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PubMed2005

Identification and thermodynamic treatment of several types of large-amplitude motions.

We present a partially automated method for the thermodynamic treatment of large-amplitude motions. Starting from the molecular geometry and the Hessian matrix, we evaluate anharmonic partition functions for selected vibrational degrees of freedom. Supported anharmonic vibration types are internal rotation and inversion (oscillation in a double-well potential). By heuristic algorithms, we identify internal rotations in most cases automatically from the Hessian eigenvectors, and we also estimate the parameters of anharmonic partition functions (e.g., potential barrier, periodicity, and symmetry number) with thermodynamically sufficient precision. We demonstrate the validity of our schemes by comparison to pointwise calculated ab initio potential curves.

Journal Article↗
PubMed2007

Thermodynamic calculations for molecules with asymmetric internal rotors--application to 1,3-butadiene.

We present quantum mechanical partition functions, free energies, entropies, and heat capacities of 1,3-butadiene derived from ab initio calculations. Our technique makes use of a reaction path-like Hamiltonian to couple all 23 vibrational modes to the large-amplitude torsion, which involves heavy asymmetric functional groups. Ab initio calculations were performed at the B3LYP, MP2, and CCSD(T) levels of theory and compared with experimental values as a reference case. By using the ab initio potentials and projected frequencies, simple perturbative expressions are presented for computing the couplings of all the vibrational modes to the large-amplitude torsion. The expressions are particularly suited for programming in the new STAR-P software platform which automatically parallelizes our codes with distributed memory via a familiar MATLAB interface. Using the efficient parallelization scheme of STAR-P, we obtain thermodynamic properties of 1,3-butadiene for temperatures ranging from 50 to 500 K. The free energies, entropies, and heat capacities obtained from our perturbative formulas are compared with conventional approximations and experimental values found in thermodynamic tables.

Journal Article↗
PubMed2005

Extended thermodynamic approach to ion interaction chromatography. Influence of the chain length of the solute ion: a chromatographic method for the determination of ion-pairing constants.

The influence of the chain length in Ion Interaction Chromatography (IIC), previously named Ion Pair Chromatography, was investigated. The system examined is a C18 stationary phase and a variable, salt-controlled, mixture of a phosphate buffer pH 2.1 in methanol containing tetrabutylammonium bromide as Ion Interaction Reagent. IIC proves to be a good alternative to the well established spectrophotometric and conductometric methods of obtaining thermodynamic ion-pairing constants. The latter increase with increasing analyte chain length and decrease with increasing methanol concentration in the eluent: both results support a physical chemical description of the hydrophobic ion-pairing process at variance with the classical, Bjerrum-type modelling of the purely electrostatic interaction between inorganic ions. The calculated deltaG(o) are reliable because they compare to non-chromatographic estimates of deltaG(o) for similar systems. The present extended thermodynamic approach is able to predict and explain why the purely electrostatic approach works better for lower analyte lipophilicity or higher organic modifier concentration.

Journal Article↗
PubMed2004

Multi-method global analysis of thermodynamics and kinetics in reconstitution of monellin.

Accurate and precise determinations of thermodynamic parameters of binding are important steps toward understanding many biological mechanisms. Here, a multi-method approach to binding analysis is applied and a detailed error analysis is introduced. Using this approach, the binding thermodynamics and kinetics of the reconstitution of the protein monellin have been quantitatively determined in detail by simultaneous analysis of data collected with fluorescence spectroscopy, surface plasmon resonance and isothermal titration calorimetry at 25 degrees C, pH 7.0 and 150 mM NaCl. Monellin is an intensely sweet protein composed of two peptide chains that form a single globular domain. The kinetics of the reconstitution reaction are slow, with an association rate constant, k(on) of 8.8 x 10(3) M(-1) s(-1) and a dissociation rate constant, k(off) of 3.1 x 10(-4) s(-1). The equilibrium constant K(A) is 2.8 x 10(7) M(-1) corresponding to a standard free energy of association, DeltaG degrees , of -42.5 kJ/mol. The enthalpic component, DeltaH degrees , is -18.7 kJ/mol and the entropic contribution, DeltaS degrees , is 79.8 J mol(-1) K(-1) (-TDeltaS degrees = -23.8 kJ/mol). The association of monellin is therefore a bimolecular intra-protein association whose energetics are slightly dominated by entropic factors.

