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PubMed2004

Prediction of multicomponent liquid adsorption using excess quantities I. Statistical thermodynamic derivation of the basic equation of excess formalism.

The utilization of excess quantities as the basis of a thermodynamic approach can simplify the prediction of multicomponent liquid adsorption from binary data. From statistical thermodynamics, the fundamental equation is derived for the prediction of ternary or higher order data from adsorption data for the constituent binary mixtures. An additive expression is obtained for the double Gibbs free excess energies, valid for adsorption on liquid mixture/air interfaces as well as liquid mixture/solid interfaces.

Journal Article↗
PubMed2004

Hybrid aniline/silica xerogel cation adsorption and thermodynamics of interaction.

Aniline groups chemically immobilized on silica through the sol-gel process were employed to extract divalent nickel and manganese from aqueous solutions at room temperature. The maximum adsorption capacity of the xerogel was studied from adsorption isotherms using a batch technique. The isotherms obtained were adjusted following the Langmuir equation. The xerogel adsorbent appears to have better affinity for nickel than manganese. From calorimetric titration, thermodynamic data on cation/nitrogen basic atom interaction in the solid/liquid interface were determined. The enthalpic values, -0.46 +/- 0.02 and -.029 +/- 0.02 kJ mol(-1) for nickel and manganese, respectively, are in agreement with the low availability of the basic nitrogen atom on the aniline group and also the possible steric hindrance of the phenyl group bonded to nitrogen. However, thermodynamics indicated the existence of favorable conditions for such cation-nitrogen interactions.

Journal Article↗
PubMed2005

Thermodynamically stable dispersions induced by depletion interactions.

When small particles are added to a colloidal dispersion of large particles, a depletion interaction between large particles occurs because the small ones are depleted from the gaps between the former particles. In the present paper, a cell model is employed to examine the behavior of a dispersion of large particles immersed in an electrolyte solution containing small particles. In this model, each cell consists of one large particle in its center and an associated atmosphere. Double-layer, van der Waals, and depletion interactions, as well as entropic effects, have been taken into account. When the change of the free energy with respect to that of the electrolyte solution is negative (and this happens in most cases), the dispersions of large particles are stable from a thermodynamic point of view. With increasing volume fraction of the small particles, the free energy change becomes more negative. The formation of gels observed experimentally in concentrated emulsions is explained through the formation of a thermodynamically stable dispersion.

Journal Article↗
PubMed2006

Thermodynamic characterization of the prevailing molecular interactions in mixed floating monolayers of phospholipids and usnic acid.

The investigation of the characteristics of mixed floating monolayers of phospholipids and usnic acid (UA), an active metabolite from lichens, can provide valuable information on how to prepare stable liposomes that could serve as carriers of UA for therapeutic proposes. The present paper is concerned with the thermodynamic analysis of the behavior of Langmuir monolayers formed by mixing different phospholipids (dibehenoylphosphatidylcholine, DBPC, dipalmitoylphosphatidylcholine, DPPC, and dioleoylphosphatidylcholine, DOPC) and UA at varied molar fractions. Relevant thermodynamic parameters such as excess areas, excess free energies and free energy of mixing were derived from the surface pressure data obtained from compression measurements performed in a Langmuir trough. For the largest lateral pressure examined (25 mN/m), negative values of the excess free energy were found only for the DOPC/UA monolayer, which should be the most stable of them. Based on the calculated values of the free energy of mixing, we note that the DBPC/UA and DPPC/UA systems present the best mixed character at low pressures and when the molar fraction of the UA is 0.5; at that relative concentration and at low values of the external pressure, the UA molecules can better mix and interact with the phospholipid molecules. The compression isotherms for mixed monolayers show no visible transitions, exhibiting a more organized phase that corresponds to a negative free energy of mixing. We have established that the most stable monolayers were those corresponding to DOPC/UA mixtures with a UA molar fraction of 0.75.

Benzofurans↗
PubMed2006

A simplified method to estimate kinetic and thermodynamic parameters on the solid-liquid separation of pollutants.

