainly occur close to the site of the mutation, and, hence, that it is possible to make a residue-by-residue map of heat exchange in the AChR gating isomerization. The structural correlates of enthalpy changes are discussed for 12 different mutations in the protein. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Thermodynamic evidence of flexibility in H2O and CO2 absorption of transition metal ion exchanged zeolite LTA.

PubMed

Guo, Xin; Wu, Lili; Navrotsky, Alexandra

2018-02-07

Gas absorption calorimetry has been employed to probe the intercation of water and carbon dioxide with transition metal ion (TM = Mn 2+ , Fe 2+ , Co 2+ , Cu 2+ , and Zn 2+ ) exchanged zeolite A samples. There appears to be a two-phase region, indicative of a guest-induced flexibility transition, separating hydrated zeolite A and its dehydrated form, both of which have variable water content in the single phase region. The differential enthalpy of absorption as a function of water loading directly identifies different strengths of multiple interactions along with possible binding mechanisms of Zn-A and Mn-A exhibiting the highest water absorption with most exothermic initial enthalpies of -125.28 ± 4.82 and -115.30 ± 2.56 kJ mol -1 . Zn-A and Mn-A also show moderately good capture ability for CO 2 with zero-coverage negative enthalpies of -55.59 ± 2.48 and -44.07 ± 1.53 kJ mol -1 . The thermodynamic information derived from differential enthalpy, chemical potential and differential entropy elucidated the multistage interactive behavior of small guest molecules (H 2 O/CO 2 ) and ion-exchanged frameworks.

Thermodynamic properties of 5(nitrophenyl) furan-2-carbaldehyde isomers.

PubMed

Dibrivnyi, Volodymyr; Sobechko, Iryna; Puniak, Marian; Horak, Yuriy; Obushak, Mykola; Van-Chin-Syan, Yuriy; Andriy, Marshalek; Velychkivska, Nadiia

2015-01-01

The aim of the current work was to determine thermo dynamical properties of 5(2-nitro phenyl)-furan-2-carbaldehyde, 5(3-nitro phenyl)-furan-2-carbaldehyde and 5(4-nitro phenyl)-furan-2-carbaldehyde. The temperature dependence of saturated vapor pressure of 5(2-nitro phenyl)-furan-2-carbaldehyde, 5(3-nitro phenyl)-furan-2-carbaldehyde and 5(4-nitro phenyl)-furan-2-carbaldehyde was determined by Knudsen's effusion method. The results are presented by the Clapeyron-Clausius equation in linear form, and via this form, the standard enthalpies, entropies and Gibbs energies of sublimation and evaporation of compounds were calculated at 298.15 K. The standard molar formation enthalpies of compounds in crystalline state at 298.15 K were determined indirectly by the corresponding standard molar combustion enthalpy, obtained using bomb calorimetry combustion. Determination of the thermodynamic properties for these compounds may contribute to solving practical problems pertaining optimization processes of their synthesis, purification and application and it will also provide a more thorough insight regarding the theoretical knowledge of their nature.Graphical abstract:Generalized structural formula of investigated compounds and their formation enthalpy determination scheme in the gaseous state.

Thermodynamics of interactions between mammalian cytochromes P450 and b5.

PubMed

Yablokov, Evgeny; Florinskaya, Anna; Medvedev, Alexei; Sergeev, Gennady; Strushkevich, Natallia; Luschik, Alexander; Shkel, Tatsiana; Haidukevich, Irina; Gilep, Andrei; Usanov, Sergey; Ivanov, Alexis

2017-04-01

Cytochromes P450 (CYPs) play an important role in the metabolism of xenobiotics and various endogenous substrates. Being a crucial component of the microsomal monooxygenase system, CYPs are involved in numerous protein-protein interactions. However, mechanisms underlying molecular interactions between components of the monooxygenase system still need better characterization. In this study thermodynamic parameters of paired interactions between mammalian CYPs and cytochromes b5 (CYB5) have been evaluated using a Surface Plasmon Resonance (SPR) based biosensor Biacore 3000. Analysis of 18 pairs of CYB5-CYP complexes formed by nine different isoforms of mammalian CYPs and two isoforms of human CYB5 has shown that thermodynamically these complexes can be subdivided into enthalpy-driven and entropy-driven groups. Formation of the enthalpy-driven complexes was observed in the case of microsomal CYPs allosterically regulated by CYB5 (CYB5A-CYP3A4, CYB5A-CYP3A5, CYB5A-CYP17A1). The entropy-driven complexes were formed when CYB5 had no effect on the CYP activity (CYB5A-CYP51A1, CYB5A-CYP1B1, CYB5B-CYP11A1). Results of this study suggest that such interactions determining protein clustering are indirectly linked to the monooxygenase functioning. Positive ΔH values typical for such interactions may be associated with displacement of the solvation shells of proteins upon clustering. CYB5-CYP complex formation accompanied by allosteric regulation of CYP activity by CYB5 is enthalpy-dependent. Copyright © 2017 Elsevier Inc. All rights reserved.

Tables and charts of equilibrium thermodynamic properties of ammonia for temperatures from 500 to 50,000 K.

NASA Technical Reports Server (NTRS)

Simmonds, A. L.; Miller, C. G., III; Nealy, J. E.

1976-01-01

Equilibrium thermodynamic properties for pure ammonia were generated for a range of temperature from 500 to 50,000 K and pressure from 0.01 to 40 MN/sq m and are presented in tabulated and graphical form. Properties include pressure, temperature, density, enthalpy, speed of sound, entropy, molecular-weight ratio, specific heat at constant pressure, specific heat at constant volume, isentropic exponent, and species mole fractions. These properties were calculated by the method which is based on minimization of the Gibbs free energy. The data presented herein are for an 18-species ammonia model. Heats of formation and spectroscopic constants used as input data are presented. Comparison of several thermodynamic properties calculated with the present program and a second computer code is performed for a range of pressure and for temperatures up to 30,000 K.

Tables of critical-flow functions and thermodynamic properties for methane and computational procedures for both methane and natural gas

NASA Technical Reports Server (NTRS)

Johnson, R. C.

1972-01-01

Procedures for calculating the mass flow rate of methane and natural gas through nozzles are given, along with the FORTRAN 4 subroutines used to make these calculations. Three sets of independent variables are permitted in these routines. In addition to the plenum pressure and temperature, the third independent variable is either nozzle exit pressure, Mach number, or temperature. A critical-flow factor that becomes a convenient means for determining the mass flow rate of methane through critical-flow nozzles is tabulated. Other tables are included for nozzle throat velocity and critical pressure, density, and temperature ratios, along with some thermodynamic properties of methane, including compressibility factor, enthalpy, entropy, specific heat, specific-heat ratio, and speed of sound. These tabulations cover a temperature range from 120 to 600 K and pressures to 3 million N/sq m.

Review of MEMS differential scanning calorimetry for biomolecular study

NASA Astrophysics Data System (ADS)

Yu, Shifeng; Wang, Shuyu; Lu, Ming; Zuo, Lei

2017-12-01

Differential scanning calorimetry (DSC) is one of the few techniques that allow direct determination of enthalpy values for binding reactions and conformational transitions in biomolecules. It provides the thermodynamics information of the biomolecules which consists of Gibbs free energy, enthalpy and entropy in a straightforward manner that enables deep understanding of the structure function relationship in biomolecules such as the folding/unfolding of protein and DNA, and ligand bindings. This review provides an up to date overview of the applications of DSC in biomolecular study such as the bovine serum albumin denaturation study, the relationship between the melting point of lysozyme and the scanning rate. We also introduce the recent advances of the development of micro-electro-mechanic-system (MEMS) based DSCs.

Selected Thermophysical Properties of 2,2 Dimethylcyclopentyl Methylphosphonofluoridate (GP) and 2,2 Dimethylcyclopentanol (DMCP)

DTIC Science & Technology

2016-09-01

Thermophysical properties, including vapor pressure, density, viscosity, surface tension, and flash point, are reported for 2,2-dimethylcyclopentyl...methylphosphonofluoridate (GP; Chemical Abstracts Service [CAS] no. 453574-97-5). Density data above the melting point, and vapor pressure of the liquid and solid...experimental vapor pressure data and were used to calculate the temperature-dependent enthalpy of vaporization , volatility, and entropy of

Interactive FORTRAN IV computer programs for the thermodynamic and transport properties of selected cryogens (fluids pack)

NASA Technical Reports Server (NTRS)

Mccarty, R. D.

1980-01-01

The thermodynamic and transport properties of selected cryogens had programmed into a series of computer routines. Input variables are any two of P, rho or T in the single phase regions and either P or T for the saturated liquid or vapor state. The output is pressure, density, temperature, entropy, enthalpy for all of the fluids and in most cases specific heat capacity and speed of sound. Viscosity and thermal conductivity are also given for most of the fluids. The programs are designed for access by remote terminal; however, they have been written in a modular form to allow the user to select either specific fluids or specific properties for particular needs. The program includes properties for hydrogen, helium, neon, nitrogen, oxygen, argon, and methane. The programs include properties for gaseous and liquid states usually from the triple point to some upper limit of pressure and temperature which varies from fluid to fluid.

Entropy-driven one-step formation of Phi29 pRNA 3WJ from three RNA fragments.

PubMed

Binzel, Daniel W; Khisamutdinov, Emil F; Guo, Peixuan

2014-04-15

The emerging field of RNA nanotechnology necessitates creation of functional RNA nanoparticles but has been limited by particle instability. It has been shown that the three-way junction of bacteriophage phi29 motor pRNA has unusual stability and can self-assemble from three fragments with high efficiency. It is generally believed that RNA and DNA folding is energy landscape-dependent, and the folding of RNA is driven by enthalpy. Here we examine the thermodynamic characteristics of the 3WJ components as 2'-fluoro RNA, DNA, and RNA. It was seen that the three fragments existed either in 3WJ complex or as monomers, with the intermediate of dimers almost undetectable. It seems that the three fragments can lead to the formation of the 3WJ complex efficiently within a rapid time. A low dissociation constant (apparent KD) of 11.4 nM was determined for RNA, inclusion of 2'-F pyrimidines strengthened the KD to 4.5 nM, and substitution of DNA weakened it to 47.7 nM. The ΔG°37, were -36, -28, and -15 kcal/mol for 3WJ2'-F, 3WJRNA, and 3WJDNA, respectively. It is found that the formation of the three-component complex was governed by entropy, instead of enthalpy, as usually found in RNA complexes. Here entropy-driven is referring to a dominating entropic contribution to the increased stability of the 3WJ(2'-F and 3WJ(RNA) compared to the 3WJ(DNA,) instead of referring to the absolute role or total energy governing 3WJ folding. [corrected].

Thermodynamic compensation upon binding to exosite 1 and the active site of thrombin.

PubMed

Treuheit, Nicholas A; Beach, Muneera A; Komives, Elizabeth A

2011-05-31

Several lines of experimental evidence including amide exchange and NMR suggest that ligands binding to thrombin cause reduced backbone dynamics. Binding of the covalent inhibitor dPhe-Pro-Arg chloromethyl ketone to the active site serine, as well as noncovalent binding of a fragment of the regulatory protein, thrombomodulin, to exosite 1 on the back side of the thrombin molecule both cause reduced dynamics. However, the reduced dynamics do not appear to be accompanied by significant conformational changes. In addition, binding of ligands to the active site does not change the affinity of thrombomodulin fragments binding to exosite 1; however, the thermodynamic coupling between exosite 1 and the active site has not been fully explored. We present isothermal titration calorimetry experiments that probe changes in enthalpy and entropy upon formation of binary ligand complexes. The approach relies on stringent thrombin preparation methods and on the use of dansyl-l-arginine-(3-methyl-1,5-pantanediyl)amide and a DNA aptamer as ligands with ideal thermodynamic signatures for binding to the active site and to exosite 1. Using this approach, the binding thermodynamic signatures of each ligand alone as well as the binding signatures of each ligand when the other binding site was occupied were measured. Different exosite 1 ligands with widely varied thermodynamic signatures cause a similar reduction in ΔH and a concomitantly lower entropy cost upon DAPA binding at the active site. The results suggest a general phenomenon of enthalpy-entropy compensation consistent with reduction of dynamics/increased folding of thrombin upon ligand binding to either the active site or exosite 1.

Characterization of racemic species of chiral drugs using thermal analysis, thermodynamic calculation, and structural studies.

PubMed

Li, Z J; Zell, M T; Munson, E J; Grant, D J

1999-03-01

The identification of the racemic species, as a racemic compound, a racemic conglomerate, or a racemic solid solution (pseudoracemate), is crucial for rationalizing the potential for resolution of racemates by crystallization. The melting points and enthalpies of fusion of a number of chiral drugs and their salts were measured by differential scanning calorimetry. Based on a thermodynamic cycle involving the solid and liquid phases of the enantiomers and racemic species, the enthalpy, entropy and Gibbs free energy of the racemic species were derived from the thermal data. The Gibbs free energy of formation, is always negative for a racemic compound, if it can exist, and the contribution from the entropy of mixing in the liquid state to the free energy of formation is the driving force for the process. For a racemic conglomerate, the entropy of mixing in the liquid state is close to the ideal value of R ln 2 (1.38 cal.mol-1. K-1). Pseudoracemates behave differently from the other two types of racemic species. When the melting points of the racemic species is about 30 K below that of the homochiral species, is approximately zero, indicating that the racemic compound and racemic conglomerate possess similar relative stabilities. The powder X-ray diffraction patterns and 13C solid-state nuclear magnetic resonance spectra are valuable for revealing structural differences between a racemic compound and a racemic conglomerate. Thermodynamic prediction, thermal analysis, and structural study are in excellent agreement for identifying the nature of the racemic species.

Thermometric titration studies of mixed ligand complexes of thorium.

PubMed

Kugler, G C; Carey, G H

1970-10-01

Mixed-ligand chelates consisting of two different multidentate ligands linked to a central thorium(IV) ion have been prepared in aqueous solution and their heats of formation studied thermo metrically. Pyrocatechol, tiron, chromotropic acid, potassium hydrogen phthalate, 8-hydroxyquinoline-S-sulphonic acid, iminodiacetic acid, 5-sulphosalicylic acid and salicylic acid were used as the secondary ligands, while ethylenediaminetetra-acetate and 1, 2-diaminocyclohexane-N,N,N',N'-tetra-acetate were used as primary ligands. DeltaH values for the overall reactions are given, and where possible, the DeltaH and DeltaS values for the specific secondary ligand addition were calculated. The overall stability of the mixed-ligand chelates and the enhanced stability of EDTA mixed chelates relative to the analogous DCTA chelates were found to be due to entropy rather than enthalpy effects.

Adsorption properties of cationic rhodamine B dye onto metals chloride-activated castor bean residue carbons.

PubMed

Zhi, Lee Lin; Zaini, Muhammad Abbas Ahmad

2017-02-01

This work was aimed to evaluate the feasibility of castor bean residue based activated carbons prepared through metals chloride activation. The activated carbons were characterized for textural properties and surface chemistry, and the adsorption data of rhodamine B were established to investigate the removal performance. Zinc chloride-activated carbon with specific surface area of 395 m 2 /g displayed a higher adsorption capacity of 175 mg/g. Magnesium chloride and iron(III) chloride are less toxic and promising agents for composite chemical activation. The adsorption data obeyed Langmuir isotherm and pseudo-second-order kinetics model. The rate-limiting step in the adsorption of rhodamine B is film diffusion. The positive values of enthalpy and entropy indicate that the adsorption is endothermic and spontaneous at high temperature.

Computer program for determining the thermodynamic properties of Freon refrigerants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riemer, D.H.; Jacobs, H.R.; Boehm, R.F.

1977-12-01

This program was written to be used as a subroutine. The program determines the thermodynamics of Freon refrigerants. The following refrigerants can be analyzed F-11, F-12, F-13, F-14, F-21, F-22, F-23, F-113, and F-114. The subroutine can evaluate a thermodynamic state for these refrigerants given any of the following pairs of state quantities: pressure and quality, pressure and entropy, pressure and enthalpy, temperature and quality, temperature and specific volume, and temperature and pressure. These six pairs of knowns allow the user to analyze any thermodynamic cycle utilizing a refrigerant as the working fluid. The Downing form of the Martin equationmore » of state was used. This report contains a brief description, flow chart and listing of all subroutines required.« less

Computer program for determining the thermodynamic properties of freon refrigerants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riemer, D.H.; Jacobs, H.R.; Boehm, R.F.

1976-07-01

This program was written to be used as a subroutine. The program determines the thermodynamics of Freon refrigerants. The following refrigerants can be analyzed F-11, F-12, F-13, F-14, F-21, F-22, F-23, F-113, and F-114. The subroutine can evaluate a thermodynamic state for these refrigerants given any of the following pairs of state quantities: pressure and quality, pressure and entropy, pressure and enthalpy, temperature and quality, temperature and specific volume and temperature and pressure. These six pairs of knowns allow the user to analyze any thermodynamic cycle utilizing a refrigerant as the working fluid. The Downing form of the Martin equationmore » of state was used. A brief description, flow chart, and listing of all subroutines required are presented.« less

Investigation of phase stability of novel equiatomic FeCoNiCuZn based-high entropy alloy prepared by mechanical alloying

NASA Astrophysics Data System (ADS)

Soni, Vinay Kumar; Sanyal, S.; Sinha, S. K.

2018-05-01

The present work reports the structural and phase stability analysis of equiatomic FeCoNiCuZn High entropy alloy (HEA) systems prepared by mechanical alloying (MA) method. In this research effort some 1287 alloy combinations were extensively studied to arrive at most favourable combination. FeCoNiCuZn based alloy system was selected on the basis of physiochemical parameters such as enthalpy of mixing (ΔHmix), entropy of mixing (ΔSmix), atomic size difference (ΔX) and valence electron concentration (VEC) such that it fulfils the formation criteria of stable multi component high entropy alloy system. In this context, we have investigated the effect of novel alloying addition in view of microstructure and phase formation aspect. XRD plots of the MA samples shows the formation of stable solid solution with FCC (Face Cantered Cubic) after 20 hr of milling time and no indication of any amorphous or intermetallic phase formation. Our results are in good agreement with calculation and analysis done on the basis of physiochemical parameters during selection of constituent elements of HEA.

Is Water at the Graphite Interface Vapor-like or Ice-like?

PubMed

Qiu, Yuqing; Lupi, Laura; Molinero, Valeria

2018-04-05

Graphitic surfaces are the main component of soot, a major constituent of atmospheric aerosols. Experiments indicate that soots of different origins display a wide range of abilities to heterogeneously nucleate ice. The ability of pure graphite to nucleate ice in experiments, however, seems to be almost negligible. Nevertheless, molecular simulations with the monatomic water model mW with water-carbon interactions parameterized to reproduce the experimental contact angle of water on graphite predict that pure graphite nucleates ice. According to classical nucleation theory, the ability of a surface to nucleate ice is controlled by the binding free energy between ice immersed in liquid water and the surface. To establish whether the discrepancy in freezing efficiencies of graphite in mW simulations and experiments arises from the coarse resolution of the model or can be fixed by reparameterization, it is important to elucidate the contributions of the water-graphite, water-ice, and ice-water interfaces to the free energy, enthalpy, and entropy of binding for both water and the model. Here we use thermodynamic analysis and free energy calculations to determine these interfacial properties. We demonstrate that liquid water at the graphite interface is not ice-like or vapor-like: it has similar free energy, entropy, and enthalpy as water in the bulk. The thermodynamics of the water-graphite interface is well reproduced by the mW model. We find that the entropy of binding between graphite and ice is positive and dominated, in both experiments and simulations, by the favorable entropy of reducing the ice-water interface. Our analysis indicates that the discrepancy in freezing efficiencies of graphite in experiments and the simulations with mW arises from the inability of the model to simultaneously reproduce the contact angle of liquid water on graphite and the free energy of the ice-graphite interface. This transferability issue is intrinsic to the resolution of the model, and arises from its lack of rotational degrees of freedom.

Side-chain conformational space analysis (SCSA): A multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities

NASA Astrophysics Data System (ADS)

Zhou, Peng; Chen, Xiang; Shang, Zhicai

2009-03-01

In this article, the concept of multi conformation-based quantitative structure-activity relationship (MCB-QSAR) is proposed, and based upon that, we describe a new approach called the side-chain conformational space analysis (SCSA) to model and predict protein-peptide binding affinities. In SCSA, multi-conformations (rather than traditional single-conformation) have received much attention, and the statistical average information on multi-conformations of side chains is determined using self-consistent mean field theory based upon side chain rotamer library. Thereby, enthalpy contributions (including electrostatic, steric, hydrophobic interaction and hydrogen bond) and conformational entropy effects to the binding are investigated in terms of occurrence probability of residue rotamers. Then, SCSA was applied into the dataset of 419 HLA-A*0201 binding peptides, and nonbonding contributions of each position in peptide ligands are well determined. For the peptides, the hydrogen bond and electrostatic interactions of the two ends are essential to the binding specificity, van der Waals and hydrophobic interactions of all the positions ensure strong binding affinity, and the loss of conformational entropy at anchor positions partially counteracts other favorable nonbonding effects.

Enthalpy-Driven RNA Folding: Single-Molecule Thermodynamics of Tetraloop–Receptor Tertiary Interaction†

PubMed Central

Fiore, Julie L.; Kraemer, Benedikt; Koberling, Felix; Edmann, Rainer; Nesbitt, David J.

2010-01-01

RNA folding thermodynamics are crucial for structure prediction, which requires characterization of both enthalpic and entropic contributions of tertiary motifs to conformational stability. We explore the temperature dependence of RNA folding due to the ubiquitous GAAA tetraloop–receptor docking interaction, exploiting immobilized and freely diffusing single-molecule fluorescence resonance energy transfer (smFRET) methods. The equilibrium constant for intramolecular docking is obtained as a function of temperature (T = 21–47 °C), from which a van’t Hoff analysis yields the enthalpy (ΔH°) and entropy (ΔS°) of docking. Tetraloop–receptor docking is significantly exothermic and entropically unfavorable in 1 mM MgCl2 and 100 mM NaCl, with excellent agreement between immobilized (ΔH° = −17.4 ± 1.6 kcal/mol, and ΔS° = −56.2 ± 5.4 cal mol−1 K−1) and freely diffusing (ΔH° = −17.2 ± 1.6 kcal/mol, and ΔS° = −55.9 ± 5.2 cal mol−1 K−1) species. Kinetic heterogeneity in the tetraloop–receptor construct is unaffected over the temperature range investigated, indicating a large energy barrier for interconversion between the actively docking and nondocking subpopulations. Formation of the tetraloop–receptor interaction can account for ~60% of the ΔH° and ΔS° of P4–P6 domain folding in the Tetrahymena ribozyme, suggesting that it may act as a thermodynamic clamp for the domain. Comparison of the isolated tetraloop–receptor and other tertiary folding thermodynamics supports a theme that enthalpy- versus entropy-driven folding is determined by the number of hydrogen bonding and base stacking interactions. PMID:19186984

Cyclopentadienone Oxidation Reaction Kinetics and Thermochemistry for the Alcohols, Hydroperoxides, and Vinylic, Alkoxy, and Alkylperoxy Radicals.

PubMed

Yommee, Suriyakit; Bozzelli, Joseph W

2016-01-28

Cyclopentadienone has one carbonyl and two olefin groups resulting in 4n + 2 π-electrons in a cyclic five-membered ring structure. Thermochemical and kinetic parameters for the initial reactions of cyclopentadienone radicals with O2 and the thermochemical properties for cyclopentadienone-hydroperoxides, alcohols, and alkenyl, alkoxy, and peroxy radicals were determined by use of computational chemistry. The CBS-QB3 composite and B3LYP density functional theory methods were used to determine the enthalpies of formation (ΔfH°298) using the isodesmic reaction schemes with several work reactions for each species. Entropy and heat capacity, S°(T) and Cp°(T) (50 K ≤ T ≤ 5000 K) are determined using geometric parameters, internal rotor potentials, and frequencies from B3LYP/6-31G(d,p) calculations. Standard enthalpies of formation are reported for parent molecules as cyclopentadienone, cyclopentadienone with alcohol, hydroperoxide substituents, and the cyclopentadienone-yl vinylic, alkoxy, and peroxy radicals corresponding to loss of a hydrogen atom from the carbon and oxygen sites. Entropy and heat capacity vs temperature also are reported for the parent molecules and for radicals. The thermochemical analysis shows The R(•) + O2 well depths are deep, on the order of 50 kcal mol(-1), and the R(•) + O2 reactions to RO + O (chain branching products) for cyclopentadienone-2-yl and cyclopentadienone-3-yl have unusually low reaction (ΔHrxn) enthalpies, some 20 or so kcal/mol below the entrance channels. Chemical activation kinetics using quantum RRK analysis for k(E) and master equation for falloff are used to show that significant chain branching as a function of temperature and pressure can occur when these vinylic radicals are formed.

Towards an understanding of the molecular mechanism of solvation of drug molecules: a thermodynamic approach by crystal lattice energy, sublimation, and solubility exemplified by paracetamol, acetanilide, and phenacetin.

PubMed

Perlovich, German L; Volkova, Tatyana V; Bauer-Brandl, Annette

2006-10-01

Temperature dependencies of saturated vapor pressure for the monoclinic modification of paracetamol (acetaminophen), acetanilide, and phenacetin (acetophenetidin) were measured and thermodynamic functions of sublimation calculated (paracetamol: DeltaGsub298=60.0 kJ/mol; DeltaHsub298=117.9+/-0.7 kJ/mol; DeltaSsub298=190+/-2 J/mol.K; acetanilide: DeltaGsub298=40.5 kJ/mol; DeltaHsub298=99.8+/-0.8 kJ/mol; DeltaSsub298=197+/-2 J/mol.K; phenacetin: DeltaGsub298=52.3 kJ/mol; DeltaHsub298=121.8+/-0.7 kJ/mol; DeltaSsub298=226+/-2 J/mol.K). Analysis of packing energies based on geometry optimization of molecules in the crystal lattices using diffraction data and the program Dmol3 was carried out. Parameters analyzed were: (a) energetic contribution of van der Waals forces and hydrogen bonding to the total packing energy; (b) contributions of fragments of the molecules to the packing energy. The fraction of hydrogen bond energy in the packing energy increases as: phenacetin (17.5%)

Vaporization behavior of an alkyl diphenyl ether and a commercial lubricant

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMurray, Jake W.; Frame, Barbara J.; Voit, Stewart L.

The equilibrium vapor pressure as a function of temperature for an alkyl diphenyl ether with a vaporization coefficient significantly smaller than unity was characterized using the combined Langmuir free evaporation and mass loss Knudsen effusion technique. Results are compared using different cell designs and discrepancies, difficulties, and complications are discussed. In conclusion, the enthalpy and entropy of vaporization are estimated using the average temperature of the measurements.

Vaporization behavior of an alkyl diphenyl ether and a commercial lubricant

DOE PAGES

McMurray, Jake W.; Frame, Barbara J.; Voit, Stewart L.

2018-05-24

The equilibrium vapor pressure as a function of temperature for an alkyl diphenyl ether with a vaporization coefficient significantly smaller than unity was characterized using the combined Langmuir free evaporation and mass loss Knudsen effusion technique. Results are compared using different cell designs and discrepancies, difficulties, and complications are discussed. In conclusion, the enthalpy and entropy of vaporization are estimated using the average temperature of the measurements.

Formation of nitric acid hydrates - A chemical equilibrium approach

NASA Technical Reports Server (NTRS)

Smith, Roland H.

1990-01-01

Published data are used to calculate equilibrium constants for reactions of the formation of nitric acid hydrates over the temperature range 190 to 205 K. Standard enthalpies of formation and standard entropies are calculated for the tri- and mono-hydrates. These are shown to be in reasonable agreement with earlier calorimetric measurements. The formation of nitric acid trihydrate in the polar stratosphere is discussed in terms of these equilibrium constants.

Folding of a LysM Domain: Entropy-Enthalpy Compensation in the Transition State of an Ideal Two-state Folder

PubMed Central

Nickson, Adrian A.; Stoll, Kate E.; Clarke, Jane

2008-01-01

Protein-engineering methods (Φ-values) were used to investigate the folding transition state of a lysin motif (LysM) domain from Escherichia coli membrane-bound lytic murein transglycosylase D. This domain consists of just 48 structured residues in a symmetrical βααβ arrangement and is the smallest αβ protein yet investigated using these methods. An extensive mutational analysis revealed a highly robust folding pathway with no detectable transition state plasticity, indicating that LysM is an example of an ideal two-state folder. The pattern of Φ-values denotes a highly polarised transition state, with significant formation of the helices but no structure within the β-sheet. Remarkably, this transition state remains polarised after circularisation of the domain, and exhibits an identical Φ-value pattern; however, the interactions within the transition state are uniformly weaker in the circular variant. This observation is supported by results from an Eyring analysis of the folding rates of the two proteins. We propose that the folding pathway of LysM is dominated by enthalpic rather than entropic considerations, and suggest that the lower entropy cost of formation of the circular transition state is balanced, to some extent, by the lower enthalpy of contacts within this structure. PMID:18538343

Removal of cadmium(II) ions from aqueous solution using Ni (15 wt.%)-doped α-Fe2O3 nanocrystals: equilibrium, thermodynamic, and kinetic studies.

PubMed

OuldM'hamed, Mohamed; Khezami, L; Alshammari, Abdulrahman G; Ould-Mame, S M; Ghiloufi, I; Lemine, O M

2015-01-01

The present publication investigates the performance of nanocrystalline Ni (15 wt.%)-doped α-Fe2O3 as an effective nanomaterial for the removal of Cd(II) ions from aqueous solutions. The nanocrystalline Ni-doped α-Fe2O3 powders were prepared by mechanical alloying, and characterized by X-ray diffraction and a vibrating sample magnetometer. Batch-mode experiments were realized to determine the adsorption equilibrium, kinetics, and thermodynamic parameters of toxic heavy metal ions by Ni (15 wt.%)-doped α-Fe2O3. The adsorption isotherms data were found to be in good agreement with the Langmuir model. The adsorption capacity of Cd(II) ion reached a maximum value of about 90.91 mg g(-1) at 328 K and pH 7. The adsorption process kinetics was found to comply with pseudo-second-order rate law. Thermodynamic parameters related to the adsorption reaction, free energy change, enthalpy change and entropy change, were evaluated. The found values of free energy and enthalpy revealed a spontaneous endothermic adsorption-process. Moreover, the positive entropy suggests an increase of randomness during the process of heavy metal removal at the adsorbent-solution interface.

Driving forces and the influence of the buffer composition on the complexation reaction between ibuprofen and HPCD.

PubMed

Perlovich, German L; Skar, Merete; Bauer-Brandl, Annette

2003-10-01

Cyclodextrins are often used in order to increase the aqueous solubility of drug substances by complexation. In order to investigate the complexation reaction of ibuprofen and hydroxypropyl-beta-cyclodextrin, titration calorimetry was used as a direct method. The thermodynamic parameters of the complexation process (stability constant, K(11); complexation enthalpy, deltaH(c) degrees ) were obtained in two different buffer systems (citric acid/sodium-phosphate and phosphoric acid) at various pH values. Based on these data the relative contributions of the enthalpic and entropic terms of the Gibbs energy to the complexation process have been analyzed. In both buffers the enthalpic and entropic terms are of different sign and this case corresponds to a 'nonclassical' model of hydrophobic interaction. In citric buffer, the main driving force of complexation is the entropy, which increases from 60 to 67% while the pH of the solution increases from 3.2 to 8.0. However, for the phosphoric buffer the entropic term decreases from 60 to 45%, while the pH-value of the solution increases from 5.0 to 8.2, and the driving force of the complexation process changes from entropy to enthalpy. The experimental data of the present study are compared to results of other authors and discrepancies discussed in detail.

Thermodynamics of Host–Guest Interactions between Fullerenes and a Buckycatcher

PubMed Central

2015-01-01

1H NMR and isothermal titration calorimetry (ITC) experiments were employed to obtain reliable thermodynamic data for the formation of the 1:1 inclusion complexes of fullerenes C60 and C70 with the buckycatcher (C60H28). NMR measurements were done in toluene-d8 and chlorobenzene-d5 at 288, 298, and 308 K, while the ITC titrations were performed in toluene, chlorobenzene, o-dichlorobenzene, anisole, and 1,1,2,2-tetrachloroethane at temperatures from 278 to 323 K. The association constants, Ka, obtained with both techniques are in very good agreement. The thermodynamic data obtained by ITC indicate that generally the host–guest association is enthalpy-driven. Interestingly, the entropy contributions are, with rare exceptions, slightly stabilizing or close to zero. Neither ΔH nor ΔS is constant over the temperature range studied, and these thermodynamic functions exhibit classical enthalpy/entropy compensation. The ΔCp values calculated from the temperature dependence of the calorimetric ΔH values are negative for the association of both fullerenes with the buckycatcher in toluene. The negative ΔCp values are consistent with some desolvation of the host-cavity and the guest in the inclusion complexes, C60@C60H28 and C70@C60H28. PMID:25248285

Solvation Effect on Complexation of Alkali Metal Cations by a Calix[4]arene Ketone Derivative.

PubMed

Požar, Josip; Nikšić-Franjić, Ivana; Cvetnić, Marija; Leko, Katarina; Cindro, Nikola; Pičuljan, Katarina; Borilović, Ivana; Frkanec, Leo; Tomišić, Vladislav

2017-09-14

The medium effect on the complexation of alkali metal cations with a calix[4]arene ketone derivative (L) was systematically examined in methanol, ethanol, N-methylformamide, N,N-dimethylformamide, dimethyl sulfoxide, and acetonitrile. In all solvents the binding of Na + cation by L was rather efficient, whereas the complexation of other alkali metal cations was observed only in methanol and acetonitrile. Complexation reactions were enthalpically controlled, while ligand dissolution was endothermic in all cases. A notable influence of the solvent on NaL + complex stability could be mainly attributed to the differences in complexation entropies. The higher NaL + stability in comparison to complexes with other alkali metal cations in acetonitrile was predominantly due to a more favorable complexation enthalpy. The 1 H NMR investigations revealed a relatively low affinity of the calixarene sodium complex for inclusion of the solvent molecule in the calixarene hydrophobic cavity, with the exception of acetonitrile. Differences in complex stabilities in the explored solvents, apart from N,N-dimethylformamide and acetonitrile, could be mostly explained by taking into account solely the cation and complex solvation. A considerable solvent effect on the complexation equilibria was proven to be due to an interesting interplay between the transfer enthalpies and entropies of the reactants and the complexes formed.

Thermodynamics of a third-generation poly(phenylene-pyridyl) dendron decorated with dodecyl groups in the range of T → 0 to 480 K

NASA Astrophysics Data System (ADS)

Smirnova, N. N.; Markin, A. V.; Tsvetkova, L. Ya.; Kuchkina, N. V.; Yuzik-Klimova, E. Yu.; Shifrina, Z. B.

2016-05-01

The heat capacity of a glassy third-generation poly(phenylene-pyridyl) dendron decorated with dodecyl groups is studied for the first time via high-precision adiabatic vacuum and differential scanning calorimetry in the temperature range of 6 to 520 K. The standard thermodynamic functions (molar heat capacity C p ° , enthalpy H°( T), entropy S°( T), and Gibbs energy G°( T)- H°(0)) in the range of T → 0 to 480 K, and the entropy of formation at 298.15 K, are calculated on the basis of the obtained data. The thermodynamic properties of the dendron and the corresponding third-generation poly(phenylene-pyridyl) dendrimer studied earlier are compared.

Hydration of an apolar solute in a two-dimensional waterlike lattice fluid

NASA Astrophysics Data System (ADS)

Buzano, C.; de Stefanis, E.; Pretti, M.

2005-05-01

In a previous work, we investigated a two-dimensional lattice-fluid model, displaying some waterlike thermodynamic anomalies. The model, defined on a triangular lattice, is now extended to aqueous solutions with apolar species. Water molecules are of the “Mercedes Benz” type, i.e., they possess a D3 (equilateral triangle) symmetry, with three equivalent bonding arms. Bond formation depends both on orientation and local density. The insertion of inert molecules displays typical signatures of hydrophobic hydration: large positive transfer free energy, large negative transfer entropy (at low temperature), strong temperature dependence of the transfer enthalpy and entropy, i.e., large (positive) transfer heat capacity. Model properties are derived by a generalized first order approximation on a triangle cluster.

Hydration of an apolar solute in a two-dimensional waterlike lattice fluid.

PubMed

Buzano, C; De Stefanis, E; Pretti, M

2005-05-01

In a previous work, we investigated a two-dimensional lattice-fluid model, displaying some waterlike thermodynamic anomalies. The model, defined on a triangular lattice, is now extended to aqueous solutions with apolar species. Water molecules are of the "Mercedes Benz" type, i.e., they possess a D3 (equilateral triangle) symmetry, with three equivalent bonding arms. Bond formation depends both on orientation and local density. The insertion of inert molecules displays typical signatures of hydrophobic hydration: large positive transfer free energy, large negative transfer entropy (at low temperature), strong temperature dependence of the transfer enthalpy and entropy, i.e., large (positive) transfer heat capacity. Model properties are derived by a generalized first order approximation on a triangle cluster.

High-temperature heat capacity of Co3O4 spinel: thermally induced spin unpairing transition

USGS Publications Warehouse

Mocala, K.; Navrotsky, A.; Sherman, David M.

1992-01-01

A strong anomaly was found in the heat capacity of Co3O4 between 1000 K and the decomposition temperature. This anomaly is not related to the decomposition of Co3O4 to CoO. The measured entropy of transition, ??S=46??4 J mol-1 K-1 of Co3O4, supports the interpretation that this anomaly reflects a spin unpairing transition in octahedrally coordinated Co3+ cations. Experimental values of heat capacity, heat content and entropy of Co3O4 in the high temperature region are provided. The enthalpy of the spin unpairing transition is 53??4 kJ mol-1 of Co3O4. ?? 1992 Springer-Verlag.

New insights into the mechanism of interaction between CO2 and polymers from thermodynamic parameters obtained by in situ ATR-FTIR spectroscopy.

PubMed

Gabrienko, Anton A; Ewing, Andrew V; Chibiryaev, Andrey M; Agafontsev, Alexander M; Dubkov, Konstantin A; Kazarian, Sergei G

2016-03-07

This work reports new physical insights of the thermodynamic parameters and mechanisms of possible interactions occurring in polymers subjected to high-pressure CO2. ATR-FTIR spectroscopy has been used in situ to determine the thermodynamic parameters of the intermolecular interactions between CO2 and different functional groups of the polymers capable of specific interactions with sorbed CO2 molecules. Based on the measured ATR-FTIR spectra of the polymer samples subjected to high-pressure CO2 (30 bar) at different temperatures (300-340 K), it was possible to characterize polymer-polymer and CO2-polymer interactions. Particularly, the enthalpy and entropy of the formation of the specific non-covalent complexes between CO2 and the hydroxy (-OH), carbonyl (C[double bond, length as m-dash]O) and hydroxyimino ([double bond, length as m-dash]N-OH) functional groups of the polymer samples have been measured. Furthermore, the obtained spectroscopic results have provided an opportunity for the structure of these complexes to be proposed. An interesting phenomenon regarding the behavior of CO2/polymer systems has also been observed. It has been found that only for the polyketone, the value of enthalpy was negative indicating an exothermic process during the formation of the CO2-polymer non-covalent complexes. Conversely, for the polyoxime and polyalcohol samples there is a positive enthalpy determined. This is a result of the initial polymer-polymer interactions requiring more energy to break than is released during the formation of the CO2-polymer complex. The effect of increasing temperature to facilitate the breaking of the polymer-polymer interactions has also been observed. Hence, a mechanism for the formation of CO2-polymer complexes was suggested based on these results, which occurs via a two-step process: (1) the breaking of the existing polymer-polymer interactions followed by (2) the formation of new CO2-polymer non-covalent interactions.

Thermodynamic compensation upon binding to exosite 1 and the active site of thrombin

PubMed Central

Treuheit, Nicholas A.; Beach, Muneera A.; Komives, Elizabeth A.

2011-01-01

Several lines of experimental evidence including amide exchange and NMR suggest that ligands binding to thrombin cause reduced backbone dynamics. Binding of the covalent inhibitor dPhe-Pro-Arg chloromethylketone to the active site serine, as well as non-covalent binding of a fragment of the regulatory protein, thrombomodulin, to exosite 1 on the back side of the thrombin molecule both cause reduced dynamics. However, the reduced dynamics do not appear to be accompanied by significant conformational changes. In addition, binding of ligands to the active site does not change the affinity of thrombomodulin fragments binding to exosite 1, however, the thermodynamic coupling between exosite 1 and the active site has not been fully explored. We present isothermal titration calorimetry experiments that probe changes in enthalpy and entropy upon formation of binary ligand complexes. The approach relies on stringent thrombin preparation methods and on the use of dansyl-L-arginine-(3-methyl-1,5-pantanediyl) amide and a DNA aptamer as ligands with ideal thermodynamic signatures for binding to the active site and to exosite 1. Using this approach, the binding thermodynamic signatures of each ligand alone as well as the binding signatures of each ligand when the other binding site was occupied were measured. Different exosite 1 ligands with widely varied thermodynamic signatures cause the same reduction in ΔH and a concomitantly lower entropy cost upon DAPA binding at the active site. The results suggest a general phenomenon of enthalpy-entropy compensation consistent with reduction of dynamics/increased folding of thrombin upon ligand binding to either the active site or to exosite 1. PMID:21526769

Detailed Investigation of Core-Shell Precipitates in a Cu-Containing High Entropy Alloy

NASA Astrophysics Data System (ADS)

Alam, T.; Gwalani, B.; Viswanathan, G.; Fraser, H.; Banerjee, R.

2018-05-01

Due to the competing influences of configurational entropy and enthalpy of mixing, in recent years, secondary (including intermetallic) phases have been reported in many high entropy alloy (HEA) systems. These secondary phases offer great potential in terms of strengthening the HEA beyond the solid solution strengthening effects, and as such are of great interest in regards to alloy design for engineering applications. The present research investigates novel nano-scale core-shell precipitates forming within the disordered bcc matrix phase of an Al2CrCuFeNi2 HEA, utilizing complementary high-resolution microscopy techniques of atom probe tomography (APT) and transmission electron microscopy (TEM). The size, morphology, and local chemistry of these core-shell precipitates was measured by APT, and the composition was further corroborated by high-resolution scanning transmission electron microscopy-energy dispersive spectroscopy in an aberration-corrected TEM. Furthermore, high-resolution TEM imaging of the core-shell structure indicates that the Cu-rich core exhibits a bcc crystal structure.

Chain architecture and micellization: A mean-field coarse-grained model for poly(ethylene oxide) alkyl ether surfactants

DOE Office of Scientific and Technical Information (OSTI.GOV)

García Daza, Fabián A.; Mackie, Allan D., E-mail: allan.mackie@urv.cat; Colville, Alexander J.

2015-03-21

Microscopic modeling of surfactant systems is expected to be an important tool to describe, understand, and take full advantage of the micellization process for different molecular architectures. Here, we implement a single chain mean field theory to study the relevant equilibrium properties such as the critical micelle concentration (CMC) and aggregation number for three sets of surfactants with different geometries maintaining constant the number of hydrophobic and hydrophilic monomers. The results demonstrate the direct effect of the block organization for the surfactants under study by means of an analysis of the excess energy and entropy which can be accurately determinedmore » from the mean-field scheme. Our analysis reveals that the CMC values are sensitive to branching in the hydrophilic head part of the surfactant and can be observed in the entropy-enthalpy balance, while aggregation numbers are also affected by splitting the hydrophobic tail of the surfactant and are manifested by slight changes in the packing entropy.« less

Heat capacity from 12 to 305°K and entropy of talc and tremolite

USGS Publications Warehouse

Robie, R.A.; Stout, J.W.