Calorimetry↗
PubMed1997

Ion Adsorption and Agglomeration Mechanism in Si3N4/H2O(l) Dispersions Compatible with Thermodynamical Stability

Adsorption isotherms from aqueous liquid phase of H+ and/or OH- ions onto Si3N4 solid surface agglomerates have been derived through titration measurements (Beruto et al., J. Chem. Soc., Faraday Trans. 91(2), 323 (1995)). The isotherms exhibit S-shape and can be fitted with Freundlich as well as with Langmuir type isotherms. In order to explain the agglomeration process based on the decrease of total solid-liquid interfacial energy, a model (ISD) has been developed. The agreement between numerical data derived by this model and the experimental data is quite good. Isotherm equation and agglomeration law should obey also the dispersion thermodynamic stability criterion. This condition yields an extra equation to select the pair of functions, thus providing a criterion to choose between the several equations that fit adsorption and agglomeration data fairly well. The solution of the problem mentioned above, from the mathematical point of view, is based on the Dini implicit function theorem (Mezzasalma and Oliva, Appl. Math. Lett., submitted). The results indicate that Van der Waals adsorption isotherm coupled with the ISD model are compatible with the thermodynamic stability of the aqueous Si3N4 dispersions.

Journal Article↗
PubMed2000

Modeling of the Internal Structure of Randomly Formed Microporous Material of Unlimited Volume, Following Thermodynamic Limitations.

The problem of pore formation in unlimited (very large) volume has been considered. General equations describing the system have been obtained for three possible situations of pore formation: Monte Carlo-like case, entropy mechanism of pore formation, and thermodynamically limited situation. The applicability of each approach to real systems has been considered. It has been proved that, in the fractal description of pore formation, the geometry of a porous cluster-random fractal does not differ from that of the initial fractal. The values of surface area and fractal dimensionality in various situations have been estimated. Solutions following thermodynamic limitations have been compared to those obtained for random (Monte Carlo approach) situations. Copyright 2000 Academic Press.

Journal Article↗
PubMed2001

Thermodynamic Investigation of the Micellization and the Adsorption of Short Perfluoroalkylated Diols via Fluorescence Spectroscopy and Tensiometry.

The micellization and adsorption of two short chain perfluorodiols 3,3,4,4,5,5,6,6,6-nonafluorohexane-1,2-diol (nFHD) and 3,3,4,4,5,5,6,6,7,7,8,8,8-tridecafluorooctane-1,2-diol (tFOD) are examined from a thermodynamic point of view as a function of temperature and methanol content. The microenvironment of the fluorinated aggregates is evaluated by the fluorescence probe method using pyrene and a molecular rotor 1,1-dicyano-4-p-dimethylaminophenyl)-1,3-butadiene (DMAPhC). The formation of micellar aggregates being evidenced, the results are discussed in terms of the polarity and of the cohesion behavior of the micellar aggregates by taking into account the methanol (MeOH) effect. The critical micellization concentrations thus determined are compared with those given by surface tension measurements. Micellar and adsorption thermodynamic parameters such as Gibbs free energies, enthalpies, and entropies are determined together with the surface areas. The results are compared with literature data and discussed. A model for describing the adsorption process of the fluorinated compounds upon the influence of methanol is finally proposed. Copyright 2001 Academic Press.

Journal Article↗
PubMed2001

Thermodynamics of Unilamellar Vesicles: Influence of Mixing on the Curvature Free Energy of a Vesicle Bilayer.

The influence of mixing on the curvature free energy of a thermodynamically open, reversibly formed vesicle bilayer is investigated by deriving expressions for the various contributions to the bilayer bending constant k(bi) as functions of the structure of aggregated surfactants as well as the solution state (electrolyte concentration, average composition in the bilayers, etc). k(bi) is shown to be lowered in surfactant mixtures as a result of the fact that a mixed vesicle bilayer that is open in the thermodynamic sense may assume different compositions in the inner and outer monolayers. The net contribution of all terms related to surfactant mixing is to lower k(bi). The magnitude of this reduction increases with increasing asymmetry between the two surfactants with respect to charge number, head group size, and tail length. The reduction of k(bi) due to mixing is most pronounced for mixtures where the surfactant that carries charge or has the highest charge number has the larger head group and the smaller tail. Copyright 2001 Academic Press.