The aim of the present study was to propose a simplified experimental-theoretical method for estimating the kinetic and thermodynamic parameters for the solid-liquid separation of pollutants by using kinetic studies with batch reactors, i.e., the removed quantity of dissolved ion as a function of time at different initial concentration. This method was applied to the removal of uranyl ion (UO(2+)(2)) from aqueous solutions onto synthetic manganese oxide (birnessite). The pseudo-second-order kinetics and one-site saturation models were proposed to fit the experimental and calculated data, the fitting parameters being estimated by nonlinear regression, using the least-squares method. For initial concentration range 0.2-11.8 microM, the results showed that the uranyl removal process in dispersed batch reactors can be efficiently modeled by the proposed models. Then, several kinetic and thermodynamic parameters were calculated, such as maximal removed quantity of uranyl, q(r,max), half-removal time, t(1/2), initial rate of uranyl-ion removal, v(0), initial uranyl-removal coefficient, K, maximal rate of uranyl removal, v(0,max), mass transfer coefficient, D(transfer), equilibrium Langmuir constant, K(L), and constant separation factor, K(s). These parameters make it possible to demonstrate that the removal of U onto birnessite is favorable, and that the maximum surface coverage of the uranyl ions represents about 3% of vacant sites in the Mn layer.

Journal Article↗
PubMed2003

Thermodynamic characterization of the folding coupled DNA binding by the monomeric transcription activator GCN4 peptide.

Dimerization is a widely believed critical requirement for the yeast transcriptional activator GCN4 specifically recognizing its DNA target sites. Nonetheless, the binding of the monomeric GCN4 to DNA target sites AP-1 and ATF/CREB was recently detected by kinetic studies. Here, for the first time, we present a detailed description of the thermodynamics of a monomeric peptide GCN4-br, the basic region (226-252) of GCN4, binding to AP-1, and ATF/CREB. GCN4 specifically binds to AP-1 and ATF/CREB in the monomeric form as shown by our circular dichroism thermal unfolding measurements. Isothermal titration calorimetry experiments indicate that the binding process of GCN4-br with DNA is enthalpically driven, accompanied by an unfavorable entropy change. The temperature dependence of DeltaH(0) reveals negative changes in heat capacity DeltaC(p): DeltaC(p) = -0.92 kJ. mol(-1) K(-1) and DeltaC(p) = -0.95 kJ. mol(-1) K(-1) for GCN4-br binding to AP-1 and ATF/CREB, respectively, which is a striking manifestation of GCN4-br specifically recognizing DNA target sites. These thermodynamic characteristics may give new insight into the mechanism by which GCN4 protein binds to DNA target sites for its transcriptional regulation.

Activating Transcription Factor 2↗
PubMed1981

Thermodynamic and kinetic studies of the interaction between T5-phages and their receptor, isolated from Escherichia coli b, in the absence and presence of Triton X-100.

Particles with receptor activity for T5-phages were isolated from the outer membrane of Escherichia coli B. We describe the interaction of these particles with T5-phages as a two-step chemical reaction. The rate constants were estimated from the inactivation kinetics. The transition-state theory permits the calculation of the entropy, enthalpy, and Gibbs free energy of activation. In the absence of Triton X-100, the reaction can be described with one set of thermodynamic constants for the temperature range from 10 degrees to 40 degrees C. The addition of Triton, which results in the splitting of receptor particles and in the building of mixed micelles, causes a complicated dependence on temperature. In this case, a subdividing of the temperature range measured into two parts yields two sets of thermodynamic constants that permit a good description of experimental kinetics.

Detergents↗
PubMed2004

Mechanistic and thermodynamic interpretations of zinc sorption onto ferrihydrite.

Elucidating the reaction mechanisms and estimating the associated transport and thermodynamic parameters are important for an accurate description of the fate of toxic metal pollutants, such as Zn(II), in soils and aquatic ecosystems rich in iron oxides. Consequently, sorption of Zn(II) ions onto ferrihydrite was investigated with macroscopic and spectroscopic studies as a function of pH (4.0-8.0), ionic strength (10(-3)-10(-1) M NaNO(3)), aqueous Zn(II) concentration (10(-8)-10(-2) M), and temperature (4-25 degrees C). Present findings suggest that, for a given set of pH and temperature conditions, Zn sorption onto ferrihydrite can best be described by one average reaction mechanism below the saturation limits. Thermodynamic analyses reveal that the Zn(II) ions sorb onto the ferrihydrite surfaces via strong endothermic chemical reactions. Consistently, X-ray absorption spectroscopic (XAS) analyses confirm that, at pH < 6.5, for all Zn loadings, Zn(II) ions form corner-sharing, mononuclear, bidentate inner-sphere complexes with ferrihydrite, where R(Zn-O) approximately 1.97 A and R(Zn-Fe) approximately 3.48 A. For pH >/=6.5, similar sorption complexes were observed at lower sorption densities. Then again, for pH >/=6.5 and at higher sorption densities, Zn(II) ions may begin to form zinc-hydroxide-like polynuclear sorption complexes on the surfaces of the ferrihydrite, where R(Zn-Zn) approximately 3.53 A. Surprisingly, small changes in temperature had a significant impact on the affinity of zinc for the ferrihydrite surface; equilibrium sorption capacity decreased by 3-4 orders of magnitude as temperature fell from 25 to 4 degrees C for all pH. Zinc sorption onto ferrihydrite, therefore, is governed by pH as well as by temperature and sorbate/sorbent ratio.