1963-01-01

The heat capacities of talc, Mg3Si4O10(OH)2, and tremolite, Ca2Mg6Si8O22(OH)2, have been measured between 12 and 305??K. Smoothed values of heat capacity, entropy, enthalpy, and free energy are tabulated. At 298.15?? K. the values of the thermodynamic functions are: talc, Cp?? = 76.89 ?? 0.23 cal. deg.-1 mole-1, S?? = 62.33 ?? 0.19 cal. deg.-1 mole-1, H?? - H6?? = 11,206 ?? 34 cal. mole-1; tremolite, Cp?? = 156.7 ?? 0.6 cal. deg.-1 mole-1, S?? = 131.2 ?? 0.5 cal. deg.-1 mole-1, H?? - H6?? = 23,335 ?? 90 cal. mole-1. From the equilibrium data of Bowen and Tuttle and the entropy of talc, the heat of formation of talc from MgO, SiO2, and H2O (liq.) is calculated to be ??H??f298 = -43.6 ?? 1 kcal.

Chain architecture and micellization: A mean-field coarse-grained model for poly(ethylene oxide) alkyl ether surfactants

NASA Astrophysics Data System (ADS)

García Daza, Fabián A.; Colville, Alexander J.; Mackie, Allan D.

2015-03-01

Microscopic modeling of surfactant systems is expected to be an important tool to describe, understand, and take full advantage of the micellization process for different molecular architectures. Here, we implement a single chain mean field theory to study the relevant equilibrium properties such as the critical micelle concentration (CMC) and aggregation number for three sets of surfactants with different geometries maintaining constant the number of hydrophobic and hydrophilic monomers. The results demonstrate the direct effect of the block organization for the surfactants under study by means of an analysis of the excess energy and entropy which can be accurately determined from the mean-field scheme. Our analysis reveals that the CMC values are sensitive to branching in the hydrophilic head part of the surfactant and can be observed in the entropy-enthalpy balance, while aggregation numbers are also affected by splitting the hydrophobic tail of the surfactant and are manifested by slight changes in the packing entropy.

Temperature Dependence of Uranium and Vanadium Adsorption on Amidoxime-Based Adsorbents in Natural Seawater

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuo, Li-Jung; Gill, Gary A.; Tsouris, Costas

The apparent enthalpy and entropy of the complexation of uranium (VI) and vanadium (V) with amidoxime ligands grafted onto polyethylene fiber was determined using time series measurements of adsorption capacities in natural seawater at three different temperatures. The complexation of uranium was highly endothermic, while the complexation of vanadium showed minimal temperature sensitivity. Amidoxime-based polymeric adsorbents exhibit significantly increased uranium adsorption capacities and selectivity in warmer waters.

Thermodynamic and hydration effects for the incorporation of a cationic 3-aminopropyl chain into DNA

PubMed Central

Soto, Ana Maria; Kankia, Besik I.; Dande, Prasad; Gold, Barry; Marky, Luis A.

2002-01-01

The introduction of cationic 5-(ω-aminoalkyl)-2′-deoxypyrimidines into duplex DNA has been shown to induce DNA bending. In order to understand the energetic and hydration contributions for the incorporation of a cationic side chain in DNA a combination of spectroscopy, calorimetry and density techniques were used. Specifically, the temperature unfolding and isothermal formation was studied for a pair of duplexes with sequence d(CGTAGUCG TGC)/d(GCACGACTACG), where U represents 2′-deoxyuridine (‘control’) or 5-(3-aminopropyl)-2′-deoxyuridine (‘modified’). Continuous variation experiments confirmed 1:1 stoichiometries for each duplex and the circular dichroism spectra show that both duplexes adopted the B conformation. UV and differential scanning calorimetry melting experiments reveal that each duplex unfolds in two-state transitions. In low salt buffer, the ‘modified’ duplex is more stable and unfolds with a lower endothermic heat and lower release of counterion and water. This electrostatic stabilization is entropy driven and disappears at higher salt concentrations. Complete thermodynamic profiles at 15°C show that the favorable formation of each duplex results from the compensation of a favorable exothermic heat with an unfavorable entropy contribution. However, the isothermal profiles yielded a differential enthalpy of 8.8 kcal/mol, which is 4.3 kcal/mol higher than the differential enthalpy observed in the unfolding profiles. This indicates that the presence of the aminopropyl chain induces an increase in base stacking interactions in the modified single strand and a decrease in base stacking interactions in the modified duplex. Furthermore, the formation of the ‘control’ duplex releases water while the ‘modified’ duplex takes up water. Relative to the control duplex, formation of the modified duplex at 15°C yielded a marginal differential ΔG° term, positive ΔΔHITC–Δ(TΔS) compensation, negative ΔΔV and a net release of counterions. The opposite signs of the differential enthalpy–entropy compensation and differential volume change terms show a net uptake of structural water around polar and non-polar groups. This indicates that incorporation of the aminopropyl chain induces a higher exposure of aromatic bases to the solvent, which may be consistent with a small and local bend in the ‘modified’ duplex. PMID:12136099

Thermodynamic properties (enthalpy, bond energy, entropy, and heat capacity) and internal rotor potentials of vinyl alcohol, methyl vinyl ether, and their corresponding radicals.

PubMed

da Silva, Gabriel; Kim, Chol-Han; Bozzelli, Joseph W

2006-06-29

Vinyl alcohols (enols) have been discovered as important intermediates and products in the oxidation and combustion of hydrocarbons, while methyl vinyl ethers are also thought to occur as important combustion intermediates. Vinyl alcohol has been detected in interstellar media, while poly(vinyl alcohol) and poly(methyl vinyl ether) are common polymers. The thermochemical property data on these vinyl alcohols and methyl vinyl ethers is important for understanding their stability, reaction paths, and kinetics in atmospheric and thermal hydrocarbon-oxygen systems. Enthalpies , entropies , and heat capacities (C(p)()(T)) are determined for CH(2)=CHOH, C(*)H=CHOH, CH(2)=C(*)OH, CH(2)=CHOCH(3), C(*)H=CHOCH(3), CH(2)=C(*)OCH(3), and CH(2)=CHOC(*)H(2). Molecular structures, vibrational frequencies, , and C(p)(T) are calculated at the B3LYP/6-31G(d,p) density functional calculation level. Enthalpies are also determined using the composite CBS-Q, CBS-APNO, and G3 methods using isodesmic work reactions to minimize calculation errors. Potential barriers for internal rotors are calculated at the B3LYP/6-31G(d,p) level and used to determine the hindered internal rotational contributions to entropy and heat capacity. The recommended ideal gas phase values calculated in this study are the following (in kcal mol(-1)): -30.0, -28.9 (syn, anti) for CH(2)=CHOH; -25.6, -23.9 for CH(2)=CHOCH(3); 31.3, 33.5 for C(*)H=CHOH; 27.1 for anti-CH(2)=C(*)OH; 35.6, 39.3 for C(*)H=CHOCH(3); 33.5, 32.2 for CH(2)=C(*)OCH(3); 21.3, 22.0 for CH(2)=CHOC(*)H(2). Bond dissociation energies (BDEs) and group additivity contributions are also determined. The BDEs reveal that the O-H, O-CH(3), C-OH, and C-OCH(3) bonds in vinyl alcohol and methyl vinyl ether are similar in energy to those in the aromatic molecules phenol and methyl phenyl ether, being on average around 3 kcal mol(-1) weaker in the vinyl systems. The keto-enol tautomerization enthalpy for the interconversion of vinyl alcohol to acetaldehyde is determined to be -9.7 kcal mol(-1), while the activation energy for this reaction is calculated as 55.9 kcal mol(-1); this is the simplest keto-enol tautomerization and is thought to be important in the reactions of vinyl alcohol. Formation of the formyl methyl radical (vinoxy radical/vinyloxy radical) from both vinyl alcohol and methyl vinyl ether is also shown to be important, and its reactions are discussed briefly.

Energy and enthalpy distribution functions for a few physical systems.

PubMed

Wu, K L; Wei, J H; Lai, S K; Okabe, Y

2007-08-02

The present work is devoted to extracting the energy or enthalpy distribution function of a physical system from the moments of the distribution using the maximum entropy method. This distribution theory has the salient traits that it utilizes only the experimental thermodynamic data. The calculated distribution functions provide invaluable insight into the state or phase behavior of the physical systems under study. As concrete evidence, we demonstrate the elegance of the distribution theory by studying first a test case of a two-dimensional six-state Potts model for which simulation results are available for comparison, then the biphasic behavior of the binary alloy Na-K whose excess heat capacity, experimentally observed to fall in a narrow temperature range, has yet to be clarified theoretically, and finally, the thermally induced state behavior of a collection of 16 proteins.

Thermodynamic Data to 20,000 K For Monatomic Gases

NASA Technical Reports Server (NTRS)

Gordon, Sanford; McBride, Bonnie J.

1999-01-01

This report contains standard-state thermodynamic functions for 50 gaseous atomic elements plus deuterium and electron gas, 51 singly ionized positive ions, and 36 singly ionized negative ions. The data were generated by the NASA Lewis computer program PAC97, a modified version of PAC91 reported in McBride and Gordon. This report is being published primarily to document part of the data currently being used in several NASA Lewis computer programs. The data are presented in tabular and graphical format and are also represented in the form of least-squares coefficients. The tables give the following data as functions of temperature : heat capacity, enthalpy, entropy Gibbs energy, enthalpy of formation, and equilibrium constant. A brief discussion and a comparison of calculated results are given for several models for calculating ideal thermodynamic data for monatomic gases.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ching-Yuan Chang; Wen-Tien Tsai; Horng-Chia Lee

Such thermodynamic properties as enthalpy, free energy, and entropy of adsorption have been computed for N,N-dimethylformamide (DMF) vapor on two commercial adsorbents: coconut shell Type PCB of activated carbon and Type DAY of hydrophobic zeolite. The computation is based on the Langmuir adsorption isotherms obtained at 293, 303, and 313 K as reported by Tsai et al. The laden adsorbents were regenerated with hot inert nitrogen gas and studied by thermal gravimetric analysis at three different heating rates. The apparent activation energies (E{sub des}) of thermal desorption were determined by using the Friedman method. The zeolite DAY has an adsorptionmore » potential higher than that of activated carbon PCB as indicated by the more negative value of the adsorption enthalpy of DMF vapor. The average value of E{sub des} of zeolite DAY is larger than that of activated carbon PCB.« less

Kinetic evaluation of the solvolysis of isobutyl chloro- and chlorothioformate esters

PubMed Central

McAneny, Matthew J; Choi, Song Hee

2011-01-01

Summary The specific rates of solvolysis of isobutyl chloroformate (1) are reported at 40.0 °C and those for isobutyl chlorothioformate (2) are reported at 25.0 °C, in a variety of pure and binary aqueous organic mixtures with wide ranging nucleophilicity and ionizing power. For 1, we also report the first-order rate constants determined at different temperatures in pure ethanol (EtOH), methanol (MeOH), 80% EtOH, and in both 97% and 70% 2,2,2-trifluoroethanol (TFE). The enthalpy (ΔH≠) and entropy (ΔS≠) of activation values obtained from Arrhenius plots for 1 in these five solvents are reported. The specific rates of solvolysis were analyzed using the extended Grunwald–Winstein equation. Results obtained from correlation analysis using this linear free energy relationship (LFER) reinforce our previous suggestion that side-by-side addition–elimination and ionization mechanisms operate, and the relative importance is dependent on the type of chloro- or chlorothioformate substrate and the solvent. PMID:21647255

Specific and highly efficient condensation of GC and IC DNA by polyaza pyridinophane derivatives.

PubMed

Stojković, Marijana Radić; Gonzalez-Garcia, Jorge; Šupljika, Filip; Galiana-Rosello, Cristina; Guijarro, Lluis; Gazze, Salvatore A; Francis, Lewis W; Piantanida, Ivo; Garcia-Espana, Enrique

2018-04-01

Two bis-polyaza pyridinophane derivatives and their monomeric reference compounds revealed strong interactions with ds-DNA and RNA. The bis-derivatives show a specific condensation of GC- and IC-DNA, which is almost two orders of magnitude more efficient than the well-known condensation agent spermine. The type of condensed DNA was identified as ψ-DNA, characterized by the exceptionally strong CD signals. At variance to the almost silent AT(U) polynucleotides, these strong CD signals allow the determination of GC-condensates at nanomolar nucleobase concentrations. Detailed thermodynamic characterisation by ITC reveals significant differences between the DNA binding of the bis-derivative compounds (enthalpy driven) and that of spermine and of their monomeric counterparts (entropy driven). Atomic force microscopy confirmed GC-DNA compaction by the bis-derivatives and the formation of toroid- and rod-like structures responsible for the ψ-type pattern in the CD spectra. Copyright © 2017 Elsevier B.V. All rights reserved.

Thermodynamic Data Rescue and Informatics for Deep Carbon Science

NASA Astrophysics Data System (ADS)

Zhong, H.; Ma, X.; Prabhu, A.; Eleish, A.; Pan, F.; Parsons, M. A.; Ghiorso, M. S.; West, P.; Zednik, S.; Erickson, J. S.; Chen, Y.; Wang, H.; Fox, P. A.

2017-12-01

A large number of legacy datasets are contained in geoscience literature published between 1930 and 1980 and not expressed external to the publication text in digitized formats. Extracting, organizing, and reusing these "dark" datasets is highly valuable for many within the Earth and planetary science community. As a part of the Deep Carbon Observatory (DCO) data legacy missions, the DCO Data Science Team and Extreme Physics and Chemistry community identified thermodynamic datasets related to carbon, or more specifically datasets about the enthalpy and entropy of chemicals, as a proof of principle analysis. The data science team endeavored to develop a semi-automatic workflow, which includes identifying relevant publications, extracting contained datasets using OCR methods, collaborative reviewing, and registering the datasets via the DCO Data Portal where the 'Linked Data' feature of the data portal provides a mechanism for connecting rescued datasets beyond their individual data sources, to research domains, DCO Communities, and more, making data discovery and retrieval more effective.To date, the team has successfully rescued, deposited and registered additional datasets from publications with thermodynamic sources. These datasets contain 3 main types of data: (1) heat content or enthalpy data determined for a given compound as a function of temperature using high-temperature calorimetry, (2) heat content or enthalpy data determined for a given compound as a function of temperature using adiabatic calorimetry, and (3) direct determination of heat capacity of a compound as a function of temperature using differential scanning calorimetry. The data science team integrated these datasets and delivered a spectrum of data analytics including visualizations, which will lead to a comprehensive characterization of the thermodynamics of carbon and carbon-related materials.

Novel carbon-ion fuel cells. Quarterly technical report No. 9, October 1, 1995--December 31, 1995

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cocks, F.H.

1995-12-31

This report presents research to develop an entirely new, fundamentally different class of fuel cell using a solid electrolyte that transports carbon ions. This fuel cell would use solid carbon dissolved in molten metal as a fuel reservoir and anode; expensive gaseous or liquid fuel would not be required. Thermodynamic factors favor a carbon-ion fuel cell over other fuel cell designs: a combination of enthalpy, entropy, and Gibbs free energy makes the reaction of solid carbon and oxygen very efficient, and the entropy change allows this efficiency to slightly increase at high temperatures. The high temperature exhaust of the fuelmore » cell would make it useful as a ``topping cycle``, to be followed by conventional steam turbine systems.« less

PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements.

PubMed

Tang, Yat T; Marshall, Garland R

2011-02-28

Binding affinity prediction is one of the most critical components to computer-aided structure-based drug design. Despite advances in first-principle methods for predicting binding affinity, empirical scoring functions that are fast and only relatively accurate are still widely used in structure-based drug design. With the increasing availability of X-ray crystallographic structures in the Protein Data Bank and continuing application of biophysical methods such as isothermal titration calorimetry to measure thermodynamic parameters contributing to binding free energy, sufficient experimental data exists that scoring functions can now be derived by separating enthalpic (ΔH) and entropic (TΔS) contributions to binding free energy (ΔG). PHOENIX, a scoring function to predict binding affinities of protein-ligand complexes, utilizes the increasing availability of experimental data to improve binding affinity predictions by the following: model training and testing using high-resolution crystallographic data to minimize structural noise, independent models of enthalpic and entropic contributions fitted to thermodynamic parameters assumed to be thermodynamically biased to calculate binding free energy, use of shape and volume descriptors to better capture entropic contributions. A set of 42 descriptors and 112 protein-ligand complexes were used to derive functions using partial least-squares for change of enthalpy (ΔH) and change of entropy (TΔS) to calculate change of binding free energy (ΔG), resulting in a predictive r2 (r(pred)2) of 0.55 and a standard error (SE) of 1.34 kcal/mol. External validation using the 2009 version of the PDBbind "refined set" (n = 1612) resulted in a Pearson correlation coefficient (R(p)) of 0.575 and a mean error (ME) of 1.41 pK(d). Enthalpy and entropy predictions were of limited accuracy individually. However, their difference resulted in a relatively accurate binding free energy. While the development of an accurate and applicable scoring function was an objective of this study, the main focus was evaluation of the use of high-resolution X-ray crystal structures with high-quality thermodynamic parameters from isothermal titration calorimetry for scoring function development. With the increasing application of structure-based methods in molecular design, this study suggests that using high-resolution crystal structures, separating enthalpy and entropy contributions to binding free energy, and including descriptors to better capture entropic contributions may prove to be effective strategies toward rapid and accurate calculation of binding affinity.

Enthalpies of formation of U-, Th-, Ce-brannerite: implications for plutonium immobilization

NASA Astrophysics Data System (ADS)

Helean, K. B.; Navrotsky, A.; Lumpkin, G. R.; Colella, M.; Lian, J.; Ewing, R. C.; Ebbinghaus, B.; Catalano, J. G.

2003-08-01

Brannerite, ideally MTi 2O 6, (M=actinides, lanthanides and Ca) occurs in titanate-based ceramics proposed for the immobilization of plutonium. Standard enthalpies of formation, Δ H0f at 298 K, for three brannerite compositions (kJ/mol): CeTi 2O 6 (-2948.8 ± 4.3), U 0.97Ti 2.03O 6 (-2977.9 ± 3.5) and ThTi 2O 6 (-3096.5 ± 4.3) were determined by high temperature oxide melt drop solution calorimetry at 975 K using 3Na 2O · 4MoO 3 solvent. The enthalpies of formation were also calculated from an oxide phase assemblage (Δ H0f-ox at 298 K): MO 2 + 2TiO 2=MTi 2O 6. Only UTi 2O 6 is energetically stable with respect to an oxide assemblage: U 0.97Ti 2.03O 6 (Δ H0f-ox=-7.7±2.8 kJ/mol). Both CeTi 2O 6 and ThTi 2O 6 are higher in enthalpy with respect to their oxide assemblages with (Δ H0f-ox=+29.4±3.6 kJ/mol) and (Δ H0f-ox=+19.4±1.6 kJ/mol) respectively. Thus, Ce- and Th-brannerite are entropy stabilized and are thermodynamically stable only at high temperature.

Comparison of hydrogen bonding in 1-octanol and 2-octanol as probed by spectroscopic techniques.

PubMed

Palombo, Francesca; Sassi, Paola; Paolantoni, Marco; Morresi, Assunta; Cataliotti, Rosario Sergio

2006-09-14

Liquid 1-octanol and 2-octanol have been investigated by infrared (IR), Raman, and Brillouin experiments in the 10-90 degrees C temperature range. Self-association properties of the neat liquids are described in terms of a three-state model in which OH oscillators differently implicated in the formation of H-bonds are considered. The results are in quantitative agreement with recent computational studies for 1-octanol. The H-bond probability is obtained by Raman data, and a stochastic model of H-bonded chains gives a consistent picture of the self-association characteristics. Average values of hydrogen bond enthalpy and entropy are evaluated. The H-bond formation enthalpy is ca. -22 kJ/mol and is slightly dependent on the structural isomerism. The different degree of self-association for the two octanols is attributed to entropic factors. The more shielded 2-isomer forms larger fractions of smaller, less cooperative, and more ordered clusters, likely corresponding to cyclic structures. Signatures of a different cluster organization are also evidenced by comparing the H-bond energy dispersion (HBED) of OH stretching IR bands. A limiting cooperative H-bond enthalpy value of 27 kJ/mol is found. It is also proposed that the different H-bonding capabilities may modulate the extent of interaggregate hydrocarbon interactions, which is important in explaining the differences in molar volume, compressibility, and vaporization enthalpy for the two isomers.

Thermodynamics of organisms in the context of dynamic energy budget theory.

PubMed

Sousa, Tânia; Mota, Rui; Domingos, Tiago; Kooijman, S A L M

2006-11-01

We carry out a thermodynamic analysis to an organism. It is applicable to any type of organism because (1) it is based on a thermodynamic formalism applicable to all open thermodynamic systems and (2) uses a general model to describe the internal structure of the organism--the dynamic energy budget (DEB) model. Our results on the thermodynamics of DEB organisms are the following. (1) Thermodynamic constraints for the following types of organisms: (a) aerobic and exothermic, (b) anaerobic and exothermic, and (c) anaerobic and endothermic; showing that anaerobic organisms have a higher thermodynamic flexibility. (2) A way to compute the changes in the enthalpy and in the entropy of living biomass that accompany changes in growth rate solving the problem of evaluating the thermodynamic properties of biomass as a function of the amount of reserves. (3) Two expressions for Thornton's coefficient that explain its experimental variability and theoretically underpin its use in metabolic studies. (4) A mechanism that organisms in non-steady-state use to rid themselves of internal entropy production: "dilution of entropy production by growth." To demonstrate the practical applicability of DEB theory to quantify thermodynamic changes in organisms we use published data on Klebsiella aerogenes growing aerobically in a continuous culture. We obtain different values for molar entropies of the reserve and the structure of Klebsiella aerogenes proving that the reserve density concept of DEB theory is essential in discussions concerning (a) the relationship between organization and entropy and (b) the mechanism of storing entropy in new biomass. Additionally, our results suggest that the entropy of dead biomass is significantly different from the entropy of living biomass.

Thermodynamic Effects of Noncoded and Coded Methionine Substitutions in Calmodulin

PubMed Central

Yamniuk, Aaron P.; Ishida, Hiroaki; Lippert, Dustin; Vogel, Hans J.

2009-01-01

The methionine residues in the calcium (Ca2+) regulatory protein calmodulin (CaM) are structurally and functionally important. They are buried within the N- and C-domains of apo-CaM but become solvent-exposed in Ca2+-CaM, where they interact with numerous target proteins. Previous structural studies have shown that methionine substitutions to the noncoded amino acids selenomethionine, ethionine, or norleucine, or mutation to leucine do not impact the main chain structure of CaM. Here we used differential scanning calorimetry to show that these substitutions enhance the stability of both domains, with the largest increase in melting temperature (19–26°C) achieved with leucine or norleucine in the apo-C-domain. Nuclear magnetic resonance spectroscopy experiments also revealed the loss of a slow conformational exchange process in the Leu-substituted apo-C-domain. In addition, isothermal titration calorimetry experiments revealed considerable changes in the enthalpy and entropy of target binding to apo-CaM and Ca2+-CaM, but the free energy of binding was largely unaffected due to enthalpy-entropy compensation. Collectively, these results demonstrate that noncoded and coded methionine substitutions can be accommodated in CaM because of the structural plasticity of the protein. However, adjustments in side-chain packing and dynamics lead to significant differences in protein stability and the thermodynamics of target binding. PMID:19217866

Effect of unsaturation on the absorption of ethane and ethylene in imidazolium-based ionic liquids.

PubMed

Moura, Leila; Mishra, Manas; Bernales, Varinia; Fuentealba, Patricio; Padua, Agilio A H; Santini, Catherine C; Costa Gomes, Margarida F

2013-06-20

The influence of the presence of imidazolium side chain unsaturation on the solubility of ethane and ethylene was studied in three ionic liquids: 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide-saturated alkyl side-chain in the cation; 1-methyl-3-(buten-3-yl)imidazolium bis(trifluorosulfonyl)imide-double bond in the side-chain of the cation; and 1-methyl-3-benzylimidazolium bis(trifluorosulfonyl)imide-benzyl group in the side-chain of the cation. The solubility of both gases decreases when the side-chain of the cations is functionalized with an unsaturated group. This can be explained by a less favorable enthalpy of solvation. The difference of solubility between ethane and ethylene can be explained from a balance of enthalpic and entropic factors: for the ionic liquid with the saturated alkyl side-chain and the benzyl-substituted side-chain, it is the favorable entropy of solvation that explains the larger ethylene solubility, whereas in the case of the saturated side-chain, it is the more favorable enthalpy of solvation. Molecular simulation allowed the identification of the mechanisms of solvation and the preferential solvation sites for each gas in the different ionic liquids. Simulations have shown that the entropy of solvation is more favorable when the presence of the gas weakens the cation-anion interactions or when the gas can be solvated near different sites of the ionic liquid.

Thermodynamics study of the dimerization equilibria of rhodamine B and 6G in different ionic strengths by photometric titration and chemometrics method

NASA Astrophysics Data System (ADS)

Ghasemi, Jahanbakhsh; Niazi, Ali; Kubista, Mikael

2005-11-01

The dimerization constants of rhodamine B and 6G have been determined by studying the dependence of their absorption spectra on the temperature in the range 20-80 °C at different total concentrations of rhodamine B (5.89 × 10 -6 to 2.36 × 10 -4 M) and rhodamine 6G (2.34 × 10 -5 to 5.89 × 10 -4 M) and in different concentrations of LiCl, NaCl and KCl salts as supporting electrolytes. The monomer-dimer equilibrium of rhodamine B and 6G have been determined by chemometrics refinement of the absorption spectra obtained by thermometric titrations performed at different ionic strengths. The quantitative analysis of the data of undefined mixtures, was carried out by simultaneous resolution of the overlapping spectral bands in the whole set of absorption spectra. The dimerization constants are varied by changing the ionic strength and the degree of dimerization are decreased by increasing of the ionic strength of the medium. The enthalpy and entropy of the dimerization reactions were determined from the dependence of the equilibrium constants on the temperature (van't Hoff equation). From the thermodynamic results the TΔ S°-Δ H° plot was sketched. It shows a fairly good positive correlation which indicates the enthalpy-entropy compensation in the dimerization reactions (compensation effect).

Thermodynamics study of the dimerization equilibria of rhodamine B and 6G in different ionic strengths by photometric titration and chemometrics method.

PubMed

Ghasemi, Jahanbakhsh; Niazi, Ali; Kubista, Mikael

2005-11-01

The dimerization constants of rhodamine B and 6G have been determined by studying the dependence of their absorption spectra on the temperature in the range 20-80 degrees C at different total concentrations of rhodamine B (5.89 x 10(-6) to 2.36 x 10(-4)M) and rhodamine 6G (2.34 x 10(-5) to 5.89 x 10(-4)M) and in different concentrations of LiCl, NaCl and KCl salts as supporting electrolytes. The monomer-dimer equilibrium of rhodamine B and 6G have been determined by chemometrics refinement of the absorption spectra obtained by thermometric titrations performed at different ionic strengths. The quantitative analysis of the data of undefined mixtures, was carried out by simultaneous resolution of the overlapping spectral bands in the whole set of absorption spectra. The dimerization constants are varied by changing the ionic strength and the degree of dimerization are decreased by increasing of the ionic strength of the medium. The enthalpy and entropy of the dimerization reactions were determined from the dependence of the equilibrium constants on the temperature (van't Hoff equation). From the thermodynamic results the TDeltaS degrees -DeltaH degrees plot was sketched. It shows a fairly good positive correlation which indicates the enthalpy-entropy compensation in the dimerization reactions (compensation effect).

Clues to understanding cold sensation: Thermodynamics and electrophysiological analysis of the cold receptor TRPM8

PubMed Central

Brauchi, Sebastian; Orio, Patricio; Latorre, Ramon

2004-01-01

The cold and menthol receptor, TRPM8, also designated CMR1, is a member of the transient receptor potential (TRP) family of excitatory ion channels. TRPM8 is a channel activated by cold temperatures, voltage, and menthol. In this study, we characterize the cold- and voltage-induced activation of TRPM8 channel in an attempt to identify the temperature- and voltage-dependent components involved in channel activation. Under equilibrium conditions, decreasing temperature has two effects. (i) It shifts the normalized conductance vs. voltage curves toward the left, along the voltage axis. This effect indicates that the degree of order is higher when the channel is in the open configuration. (ii) It increases the maximum channel open probability, suggesting that temperature affects both voltage-dependent and -independent pathways. In the temperature range between 18°C and 25°C, large changes in enthalpy (ΔH = -112 kcal/mol) and entropy (ΔS = -384 cal/mol K) accompany the activation process. The Q10 calculated in the same temperature range is 24. This thermodynamic analysis strongly suggests that the process of opening involves large conformational changes of the channel-forming protein. Therefore, the highly temperature-dependent transition between open and closed configurations is possible because enthalpy and entropy are both large and compensate each other. Our data also demonstrate that temperature and voltage interact allosterically to enhance channel opening. PMID:15492228

Thermodynamics of natural selection III: Landauer's principle in computation and chemistry.

PubMed

Smith, Eric

2008-05-21

This is the third in a series of three papers devoted to energy flow and entropy changes in chemical and biological processes, and their relations to the thermodynamics of computation. The previous two papers have developed reversible chemical transformations as idealizations for studying physiology and natural selection, and derived bounds from the second law of thermodynamics, between information gain in an ensemble and the chemical work required to produce it. This paper concerns the explicit mapping of chemistry to computation, and particularly the Landauer decomposition of irreversible computations, in which reversible logical operations generating no heat are separated from heat-generating erasure steps which are logically irreversible but thermodynamically reversible. The Landauer arrangement of computation is shown to produce the same entropy-flow diagram as that of the chemical Carnot cycles used in the second paper of the series to idealize physiological cycles. The specific application of computation to data compression and error-correcting encoding also makes possible a Landauer analysis of the somewhat different problem of optimal molecular recognition, which has been considered as an information theory problem. It is shown here that bounds on maximum sequence discrimination from the enthalpy of complex formation, although derived from the same logical model as the Shannon theorem for channel capacity, arise from exactly the opposite model for erasure.

Translational Diffusion Coefficient and Partition Coefficient of a Spin-Labeled Solute in Lecithin Bilayer Membranes

PubMed Central

Dix, James A.; Diamond, Jared M.; Kivelson, Daniel

1974-01-01

The translational diffusion coefficient and the partition coefficient of a spin-labeled solute, di-t-butyl nitroxide, in an aqueous suspension of dipalmitoyl lecithin vesicles have been studied by electron spin resonance spectroscopy. When the lecithin is cooled through its phase transition temperature near 41°C, some solute is “frozen out” of the bilayer, and the standard partial molar enthalpy and entropy of partition go more positive by a factor of 8 and 6, respectively. However, the apparent diffusion constant in the lecithin phase is only slightly smaller than that in water, both above and below the transition temperature. The fraction of bilayer volume within which solute is distributed may increase with temperature, contributing to the positive enthalpy of partition. Comparison of time constants suggests that there is a permeability barrier to this solute in the periphery of the bilayer. PMID:4360944

Molecular basis for the specific recognition of the metazoan cyclic GMP-AMP by the innate immune adaptor protein STING

DOE PAGES

Shi, Heping; Wu, Jiaxi; Chen, Zhijian J.; ...

2015-07-06

Cyclic GMP-AMP containing a unique combination of mixed phosphodiester linkages (2'3'-cGAMP) is an endogenous second messenger molecule that activates the type-I IFN pathway upon binding to the homodimer of the adaptor protein STING on the surface of endoplasmic reticulum membrane. However, the preferential binding of the asymmetric ligand 2'3'-cGAMP to the symmetric dimer of STING represents a physicochemical enigma. In this paper, we show that 2'3'-cGAMP, but not its linkage isomers, adopts an organized free-ligand conformation that resembles the STING-bound conformation and pays low entropy and enthalpy costs in converting into the active conformation. Finally, our results demonstrate that analysesmore » of free-ligand conformations can be as important as analyses of protein conformations in understanding protein–ligand interactions.« less

The stability of N-[2-(4-o-fluorophenylpiperazin-1-yl)ethyl]-2,5-dimethyl-1 -phenylpyrrole-3,4-dicarboximide in aqueous-organic solutions.

PubMed

Zajac, Marianna; Sobczak, Agnieszka; Malinka, Wiesław; Redzicka, Aleksandra

2010-01-01

The first-order reaction of solvolysis of N-[2-(4-o-fluorophenylpiperazin-1-yl)ethyl]-2,5-dimethyl-1-phenylpyrrole-3,4-dicarboximide (PDI) was investigated as a function of pH at 333, 328, 323, 318 and 308 K in the pH range 1.11 - 12.78. The decomposition of PDI was followed by the HPLC method (Nucleosil 10-C8 column (250 x 4 mm I.D., dp = 10 microm), mobile phase: 0.018 mol/L ammonia acetate - acetonitrile (40: 60 v/v), UV detector: 240 nm, flow rate: 1 mL/min. Specific acid-base catalysis involves solvolysis of the undissociated molecules of PDI catalyzed by hydroxide ions and spontaneous solvolysis of the undissociated and monoprotonated forms of PDI under the influence of solvents. The thermodynamic parameters of the reactions--activation energy (E(a)), enthalpy (DH(#)), entropy (DS(#))--were calculated.

Structures, internal rotor potentials, and thermochemical properties for a series of nitrocarbonyls, nitroolefins, corresponding nitrites, and their carbon centered radicals.

PubMed

Snitsiriwat, Suarwee; Asatryan, Rubik; Bozzelli, Joseph W

2011-12-01

Structures, enthalpy (Δ(f)H°(298)), entropy (S°(T)), and heat capacity (C(p)(T)) are determined for a series of nitrocarbonyls, nitroolefins, corresponding nitrites, and their carbon centered radicals using the density functional B3LYP and composite CBS-QB3 calculations. Enthalpies of formation (Δ(f)H°(298)) are determined at the B3LYP/6-31G(d,p), B3LYP/6-31+G(2d,2p), and composite CBS-QB3 levels using several work reactions for each species. Entropy (S) and heat capacity (C(p)(T)) values from vibration, translational, and external rotational contributions are calculated using the rigid-rotor-harmonic-oscillator approximation based on the vibration frequencies and structures obtained from the density functional studies. Contribution to Δ(f)H(T), S, and C(p)(T) from the analysis on the internal rotors is included. Recommended values for enthalpies of formation of the most stable conformers of nitroacetone cc(═o)cno2, acetonitrite cc(═o)ono, nitroacetate cc(═o)no2, and acetyl nitrite cc(═o)ono are -51.6 kcal mol(-1), -51.3 kcal mol(-1), -45.4 kcal mol(-1), and -58.2 kcal mol(-1), respectively. The calculated Δ(f)H°(298) for nitroethylene c═cno2 is 7.6 kcal mol(-1) and for vinyl nitrite c═cono is 7.2 kcal mol(-1). We also found an unusual phenomena: an intramolecular transfer reaction (isomerization) with a low barrier (3.6 kcal mol(-1)) in the acetyl nitrite. The NO of the nitrite (R-ONO) in CH(3)C(═O')ONO moves to the C═O' oxygen in a motion of a stretching frequency and then a shift to the carbonyl oxygen (marked as O' for illustration purposes). © 2011 American Chemical Society

Biochemical thermodynamics: applications of Mathematica.

PubMed

Alberty, Robert A

2006-01-01

The most efficient way to store thermodynamic data on enzyme-catalyzed reactions is to use matrices of species properties. Since equilibrium in enzyme-catalyzed reactions is reached at specified pH values, the thermodynamics of the reactions is discussed in terms of transformed thermodynamic properties. These transformed thermodynamic properties are complicated functions of temperature, pH, and ionic strength that can be calculated from the matrices of species values. The most important of these transformed thermodynamic properties is the standard transformed Gibbs energy of formation of a reactant (sum of species). It is the most important because when this function of temperature, pH, and ionic strength is known, all the other standard transformed properties can be calculated by taking partial derivatives. The species database in this package contains data matrices for 199 reactants. For 94 of these reactants, standard enthalpies of formation of species are known, and so standard transformed Gibbs energies, standard transformed enthalpies, standard transformed entropies, and average numbers of hydrogen atoms can be calculated as functions of temperature, pH, and ionic strength. For reactions between these 94 reactants, the changes in these properties can be calculated over a range of temperatures, pHs, and ionic strengths, and so can apparent equilibrium constants. For the other 105 reactants, only standard transformed Gibbs energies of formation and average numbers of hydrogen atoms at 298.15 K can be calculated. The loading of this package provides functions of pH and ionic strength at 298.15 K for standard transformed Gibbs energies of formation and average numbers of hydrogen atoms for 199 reactants. It also provides functions of temperature, pH, and ionic strength for the standard transformed Gibbs energies of formation, standard transformed enthalpies of formation, standard transformed entropies of formation, and average numbers of hydrogen atoms for 94 reactants. Thus loading this package makes available 774 mathematical functions for these properties. These functions can be added and subtracted to obtain changes in these properties in biochemical reactions and apparent equilibrium constants.

Effect of hydrostatic pressure, temperature, and solvent on the rate of the Diels-Alder reaction between 9,10-anthracenedimethanol and maleic anhydride

NASA Astrophysics Data System (ADS)

Kiselev, V. D.; Kornilov, D. A.; Anikin, O. V.; Latypova, L. I.; Konovalov, A. I.

2017-03-01

The rate of the reaction between 9,10-anthracenedimethanol and maleic anhydride in 1,4-dioxane, acetonitrile, trichloromethane, and toluene is studied at 25, 35, 45°C in the pressure range of 1-1772 bar. The rate constants, enthalpies, entropies and activation volumes are determined. It is shown that the rate of reaction with 9,10-anthracenedimethanol is approximately one order of magnitude higher than with 9-anthracenemethanol.

Thermodynamic Properties of HCFC142b

NASA Astrophysics Data System (ADS)

Fukushima, Masato; Watanabe, Naohiro

Thermodynamic properties of HCFC142b,namely saturated densities,vapor pressures and PVT properties,were measured and the critical parameters were determined through those experimental results. The correlations for vpor pressure, saturated liquid density and PVT properties deduced from those experimental results were compared with the measured data and also with the estimates of the other correlations published in literatures. The thermodynamic functions,such as enthalpy,entropy,heat capacity and etc.,could be considered to be reasonab1y estimatedby the expression reported in this paper.

Computer simulation of the carbon activity in austenite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murch, G.E.; Thorn, R.J.

1979-02-01

Carbon activity in austenite is described in terms of an Ising-like f.c.c. lattice gas model in which carbon interstitials repel only at the distance of nearest neighbors. A Monte Carlo simulation method in the petit canonical ensemble is employed to calculate directly the carbon activity as a function of composition and temperature. The computed activities are in satisfactory agreement with the experimental data, similarly for the decompostion of the activity to the partial molar enthalpy and entropy.

The study of dielectric relaxation in aqueous carbohydrates solutions using time domain reflectometry technique

NASA Astrophysics Data System (ADS)

Hudge, Pravin G.; Lokhande, Milind P.; Kumbharkhane, Ashok C.

2012-09-01

Complex permittivity spectra of aqueous solutions of monosaccharide ( d-glucose) and disaccharides ( d-sucrose) in the frequency range from 10 MHz to 30 GHz at various concentrations and temperatures have been determined using time domain reflectometry technique. The complex dielectric permittivity spectrum of d-glucose and d-sucrose in water shows Cole-Davidson type behaviour. Dielectric constant (ɛ0) and relaxation time (τ), Kirkwood correlation factor, activation enthalpy and entropy parameters have been determined.

Electrochemistry of cations in diopsidic melt - Determining diffusion rates and redox potentials from voltammetric curves

NASA Technical Reports Server (NTRS)

Colson, Russell O.; Haskin, Larry A.; Crane, Daniel

1990-01-01

Results are presented on determinations of reduction potentials and their temperature dependence of selected ions in diopsidic melt, by using linear sweep voltammetry. Diffusion coefficients were measured for cations of Eu, Mn, Cr, and In. Enthalpies and entropies of reduction were determined for the cations V(V), Cr(3+), Mn(2+), Mn(3+), Fe(2+), Cu(2+), Mo(VI), Sn(IV), and Eu(3+). Reduction potentials were used to study the structural state of cations in the melt.

The sublimation kinetics of GeSe single crystals

NASA Technical Reports Server (NTRS)

Irene, E. A.; Wiedemeier, H.

1975-01-01

The sublimation kinetics of (001) oriented GeSe single crystal platelets was studied by high-temperature mass spectroscopy, quantitative vacuum microbalance techniques, and hot stage optical microscopy. For a mean experimental temperature of 563 K, the activation enthalpy and entropy are found to equal 32.3 kcal/mole and 19.1 eu, respectively. The vaporization coefficient is less than unity for the range of test temperatures, and decreases with increasing temperature. The combined experimental data are correlated by means of a multistep surface adsorption mechanism.

Conformational Entropy as Collective Variable for Proteins.

PubMed

Palazzesi, Ferruccio; Valsson, Omar; Parrinello, Michele

2017-10-05

Many enhanced sampling methods rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate descriptors has proven challenging. Here we suggest that the NMR S 2 order parameter can be used to this effect. We trace the validity of this statement to the suggested relation between S 2 and conformational entropy. Using the S 2 order parameter and a surrogate for the protein enthalpy in conjunction with metadynamics or variationally enhanced sampling, we are able to reversibly fold and unfold a small protein and draw its free energy at a fraction of the time that is needed in unbiased simulations. We also use S 2 in combination with the free energy flooding method to compute the unfolding rate of this peptide. We repeat this calculation at different temperatures to obtain the unfolding activation energy.

Effect of cold rolling on the microstructure and mechanical properties of Al 0.25CoCrFe 1.25Ni 1.25 high-entropy alloy

DOE PAGES

Wang, Z.; Gao, M. C.; Ma, S. G.; ...

2015-08-05

Cold rolling can break down the as-cast dendrite microstructure and thus may have pronounced impact on the mechanical behavior of the alloy. In the present study, the effect of cold rolling on the microstructure and mechanical properties of Al 0.25CoCrFe 1.25Ni 1.25 high-entropy alloy in the face-centered cubic structure was investigated. With increasing the thickness reduction from cold rolling, the hardness, the yield strength, and the fracture strength increased at the cost of reducing ductility. At the thickness reduction of 80%, the tensile strength (hardness) was 702 MPa (406 MPa), 1.62 (2.43) times that in the as-cast condition. Compared tomore » traditional alloys, Al 0.25CoCrFe 1.25Ni 1.25 has the highest hardening rate with respect to CR thickness reduction. Lastly, the phase relation and the mixing properties of Gibbs free energy, enthalpy and entropy of Al xCoCrFe 1.25Ni 1.25 were predicted using the CALPHAD method.« less

Binding of volatile anesthetics to serum albumin: measurements of enthalpy and solvent contributions.