Journal Article↗
PubMed2002

Electrokinetic and thermodynamic analysis of the adsorption process of N-cetylpyridinium chloride on polyester fabric.

An electrokinetic and thermodynamic analysis of the adsorption process of N-cetylpyridinium chloride on polyester fabric is described in the present work. The electrokinetic study was performed by means of electrophoretic mobility measurements of the polyester-surfactant system. The most significant result is the increase in electrokinetic potential, zeta, toward more positive values as the surfactant concentration in the dispersion medium is raised. Given the molecular structure of N-cetylpyridinium chloride (N-CP-Cl), which contains a pyridinium group, positively charged, it is feasible that such increase in |zeta| is due to the electrostatic attraction between the carboxyl groups of polyester, ionized at pH 8.5, and the pyridinium group of the surfactant. The uptake of N-CP-Cl by the fiber is experimentally determined at four temperatures: the strong increase in the amount of the surfactant incorporated onto the fiber as the initial concentration of N-CP-Cl is larger shows that the electrostatic attraction between the fiber and the surfactant is the main mechanism of the adsorption of the surfactant onto the fiber. The obtained data on the kinetics and thermodynamics of adsorption of N-cetylpyridinium chloride onto the polyester, standard free energy, enthalpy, and entropy related to the process of adsorption are in accordance with our hypothesis on the mechanisms of adsorption. From a different point of view, the efficient coverage of polyester by N-CP-Cl is also demonstrated by the changes experienced by the surface free energy of polyester upon treatment with N-CP-Cl.

Journal Article↗
PubMed1999

Analysis of cross-polarization dynamics between two abundant nuclei, (19)F and (1)H, based on spin thermodynamics theory

The phenomenological theory of spin thermodynamics based on the spin temperature hypothesis was employed to describe the cross-polarization (CP) dynamics between two abundant nuclei, (19)F and (1)H, when the number of fluorine atoms is not substantially less than the number of hydrogens. The influence of T(1rho)'s of both nuclei and the relative magnitude (heat capacity) of the two spin baths must be incorporated explicitly into the analysis in order to derive values for the parameters involved in the CP dynamics. Numerical calculations were performed to clarify the difference in the evolution of magnetization in variable contact time CP experiments between the (1)H --> (13)C and (1)H --> (19)F cases. A new type of CP-drain experiment was developed for observing the residual (1)H magnetization after (1)H --> (19)F CP. (19)F direct polarization magic-angle spinning (MAS), (1)H --> (19)F CP, and (1)H --> (19)F CP-drain MAS NMR spectra have been measured for a fluorinated polyimide, 6FDA/ODA. The CP dynamics between (1)H and (19)F for the polyimide were analyzed on the basis of the spin thermodynamics theory. The constant for polarization transfer (T(HF)) was determined by the analysis using the effective CP parameters, which were directly obtained from the CP and CP-drain experiments, together with independently measured values of T(H)(1rho) and T(F)(1rho). Copyright 1999 Academic Press.

Journal Article↗
PubMed1986

The reactions of the phosphorylated pathway of L-serine biosynthesis: thermodynamic relationships in rat liver in vivo.