Journal Article↗
PubMed2002

Approach of evolutionary theories of ageing, stress, senescence-like phenotypes, calorie restriction and hormesis from the view point of far-from-equilibrium thermodynamics.

B. L. Strehler wrote that "Any system that is not in thermodynamic equilibrium will approach that state at a rate that is a function of absolute temperature and the energy barriers to the rearrangements of components". Far-from-equilibrium thermodynamics allows a global systemic description of the cellular behaviour. This approach transcends the genetic and stochastic considerations on ageing as well as some evolutionary questions about ageing. The fundamental difference between the processes of development and ageing could reflect the intrinsic differences existing between biological systems where an increase in specific entropy production (SEP) is, respectively, still possible or not. The increase of the potential of SEP which probably occurred with evolution might explain in part why life span could increase. However, this SEP-driven increase in life span was possible only in those species which did not take advantage of their increased potential of SEP to ameliorate their reproductive capacity at the expense of possible increases in repair capacity. The criteria of stability of far-from-equilibrium open systems and the theory of attractors also help to sort the possible types of cellular stress responses: normal ageing, hormesis, stress-induced premature senescence, apoptosis or necrosis.

Aging↗
PubMed1996

Thermodynamics of sequence-specific protein-DNA interactions.

The molecular recognition processes in sequence-specific protein-DNA interactions are complex. The only feature common to all sequence-specific protein-DNA structures is a large interaction interface, which displays a high degree of complementarity in terms of shape, polarity and electrostatics. Many molecular mechanisms act in concert to form the specific interface. These include conformational changes in DNA and protein, dehydration of surfaces, reorganization of ion atmospheres, and changes in dynamics. Here we review the current understanding of how different mechanisms contribute to the thermodynamics of the binding equilibrium and the stabilizing effect of the different types of noncovalent interactions found in protein-DNA complexes. The relation to the thermodynamics of small molecule-DNA binding and protein folding is also briefly discussed.

Journal Article↗
PubMed1997

Thermodynamics of protein unfolding: questions pertinent to testing the validity of the two-state model.

We discuss a number of questions pertaining to the analysis of data to extract thermodynamic parameters for the reversible unfolding of proteins. Simulations are presented to illustrate problems in trying to test the validity of the two-state model, vis-a-vis a more complicated unfolding model. A conceptual and practical problem is how to consider the unfolded state and how to relate the observed signal to this state. We discuss the idea that the unfolded state can be described as a single macrostate, comprising a distribution of microstates having different degrees of solvent-accessible surface area. We also discuss the possibilities and thermodynamic consequences of having more than one unfolded state and of having a denaturant which both stabilizes and destabilizes the protein's native state.

Journal Article↗
PubMed1998

Thermodynamics of aliphatic and aromatic hydrocarbons in water.

Makhatadze and Privalov have analyzed the thermodynamics of transfer of aliphatic and aromatic hydrocarbons from the gas phase into water. Finding that the hydration free energy of aliphatic and aromatic hydrocarbons have different signs, they conclude that the mechanism causing hydrophobicity of these solutes is of a different nature. Here, we offer an alternative analysis of the dissolution of these non-polar compounds into water based on a recently published interpretation scheme for thermodynamic transfer functions. Our analysis shows that the hydrophobicity of aromatic and aliphatic hydrocarbons is qualitatively the same, i.e. its causes are the same namely the extremely high cohesive energy of water which overcomes the favorable solute-solute and solute-water interactions. However, both analyses conclude that the experimentally observed quantitative difference between the interactions of water with aliphatic and aromatic hydrocarbons, can be assigned to the formation of aromatic ring-water H-bonds.