PubMed

Sawas, Abdul H; Pentyala, Srinivas N; Rebecchi, Mario J

2004-10-05

This study directly examines the enthalpic contributions to binding in aqueous solution of closely related anesthetic haloethers (desflurane, isoflurane, enflurane, and sevoflurane), a haloalkane (halothane), and an intravenous anesthetic (propofol) to bovine and human serum albumin (BSA and HSA) using isothermal titration calorimetry. Binding to serum albumin is exothermic, yielding enthalpies (DeltaH(obs)) of -3 to -6 kcal/mol for BSA with a rank order of apparent equilibrium association constants (K(a) values): desflurane > isoflurane approximately enflurane > halothane >or= sevoflurane, with the differences being largely ascribed to entropic contributions. Competition experiments indicate that volatile anesthetics, at low concentrations, share the same sites in albumin previously identified in crystallographic and photo-cross-linking studies. The magnitude of the observed DeltaH increased linearly with increased reaction temperature, reflecting negative changes in heat capacities (DeltaC(p)). These -DeltaC(p) values significantly exceed those calculated for burial of each anesthetic in a hydrophobic pocket. The enhanced stabilities of the albumin/anesthetic complexes and -DeltaC(p) are consistent with favorable solvent rearrangements that promote binding. This idea is supported by substitution of D(2)O for H(2)O that significantly reduces the favorable binding enthalpy observed for desflurane and isoflurane, with an opposing increase of DeltaS(obs). From these results, we infer that solvent restructuring, resulting from release of water weakly bound to anesthetic and anesthetic-binding sites, is a dominant and favorable contributor to the enthalpy and entropy of binding to proteins.

Undergraduate Students' Conceptions of Enthalpy, Enthalpy Change and Related Concepts

ERIC Educational Resources Information Center

Nilsson, Tor; Niedderer, Hans

2014-01-01

Research shows that students have problems understanding thermodynamic concepts and that a gap exists at the tertiary level related to more specific chemistry concepts such as enthalpy. Therefore, the aim of this study is to construct undergraduate students' conceptions of enthalpy, its change and related concepts. Three explorative small-scale…

Role of specific cations and water entropy on the stability of branched DNA motif structures.

PubMed

Pascal, Tod A; Goddard, William A; Maiti, Prabal K; Vaidehi, Nagarajan

2012-10-11

DNA three-way junctions (TWJs) are important intermediates in various cellular processes and are the simplest of a family of branched nucleic acids being considered as scaffolds for biomolecular nanotechnology. Branched nucleic acids are stabilized by divalent cations such as Mg(2+), presumably due to condensation and neutralization of the negatively charged DNA backbone. However, electrostatic screening effects point to more complex solvation dynamics and a large role of interfacial waters in thermodynamic stability. Here, we report extensive computer simulations in explicit water and salt on a model TWJ and use free energy calculations to quantify the role of ionic character and strength on stability. We find that enthalpic stabilization of the first and second hydration shells by Mg(2+) accounts for 1/3 and all of the free energy gain in 50% and pure MgCl(2) solutions, respectively. The more distorted DNA molecule is actually destabilized in pure MgCl(2) compared to pure NaCl. Notably, the first shell, interfacial waters have very low translational and rotational entropy (i.e., mobility) compared to the bulk, an entropic loss that is overcompensated by increased enthalpy from additional electrostatic interactions with Mg(2+). In contrast, the second hydration shell has anomalously high entropy as it is trapped between an immobile and bulklike layer. The nonmonotonic entropic signature and long-range perturbations of the hydration shells to Mg(2+) may have implications in the molecular recognition of these motifs. For example, we find that low salt stabilizes the parallel configuration of the three-way junction, whereas at normal salt we find antiparallel configurations deduced from the NMR. We use the 2PT analysis to follow the thermodynamics of this transition and find that the free energy barrier is dominated by entropic effects that result from the decreased surface area of the antiparallel form which has a smaller number of low entropy waters in the first monolayer.

Transition state-based ST6Gal I inhibitors: Mimicking the phosphodiester linkage with a triazole or carbamate through an enthalpy-entropy compensation.

PubMed

Montgomery, Andrew P; Skropeta, Danielle; Yu, Haibo

2017-10-31

Human β-galactoside α-2,6-sialyltransferase I (ST6Gal I) catalyses the synthesis of sialylated glycoconjugates. Overexpression of ST6Gal I is observed in many cancers, where it promotes metastasis through altered cell surface sialylation. A wide range of sialyltransferase inhibitors have been developed, with analogues structurally similar to the transition state exhibiting the highest inhibitory activity. To improve synthetic accessibility and pharmacokinetics of previously reported inhibitors, the replacement of the charged phosphodiester linker with a potential neutral isostere such as a carbamate or a 1,2,3-triazole has been investigated. Extensive molecular dynamics simulations have demonstrated that compounds with the alternate linkers could maintain key interactions with the human ST6Gal I active site, demonstrating the potential of a carbamate or a 1,2,3-triazole as a phosphodiester isostere. Free energy perturbation calculations provided energetic evidence suggesting that the carbamate and 1,2,3-triazole were slightly more favourable than the phosphodiester. Further exploration with free energy component, quasi-harmonic and cluster analysis suggested that there is an enthalpy-entropy compensation accounting for the replacement of the flexible charged phosphodiester with a neutral and rigid isostere. Overall, these simulations provide a strong rationale for the use of a carbamate or 1,2,3-triazole as a phosphodiester isostere in the development of novel inhibitors of human ST6Gal I.

Akermanite: phase transitions in heat capacity and thermal expansion, and revised thermodynamic data.

USGS Publications Warehouse

Hemingway, B.S.; Evans, H.T.; Nord, G.L.; Haselton, H.T.; Robie, R.A.; McGee, J.J.

1986-01-01

A small but sharp anomaly in the heat capacity of akermanite at 357.9 K, and a discontinuity in its thermal expansion at 693 K, as determined by XRD, have been found. The enthalpy and entropy assigned to the heat-capacity anomaly, for the purpose of tabulation, are 679 J/mol and 1.9 J/(mol.K), respectively. They were determined from the difference between the measured values of the heat capacity in the T interval 320-365 K and that obtained from an equation which fits the heat-capacity and heat-content data for akermanite from 290 to 1731 K. Heat-capacity measurements are reported for the T range from 9 to 995 K. The entropy and enthalpy of formation of akermanite at 298.15 K and 1 bar are 212.5 + or - 0.4 J/(mol.K) and -3864.5 + or - 4.0 kJ/mol, respectively. Weak satellite reflections have been observed in hk0 single-crystal X-ray precession photographs and electron-diffraction patterns of this material at room T. With in situ heating by TEM, the satellite reflections decreased significantly in intensity above 358 K and disappeared at about 580 K and, on cooling, reappeared. These observations suggest that the anomalies in the thermal behaviour of akermanite are associated with local displacements of Ca ions from the mirror plane (space group P421m) and accompanying distortion of the MgSi2O7 framework.-L.C.C.

Extrathermodynamic interpretation of retention equilibria in reversed-phase liquid chromatography using octadecylsilyl-silica gels bonded to C1 and C18 ligands of different densities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miyabe, Kanji; Guiochon, Georges A

2005-09-01

The retention behavior on silica gels bonded to C{sub 18} and C{sub 1} alkyl ligands of different densities was studied in reversed-phase liquid chromatography (RPLC) from the viewpoints of two extrathermodynamic relationships, enthalpy-entropy compensation (EEC) and linear free energy relationship (LFER). First, the four tests proposed by Krug et al. were applied to the values of the retention equilibrium constants (K) normalized by the alkyl ligand density. These tests showed that a real EEC of the retention equilibrium originates from substantial physico-chemical effects. Second, we derived a new model based on the EEC to explain the LFER between the retentionmore » equilibria under different RPLC conditions. The new model indicates how the slope and intercept of the LFER are correlated to the compensation temperatures derived from the EEC analyses and to several parameters characterizing the molecular contributions to the changes in enthalpy and entropy. Finally, we calculated K under various RPLC conditions from only one original experimental K datum by assuming that the contributions of the C{sub 18} and C{sub 1} ligands to K are additive and that their contributions are proportional to the density of each ligand. The estimated K values are in agreement with the corresponding experimental data, demonstrating that our model is useful to explain the variations of K due to changes in the RPLC conditions.« less

Modeling solubility of CO2/hydrocarbon gas in ionic liquid ([emim][FAP]) using Aspen Plus simulations.

PubMed

Bagchi, Bishwadeep; Sati, Sushmita; Shilapuram, Vidyasagar

2017-08-01

The Peng-Robinson equation of state with quadratic van der Waals (vdW) mixing rule model was chosen to perform the thermodynamic calculations in Flash3 column of Aspen Plus to predict the solubility of CO 2 or any one of the hydrocarbons (HCs) among methane, ethane, propane, and butane in an ionic liquid 1-ethyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate ([emim][FAP]). Bubble point pressure, solubility, bubble point temperature, fugacity, and partial molar volume at infinite dilution were obtained from the simulations, and enthalpy of absorption, Gibbs free energy of solvation, and entropy change of absorption were estimated by thermodynamic relations. Results show that carbon chain length has a significant effect on the bubble point pressure. Methane has the highest bubble point pressure among all the considered HCs and CO 2 . The bubble point pressure and fugacity variation with temperature is different for CO 2 as compared to HCs for mole fractions above 0.2. Two different profiles are noticed for enthalpy of absorption when plotted as a function of mole fraction of gas soluble in IL. Partial molar volume of CO 2 decreases with increase in temperature in [emim][FAP], while it is increased for HCs. Bubble point temperature decreases with increase in the mole fraction of the solute. Entropy of solvation increases with temperature till a particular value followed by a decrease with further increase in temperature. Gibbs free energy change of solvation showed that the process of solubility was spontaneous.

Coordination-induced spin crossover (CISCO) through axial bonding of substituted pyridines to nickel-porphyrins: sigma-donor versus pi-acceptor effects.

PubMed

Thies, Steffen; Bornholdt, Claudia; Köhler, Felix; Sönnichsen, Frank D; Näther, Christian; Tuczek, Felix; Herges, Rainer

2010-09-03

Nickel-porphyrins, with their rigid quadratic planar coordination framework, provide an excellent model to study the coordination-induced spin crossover (CISCO) effect because bonding of one or two axial ligands to the metal center leads to a spin transition from S=0 to S=1. Herein, both equilibrium constants K(1S) and K(2), and for the first time also the corresponding thermodynamic parameters DeltaH(1S), DeltaH(2), DeltaS(1S), and DeltaS(2), are determined for the reaction of a nickel-porphyrin (Ni-tetrakis(pentafluorophenyl)porphyrin) with different 4-substituted pyridines by temperature-dependent NMR spectroscopy. The association constants K(1S) and K(2) are correlated with the basicity of the 4-substituted pyridines (R: OMe>H>CO(2)Et>NO(2)) whereas the DeltaH(1S) values exhibit a completely different order (OMeCO(2)Et>NO(2)). 4-Nitropyridine exhibits the largest binding enthalpy, which, however, is overcompensated by a large negative binding entropy. We attribute the large association enthalpy of nitropyridine with porphyrin to the back donation of electrons from the Ni d(xz) and d(yz) orbitals into the pi orbitals of pyridine, and the negative association entropy to a decrease in vibrational and internal rotation entropy of the more rigid porphyrin-pyridine complex. Back donation for the nitro- and cyanopyridine complexes is also confirmed by IR spectroscopy, and shows a shift of the N-O and C-N vibrations, respectively, to lower wave numbers. X-ray structures of 2:1 complexes with nitro-, cyano-, and dimethylaminopyridine provide further indication of a back donation. A further trend has been observed: the more basic the pyridine the larger is K(1S) relative to K(2). For nitropyridine K(2) is 17 times larger than K(1S) and in the case of methoxypyridine K(2) and K(1S) are almost equal.

Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium.

PubMed

Qian, Hong; Beard, Daniel A

2005-04-22

The principles of thermodynamics apply to both equilibrium and nonequilibrium biochemical systems. The mathematical machinery of the classic thermodynamics, however, mainly applies to systems in equilibrium. We introduce a thermodynamic formalism for the study of metabolic biochemical reaction (open, nonlinear) networks in both time-dependent and time-independent nonequilibrium states. Classical concepts in equilibrium thermodynamics-enthalpy, entropy, and Gibbs free energy of biochemical reaction systems-are generalized to nonequilibrium settings. Chemical motive force, heat dissipation rate, and entropy production (creation) rate, key concepts in nonequilibrium systems, are introduced. Dynamic equations for the thermodynamic quantities are presented in terms of the key observables of a biochemical network: stoichiometric matrix Q, reaction fluxes J, and chemical potentials of species mu without evoking empirical rate laws. Energy conservation and the Second Law are established for steady-state and dynamic biochemical networks. The theory provides the physiochemical basis for analyzing large-scale metabolic networks in living organisms.

A new strategy to design eutectic high-entropy alloys using simple mixture method

DOE PAGES

Jiang, Hui; Han, Kaiming; Gao, Xiaoxia; ...

2018-01-13

Eutectic high entropy alloys (EHEAs) hold promising industrial application potential, but how to design EHEA compositions remains challenging. In the present work, a simple and effective strategy by combining mixing enthalpy and constituent binary eutectic compositions was proposed to design EHEA compositions. This strategy was then applied to a series of (CoCrFeNi)M x (M = Nb, Ta, Zr, Hf) HEAs, leading to the discovery of new EHEAs, namely, CoCrFeNiNb 0.45, CoCrFeNiTa 0.4, CoCrFeNiZr 0.55 and CoCrFeNiHf 0.4. The microstructure of these new EHEAs comprised of FCC and Laves phases in the as-cast state. In conclusion, the experimental result shows thatmore » this new alloy design strategy can be used to locate new EHEAs effectively.« less

Thermokinetic comparison of trypan blue decolorization by free laccase and fungal biomass.

PubMed

Razak, N N A; Annuar, M S M

2014-03-01

Free laccase and fungal biomass from white-rot fungi were compared in the thermokinetics study of the laccase-catalyzed decolorization of an azo dye, i.e., Trypan Blue. The decolorization in both systems followed a first-order kinetics. The apparent first-order rate constant, k1', value increases with temperature. Apparent activation energy of decolorization was similar for both systems at ∼ 22 kJ mol(-1), while energy for laccase inactivation was 18 kJ mol(-1). Although both systems were endothermic, fungal biomass showed higher enthalpy, entropy, and Gibbs free energy changes for the decolorization compared to free laccase. On the other hand, free laccase showed reaction spontaneity over a wider range of temperature (ΔT = 40 K) as opposed to fungal biomass (ΔT = 15 K). Comparison of entropy change (ΔS) values indicated metabolism of the dye by the biomass.

Thermodynamic and Spectroscopic Investigation of Interactions between Reactive Red 223 and Reactive Orange 122 Anionic Dyes and Cetyltrimethyl Ammonium Bromide (CTAB) Cationic Surfactant in Aqueous Solution

PubMed Central

Irfan, Muhammad; Usman, Muhammad; Mansha, Asim; Rasool, Nasir; Ibrahim, Muhammad; Rana, Usman Ali; Siddiq, Mohammad; Zia-Ul-Haq, Muhammad; Jaafar, Hawa Z. E.; Khan, Salah Ud-Din

2014-01-01

The present study describes the conductometric and spectroscopic study of the interaction of reactive anionic dyes, namely, reactive red 223 and reactive orange 122 with the cationic surfactant cetyltrimethyl ammonium bromide (CTAB). In a systematic investigation, the electrical conductivity data was used to calculate various thermodynamic parameters such as free energy (ΔG), enthalpy (ΔH), and the entropy (ΔS) of solubilization. The trend of change in these thermodynamic quantities indicates toward the entropy driven solubilization process. Moreover, the results from spectroscopic data reveal high degree of solubilization, with strong interactions observed in the cases of both dyes and the CTAB. The spontaneous nature of solubilization and binding was evident from the observed negative values of free energies (ΔG p and ΔG b). PMID:25243216

Chemical reaction mechanisms in solution from brute force computational Arrhenius plots.

PubMed

Kazemi, Masoud; Åqvist, Johan

2015-06-01

Decomposition of activation free energies of chemical reactions, into enthalpic and entropic components, can provide invaluable signatures of mechanistic pathways both in solution and in enzymes. Owing to the large number of degrees of freedom involved in such condensed-phase reactions, the extensive configurational sampling needed for reliable entropy estimates is still beyond the scope of quantum chemical calculations. Here we show, for the hydrolytic deamination of cytidine and dihydrocytidine in water, how direct computer simulations of the temperature dependence of free energy profiles can be used to extract very accurate thermodynamic activation parameters. The simulations are based on empirical valence bond models, and we demonstrate that the energetics obtained is insensitive to whether these are calibrated by quantum mechanical calculations or experimental data. The thermodynamic activation parameters are in remarkable agreement with experiment results and allow discrimination among alternative mechanisms, as well as rationalization of their different activation enthalpies and entropies.

Chemical reaction mechanisms in solution from brute force computational Arrhenius plots

PubMed Central

Kazemi, Masoud; Åqvist, Johan

2015-01-01

Decomposition of activation free energies of chemical reactions, into enthalpic and entropic components, can provide invaluable signatures of mechanistic pathways both in solution and in enzymes. Owing to the large number of degrees of freedom involved in such condensed-phase reactions, the extensive configurational sampling needed for reliable entropy estimates is still beyond the scope of quantum chemical calculations. Here we show, for the hydrolytic deamination of cytidine and dihydrocytidine in water, how direct computer simulations of the temperature dependence of free energy profiles can be used to extract very accurate thermodynamic activation parameters. The simulations are based on empirical valence bond models, and we demonstrate that the energetics obtained is insensitive to whether these are calibrated by quantum mechanical calculations or experimental data. The thermodynamic activation parameters are in remarkable agreement with experiment results and allow discrimination among alternative mechanisms, as well as rationalization of their different activation enthalpies and entropies. PMID:26028237

Kinetic, Spectroscopic, and Theoretical Assessment of Associative and Dissociative Methanol Dehydration Routes in Zeolites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Andrew J.; Iglesia, Enrique

Mechanistic interpretations of rates and in situ IR spectra combined with density functionals that account for van der Waals interactions of intermediates and transition states within confining voids show that associative routes mediate the formation of dimethyl ether from methanol on zeolitic acids at the temperatures and pressures of practical dehydration catalysis. Methoxy-mediated dissociative routes become prevalent at higher temperatures and lower pressures, because they involve smaller transition states with higher enthalpy, but also higher entropy, than those in associative routes. These enthalpy–entropy trade-offs merely reflect the intervening role of temperature in activation free energies and the prevalence of moremore » complex transition states at low temperatures and high pressures. This work provides a foundation for further inquiry into the contributions of H-bonded methanol and methoxy species in homologation and hydrocarbon synthesis reactions from methanol.« less

Reaction of the Anticancer Organometallic Ruthenium Compound, [(η6-p-Cymene)Ru(ATSC)Cl]PF6 with Human Serum Albumin

PubMed Central

Beckford, Floyd A.

2010-01-01

The reaction of [(η6-p-cymene)Ru(ATSC)Cl]PF6 (ATSC = 9-anthraldehyde thiosemicarbazone) with human serum albumin was investigated at different temperatures using fluorescence and infrared spectrophotometry. The binding constant, K, for the reaction was determined using a number of different methods. Using a modified Stern-Volmer equation, K was determined to be 9.09 × 104, 12.1 × 104, and 13.1 × 104 M−1 at 293 K, 298 K, and 308 K, respectively. A thermodynamic analysis showed that the reaction is spontaneous with ΔG being negative. The enthalpy of reaction ΔH = 16.5kJ mol−1 and the entropy of reaction ΔS = 152 Jmol−1K−1. The values of ΔH and ΔS suggest that hydrophobic forces are dominant in the mode of interaction and that the process is mostly entropy driven. PMID:20671814

Study on the intrinsic defects in tin oxide with first-principles method

NASA Astrophysics Data System (ADS)

Sun, Yu; Liu, Tingyu; Chang, Qiuxiang; Ma, Changmin

2018-04-01

First-principles and thermodynamic methods are used to study the contribution of vibrational entropy to defect formation energy and the stability of the intrinsic point defects in SnO2 crystal. According to thermodynamic calculation results, the contribution of vibrational entropy to defect formation energy is significant and should not be neglected, especially at high temperatures. The calculated results indicate that the oxygen vacancy is the major point defect in undoped SnO2 crystal, which has a higher concentration than that of the other point defect. The property of negative-U is put forward in SnO2 crystal. In order to determine the most stable defects much clearer under different conditions, the most stable intrinsic defect as a function of Fermi level, oxygen partial pressure and temperature are described in the three-dimensional defect formation enthalpy diagrams. The diagram visually provides the most stable point defects under different conditions.

A new strategy to design eutectic high-entropy alloys using simple mixture method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Hui; Han, Kaiming; Gao, Xiaoxia

Eutectic high entropy alloys (EHEAs) hold promising industrial application potential, but how to design EHEA compositions remains challenging. In the present work, a simple and effective strategy by combining mixing enthalpy and constituent binary eutectic compositions was proposed to design EHEA compositions. This strategy was then applied to a series of (CoCrFeNi)M x (M = Nb, Ta, Zr, Hf) HEAs, leading to the discovery of new EHEAs, namely, CoCrFeNiNb 0.45, CoCrFeNiTa 0.4, CoCrFeNiZr 0.55 and CoCrFeNiHf 0.4. The microstructure of these new EHEAs comprised of FCC and Laves phases in the as-cast state. In conclusion, the experimental result shows thatmore » this new alloy design strategy can be used to locate new EHEAs effectively.« less

Revised values for the thermodynamic properties of boehmite, AlO(OH) , and related species and phases in the system Al-H-O

USGS Publications Warehouse

Hemingway, B.S.; Robie, R.A.; Apps, J.A.

1991-01-01

Heat capacity measurements are reported for a well-characterized boehmite that differ significantly from results reported earlier by Shomate and Cook (1946) for a monohydrate of alumina. It is suggested that the earlier measurements were made on a sample that was a mixture of phases and that use of that heat-capacity and derived thermodynamic data be discontinued. The entropy of boehmite derived in this study is 37.19 ?? 0.10 J/(mol.K) at 298.15 K. Based on our value for the entropy and accepting the recommended Gibbs free energy for Al(OH)-4, the Gibbs free energy and enthalpy of formation of boehmite are calculated to be -918.4 ?? 2.1 and -996.4 ?? 2.2 kJ/mol, respectively, from solubility data for boehmite. The Gibbs energy for boehmite is unchanged from that given by Hemingway et al. (1978). -from Authors

Thermodynamic characterization of hydrogen interaction with iridium polyhydride complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zidan, R.A.; Rocheleau, R.E.

1999-01-01

Hydrogen interaction with solid iridium complexes IrXH{sub 2}(PPr3{sup i}){sub 2} (X=Cl, I) was investigated. Gaseous hydrogen was found to react reversibly with solid chloro-iridium complex IrClH{sub 2}(PPr3{sup i}){sub 2} forming IrClH{sub 2}(PPr3{sup i}){sub 2}H{sub 2}. The relative partial molal enthalpy and entropy were obtained from equilibrium isotherms at different hydrogen concentrations. The decrease in entropy with increasing hydrogen concentration and the absence of plateaus in the equilibrium isotherms were consistent with a single phase solid solution with two chemical components. Hydrogen release from solid iodo-iridium complex IrIH{sub 2}(PPr3{sup i}){sub 2}H{sub 2} was not observed at temperatures up to 350 K,more » indicating stronger hydrogen bonding. {copyright} {ital 1999 Materials Research Society.}« less

Allostery: Absence of a change in shape does not imply that allostery is not at play

PubMed Central

Tsai, Chung-Jung; Sol, Antonio del; Nussinov, Ruth

2009-01-01

Allostery is essential for controlled catalysis, signal transmission, receptor trafficking, turning genes on and off, and apoptosis. It governs the organism’s response to environmental and metabolic cues, dictating transient partner interactions in the cellular network. Textbooks taught us that allostery is a change of shape at one site on the protein surface brought about by ligand binding to another. For already several years it has been broadly accepted that the change of shape is not induced; rather, it is observed simply because a larger protein population presents it. Current data indicate that while side-chains can reorient and rewire, allostery may not even involve a change of (backbone) shape. Assuming that the enthalpy change does not reverse the free energy change due to the change in entropy, entropy is mainly responsible for binding. PMID:18353365

X-ray and simulation studies of water

NASA Astrophysics Data System (ADS)

Nilsson, A.; Schlesinger, D.; G. M. Pettersson, L.

Here we present a picture that combines discussions regarding the thermodynamic anomalies in ambient and supercooled water with recent interpretations of X-ray spectroscopy and scattering data of water. At ambient temperatures most molecules favor a closer packing than tetrahedral, with strongly distorted hydrogen bonds, which allows the quantized librational modes to be excited and contribute to the entropy, but with enthalpically favored tetrahedrally bonded water patches appearing as fluctuations, a competition between entropy and enthalpy. Upon cooling water the amount of molecules participating in tetrahedral structures and the size of the tetrahedral patches increase. The two local structures are connected to the liquid-liquid critical point hypothesis in supercooled water corresponding to high-density liquid (HDL) and low-density liquid (LDL). We demonstrate that the HDL local structure deviates from a tetrahedral coordination not only through a collapse of the 2nd shell but also through severe distortions around the 1st coordination shell.

Influence of specific contacts on the stability and structure of proteins. Theory for the perturbation of a harmonic system.

PubMed Central

Jackson, M B

1987-01-01

The question of how specific contacts within a protein influence its stability and structure is examined within a formal theoretical framework. A mathematical model is developed in which the potential energy of a protein is taken as a harmonic expansion of all of its internal or normal coordinates. With classical statistical mechanics the properties of the system can be derived from this potential energy function. A few new contacts are then introduced as additional energy terms, each having a quadratic dependence on a single internal coordinate. These terms are added as perturbations to the original potential energy, and the attendant changes in the properties of the system are obtained. Exact expressions can be derived for changes in the enthalpy, entropy, and for any arbitrary internal degree of freedom. These quantities are expressed in terms of the parameters of the potential energy functions of the new contacts, and the mean square displacements and positional correlation functions of the internal coordinates. These results provide qualitative insights into the role of contacts in stabilizing a particular conformation. Estimates are given for the entropy of formation of a hydrogen bond in a protein. A criterion is proposed for determining whether a contact is essential to the stability of a protein conformation. This model may be applicable to many experimental systems in which mutant or modified proteins are available that differ by one or a few amino acids. The results may also be useful in thermodynamic analyses of computer simulations. PMID:3828463

Enhancement of the Rate of Pyrophosphate Hydrolysis by Nonenzymatic Catalysts and by Inorganic Pyrophosphatase*

PubMed Central

Stockbridge, Randy B.; Wolfenden, Richard

2011-01-01

To estimate the proficiency of inorganic pyrophosphatase as a catalyst, 31P NMR was used to determine rate constants and thermodynamics of activation for the spontaneous hydrolysis of inorganic pyrophosphate (PPi) in the presence and absence of Mg2+ at elevated temperatures. These values were compared with rate constants and activation parameters determined for the reaction catalyzed by Escherichia coli inorganic pyrophosphatase using isothermal titration calorimetry. At 25 °C and pH 8.5, the hydrolysis of MgPPi2− proceeds with a rate constant of 2.8 × 10−10 s−1, whereas E. coli pyrophosphatase was found to have a turnover number of 570 s−1 under the same conditions. The resulting rate enhancement (2 × 1012-fold) is achieved entirely by reducing the enthalpy of activation (ΔΔH‡ = −16.6 kcal/mol). The presence of Mg2+ ions or the transfer of the substrate from bulk water to dimethyl sulfoxide was found to increase the rate of pyrophosphate hydrolysis by as much as ∼106-fold. Transfer to dimethyl sulfoxide accelerated PPi hydrolysis by reducing the enthalpy of activation. Mg2+ increased the rate of PPi hydrolysis by both increasing the entropy of activation and reducing the enthalpy of activation. PMID:21460215

Correlation between structural and thermodynamic properties of some selenium based phase-change materials

NASA Astrophysics Data System (ADS)

Chandel, Namrata; Mehta, Neeraj

2018-04-01

In this study, we prepared novel selenium rich multi-component glasses by incorporating In, Cd and Sb as foreign elements in an Sn containing Sesbnd Te system in order to study their metal-induced effects on the thermal properties of the parent ternary glass. In particular, we determined the thermodynamic parameters of Se80Te18Sn2 and Se80Te8Sn2M10 (M = Cd, In, Sb) glassy semiconductors in a non-isothermal environment using the differential scanning calorimetry. Calorimetric measurements were obtained in the glass transition regions for Se80Te18Sn2 and Se80Te8Sn2M10 (M = Cd, In, Sb) glasses to determine their thermodynamic parameters such as the specific heat, enthalpy, and entropy during glass transition. We analyzed the variation in the specific heat before and after the heat capacity jump in these alloys. The metal-induced effects of foreign elements on the thermodynamic properties of the parent glass were also investigated in terms of the influence of the elemental specific heat of the added elemental metal as well as the thermal stability and glass-forming ability of the glasses.

YamiPred: A Novel Evolutionary Method for Predicting Pre-miRNAs and Selecting Relevant Features.

PubMed

Kleftogiannis, Dimitrios; Theofilatos, Konstantinos; Likothanassis, Spiros; Mavroudi, Seferina

2015-01-01

MicroRNAs (miRNAs) are small non-coding RNAs, which play a significant role in gene regulation. Predicting miRNA genes is a challenging bioinformatics problem and existing experimental and computational methods fail to deal with it effectively. We developed YamiPred, an embedded classification method that combines the efficiency and robustness of support vector machines (SVM) with genetic algorithms (GA) for feature selection and parameters optimization. YamiPred was tested in a new and realistic human dataset and was compared with state-of-the-art computational intelligence approaches and the prevalent SVM-based tools for miRNA prediction. Experimental results indicate that YamiPred outperforms existing approaches in terms of accuracy and of geometric mean of sensitivity and specificity. The embedded feature selection component selects a compact feature subset that contributes to the performance optimization. Further experimentation with this minimal feature subset has achieved very high classification performance and revealed the minimum number of samples required for developing a robust predictor. YamiPred also confirmed the important role of commonly used features such as entropy and enthalpy, and uncovered the significance of newly introduced features, such as %A-U aggregate nucleotide frequency and positional entropy. The best model trained on human data has successfully predicted pre-miRNAs to other organisms including the category of viruses.

Thermophysical properties of hydrogen along the liquid-vapor coexistence

NASA Astrophysics Data System (ADS)

Osman, S. M.; Sulaiman, N.; Bahaa Khedr, M.

2016-05-01

We present Theoretical Calculations for the Liquid-Vapor Coexistence (LVC) curve of fluid Hydrogen within the first order perturbation theory with a suitable first order quantum correction to the free energy. In the present equation of state, we incorporate the dimerization of H2 molecule by treating the fluid as a hard convex body fluid. The thermophysical properties of fluid H2 along the LVC curve, including the pressure-temperature dependence, density-temperature asymmetry, volume expansivity, entropy and enthalpy, are calculated and compared with computer simulation and empirical results.

Why is hydrofluoric acid a weak acid?

PubMed

Ayotte, Patrick; Hébert, Martin; Marchand, Patrick

2005-11-08

The infrared vibrational spectra of amorphous solid water thin films doped with HF at 40 K reveal a strong continuous absorbance in the 1000-3275 cm(-1) range. This so-called Zundel continuum is the spectroscopic hallmark for aqueous protons. The extensive ionic dissociation of HF at such low temperature suggests that the reaction enthalpy remains negative down to 40 K. These observations support the interpretation that dilute HF aqueous solutions behave as weak acids largely due to the large positive reaction entropy resulting from the structure making character of the hydrated fluoride ion.

Study of charge transfer complexes of menadione (vitamin K 3) with a series of anilines

NASA Astrophysics Data System (ADS)

Pal, Purnendu; Saha, Avijit; Mukherjee, Asok K.; Mukherjee, Dulal C.

2004-01-01

Menadione (vitamin K 3) has been shown to form charge transfer complexes with N, N-dimethyl aniline, N, N-dimethyl p-toluidine and N, N-dimethyl m-toluidine in CCl 4 medium. The CT transition energies are well correlated with the ionisation potentials of the anilines. The formation constants of the complexes have been determined at a number of temperatures from which the enthalpies and entropies of formation have been obtained. The formation constants exhibit a very good linear free energy relationship (Hammett) at all the temperatures studied.

Thermodynamics of the sorption of water-soluble vitamins in reverse-phase high performance liquid chromatography

NASA Astrophysics Data System (ADS)

Chirkin, V. A.; Karpov, S. I.; Selemenev, V. F.

2012-12-01

The thermodynamics of the sorption of certain water-soluble vitamins on a C18 reverse phase from water-acetonitrile solutions of different compositions is studied. The thermodynamic characteristics of the investigated chromatographic systems are calculated. The dependences of standard molar enthalpy and changes in entropy when the sorbate transfers from the bulk solution to the surface layer on the concentration of the organic component in the mobile phase are analyzed. The boundaries for applying the main retention models describing the sorption of the investigated compounds are discussed.

A simple thermodynamic approach to predict responses from polymer-coated quartz crystal microbalance sensors exposed to organic vapors.

PubMed

Palmas, P; Klingenfus, J; Vedeau, B; Girard, E; Montmeat, P; Hairault, L; Pradier, C M; Méthivier, C

2013-10-15

As of lately, the demand for developing artificial sensors with improved capabilities for the detection of explosives, toxics or drugs has increased. Ideally, sensor devices should provide high sensitivity and give a response that is specific to a given target molecule without being influenced by possible interfering molecules in the atmosphere. These properties strongly depend on the structure of the chemical compound used as a sensitive material. It is thus crucial to select the right compound and this step would be facilitated with the aid of predictive tools. The present investigations have been focused on a family of functionalized polysiloxane polymers deposited on a QCM device, producing only weak interactions compatible with reversible sensors. The quartz frequency variation at equilibrium has been linked to the partition coefficient that was evaluated using a thermodynamic description of the adsorption process. We have shown that the relative responses of two polymers can be directly determined from the Gibbs free enthalpy of mixing as determined from NMR measurements performed on neat liquid mixtures. An equivalence of this term-including both enthalpy and entropy contributions-to the energy interaction term calculated using Hansen solubility coefficients, has been demonstrated previously. These results constitute a basis for the development of a numerical program for calculating equilibrium sensor responses. For small molecules, the adsorption kinetics can be easily accounted for by a Fick diffusion coefficient estimated from the Van der Waals volume. Copyright © 2013 Elsevier B.V. All rights reserved.

Evolution of biofunctional semiconductor nanocrystals: a calorimetric investigation.

PubMed

Ghosh, Debasmita; Mondal, Somrita; Roy, Chandra Nath; Saha, Abhijit

2013-12-14

Semiconductor nanomaterials have found numerous applications in optoelectronic device fabrication and in platforms for drug delivery and hyperthermia cancer treatment, and in various other biomedical fields because of their high photochemical stability and size-tunable photoluminescence (PL). However, little attention has been paid to exploring the energetics of formation of these semiconductor nanoparticles. We demonstrate that formation of nanocrystals with biofunctionalization supported by widely used groups, BSA and cysteine, is an exothermic spontaneous process driven by enthalpy. The whole energetics of the reaction shows that formation of smaller particles is favored with lower synthesis temperature. Further, it is shown that the thermodynamics of nanoparticle formation is strongly influenced by the conformation of the protein matrix. We also demonstrate that protein supported formation of nanocrystals is thermodynamically more favorable compared to that involving smaller organic thiol groups. The favorable enthalpy of formation compensates unfavorable entropy, resulting in favorable Gibbs free energy. Thus, this study can open up new avenues for establishing a thermodynamic basis for the design of nanosystems with new and tunable properties.

High-Definition Self-Assemblies driven by the Hydrophobic Effect: Synthesis and Properties of a Supramolecular Nano-Capsule

PubMed Central

Liu, Simin

2008-01-01

High definition self-assemblies, those that possess order at the molecular level, are most commonly made from subunits possessing metals and metal coordination sites, or groups capable of partaking in hydrogen bonding. In other words, enthalpy is the driving force behind the free energy of assembly. The hydrophobic effect engenders the possibility of (nominally) relying not on enthalpy but entropy to drive assembly. Towards this idea, we describe how template molecules can trigger the dimerization of a cavitand in aqueous solution, and in doing so are encapsulated within the resulting capsule. Although not held together by (enthalpically) strong and directional non-covalent forces, these capsules possess considerable thermodynamic and kinetic stability. As a result, they display unusual and even unique properties. We discuss some of these, including the use of the capsule as a nano-scale reaction chamber and how they can bring about the separation of hydrocarbon gases. PMID:18685753

He-Ne laser-induced changes in germination, thermodynamic parameters, internal energy, enzyme activities and physiological attributes of wheat during germination and early growth

NASA Astrophysics Data System (ADS)

Jamil, Yasir; Perveen, Rashida; Ashraf, Muhammad; Ali, Qasim; Iqbal, Munawar; Ahmad, Muhammad Raza

2013-04-01

Using low power continuous wave He-Ne laser irradiation of seeds, the germination characteristics, thermodynamic changes and enzyme activities as well as changes in morphological attributes were explored for wheat (Triticum aestivum L. cv. S-24) cultivar. The changes in thermodynamic properties such as change in enthalpy (ΔH), entropy generation [(ΔSe)], entropy flux [(ΔSc)], entropy generation ratio [(ΔS)e/Δt], and entropy flux ratio [(ΔS)c/Δt] showed significant (P < 0.05) changes at an energy level of 500 mJ. The germination energy (GE), germination percentage (G%), germination index (GI) as well as α-amylase and protease activities was also found to be higher at 500 mJ, while the mean emergence time (MET) and time for 50% germination (E50) decreased for 300 mJ irradiance. The internal energy of the seeds increased significantly at all laser energy levels, but was highest for 500 mJ 72 h after sowing. The enzyme activities increased up to 24 h after sowing and then declined. The activities of α-amylase and protease were found to be positively correlated with the plant physiological attributes. These results indicate that low power continuous wave He-Ne laser (632 nm) treatment has considerable biological effects on seed metabolism during germination as well as on later vegetative growth.

Energetics of photosynthetic glow peaks

PubMed Central

DeVault, Don; Govindjee; Arnold, William

1983-01-01

By postulating temperature-dependent equilibria between two or more electron carriers acting as traps for electrons or holes, it is possible to modify the Randall-Wilkins theory of thermoluminescence so as to explain the abnormally large apparent activation energies and apparent frequency factors observed in photosynthetic glow curves when fitted by unmodified Randall-Wilkins theory. The equilibria serve to inhibit the formation of the light-emitting excited state by withholding the needed precursor state. When the inhibition is released at higher temperature by shift of equilibrium with temperature, the rise of the glow peak can be much faster than would result from Arrhenius behavior based on the true activation energy and so appears to correspond to a higher activation energy accompanied by a larger frequency factor. From another viewpoint, the enthalpy changes, ΔH, of the equilibria tend to add to the activation energy. Similarly the entropy changes, ΔS, of the equilibria tend to add to the entropy of activation, giving the large apparent frequency factors. The positive values of ΔS needed would correspond to entropy decreases in the forward early electron transport. A comparison of the glow peaks obtained by different workers is also presented. PMID:16593283

Investigating the impacts of DNA binding mode and sequence on thermodynamic quantities and water exchange values for two small molecule drugs.

PubMed

Kenney, Rachael M; Buxton, Katherine E; Glazier, Samantha

2016-09-01

Doxorubicin and nogalamycin are antitumor antibiotics that interact with DNA via intercalation and threading mechanisms, respectively. Because the importance of water, particularly its impact on entropy changes, has been established in other biological processes, we investigated the role of water in these two drug-DNA binding events. We used the osmotic stress method to calculate the number of water molecules exchanged (Δnwater), and isothermal titration calorimetry to measure Kbinding, ΔH, and ΔS for two synthetic DNAs, poly(dA·dT) and poly(dG·dC), and calf thymus DNA (CT DNA). For nogalamycin, Δnwater<0 for CT DNA and poly(dG·dC). For doxorubicin, Δnwater>0 for CT DNA and Δnwater<0 for poly(dG·dC). For poly(dA·dT), Δnwater~0 with both drugs. Net enthalpy changes were always negative, but net entropy changes depended on the drug. The effect of water exchange on the overall sign of entropy change appears to be smaller than other contributions. Copyright © 2016 Elsevier B.V. All rights reserved.

Concentration Waves in High-Entropy Alloys - a new alloy design approach

NASA Astrophysics Data System (ADS)

Singh, Prashant; Johnson, Duane D.

2015-03-01

Chemical short-range order (SRO) in solid solutions can be interpreted as a ``concentration wave'' - a Fourier decomposition of nascent order - identified experimentally via Warren-Cowley SRO parameters. We present a rigorous thermodynamic theory to predict and uniquely interpret the SRO in N -component alloys. Based on KKR-CPA electronic structure, we implemented this method using thermodynamic linear-response to include all alloying effects, e.g., band-filling, hybridization, Fermi -surface nesting and van Hove instabilities. We apply this first-principles method to high-entropy alloys (HEAs), i.e., solid solutions with N >4 that inhibit small-cell order due to large entropy competing against ordering enthalpy, as their properties are sensitive to SRO. We validated theory with comparison to experiments in A2 Nb-Al-Ti and A1 Cu-Ni-Zn . We then predict and analyze SRO and mechanical trends in Ni-Ti-Zr-Cu-Al and Co-Cr-Fe-Mn-Ni systems - showcasing this new first-principles-based alloy design method. Work was supported by the USDoE, Office of Sci., Basic Energy Sci., Materials Sci. and Eng. Division for `Materials Discovery.' Research was performed at Ames Lab, operated by Iowa State University under Contract #DE-AC02-07CH11358.

Dual and mixed nonsymmetric stress-based variational formulations for coupled thermoelastodynamics with second sound effect

NASA Astrophysics Data System (ADS)

Tóth, Balázs

2018-03-01

Some new dual and mixed variational formulations based on a priori nonsymmetric stresses will be developed for linearly coupled irreversible thermoelastodynamic problems associated with second sound effect according to the Lord-Shulman theory. Having introduced the entropy flux vector instead of the entropy field and defining the dissipation and the relaxation potential as the function of the entropy flux, a seven-field dual and mixed variational formulation will be derived from the complementary Biot-Hamilton-type variational principle, using the Lagrange multiplier method. The momentum-, the displacement- and the infinitesimal rotation vector, and the a priori nonsymmetric stress tensor, the temperature change, the entropy field and its flux vector are considered as the independent field variables of this formulation. In order to handle appropriately the six different groups of temporal prescriptions in the relaxed- and/or the strong form, two variational integrals will be incorporated into the seven-field functional. Then, eliminating the entropy from this formulation through the strong fulfillment of the constitutive relation for the temperature change with the use of the Legendre transformation between the enthalpy and Gibbs potential, a six-field dual and mixed action functional is obtained. As a further development, the elimination of the momentum- and the velocity vector from the six-field principle through the a priori satisfaction of the kinematic equation and the constitutive relation for the momentum vector leads to a five-field variational formulation. These principles are suitable for the transient analyses of the structures exposed to a thermal shock of short temporal domain or a large heat flux.

Alternate binding modes for a ubiquitin-SH3 domain interaction studied by NMR spectroscopy.

PubMed

Korzhnev, Dmitry M; Bezsonova, Irina; Lee, Soyoung; Chalikian, Tigran V; Kay, Lewis E

2009-02-20

Surfaces of many binding domains are plastic, enabling them to interact with multiple targets. An understanding of how they bind and recognize their partners is therefore predicated on characterizing such dynamic interfaces. Yet, these interfaces are difficult to study by standard biophysical techniques that often 'freeze' out conformations or that produce data averaged over an ensemble of conformers. In this study, we used NMR spectroscopy to study the interaction between the C-terminal SH3 domain of CIN85 and ubiquitin that involves the 'classical' binding sites of these proteins. Notably, chemical shift titration data of one target with another and relaxation dispersion data that report on millisecond time scale exchange processes are both well fit to a simple binding model in which free protein is in equilibrium with a single bound conformation. However, dissociation constants and chemical shift differences between free and bound states measured from both classes of experiment are in disagreement. It is shown that the data can be reconciled by considering three-state binding models involving two distinct bound conformations. By combining titration and dispersion data, kinetic and thermodynamic parameters of the three-state binding reaction are obtained along with chemical shifts for each state. A picture emerges in which one bound conformer has increased entropy and enthalpy relative to the second and chemical shifts similar to that of the free state, suggesting a less packed interface. This study provides an example of the interplay between entropy and enthalpy to fine-tune molecular interactions involving the same binding surfaces.