The effect of the induction of the enzymes of the phosphorylated pathway of L-serine biosynthesis on the thermodynamic relationships among the reactions has been determined in rat liver in vivo. The mass action ratios of the reactions involved were calculated from the concentrations of appropriate metabolites in freeze-clamped liver from animals fed normal and low-protein diets for 2 weeks. These ratios were compared with the equilibrium constants of the same reactions previously determined under physiological conditions and the results previously obtained in the rabbit. The thermodynamic relationships in the pathway were different between the normal rat and rabbit as might have been expected, because of the significantly lower activities of the L-serine biosynthetic enzymes in the former animal. Although the delta G for the overall pathway is nearly identical in the rat and rabbit (-5.8 versus -5.5 kcal/mol, respectively), the distribution of delta G among the reactions is different. The disequilibrium in the pathway in rat liver is nearly equally divided between the L-phosphoserine phosphatase (EC 3.1.3.3) step and the other two reactions [D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) and L-phosphoserine aminotransferase (EC 2.6.1.52)], whereas in rabbit the phosphatase reaction accounts for nearly the entire delta G. Feeding the rat a low protein diet, however, induced the activity of D-3-phosphoglycerate dehydrogenase 12-fold, that of L-phosphoserine aminotransferase 20-fold, and that of L-phosphoserine phosphatase 2-fold. With the induction of the pathway, L-phosphoserine appeared in the tissue, there was a more than 3-fold rise in L-serine in the liver, and the pattern of delta G in the rat liver approached that in the rabbit.

Animals↗
PubMed1983

Kinetic and thermodynamic parameters for oxygen binding to the allosteric states of Panulirus interruptus hemocyanin.

The temperature dependence of the oxygen binding equilibria and kinetics of Panulirus interruptus hemocyanin has been analyzed within the context of the two-state allosteric model. Oxygenation of the T-state is characterized by a more negative value of DeltaH than that of the R-state; therefore, cooperative effects in oxygen binding to P. interruptus hemocyanin are thermodynamically governed by favorable entropy changes. The allosteric transition in the unliganded derivative shows an enthalpy-entropy compensation effect. The activation enthalpies for oxygenation and deoxygenation of the T-state are larger than those for the R-state, while the activation entropies are favorable for the T-state and unfavorable for the R-state. Thus, the activation free energies for oxygen binding to the T- and R-states are similar, while for the deoxygenation reaction DeltaG++ is smaller for the T-state. The analysis reported confirms the applicability of the Monod-Wyman-Changeux two-state allosteric model to P. interruptus hemocyanin and yields a complete thermodynamic characterization of oxygen binding under both equilibrium and dynamic regimes.

Journal Article↗
PubMed1986

Thermodynamics of carbohydrate isomerization reactions. The conversion of aqueous allose to psicose.

The thermodynamics of the conversion of aqueous D-psicose to D-allose has been investigated using high-pressure liquid chromatography. The reaction was carried out in phosphate buffer at pH 7.4 over the temperature range 317.25-349.25 K. The following results are obtained for the conversion process at 298.15 K: DeltaG degrees = - 1.41 +/- 0.09 kJ mol(-1), DeltaH degrees = 7.42 +/- 1.7 kJ mol(-1), and DeltaC(p) degrees = 67 +/- 50 J mol(-1) K(-1). An approximate equilibrium constant of 0.30 is obtained at 333.15 K for the conversion of aqueous D-psicose to D-altrose. Available thermodynamic data for isomerization reactions involving aldohexoses and aldopentoses are summarized.

Journal Article↗
PubMed1991

Thermodynamics of the disproportionation of adenosine 5'-diphosphate to adenosine 5'-triphosphate and adenosine 5'-monophosphate. I. Equilibrium model.

The thermodynamic treatment of the disproportionation reaction of adenosine 5'-diphosphate to adenosine 5'-triphosphate and adenosine 5'-monophosphate is discussed in terms of an equilibrium model which includes the effects of the multiplicity of ionic and metal bound species and the presence of long range electrostatic and short range repulsive interactions. Calculated quantities include equilibrium constants, enthalpies, heat capacities, entropies, and the stoichiometry of the overall reaction. The matter of how these calculations can be made self-consistent with respect to both calculated values of the ionic strength and the molality of the free magnesium ion is discussed. The thermodynamic data involving proton and magnesium-ion binding data for the nucleotides involved in this reaction have been evaluated.

Journal Article↗
PubMed1991

Interfacial thermodynamics of protein adsorption, ion co-adsorption and ion binding in solution. I. Phenomenological linkage relations for ion exchange in lysozyme chromatography and titration in solution.