Journal Article↗
PubMed1998

The effects of temperature and pressure on the thermodynamic activity of anesthetics.

Anesthetic potency is often expressed by volume percent or partial pressure in the gas phase, concentrations in the aqueous phase, etc. However. these values do not represent the anesthetic activity at the action sites. Because the activity at the action sites is difficult to obtain. Ferguson (Ferguson, J., 1939. Proc. R. Soc. Lond. B 127 387-404) defined the thermodynamic activity, which is the ratio between the anesthetizing partial pressure and the vapor pressure of the pure anesthetic at the same temperature. This paper discusses the effects of temperature and pressure on the thermodynamic activity of anesthetics. It also discusses the limitations of the Meyer-Overton rule.

Anesthetics↗
PubMed2000

Structural and thermodynamic strategies for site-specific DNA binding proteins.

BACKGROUND: Site-specific protein-DNA complexes vary greatly in structural properties and in the thermodynamic strategy for achieving an appropriate binding free energy. A better understanding of the structural and energetic engineering principles might lead to rational methods for modification or design of such proteins. RESULTS: A novel analysis of ten site-specific protein-DNA complexes reveals a striking correspondence between the degree of imposed DNA distortion and the thermodynamic parameters of each system. For complexes with relatively undistorted DNA, favorable enthalpy change drives unfavorable entropy change, whereas for complexes with highly distorted DNA, unfavorable DeltaH degrees is driven by favorable DeltaS degrees. We show for the first time that protein-DNA associations have isothermal enthalpy-entropy compensation, distinct from temperature-dependent compensation, so DeltaH degrees and DeltaS degrees do not vary independently. All complexes have favorable DeltaH degrees from direct protein-DNA recognition interactions and favorable DeltaS degrees from water release. Systems that strongly distort the DNA nevertheless have net unfavorable DeltaH degrees as the result of molecular strain, primarily associated with the base pair destacking. These systems have little coupled protein folding and the strained interface suffers less immobilization, so DeltaS degrees is net favorable. By contrast, systems with little DNA distortion have net favorable DeltaH degrees, which must be counterbalanced by net unfavorable DeltaS degrees, derived from loss of vibrational entropy (a result of isothermal enthalpy-entropy compensation) and from coupling between DNA binding and protein folding. CONCLUSIONS: Isothermal enthalpy-entropy compensation implies that a structurally optimal, unstrained fit is achieved only at the cost of entropically unfavorable immobilization, whereas an enthalpically weaker, strained interface entails smaller entropic penalties.

Binding Sites↗
PubMed1997

Some comments on the thermodynamics of sonoluminescence--a personal view.

The path of the gas in a sonoluminescent bubble must enclose an area in a P-V plot if the gas itself emits photons. Thermodynamic analysis thus delineates the playing field that may enable us to distinguish liquid-phase emissions from gas-phase emissions. The apparent importance of the van der Waals a (which parameterizes mean-square induced dipole attractions) in light intensity supports collision-induced emission as a likely mechanism. The suggested emitting object, containing 10(10) molecules in picosecond-long van der Waals contact, is novel, being neither plasma, gas, liquid nor blackbody. The bubble pursues a unique thermodynamic path.

Journal Article↗
PubMed2000

Justification of statistical overlap theory in programmed temperature gas chromatography: thermodynamic origin of random distribution of retention times.

A specific distribution of compounds' standard-state changes of enthalpy and entropy between mobile and stationary phases in programmed temperature gas chromatography (PTGC) is shown to produce the Poisson distribution of retention times often postulated in statistical-overlap theory (SOT). A three-part model is proposed, in which the enthalpy change is Poisson distributed, the average entropy change depends on the enthalpy change, and the actual entropy change varies in a uniformly random manner about the average entropy change. To test the model, the entropy and enthalpy changes of 350 aliphatic and aromatic hydrocarbons in petroleum were calculated with commercial GC software. These changes are shown to follow the three-part model. The model then was used with Monte Carlo methods to mimic the enthalpy and entropy changes. The substitution of the mimicked enthalpy and entropy changes into an equation for the retention temperature in PTGC is shown to produce a Poisson distribution of retention times that is statistically significant. This finding establishes a scientific link between the thermodynamics governing retention in PTGC and the superficially ad hoc assumption of the Poisson retention time distribution in SOT. Similar thermodynamic distributions are found for flavors and fragrances and for tetrachlorodibenzo-p-dioxins and furans, which follow SOT based on the Poisson distribution, but not for polychloronaphthalenes, which do not follow that SOT.