Theoretical and experimental study on the effects of particle size and temperature on the reaction kinetics of cubic nano-Cu2O

NASA Astrophysics Data System (ADS)

Tang, Huanfeng; Huang, Zaiyin; Xiao, Ming; Liang, Min; Chen, Liying; Tan, XueCai

2017-09-01

The activities, selectivities, and stabilities of nanoparticles in heterogeneous reactions are size-dependent. In order to investigate the influencing laws of particle size and temperature on kinetic parameters in heterogeneous reactions, cubic nano-Cu2O particles of four different sizes in the range of 40-120 nm have been controllably synthesized. In situ microcalorimetry has been used to attain thermodynamic data on the reaction of Cu2O with aqueous HNO3 and, combined with thermodynamic principles and kinetic transition-state theory, the relevant reaction kinetic parameters have been evaluated. The size dependences of the kinetic parameters are discussed in terms of the established kinetic model and the experimental results. It was found that the reaction rate constants increased with decreasing particle size. Accordingly, the apparent activation energy, pre-exponential factor, activation enthalpy, activation entropy, and activation Gibbs energy decreased with decreasing particle size. The reaction rate constants and activation Gibbs energies increased with increasing temperature. Moreover, the logarithms of the apparent activation energies, pre-exponential factors, and rate constants were found to be linearly related to the reciprocal of particle size, consistent with the kinetic models. The influence of particle size on these reaction kinetic parameters may be explained as follows: the apparent activation energy is affected by the partial molar enthalpy, the pre-exponential factor is affected by the partial molar entropy, and the reaction rate constant is affected by the partial molar Gibbs energy. [Figure not available: see fulltext.

Interaction of small molecules with double-stranded RNA: spectroscopic, viscometric, and calorimetric study of hoechst and proflavine binding to PolyCG structures.

PubMed

Sinha, Rangana; Hossain, Maidul; Kumar, Gopinatha Suresh

2009-04-01

Design and synthesis of new small molecules binding to double-stranded RNA necessitate complete understanding of the molecular aspects of the binding of many existing molecules. Toward this goal, in this work we evaluated the biophysical aspects of the interaction of a DNA intercalator (proflavine) and a minor groove binder (hoechst 33258) with two polymorphic forms of polyCG, namely, the right-handed Watson-Crick base paired A-form and the left-handed Hoogsteen base paired H(L)-form, by absorption, fluorescence, and viscometry experiments. The energetics of the interaction of these molecules with the RNA structures has also been elucidated by isothermal titration calorimetry (ITC). Results suggest that proflavine strongly intercalates in both forms of polyCG, whereas hoechst shows mainly groove-binding modes. The binding of both drugs to both forms of RNA resulted in significant conformational change to the RNA structure with the bound molecules being placed in the chiral RNA helix. ITC profiles for both proflavine and hoechst show two binding sites. Binding of proflavine to both forms of RNA is endothermic and entropy driven in the first site and exothermic and enthalpy driven in the second site, whereas hoechst binding to both forms of RNA is exothermic and enthalpy driven in the first site and endothermic and entropy driven in the second site. This study suggests that the binding affinity characteristics and energetics of interaction of these DNA binding molecules with the RNA conformations are significantly different and may serve as data for future development of effective structure-selective RNA-based drugs.

Proline cis-trans isomerization in staphylococcal nuclease: multi-substrate free energy perturbation calculations.

PubMed Central

Hodel, A.; Rice, L. M.; Simonson, T.; Fox, R. O.; Brünger, A. T.

1995-01-01

Staphylococcal nuclease A exists in two folded forms that differ in the isomerization state of the Lys 116-Pro 117 peptide bond. The dominant form (90% occupancy) adopts a cis peptide bond, which is observed in the crystal structure. NMR studies show that the relatively small difference in free energy between the cis and trans forms (delta Gcis-->trans approximately 1.2 kcal/mol) results from large and nearly compensating differences in enthalpy and entropy (delta Hcis-->trans approximately delta TScis-->trans approximately 10 kcal/mol). There is evidence from X-ray crystal structures that the structural differences between the cis and the trans forms of nuclease are confined to the conformation of residues 112-117, a solvated protein loop. Here, we obtain a thermodynamic and structural description of the conformational equilibrium of this protein loop through an exhaustive conformational search that identified several substates followed by free energy simulations between the substrates. By partitioning the search into conformational substates, we overcame the multiple minima problem in this particular case and obtained precise and reproducible free energy values. The protein and water environment was implicitly modeled by appropriately chosen nonbonded terms between the explicitly treated loop and the rest of the protein. These simulations correctly predicted a small free energy difference between the cis and trans forms composed of larger, compensating differences in enthalpy and entropy. The structural predictions of these simulations were qualitatively consistent with known X-ray structures of nuclease variants and yield a model of the unknown minor trans conformation. PMID:7613463

SteamTables: An approach of multiple variable sets

NASA Astrophysics Data System (ADS)

Verma, Mahendra P.

2009-10-01

Using the IAPWS-95 formulation, an ActiveX component SteamTablesIIE in Visual Basic 6.0 is developed to calculate thermodynamic properties of pure water as a function of two independent intensive variables: (1) temperature ( T) or pressure ( P) and (2) T, P, volume ( V), internal energy ( U), enthalpy ( H), entropy ( S) or Gibbs free energy ( G). The second variable cannot be the same as variable 1. Additionally, it calculates the properties along the separation boundaries (i.e., sublimation, saturation, critical isochor, ice I melting, ice III to ice IIV melting and minimum volume curves) considering the input parameter as T or P for the variable 1. SteamTablesIIE is an extension of the ActiveX component SteamTables implemented earlier considering T (190 to 2000 K) and P (3.23×10 -8 to 10000 MPa) as independent variables. It takes into account the following 27 intensive properties: temperature ( T), pressure ( P), fraction, state, volume ( V), density ( Den), compressibility factor ( Z0), internal energy ( U), enthalpy ( H), Gibbs free energy ( G), Helmholtz free energy ( A), entropy ( S), heat capacity at constant pressure ( C p), heat capacity at constant volume ( C v), coefficient of thermal expansion ( CTE), isothermal compressibility ( Z iso), speed of sound ( VelS), partial derivative of P with T at constant V ( dPdT), partial derivative of T with V at constant P ( dTdV), partial derivative of V with P at constant T ( dVdP), Joule-Thomson coefficient ( JTC), isothermal throttling coefficient ( IJTC), viscosity ( Vis), thermal conductivity ( ThrmCond), surface tension ( SurfTen), Prandtl number ( PrdNum) and dielectric constant ( DielCons).

Heat capacity and thermodynamic properties for coesite and jadeite, reexamination of the quartz-coesite equilibrium boundary

USGS Publications Warehouse

Hemingway, B.S.; Bohlen, S.R.; Hankins, W.B.; Westrum, E.F.; Kuskov, O.L.

1998-01-01

The heat capacities of synthetic coesite and jadeite were measured between about 15 and 850 K by adiabatic and differential scanning calorimetry. The experimental data were smoothed and estimates were made of heat capacities to 1800 K. The following equations represent our estimate of the heat capacities of coesite and jadeite between 298.15 and 1800 K: [see original article for formula]. Tables of thermodynamic values for coesite and jadeite to 1800 K are presented. The entropies of coesite and jadeite are 40.38 ?? 0.12 and 136.5 ?? 0.32 J/(mol.K), respectively, at 298.15 K. The entropy for coesite derived here confirms the value published earlier by Holm et al. (1967). We have derived an equation to describe the quartz-coesite boundary over the temperature range of 600 to 1500 K, P(GPa) = 1.76 + 0.001T(K). Our results are in agreement with the enthalpy of transition reported by Akaogi and Navrotsky (1984) and yield -907.6 ?? 1.4 kJ/mol for the enthalpy of formation of coesite from the elements at 298.15 K and 1 bar, in agreement with the value recommended by CODATA (Khodakovsky et al. 1995). Several sources of uncertainty remain unacceptably high, including: the heat capacities of coesite at temperatures above about 1000 K; the heat capacities and volumetric properties of ?? quartz at higher pressures and at temperatures above 844 K; the pressure corrections for the piston cylinder apparatus used to determine the quartz-coesite equilibrium boundary.

Tunable thermodynamic activity of La x Sr1-x Mn y Al1-y O3-δ (0 ≤ x ≤ 1, 0 ≤ y ≤ 1) perovskites for solar thermochemical fuel synthesis.

PubMed

Ezbiri, M; Takacs, M; Theiler, D; Michalsky, R; Steinfeld, A

2017-02-28

Nonstoichiometric metal oxides with variable valence are attractive redox materials for thermochemical and electrochemical fuel processing. To guide the design of advanced redox materials for solar-driven splitting of CO 2 and/or H 2 O to produce CO and/or H 2 (syngas), we investigate the equilibrium thermodynamics of the La x Sr 1- x Mn y Al 1- y O 3- δ perovskite family (0 ≤ x ≤ 1, 0 ≤ y ≤ 1) and La 0.6 Ca 0.4 Mn 0.8 Al 0.2 O 3- δ , and compare them to those of CeO 2 as the baseline. Oxygen nonstoichiometry measurements from 1573 to 1773 K and from 0.206 to 180 mbar O 2 show a tunable reduction extent, increasing with increasing Sr content. Maximal nonstoichiometry of 0.32 is established with La 0.2 Sr 0.8 Mn 0.8 Al 0.2 O 3- δ at 1773 K and 2.37 mbar O 2 . As a trend, we find that oxygen capacities are most sensitive to the A-cation composition. Partial molar enthalpy, entropy and Gibbs free energy changes for oxide reduction are extracted from the experimental data using defect models for Mn 4+ /Mn 3+ and Mn 3+ /Mn 2+ redox couples. We find that perovskites exhibit typically decreasing enthalpy changes with increasing nonstoichiometries. This desirable characteristic is most pronounced by La 0.6 Sr 0.4 Mn 0.4 Al 0.6 O 3- δ , rendering it attractive for CO 2 and H 2 O splitting. Generally, perovskites show lower enthalpy and entropy changes than ceria, resulting in more favorable reduction but less favorable oxidation equilibria. The energy penalties due to larger temperature swings and excess oxidants are discussed in particular. Using electronic structure theory, we conclude with a practical methodology estimating thermodynamic activity to rationally design perovskites with variable stoichiometry and valence.

The molecular origins of specificity in the assembly of a multienzyme complex.

PubMed

Frank, René A W; Pratap, J Venkatesh; Pei, Xue Y; Perham, Richard N; Luisi, Ben F

2005-08-01

The pyruvate dehydrogenase (PDH) multienzyme complex is central to oxidative metabolism. We present the first crystal structure of a complex between pyruvate decarboxylase (E1) and the peripheral subunit binding domain (PSBD) of the dihydrolipoyl acetyltransferase (E2). The interface is dominated by a "charge zipper" of networked salt bridges. Remarkably, the PSBD uses essentially the same zipper to alternately recognize the dihydrolipoyl dehydrogenase (E3) component of the PDH assembly. The PSBD achieves this dual recognition largely through the addition of a network of interfacial water molecules unique to the E1-PSBD complex. These structural comparisons illuminate our observations that the formation of this water-rich E1-E2 interface is largely enthalpy driven, whereas that of the E3-PSBD complex (from which water is excluded) is entropy driven. Interfacial water molecules thus diversify surface complementarity and contribute to avidity, enthalpically. Additionally, the E1-PSBD structure provides insight into the organization and active site coupling within the approximately 9 MDa PDH complex.

Revisiting Hansen Solubility Parameters by Including Thermodynamics.

PubMed

Louwerse, Manuel J; Maldonado, Ana; Rousseau, Simon; Moreau-Masselon, Chloe; Roux, Bernard; Rothenberg, Gadi

2017-11-03

The Hansen solubility parameter approach is revisited by implementing the thermodynamics of dissolution and mixing. Hansen's pragmatic approach has earned its spurs in predicting solvents for polymer solutions, but for molecular solutes improvements are needed. By going into the details of entropy and enthalpy, several corrections are suggested that make the methodology thermodynamically sound without losing its ease of use. The most important corrections include accounting for the solvent molecules' size, the destruction of the solid's crystal structure, and the specificity of hydrogen-bonding interactions, as well as opportunities to predict the solubility at extrapolated temperatures. Testing the original and the improved methods on a large industrial dataset including solvent blends, fit qualities improved from 0.89 to 0.97 and the percentage of correct predictions rose from 54 % to 78 %. Full Matlab scripts are included in the Supporting Information, allowing readers to implement these improvements on their own datasets. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations.

PubMed

Liu, Fengjiao; Zhang, John Z H; Mei, Ye

2016-06-01

Previous experimental study measuring the binding affinities of biotin to the wild type streptavidin (WT) and three mutants (S45A, D128A and S45A/D128A double mutant) has shown that the loss of binding affinity from the double mutation is larger than the direct sum of those from two single mutations. The origin of this cooperativity has been investigated in this work through molecular dynamics simulations and the end-state free energy method using the polarized protein-specific charge. The results show that this cooperativity comes from both the enthalpy and entropy contributions. The former contribution mainly comes from the alternations of solvation free energy. Decomposition analysis shows that the mutated residues nearly have no contributions to the cooperativity. Instead, N49 and S88, which are located at the entry of the binding pocket and interact with the carboxyl group of biotin, make the dominant contribution among all the residues in the first binding shell around biotin.

The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Liu, Fengjiao; Zhang, John Z. H.; Mei, Ye

2016-06-01

Previous experimental study measuring the binding affinities of biotin to the wild type streptavidin (WT) and three mutants (S45A, D128A and S45A/D128A double mutant) has shown that the loss of binding affinity from the double mutation is larger than the direct sum of those from two single mutations. The origin of this cooperativity has been investigated in this work through molecular dynamics simulations and the end-state free energy method using the polarized protein-specific charge. The results show that this cooperativity comes from both the enthalpy and entropy contributions. The former contribution mainly comes from the alternations of solvation free energy. Decomposition analysis shows that the mutated residues nearly have no contributions to the cooperativity. Instead, N49 and S88, which are located at the entry of the binding pocket and interact with the carboxyl group of biotin, make the dominant contribution among all the residues in the first binding shell around biotin.

Energetics of zirconia stabilized by cation and nitrogen substitution

NASA Astrophysics Data System (ADS)

Molodetsky, Irina

Tetragonal and cubic zirconia are used in advanced structural ceramics, fuel cells, oxygen sensors, nuclear waste ceramics and many other applications. These zirconia phases are stabilized at room temperature (relative to monoclinic phase for pure zirconia) by cation and nitrogen substitution. This work is aimed at a better understanding of the mechanisms of stabilization of the high-temperature zirconia. phases. Experimental data are produced on the energetics of zirconia stabilized by yttria and calcia, energetics of nitrogen-oxygen substitution in zirconia and cation doped zirconia, and energetics of x-ray amorphous zirconia. obtained by low-temperature synthesis. High-temperature oxide melt solution enables direct measurement of enthalpies of formation of these refractory oxides. The enthalpy of the monoclinic to cubic phase transition of zirconia is DeltaHm-c = 12.2 +/- 1.2 kJ/mol. For cubic phases of YSZ at low yttria contents, a straight line DeltaH f,YSZ = -(52.4 +/- 3.6)x + (12.2 +/- 1.2) approximates the enthalpy of formation as a function of the yttria content, x (0. 1 < x < 0.3). Use of the quadratic fit DeltaHf,YSZ = 126.36 x 2 - 81.29 x + 12.37 (0.1 ≲ x ≲ 0.53) indicates that yttria stabilizes the cubic phase in enthalpy at low dopant content and destabilizes the cubic phase as yttria content increases. Positive entropy of mixing in YSZ and small enthalpy of long range ordering in 0.47ZrO2-0.53YO1.5, DeltaHord = -2.4 +/- 3.0 kJ/mol, indicate presence of short range ordering in YSZ. The enthalpy of formation of calcia stabilized zirconia as a function of calcia content x, is approximated as DeltaHf,c = (-91.4 +/- 3.8) x + (13.5 +/- 1.7) kJ/mol. The enthalpy of oxygen-nitrogen substitution, DeltaHO-N, in zirconium oxynitrides is a linear function of nitrogen content. DeltaH O-N ˜ -500 kJ/mol N is for Ca (Y)-Zr-N-O and Zr-N-O oxynitrides and DeltaHO-N ˜ -950 kJ/mol N is for Mg-Zr-N-O oxynitrides. X-ray amorphous zirconia is 58.6 +/- 3.3 kJ/mol less stable in enthalpy than monoclinic zirconia. The difference between the surface energies of amorphous and tetragonal zirconia phases is ˜1.19 +/- 0.05 J/m2, with a lower surface energy for the amorphous material.

Trends in Ground-State Entropies for Transition Metal Based Hydrogen Atom Transfer Reactions

PubMed Central

Mader, Elizabeth A.; Manner, Virginia W.; Markle, Todd F.; Wu, Adam; Franz, James A.; Mayer, James M.

2009-01-01

Reported herein are thermochemical studies of hydrogen atom transfer (HAT) reactions involving transition metal H-atom donors MIILH and oxyl radicals. [FeII(H2bip)3]2+, [FeII(H2bim)3]2+, [CoII(H2bim)3]2+ and RuII(acac)2(py-imH) [H2bip = 2,2’-bi-1,4,5,6-tetrahydropyrimidine, H2bim = 2,2’-bi-imidazoline, acac = 2,4-pentandionato, py-imH = 2-(2’-pyridyl)-imidazole)] each react with TEMPO (2,2,6,6-tetramethyl-1-piperidinoxyl) or tBu3PhO• (2,4,6-tri-tert-butylphenoxyl) to give the deprotonated, oxidized metal complex MIIIL, and TEMPOH or tBu3PhOH. Solution equilibrium measurements for the reaction of [CoII(H2bim)3]2+ with TEMPO show a large, negative ground-state entropy for hydrogen atom transfer, −41 ± 2 cal mol−1 K−1. This is even more negative than the ΔSoHAT = −30 ± 2 cal mol−1 K−1 for the two iron complexes and the ΔSoHAT for RuII(acac)2(py-imH) + TEMPO, 4.9 ± 1.1 cal mol−1 K−1, as reported earlier. Calorimetric measurements quantitatively confirm the enthalpy of reaction for [FeII(H2bip)3]2+ + TEMPO, thus also confirming ΔSoHAT. Calorimetry on TEMPOH + tBu3PhO• gives ΔHoHAT = −11.2 ± 0.5 kcal mol−1 which matches the enthalpy predicted from the difference in literature solution BDEs. A brief evaluation of the literature thermochemistry of TEMPOH and tBu3PhOH supports the common assumption that ΔSoHAT ≈ 0 for HAT reactions of organic and small gas-phase molecules. However, this assumption does not hold for transition metal based HAT reactions. The trend in magnitude of |ΔSoHAT| for reactions with TEMPO, RuII(acac)2(py-imH) << [FeII(H2bip)3]2+ = [FeII(H2bim)3]2+ < [CoII(H2bim)3]2+, is surprisingly well predicted by the trends for electron transfer half-reaction entropies, ΔSoET, in aprotic solvents. This is because both ΔSoET and ΔSoHAT have substantial contributions from vibrational entropy, which varies significantly with the metal center involved. The close connection between ΔSoHAT and ΔSoET provides an important link between these two fields and provides a starting point from which to predict which HAT systems will have important ground-state entropy effects. PMID:19275235

Thermodynamic properties of model CdTe/CdSe mixtures

DOE PAGES

van Swol, Frank; Zhou, Xiaowang W.; Challa, Sivakumar R.; ...

2015-02-20

We report on the thermodynamic properties of binary compound mixtures of model groups II–VI semiconductors. We use the recently introduced Stillinger–Weber Hamiltonian to model binary mixtures of CdTe and CdSe. We use molecular dynamics simulations to calculate the volume and enthalpy of mixing as a function of mole fraction. The lattice parameter of the mixture closely follows Vegard's law: a linear relation. This implies that the excess volume is a cubic function of mole fraction. A connection is made with hard sphere models of mixed fcc and zincblende structures. We found that the potential energy exhibits a positive deviation frommore » ideal soluton behaviour; the excess enthalpy is nearly independent of temperatures studied (300 and 533 K) and is well described by a simple cubic function of the mole fraction. Using a regular solution approach (combining non-ideal behaviour for the enthalpy with ideal solution behaviour for the entropy of mixing), we arrive at the Gibbs free energy of the mixture. The Gibbs free energy results indicate that the CdTe and CdSe mixtures exhibit phase separation. The upper consolute temperature is found to be 335 K. Finally, we provide the surface energy as a function of composition. Moreover, it roughly follows ideal solution theory, but with a negative deviation (negative excess surface energy). This indicates that alloying increases the stability, even for nano-particles.« less

Metal-coupled folding as the driving force for the extreme stability of Rad50 zinc hook dimer assembly

NASA Astrophysics Data System (ADS)

Kochańczyk, Tomasz; Nowakowski, Michał; Wojewska, Dominika; Kocyła, Anna; Ejchart, Andrzej; Koźmiński, Wiktor; Krężel, Artur

2016-11-01

The binding of metal ions at the interface of protein complexes presents a unique and poorly understood mechanism of molecular assembly. A remarkable example is the Rad50 zinc hook domain, which is highly conserved and facilitates the Zn2+-mediated homodimerization of Rad50 proteins. Here, we present a detailed analysis of the structural and thermodynamic effects governing the formation and stability (logK12 = 20.74) of this evolutionarily conserved protein assembly. We have dissected the determinants of the stability contributed by the small β-hairpin of the domain surrounding the zinc binding motif and the coiled-coiled regions using peptides of various lengths from 4 to 45 amino acid residues, alanine substitutions and peptide bond-to-ester perturbations. In the studied series of peptides, an >650 000-fold increase of the formation constant of the dimeric complex arises from favorable enthalpy because of the increased acidity of the cysteine thiols in metal-free form and the structural properties of the dimer. The dependence of the enthalpy on the domain fragment length is partially compensated by the entropic penalty of domain folding, indicating enthalpy-entropy compensation. This study facilitates understanding of the metal-mediated protein-protein interactions in which the metal ion is critical for the tight association of protein subunits.

Metal-coupled folding as the driving force for the extreme stability of Rad50 zinc hook dimer assembly

PubMed Central

Kochańczyk, Tomasz; Nowakowski, Michał; Wojewska, Dominika; Kocyła, Anna; Ejchart, Andrzej; Koźmiński, Wiktor; Krężel, Artur

2016-01-01

The binding of metal ions at the interface of protein complexes presents a unique and poorly understood mechanism of molecular assembly. A remarkable example is the Rad50 zinc hook domain, which is highly conserved and facilitates the Zn2+-mediated homodimerization of Rad50 proteins. Here, we present a detailed analysis of the structural and thermodynamic effects governing the formation and stability (logK12 = 20.74) of this evolutionarily conserved protein assembly. We have dissected the determinants of the stability contributed by the small β-hairpin of the domain surrounding the zinc binding motif and the coiled-coiled regions using peptides of various lengths from 4 to 45 amino acid residues, alanine substitutions and peptide bond-to-ester perturbations. In the studied series of peptides, an >650 000-fold increase of the formation constant of the dimeric complex arises from favorable enthalpy because of the increased acidity of the cysteine thiols in metal-free form and the structural properties of the dimer. The dependence of the enthalpy on the domain fragment length is partially compensated by the entropic penalty of domain folding, indicating enthalpy-entropy compensation. This study facilitates understanding of the metal-mediated protein-protein interactions in which the metal ion is critical for the tight association of protein subunits. PMID:27808280

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salud, J.; Lopez, D.O.; Barrio, M.

The experimental two-component phase diagram between the orientationally disordered crystals 2-amino-2-methyl-1,3-propanediol (AMP) and 1,1,1-tris(hydroxymethyl)propane (PG) has been established from room temperature to the liquid state using thermal analysis and X-ray powder diffraction techniques. The intermolecular interactions in the orientationally disordered mixed crystals of the mentioned system and other related two-component systems are discussed by analyzing the evolution of the packing coefficient as a function of the composition. A thermodynamic analysis of the presented phase diagram and the redetermined AMP/NPG (2,2-dimethyl-1,3-propanediol) is reported on the basis of the enthalpy-entropy compensation theory.

Physicochemical application of capillary chromatography

NASA Astrophysics Data System (ADS)

Vasil'ev, A. V.; Aleksandrov, E. N.

1992-04-01

The application of capillary gas chromatography in the determination of the free energy, enthalpy, and entropy of sorption, the saturated vapour pressure and activity coefficients, the assessment of the lipophilicity of volatile compounds, and the study of the properties of polymers and liquid crystals is described. The use of reaction cappillary chromatography in kinetic studies of conformational conversions, thermal degradation, and photochemical reactions is examined. Studies on the use of capillary columns for determination of the second virial coefficients and viscosity of gases and the diffusion coefficients in gases, liquids, supercritical fluids, and polymers are analysed. The bibliography includes 114 references.

On the interaction of luminol with human serum albumin: Nature and thermodynamics of ligand binding

NASA Astrophysics Data System (ADS)

Moyon, N. Shaemningwar; Mitra, Sivaprasad

2010-09-01

The mechanism and thermodynamic parameters for the binding of luminol (LH 2) with human serum albumin was explored by steady state and picosecond time-resolved fluorescence spectroscopy. It was shown that out of two possible LH 2 conformers present is solution, only one is accessible for binding with HSA. The thermodynamic parameters like enthalpy (Δ H) and entropy (Δ S) change corresponding to the ligand binding process were also estimated by performing the experiment at different temperatures. The ligand replacement experiment with bilirubin confirms that LH 2 binds into the sub-domain IIA of the protein.

Liquid-vapor phase equilibria and the thermodynamic properties of 2-methylpropanol- n-alkyl propanoate solutions

NASA Astrophysics Data System (ADS)

Suntsov, Yu. K.; Goryunov, V. A.; Chuikov, A. M.; Meshcheryakov, A. V.

2016-08-01

The boiling points of solutions of five binary systems are measured via ebulliometry in the pressure range of 2.05-103.3 kPa. Equilibrium vapor phase compositions, the values of the excess Gibbs energies, enthalpies, and entropies of solution of these systems are calculated. Patterns in the changes of phase equilibria and thermodynamic properties of solutions are established, depending on the compositions and temperatures of the systems. Liquid-vapor equilibria in the systems are described using the equations of Wilson and the NRTL (Non-Random Two-Liquid Model).

The application of the thermodynamic perturbation theory to study the hydrophobic hydration.

PubMed

Mohoric, Tomaz; Urbic, Tomaz; Hribar-Lee, Barbara

2013-07-14

The thermodynamic perturbation theory was tested against newly obtained Monte Carlo computer simulations to describe the major features of the hydrophobic effect in a simple 3D-Mercedes-Benz water model: the temperature and hydrophobe size dependence on entropy, enthalpy, and free energy of transfer of a simple hydrophobic solute into water. An excellent agreement was obtained between the theoretical and simulation results. Further, the thermodynamic perturbation theory qualitatively correctly (with respect to the experimental data) describes the solvation thermodynamics under conditions where the simulation results are difficult to obtain with good enough accuracy, e.g., at high pressures.

Heat capacities and entropies of sillimanite, fibrolite, andalusite, kyanite, and quartz and the Al2SiO5 phase diagram

USGS Publications Warehouse

Hemingway, B.S.; Robie, R.A.; Evans, H.T.; Kerrick, Derrill M.

1991-01-01

Low-temperature heat capacities for sillimanite, fibrolite, and both fine-grained and coarse-grained quartz have been measured. Superambient heat capacities have been measured for four sillimanite, two andalusite, one kyanite, and two fibrolite samples. Equations are recommended for the temperature dependence of the heat capacities of kyanite, andalusite, sillimanite, and fibrolite. The heat capacity functions have been combined with thermal expansion (fibrolite and sillimanite reported here), enthalpy of solution, and phase equilibrium data in order to construct a phase diagram for the Al2SiO5 polymorphs. -from Authors

The application of the thermodynamic perturbation theory to study the hydrophobic hydration

NASA Astrophysics Data System (ADS)

Mohorič, Tomaž; Urbic, Tomaz; Hribar-Lee, Barbara

2013-07-01

The thermodynamic perturbation theory was tested against newly obtained Monte Carlo computer simulations to describe the major features of the hydrophobic effect in a simple 3D-Mercedes-Benz water model: the temperature and hydrophobe size dependence on entropy, enthalpy, and free energy of transfer of a simple hydrophobic solute into water. An excellent agreement was obtained between the theoretical and simulation results. Further, the thermodynamic perturbation theory qualitatively correctly (with respect to the experimental data) describes the solvation thermodynamics under conditions where the simulation results are difficult to obtain with good enough accuracy, e.g., at high pressures.

Experimental Techniques for Thermodynamic Measurements of Ceramics

NASA Technical Reports Server (NTRS)

Jacobson, Nathan S.; Putnam, Robert L.; Navrotsky, Alexandra

1999-01-01

Experimental techniques for thermodynamic measurements on ceramic materials are reviewed. For total molar quantities, calorimetry is used. Total enthalpies are determined with combustion calorimetry or solution calorimetry. Heat capacities and entropies are determined with drop calorimetry, differential thermal methods, and adiabatic calorimetry . Three major techniques for determining partial molar quantities are discussed. These are gas equilibration techniques, Knudsen cell methods, and electrochemical techniques. Throughout this report, issues unique to ceramics are emphasized. Ceramic materials encompass a wide range of stabilities and this must be considered. In general data at high temperatures is required and the need for inert container materials presents a particular challenge.

Spatial Analysis and Quantification of the Thermodynamic Driving Forces in Protein-Ligand Binding: Binding Site Variability

PubMed Central

Raman, E. Prabhu; MacKerell, Alexander D.

2015-01-01

The thermodynamic driving forces behind small molecule-protein binding are still not well understood, including the variability of those forces associated with different types of ligands in different binding pockets. To better understand these phenomena we calculate spatially resolved thermodynamic contributions of the different molecular degrees of freedom for the binding of propane and methanol to multiple pockets on the proteins Factor Xa and p38 MAP kinase. Binding thermodynamics are computed using a statistical thermodynamics based end-point method applied on a canonical ensemble comprising the protein-ligand complexes and the corresponding free states in an explicit solvent environment. Energetic and entropic contributions of water and ligand degrees of freedom computed from the configurational ensemble provides an unprecedented level of detail into the mechanisms of binding. Direct protein-ligand interaction energies play a significant role in both non-polar and polar binding, which is comparable to water reorganization energy. Loss of interactions with water upon binding strongly compensates these contributions leading to relatively small binding enthalpies. For both solutes, the entropy of water reorganization is found to favor binding in agreement with the classical view of the “hydrophobic effect”. Depending on the specifics of the binding pocket, both energy-entropy compensation and reinforcement mechanisms are observed. Notable is the ability to visualize the spatial distribution of the thermodynamic contributions to binding at atomic resolution showing significant differences in the thermodynamic contributions of water to the binding of propane versus methanol. PMID:25625202

Predicting loop–helix tertiary structural contacts in RNA pseudoknots

PubMed Central

Cao, Song; Giedroc, David P.; Chen, Shi-Jie

2010-01-01

Tertiary interactions between loops and helical stems play critical roles in the biological function of many RNA pseudoknots. However, quantitative predictions for RNA tertiary interactions remain elusive. Here we report a statistical mechanical model for the prediction of noncanonical loop–stem base-pairing interactions in RNA pseudoknots. Central to the model is the evaluation of the conformational entropy for the pseudoknotted folds with defined loop–stem tertiary structural contacts. We develop an RNA virtual bond-based conformational model (Vfold model), which permits a rigorous computation of the conformational entropy for a given fold that contains loop–stem tertiary contacts. With the entropy parameters predicted from the Vfold model and the energy parameters for the tertiary contacts as inserted parameters, we can then predict the RNA folding thermodynamics, from which we can extract the tertiary contact thermodynamic parameters from theory–experimental comparisons. These comparisons reveal a contact enthalpy (ΔH) of −14 kcal/mol and a contact entropy (ΔS) of −38 cal/mol/K for a protonated C+•(G–C) base triple at pH 7.0, and (ΔH = −7 kcal/mol, ΔS = −19 cal/mol/K) for an unprotonated base triple. Tests of the model for a series of pseudoknots show good theory–experiment agreement. Based on the extracted energy parameters for the tertiary structural contacts, the model enables predictions for the structure, stability, and folding pathways for RNA pseudoknots with known or postulated loop–stem tertiary contacts from the nucleotide sequence alone. PMID:20100813

Dynamics, Conformational Entropy, and Frustration in Protein-Protein Interactions Involving an Intrinsically Disordered Protein Domain.

PubMed

Lindström, Ida; Dogan, Jakob

2018-05-18

Intrinsically disordered proteins (IDPs) are abundant in the eukaryotic proteome. However, little is known about the role of subnanosecond dynamics and the conformational entropy that it represents in protein-protein interactions involving IDPs. Using nuclear magnetic resonance side chain and backbone relaxation, stopped-flow kinetics, isothermal titration calorimetry, and computational studies, we have characterized the interaction between the globular TAZ1 domain of the CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2). We show that the TAZ1/TAD-STAT2 complex retains considerable subnanosecond motions, with TAD-STAT2 undergoing only a partial disorder-to-order transition. We report here the first experimental determination of the conformational entropy change for both binding partners in an IDP binding interaction and find that the total change even exceeds in magnitude the binding enthalpy and is comparable to the contribution from the hydrophobic effect, demonstrating its importance in the binding energetics. Furthermore, we show that the conformational entropy change for TAZ1 is also instrumental in maintaining a biologically meaningful binding affinity. Strikingly, a spatial clustering of very high amplitude motions and a cluster of more rigid sites in the complex exist, which through computational studies we found to overlap with regions that experience energetic frustration and are less frustrated, respectively. Thus, the residual dynamics in the bound state could be necessary for faster dissociation, which is important for proteins that interact with multiple binding partners.

Single molecule thermodynamics in biological motors.

PubMed

Taniguchi, Yuichi; Karagiannis, Peter; Nishiyama, Masayoshi; Ishii, Yoshiharu; Yanagida, Toshio

2007-04-01

Biological molecular machines use thermal activation energy to carry out various functions. The process of thermal activation has the stochastic nature of output events that can be described according to the laws of thermodynamics. Recently developed single molecule detection techniques have allowed each distinct enzymatic event of single biological machines to be characterized providing clues to the underlying thermodynamics. In this study, the thermodynamic properties in the stepping movement of a biological molecular motor have been examined. A single molecule detection technique was used to measure the stepping movements at various loads and temperatures and a range of thermodynamic parameters associated with the production of each forward and backward step including free energy, enthalpy, entropy and characteristic distance were obtained. The results show that an asymmetry in entropy is a primary factor that controls the direction in which the motor will step. The investigation on single molecule thermodynamics has the potential to reveal dynamic properties underlying the mechanisms of how biological molecular machines work.

Thermodynamic variables of first-order entropy corrected Lovelock-AdS black holes: P{-}V criticality analysis

NASA Astrophysics Data System (ADS)

Haldar, Amritendu; Biswas, Ritabrata

2018-06-01

We investigate the effect of thermal fluctuations on the thermodynamics of a Lovelock-AdS black hole. Taking the first order logarithmic correction term in entropy we analyze the thermodynamic potentials like Helmholtz free energy, enthalpy and Gibbs free energy. We find that all the thermodynamic potentials are decreasing functions of correction coefficient α . We also examined this correction coefficient must be positive by analysing P{-}V diagram. Further we study the P{-}V criticality and stability and find that presence of logarithmic correction in it is necessary to have critical points and stable phases. When P{-}V criticality appears, we calculate the critical volume V_c, critical pressure P_c and critical temperature T_c using different equations and show that there is no critical point for this black hole without thermal fluctuations. We also study the geometrothermodynamics of this kind of black holes. The Ricci scalar of the Ruppeiner metric is graphically analysed.

LOW-TEMPERATURE HEAT CAPACITIES AND THERMODYNAMIC FUNCTIONS OF SOME PLATINUM AND PALLADIUM GROUP CHALCOGENIDES. I. MONO-CHALCOGENIDES. Pts, PtTe, AND PdTe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Groenvold, F.; Thurmann-Moe, T.; Westrum, E.F. Jr.

1961-11-01

Heat capacities of platinum monosulfide, platinum monotelluride, and palladium monotelluride were measured in the range 5--350 deg K. They show the normal sigmoidal temperature dependence with no evidence of transivions or other anomalies. The derived heat-capacity equations were integrated. Values of heat capacitles, entropy, and enthalpy increments, and of the free-energy function are tabulated for selected temperatures. Av 298,15 deg K, the third-law entroples are 13,16 cal gfw/sup -1/ deg K/sup -1/ for PtS 19.41 cal gfw/sup -1/ deg K/sup - 1/ for PtTe, and 2l.42 cal gfw/sup -1/ deg K/sup -1/ for PdTe. The new dava on PvS weremore » correlaved wlvh exlstlng decomposlvlonpressure data vo evaluate DELTA Hf, DELTA Ff, and DELTA Sf 298.15 deg K. Entropies for other platlnum-metal monochalcogenides were estimated. (auth)« less

Unusual Entropy of Adsorbed Methane on Zeolite-Templated Carbon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stadie, Nicholas P.; Murialdo, Maxwell; Ahn, Channing C.

2015-11-25

Methane adsorption at high pressures and across a wide range of temperatures was investigated on the surface of three porous carbon adsorbents with complementary structural properties. The measured adsorption equilibria were analyzed using a method that can accurately account for nonideal fluid properties and distinguish between absolute and excess quantities of adsorption, and that also allows the direct calculation of the thermodynamic potentials relevant to adsorption. On zeolite-templated carbon (ZTC), a material that exhibits extremely high surface area with optimal pore size and homogeneous structure, methane adsorption occurs with unusual thermodynamic properties that are greatly beneficial for deliverable gas storage:more » an enthalpy of adsorption that increases with site occupancy, and an unusually low entropy of the adsorbed phase. The origin of these properties is elucidated by comparison of the experimental results with a statistical mechanical model. The results indicate that temperature-dependent clustering (i.e., reduced configurations) of the adsorbed phase due to enhanced lateral interactions can account for the peculiarities of methane adsorbed on ZTC.« less

A fast and simple spectrofluorometric method for the determination of alendronate sodium in pharmaceuticals

PubMed Central

Ezzati Nazhad Dolatabadi, Jafar; Hamishehkar, Hamed; de la Guardia, Miguel; Valizadeh, Hadi

2014-01-01

Introduction: Alendronate sodium enhances bone formation and increases osteoblast proliferation and maturation and leads to the inhibition of osteoblast apoptosis. Therefore, a rapid and simple spectrofluorometric method has been developed and validated for the quantitative determination of it. Methods: The procedure is based on the reaction of primary amino group of alendronate with o-phthalaldehyde (OPA) in sodium hydroxide solution. Results: The calibration graph was linear over the concentration range of 0.0-2.4 μM and limit of detection and limit of quantification of the method was 8.89 and 29 nanomolar, respectively. The enthalpy and entropy of the reaction between alendronate sodium and OPA showed that the reaction is endothermic and entropy favored (ΔH = 154.08 kJ/mol; ΔS = 567.36 J/mol K) which indicates that OPA interaction with alendronate is increased at elevated temperature. Conclusion: This simple method can be used as a practical technique for the analysis of alendronate in various samples. PMID:24790897

Design of high-strength refractory complex solid-solution alloys

DOE PAGES

Singh, Prashant; Sharma, Aayush; Smirnov, A. V.; ...

2018-03-28

Nickel-based superalloys and near-equiatomic high-entropy alloys containing molybdenum are known for higher temperature strength and corrosion resistance. Yet, complex solid-solution alloys offer a huge design space to tune for optimal properties at slightly reduced entropy. For refractory Mo-W-Ta-Ti-Zr, we showcase KKR electronic structure methods via the coherent-potential approximation to identify alloys over five-dimensional design space with improved mechanical properties and necessary global (formation enthalpy) and local (short-range order) stability. Deformation is modeled with classical molecular dynamic simulations, validated from our first-principle data. We predict complex solid-solution alloys of improved stability with greatly enhanced modulus of elasticity (3× at 300 K)more » over near-equiatomic cases, as validated experimentally, and with higher moduli above 500 K over commercial alloys (2.3× at 2000 K). We also show that optimal complex solid-solution alloys are not described well by classical potentials due to critical electronic effects.« less

Effect of temperature on the complexation of NpO 2 + with benzoic acid: Spectrophotometric and calorimetric studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Yanqiu; Zhang, Zhicheng; Liu, Guokui

The equilibrium constants of the 1:1 NpO2+/benzoate complex were determined by spectrophotometric titrations at variable temperatures (T = 283 to 343 K) and the ionic strength of 1.05 mol · kg-1. The enthalpy of complexation at T = 298 K was determined by microcalorimetric titrations. Similar to other monocarboxylates, benzoate forms a weak complex with NpO2+ and the complexation is strengthened as the temperature is increased. The complexation is endothermic and is entropy-driven. The enhancement of the complexation at elevated temperatures is primarily attributed to the increasingly larger entropy gain when the water molecules are released from the highly-ordered solvationmore » spheres of NpO2+ and benzoate to the bulk solvent where the degree of disorder is higher at higher temperatures. The spectroscopic features of the Np(V)/benzoate system, including the effect of temperature on the absorption bands, are discussed in terms of ligand field splitting and a thermal expansion mechanism.« less

Design of high-strength refractory complex solid-solution alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Prashant; Sharma, Aayush; Smirnov, A. V.

Nickel-based superalloys and near-equiatomic high-entropy alloys containing molybdenum are known for higher temperature strength and corrosion resistance. Yet, complex solid-solution alloys offer a huge design space to tune for optimal properties at slightly reduced entropy. For refractory Mo-W-Ta-Ti-Zr, we showcase KKR electronic structure methods via the coherent-potential approximation to identify alloys over five-dimensional design space with improved mechanical properties and necessary global (formation enthalpy) and local (short-range order) stability. Deformation is modeled with classical molecular dynamic simulations, validated from our first-principle data. We predict complex solid-solution alloys of improved stability with greatly enhanced modulus of elasticity (3× at 300 K)more » over near-equiatomic cases, as validated experimentally, and with higher moduli above 500 K over commercial alloys (2.3× at 2000 K). We also show that optimal complex solid-solution alloys are not described well by classical potentials due to critical electronic effects.« less

Determining Membrane Protein-Lipid Binding Thermodynamics Using Native Mass Spectrometry.

PubMed

Cong, Xiao; Liu, Yang; Liu, Wen; Liang, Xiaowen; Russell, David H; Laganowsky, Arthur

2016-04-06

Membrane proteins are embedded in the biological membrane where the chemically diverse lipid environment can modulate their structure and function. However, the thermodynamics governing the molecular recognition and interaction of lipids with membrane proteins is poorly understood. Here, we report a method using native mass spectrometry (MS), to determine thermodynamics of individual ligand binding events to proteins. Unlike conventional methods, native MS can resolve individual ligand binding events and, coupled with an apparatus to control the temperature, determine binding thermodynamic parameters, such as for protein-lipid interactions. We validated our approach using three soluble protein-ligand systems (maltose binding protein, lysozyme, and nitrogen regulatory protein) and obtained similar results to those using isothermal titration calorimetry and surface plasmon resonance. We also determined for the first time the thermodynamics of individual lipid binding to the ammonia channel (AmtB), an integral membrane protein from Escherichia coli. Remarkably, we observed distinct thermodynamic signatures for the binding of different lipids and entropy-enthalpy compensation for binding lipids of variable chain length. Additionally, using a mutant form of AmtB that abolishes a specific phosphatidylglycerol (PG) binding site, we observed distinct changes in the thermodynamic signatures for binding PG, implying these signatures can identify key residues involved in specific lipid binding and potentially differentiate between specific lipid binding sites.