In this paper we discuss the thermodynamics of ion binding in solution, protein adsorption and ion co-adsorption. The emphasis is on charge regulation effects. To this end, we introduce phenomenological linkage relations from which the ion binding can be calculated from the electrolyte dependency of proton titration curves and the co-adsorption from the electrolyte dependency of protein adsorption isotherms. The linkage relations are derived from classical interfacial thermodynamics, and thus offer an alternative approach as compared to the mass balance equations which are currently used in biotechnology, and Record et al.'s 1978 analysis of Wyman's Binding Polynomial for protein interactions. The co-adsorption theory is an extension of our previous analysis of ion binding in solution, which we include here for comparison of the ion co-adsorption with the ion binding in solution. The theory is applied to the chromatography of lysozyme on the strong cation exchanger 'mono S' and to the proton titration of lysozyme in solution. In the accompanying Part 2 of this paper the results are interpreted with a simple model.

Journal Article↗
PubMed2004

A molecular thermodynamic view of DNA-drug interactions: a case study of 25 minor-groove binders.

Developing a molecular view of the thermodynamics of DNA recognition is essential to the design of ligands for regulating gene expression. In a first comprehensive attempt at sketching an atlas of DNA-drug energetics, we present here a detailed thermodynamic view of minor-groove recognition by small molecules via a computational study on 25 DNA-drug complexes. The studies are configured in the MMGBSA (Molecular Mechanics-Generalized Born-Solvent Accessibility) framework at the current state of the art and facilitate a structure-energy component correlation. Analyses were conducted on both energy minimized structures of DNA-drug complexes and molecular dynamics trajectories developed for the purpose of this study. While highlighting the favorable role of packing, shape complementarity, and van der Waals and hydrophobic interactions of the drugs in the minor groove in conformity with experiment, the studies reveal an interesting annihilation of favorable electrostatics by desolvation. Structural modifications attempted on the ligands point to the requisite physico-chemical factors for obtaining improved binding energies. Hydrogen bonds predicted to be important for specificity based on structural considerations do not always turn out to be significant to binding in post facto analyses of molecular dynamics trajectories, which treat thermal averaging, solvent, and counterion effects rigorously. The strength of the hydrogen bonds retained between the DNA and drug during the molecular dynamics simulations is approximately 1kcal/mol. Overall, the study reveals the compensatory nature of the diverse binding free energy components, possible threshold limits for some of these properties, and the availability of a computationally viable free energy methodology which could be of value in drug-design endeavors.

Binding Sites↗
PubMed2004

Aliphatics vs. aromatics hydration thermodynamics.

By comparing the hydration thermodynamics of benzene with that of a hypothetical aliphatic hydrocarbon having the same accessible surface area (ASA) of benzene, Makhatadze and Privalov concluded that the whole difference is due to the weak H-bonds that water forms with the aromatic ring. The formation of such H-bonds would be characterized by a negative Gibbs energy change, slightly increasing in magnitude with temperature, and a positive entropy change over a large temperature range. The latter thermodynamic feature is not physically reliable for the formation of H-bonds. In the present article, by using a statistical mechanical dissection scheme of hydration, a microscopic interpretation for the numbers obtained by Makhatadze and Privalov is proposed. The difference in hydration Gibbs energy should be attributed to the different strength of van der Waals interactions that benzene can do with water, owing to the larger polarizability of the aromatic ring with respect to an aliphatic hydrocarbon of equal size. In addition, the difference in hydration entropy should account for the different extent of H-bond reorganization upon the insertion of benzene and the corresponding aliphatic hydrocarbon in water.

Benzene↗
PubMed2004

Aggregate formation in oil and adsorption at oil/water interface: thermodynamics and its application to the oleyl alcohol system.

The thermodynamic equations for examining aggregate formation in an oil phase and adsorption at the oil/water interface of a nonionic solute were derived. The total differentials of chemical potentials of species and the oil/water interfacial tension were expressed as functions of temperature, pressure, and the total concentration of solute in the oil phase after explicit consideration of aggregate formation. The partial derivatives of the chemical potentials and the interfacial tension with respect to the independent variables were found to provide the thermodynamic quantities of aggregate formation and adsorption from oil phase to the interface by introducing the concept of an ideally dilute associated solution. These equations were applied to the cyclohexane solution of oleyl alcohol/water system, and the adsorption and aggregate formation was examined.

Journal Article↗