Journal Article↗
PubMedDate not supplied

Prediction of thermodynamic parameters in gas chromatography from molecular structure: hydrocarbons.

Theoretical prediction of gas-chromatographic retention times could be used as an additional method for a more accurate identification of organic compounds during GC/MS analysis. Two separate quantitative structure-property relationship models were introduced for the calculation of thermodynamic values (DeltaH degrees, DeltaS degrees) for aliphatic and aromatic hydrocarbons. These values are required for the calculation of retention times in temperature programmed gas chromatography. Seven-descriptor and five-descriptor MLR models were selected for the calculation of DeltaH degrees and DeltaS degrees values, respectively, based on the best cross-validation abilities. The final prediction capabilities of the models were evaluated by a test set procedure. RMS errors calculated from the test set were 207 cal mol(-1) and 0.58 cal mol(-1) K(-1) for DeltaH degrees and DeltaS degrees prediction models, respectively. To evaluate the error of the models represented in the time scale, several chromatograms were simulated using experimental Pro ezGC and theoretically calculated thermodynamic data. Afterward a standard deviation of retention time residuals was calculated. It was found out that, although the standard deviation varies from one chromatographic condition to another, the ratio between the standard deviation and the maximum available separation space for the particular set of organic compounds remains constant and was around 5% of the maximum separation space available at selected chromatographic conditions. Our prediction model was able to accurately differentiate between the retention times of the consecutive compounds in the n-alkanes, 1-alkenes, and 2-alkenes homological series.

Journal Article↗
PubMed2002

Modeling reactive metal oxides. Kinetics, thermodynamics, and mechanism of M(3) cap isomerization in polyoxometalates.

An investigation of M(3)O(13) unit ("M(3) cap") isomerization in the classical polytungstodiphosphates alpha- and beta-P(2)W(18)O(62)(6)(-) has been undertaken because cap isomerism is an important and structurally well-studied phenomenon in many polyoxometalate families. The relative thermodynamic stabilities of the alpha (more stable) versus beta isomers were established both in the solid state by differential scanning calorimetry (4.36 +/- 0.64 kcal/mol) and in solution by (31)P NMR (3.80 +/- 0.57 kcal/mol). The isomerization of beta-P(2)W(18)O(62)(6)(-) to alpha-P(2)W(18)O(62)(6)(-), followed by (31)P NMR, has a bimolecular rate constant k(2) of 9.3 x 10(-)(1) M(-)(1) s(-)(1) at 343 K in pH 4.24 acetate buffer. Several lines of evidence establish the validity of suggestions in the literature that isomerization goes through a lacunary (defect) intermediate. First, the rate is proportional to [OH(-)]. Second, isomerization increases at higher ionic strengths, and a Debye-Hückel plot is consistent with a rate-limiting reaction between beta-P(2)W(18)O(62)(6)(-) and OH(-) (two species with a charge product of 6). Third, alkali-metal cations stabilize the bimolecular transition state (K(+) > Na(+) > Li(+)), consistent with recent ion-pairing studies in polyoxometalate systems. Fourth, the monovanadium-substituted products alpha(1)- and alpha(2)-P(2)VW(17)O(62)(7)(-) ((51)V NMR delta -554 ppm) form during isomerization in the presence of VO(2+). The known lacunary compounds (alpha(1)- and alpha(2)-P(2)W(17)O(61)(10)(-)) also react rapidly with the same vanadium precursor. Fifth, solvent studies establish that isomerization does not occur when OH(-) is absent. A mechanism is proposed involving attack of OH(-) on beta-P(2)W(18)O(62)(6)(-), loss of monomeric W(VI) from the M(3) (M(3)O(13)) terminal cap, isomerization of the resulting lacunary compound to alpha-P(2)W(17)O(61)(10)(-), and finally reaction of this species with monomeric W(VI) to form the thermodynamic and observed product, alpha-P(2)W(18)O(62)(6)(-).

Journal Article↗