HIGH-AFFINITY T CELL RECEPTOR DIFFERENTIATES COGNATE PEPTIDE-MHC AND ALTERED PEPTIDE LIGANDS WITH DISTINCT KINETICS AND THERMODYNAMICS

PubMed Central

Persaud, Stephen P.; Donermeyer, David L.; Weber, K. Scott; Kranz, David M.; Allen, Paul M.

2010-01-01

Interactions between the T cell receptor and cognate peptide-MHC are crucial initiating events in the adaptive immune response. These binding events are highly specific yet occur with micromolar affinity. Even weaker interactions between TCR and self-pMHC complexes play critical regulatory roles in T cell development, maintenance and coagonist activity. Due to their low affinity, the kinetics and thermodynamics of such weak interactions are difficult to study. In this work, we used M15, a high-affinity TCR engineered from the 3.L2 TCR system, to study the binding properties, thermodynamics, and specificity of two altered peptide ligands (APLs). Our affinity measurements of the high-affinity TCR support the view that the wild type TCR binds these APLs in the millimolar affinity range, and hence very low affinities can still elicit biological functions. Finally, single methylene differences among the APLs gave rise to strikingly different binding thermodynamics. These minor changes in the pMHC antigen were associated with significant and unpredictable changes in both the entropy and enthalpy of the reaction. As the identical TCR was analyzed with several structurally similar ligands, the distinct thermodynamic binding profiles provide a mechanistic perspective on how exquisite antigen specificity is achieved by the T cell receptor. PMID:20334923

Cleavage Entropy as Quantitative Measure of Protease Specificity

PubMed Central

Fuchs, Julian E.; von Grafenstein, Susanne; Huber, Roland G.; Margreiter, Michael A.; Spitzer, Gudrun M.; Wallnoefer, Hannes G.; Liedl, Klaus R.

2013-01-01

A purely information theory-guided approach to quantitatively characterize protease specificity is established. We calculate an entropy value for each protease subpocket based on sequences of cleaved substrates extracted from the MEROPS database. We compare our results with known subpocket specificity profiles for individual proteases and protease groups (e.g. serine proteases, metallo proteases) and reflect them quantitatively. Summation of subpocket-wise cleavage entropy contributions yields a measure for overall protease substrate specificity. This total cleavage entropy allows ranking of different proteases with respect to their specificity, separating unspecific digestive enzymes showing high total cleavage entropy from specific proteases involved in signaling cascades. The development of a quantitative cleavage entropy score allows an unbiased comparison of subpocket-wise and overall protease specificity. Thus, it enables assessment of relative importance of physicochemical and structural descriptors in protease recognition. We present an exemplary application of cleavage entropy in tracing substrate specificity in protease evolution. This highlights the wide range of substrate promiscuity within homologue proteases and hence the heavy impact of a limited number of mutations on individual substrate specificity. PMID:23637583

Enthalpy-based equation of state for highly porous materials employing modified soft sphere fluid model

NASA Astrophysics Data System (ADS)

Nayak, Bishnupriya; Menon, S. V. G.

2018-01-01

Enthalpy-based equation of state based on a modified soft sphere model for the fluid phase, which includes vaporization and ionization effects, is formulated for highly porous materials. Earlier developments and applications of enthalpy-based approach had not accounted for the fact that shocked states of materials with high porosity (e.g., porosity more than two for Cu) are in the expanded fluid region. We supplement the well known soft sphere model with a generalized Lennard-Jones formula for the zero temperature isotherm, with parameters determined from cohesive energy, specific volume and bulk modulus of the solid at normal condition. Specific heats at constant pressure, ionic and electronic enthalpy parameters and thermal excitation effects are calculated using the modified approach and used in the enthalpy-based equation of state. We also incorporate energy loss from the shock due to expansion of shocked material in calculating porous Hugoniot. Results obtained for Cu, even up to initial porosities ten, show good agreement with experimental data.

Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water

PubMed Central

Athawale, Manoj V.; Goel, Gaurav; Ghosh, Tuhin; Truskett, Thomas M.; Garde, Shekhar

2007-01-01

We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on folding. Hydrophobic polymers display parabolic, protein-like, temperature-dependent free energy of unfolding. Folded states of small attractive polymers are marginally stable at 300 K and can be unfolded by heating or cooling. Increasing the lengthscale or decreasing the polymer–water attractions stabilizes folded states significantly, the former dominated by the hydration contribution. That hydration contribution can be described by the surface tension model, ΔG = γ(T)ΔA, where the surface tension, γ, is lengthscale-dependent and decreases monotonically with temperature. The resulting variation of the hydration entropy with polymer lengthscale is consistent with theoretical predictions of Huang and Chandler [Huang DM, Chandler D (2000) Proc Natl Acad Sci USA 97:8324–8327] that explain the blurring of entropy convergence observed in protein folding thermodynamics. Analysis of water structure shows that the polymer–water hydrophobic interface is soft and weakly dewetted, and is characterized by enhanced interfacial density fluctuations. Formation of this interface, which induces polymer folding, is strongly opposed by enthalpy and favored by entropy, similar to the vapor–liquid interface. PMID:17215352

On the polymer physics origins of protein folding thermodynamics.

PubMed

Taylor, Mark P; Paul, Wolfgang; Binder, Kurt

2016-11-07

A remarkable feature of the spontaneous folding of many small proteins is the striking similarity in the thermodynamics of the folding process. This process is characterized by simple two-state thermodynamics with large and compensating changes in entropy and enthalpy and a funnel-like free energy landscape with a free-energy barrier that varies linearly with temperature. One might attribute the commonality of this two-state folding behavior to features particular to these proteins (e.g., chain length, hydrophobic/hydrophilic balance, attributes of the native state) or one might suspect that this similarity in behavior has a more general polymer-physics origin. Here we show that this behavior is also typical for flexible homopolymer chains with sufficiently short range interactions. Two-state behavior arises from the presence of a low entropy ground (folded) state separated from a set of high entropy disordered (unfolded) states by a free energy barrier. This homopolymer model exhibits a funneled free energy landscape that reveals a complex underlying dynamics involving competition between folding and non-folding pathways. Despite the presence of multiple pathways, this simple physics model gives the robust result of two-state thermodynamics for both the cases of folding from a basin of expanded coil states and from a basin of compact globule states.

On the polymer physics origins of protein folding thermodynamics

NASA Astrophysics Data System (ADS)

Taylor, Mark P.; Paul, Wolfgang; Binder, Kurt

2016-11-01

A remarkable feature of the spontaneous folding of many small proteins is the striking similarity in the thermodynamics of the folding process. This process is characterized by simple two-state thermodynamics with large and compensating changes in entropy and enthalpy and a funnel-like free energy landscape with a free-energy barrier that varies linearly with temperature. One might attribute the commonality of this two-state folding behavior to features particular to these proteins (e.g., chain length, hydrophobic/hydrophilic balance, attributes of the native state) or one might suspect that this similarity in behavior has a more general polymer-physics origin. Here we show that this behavior is also typical for flexible homopolymer chains with sufficiently short range interactions. Two-state behavior arises from the presence of a low entropy ground (folded) state separated from a set of high entropy disordered (unfolded) states by a free energy barrier. This homopolymer model exhibits a funneled free energy landscape that reveals a complex underlying dynamics involving competition between folding and non-folding pathways. Despite the presence of multiple pathways, this simple physics model gives the robust result of two-state thermodynamics for both the cases of folding from a basin of expanded coil states and from a basin of compact globule states.

A combined spectroscopic, molecular docking and molecular dynamic simulation study on the interaction of quercetin with β-casein nanoparticles.

PubMed

Mehranfar, Fahimeh; Bordbar, Abdol-Khalegh; Parastar, Hadi

2013-10-05

The interaction of quercetin with β-casein nanoparticle micelle was studied at various temperatures in order to do a complete thermodynamic and molecular analysis on the binding process. The results of fluorescence studies showed the possibility of fluorescence energy transfer between excited tryptophan and quercetin. The determined values of critical transfers distance and the mean distance of ligand from Trp-143 residues in β-casein micelle represents a non-radiative energy transfer mechanism for quenching and the existence of a significant interaction between this flavonoid and β-casein nanoparticle. The equilibrium binding of quercetin with β-casein micelle at different temperatures was studied by using UV-Vis absorption spectroscopy. The chemometric analysis (principal component analysis (PCA) and multivariate curve resolution-alternating least squares (MCR-ALS) methods) on spectrophotometric data revealed the existence of two components in solution (quercetin and β-casein-quercetin complex) and resolved their pure concentration and spectral profiles. This information let us to calculate the equilibrium binding constant at various temperatures and the relevant thermodynamic parameters of interaction (enthalpy, entropy and Gibbs free energy) with low uncertainty. The negative values of entropy and enthalpy changes represent the predominate role of hydrogen binding and van der Waals interactions in the binding process. Docking calculations showed the probable binding site of quercetin is located in the hydrophobic core of β-casein where the quercetin molecule is lined by hydrophobic residues and make five hydrogen bonds and several van der Waals contacts with them. Moreover, molecular dynamic (MD) simulation results suggested that this flavonoid can interact with β-casein, without affecting the secondary structure of β-casein. Simulations, molecular docking and experimental data reciprocally supported each other. Copyright © 2013 Elsevier B.V. All rights reserved.

Lattice dynamical investigation of the Raman and infrared wave numbers and heat capacity properties of the pyrochlores R2Zr2O7 (R = La, Nd, Sm, Eu)

NASA Astrophysics Data System (ADS)

Nandi, S.; Jana, Y. M.; Gupta, H. C.

2018-04-01

A short-range electrostatic forcefield model has been applied for the first time to investigate the Raman and infrared wave numbers in pyrochlore zirconates R2Zr2O7 (R3+ = La, Nd, Sm, Eu). The calculations of phonons involve five stretching and four bending force constants in the Wilson GF matrix method. The calculated phonon wave numbers are in reasonable agreement with the observed spectra in infrared and Raman excitation zones for all of these isomorphous compounds. The contributions of force constants to each mode show a similar trend of variation for all of these compounds. Furthermore, to validate the established forcefield model, we calculated the standard thermodynamic functions, e.g., molar heat capacity, entropy and enthalpy, and compared the results with the previous experimental data for each compound. Using the derived wave numbers for the acoustic and optical modes, the total phonon contribution to the heat capacity was calculated for all these zirconate compounds. The Schottky heat capacity contributions were also calculated for the magnetic compounds, Nd2Zr2O7, Sm2Zr2O7 and Eu2Zr2O7, taking account of crystal-field level schemes of the lanthanide ions. The derived total heat capacity and the integrated values of molar entropy and molar enthalpy showed satisfactory correlations at low temperatures with the experimental results available in the literature for these compounds. At higher temperatures, the discrepancies may be caused by the anharmonic effects of vibrations, phonon dispersion, distribution of phonon density of states, etc.

Modeling the dynamic equilibrium between oligomers of (AlOCH3)n in methylaluminoxane (MAO). A theoretical study based on a combined quantum mechanical and statistical mechanical approach.

PubMed

Zurek, E; Woo, T K; Firman, T K; Ziegler, T

2001-01-15

Density functional theory (DFT) has been used to calculate the energies of 36 different methylaluminoxane (MAO) cage structures with the general formula (MeAlO)n, where n ranges from 4 to 16. A least-squares fit has been used to devise a formula which predicts the total energies of the MAO with different n's giving an rms deviation of 4.70 kcal/mol. These energies in conjunction with frequency calculations based on molecular mechanics have been used to estimate the finite temperature enthalpies, entropies, and free energies for these MAO structures. Furthermore, formulas have been devised which predict finite temperature enthalpies and entropies for MAO structures of any n for a temperature range of 198.15-598.15 K. Using these formulas, the free energies at different temperatures have been predicted for MAO structures where n ranges from 17 to 30. The free energy values were then used to predict the percentage of each n found at a given temperature. Our calculations give an average n value of 18.41, 17.23, 16.89, and 15.72 at 198.15, 298.15, 398.15, and 598.15 K, respectively. Topological arguments have also been used to show that the MAO cage structure contains a limited amount of square faces as compared to octagonal and hexagonal ones. It is also suggested that the limited number of square faces with their strained Al-O bonds explain the high molar Al:catalyst ratio required for activation. Moreover, in this study we outline a general methodology which may be used to calculate the percent abundance of an equilibrium mixture of oligomers with the general formula (X)n.

Spectroscopic and chemical reactivity analysis of D-Myo-Inositol using quantum chemical approach and its experimental verification

NASA Astrophysics Data System (ADS)

Mishra, Devendra P.; Srivastava, Anchal; Shukla, R. K.

2017-07-01

This paper describes the spectroscopic (^1H and ^{13}C NMR, FT-IR and UV-Visible), chemical, nonlinear optical and thermodynamic properties of D-Myo-Inositol using quantum chemical technique and its experimental verification. The structural parameters of the compound are determined from the optimized geometry by B3LYP method with 6 {-}311{+}{+}G(d,p) basis set. It was found that the optimized parameters thus obtained are almost in agreement with the experimental ones. A detailed interpretation of the infrared spectra of D-Myo-Inositol is also reported in the present work. After optimization, the proton and carbon NMR chemical shifts of the studied compound are calculated using GIAO and 6 {-}311{+}{+}G(d,p) basis set. The search of organic materials with improved charge transfer properties requires precise quantum chemical calculations of space-charge density distribution, state and transition dipole moments and HOMO-LUMO states. The nature of the transitions in the observed UV-Visible spectrum of the compound has been studied by the time-dependent density functional theory (TD-DFT). The global reactivity descriptors like chemical potential, electronegativity, hardness, softness and electrophilicity index, have been calculated using DFT. The thermodynamic calculation related to the title compound was also performed at B3LYP/ 6 {-}311{+}{+}G(d,p) level of theory. The standard statistical thermodynamic functions like heat capacity at constant pressure, entropy and enthalpy change were obtained from the theoretical harmonic frequencies of the optimized molecule. It is observed that the values of heat capacity, entropy and enthalpy increase with increase in temperature from 100 to 1000 K, which is attributed to the enhancement of molecular vibration with the increase in temperature.

Transition state characterization for the reversible binding of dihydrogen to bis(2,2'-bipyridine)rhodium(I) from temperature- and pressure-dependent experimental and theoretical studies.

PubMed

Fujita, Etsuko; Brunschwig, Bruce S; Creutz, Carol; Muckerman, James T; Sutin, Norman; Szalda, David; van Eldik, Rudi

2006-02-20

Thermodynamic and kinetic parameters for the oxidative addition of H2 to [Rh(I)(bpy)2]+ (bpy = 2,2'-bipyridine) to form [Rh(III)(H)2(bpy)2]+ were determined from either the UV-vis spectrum of equilibrium mixtures of [Rh(I)(bpy)2]+ and [Rh(III)(H)2(bpy)2]+ or from the observed rates of dihydride formation following visible-light irradiation of solutions containing [Rh(III)(H)2(bpy)2]+ as a function of H2 concentration, temperature, and pressure in acetone and methanol. The activation enthalpy and entropy in methanol are 10.0 kcal mol(-1) and -18 cal mol(-1) K(-1), respectively. The reaction enthalpy and entropy are -10.3 kcal mol(-1) and -19 cal mol(-1) K(-1), respectively. Similar values were obtained in acetone. Surprisingly, the volumes of activation for dihydride formation (-15 and -16 cm(3) mol(-1) in methanol and acetone, respectively) are very close to the overall reaction volumes (-15 cm(3) mol(-1) in both solvents). Thus, the volumes of activation for the reverse reaction, elimination of dihydrogen from the dihydrido complex, are approximately zero. B3LYP hybrid DFT calculations of the transition-state complex in methanol and similar MP2 calculations in the gas phase suggest that the dihydrogen has a short H-H bond (0.823 and 0.810 Angstroms, respectively) and forms only a weak Rh-H bond (1.866 and 1.915 Angstroms, respectively). Equal partial molar volumes of the dihydrogenrhodium(I) transition state and dihydridorhodium(III) can account for the experimental volume profile found for the overall process.

Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses

PubMed Central

Nakayama, Taisuke; Mizohata, Eiichi; Yamashita, Takefumi; Nagatoishi, Satoru; Nakakido, Makoto; Iwanari, Hiroko; Mochizuki, Yasuhiro; Kado, Yuji; Yokota, Yuki; Satoh, Reiko; Tsumoto, Kouhei; Fujitani, Hideaki; Kodama, Tatsuhiko; Hamakubo, Takao; Inoue, Tsuyoshi

2015-01-01

ROBO1, fibronectin Type-III domain (Fn)-containing protein, is a novel immunotherapeutic target for hepatocellular carcinoma in humans. The crystal structure of the antigen-binding fragment (Fab) of B2212A, the monoclonal antibody against the third Fn domain (Fn3) of ROBO1, was determined in pursuit of antibody drug for hepatocellular carcinoma. This effort was conducted in the presence or absence of the antigen, with the chemical features being investigated by determining the affinity of the antibody using molecular dynamics (MD) and thermodynamics. The structural comparison of B2212A Fab between the complex and the free form revealed that the interfacial TyrL50 (superscripts L, H, and F stand for the residues in the light chain, heavy chain, and Fn3, respectively) played important roles in Fn3 recognition. That is, the aromatic ring of TyrL50 pivoted toward PheF68, forming a CH/π interaction and a new hydrogen bond with the carbonyl O atom of PheF68. MD simulations predicted that the TyrL50-PheF68 interaction almost entirely dominated Fab-Fn3 binding, and Ala-substitution of TyrL50 led to a reduced binding of the resultant complex. On the contrary, isothermal titration calorimetry experiments underscored that Ala-substitution of TyrL50 caused an increase of the binding enthalpy between B2212A and Fn3, but importantly, it induced an increase of the binding entropy, resulting in a suppression of loss in the Gibbs free energy in total. These results suggest that mutation analysis considering the binding entropy as well as the binding enthalpy will aid in the development of novel antibody drugs for hepatocellular carcinoma. PMID:25492858

Thermodynamic and structural signatures of water-driven methane-methane attraction in coarse-grained mW water.

PubMed

Song, Bin; Molinero, Valeria

2013-08-07

Hydrophobic interactions are responsible for water-driven processes such as protein folding and self-assembly of biomolecules. Microscopic theories and molecular simulations have been used to study association of a pair of methanes in water, the paradigmatic example of hydrophobic attraction, and determined that entropy is the driving force for the association of the methane pair, while the enthalpy disfavors it. An open question is to which extent coarse-grained water models can still produce correct thermodynamic and structural signatures of hydrophobic interaction. In this work, we investigate the hydrophobic interaction between a methane pair in water at temperatures from 260 to 340 K through molecular dynamics simulations with the coarse-grained monatomic water model mW. We find that the coarse-grained model correctly represents the free energy of association of the methane pair, the temperature dependence of free energy, and the positive change in entropy and enthalpy upon association. We investigate the relationship between thermodynamic signatures and structural order of water through the analysis of the spatial distribution of the density, energy, and tetrahedral order parameter Qt of water. The simulations reveal an enhancement of tetrahedral order in the region between the first and second hydration shells of the methane molecules. The increase in tetrahedral order, however, is far from what would be expected for a clathrate-like or ice-like shell around the solutes. This work shows that the mW water model reproduces the key signatures of hydrophobic interaction without long ranged electrostatics or the need to be re-parameterized for different thermodynamic states. These characteristics, and its hundred-fold increase in efficiency with respect to atomistic models, make mW a promising water model for studying water-driven hydrophobic processes in more complex systems.

Thermodynamic properties of chlorite and berthierine derived from calorimetric measurements

NASA Astrophysics Data System (ADS)

Blanc, Philippe; Gailhanou, Hélène; Rogez, Jacques; Mikaelian, Georges; Kawaji, Hitoshi; Warmont, Fabienne; Gaboreau, Stéphane; Grangeon, Sylvain; Grenèche, Jean-Marc; Vieillard, Philippe; Fialips, Claire I.; Giffaut, Eric; Gaucher, Eric C.; Claret, F.

2014-09-01

In the context of the deep waste disposal, we have investigated the respective stabilities of two iron-bearing clay minerals: berthierine ISGS from Illinois [USA; (Al0.975FeIII0.182FeII1.422Mg0.157Li0.035Mn0.002)(Si1.332Al0.668)O5(OH)4] and chlorite CCa-2 from Flagstaff Hill, California [USA; (Si2.633Al1.367)(Al1.116FeIII0.215Mg2.952FeII1.712Mn0.012Ca0.011)O10(OH)8]. For berthierine, the complete thermodynamic dataset was determined at 1 bar and from 2 to 310 K, using calorimetric methods. The standard enthalpies of formation were obtained by solution-reaction calorimetry at 298.15 K, and the heat capacities were measured by heat-pulse calorimetry. For chlorite, the standard enthalpy of formation is measured by solution-reaction calorimetry at 298.15 K. This is completing the entropy and heat capacity obtained previously by Gailhanou et al. (Geochim Cosmochim Acta 73:4738-4749, 2009) between 2 and 520 K, by using low-temperature adiabatic calorimetry and differential scanning calorimetry. For both minerals, the standard entropies and the Gibbs free energies of formation at 298.15 K were then calculated. An assessment of the measured properties could be carried out with respect to literature data. Eventually, the thermodynamic dataset allowed realizing theoretical calculations concerning the berthierine to chlorite transition. The latter showed that, from a thermodynamic viewpoint, the main factor controlling this transition is probably the composition of the berthierine and chlorite minerals and the nature of the secondary minerals rather than temperature.

Intrinsic thermodynamics of ethoxzolamide inhibitor binding to human carbonic anhydrase XIII

PubMed Central

2012-01-01

Background Human carbonic anhydrases (CAs) play crucial role in various physiological processes including carbon dioxide and hydrocarbon transport, acid homeostasis, biosynthetic reactions, and various pathological processes, especially tumor progression. Therefore, CAs are interesting targets for pharmaceutical research. The structure-activity relationships (SAR) of designed inhibitors require detailed thermodynamic and structural characterization of the binding reaction. Unfortunately, most publications list only the observed thermodynamic parameters that are significantly different from the intrinsic parameters. However, only intrinsic parameters could be used in the rational design and SAR of the novel compounds. Results Intrinsic binding parameters for several inhibitors, including ethoxzolamide, trifluoromethanesulfonamide, and acetazolamide, binding to recombinant human CA XIII isozyme were determined. The parameters were the intrinsic Gibbs free energy, enthalpy, entropy, and the heat capacity. They were determined by titration calorimetry and thermal shift assay in a wide pH and temperature range to dissect all linked protonation reaction contributions. Conclusions Precise determination of the inhibitor binding thermodynamics enabled correct intrinsic affinity and enthalpy ranking of the compounds and provided the means for SAR analysis of other rationally designed CA inhibitors. PMID:22676044

A comparative study on the B12N12, Al12N12, B12P12 and Al12P12 fullerene-like cages.

PubMed

Beheshtian, Javad; Bagheri, Zargham; Kamfiroozi, Mohammad; Ahmadi, Ali

2012-06-01

The stability, geometry and electronic structure of the title nanoclusters were compared by using density functional theory (DFT) calculations. Their electrical property analysis showed that the relative magnitude of the HOMO-LUMO gaps (eV) that are average values from the calculated results with five different DFT functionals is as follows: B12N12(7:02)>Al12N12(4.09)>B12P12(3.80)>Al12P12(3.39). Computing the standard enthalpy and the Gibbs free energy of formation, it was found that the B(12)N(12) structure is thermodynamically stable at 298 K and 1 atmosphere of pressure, while the Al(12)N(12) structure may be stable at low temperatures. Due to positive values of change of enthalpy and entropy of formation for both the B(12)P(12) and Al(12)P(12) clusters, it seems that their formation from the consisting atoms is not spontaneous at any temperature.

The Influence of Concentration and Temperature on the Formation of γ-Oryzanol + β-Sitosterol Tubules in Edible Oil Organogels

PubMed Central

Venema, Paul; Bot, Arjen; Flöter, Eckhard; van der Linden, Erik

2010-01-01

The gelation process of mixtures of γ-oryzanol and sitosterol structurants in sunflower oil was studied using light scattering, rheology, and micro-scanning calorimetry (Micro-DSC). The relation between temperature and the critical aggregation concentration (CAC) of tubule formation of γ-oryzanol and sitosterol was determined using these techniques. The temperature dependence of the CAC was used to estimate the binding energy and enthalpic and entropic contribution to the tubular formation process. The binding energy calculated at the corresponding temperatures and CACs were relatively low, in order of 2 RT (4.5 kJ mol−1), which is in accord with the reversibility of the tubular formation process. The formation of the tubules was associated with negative (exothermic) enthalpy change (ΔH0) compared with positive entropy term (−T ΔS0 >0), indicating that the aggregation into tubules is an enthalpy-driven process. The oryzanol–sitosterol ratio affected the aggregation process; solutions with ratio of (60 oryzanol–40 sitosterol) started aggregation at higher temperature compared with other ratios. PMID:21423326

The Influence of Concentration and Temperature on the Formation of γ-Oryzanol + β-Sitosterol Tubules in Edible Oil Organogels.

PubMed

Sawalha, Hassan; Venema, Paul; Bot, Arjen; Flöter, Eckhard; van der Linden, Erik

2011-03-01

The gelation process of mixtures of γ-oryzanol and sitosterol structurants in sunflower oil was studied using light scattering, rheology, and micro-scanning calorimetry (Micro-DSC). The relation between temperature and the critical aggregation concentration (CAC) of tubule formation of γ-oryzanol and sitosterol was determined using these techniques. The temperature dependence of the CAC was used to estimate the binding energy and enthalpic and entropic contribution to the tubular formation process. The binding energy calculated at the corresponding temperatures and CACs were relatively low, in order of 2 RT (4.5 kJ mol(-1)), which is in accord with the reversibility of the tubular formation process. The formation of the tubules was associated with negative (exothermic) enthalpy change (ΔH(0)) compared with positive entropy term (-T ΔS(0) >0), indicating that the aggregation into tubules is an enthalpy-driven process. The oryzanol-sitosterol ratio affected the aggregation process; solutions with ratio of (60 oryzanol-40 sitosterol) started aggregation at higher temperature compared with other ratios.

Moisture Sorption and Thermodynamic Properties of Vacuum-Dried Capsosiphon fulvescens Powder

PubMed Central

Zuo, Li; Rhim, Jong-Whan; Lee, Jun Ho

2015-01-01

The moisture sorption isotherms of vacuum-dried edible green alga (Capsosiphon fulvescens) powders were determined at 25, 35, and 45°C and water activity (aw) in the range of 0.11~0.94. An inversion effect of temperature was found at high water activity (>0.75). Various mathematical models were fitted to the experimental data, and Brunauer, Emmett, and Teller model was found to be the most suitable model describing the relationship between equilibrium moisture content and water activity (<0.45). Henderson model could also provide excellent agreement between the experimental and predicted values despite of the intersection point. Net isosteric heat of adsorption decreased from 15.77 to 9.08 kJ/mol with an increase in equilibrium moisture content from 0.055 to 0.090 kg H2O/kg solids. The isokinetic temperature (Tβ) was 434.79 K, at which all the adsorption reactions took place at the same rate. The enthalpy-entropy compensation suggested that the mechanism of the adsorption process was shown to be enthalpy-driven. PMID:26451360

Spectroscopic Study of the Binding of Netropsin and Hoechst 33258 to Nucleic Acids

NASA Astrophysics Data System (ADS)

Vardevanyan, P. O.; Parsadanyan, M. A.; Antonyan, A. P.; Sahakyan, V. G.

2018-05-01

The interaction of groove binding compounds — peptide antibiotic (polyamide) netropsin and fluorescent dye (bisbenzimidazole) Hoechst 33258 — with the double-stranded DNA and synthetic double-stranded polynucleotide poly(rA)-poly(rU) has been studied by spectrophotometry. Absorption spectra of these ligand complexes with nucleic acids have been obtained. Spectral changes at the complexation of individual ligands with the mentioned nucleic acids reveal the similarity of binding of each of these ligands with both DNA and RNA. Based on the spectroscopic measurements, the binding parameters of netropsin and Hoechst 33258 binding to DNA and poly(rA)-poly(rU) - K and n, as well as the thermodynamic parameters ΔS, ΔG, and ΔH have been determined. It was found that the binding of Hoechst 33258 to both nucleic acids is accompanied by a positive change in enthalpy, while in the case of netropsin the change in enthalpy is negative. Moreover, the contribution of entropy to the formation of the complexes is more pronounced in the case of Hoechst 33258.

Thermodynamic and structure-property study of liquid-vapor equilibrium for aroma compounds.

PubMed

Tromelin, Anne; Andriot, Isabelle; Kopjar, Mirela; Guichard, Elisabeth

2010-04-14

Thermodynamic parameters (T, DeltaH degrees , DeltaS degrees , K) were collected from the literature and/or calculated for five esters, four ketones, two aldehydes, and three alcohols, pure compounds and compounds in aqueous solution. Examination of correlations between these parameters and the range values of DeltaH degrees and DeltaS degrees puts forward the key roles of enthalpy for vaporization of pure compounds and of entropy in liquid-vapor equilibrium of compounds in aqueous solution. A structure-property relationship (SPR) study was performed using molecular descriptors on aroma compounds to better understand their vaporization behavior. In addition to the role of polarity for vapor-liquid equilibrium of compounds in aqueous solution, the structure-property study points out the role of chain length and branching, illustrated by the correlation between the connectivity index CHI-V-1 and the difference between T and log K for vaporization of pure compounds and compounds in aqueous solution. Moreover, examination of the esters' enthalpy values allowed a probable conformation adopted by ethyl octanoate in aqueous solution to be proposed.

Elastic properties, thermal stability, and thermodynamic parameters of MoAlB

NASA Astrophysics Data System (ADS)

Kota, Sankalp; Agne, Matthias; Zapata-Solvas, Eugenio; Dezellus, Olivier; Lopez, Diego; Gardiola, Bruno; Radovic, Miladin; Barsoum, Michel W.

2017-04-01

MoAlB is the first and, so far, the only transition-metal boride that forms alumina when heated in air and is thus potentially useful for high-temperature applications. Herein, the thermal stability in argon and vacuum atmospheres and the thermodynamic parameters of bulk polycrystalline MoAlB were investigated experimentally. At temperatures above 1708 K, in vacuum and inert atmospheres, this compound incongruently melts into the binary MoB and liquid aluminum metal as confirmed by differential thermal analysis, quenching experiments, x-ray diffraction, and scanning electron microscopy. Making use of that information together with heat-capacity measurements in the 4-1000-K temperature range—successfully modeled as the sum of lattice, electronic, and dilation contributions—the standard enthalpy, entropy, and free energy of formation are computed and reported for the full temperature range. The standard enthalpy of formation of MoAlB at 298 K was found to be -132 ±3.2 kJ/mol. Lastly, the thermal conductivity values are computed and modeled using a variation of the Slack model in the 300-1600-K temperature range.

First-principles theoretical assessment of catalysis by confinement: NO-O2 reactions within voids of molecular dimensions in siliceous crystalline frameworks.

PubMed

Maestri, Matteo; Iglesia, Enrique

2018-06-01

Density functional theory methods that include dispersive forces are used to show how voids of molecular dimensions enhance reaction rates by the mere confinement of transition states analogous to those involved in homogeneous routes and without requiring specific binding sites or structural defects within confining voids. These van der Waals interactions account for the observed large rate enhancements for NO oxidation in the presence of purely siliceous crystalline frameworks. The minimum free energy paths for NO oxidation within chabazite (CHA) and silicalite (SIL) frameworks involve intermediates similar in stoichiometry, geometry, and kinetic relevance to those involved in the homogeneous route. The termolecular transition state for the kinetically-relevant cis-NOO2NO isomerization to trans-NOO2NO is strongly stabilized by confinement within CHA (by 36.3 kJ mol-1 in enthalpy) and SIL (by 39.2 kJ mol-1); such enthalpic stabilization is compensated, in part, by concomitant entropy losses brought forth by confinement (CHA: 44.9; SIL: 45.3, J mol-1 K-1 at 298 K). These enthalpy and entropy changes upon confinement agree well with those measured and combine to significantly decrease activation free energies and are consistent with the rate enhancements that become larger as temperature decreases because of the more negative apparent activation energies in confined systems compared with homogeneous routes. Calculated free energies of confinement are in quantitative agreement with measured rate enhancements and with their temperature sensitivity. Such quantitative agreements reflect preeminent effects of geometry in determining the van der Waals contributions from contacts between the transition states (TS) and the confining walls and the weak effects of the level of theory on TS geometries. NO oxidation reactions are chosen here to illustrate these remarkable effects of confinement because detailed kinetic analysis of rate data are available, but also because of their critical role in the treatment of combustion effluents and in the synthesis of nitric acid and nitrates. Similar effects are evident from rate enhancements by confinement observed for Diels-Alder and alkyne oligomerization reactions. These reactions also occur in gaseous media at near ambient temperatures, for which enthalpic stabilization upon confinement of their homogeneous transition states becomes the preeminent component of activation free energies.

Evolutionary dynamics of enzymes.

PubMed

Demetrius, L

1995-08-01

This paper codifies and rationalizes the large diversity in reaction rates and substrate specificity of enzymes in terms of a model which postulates that the kinetic properties of present-day enzymes are the consequence of the evolutionary force of mutation and selection acting on a class of primordial enzymes with poor catalytic activity and broad substrate specificity. Enzymes are classified in terms of their thermodynamic parameters, activation enthalpy delta H* and activation entropy delta S*, in their kinetically significant transition states as follows: type 1, delta H* > 0, delta S* < 0; type 2, delta H* < or = 0, delta S* < or = 0; type 3, delta H* > 0, delta S* > 0. We study the evolutionary dynamics of these three classes of enzymes subject to mutation, which acts at the level of the gene which codes for the enzyme and selection, which acts on the organism that contains the enzyme. Our model predicts the following evolutionary trends in the reaction rate and binding specificity for the three classes of molecules. In type 1 enzymes, evolution results in random, non-directional changes in the reaction rate and binding specificity. In type 2 and 3 enzymes, evolution results in a unidirectional increase in both the reaction rate and binding specificity. We exploit these results in order to codify the diversity in functional properties of present-day enzymes. Type 1 molecules will be described by intermediate reaction rates and broad substrate specificity. Type 2 enzymes will be characterized by diffusion-controlled rates and absolute substrate specificity. The type 3 catalysts can be further subdivided in terms of their activation enthalpy into two classes: type 3a (delta H* small) and type 3b (delta H* large). We show that type 3a will be represented by the same functional properties that identify type 2, namely, diffusion-controlled rates and absolute substrate specificity, whereas type 3b will be characterized by non-diffusion-controlled rates and absolute substrate specificity. We infer from this depiction of the three classes of enzymes, a general relation between the two functional properties, reaction rate and substrate specificity, namely, enzymes with diffusion-controlled rates have absolute substrate specificity. By appealing to energetic considerations, we furthermore show that enzymes with diffusion-controlled rates (types 2 and 3a) form a small subset of the class of all enzymes. This codification of present-day enzymes derived from an evolutionary model, essentially relates the structural properties of enzymes, as described by their thermodynamic parameters, to their functional properties, as represented by the reaction rate and substrate specificity.

Extended Subadiabatic Layer in Simulations of Overshooting Convection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Käpylä, Petri J.; Arlt, Rainer; Rheinhardt, Matthias

2017-08-20

We present numerical simulations of hydrodynamic overshooting convection in local Cartesian domains. We find that a substantial fraction of the lower part of the convection zone (CZ) is stably stratified according to the Schwarzschild criterion while the enthalpy flux is outward directed. This occurs when the heat conduction profile at the bottom of the CZ is smoothly varying, based either on a Kramers-like opacity prescription as a function of temperature and density or a static profile of a similar shape. We show that the subadiabatic layer arises due to nonlocal energy transport by buoyantly driven downflows in the upper partsmore » of the CZ. Analysis of the force balance of the upflows and downflows confirms that convection is driven by cooling at the surface. We find that the commonly used prescription for the convective enthalpy flux being proportional to the negative entropy gradient does not hold in the stably stratified layers where the flux is positive. We demonstrate the existence of a non-gradient contribution to the enthalpy flux, which is estimated to be important throughout the convective layer. A quantitative analysis of downflows indicates a transition from a tree-like structure where smaller downdrafts merge into larger ones in the upper parts to a structure in the deeper parts where a height-independent number of strong downdrafts persist. This change of flow topology occurs when a substantial subadiabatic layer is present in the lower part of the CZ.« less

The Superorbital Expansion Tube concept, experiment and analysis

NASA Technical Reports Server (NTRS)

Neely, A. J.; Morgan, R. G.

1995-01-01

In response to the need for ground testing facilities for super orbital re-entry research, a small scale facility has been set up at the University of Queensland to demonstrate the superorbital expansion tube concept. This unique device is a free piston driven, triple diaphragm, impulse shock facility which uses the enthalpy multiplication mechanism of the unsteady expansion process and the addition of a secondary shock driver to further heat the driver gas. The pilot facility has been operated to produce quasi-steady test flows in air with shock velocities in excess of 13 km/s and with a usable test flow duration of the order of 15 micro sec. an experimental condition produced in the facility with total enthalpy of 108 MJ/kg and a total pressure of 335 MPa is reported. A simple analytical flow model which accounts for non-ideal rupture of the light tertiary diaphragm and the resulting entropy increase in the test gas is discussed. It is shown that equilibrium calculations more accurately model the unsteady expansion process than calculations assuming frozen chemistry. This is because the high enthalpy flows produced in the facility can only be achieved if the chemical energy stored in the test flow during shock heating of the test gas is partially returned to the flow during the process of unsteady expansion. Measurements of heat transfer rates to a flat plate demonstrate the usability of test flow for aerothermodynamic testing and comparison of these rates with empirical calculations confirms the usable accuracy of the flow model.

Kinetics of degradation of enalapril maleate in dosage forms.

PubMed

Stanisz, Beata

2004-01-01

The effect of humidity and temperature on the stability of enalapril maleate (ENA) in tablets have been studied. Tablets with ENA were stored in final packs (blisters) and without final packs in the atmosphere of increased humidity (76.4 % RH) and in the temperature range from 313 K to 333 K (forced degradation test). Degradation of ENA in tablets stored in final packs and without final packs followed the first order reaction model. During this study, the product of hydrolysis of the ester group and intramolecular cyclization have been observed. Thermodynamic parameters (activation energies, enthalpy and entropy) for the decomposition of ENA in tablets were calculated.

Mollier-I, S-Diagrams for Combustion Gases in Data Processing

NASA Technical Reports Server (NTRS)

Zacharias, F.

1982-01-01

In order to have all the thermal and caloric states of combustion gases accessible in a computer, closed mathematical approximation equations were established for the real factors, the enthalpy and the entropy of a real combustion gas. The equations approximate the various effects of molecular forces real gas influence and dissociation - at temperatures of 200 K to 6,000 K, pressures of 0.001 to 1,000 bar, and in the range from stoichiometric composition to air. A system of subprograms is listed in FORTRAN, by means of which thermodynamic calculations can be carried out in the same manner as with Mollier I,S diagrams.

Methods for thermodynamic evaluation of battery state of health

DOEpatents

Yazami, Rachid; McMenamin, Joseph; Reynier, Yvan; Fultz, Brent T

2013-05-21

Described are systems and methods for accurately characterizing thermodynamic and materials properties of electrodes and battery systems and for characterizing the state of health of electrodes and battery systems. Measurement of physical attributes of electrodes and batteries corresponding to thermodynamically stabilized electrode conditions permit determination of thermodynamic parameters, including state functions such as the Gibbs free energy, enthalpy and entropy of electrode/electrochemical cell reactions, that enable prediction of important performance attributes of electrode materials and battery systems, such as energy, power density, current rate, cycle life and state of health. Also provided are systems and methods for charging a battery according to its state of health.

Methods and systems for thermodynamic evaluation of battery state of health

DOEpatents

Yazami, Rachid; McMenamin, Joseph; Reynier, Yvan; Fultz, Brent T

2014-12-02

Described are systems and methods for accurately characterizing thermodynamic and materials properties of electrodes and battery systems and for characterizing the state of health of electrodes and battery systems. Measurement of physical attributes of electrodes and batteries corresponding to thermodynamically stabilized electrode conditions permit determination of thermodynamic parameters, including state functions such as the Gibbs free energy, enthalpy and entropy of electrode/electrochemical cell reactions, that enable prediction of important performance attributes of electrode materials and battery systems, such as energy, power density, current rate, cycle life and state of health. Also provided are systems and methods for charging a battery according to its state of health.

The application of the thermodynamic perturbation theory to study the hydrophobic hydration

PubMed Central

Mohorič, Tomaž; Urbic, Tomaz; Hribar-Lee, Barbara

2013-01-01

The thermodynamic perturbation theory was tested against newly obtained Monte Carlo computer simulations to describe the major features of the hydrophobic effect in a simple 3D-Mercedes-Benz water model: the temperature and hydrophobe size dependence on entropy, enthalpy, and free energy of transfer of a simple hydrophobic solute into water. An excellent agreement was obtained between the theoretical and simulation results. Further, the thermodynamic perturbation theory qualitatively correctly (with respect to the experimental data) describes the solvation thermodynamics under conditions where the simulation results are difficult to obtain with good enough accuracy, e.g., at high pressures. PMID:23862923

Optimization of binary thermodynamic and phase diagram data

NASA Astrophysics Data System (ADS)

Bale, Christopher W.; Pelton, A. D.

1983-03-01

An optimization technique based upon least squares regression is presented to permit the simultaneous analysis of diverse experimental binary thermodynamic and phase diagram data. Coefficients of polynomial expansions for the enthalpy and excess entropy of binary solutions are obtained which can subsequently be used to calculate the thermodynamic properties or the phase diagram. In an interactive computer-assisted analysis employing this technique, one can critically analyze a large number of diverse data in a binary system rapidly, in a manner which is fully self-consistent thermodynamically. Examples of applications to the Bi-Zn, Cd-Pb, PbCl2-KCl, LiCl-FeCl2, and Au-Ni binary systems are given.

Thermodynamic characteristics of the interaction between nicotinic acid and phenylalanine in an aqueous buffer solution at 298 K

NASA Astrophysics Data System (ADS)

Badelin, V. G.; Tyunina, E. Yu.; Mezhevoi, I. N.; Tarasova, G. N.

2013-08-01

The interaction between L-phenylalanine and nicotinic acid is studied by solution calorimetry in an aqueous buffer solution (pH 7.35) at different ratios of the reagents. Experimental data on the enthalpy of dissolution of amino acid in the buffer solution of nicotinic acid at 298.15 K are calculated. The values of thermodynamic parameters for the complexation of L-phenylalanine with nicotinic acid are calculated. It is shown that the formation of a 1: 2 molecular complex is stabilized by the entropy factor due to the dominant role of the dehydration effect of initial reagents.

The solubility of hydrogen in rhodium, ruthenium, iridium and nickel.

NASA Technical Reports Server (NTRS)

Mclellan, R. B.; Oates, W. A.

1973-01-01

The temperature variation of the solubility of hydrogen in rhodium, ruthenium, iridium, and nickel in equilibrium with H2 gas at 1 atm pressure has been measured by a technique involving saturating the solvent metal with hydrogen, quenching, and analyzing in resultant solid solutions. The solubilities determined are small (atom fraction of H is in the range from 0.0005 to 0.00001, and the results are consistent with the simple quasi-regular model for dilute interstitial solid solutions. The relative partial enthalpy and excess entropy of the dissolved hydrogen atoms have been calculated from the solubility data and compared with well-known correlations between these quantities.

Table and charts of equilibrium normal shock and shock tube properties for pure argon with velocities to 18 km/sec

NASA Technical Reports Server (NTRS)

Miller, C. G., III; Wilder, S. E.

1976-01-01

Equilibrium thermodynamic and flow properties are presented in tabulated and graphical form for moving, standing, and reflected normal shock waves in pure argon. Properties include pressure, temperature, density, enthalpy, speed of sound, entropy, molecular-weight ratio, isentropic exponent, velocity, and species mole fractions. Incident (moving) shock velocities are varied from 2 to 18 km/sec for a range of initial pressure of 5 N/sq m to 500 kN/sq m. Working charts illustrating shock tube performance with argon test gas and heated helium and hydrogen driver gases are also presented.

Thermodynamic parameters for adsorption equilibrium of heavy metals and dyes from wastewaters.

PubMed

Liu, Xiang; Lee, Duu-Jong

2014-05-01

This meta-analysis evaluates adsorption studies that report thermodynamic parameters for heavy metals and dyes from wastewaters. The adsorbents were derived from agricultural waste, industrial wastes, inorganic particulates, or some natural products. The adsorption mechanisms, derivation of thermodynamic relationships, and possible flaws made in such evaluation are discussed. This analysis shows that conclusions from the examined standard enthalpy and entropy changes are highly contestable. The reason for this flaw may be the poor physical structure of adsorbents tested, such that pore transport controlled the solute flux, leaving a surface reaction process near equilibrium. Copyright © 2013 Elsevier Ltd. All rights reserved.

Thermochemistry of the specific binding of C12 surfactants to bovine serum albumin.

PubMed

Nielsen, A D; Borch, K; Westh, P

2000-06-15

The specific binding to bovine serum albumin (BSA) of anionic and non-ionic surfactants with C12 acyl chains has been studied by high sensitivity isothermal titration calorimetry. This method proved particularly effective in resolving the binding of anionic surfactants into separate classes of sites with different affinity. For sodium dodecylsulfate (SDS) the measured binding curves could be rationalized as association to two classes (high affinity/low affinity) of sites comprising, respectively, three and six similar (i.e. thermodynamically equivalent), independent sites. Changes in the thermodynamic functions enthalpy, standard free energy, standard entropy and heat capacity could be discerned for each class of binding site, as well as for micelle formation. These data suggest that binding to low affinity sites (in analogy with micelle formation) exhibits energetic parameters; in particular, a large negative change in heat capacity, which is characteristic of hydrophobic interactions. The thermodynamics of high affinity binding, on the other hand, is indicative of other dominant forces; most likely electrostatic interactions. Other anionic ligands investigated (laurate and dodecyl benzylsulfonate) showed a behavior similar to SDS, the most significant difference being the high affinity binding of the alkylbenzyl sulfonate. For this ligand, the thermodynamic data is indicative of a more loosely associated complex than for SDS and laurate. BSA was found to bind one or two of the non-ionic surfactants (NIS) hepta- or penta(ethylene glycol) monododecyl ether (C12EO7 and C12EO5) with binding constants about three orders of magnitude lower than for SDS. Hence, the free energy of the surfactant in the weakly bound BSA-NIS complex is only slightly favored over the micellar state. The binding process is characterized by very large exothermic enthalpy changes (larger than for the charged surfactants) and a large, positive increment in heat capacity. These observations cannot be reconciled with a molecular picture based on simple hydrophobic condensation onto non-polar patches on the protein surface.

Physicochemical studies of mixed surfactant microemulsions with isopropyl myristate as oil.

PubMed

Bardhan, Soumik; Kundu, Kaushik; Saha, Swapan K; Paul, Bidyut K

2013-07-15

The present study is focused on evaluation of interfacial compositions and thermodynamic properties of w/o mixed surfactant [(sodium dodecylsulfate, SDS/polyoxyethylene (23) lauryl ether, Brij-35)/1-pentanol (Pn)/isopropyl myristate (IPM)] microemulsions under various physicochemical conditions by the dilution method. The number of moles of Pn at the interface (n(a)(i)) and bulk oil (n(a)(o)), and various thermodynamic parameters [viz. standard Gibbs free energy (ΔG(o→i)(0)), standard enthalpy (ΔH(o→i)(0)), and standard entropy (ΔS(o→i)(0)) of the transfer of Pn from bulk oil to the interface] have been found to be dependent on the molar ratio of water to surfactant (ω), concentration of Brij-35 (X(Brij-35)), and temperature. Temperature-insensitive microemulsions with zero specific heat capacity (ΔC(p)(0))(o→i) have been formed at specific compositions. The intrinsic enthalpy change of the transfer process (ΔH(0))(o→i)* has been evaluated from linear correlation between ΔH(o→i)(0) and ΔS(o→i)(0) at different experimental temperatures. The present report also aims at a precise characterization on the basis of molecular interactions between the constituents and provides insight into the nature of the oil/water interfaces of these systems by conductivity and dynamic light scattering studies as a function of ω and X(Brij-35). Conductivity studies reveal that incorporation of Brij-35 in non-percolating water/SDS/Pn/IPM systems makes them favorable for ω-induced percolation behavior up to X(Brij-35) ≤ 0.5. But further addition of Brij-35 causes a decrease in conductivity with increasing ω. Furthermore, the hydrodynamic diameters of the microemulsion droplets increase with increase in both X(Brij-35) and ω. Correlations of the results in terms of the evaluated physicochemical parameters have been attempted. Copyright © 2013 Elsevier Inc. All rights reserved.

DNA entropy reveals a significant difference in complexity between housekeeping and tissue specific gene promoters.

PubMed

Thomas, David; Finan, Chris; Newport, Melanie J; Jones, Susan

2015-10-01

The complexity of DNA can be quantified using estimates of entropy. Variation in DNA complexity is expected between the promoters of genes with different transcriptional mechanisms; namely housekeeping (HK) and tissue specific (TS). The former are transcribed constitutively to maintain general cellular functions, and the latter are transcribed in restricted tissue and cells types for specific molecular events. It is known that promoter features in the human genome are related to tissue specificity, but this has been difficult to quantify on a genomic scale. If entropy effectively quantifies DNA complexity, calculating the entropies of HK and TS gene promoters as profiles may reveal significant differences. Entropy profiles were calculated for a total dataset of 12,003 human gene promoters and for 501 housekeeping (HK) and 587 tissue specific (TS) human gene promoters. The mean profiles show the TS promoters have a significantly lower entropy (p<2.2e-16) than HK gene promoters. The entropy distributions for the 3 datasets show that promoter entropies could be used to identify novel HK genes. Functional features comprise DNA sequence patterns that are non-random and hence they have lower entropies. The lower entropy of TS gene promoters can be explained by a higher density of positive and negative regulatory elements, required for genes with complex spatial and temporary expression. Copyright © 2015 Elsevier Ltd. All rights reserved.

Facing the challenge of predicting the standard formation enthalpies of n-butyl-phosphate species with ab initio methods

NASA Astrophysics Data System (ADS)

Saab, Mohamad; Réal, Florent; Šulka, Martin; Cantrel, Laurent; Virot, François; Vallet, Valérie

2017-06-01

Tributyl-phosphate (TBP), a ligand used in the PUREX liquid-liquid separation process of spent nuclear fuel, can form an explosive mixture in contact with nitric acid that might lead to a violent explosive thermal runaway. In the context of safety of a nuclear reprocessing plant facility, it is crucial to predict the stability of TBP at elevated temperatures. So far, only the enthalpies of formation of TBP are available in the literature with rather large uncertainties, while those of its degradation products, di-(HDBP) and mono-(H2MBP), are unknown. In this goal, we have used state-of-the art quantum chemical methods to compute the formation enthalpies and entropies of TBP and its degradation products di-(HDBP) and mono-(H2MBP) in gas and liquid phases. Comparisons of levels of quantum chemical theory revealed that there are significant effects of correlation on their electronic structures, pushing for the need of not only high level of electronic correlation treatment, namely, local coupled cluster with single and double excitation operators and perturbative treatment of triple excitations, but also extrapolations to the complete basis to produce reliable and accurate thermodynamics data. Solvation enthalpies were computed with the conductor-like screening model for real solvents [COSMO-RS], for which we observe errors not exceeding 22 kJ mol-1. We thus propose with final uncertainty of about 20 kJ mol-1 standard enthalpies of formation of TBP, HDBP, and H2MBP which amounts to -1281.7 ± 24.4, -1229.4 ± 19.6, and -1176.7 ± 14.8 kJ mol-1, respectively, in the gas phase. In the liquid phase, the predicted values are -1367.3 ± 24.4, -1348.7 ± 19.6, and -1323.8± 14.8 kJ mol-1, to which we may add about -22 kJ mol-1 error from the COSMO-RS solvent model. From these data, the complete hydrolysis of TBP is predicted as an exothermic phenomena but showing a slightly endergonic process.

Application of an enthalpy balance model of the relation between growth and respiration to temperature acclimation of Eucalyptus globulus seedlings.

PubMed Central

Macfarlane, Craig; Adams, Mark A; Hansen, Lee D

2002-01-01

The enthalpy balance model of growth uses measurements of the rates of heat and CO(2) production to quantify rates of decarboxylation, oxidative phosphorylation and net anabolism. Enthalpy conversion efficiency (eta(H)) and the net rate of conservation of enthalpy in reduced biosynthetic products (R(SG)DeltaH(B)) can be calculated from metabolic heat rate (q) and CO(2) rate (R(CO2)). eta(H) is closely related to carbon conversion efficiency and the efficiency of conservation of available electrons in biosynthetic products. R(SG)DeltaH(B) and eta(H) can be used, together with biomass composition, to describe the rate and efficiency of growth of plant tissues. q is directly related to the rate of O(2) consumption and the ratio q:R(CO2) is inversely related to the respiratory quotient. We grew seedlings of Eucalyptus globulus at 16 and 28 degrees C for four to six weeks, then measured q and R(CO2) using isothermal calorimetry. Respiratory rate at a given temperature was increased by a lower growth temperature but eta(H) was unaffected. Enthalpy conversion efficiency - and, therefore, carbon conversion efficiency - decreased with increasing temperature from 15 to 35 degrees C. The ratio of oxidative phosphorylation to oxygen consumption (P/O ratio) was inferred in vivo from eta(H) and by assuming a constant ratio of growth to maintenance respiration with changing temperature. The P/O ratio decreased from 2.1 at 10-15 degrees C to less than 0.3 at 35 degrees C, suggesting that decreased efficiency was not only due to activity of the alternative oxidase pathway. In agreement with predictions from non-equilibrium thermodynamics, growth rate was maximal near 25 degrees C, where the calculated P/O ratio was about half maximum. We propose that less efficient pathways, such as the alternative oxidase pathway, are necessary to satisfy the condition of conductance matching whilst maintaining a near constant phosphorylation potential. These conditions minimize entropy production and maximize the efficiency of mitochondrial energy conversions as growing conditions change, while maintaining adequate finite rates of energy processing. PMID:12137581

Measurement of the aerothermodynamic state in a high enthalpy plasma wind-tunnel flow

NASA Astrophysics Data System (ADS)

Hermann, Tobias; Löhle, Stefan; Zander, Fabian; Fasoulas, Stefanos

2017-11-01

This paper presents spatially resolved measurements of absolute particle densities of N2, N2+, N, O, N+ , O+ , e- and excitation temperatures of electronic, rotational and vibrational modes of an air plasma free stream. All results are based on optical emission spectroscopy data. The measured parameters are combined to determine the local mass-specific enthalpy of the free stream. The analysis of the radiative transport, relative and absolute intensities, and spectral shape is used to determine various thermochemical parameters. The model uncertainty of each analysis method is assessed. The plasma flow is shown to be close to equilibrium. The strongest deviations from equilibrium occur for N, N+ and N2+ number densities in the free stream. Additional measurements of the local mass-specific enthalpy are conducted using a mass injection probe as well as a heat flux and total pressure probe. The agreement between all methods of enthalpy determination is good.

Estimation and application of the thermodynamic properties of aqueous phenanthrene and isomers of methylphenanthrene at high temperature

NASA Astrophysics Data System (ADS)

Dick, Jeffrey M.; Evans, Katy A.; Holman, Alex I.; Jaraula, Caroline M. B.; Grice, Kliti

2013-12-01

Estimates of standard molal Gibbs energy (ΔGf°) and enthalpy (ΔHf°) of formation, entropy (S°), heat capacity (CP°) and volume (V°) at 25 °C and 1 bar of aqueous phenanthrene (P) and 1-, 2-, 3-, 4- and 9-methylphenanthrene (1-MP, 2-MP, 3-MP, 4-MP, 9-MP) were made by combining reported standard-state properties of the crystalline compounds, solubilities and enthalpies of phenanthrene and 1-MP, and relative Gibbs energies, enthalpies and entropies of aqueous MP isomers from published quantum chemical simulations. The calculated properties are consistent with greater stabilities of the β isomers (2-MP and 3-MP) relative to the α isomers (1-MP and 9-MP) at 25 °C. However, the metastable equilibrium values of the abundance ratios 2-MP/1-MP (MPR) and (2-MP + 3-MP)/(1-MP + 9-MP) (MPI-3) decrease with temperature, becoming <1 at ∼375-455 °C. The thermodynamic model is consistent with observations of reversals of these organic maturity parameters at high temperature in hydrothermal and metamorphic settings. Application of the model to data reported for the Paleoproterozoic Here’s Your Chance (HYC) Pb-Zn-Ag ore deposit (McArthur River, Northern Territory, Australia) indicates a likely effect of high-temperature equilibration on reported values of MPR and MPI-3, but this finding is contingent on the location within the deposit. If metastable equilibrium holds, a third aromatic maturity ratio, 1.5 × (2-MP + 3-MP)/(P + 1-MP + 9-MP) (MPI-1), can be used as a proxy for oxidation potential. Values of logaH2aq determined from data reported for HYC and for a sequence of deeply buried source rocks are indicative of more reducing conditions at a given temperature than those inferred from data reported for two sets of samples exposed to contact or regional metamorphism. These results are limiting-case scenarios for the modeled systems that do not account for effects of non-ideal mixing or kinetics, or external sources or transport of the organic matter. Nevertheless, quantifying the temperature dependence of equilibrium constants of organic reactions enables the utilization of organic maturity parameters as relative geothermometers at temperatures higher than the nominal limits of the oil window.

Thermochemical Properties Enthalpy, Entropy, and Heat Capacity of C1-C4 Fluorinated Hydrocarbons: Fluorocarbon Group Additivity.

PubMed

Wang, Heng; Castillo, Álvaro; Bozzelli, Joseph W

2015-07-23

Enthalpies of formation for 14 C2–C4 fluorinated hydrocarbons were calculated with nine popular ab initio and density functional theory methods: B3LYP, CBS-QB3, CBS-APNO, M06, M06-2X, ωB97X, G4, G4(MP2)-6X, and W1U via several series of isodesmic reactions. The recommended ideal gas phase ΔHf298° (kcal mol(–1)) values calculated in this study are the following: −65.4 for CH3CH2F; −70.2 for CH3CH2CH2F; −75.3 for CH3CHFCH3; −75.2 for CH3CH2CH2CH2F; −80.3 for CH3CHFCH2CH3; −108.1 for CH2F2; −120.9 for CH3CHF2; −125.8 for CH3CH2CHF2; −133.3 for CH3CF2CH3; −166.7 for CHF3; −180.5 for CH3CF3; −185.5 for CH3CH2CF3; −223.2 for CF4; and −85.8 for (CH3)3CF. Entropies (S298° in cal mol(–1) K(–1)) were estimated using B3LYP/6-31+G(d,p) computed frequencies and geometries. Rotational barriers were determined and hindered internal rotational contributions for S298°, and Cp(T) were calculated using the rigid rotor harmonic oscillator approximation, with direct integration over energy levels of the intramolecular rotation potential energy curve. Thermochemical properties for the fluorinated carbon groups C/C/F/H2, C/C2/F/H, C/C/F2/H, C/C2/F2, and C/C/F3 were derived from the above target fluorocarbons. Previously published enthalpies and groups for 1,2-difluoroethane, 1,1,2-trifluoroethane, 1,1,2,2-tetrafluoroethane, 1,1,1,2-tetrafluoroethane, 1,1,1,2,2-pentafluoroethane, 2-fluoro-2-methylpropane that were previously determined via work reaction schemes are revised using updated reference species values. Standard deviations are compared for the calculation methods.

Tunable thermodynamic activity of LaxSr1–xMnyAl1–yO3–δ (0 ≤ x ≤ 1, 0 ≤ y ≤ 1) perovskites for solar thermochemical fuel synthesis† †Electronic supplementary information (ESI) available: Computational details, comprehensive XRD analyses, oxygen nonstoichiometry measurements and thermodynamic characterization of the perovskites. See DOI: 10.1039/c6ta06644e Click here for additional data file.

PubMed Central

Ezbiri, M.; Takacs, M.; Theiler, D.; Steinfeld, A.

2017-01-01

Nonstoichiometric metal oxides with variable valence are attractive redox materials for thermochemical and electrochemical fuel processing. To guide the design of advanced redox materials for solar-driven splitting of CO2 and/or H2O to produce CO and/or H2 (syngas), we investigate the equilibrium thermodynamics of the LaxSr1–xMnyAl1–yO3–δ perovskite family (0 ≤ x ≤ 1, 0 ≤ y ≤ 1) and La0.6Ca0.4Mn0.8Al0.2O3–δ, and compare them to those of CeO2 as the baseline. Oxygen nonstoichiometry measurements from 1573 to 1773 K and from 0.206 to 180 mbar O2 show a tunable reduction extent, increasing with increasing Sr content. Maximal nonstoichiometry of 0.32 is established with La0.2Sr0.8Mn0.8Al0.2O3–δ at 1773 K and 2.37 mbar O2. As a trend, we find that oxygen capacities are most sensitive to the A-cation composition. Partial molar enthalpy, entropy and Gibbs free energy changes for oxide reduction are extracted from the experimental data using defect models for Mn4+/Mn3+ and Mn3+/Mn2+ redox couples. We find that perovskites exhibit typically decreasing enthalpy changes with increasing nonstoichiometries. This desirable characteristic is most pronounced by La0.6Sr0.4Mn0.4Al0.6O3–δ, rendering it attractive for CO2 and H2O splitting. Generally, perovskites show lower enthalpy and entropy changes than ceria, resulting in more favorable reduction but less favorable oxidation equilibria. The energy penalties due to larger temperature swings and excess oxidants are discussed in particular. Using electronic structure theory, we conclude with a practical methodology estimating thermodynamic activity to rationally design perovskites with variable stoichiometry and valence. PMID:28580143

Water Mediated Ligand Functional Group Cooperativity: The Contribution of a Methyl Group to Binding Affinity is Enhanced by a COO− Group Through Changes in the Structure and Thermo dynamics of the Hydration Waters of Ligand-Thermolysin Complexes

PubMed Central

Nasief, Nader N; Tan, Hongwei; Kong, Jing; Hangauer, David

2012-01-01

Ligand functional groups can modulate the contributions of one another to the ligand-protein binding thermodynamics, producing either positive or negative cooperativity. Data presented for four thermolysin phosphonamidate inhibitors demonstrate that the differential binding free energy and enthalpy caused by replacement of a H with a Me group, which binds in the well-hydrated S2′ pocket, are more favorable in presence of a ligand carboxylate. The differential entropy is however less favorable. Dissection of these differential thermodynamic parameters, X-ray crystallography, and density-functional theory calculations suggest that these cooperativities are caused by variations in the thermodynamics of the complex hydration shell changes accompanying the H→Me replacement. Specifically, the COO− reduces both the enthalpic penalty and the entropic advantage of displacing water molecules from the S2′ pocket, and causes a subsequent acquisition of a more enthalpically, less entropically, favorable water network. This study contributes to understanding the important role water plays in ligand-protein binding. PMID:22894131

Correlation of the Rates of Solvolysis of i-Butyl Fluoroformate and a Consideration of Leaving-Group Effects

PubMed Central

Lee, Yelin; Park, Kyoung-Ho; Seong, Mi Hye; Kyong, Jin Burm; Kevill, Dennis N.

2011-01-01

The specific rates of solvolysis of isobutyl fluoroformate (1) have been measured at 40.0 °C in 22 pure and binary solvents. These results correlated well with the extended Grunwald-Winstein (G-W) equation, which incorporated the NT solvent nucleophilicity scale and the YCl solvent ionizing power scale. The sensitivities (l and m-values) to changes in solvent nucleophilicity and solvent ionizing power, and the kF/kCl values are very similar to those observed previously for solvolyses of n-octyl fluoroformate, consistent with the additional step of an addition-elimination pathway being rate-determining. The solvent deuterium isotope effect value (kMeOH/kMeOD) for methanolysis of 1 was determined, and for solvolyses in ethanol, methanol, 80% ethanol, and 70% TFE, the values of the enthalpy and the entropy of activation for the solvolysis of 1 were also determined. The results are compared with those reported earlier for isobutyl chloroformate (2) and other alkyl haloformate esters and mechanistic conclusions are drawn. PMID:22174633

Molecular Interactions in 1,4-Dioxane, Tetrahydrofuran, and Ethyl Acetate Solutions of 1,1'-Bis(4-isopropyloxyacetylphenoxy)cyclohexane on Reological, Density, and Acoustic Behavior

NASA Astrophysics Data System (ADS)

Dhaduk, B. B.; Patel, Ch. B.; Parsania, P. H.

2017-12-01

Various thermo-acoustical parameters of 1,4-dioxane, tetrahydofuran and ethylacetae solutions of 1,1'-bis(4-isopropyloxyacetylphenoxy)cyclohexane were determined at different temperatures using density, viscosity and ultrasonic speed and correlated with concentration. Linear increase of ultrasonic speed, specific acoustical impedance, Rao's molar sound function, Van der Waals constant and free volume with concentration C and decreased with temperature. Linear decrease of adiabatic compressibility, internal pressure, intermolecular free path length, classical absorption coefficient, and viscous relaxation time with concentration and increased with temperature indicated existence of strong molecular interactions in solutions and further supported by positive values of solvation number. Gibbs free energy of activation decreased with C in all three systems. It is decreased with T in 1,4-dioxane, while increased in tetrahydrofuran and ethyl acetate. Both enthalpy of activation and entropy of activation are increased gradually with C in 1,4-dioxane, while they are negative and remained practically independent of concentration in 1,4-dioxane and tetrahydofuran systems.

Predicting Molecular Crystal Properties from First Principles: Finite-Temperature Thermochemistry to NMR Crystallography.

PubMed

Beran, Gregory J O; Hartman, Joshua D; Heit, Yonaton N

2016-11-15

Molecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties. First, it describes the coupling of fragment electronic structure models with quasi-harmonic techniques for modeling the thermal expansion of molecular crystals, and what effects this expansion has on thermochemical and mechanical properties. Excellent agreement with experiment is demonstrated for the molar volume, sublimation enthalpy, entropy, and free energy, and the bulk modulus of phase I carbon dioxide when large basis second-order Møller-Plesset perturbation theory (MP2) or coupled cluster theories (CCSD(T)) are used. In addition, physical insight is offered into how neglect of thermal expansion affects these properties. Zero-point vibrational motion leads to an appreciable expansion in the molar volume; in carbon dioxide, it accounts for around 30% of the overall volume expansion between the electronic structure energy minimum and the molar volume at the sublimation point. In addition, because thermal expansion typically weakens the intermolecular interactions, neglecting thermal expansion artificially stabilizes the solid and causes the sublimation enthalpy to be too large at higher temperatures. Thermal expansion also frequently weakens the lower-frequency lattice phonon modes; neglecting thermal expansion causes the entropy of sublimation to be overestimated. Interestingly, the sublimation free energy is less significantly affected by neglecting thermal expansion because the systematic errors in the enthalpy and entropy cancel somewhat. Second, because solid state nuclear magnetic resonance (NMR) plays an increasingly important role in molecular crystal studies, this Account discusses how fragment methods can be used to achieve higher-accuracy chemical shifts in molecular crystals. Whereas widely used plane wave density functional theory models are largely restricted to generalized gradient approximation (GGA) functionals like PBE in practice, fragment methods allow the routine use of hybrid density functionals with only modest increases in computational cost. In extensive molecular crystal benchmarks, hybrid functionals like PBE0 predict chemical shifts with 20-30% higher accuracy than GGAs, particularly for 1 H, 13 C, and 15 N nuclei. Due to their higher sensitivity to polarization effects, 17 O chemical shifts prove slightly harder to predict with fragment methods. Nevertheless, the fragment model results are still competitive with those from GIPAW. The improved accuracy achievable with fragment approaches and hybrid density functionals increases discrimination between different potential assignments of individual shifts or crystal structures, which is critical in NMR crystallography applications. This higher accuracy and greater discrimination are highlighted in application to the solid state NMR of different acetaminophen and testosterone crystal forms.

The specific entropy of elliptical galaxies: an explanation for profile-shape distance indicators?

NASA Astrophysics Data System (ADS)

Lima Neto, G. B.; Gerbal, D.; Márquez, I.

1999-10-01

Dynamical systems in equilibrium have a stationary entropy; we suggest that elliptical galaxies, as stellar systems in a stage of quasi-equilibrium, may have in principle a unique specific entropy. This uniqueness, a priori unknown, should be reflected in correlations between the fundamental parameters describing the mass (light) distribution in galaxies. Following recent photometrical work on elliptical galaxies by Caon et al., Graham & Colless and Prugniel & Simien, we use the Sérsic law to describe the light profile and an analytical approximation to its three-dimensional deprojection. The specific entropy is then calculated, supposing that the galaxy behaves as a spherical, isotropic, one-component system in hydrostatic equilibrium, obeying the ideal-gas equations of state. We predict a relation between the three parameters of the Sérsic law linked to the specific entropy, defining a surface in the parameter space, an `Entropic Plane', by analogy with the well-known Fundamental Plane. We have analysed elliptical galaxies in two rich clusters of galaxies (Coma and ABCG 85) and a group of galaxies (associated with NGC 4839, near Coma). We show that, for a given cluster, the galaxies follow closely a relation predicted by the constant specific entropy hypothesis with a typical dispersion (one standard deviation) of 9.5per cent around the mean value of the specific entropy. Moreover, assuming that the specific entropy is also the same for galaxies of different clusters, we are able to derive relative distances between Coma, ABGC 85, and the group of NGC 4839. If the errors are due only to the determination of the specific entropy (about 10per cent), then the error in the relative distance determination should be less than 20per cent for rich clusters. We suggest that the unique specific entropy may provide a physical explanation for the distance indicators based on the Sérsic profile put forward by Young & Currie and recently discussed by Binggeli & Jerjen.

Group vector space method for estimating enthalpy of vaporization of organic compounds at the normal boiling point.

PubMed

Wenying, Wei; Jinyu, Han; Wen, Xu

2004-01-01

The specific position of a group in the molecule has been considered, and a group vector space method for estimating enthalpy of vaporization at the normal boiling point of organic compounds has been developed. Expression for enthalpy of vaporization Delta(vap)H(T(b)) has been established and numerical values of relative group parameters obtained. The average percent deviation of estimation of Delta(vap)H(T(b)) is 1.16, which show that the present method demonstrates significant improvement in applicability to predict the enthalpy of vaporization at the normal boiling point, compared the conventional group methods.

Thermodynamic aspects of dicarboxylate recognition by simple artificial receptors.

PubMed

Linton, B R; Goodman, M S; Fan, E; van Arman, S A; Hamilton, A D

2001-11-02

Recognition of dicarboxylates by bis-functional hydrogen-bonding receptors displays divergent thermodynamics in different solvent systems. NMR titration and isothermal titration calorimetry indicated that neutral bis-urea and bis-thiourea receptors form exothermic complexes with dicarboxylates in DMSO, with a near zero entropic contribution to binding. The increased binding strength of bis-guanidinium receptors precluded quantitative measurement of binding constants in DMSO, but titration calorimetry offered a qualitative picture of the association. Formation of these 1:1 complexes was also exothermic, but additional endothermic events occurred at both lower and higher host-guest ratios. These events indicated multiple binding equilibria but did not always occur at a discrete 2:1 or 1:2 host-guest molar ratio, suggesting higher aggregates. With increasing amounts of methanol as solvent, bis-guanidinium receptors form more endothermic complexes with dicarboxylates, with a favorable entropy of association. This switch from association driven by enthalpy to one driven by entropy may reflect a change from complexation involving the formation of hydrogen bonds to that promoted by solvent liberation from binding sites.

Entropy and enthalpy of interaction between amino acid side chains in nanopores

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vaitheeswaran, S., E-mail: vaithee05@gmail.com; Thirumalai, D.; Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742

2014-12-14

Understanding the stabilities of proteins in nanopores requires a quantitative description of confinement induced interactions between amino acid side chains. We use molecular dynamics simulations to study the nature of interactions between the side chain pairs ALA-PHE, SER-ASN, and LYS-GLU in bulk water and in water-filled nanopores. The temperature dependence of the bulk solvent potentials of mean force and the interaction free energies in cylindrical and spherical nanopores is used to identify the corresponding entropic and enthalpic components. The entropically stabilized hydrophobic interaction between ALA and PHE in bulk water is enthalpically dominated upon confinement depending on the relative orientationsmore » between the side chains. In the case of SER-ASN, hydrogen bonded configurations that are similar in bulk water are thermodynamically distinct in a cylindrical pore, thus making rotamer distributions different from those in the bulk. Remarkably, salt bridge formation between LYS-GLU is stabilized by entropy in contrast to the bulk. Implications of our findings for confinement-induced alterations in protein stability are briefly outlined.« less

Thermodynamics and Mechanism of the Interaction of Willardiine Partial Agonists with a Glutamate Receptor: Implications for Drug Development

PubMed Central

2015-01-01

Understanding the thermodynamics of binding of a lead compound to a receptor can provide valuable information for drug design. The binding of compounds, particularly partial agonists, to subtypes of the α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptor is, in some cases, driven by increases in entropy. Using a series of partial agonists based on the structure of the natural product, willardiine, we show that the charged state of the ligand determines the enthalpic contribution to binding. Willardiines have uracil rings with pKa values ranging from 5.5 to 10. The binding of the charged form is largely driven by enthalpy, while that of the uncharged form is largely driven by entropy. This is due at least in part to changes in the hydrogen bonding network within the binding site involving one water molecule. This work illustrates the importance of charge to the thermodynamics of binding of agonists and antagonists to AMPA receptors and provides clues for further drug discovery. PMID:24850223

Calculation of the thermoneutral potential of NiCd and NiH2 cells

NASA Technical Reports Server (NTRS)

Zimmerman, Albert H.

1994-01-01

The thermoneutral potential of a nickel cadmium or nickel hydrogen cell is the potential at which the cell charge or discharge process puts out zero heat, and thus is the potential corresponding to the enthalpy change of the charge/discharge reaction, delta H. A relatively straightforward method for obtaining the thermoneutral potential E(sub tn), is based on the measured potential and temperature derivative of the cell reactions, which are related to the free energy change delta G, and entropy change delta S, respectively. Particularly in the nickel hydrogen cell, the pressure of hydrogen can often vary over an order of magnitude or more during the course of a charge or discharge. In a nickel cadmium cell, although significant changes in oxygen pressure can occur during charge or discharge, since oxygen does not enter into the charge/discharge reaction, these pressure changes are related to the heat generated from oxygen evolution and recombination. However, the entropy changes due to changes in hydrogen pressure relative to the 1 atm standard state must be included to apply this method to the nickel hydrogen cell.

Effect of Quenched Disorder in the Entropy-Jump at the First-Order Vortex Phase Transition of Bi $_{2} 2 Sr _{2} 2 CaCu _{2} 2 O _{8 + delta }$ 8 + δ

NASA Astrophysics Data System (ADS)

Dolz, M. I.; Pedrazzini, P.; Pastoriza, H.; Konczykowski, M.; Fasano, Y.

2015-04-01

We study the effect of quenched disorder in the thermodynamic magnitudes entailed in the first-order vortex phase transition of the extremely layered BiSrCaCuO compound. We track the temperature-evolution of the enthalpy and the entropy jump at the vortex solidification transition by means of AC local magnetic measurements. Quenched disorder is introduced to the pristine samples by means of heavy-ion irradiation with Pb and Xe producing a random columnar-track pins distribution with different densities (matching field ). In contrast with previous magneto-optical reports, we find that the first-order phase transition persists for samples with up to 100 Gauss. For very low densities of quenched disorder (pristine samples), the evolution of the thermodynamic properties can be satisfactorily explained considering a negligible effect of pinning and only electromagnetic coupling between pancake vortices lying in adjacent CuO planes. This description is not satisfactory on increasing magnitude of quenched disorder.

Design of refractory high-entropy alloys

DOE PAGES

Gao, M. C.; Carney, C. S.; Dogan, O. N.; ...

2015-09-15

Here, this report presents a design methodology for refractory high-entropy alloys with a body-centered cubic (bcc) structure using select empirical parameters (i.e., enthalpy of mixing, atomic size difference, Ω-parameter, and electronegativity difference) and CALPHAD approach. Sixteen alloys in equimolar compositions ranging from quinary to ennead systems were designed with experimental verification studies performed on two alloys using x-ray diffraction, energy-dispersive spectroscopy, and scanning electron microscopy. Two bcc phases were identified in the as-cast HfMoNbTaTiVZr, whereas multiple phases formed in the as-cast HfMoNbTaTiVWZr. Observed elemental segregation in the alloys qualitatively agrees with CALPHAD prediction. Comparisons of the thermodynamic mixing properties formore » liquid and bcc phases using the Miedema model and CALPHAD are presented. This study demonstrates that CALPHAD is more effective in predicting HEA formation than empirical parameters, and new single bcc HEAs are suggested: HfMoNbTiZr, HfMoTaTiZr, NbTaTiVZr, HfMoNbTaTiZr, HfMoTaTiVZr, and MoNbTaTiVZr.« less

Domain-specific interactions between MLN8237 and human serum albumin estimated by STD and WaterLOGSY NMR, ITC, spectroscopic, and docking techniques.

PubMed

Yang, Hongqin; Liu, Jiuyang; Huang, Yanmei; Gao, Rui; Tang, Bin; Li, Shanshan; He, Jiawei; Li, Hui

2017-03-30

Alisertib (MLN8237) is an orally administered inhibitor of Aurora A kinase. This small-molecule inhibitor is under clinical or pre-clinical phase for the treatment of advanced malignancies. The present study provides a detailed characterization of the interaction of MLN8237 with a drug transport protein called human serum albumin (HSA). STD and WaterLOGSY nuclear magnetic resonance (NMR)-binding studies were conducted first to confirm the binding of MLN8237 to HSA. In the ligand orientation assay, the binding sites of MLN8237 were validated through two site-specific spy molecules (warfarin sodium and ibuprofen, which are two known site-selective probes) by using STD and WaterLOGSY NMR competition techniques. These competition experiments demonstrate that both spy molecules do not compete with MLN8237 for the specific binding site. The AutoDock-based blind docking study recognizes the hydrophobic subdomain IB of the protein as the probable binding site for MLN8237. Thermodynamic investigations by isothermal titration calorimetry (ITC) reveal that the non-covalent interaction between MLN8237 and HSA (binding constant was approximately 10 5  M -1 ) is driven mainly by favorable entropy and unfavorable enthalpy. In addition, synchronous fluorescence, circular dichroism (CD), and 3D fluorescence spectroscopy suggest that MLN8237 may induce conformational changes in HSA.

Non-autoclaved aerated concrete with mineral additives

NASA Astrophysics Data System (ADS)

Il'ina, L. V.; Rakov, M. A.

2016-01-01

We investigated the effect of joint grinding of Portland cement clinker, silica and carbonate components and mineral additives to specific surface of 280 - 300 m2/kg on the properties (strength, average density and thermal conductivity) of non-autoclaved aerated concrete, and the porosity of the hardened cement paste produced from Portland cement clinker with mineral additives. The joint grinding of the Portland cement clinker with silica and carbonate components and mineral additives reduces the energy consumption of non-autoclaved aerated concrete production. The efficiency of mineral additives (diopside, wollastonite) is due to the closeness the composition, the type of chemical bonds, physical and chemical characteristics (specific enthalpy of formation, specific entropy) to anhydrous clinker minerals and their hydration products. Considering the influence of these additions on hydration of clinker minerals and formation of hardened cement paste structure, dispersed wollastonite and diopside should be used as mineral additives. The hardness and, consequently, the elastic modulus of diopside are higher than that of hardened cement paste. As a result, there is a redistribution of stresses in the hardened cement paste interporous partitions and hardening, both the partitions and aerated concrete on the whole. The mineral additives introduction allowed to obtain the non-autoclaved aerated concrete with average density 580 kg/m3, compressive strength of 3.3 MPa and thermal conductivity of 0.131 W/(m.°C).

Domain-specific interactions between MLN8237 and human serum albumin estimated by STD and WaterLOGSY NMR, ITC, spectroscopic, and docking techniques

PubMed Central

Yang, Hongqin; Liu, Jiuyang; Huang, Yanmei; Gao, Rui; Tang, Bin; Li, Shanshan; He, Jiawei; Li, Hui

2017-01-01

Alisertib (MLN8237) is an orally administered inhibitor of Aurora A kinase. This small-molecule inhibitor is under clinical or pre-clinical phase for the treatment of advanced malignancies. The present study provides a detailed characterization of the interaction of MLN8237 with a drug transport protein called human serum albumin (HSA). STD and WaterLOGSY nuclear magnetic resonance (NMR)-binding studies were conducted first to confirm the binding of MLN8237 to HSA. In the ligand orientation assay, the binding sites of MLN8237 were validated through two site-specific spy molecules (warfarin sodium and ibuprofen, which are two known site-selective probes) by using STD and WaterLOGSY NMR competition techniques. These competition experiments demonstrate that both spy molecules do not compete with MLN8237 for the specific binding site. The AutoDock-based blind docking study recognizes the hydrophobic subdomain IB of the protein as the probable binding site for MLN8237. Thermodynamic investigations by isothermal titration calorimetry (ITC) reveal that the non-covalent interaction between MLN8237 and HSA (binding constant was approximately 105 M−1) is driven mainly by favorable entropy and unfavorable enthalpy. In addition, synchronous fluorescence, circular dichroism (CD), and 3D fluorescence spectroscopy suggest that MLN8237 may induce conformational changes in HSA. PMID:28358124

Domain-specific interactions between MLN8237 and human serum albumin estimated by STD and WaterLOGSY NMR, ITC, spectroscopic, and docking techniques

NASA Astrophysics Data System (ADS)

Yang, Hongqin; Liu, Jiuyang; Huang, Yanmei; Gao, Rui; Tang, Bin; Li, Shanshan; He, Jiawei; Li, Hui

2017-03-01

Alisertib (MLN8237) is an orally administered inhibitor of Aurora A kinase. This small-molecule inhibitor is under clinical or pre-clinical phase for the treatment of advanced malignancies. The present study provides a detailed characterization of the interaction of MLN8237 with a drug transport protein called human serum albumin (HSA). STD and WaterLOGSY nuclear magnetic resonance (NMR)-binding studies were conducted first to confirm the binding of MLN8237 to HSA. In the ligand orientation assay, the binding sites of MLN8237 were validated through two site-specific spy molecules (warfarin sodium and ibuprofen, which are two known site-selective probes) by using STD and WaterLOGSY NMR competition techniques. These competition experiments demonstrate that both spy molecules do not compete with MLN8237 for the specific binding site. The AutoDock-based blind docking study recognizes the hydrophobic subdomain IB of the protein as the probable binding site for MLN8237. Thermodynamic investigations by isothermal titration calorimetry (ITC) reveal that the non-covalent interaction between MLN8237 and HSA (binding constant was approximately 105 M-1) is driven mainly by favorable entropy and unfavorable enthalpy. In addition, synchronous fluorescence, circular dichroism (CD), and 3D fluorescence spectroscopy suggest that MLN8237 may induce conformational changes in HSA.

Thermodynamics of the binding of L-arabinose and of D-galactose to the L-arabinose-binding protein of Escherichia coli.

PubMed

Fukada, H; Sturtevant, J M; Quiocho, F A

1983-11-10

The thermodynamics of the binding of L-arabinose and of D-galactose to the L-arabinose-binding protein of Escherichia coli have been studied by isothermal and scanning calorimetry. The binding reaction with arabinose is characterized by an enthalpy change of -15.3 +/- 0.5 kcal mol-1 at 25 degrees C, and a large decrease in apparent heat capacity, amounting to -0.44 +/- 0.05 kcal K-1 mol-1, which is constant over the temperature range 8 to 30 degrees C. Very similar results were obtained with D-galactose. These calorimetric results have been combined with binding constants determined by equilibrium dialysis (Clark, A. F., Gerken, T. A., and Hogg, R. W. (1982) Biochemistry 21, 2227-2233) to obtain free energy and entropy changes over the range 5 to 30 degrees C, and by extrapolation to 60 degrees C. The protein undergoes reversible unfolding on being heated with an increase in enthalpy at 53.5 degrees C of 151.8 +/- 1.1 kcal mol-1 (169.2 +/- 1.2 kcal mol-1 at 59.0 degrees C) and in apparent heat capacity of 3.16 +/- 0.07 kcal K-1 mol-1. In the presence of arabinose, the unfolding enthalpy is increased to 200.7 +/- 1.8 kcal mol-1 at 59.0 degrees C, the increase being due to the enthalpy of dissociation of the ligand which amounts to 31 kcal mol-1 at the unfolding temperature. The unfolding temperature is increased by the presence of excess arabinose or galactose, an effect which is due solely to displacement by the added ligand of the unfolding-dissociation equilibrium. The thermodynamic data are discussed in connection with the detailed structural information available for this system from x-ray crystallography (Newcomer, M. E., Gilliland, G. L. and Quiocho, F. A. (1981) J. Biol. Chem. 256, 13213-13217, and references cited therein).

New Standard State Entropy for Sphene (Titanite)

NASA Astrophysics Data System (ADS)

Manon, M. R.; Dachs, E.; Essene, E. J.

2004-12-01

Several recent papers have questioned the accepted standard state (STP) entropy of sphene (CaTiSiO5), which had been considered to be in the range 129-132 J/mol.K (Berman, 1988: 129.3 Robie and Hemingway, 1995: 129.2 J/mol.K; Holland and Powell, 1995: 131.2 J/mol.K.). However, Xirouchakis and Lindsley (1998) recommended a much lower value of 106 J/mol.K for the STP entropy of sphene. Tangeman and Xirouchakis (2001) inferred a value less than 124 or 120 J/mol.K, based on based on enthalpy constraints combined with the tightly reversed reaction sphene+kyanite=rutile+anorthite by Bohlen and Manning (1991). Their recommendations are in conflict with the accepted values for STP entropy for sphene, including values calculated by direct measurement of Cp from 50 to 300 K by King (1954). In order to resolve this discrepancy, we have collected new data on the Cp of sphene between 5 and 300 K. Our measurements were made in the PPMS at Salzburg on a 21.4 g sample of sphene generously furnished by Tangeman and Xirouchakis (2001), the same sample as used in their experiments. The Cp data are slightly lower than those of King (1954) but merge smoothly with data of Tangeman and Xirouchakis (2001) from 330 to 483 K (or whatever) where a transition is recorded in the Cp data as a lambda anomaly. Tangeman and Xirouchakis also obtained data above the transition up to 950K. Integration of the new Cp data yields a STP entropy of 127.3 J/mol.K, lower than the generally accepted value by ca. 2 J/mol.K. A change in the STP entropy of sphene will have an effect on many Ti-bearing reactions which occur within the earth, although the magnitude of this change is not nearly as large as that suggested by Xirouchakis and Lindsley (1998). Above 700 K, the entropy calculated using the new STP entropy with the heat capacity equation of Tangeman and Xirouchakis (2001) is within 1 J/mol.K of the value tabulated in Robie and Hemingway (1995) and of that calculated from Berman (1988). The effect on most phase equilibrium calculations will not be large except for reactions with small Δ S. The use of 127.2 J/mol.K as the standard entropy of sphene is recommended especially in calculations of geobarometers involving that phase.

Thermodynamic analysis of cavity creating mutations in an engineered leucine zipper and energetics of glycerol-induced coiled coil stabilization.

PubMed

Dürr, E; Jelesarov, I

2000-04-18

Protein stability in vitro can be influenced either by introduction of mutations or by changes in the chemical composition of the solvent. Recently, we have characterized the thermodynamic stability and the rate of folding of the engineered dimeric leucine zipper A(2), which has a strengthened hydrophobic core [Dürr, E., Jelesarov, I., and Bosshard, H. R. (1999) Biochemistry 38, 870-880]. Here we report on the energetic consequences of a cavity introduced by Leu/Ala substitution at the tightly packed dimeric interface and how addition of 30% glycerol affects the folding thermodynamics of A(2) and the cavity mutants. Folding could be described by a two-state transition from two unfolded monomers to a coiled coil dimer. Removal of six methylene groups by Leu/Ala substitutions destabilized the dimeric coiled coil by 25 kJ mol(-1) at pH 3.5 and 25 degrees C in aqueous buffer. Destabilization was purely entropic at around room temperature and became increasingly enthalpic at elevated temperatures. Mutations were accompanied by a decrease of the unfolding heat capacity by 0.5 kJ K(-1) mol(-1). Addition of 30% glycerol increased the free energy of folding of A(2) and the cavity mutants by 5-10 kJ mol(-1) and lowered the unfolding heat capacity by 25% for A(2) and by 50% for the Leu/Ala mutants. The origin of the stabilizing effect of glycerol varied with temperature. Stabilization of the parent leucine zipper A(2) was enthalpic with an unfavorable entropic component between 0 and 100 degrees C. In the case of cavity mutants, glycerol induced enthalpic stabilization below 50 degrees C and entropic stabilization above 50 degrees C. The effect of glycerol could not be accounted for solely by the enthalpy and entropy of transfer or protein surface from water to glycerol/water mixture. We propose that in the presence of glycerol the folded coiled coil dimer is better packed and displays less intramolecular fluctuations, leading to enhanced enthalpic interactions and to an increase of the entropy of folding. This work demonstrates that mutational and solvent effects on protein stability can be thermodynamically complex and that it may not be sufficient to only analyze changes of enthalpy and entropy at the unfolding temperature (T(m)) to understand the mechanisms of protein stabilization.

Hydrogen uptake characteristics of mischmetal based alloy

NASA Astrophysics Data System (ADS)

Jain, Ankur; Jain, R. K.; Jain, I. P.

Hydrogen storage properties of Mm 39.2Ni 42.1Mn 4.9Al 1.25Co 10.2Fe 2.35 alloy have been systematically studied in the present work. An attempt is made to relate the content of hydrogen with change in resistance. It is found that the resistance of material increases with the increase in value of H/ M due to hydrogen absorption. Pressure composition (P-C-T) isotherm using water displacement method has been investigated in the temperature and pressure ranges of 308 ≤ T ≤ 338 K and 0.5 ≤ P ≤ 10 bar, respectively. The P-C isotherms show the presence of two single α and β regions one mixed α + β phase. The maximum H (wt%) was found to be around 1.53 at 308 K and around 6 bar. Since enthalpy is an index of thermochemical stability of metal hydride the thermo dynamical parameters viz., the relative partial molar enthalpy (Δ H) and relative partial molar entropy (Δ S) of dissolved hydrogen have been calculated by plotting the Van't Hoff plot. The variation of Δ H and Δ S with the hydrogen concentration confirm the phase boundaries.

Evaluation of water displacement energetics in protein binding sites with grid cell theory.

PubMed

Gerogiokas, G; Southey, M W Y; Mazanetz, M P; Heifetz, A; Hefeitz, A; Bodkin, M; Law, R J; Michel, J

2015-04-07

Excess free energies, enthalpies and entropies of water in protein binding sites were computed via classical simulations and Grid Cell Theory (GCT) analyses for three pairs of congeneric ligands in complex with the proteins scytalone dehydratase, p38α MAP kinase and EGFR kinase respectively. Comparative analysis is of interest since the binding modes for each ligand pair differ in the displacement of one binding site water molecule, but significant variations in relative binding affinities are observed. Protocols that vary in their use of restraints on protein and ligand atoms were compared to determine the influence of protein-ligand flexibility on computed water structure and energetics, and to assess protocols for routine analyses of protein-ligand complexes. The GCT-derived binding affinities correctly reproduce experimental trends, but the magnitude of the predicted changes in binding affinities is exaggerated with respect to results from a previous Monte Carlo Free Energy Perturbation study. Breakdown of the GCT water free energies into enthalpic and entropic components indicates that enthalpy changes dominate the observed variations in energetics. In EGFR kinase GCT analyses revealed that replacement of a pyrimidine by a cyanopyridine perturbs water energetics up three hydration shells away from the ligand.

Experimental and Theoretical Study of Thermodynamics of the Reaction of Titania and Water at High Temperatures

NASA Technical Reports Server (NTRS)

Nguyen, Quynhgiao N.; Myers, Dwight L.; Jacobson, Nathan S.; Opila, Elizabeth J.

2014-01-01

The transpiration method was used to determine the volatility of titanium dioxide (TiO2) in water vapor-containing environments at temperatures between 1473 and 1673 K. Water contents ranged from 0 to 76 mole % in oxygen or argon carrier gases for 20 to 250 hr exposure times. Results indicate that oxygen is not a key contributor to volatilization and the primary reaction for volatilization in this temperature range is: TiO2(s) + H2O(g) = TiO(OH)2(g). Data were analyzed with both the second and third law methods to extract an enthalpy and entropy of formation. The geometry and vibrational frequencies of TiO(OH)2(g) were computed using B3LYP density functional theory, and the enthalpy of formation was computed using the coupled-cluster singles and doubles method with a perturbative correction for connected triple substitutions [CCSD(T)]. Thermal functions are calculated using both a structure with bent and linear hydroxyl groups. Calculated second and third heats show closer agreement with the linear hydroxyl group, suggesting more experimental and computational spectroscopic and structural work is needed on this system.

Spectroscopic and microcalorimetric studies on the molecular binding of food colorant acid red 27 with deoxyribonucleic acid.

PubMed

Basu, Anirban; Kumar, Gopinatha Suresh

2016-08-01

Interaction of the food colorant acid red 27 with double stranded DNA was investigated using spectroscopic and calorimetric methods. Absorbance and fluorescence studies suggested an intimate binding interaction between the dye and DNA. The quantum efficiency value testified an effective energy transfer from the DNA base pairs to the dye molecules. Minor groove displacement assay with Hoechst 33258 revealed that the binding occurs in the minor groove of DNA. Circular dichroism studies revealed that acid red 27 induces moderate conformational perturbations in DNA. Results of calorimetric studies suggested that the complexation process was driven largely by positive entropic contribution with a smaller favorable enthalpy contribution. The equilibrium constant of the binding was calculated to be (3.04 ± 0.09) × 10(4)  M(-1) at 298.15 K. Negative heat capacity value along with the enthalpy-entropy compensation phenomenon established the involvement of dominant hydrophobic forces in the binding process. Differential scanning calorimetry studies presented evidence for an increased thermal stability of DNA on binding of acid red 27. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Misuse of thermodynamics in the interpretation of isothermal titration calorimetry data for ligand binding to proteins.

PubMed

Pethica, Brian A

2015-03-01

Isothermal titration calorimetry (ITC) has given a mass of data on the binding of small molecules to proteins and other biopolymers, with particular interest in drug binding to proteins chosen as therapeutic indicators. Interpretation of the enthalpy data usually follows an unsound protocol that uses thermodynamic relations in circumstances where they do not apply. Errors of interpretation include incomplete definitions of ligand binding and equilibrium constants and neglect of the non-ideality of the solutions under study, leading to unreliable estimates of standard free energies and entropies of binding. The mass of reported thermodynamic functions for ligand binding to proteins estimated from ITC enthalpies alone is consequently of uncertain thermodynamic significance and utility. ITC and related experiments to test the protocol assumptions are indicated. A thermodynamic procedure avoiding equilibrium constants or other reaction models and not requiring protein activities is given. The discussion draws attention to the fundamental but neglected relation between the thermodynamic activity and bioactivity of drugs and to the generally unknown thermodynamic status of ligand solutions, which for drugs relates directly to effective therapeutic dosimetry. Copyright © 2014 Elsevier Inc. All rights reserved.

Microhydration of caesium compounds: Cs, CsOH, CsI and Cs₂I₂ complexes with one to three H₂O molecules of nuclear safety interest.

PubMed

Sudolská, Mária; Cantrel, Laurent; Cernušák, Ivan

2014-04-01

Structure and thermodynamic properties (standard enthalpies of formation and Gibbs free energies) of hydrated caesium species of nuclear safety interest, Cs, CsOH, CsI and its dimer Cs₂I₂, with one up to three water molecules, are calculated to assess their possible existence in severe accident occurring to a pressurized water reactor. The calculations were performed using the coupled cluster theory including single, double and non-iterative triple substitutions (CCSD(T)) in conjunction with the basis sets (ANO-RCC) developed for scalar relativistic calculations. The second-order spin-free Douglas-Kroll-Hess Hamiltonian was used to account for the scalar relativistic effects. Thermodynamic properties obtained by these correlated ab initio calculations (entropies and thermal capacities at constant pressure as a function of temperature) are used in nuclear accident simulations using ASTEC/SOPHAEROS software. Interaction energies, standard enthalpies and Gibbs free energies of successive water molecules addition determine the ordering of the complexes. CsOH forms the most hydrated stable complexes followed by CsI, Cs₂I₂, and Cs. CsOH still exists in steam atmosphere even at quite high temperature, up to around 1100 K.

Mass spectrometric measurements of the freestream composition in the T4 free-piston shock-tunnel

NASA Astrophysics Data System (ADS)

Boyce, R. R.; Takahashi, M.; Stalker, R. J.

2005-12-01

The freestream composition is an important parameter in ground-based aerodynamic testing, and direct measurement of it is very important. This paper reports extensive composition measurements in the freestream of the T4 free-piston shock-tunnel, employing a recently improved time-of-flight mass spectrometer. A wide range of nozzle reservoir conditions were used. The results show good agreement between measured and theoretical values for nitric oxide over the entire enthalpy range reported (2.5 13 MJ/kg). This provides confidence that the chemistry model is correctly predicting sudden freezing of NO in the nozzle expansion. On the other hand, no monatomic species have been measured other than those produced by dissociative ionisation within the mass spectrometer, even at flow conditions where significant freestream dissociation is expected. Furthermore, excess diatomic oxygen is detected at high enthalpies. These observations are consistent with the possibility that oxygen recombination is not correctly predicted in the nozzle expansion, with sudden freezing occurring significantly later than predicted. However, the observations are also consistent with possible catalytic recombination in the skimmer system. The possibility for producing an empirical correlation between the freestream composition and the reservoir entropy has also been observed.

Influence of polymorphism on the surface energetics of salmeterol xinafoate crystallized from supercritical fluids.

PubMed

Tong, Henry H Y; Shekunov, Boris Yu; York, Peter; Chow, Albert H L

2002-05-01

To characterize the surface thermodynamic properties of two polymorphic forms (I and II) of salmeterol xinafoate (SX) prepared from supercritical fluids and a commercial micronized SX (form 1) sample (MSX). Inverse gas chromatographic analysis was conducted on the SX samples at 30, 40, 50, and 60 degrees C using the following probes at infinite dilution: nonpolar probes (NPs; alkane C5-C9 series); and polar probes (PPs; i.e., dichloromethane, chloroform, acetone, ethyl acetate, diethyl ether, and tetrahydrofuran). Surface thermodynamic parameters of adsorption and Hansen solubility parameters were calculated from the retention times of the probes. The free energies of adsorption (- deltaG(A)) of the three samples obtained at various temperatures follow this order: SX-II > MSX approximately/= SX-I for the NPs; and SX-II > MSX > SX-I for the PPs. For both NPs and PPs, SX-II exhibits a less negative enthalpy of adsorption (deltaH(A)) and a much less negative entropy of adsorption (ASA) than MSX and SX-I, suggesting that the high -AGA of SX-II is contributed by a considerably reduced entropy loss. The dispersive component of surface free energy (gammas(D)) is the highest for MSX but the lowest for SX-II at all temperatures studied, whereas the specific component of surface free energy of adsorption (-deltaG(A)SP) is higher for SX-II than for SX-I. That SX-II displays the highest -deltaG(A) for the NP but the lowest gammasD of all the SX samples may be explained by the additional -AGA change associated with an increased mobility of the probe molecules on the less stable and more disordered SX-II surface. The acid and base parameters, K(A) and K(D) that were derived from deltaH(A)SP reveal significant differences in the relative acid and base properties among the samples. The calculated Hansen solubility parameters (deltaD, deltap, and deltaH) indicate that the surface of SX-II is the most polar and most energetic of all the three samples in terms of specific interactions (mostly hydrogen bonding). The metastable SX-II polymorph possesses a higher surface free energy, higher surface entropy, and a more polar surface than the stable SX-I polymorph.

Boundary-Layer Edge Conditions and Transition Reynolds Number Data for a Flight Test at Mach 20 (Reentry F)

NASA Technical Reports Server (NTRS)

Johnson, Charles B.; Stainback, P. Calvin; Wicker, Kathleen C.; Boney, Lillian R.

1972-01-01

A flight experiment, designated Reentry F, was conducted to measure heat-transfer rates for laminar, transitional, and turbulent boundary layers on a 5 deg half-angle cone 3.962 m (13 ft) long with a preflight nose radius of 2.54 mm (0.10 in.). Data were obtained over an altitude range from 36.58 to 18.29 km (120 000 to 60 000 ft) at a flight velocity of about 6.096 km/sec (20 000 ft/sec). The nominal values of the free-stream total enthalpy, sharp-cone Mach number, and the wall-to-total enthalpy ratio were 18 MJ/kg (8000 Btu/lb), 15, and 0.03, respectively. Calculated boundary-layer edge conditions that account for effects of the entropy layer and corresponding local transition Reynolds numbers are reported in the present paper. Fully developed turbulent flow occurred with essentially constant boundary-layer edge conditions near the sharp-cone values. Transition data were obtained with local edge Mach numbers ranging from about 5.55 to 15. Transition Reynolds numbers, based on local condition, were as high as 6.6 x 10(exp 7) with an edge Mach number of about 14.4 at an altitude of 24.38 km (80 000 ft). The transition could be correlated with previous flight data taken over a Mach number range from 3 to 12 in terms of parameters including the effects of local unit Reynolds number, boundary-layer wall-to-edge enthalpy ratio, and local Mach number.

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMurray, J. W.; Zhou, Y.; Luo, H. M.

We determined the equilibrium vapor pressures, p e, of the ionic liquid tetraoctylphosphonium bis(2-ethylhexyl)phosphate ([P 8888][DEHP]) over the temperature range 409–495 K using mass loss Knudsen effusion. The p e versus temperature relationship compares well to 1-methyl-3-octylimidazolium bis(trifluoromethylsulfonyl)imide ([C 8mim][NTf 2]) but is lower than that of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C 2mim][NTf 2]) when measured using the same technique. Here, we determined the discrepancies between the p e for [C 8mim][NTf 2] and [C 2mim][NTf 2] with previous studies is discussed. Finally, the enthalpy and entropy of vaporization for all three fluids are estimated from the Clasius-Clapeyron relation.

GASPLOT - A computer graphics program that draws a variety of thermophysical property charts

NASA Technical Reports Server (NTRS)

Trivisonno, R. J.; Hendricks, R. C.

1977-01-01

A FORTRAN V computer program, written for the UNIVAC 1100 series, is used to draw a variety of precision thermophysical property charts on the Calcomp plotter. In addition to the program (GASPLOT), which requires (15 160) sub 10 storages, a thermophysical properties routine needed to produce plots. The program is designed so that any two of the state variables, the derived variables, or the transport variables may be plotted as the ordinate - abscissa pair with as many as five parametric variables. The parameters may be temperature, pressure, density, enthalpy, and entropy. Each parameter may have as many a 49 values, and the range of the variables is limited only by the thermophysical properties routine.

Thermodynamic properties of La-Ga-Al and U-Ga-Al alloys and the separation factor of U/La couple in the molten salt-liquid metal system

NASA Astrophysics Data System (ADS)

Novoselova, A.; Smolenski, V.; Volkovich, V. A.; Ivanov, A. B.; Osipenko, A.; Griffiths, T. R.

2015-11-01

The electrochemical behaviour of lanthanum and uranium was studied in fused 3LiCl-2KCl eutectic and Ga-Al eutectic liquid metal alloy between 723 and 823 K. Electrode potentials were recorded vs. Cl-/Cl2 reference electrode and the temperature dependencies of the apparent standard potentials of La-(Ga-Al) and U-(Ga-Al) alloys were determined. Lanthanum and uranium activity coefficients and U/La couple separation factor were calculated. Partial excess free Gibbs energy, partial enthalpy of mixing and partial excess entropy of La-(Ga-Al) and U-(Ga-Al) alloys were estimated.

Thermal degradation of ternary blend films containing PVA/chitosan/vanillin

NASA Astrophysics Data System (ADS)

Kasai, Deepak; Chougale, Ravindra; Masti, Saraswati; Narasgoudar, Shivayogi

2018-05-01

The ternary chitosan/poly (vinyl alcohol)/vanillin blend films were prepared by solution casting method. The influence of equal weight percent of poly (vinyl alcohol) and vanillin on thermal stability of the chitosan blend films were investigated by using thermogravimetric analysis (TGA). The kinetic parameters such as enthalpy (ΔH*), entropy (ΔS*), and Gibbs free energy (ΔG*) in the first and second decomposition steps based on the thermogravimetric data were calculated. The thermal stabilities of the blend films were confirmed by thermodynamic parameters obtained in the activation energies, which indicated that increase in the equal weight percent of PVA/vanillin decreased the thermal stability of the chitosan film.

The Theory of Thermodynamics for Chemical Reactions in Dispersed Heterogeneous Systems

PubMed

Yongqiang; Baojiao; Jianfeng

1997-07-01

In this paper, the expressions of Gibbs energy change, enthalpy change, entropy change, and equilibrium constant for chemical reactions in dispersed heterogeneous systems are derived using classical thermodynamics theory. The thermodynamical relations for the same reaction system between the dispersed and the block state are also derived. The effects of degree of dispersion on thermodynamical properties, reaction directions, and chemical equilibria are discussed. The results show that the present equation of thermodynamics for chemical reactions is only a special case of the above-mentioned formulas and that the effect of the dispersity of a heterogeneous system on the chemical reaction obeys the Le Chatelier principle of movement of equilibria.

Thermodynamics of R-(+)-2-(4-Hydroxyphenoxy)propanoic Acid Dissolution in Methanol, Ethanol, and Methanol-Ethanol Mixture

NASA Astrophysics Data System (ADS)

Liu, Wei; Ma, Jinju; Yao, Xinding; Fang, Ruina; Cheng, Liang

2018-05-01

The solubilities of R-(+)-2-(4-hydroxyphenoxy)propanoic acid (D-HPPA) in methanol, ethanol and various methanol-ethanol mixtures are determined in the temperature range from 273.15 to 323.15 K at atmospheric pressure using a laser detecting system. The solubilities of D-HPPA increase with increasing mole fraction of ethanol in the methanol-ethanol mixtures. Experimental data were correlated with Buchowski-Ksiazczak λ h equation and modified Apelblat equation; the first one gives better approximation for the experimental results. The enthalpy, entropy and Gibbs free energy of D-HPPA dissolution in methanol, ethanol and methanol-ethanol mixtures were also calculated from the solubility data.

Mechanism of curcumin-induced trypsin inhibition: Computational and experimental studies

NASA Astrophysics Data System (ADS)

Wang, Yan-Qing; Zhang, Hong-Mei; Kang, Yi-Jun; Gu, Yun-Lan; Cao, Jian

2016-03-01

In the present study, the experimental and theoretical methods were used to analyze the binding interaction of food dye, curcumin with trypsin. The results of fluorescence spectroscopic measurements indicated that curcumin binding resulted in the obviously intrinsic fluorescence quenching with the increase concentration of curcumin. This binding interaction is a spontaneous process with the estimated enthalpy and entropy changes being -15.70 kJ mol-1 and 40.25 J mol-1 K-1, respectively. Hydrogen bonds and hydrophobic forces played an important role in the complex formation between curcumin and trypsin. Moreover, curcumin could enter into the primary substrate-binding pocket and makes the activity of trypsin decrease remarkably with the increasing concentration of curcumin.

Spectroscopic and thermogravimetric study of nickel sulfaquinoxaline complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tailor, Sanjay M., E-mail: sanjay-tailor10@yahoo.com; Patel, Urmila H.

2016-05-06

The ability of sulfaquinoxaline (4-Amino-N-2-quinoxalinylbenzenesulfonamide) to form metal complexes are investigated. The nickel complex of sulfaquinoxaline is prepared by reflux method and characterized by CHN analysis and IR spectra. The results of IR spectral data suggest that the binding of nickel atom to the sulfonamidic nitrogen are in good agreement. The thermogravimetric analysis (TGA), differential thermal analysis (DTA) and differential thermogravimetric (DTG) analysis of nickel sulfaquinoxaline are carried out from ambient temperature to 750°C in inert nitrogen atmosphere. The activation energy, enthalpy, entropy and Gibbs free energy of nickel sulfaquinoxaline complex is determined from the thermal curves using Broido method.more » The results are reported in this paper.« less

Spectroscopic and thermodynamic study of charge transfer complex formation between cloxacillin sodium and riboflavin in aqueous ethanol media of varying composition

NASA Astrophysics Data System (ADS)

Roy, Dalim Kumar; Saha, Avijit; Mukherjee, Asok K.

2006-03-01

Cloxacillin sodium has been shown to form a charge transfer complex of 2:1 stoichiometry with riboflavin (Vitamin B 2) in aqueous ethanol medium. The enthalpy and entropy of formation of this complex have been determined by estimating the formation constant spectrophotometrically at five different temperatures in pure water medium. Pronounced effect of dielectric constant of the medium on the magnitude of K has been observed by determining K in aqueous ethanol mixtures of varying composition. This has been rationalized in terms of ionic dissociation of the cloxacillin sodium (D -Na +), hydrolysis of the anion D - and complexation of the free acid, DH with riboflavin.

Computer program for calculating and fitting thermodynamic functions

NASA Technical Reports Server (NTRS)

Mcbride, Bonnie J.; Gordon, Sanford

1992-01-01

A computer program is described which (1) calculates thermodynamic functions (heat capacity, enthalpy, entropy, and free energy) for several optional forms of the partition function, (2) fits these functions to empirical equations by means of a least-squares fit, and (3) calculates, as a function of temperture, heats of formation and equilibrium constants. The program provides several methods for calculating ideal gas properties. For monatomic gases, three methods are given which differ in the technique used for truncating the partition function. For diatomic and polyatomic molecules, five methods are given which differ in the corrections to the rigid-rotator harmonic-oscillator approximation. A method for estimating thermodynamic functions for some species is also given.

Solubility and dissolution thermodynamics of phthalic anhydride in organic solvents at 283-313 K

NASA Astrophysics Data System (ADS)

Wang, Long; Zhang, Fang; Gao, Xiaoqiang; Luo, Tingliang; Xu, Li; Liu, Guoji

2017-08-01

The solubility of phthalic anhydride was measured at 283-313 K under atmospheric pressure in ethyl acetate, n-propyl acetate, methyl acetate, acetone, 1,4-dioxane, n-hexane, n-butyl acetate, cyclohexane, and dichloromethane. The solubility of phthalic anhydride in all solvents increased with the increasing temperature. The Van't Hoff equation, modified Apelblat equation, λ h equation, and Wilson model were used to correlate the experimental solubility data. The standard dissolution enthalpy, the standard entropy, and the standard Gibbs energy were evaluated based on the Van't Hoff analysis. The experimental data and model parameters would be useful for optimizing of the separation processes involving phthalic anhydride.

Thermophysical Properties of Cold and Vacuum Plasma Sprayed Cu-Cr-X Alloys, NiAl and NiCrAlY Coatings. Part 2; Specific Heat Capacity

NASA Technical Reports Server (NTRS)

Raj, S. V.

2017-01-01

Part I of the paper discussed the temperature dependencies of the electrical resistivities, thermal conductivities, thermal diffusivities and total hemispherical emissivities of several vacuum plasma sprayed (VPS) and cold sprayed copper alloy monolithic coatings, VPS NiAl, VPS NiCrAlY, extruded GRCop-84 and as-cast Cu-17(wt.%)Cr-5%Al. Part II discusses the temperature dependencies of the constant pressure specific heat capacities, CP, of these coatings. The data were empirically were regression-fitted with the equation: CP = AT4 + BT3 + CT2 + DT +E where T is the absolute temperature and A, B, C, D and E are regression constants. The temperature dependencies of the molar enthalpy, molar entropy and Gibbs molar free energy determined from experimental values of molar specific heat capacity are reported. Calculated values of CP using the Neumann-Kopp (NK) rule were in poor agreement with experimental data. Instead, a modification of the Neumann-Kopp rule was found to predict values closer to the experimental data with an absolute deviation less than 6.5%. The specific molar heat capacities for all the alloys did not agree with the Dulong-Petit law, and CP is greater than 3R, where R is the universal gas constant, were measured for all the alloys except NiAl for which CP is less than 3R at all temperatures.

Thermophysical Properties of Cold- and Vacuum Plasma-Sprayed Cu-Cr-X Alloys, NiAl and NiCrAlY Coatings II: Specific Heat Capacity

NASA Astrophysics Data System (ADS)

Raj, S. V.

2017-11-01

Part I of the paper discussed the temperature dependencies of the electrical resistivities, thermal conductivities, thermal diffusivities and total hemispherical emissivities of several vacuum plasma-sprayed (VPS) and cold-sprayed (CS) copper alloy monolithic coatings, VPS NiAl, VPS NiCrAlY, extruded GRCop-84 and as-cast Cu-17(wt.%)Cr-5%Al. Part II discusses the temperature dependencies of the constant-pressure specific heat capacities, C P, of these coatings. The data were empirically regression-fitted with the equation: \\varvec{C}_{P} = {AT}^{4} + {BT}^{3} + {CT}^{2} + DT + \\varvec{E}where T is the absolute temperature and A, B, C, D and E are regression constants. The temperature dependencies of the molar enthalpy, molar entropy and Gibbs molar free energy determined from experimental values of molar specific heat capacity are reported. Calculated values of C P using the Neumann-Kopp (NK) rule were in poor agreement with experimental data. Instead, a modification of the NK rule was found to predict values closer to the experimental data with an absolute deviation less than 6.5%. The specific molar heat capacities for all the alloys did not agree with the Dulong-Petit law, and C P > 3 R, where R is the universal gas constant, were measured for all the alloys except NiAl for which C P < 3 R at all temperatures.

Dynamics of glass-forming liquids. XIX. Rise and decay of field induced anisotropy in the non-linear regime

NASA Astrophysics Data System (ADS)

Young-Gonzales, Amanda R.; Samanta, Subarna; Richert, Ranko

2015-09-01

For glycerol and three monohydroxy alcohols, we have measured the non-linear dielectric effects resulting from the application and removal of a high dc bias electric field. The field effects are detected by virtue of a small amplitude harmonic field, from which time resolved changes in the dielectric loss are derived. The changes in permittivity are dominated by modifications of the time constants (rather than amplitudes) which display two contributions: a heating-like decrease of relaxation times that originates from the time dependent field when the bias is switched on and off and a slowing down of the dynamics resulting from the field induced reduction of configurational entropy. As observed for the electro-optical Kerr effect, the rise of the entropy change is slower than its decay, a feature that we rationalize on the basis of the quadratic dependence of the entropy change on polarization. For glycerol, the observed steady state level of the field induced shift of the glass transition temperature (+84 mK) matches the expectation based on the entropy change and its impact on dynamics via the Adam-Gibbs relation (+88 mK). For the alcohols, these non-linear effects rise and decay on the time scales of the prominent dielectric Debye process, underscoring the relation of these features to polarization anisotropy, opposed to mechanical or enthalpy relaxation which are orders of magnitude faster in these systems. A model is discussed which captures the observed magnitudes as well as time dependences in a near quantitative fashion. It is demonstrated that the high bias field modifies the response of polarization to the ac field, including a temporary change in the low field susceptibility.

Thermodynamic characterization of a triple-helical three-way junction containing a Hoogsteen branch point.

PubMed

Hüsler, P L; Klump, H H

1995-09-10

We have designed a Hoogsteen (HG) triple-helical three-way junction (ternary complex) constructed from three 33-mer oligonucleotides based on the same subset of sequences used for the Watson-Crick (WC) triple-helical three-way junction, characterized previously (P. L. Hüsler and H. H. Klump (1994) Arch. Biochem. Biophys., 313, 29-38). The junction differs primarily in the assembly of the branch point and the ends of the arms. The three oligonucleotides can each fold into a WC hairpin, linked by a four-member cytosine loop, each containing a homo-pyrimidine 10-mer single-strand extension. On lowering the pH (between 6 and 4), the extensions mutually associate to one of the other hairpins via Hoogsteen (HG) hydrogen bonding. Collectively, this process results in the formation of the branch point and the triple-helical arms. The HG triple-helical three-way junction is characterized by gel electrophoresis, circular dichroism, uv melting, and differential scanning calorimetry. The junction undergoes thermal unfolding in two distinct temperature regions. In the temperature range 15 to 50 degrees C loss of HG base pairing results in the dissociation of the three-way junction. Between 55 and 95 degrees C the resulting hairpins undergo further successive unfolding. The overall calorimetric unfolding enthalpy and entropy changes associated with the loss of HG base pairing are approximately equal to the sum of the enthalpy and entropy changes associated with the dissociation of the HG base pairing in the isolated arms (170.6 kcal.mol-1; 540.1 cal.mol-1.K-1). It is apparent from these results that in the proximity of the branch point the structure is not perturb or strain. This result is contrary to the results obtained for the WC triple-helical three-way and for three-way junctions constructed from canonical double-helical DNA. Complete folding of the junction requires either high Na+ (600 mM) ion concentrations or 40-60 mM Mg2+.

Mechanisms of chain adsorption on porous substrates and critical conditions of polymer chromatography.

PubMed

Cimino, Richard T; Rasmussen, Christopher J; Brun, Yefim; Neimark, Alexander V

2016-11-01

Polymer adsorption is a ubiquitous phenomenon with numerous technological and healthcare applications. The mechanisms of polymer adsorption on surfaces and in pores are complex owing to a competition between various entropic and enthalpic factors. Due to adsorption of monomers to the surface, the chain gains in enthalpy yet loses in entropy because of confining effects. This competition leads to the existence of critical conditions of adsorption when enthalpy gain and entropy loss are in balance. The critical conditions are controlled by the confining geometry and effective adsorption energy, which depends on the solvent composition and temperature. This phenomenon has important implications in polymer chromatography, since the retention at the critical point of adsorption (CPA) is chain length independent. However, the mechanisms of polymer adsorption in pores are poorly understood and there is an ongoing discussion in the theoretical literature about the very existence of CPA for polymer adsorption on porous substrates. In this work, we examine the mechanisms of chain adsorption on a model porous substrate using Monte Carlo (MC) simulations. We distinguish three adsorption mechanisms depending on the chain location: on external surface, completely confined in pores, and also partially confined in pores in so-called "flower" conformations. The free energies of different conformations of adsorbed chains are calculated by the incremental gauge cell MC method that allows one to determine the partition coefficient as a function of the adsorption potential, pore size, and chain length. We confirm the existence of the CPA for chain length independent separation on porous substrates, which is explained by the dominant contributions of the chain adsorption at the external surface, in particular in flower conformations. Moreover, we show that the critical conditions for porous and nonporous substrates are identical and depend only on the surface chemistry. The theoretical results are confirmed by comparison with experimental data on chromatographic separation of a series of linear polystyrenes. Copyright © 2016 Elsevier Inc. All rights reserved.

Interaction of new kinase inhibitors cabozantinib and tofacitinib with human serum alpha-1 acid glycoprotein. A comprehensive spectroscopic and molecular Docking approach

NASA Astrophysics Data System (ADS)

Ajmal, Mohammad Rehan; Abdelhameed, Ali Saber; Alam, Parvez; Khan, Rizwan Hasan

2016-04-01

In the current study we have investigated the interaction of newly approved kinase inhibitors namely Cabozantinib (CBZ) and Tofacitinib (TFB) with human Alpha-1 acid glycoprotein (AAG) under simulated physiological conditions using fluorescence quenching measurements, circular dichroism, dynamic light scattering and molecular docking methods. CBZ and TFB binds to AAG with significant affinity and the calculated binding constant for the drugs lie in the order of 104. With the increase in temperature the binding constant values decreased for both CBZ and TFB. The fluorescence resonance energy transfer (FRET) from AAG to CBZ and TFB suggested the fluorescence intensity of AAG was quenched by the two studied drugs via the formation of a non-fluorescent complex in the static manner. The molecular distance r value calculated from FRET is around 2 nm for both drugs, fluorescence spectroscopy data was employed for the study of thermodynamic parameters, standard Gibbs free energy change at 300K was calculated as - 5.234 kcal mol- 1 for CBZ-AAG interaction and - 6.237 kcal mol- 1 for TFB-AAG interaction, standard enthalpy change and standard entropy change for CBZ-AAG interaction are - 9.553 kcal mol- 1 and - 14.618 cal mol- 1K- 1 respectively while for AAG-TFB interaction, standard enthalpy and standard entropy change was calculated as 4.019 kcal mol- 1 and 7.206 cal mol- 1K- 1 respectively. Protein binding of the two drugs caused the tertiary structure alterations. Dynamic light scattering measurements demonstrated the reduction in the hydrodynamic radii of the protein. Furthermore molecular docking results suggested the Hydrophobic interaction and hydrogen bonding were the interactive forces in the binding process of CBZ to AAG while in case of TFB only hydrophobic interactions were found to be involved, overlap of the binding site for two studied drugs on the AAG molecule was revealed by docking results.

Black hole enthalpy and an entropy inequality for the thermodynamic volume

NASA Astrophysics Data System (ADS)

Cvetič, M.; Gibbons, G. W.; Kubizňák, D.; Pope, C. N.

2011-07-01

In a theory where the cosmological constant Λ or the gauge coupling constant g arises as the vacuum expectation value, its variation should be included in the first law of thermodynamics for black holes. This becomes dE=TdS+ΩidJi+ΦαdQα+ΘdΛ, where E is now the enthalpy of the spacetime, and Θ, the thermodynamic conjugate of Λ, is proportional to an effective volume V=-(16πΘ)/(D-2) “inside the event horizon.” Here we calculate Θ and V for a wide variety of D-dimensional charged rotating asymptotically anti-de Sitter (AdS) black hole spacetimes, using the first law or the Smarr relation. We compare our expressions with those obtained by implementing a suggestion of Kastor, Ray, and Traschen, involving Komar integrals and Killing potentials, which we construct from conformal Killing-Yano tensors. We conjecture that the volume V and the horizon area A satisfy the inequality R≡((D-1)V/AD-2)1/(D-1)(AD-2/A)1/(D-2)≥1, where AD-2 is the volume of the unit (D-2) sphere, and we show that this is obeyed for a wide variety of black holes, and saturated for Schwarzschild-AdS. Intriguingly, this inequality is the “inverse” of the isoperimetric inequality for a volume V in Euclidean (D-1) space bounded by a surface of area A, for which R≤1. Our conjectured reverse isoperimetric inequality can be interpreted as the statement that the entropy inside a horizon of a given ”volume” V is maximized for Schwarzschild-AdS. The thermodynamic definition of V requires a cosmological constant (or gauge coupling constant). However, except in seven dimensions, a smooth limit exists where Λ or g goes to zero, providing a definition of V even for asymptotically flat black holes.

Quasithermodynamic Contributions to the Fluctuations of a Protein Nanopore

PubMed Central

2015-01-01

Proteins undergo thermally activated conformational fluctuations among two or more substates, but a quantitative inquiry on their kinetics is persistently challenged by numerous factors, including the complexity and dynamics of various interactions, along with the inability to detect functional substates within a resolvable time scale. Here, we analyzed in detail the current fluctuations of a monomeric β-barrel protein nanopore of known high-resolution X-ray crystal structure. We demonstrated that targeted perturbations of the protein nanopore system, in the form of loop-deletion mutagenesis, accompanying alterations of electrostatic interactions between long extracellular loops, produced modest changes of the differential activation free energies calculated at 25 °C, ΔΔG⧧, in the range near the thermal energy but substantial and correlated modifications of the differential activation enthalpies, ΔΔH⧧, and entropies, ΔΔS⧧. This finding indicates that the local conformational reorganizations of the packing and flexibility of the fluctuating loops lining the central constriction of this protein nanopore were supplemented by changes in the single-channel kinetics. These changes were reflected in the enthalpy–entropy reconversions of the interactions between the loop partners with a compensating temperature, TC, of ∼300 K, and an activation free energy constant of ∼41 kJ/mol. We also determined that temperature has a much greater effect on the energetics of the equilibrium gating fluctuations of a protein nanopore than other environmental parameters, such as the ionic strength of the aqueous phase as well as the applied transmembrane potential, likely due to ample changes in the solvation activation enthalpies. There is no fundamental limitation for applying this approach to other complex, multistate membrane protein systems. Therefore, this methodology has major implications in the area of membrane protein design and dynamics, primarily by revealing a better quantitative assessment on the equilibrium transitions among multiple well-defined and functionally distinct substates of protein channels and pores. PMID:25479108

Thermodynamic Characterization of Binding Oxytricha nova Single Strand Telomere DNA with the Alpha Protein N-terminal Domain

PubMed Central

Buczek, Pawel; Horvath, Martin P.

2010-01-01

The Oxytricha nova telomere binding protein alpha subunit binds single strand DNA and participates in a nucleoprotein complex that protects the very ends of chromosomes. To understand how the N-terminal, DNA binding domain of alpha interacts with DNA we measured the stoichiometry, enthalpy (ΔH), entropy (ΔS), and dissociation constant (KD-DNA) for binding telomere DNA fragments at different temperatures and salt concentrations using native gel electrophoresis and isothermal titration calorimetry (ITC). About 85% of the total free energy of binding corresponded with non-electrostatic interactions for all DNAs. Telomere DNA fragments d(T2G4), d(T4G4), d(G3T4G4), and d(G4T4G4) each formed monovalent protein complexes. In the case of d(T4G4T4G4), which has two tandemly repeated d(TTTTTGGGG) telomere motifs, two binding sites were observed. The high-affinity “A site” has a dissociation constant, KD-DNA(A)=13(±4) nM, while the low-affinity “B site” is characterized by KD-DNA(B)=5600(±600) nM at 25 °C. Nucleotide substitution variants verified that the A site corresponds principally with the 3′-terminal portion of d(T4G4T4G4). The relative contributions of entropy (ΔS) and enthalpy (ΔH) for binding reactions were DNA length-dependent as was heat capacity (ΔCp). These trends with respect to DNA length likely reflect structural transitions in the DNA molecule that are coupled with DNA–protein association. Results presented here are important for understanding early intermediates and subsequent stages in the assembly of the full telomere nucleoprotein complex and how binding events can prepare the telomere DNA for extension by telomerase, a critical event in telomere biology. PMID:16678852

Thermodynamic characterization of binding Oxytricha nova single strand telomere DNA with the alpha protein N-terminal domain.

PubMed

Buczek, Pawel; Horvath, Martin P

2006-06-23

The Oxytricha nova telemere binding protein alpha subunit binds single strand DNA and participates in a nucleoprotein complex that protects the very ends of chromosomes. To understand how the N-terminal, DNA binding domain of alpha interacts with DNA we measured the stoichiometry, enthalpy (DeltaH), entropy (DeltaS), and dissociation constant (K(D-DNA)) for binding telomere DNA fragments at different temperatures and salt concentrations using native gel electrophoresis and isothermal titration calorimetry (ITC). About 85% of the total free energy of binding corresponded with non-electrostatic interactions for all DNAs. Telomere DNA fragments d(T(2)G(4)), d(T(4)G(4)), d(G(3)T(4)G(4)), and d(G(4)T(4)G(4)) each formed monovalent protein complexes. In the case of d(T(4)G(4)T(4)G(4)), which has two tandemly repeated d(TTTTTGGGG) telomere motifs, two binding sites were observed. The high-affinity "A site" has a dissociation constant, K(D-DNA(A)) = 13(+/-4) nM, while the low-affinity "B site" is characterized by K(D-DNA(B)) = 5600(+/-600) nM at 25 degrees C. Nucleotide substitution variants verified that the A site corresponds principally with the 3'-terminal portion of d(T(4)G(4)T(4)G(4)). The relative contributions of entropy (DeltaS) and enthalpy (DeltaH) for binding reactions were DNA length-dependent as was heat capacity (DeltaCp). These trends with respect to DNA length likely reflect structural transitions in the DNA molecule that are coupled with DNA-protein association. Results presented here are important for understanding early intermediates and subsequent stages in the assembly of the full telomere nucleoprotein complex and how binding events can prepare the telomere DNA for extension by telomerase, a critical event in telomere biology.

Mechanochemical effect in the iron(III) spin crossover complex [Fe(3-MeO-salenEt2]PF6 as studied by heat capacity calorimetry.

PubMed

Sorai, Michio; Burriel, Ramón; Westrum, Edgar F; Hendrickson, David N

2008-04-10

Magnetic and thermal properties of the iron(III) spin crossover complex [Fe(3MeO-salenEt)(2)]PF(6) are very sensitive to mechanochemical perturbations. Heat capacities for unperturbed and differently perturbed samples were precisely determined by adiabatic calorimetry at temperatures in the 10-300 K range. The unperturbed compound shows a cooperative spin crossover transition at 162.31 K, presenting a hysteresis of 2.8 K. The anomalous enthalpy and entropy contents of the transition were evaluated to be Delta(trs)H = 5.94 kJ mol(-1) and Delta(trs)S = 36.7 J K(-1) mol(-1), respectively. By mechanochemical treatments, (1) the phase transition temperature was lowered by 1.14 K, (2) the enthalpy and entropy gains at the phase transition due to the spin crossover phenomenon were diminished to Delta(trs)H = 4.94 kJ mol(-1) and Delta(trs)S = 31.1 J K(-1) mol(-1), and (3) the lattice heat capacities were larger than those of the unperturbed sample over the whole temperature range. In spite of different mechanical perturbations (grinding with a mortar and pestle and grinding in a ball-mill), two sets of heat capacity measurements provided basically the same results. The mechanochemical perturbation exerts its effect more strongly on the low-spin state than on the high-spin state. It shows a substantial increase of the number of iron(III) ions in the high-spin state below the transition temperature. The heat capacities of the diamagnetic cobalt(III) analogue [Co(3MeO-salenEt)(2)]PF(6) also were measured. The lattice heat capacity of the iron compounds has been estimated from either the measurements on the cobalt complex using a corresponding states law or the effective frequency distribution method. These estimations have been used for the evaluation of the transition anomaly.

Predictive thermodynamics for ionic solids and liquids.

PubMed

Glasser, Leslie; Jenkins, H Donald Brooke

2016-08-21

The application of thermodynamics is simple, even if the theory may appear intimidating. We describe tools, developed over recent years, which make it easy to estimate often elusive thermodynamic parameter values, generally (but not exclusively) for ionic materials, both solid and liquid, as well as for their solid hydrates and solvates. The tools are termed volume-based thermodynamics (VBT) and thermodynamic difference rules (TDR), supplemented by the simple salt approximation (SSA) and single-ion values for volume, Vm, heat capacity, , entropy, , formation enthalpy, ΔfH°, and Gibbs formation energy, ΔfG°. These tools can be applied to provide values of thermodynamic and thermomechanical properties such as standard enthalpy of formation, ΔfH°, standard entropy, , heat capacity, Cp, Gibbs function of formation, ΔfG°, lattice potential energy, UPOT, isothermal expansion coefficient, α, and isothermal compressibility, β, and used to suggest the thermodynamic feasibility of reactions among condensed ionic phases. Because many of these methods yield results largely independent of crystal structure, they have been successfully extended to the important and developing class of ionic liquids as well as to new and hypothesised materials. Finally, these predictive methods are illustrated by application to K2SnCl6, for which known experimental results are available for comparison. A selection of applications of VBT and TDR is presented which have enabled input, usually in the form of thermodynamics, to be brought to bear on a range of topical problems. Perhaps the most significant advantage of VBT and TDR methods is their inherent simplicity in that they do not require a high level of computational expertise nor expensive high-performance computation tools - a spreadsheet will usually suffice - yet the techniques are extremely powerful and accessible to non-experts. The connection between formula unit volume, Vm, and standard thermodynamic parameters represents a major advance exploited by these techniques.

Thermodynamics and docking of agonists to the β(2)-adrenoceptor determined using [(3)H](R,R')-4-methoxyfenoterol as the marker ligand.

PubMed

Toll, Lawrence; Pajak, Karolina; Plazinska, Anita; Jozwiak, Krzysztof; Jimenez, Lucita; Kozocas, Joseph A; Tanga, Mary J; Bupp, James E; Wainer, Irving W

2012-06-01

G protein-coupled receptors (GPCRs) are integral membrane proteins that change conformation after ligand binding so that they can transduce signals from an extracellular ligand to a variety of intracellular components. The detailed interaction of a molecule with a G protein-coupled receptor is a complicated process that is influenced by the receptor conformation, thermodynamics, and ligand conformation and stereoisomeric configuration. To better understand the molecular interactions of fenoterol analogs with the β(2)-adrenergic receptor, we developed a new agonist radioligand for binding assays. [(3)H](R,R')-methoxyfenoterol was used to probe the binding affinity for a series of fenoterol stereoisomers and derivatives. The results suggest that the radioligand binds with high affinity to an agonist conformation of the receptor, which represents approximately 25% of the total β(2)-adrenoceptor (AR) population as determined with the antagonist [(3)H]CGP-12177. The β(2)-AR agonists tested in this study have considerably higher affinity for the agonist conformation of the receptor, and K(i) values determined for fenoterol analogs model much better the cAMP activity of the β(2)-AR elicited by these ligands. The thermodynamics of binding are also different when interacting with an agonist conformation, being purely entropy-driven for each fenoterol isomer, rather than a mixture of entropy and enthalpy when the fenoterol isomers binding was determined using [(3)H]CGP-12177. Finally, computational modeling identified the molecular interactions involved in agonist binding and allow for the prediction of additional novel β(2)-AR agonists. The study underlines the possibility of using defined radioligand structure to probe a specific conformation of such shape-shifting system as the β(2)-adrenoceptor.

The ground states of iron(III) porphines: role of entropy-enthalpy compensation, Fermi correlation, dispersion, and zero-point energies.

PubMed

Kepp, Kasper P

2011-10-01

Porphyrins are much studied due to their biochemical relevance and many applications. The density functional TPSSh has previously accurately described the energy of close-lying electronic states of transition metal systems such as porphyrins. However, a recent study questioned this conclusion based on calculations of five iron(III) porphines. Here, we compute the geometries of 80 different electronic configurations and the free energies of the most stable configurations with the functionals TPSSh, TPSS, and B3LYP. Zero-point energies and entropy favor high-spin by ~4kJ/mol and 0-10kJ/mol, respectively. When these effects are included, and all electronic configurations are evaluated, TPSSh correctly predicts the spin of all the four difficult phenylporphine cases and is within the lower bound of uncertainty of any known theoretical method for the fifth, iron(III) chloroporphine. Dispersion computed with DFT-D3 favors low-spin by 3-53kJ/mol (TPSSh) or 4-15kJ/mol (B3LYP) due to the attractive r(-6) term and the shorter distances in low-spin. The very large and diverse corrections from TPSS and TPSSh seem less consistent with the similarity of the systems than when calculated from B3LYP. If the functional-specific corrections are used, B3LYP and TPSSh are of equal accuracy, and TPSS is much worse, whereas if the physically reasonable B3LYP-computed dispersion effect is used for all functionals, TPSSh is accurate for all systems. B3LYP is significantly more accurate when dispersion is added, confirming previous results. Copyright © 2011 Elsevier Inc. All rights reserved.

Thermodynamics and Docking of Agonists to the β2-Adrenoceptor Determined Using [3H](R,R′)-4-Methoxyfenoterol as the Marker Ligand

PubMed Central

Pajak, Karolina; Plazinska, Anita; Jozwiak, Krzysztof; Jimenez, Lucita; Kozocas, Joseph A.; Tanga, Mary J.; Bupp, James E.; Wainer, Irving W.

2012-01-01

G protein-coupled receptors (GPCRs) are integral membrane proteins that change conformation after ligand binding so that they can transduce signals from an extracellular ligand to a variety of intracellular components. The detailed interaction of a molecule with a G protein-coupled receptor is a complicated process that is influenced by the receptor conformation, thermodynamics, and ligand conformation and stereoisomeric configuration. To better understand the molecular interactions of fenoterol analogs with the β2-adrenergic receptor, we developed a new agonist radioligand for binding assays. [3H](R,R′)-methoxyfenoterol was used to probe the binding affinity for a series of fenoterol stereoisomers and derivatives. The results suggest that the radioligand binds with high affinity to an agonist conformation of the receptor, which represents approximately 25% of the total β2-adrenoceptor (AR) population as determined with the antagonist [3H]CGP-12177. The β2-AR agonists tested in this study have considerably higher affinity for the agonist conformation of the receptor, and Ki values determined for fenoterol analogs model much better the cAMP activity of the β2-AR elicited by these ligands. The thermodynamics of binding are also different when interacting with an agonist conformation, being purely entropy-driven for each fenoterol isomer, rather than a mixture of entropy and enthalpy when the fenoterol isomers binding was determined using [3H]CGP-12177. Finally, computational modeling identified the molecular interactions involved in agonist binding and allow for the prediction of additional novel β2-AR agonists. The study underlines the possibility of using defined radioligand structure to probe a specific conformation of such shape-shifting system as the β2-adrenoceptor. PMID:22434858

On the recent warming in the subcloud layer entropy and vertically integrated moist static energy over South Asian Monsoon region.

NASA Astrophysics Data System (ADS)

Konduru, R.; Gupta, A.; Matsumoto, J.; Takahashi, H. G.

2017-12-01

In order to explain monsoon circulation, surface temperature gradients described as most traditional concept. However, it cannot explain certain important aspects of monsoon circulation. Later, convective quasi-equilibrium framework and vertically integrated atmospheric energy budget has become recognized theories to explain the monsoon circulation. In this article, same theories were analyzed and observed for the duration 1979-2010 over south Asian summer monsoon region. With the help of NCEP-R2, NOAA 20th Century, and Era-Interim reanalysis an important feature was noticed pertained to subcloud layer entropy and vertical moist static energy. In the last 32 years, subcloud layer entropy and vertically integrated moist static energy has shown significant seasonal warming all over the region with peak over the poleward flank of the cross-equatorial cell. The important reason related to the warming was found to be increase in surface enthalpy fluxes. Instead, other dynamical contributions pertained to the warming was also observed. Increase in positive anomalies of vertical advection of moist static energy over northern Bay of Bengal, Central India, Peninsular India, Eastern Arabian Sea, and Equatorial Indian Ocean was found to be an important dynamic factor contributing for warming of vertically integrated moist static energy. Along with it vertical moist stability has also supported the argument. Similar interpretations were perceived in the AMIP simulation of CCSM4 model. Further modeling experiments on this warming will be helpful to know the exact mechanism behind it.

Molecular Dynamics Simulation of Surface Tension of NaCl Aqueous Solution at 298.15K: from Diluted to Highly Supersaturated Concentrations

NASA Astrophysics Data System (ADS)

Wang, Xiaoxiang; Chen, Chuchu; Poeschl, Ulirch; Su, Hang; Cheng, Yafang

2017-04-01

Sodium chloride (NaCl) is one of the key components of atmospheric aerosol particles. Concentration-depend surface tension of aqueous NaCl solution is essential to determine the equilibrium between droplet NaCl solution and water vapor, which is important in regards to aerosol-cloud interaction and aerosol climate effects. Although supersaturated NaCl droplets can be widely found under atmospheric conditions, the experimental determined concentration dependency of surface tension is limited up to the saturated concentration range due to technical difficulties, i.e., heterogeneous nucleation since nearly all surface tension measurement techniques requires contact of the sensor and solution surface. In this study, the surface tension of NaCl aqueous solution with solute mass fraction from 0 to 1 was calculated using molecular dynamics (MD) simulation. The surface tension increases monotonically and near linearly when mass fraction of NaCl (xNaCl) is lower than 0.265 (saturation point), which follows theoretical predictions (e.g., E-AIM, SP parameterization, and PK parameterization). Once entering into the supersaturated concentration range, the calculated surface tension starts to deviate from the near-linear extrapolation and adopts a slightly higher increasing rate until xNaCl of 0.35. We found that these two increasing phases (xNaCl 0.35) is mainly driven by the increase of excessive surface enthalpy when the solution becomes concentrated. After that, the surface tension remains almost unchanged until xNaCl of 0.52. This phenomenon is supported by the results from experiment based Differential Koehler Analyses. The stable surface tension in this concentration range is attributed to a simultaneous change of surface excess enthalpy and entropy at similar degree. When the NaCl solution is getting more concentrated than xNaCl of 0.52, the simulated surface tension regains an even faster growing momentum and shows the tendency of ultimately approaching the surface tension of molten NaCl at 298.15 K ( 148.4 mN/m by MD simulation). Energetic analyses imply that this fast increase is primarily still an excessive surface enthalpy-driven process, although concurrent fluctuation of excessive surface entropy is also expected but in a much smaller scale. Our results unfold the global landscape of concentration dependence of aqueous NaCl solution and its driven forces: a water surface tension dominated regime (xNaCl from 0 to 0.35), a transition regime (xNaCl from 0.35 to 0.52) and a molten NaCl surface tension dominated regime (xNaCl beyond 0.52).

Thermophysical properties and oxygen transport in (Th x,Pu 1-x)O 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galvin, C. O. T.; Cooper, M. W. D.; Rushton, M. J. D.

Using Molecular Dynamics, this paper investigates the thermophysical properties and oxygen transport of (Th x,Pu 1–x)O 2 (0 ≤ x ≤ 1) between 300–3500 K. Specifically, the superionic transition is investigated and viewed via the thermal dependence of lattice parameter, linear thermal expansion coefficient, enthalpy and specific heat at constant pressure. Oxygen diffusivity and activation enthalpy are also investigated. Below the superionic temperature an increase of oxygen diffusivity for certain compositions of (Th x,Pu 1–x)O 2 compared to the pure end members is predicted. Oxygen defect formation enthalpies are also examined, as they underpin the superionic transition temperature and themore » increase in oxygen diffusivity. The increase in oxygen diffusivity for (Th x,Pu 1–x)O 2 is explained in terms of lower oxygen defect formation enthalpies for (Th x,Pu 1–x)O 2 than PuO 2 and ThO 2, while links are drawn between the superionic transition temperature and oxygen Frenkel disorder.« less

Thermophysical properties and oxygen transport in (Th x,Pu 1-x)O 2

DOE PAGES

Galvin, C. O. T.; Cooper, M. W. D.; Rushton, M. J. D.; ...

2016-10-31

Using Molecular Dynamics, this paper investigates the thermophysical properties and oxygen transport of (Th x,Pu 1–x)O 2 (0 ≤ x ≤ 1) between 300–3500 K. Specifically, the superionic transition is investigated and viewed via the thermal dependence of lattice parameter, linear thermal expansion coefficient, enthalpy and specific heat at constant pressure. Oxygen diffusivity and activation enthalpy are also investigated. Below the superionic temperature an increase of oxygen diffusivity for certain compositions of (Th x,Pu 1–x)O 2 compared to the pure end members is predicted. Oxygen defect formation enthalpies are also examined, as they underpin the superionic transition temperature and themore » increase in oxygen diffusivity. The increase in oxygen diffusivity for (Th x,Pu 1–x)O 2 is explained in terms of lower oxygen defect formation enthalpies for (Th x,Pu 1–x)O 2 than PuO 2 and ThO 2, while links are drawn between the superionic transition temperature and oxygen Frenkel disorder.« less

Thermophysical property of undercooled liquid binary alloy composed of metallic and semiconductor elements

NASA Astrophysics Data System (ADS)

Wang, H. P.; Wei, B.

2009-02-01

The thermophysical properties of the liquid Ni-Si binary alloy system were investigated by the molecular dynamics method. The properties investigated include density, excessive volume, enthalpy, mixing enthalpy and specific heat at both superheated and undercooled states. It is found that the density decreases with an increase in the Si content, and so do the temperature coefficients. If the Si content is smaller than 30%, the density changes linearly with the temperature. If it is larger than 30%, the density is a quadratic function of the temperature. The simulated enthalpies of different composition alloys increase linearly with a rise in temperature. This indicates that the specific heats of Ni-Si alloys change little with temperature. The specific heat versus composition first decreases to a minimum value at 50% Si, then experiences a rise to a maximum value at 90% Si and finally falls again. According to the excessive volume and mixing enthalpy, it can be deduced that the Ni-Si alloy system seriously deviates from the ideal solution. Moreover, a comparison was also performed between the present results and the approximated values by the Neumann-Kopp rule. It reveals that this work provides reasonable data in a broad temperature range, especially for the metastable undercooled liquid state.

Direct Nanoscale Characterization of Submolecular Mobility in Complex Organic Non-linear Optical Systems

NASA Astrophysics Data System (ADS)

Knorr, Daniel; Gray, Tomoko; Kim, Tae-Dong; Luo, Jingdong; Jen, Alex; Overney, Rene

2008-03-01

For organic non-linear optical (NLO) materials composed of intricate molecular building blocks, the challenge is to deduce meaningful molecular scale mobility information to understand complex relaxation and phase behavior. This is crucial, as the process of achieving a robust acentric alignment strongly depends on the availability of inter- and intra-molecular mobilities outside the temperature range of the device operation window. Here, we introduce a nanoscale methodology based on scanning probe microscopy that provides direct insight into structural relaxations and shows great potential to direct material design of sophisticated macromolecules. It also offers a means by which mesoscale dynamics and cooperativity involved in relaxation processes can be quantified in terms of dynamic entropy and enthalpy. This study demonstrates this methodology to describe the mesocale dynamics of two systems (1) organic networking dendronized NLO molecular glasses that self-assemble into physically linked polymers due to quadrupolar phenyl-perfluorophenyl interactions and (2) dendronized side-chain electro-optic (EO) polymers. For the self assembling glasses, the degree of intermolecular cooperativity can be deduced using this methodology, while for the dendronized side-chain polymers, specific side chain mobilities are exploited to improve EO properties.

Effects of non-CpG site methylation on DNA thermal stability: a fluorescence study

PubMed Central

Nardo, Luca; Lamperti, Marco; Salerno, Domenico; Cassina, Valeria; Missana, Natalia; Bondani, Maria; Tempestini, Alessia; Mantegazza, Francesco

2015-01-01

Cytosine methylation is a widespread epigenetic regulation mechanism. In healthy mature cells, methylation occurs at CpG dinucleotides within promoters, where it primarily silences gene expression by modifying the binding affinity of transcription factors to the promoters. Conversely, a recent study showed that in stem cells and cancer cell precursors, methylation also occurs at non-CpG pairs and involves introns and even gene bodies. The epigenetic role of such methylations and the molecular mechanisms by which they induce gene regulation remain elusive. The topology of both physiological and aberrant non-CpG methylation patterns still has to be detailed and could be revealed by using the differential stability of the duplexes formed between site-specific oligonucleotide probes and the corresponding methylated regions of genomic DNA. Here, we present a systematic study of the thermal stability of a DNA oligonucleotide sequence as a function of the number and position of non-CpG methylation sites. The melting temperatures were determined by monitoring the fluorescence of donor-acceptor dual-labelled oligonucleotides at various temperatures. An empirical model that estimates the methylation-induced variations in the standard values of hybridization entropy and enthalpy was developed. PMID:26354864

Enthalpic and Entropic Competition in Blends of Self-Suspended Hairy Nanoparticles

NASA Astrophysics Data System (ADS)

Choudhury, Snehashis; Agrawal, Akanksha; Archer, Lynden

Self-suspended hairy nanoparticles, where polymer chains are grafted onto nanoparticles, have attracted significant recent attention. These materials have been reported to manifest several interesting phenomena like thermal jamming, slowing-down of polymer chain dynamics, as well as small-strain stress overshoots during start-up of steady shear. The entropic penalty on tethered polymers produced by the requirement that they fill the space between the nanoparticle cores explain most of these behaviors. Here, we show that the entropic attraction between tethered polymer chains can be manipulated in mixtures of hairy nanoparticles using different polymer chemistry to design materials with unusual characteristics. Specifically, the degree of interpenetration of polymer chains can be controlled by tuning their interaction parameter (χ) . For SiO2-PEG/SiO2-PMMA blends, oscillatory rheological measurements show that the plateau modulus and yielding energy are significantly increased, while an opposite effect is seen with SiO2-PEG/SiO2-PI blends. More subtle effects of this enthalpy-entropy competition are well captured in Dielectric Spectroscopy measurements and SAXS experiments that can be used to quantify the degree of stretch and interdigitation of polymer chains.

Pressure-Dependent Electronic and Transport Properties of Bulk Platinum Oxide by Density Functional Theory

NASA Astrophysics Data System (ADS)

Kansara, Shivam; Gupta, Sanjeev K.; Sonvane, Yogesh; Nekrasov, Kirill A.; Kichigina, Natalia V.

2018-02-01

The structural, electronic, and vibrational properties of bulk platinum oxide (PtO) at compressive pressures in the interval from 0 GPa to 35 GPa are investigated using the density functional theory. The calculated electronic band structure of PtO shows poor metallicity at very low density of states on the Fermi level. However, the hybrid pseudopotential calculation yielded 0.78 eV and 1.30 eV direct band and indirect gap, respectively. Importantly, our results predict that PtO has a direct band gap within the framework of HSE06, and it prefers equally zero magnetic order at different pressures. In the Raman spectra, peaks are slightly shifted towards higher frequency with the decrease in pressure. We have also calculated the thermoelectric properties, namely the electronic thermal conductivity and electrical conductivity, with respect to temperature and thermodynamic properties such as entropy, specific heat at constant volume, enthalpy and Gibbs free energy with respect to pressure. The result shows that PtO is a promising candidate for use as a catalyst, in sensors, as a photo-cathode in water electrolysis, for thermal decomposition of inorganic salt and fuel cells.

Analysis of biomolecular solvation sites by 3D-RISM theory.

PubMed

Sindhikara, Daniel J; Hirata, Fumio

2013-06-06

We derive, implement, and apply equilibrium solvation site analysis for biomolecules. Our method utilizes 3D-RISM calculations to quickly obtain equilibrium solvent distributions without either necessity of simulation or limits of solvent sampling. Our analysis of these distributions extracts highest likelihood poses of solvent as well as localized entropies, enthalpies, and solvation free energies. We demonstrate our method on a structure of HIV-1 protease where excellent structural and thermodynamic data are available for comparison. Our results, obtained within minutes, show systematic agreement with available experimental data. Further, our results are in good agreement with established simulation-based solvent analysis methods. This method can be used not only for visual analysis of active site solvation but also for virtual screening methods and experimental refinement.

Electrochemical thermodynamic measurement system

DOEpatents

Reynier, Yvan [Meylan, FR; Yazami, Rachid [Los Angeles, CA; Fultz, Brent T [Pasadena, CA

2009-09-29

The present invention provides systems and methods for accurately characterizing thermodynamic and materials properties of electrodes and electrochemical energy storage and conversion systems. Systems and methods of the present invention are configured for simultaneously collecting a suite of measurements characterizing a plurality of interconnected electrochemical and thermodynamic parameters relating to the electrode reaction state of advancement, voltage and temperature. Enhanced sensitivity provided by the present methods and systems combined with measurement conditions that reflect thermodynamically stabilized electrode conditions allow very accurate measurement of thermodynamic parameters, including state functions such as the Gibbs free energy, enthalpy and entropy of electrode/electrochemical cell reactions, that enable prediction of important performance attributes of electrode materials and electrochemical systems, such as the energy, power density, current rate and the cycle life of an electrochemical cell.

Sorption characteristic of uranium(VI) ion onto K-feldspar.

PubMed

Gao, Xiaoqing; Bi, Mingliang; Shi, Keliang; Chai, Zhifang; Wu, Wangsuo

2017-10-01

The effect of pH, contact time, temperature, ionic strength and initial U(VI) concentration on U(VI) sorption onto K-feldspar was investigated using batch techniques. The sorption kinetics was evaluated and the activation energy was obtained based on the rate constants at different temperature. Graphical correlations of sorption isotherm models have been evaluated and applied for U(VI) uptake by K-feldspar. Various thermodynamic parameters, such as, Gibb's free energy, entropy and enthalpy of the on-going sorption process have been calculated and the possible sorption mechanism of U(VI) was deduced. The results are expected to help better understand the migration of uranium in the host materials of granite. Copyright © 2017 Elsevier Ltd. All rights reserved.

Vaporization behavior of tetraoctylphosphonium bis(2-ethylhexyl)phosphate ionic liquid

DOE PAGES

McMurray, J. W.; Zhou, Y.; Luo, H. M.; ...

2016-11-18

We determined the equilibrium vapor pressures, p e, of the ionic liquid tetraoctylphosphonium bis(2-ethylhexyl)phosphate ([P 8888][DEHP]) over the temperature range 409–495 K using mass loss Knudsen effusion. The p e versus temperature relationship compares well to 1-methyl-3-octylimidazolium bis(trifluoromethylsulfonyl)imide ([C 8mim][NTf 2]) but is lower than that of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C 2mim][NTf 2]) when measured using the same technique. Here, we determined the discrepancies between the p e for [C 8mim][NTf 2] and [C 2mim][NTf 2] with previous studies is discussed. Finally, the enthalpy and entropy of vaporization for all three fluids are estimated from the Clasius-Clapeyron relation.

Use of a residual distribution Euler solver to study the occurrence of transonic flow in Wells turbine rotor blades

NASA Astrophysics Data System (ADS)

Henriques, J. C. C.; Gato, L. M. C.

The aim of the present study is to investigate the occurrence of transonic flow in several cascade geometries and blade sections that have been considered in the design of Wells turbine rotor blades. The calculations were performed using an implicit Euler solver for two-dimensional flow. The numerical method uses a multi-dimensional upwind matrix residual distribution scheme formulated on a new symmetrized form of the Euler equations, both in time and in space, that decouples the entropy and the enthalpy equations. Second-order accurate steady-state solutions where obtained using a compact three-point stencil. The results show that unwanted transonic flow may occur in the turbine rotor at relatively low mean-flow Mach numbers.

Vaporization behavior of tetraoctylphosphonium bis(2-ethylhexyl)phosphate ionic liquid

NASA Astrophysics Data System (ADS)

McMurray, J. W.; Zhou, Y.; Luo, H. M.; Qu, J.

2017-01-01

The equilibrium vapor pressures, pe, of the ionic liquid tetraoctylphosphonium bis(2-ethylhexyl)phosphate ([P8888][DEHP]) over the temperature range 409-495 K were determined for the first time using mass loss Knudsen effusion. The pe versus temperature relationship compares well to 1-methyl-3-octylimidazolium bis(trifluoromethylsulfonyl)imide ([C8mim][NTf2]) but is lower than that of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C2mim][NTf2]) when measured using the same technique. The discrepancies between the pe determined in this work for [C8mim][NTf2] and [C2mim][NTf2] with previous studies is discussed. The enthalpy and entropy of vaporization for all three fluids are estimated from the Clasius-Clapeyron relation.

Potential of mean force between two hydrophobic solutes in water.

PubMed

Southall, Noel T; Dill, Ken A

2002-12-10

We study the potential of mean force between two nonpolar solutes in the Mercedes Benz model of water. Using NPT Monte Carlo simulations, we find that the solute size determines the relative preference of two solute molecules to come into contact ('contact minimum') or to be separated by a single layer of water ('solvent-separated minimum'). Larger solutes more strongly prefer the contacting state, while smaller solutes have more tendency to become solvent-separated, particularly in cold water. The thermal driving forces oscillate with solute separation. Contacts are stabilized by entropy, whereas solvent-separated solute pairing is stabilized by enthalpy. The free energy of interaction for small solutes is well-approximated by scaled-particle theory. Copyright 2002 Elsevier Science B.V.

[Oligonucleotide derivatives in the nucleic acid hybridization analysis. III. Synthesis and investigation of properties of oligonucleotides, bearing bifunctional non-nucleotide insert].

PubMed

Kupriushkin, M S; Pyshnyĭ, D V

2012-01-01

Non-nucleotide phosporamidites were synthetized, having branched backbone with different position of functional groups. Obtained phosphoramidite monomers contain intercalator moiety--6-chloro-2-methoxyacridine, and additional hydroxyl residue protected with dimethoxytrityl group or with tert-butyldimethylsilyl group for post-synthetic modification. Synthesized oligothymidilates contain one or more modified units in different positions of sequence. Melting temperature and thermodynamic parameters of formation of complementary duplexes formed by modified oligonucleotides was defined (change in enthalpy and entropy). The introduction of intercalating residue causes a significant stabilization of DNA duplexes. It is shown that the efficiency of the fluorescence of acridine residue in the oligonucleotide conjugate significantly changes upon hybridization with DNA.

Ultra-High Pressure Driver and Nozzle Survivability in the RDHWT/MARIAH II Hypersonic Wind Tunnel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Costantino, M.; Brown, G.; Raman, K.

2000-06-02

An ultra-high pressure device provides a high enthalpy (> 2500 kJ/kg), low entropy (< 5 kJ/kg-K) air source for the RDHWT/MARIAH II Program Medium Scale Hypersonic Wind Tunnel. The design uses stagnation conditions of 2300 MPa (330,000 Psi) and 750 K (900 F) in a radial configuration of intensifiers around an axial manifold to deliver pure air at 100 kg/s mass flow rates for run times suitable for aerodynamic, combustion, and test and evaluation applications. Helium injection upstream of the nozzle throat reduces the throat wall recovery temperature to about 1200 K and reduces the oxygen concentration at the nozzlemore » wall.« less

Oxidation kinetics of crystal violet by potassium permanganate in acidic medium

NASA Astrophysics Data System (ADS)

Khan, Sameera Razi; Ashfaq, Maria; Mubashir; Masood, Summyia

2016-05-01

The oxidation kinetics of crystal violet (a triphenylmethane dye) by potassium permanganate was focused in an acidic medium by the spectrophotometric method at 584 nm. The oxidation reaction of crystal violet by potassium permanganate is carried out in an acidic medium at different temperatures ranging within 298-318 K. The kinetic study was carried out to investigate the effect of the concentration, ionic strength and temperature. The reaction followed first order kinetics with respect to potassium permanganate and crystal violet and the overall rate of the reaction was found to be second order. Thermodynamic activation parameters like the activation energy ( E a), enthalpy change (Δ H*), free energy change (Δ G*), and entropy change (Δ S*) have also been evaluated.

Theoretical Insights into Monometallofullerene Th@C76: Strong Covalent Interaction between Thorium and the Carbon Cage.

PubMed

Zhao, Pei; Zhao, Xiang; Ehara, Masahiro

2018-03-19

Th@C 76 has been studied by density functional theory combined with statistical mechanics calculations. The results reveal that Th@ T d (19151)-C 76 satisfying the isolated pentagon rule possesses the lowest energy. Nevertheless, considering the enthalpy-entropy interplay, Th@ C 1 (17418)-C 76 with one pair of adjacent pentagons is thermodynamically favorable at elevated temperatures, which is reported for the first time. The bonding critical points in both isomers were analyzed to disclose covalent interactions between the inner Th and cages. In addition, the Wiberg bond orders of M-C bonding in different endohedral metallofullerenes (EMFs) were investigated to prove stronger covalent interactions of Th-C in Th-based EMFs.

Removal of Reactofix Navy Blue 2 GFN from aqueous solutions using adsorption techniques.

PubMed

Gupta, Vinod Kumar; Jain, Rajeev; Varshney, Shaily; Saini, Vipin Kumar

2007-03-15

The wheat husk, an agricultural by-product, has been activated and used as an adsorbent for the adsorption of Reactofix Navy Blue 2 GFN from aqueous solution. In this work, adsorption of Reactofix Navy Blue 2 GFN on wheat husk and charcoal has been studied by using batch studies. The equilibrium adsorption level was determined to be a function of the solution pH, adsorbent dosage, dye concentration and contact time. The equilibrium adsorption capacities of wheat husk and charcoal for dye removal were obtained using Freundlich and Langmuir isotherms. Thermodynamic parameters such as the free energies, enthalpies and entropies of adsorption were also evaluated. Adsorption process is considered suitable for removing color, COD from waste water.

Thermophysical characteristics of EuF2.136 crystal

NASA Astrophysics Data System (ADS)

Popov, P. A.; Moiseev, N. V.; Karimov, D. N.; Sorokin, N. I.; Sulyanova, E. A.; Sobolev, B. P.

2015-09-01

Single crystals of EuF2.136 solid solution with a f luorite-type structure (sp. gr. , a = 5.82171(5) Å) have been grown by the Bridgeman method from a melt. Their thermal conductivity k( T) in the temperature range of 50-300 K and heat capacity С Р ( T) at 63-300 K have been studied experimentally for the first time. At T = 300 K the thermophysical characteristics are as follows: thermal conductivity k = 2.13 W/(m K), heat capacity С Р = 73 J/(mol K), and phonon mean free path l ≈ 11 Å. The temperature dependences of entropy S( T), enthalpy H( T), and phonon mean free path l( T) in EuF2.136 crystal are determined.

Thermal behavior and compatibility study of dihydroxylammonium 3,4-dinitraminofurazan

NASA Astrophysics Data System (ADS)

Huang, Haifeng; Shi, Yameng; Yu, Yao; Yang, Jun

2018-04-01

A large number of nitramino-featured energetic salts have been reported and some of them show promising properties. Among them, the dihydroxylammonium 3,4-dinitraminofurazan (HADNAF) is easy to synthesize and shows high calculated detonation performances and acceptable thermal stability. The non-isothermal kinetics parameters of HADNAF including the apparent activation energy (E) and pre-exponential factor (A) of the exothermic decomposition reaction, and activation entropy (ΔS≠), activation enthalpy (ΔH≠), activation Gibbs free energy (ΔG≠) at TP0 of the reaction and the critical temperature of thermal explosion (Tb) were obtained by Kissinger's and Ozawa's method, respectively. Additionally, the compatibility of HADNAF with other materials (e.g. TNT, RDX, HMX, B, Mg) was tested by DSC method.

Thermodynamic Diagrams

NASA Astrophysics Data System (ADS)

Chaston, Scot

1999-02-01

Thermodynamic data such as equilibrium constants, standard cell potentials, molar enthalpies of formation, and standard entropies of substances can be a very useful basis for an organized presentation of knowledge in diverse areas of applied chemistry. Thermodynamic data can become particularly useful when incorporated into thermodynamic diagrams that are designed to be easy to recall, to serve as a basis for reconstructing previous knowledge, and to determine whether reactions can occur exergonically or only with the help of an external energy source. Few students in our chemistry-based courses would want to acquire the depth of knowledge or rigor of professional thermodynamicists. But they should nevertheless learn how to make good use of thermodynamic data in their professional occupations that span the chemical, biological, environmental, and medical laboratory fields. This article discusses examples of three thermodynamic diagrams that have been developed for this purpose. They are the thermodynamic energy account (TEA), the total entropy scale, and the thermodynamic scale diagrams. These diagrams help in the teaching and learning of thermodynamics by bringing the imagination into the process of developing a better understanding of abstract thermodynamic functions, and by allowing the reader to keep track of specialist thermodynamic discourses in the literature.

Lattice model of linear telechelic polymer melts. II. Influence of chain stiffness on basic thermodynamic properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Wen-Sheng, E-mail: wsxu@uchicago.edu; Freed, Karl F., E-mail: freed@uchicago.edu; Department of Chemistry, The University of Chicago, Chicago, Illinois 60637

2015-07-14

The lattice cluster theory (LCT) for semiflexible linear telechelic melts, developed in Paper I, is applied to examine the influence of chain stiffness on the average degree of self-assembly and the basic thermodynamic properties of linear telechelic polymer melts. Our calculations imply that chain stiffness promotes self-assembly of linear telechelic polymer melts that assemble on cooling when either polymer volume fraction ϕ or temperature T is high, but opposes self-assembly when both ϕ and T are sufficiently low. This allows us to identify a boundary line in the ϕ-T plane that separates two regions of qualitatively different influence of chainmore » stiffness on self-assembly. The enthalpy and entropy of self-assembly are usually treated as adjustable parameters in classical Flory-Huggins type theories for the equilibrium self-assembly of polymers, but they are demonstrated here to strongly depend on chain stiffness. Moreover, illustrative calculations for the dependence of the entropy density of linear telechelic polymer melts on chain stiffness demonstrate the importance of including semiflexibility within the LCT when exploring the nature of glass formation in models of linear telechelic polymer melts.« less

Interaction of cinnamic acid derivatives with serum albumins: A fluorescence spectroscopic study

NASA Astrophysics Data System (ADS)

Singh, T. Sanjoy; Mitra, Sivaprasad

2011-03-01

Cinnamic acid (CA) derivatives are known to possess broad therapeutic applications including anti-tumor activity. The present study was designed to determine the underlying mechanism and thermodynamic parameters for the binding of two CA based intramolecular charge transfer (ICT) fluorescent probes, namely, 4-(dimethylamino) cinnamic acid (DMACA) and trans-ethyl p-(dimethylamino) cinnamate (EDAC), with albumins by fluorescence spectroscopy. Stern-Volmer analysis of the tryptophan fluorescence quenching data in presence of the added ligand reveals fluorescence quenching constant ( κq), Stern-Volmer constant ( KSV) and also the ligand-protein association constant ( Ka). The thermodynamic parameters like enthalpy (Δ H) and entropy (Δ S) change corresponding to the ligand binding process were also estimated. The results show that the ligands bind into the sub-domain IIA of the proteins in 1:1 stoichiometry with an apparent binding constant value in the range of 10 4 dm 3 mol -1. In both the cases, the spontaneous ligand binding to the proteins occur through entropy driven mechanism, although the interaction of DMACA is relatively stronger in comparison with EDAC. The temperature dependence of the binding constant indicates the induced change in protein secondary structure.

Entropy as a collective variable

NASA Astrophysics Data System (ADS)

Parrinello, Michele

Sampling complex free energy surfaces that exhibit long lived metastable states separated by kinetic bottlenecks is one of the most pressing issues in the atomistic simulations of matter. Not surprisingly many solutions to this problem have been suggested. Many of them are based on the identification of appropriate collective variables that span the manifold of the slow varying modes of the system. While much effort has been put in devising and even constructing on the fly appropriate collective variables there is still a cogent need of introducing simple, generic, physically transparent, and yet effective collective variables. Motivated by the physical observation that in many case transitions between one metastable state and another result from a trade off between enthalpy and entropy we introduce appropriate collective variables that are able to represent in a simple way these two physical properties. We use these variables in the context of the recently introduced variationally enhanced sampling and apply it them with success to the simulation of crystallization from the liquid and to conformational transitions in protein. Department of Chemistry and Applied Biosciences, ETH Zurich, and Facolta' di Informatica, Istituto di Scienze Computazionali, Universita' della Svizzera Italiana, Via G. Buffi 13, 6900 Lugano, Switzerland.

Inhibition of calcite precipitation by natural organic material: Kinetics, mechanism, and thermodynamics

USGS Publications Warehouse

Lin, Y.-P.; Singer, P.C.; Aiken, G.R.

2005-01-01

The inhibition of calcite precipitation by natural organic material (NOM) in solutions seeded with calcite was investigated using a pH-stat system. Experiments were carried out using three NOMs with different physical/chemical properties. For each of the materials, inhibition was found to be more effective at lower carbonate/calcium ratios and lower pH values. The reduction in the precipitation rate could be explained by a Langmuir adsorption model using a conditional equilibrium constant. By identification of the type of site on the NOM molecules that is involved in the adsorption reaction, the "conditional" equilibrium constants obtained at different solution compositions converged to a single "nonconditional" value. The thermodynamic data determined at 25??C and 1 atm suggest that the interaction between NOM molecules and the calcite surface is chemisorptive in nature and that adsorption is an endothermic reaction driven by the entropy change. The greatest degree of inhibition was observed for the NOM with the highest molecular weight and aromatic carbon content. For a given type of NOM, the degree of inhibition of calcite precipitation was dictated by the balance between the enthalpy change and the entropy change of the adsorption reaction. ?? 2005 American Chemical Society.

An Empirical Temperature Variance Source Model in Heated Jets

NASA Technical Reports Server (NTRS)

Khavaran, Abbas; Bridges, James

2012-01-01

An acoustic analogy approach is implemented that models the sources of jet noise in heated jets. The equivalent sources of turbulent mixing noise are recognized as the differences between the fluctuating and Favre-averaged Reynolds stresses and enthalpy fluxes. While in a conventional acoustic analogy only Reynolds stress components are scrutinized for their noise generation properties, it is now accepted that a comprehensive source model should include the additional entropy source term. Following Goldstein s generalized acoustic analogy, the set of Euler equations are divided into two sets of equations that govern a non-radiating base flow plus its residual components. When the base flow is considered as a locally parallel mean flow, the residual equations may be rearranged to form an inhomogeneous third-order wave equation. A general solution is written subsequently using a Green s function method while all non-linear terms are treated as the equivalent sources of aerodynamic sound and are modeled accordingly. In a previous study, a specialized Reynolds-averaged Navier-Stokes (RANS) solver was implemented to compute the variance of thermal fluctuations that determine the enthalpy flux source strength. The main objective here is to present an empirical model capable of providing a reasonable estimate of the stagnation temperature variance in a jet. Such a model is parameterized as a function of the mean stagnation temperature gradient in the jet, and is evaluated using commonly available RANS solvers. The ensuing thermal source distribution is compared with measurements as well as computational result from a dedicated RANS solver that employs an enthalpy variance and dissipation rate model. Turbulent mixing noise predictions are presented for a wide range of jet temperature ratios from 1.0 to 3.20.

The new insight into dynamic crossover in glass forming liquids from the apparent enthalpy analysis

NASA Astrophysics Data System (ADS)

Martinez-Garcia, Julio Cesar; Martinez-Garcia, Jorge; Rzoska, Sylwester J.; Hulliger, Jürg

2012-08-01

One of the most intriguing phenomena in glass forming systems is the dynamic crossover (TB), occurring well above the glass temperature (Tg). So far, it was estimated mainly from the linearized derivative analysis of the primary relaxation time τ(T) or viscosity η(T) experimental data, originally proposed by Stickel et al. [J. Chem. Phys. 104, 2043 (1996), 10.1063/1.470961; Stickel et al. J. Chem. Phys. 107, 1086 (1997)], 10.1063/1.474456. However, this formal procedure is based on the general validity of the Vogel-Fulcher-Tammann equation, which has been strongly questioned recently [T. Hecksher et al. Nature Phys. 4, 737 (2008), 10.1038/nphys1033; P. Lunkenheimer et al. Phys. Rev. E 81, 051504 (2010), 10.1103/PhysRevE.81.051504; J. C. Martinez-Garcia et al. J. Chem. Phys. 134, 024512 (2011)], 10.1063/1.3514589. We present a qualitatively new way to identify the dynamic crossover based on the apparent enthalpy space (H_a^' = {{dln τ }/{d({1/T})}}) analysis via a new plot ln H_a^' vs. 1/T supported by the Savitzky-Golay filtering procedure for getting an insight into the noise-distorted high order derivatives. It is shown that depending on the ratio between the "virtual" fragility in the high temperature dynamic domain (mhigh) and the "real" fragility at Tg (the low temperature dynamic domain, m = mlow) glass formers can be splitted into two groups related to f < 1 and f > 1, (f = mhigh/mlow). The link of this phenomenon to the ratio between the apparent enthalpy and activation energy as well as the behavior of the configurational entropy is indicated.

Gender-specific heart rate dynamics in severe intrauterine growth-restricted fetuses.

PubMed

Gonçalves, Hernâni; Bernardes, João; Ayres-de-Campos, Diogo

2013-06-01

Management of intrauterine growth restriction (IUGR) remains a major issue in perinatology. The objective of this paper was the assessment of gender-specific fetal heart rate (FHR) dynamics as a diagnostic tool in severe IUGR. FHR was analyzed in the antepartum period in 15 severe IUGR fetuses and 18 controls, matched for gestational age, in relation to fetal gender. Linear and entropy methods, such as mean FHR (mFHR), low (LF), high (HF) and movement frequency (MF), approximate, sample and multiscale entropy. Sensitivities and specificities were estimated using Fisher linear discriminant analysis and the leave-one-out method. Overall, IUGR fetuses presented significantly lower mFHR and entropy compared with controls. However, gender-specific analysis showed that significantly lower mFHR was only evident in IUGR males and lower entropy in IUGR females. In addition, lower LF/(MF+HF) was patent in IUGR females compared with controls, but not in males. Rather high sensitivities and specificities were achieved in the detection of the FHR recordings related with IUGR male fetuses, when gender-specific analysis was performed at gestational ages less than 34 weeks. Severe IUGR fetuses present gender-specific linear and entropy FHR changes, compared with controls, characterized by a significantly lower entropy and sympathetic-vagal balance in females than in males. These findings need to be considered in order to achieve better diagnostic results. Copyright © 2013 Elsevier Ltd. All rights reserved.

Thermophysical properties of undercooled liquid Co-Mo alloys

NASA Astrophysics Data System (ADS)

Han, X. J.; Wei, B.

2003-05-01

Using electromagnetic levitation in combination with the oscillating drop technique and drop calorimeter method, the surface tensions and specific heats of undercooled liquid Co-10 wt% Mo, Co-26.3 wt% Mo, and Co-37.6 wt% Mo alloys were measured. The containerless state during levitation produces substantial undercoolings up to 223 K (0.13TL), 213 K (0.13TL) and 110 K (0.07TL) respectively for these three alloys. In their respective undercooling ranges, the surface tensions were determined to be 1895 m 0.31(T m 1744), 1932 m 0.33(T m 1682), and 1989 m 0.34(T m 1607) mN mу. According to the Butler equation, the surface tensions of these three Co-Mo alloys were also calculated, and the results agree well with the experimental data. The specific heats of these three alloys are determined to be 41.85, 43.75 and 44.92 J molу Kу. Based on the determined surface tensions and specific heats, the changes in thermodynamics functions such as enthalpy, entropy and Gibbs free energy are predicted. Furthermore, the crystal nucleation, dendrite growth and Marangoni convection of undercooled Co-Mo alloys are investigated in the light of these measured thermophysical properties.