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PubMed1995

Comparative CD and thermodynamic studies between sheared A:G and Watson-Crick A:U(T) base pairs in RNA and DNA.

Thermodynamic parameters for duplex formation were determined from CD melting curves for r(GGACGAGUCC)2 and d(GGACGAGTCC)2, both of which have been demonstrated to form two consecutive 'sheared' A:G base pairs at the center by our previous studies. The parameters were determined also for r(GGACUAGUCC)2 and d(GGACTAGTCC)2, where the A:G mismatches are replaced by Watson-Crick A:U(T) base pairs. Thermodynamic properties for duplex formation are compared between the sheared and the Watson-Crick base pairs, and between RNA and DNA. Difference in the thermodynamic stability is analyzed and discussed in terms of enthalpy and entropy changes.

Base Composition↗
PubMedDate not supplied

[The thermodynamic direction of biological evolution. The model and the reality].

A macrothermodynamic model of evolution of the supramolecular structures and chemical composition of living objects during ontogenesis and at long-term stages of general biological evolution is presented. A study of quasiclosed (thermodynamically and kinetically) systems, phases of the biomass supramolecular structures, enables a conclusion on the thermodynamic direction of biological evolution to be made. In correspondence with the second principle, this direction leads to variations in the chemical composition and structure of the living systems during their development. Indirect and direct evidence of the trend to a minimal Gibbs specific function of formation of the supramolecular structures in animal tissues during ontogenesis are presented. The conclusion that thermodynamics is the "driving force" of evolution of the biological world is confirmed.

Animals↗
PubMed2003

Kinetic versus thermodynamic control during the formation of [2]rotaxanes by a dynamic template-directed clipping process.

A template-directed dynamic clipping procedure has generated a library of nine [2]rotaxanes that have been formed from three dialkylammonium salts-acting as the dumbbell-shaped components-and three dynamic, imino bond-containing, [24]crown-8-like macrocycles-acting as the ring-shaped components-which are themselves assembled from three dialdehydes and one diamine. The rates of formation of these [2]rotaxanes differ dramatically, from minutes to days depending on the choice of dialkylammonium ion and dialdehyde, as do their thermodynamic stabilities. Generally, [2]rotaxanes formed by using 2,6-diformylpyridine as the dialdehyde component, or bis(3,5-bis(trifluoromethyl)benzyl)ammonium hexafluorophosphate as the dumbbell-shaped component, assembled the most rapidly. Those rotaxanes containing this particular electron-deficient dumbbell-shaped unit, or 2,5-diformylfuran units in the macroring, were the most stable thermodynamically. The relative thermodynamic stabilities of all nine of the [2]rotaxanes were determined by competition experiments that were monitored by (1)H NMR spectroscopy.

Journal Article↗
PubMed2006

Conformational, concomitant polymorphs of 4,4-diphenyl-2,5-cyclohexadienone: conformation and lattice energy compensation in the kinetic and thermodynamic forms.

4,4-Diphenyl-2,5-cyclohexadienone (1) crystallized as four conformational polymorphs and a record number of 19 crystallographically independent molecules have been characterized by low-temperature X-ray diffraction: form A (P2(1), Z'=1), form B (P1, Z'=4), form C (P1, Z'=12), and form D (Pbca, Z'=2). We have now confirmed by variable-temperature powder X-ray diffraction that form A is the thermodynamic polymorph and B is the kinetic form of the enantiotropic system A-D. Differences in the packing of the molecules in these polymorphs result from different acidic C-H donors approaching the C=O acceptor in C-H...O chains and in synthons I-III, depending on the molecular conformation. The strength of the C-HO interaction in a particular structure correlates with the number of symmetry-independent conformations (Z') in that polymorph, that is, a short C-HO interaction leads to a high Z' value. Molecular conformation (Econf) and lattice energy (Ulatt) contributions compensate each other in crystal structures A, B, and D resulting in very similar total energies: Etotal of the stable form A=1.22 kcal mol(-1), the metastable form B=1.49 kcal mol(-1), and form D=1.98 kcal mol(-1). Disappeared polymorph C is postulated as a high-Z', high-energy precursor of kinetic form B. Thermodynamic form A matches with the third lowest energy frame based on the value of Ulatt determined in the crystal structure prediction (Cerius2, COMPASS) by full-body minimization. Re-ranking the calculated frames on consideration of both Econf (Spartan 04) and Ulatt energies gives a perfect match of frame #1 with stable structure A. Diphenylquinone 1 is an experimental benchmark used to validate accurate crystal structure energies of the kinetic and thermodynamic polymorphs separated by <0.3 kcal mol(-1) (approximately 1.3 kJ mol(-1)).

Journal Article↗
PubMed2004

Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal "Alchemical" path, and practical solutions.

Thermodynamic integration is a widely used method to calculate and analyze the effect of a chemical modification on the free energy of a chemical or biochemical process, for example, the impact of an amino acid substitution on protein association. Numerical fluctuations can introduce large uncertainties, limiting the domain of application of the method. The parametric energy function describing the chemical modification in the thermodynamic integration, the "Alchemical path," determines the amplitudes of the fluctuations. In the present work, I propose a measure of the fluctuations in the thermodynamic integration and an approach to search for a parametric energy path minimizing that measure. The optimal path derived with this approach is very close to the theoretical minimum of the measure, but produces nonergodic sampling. Nevertheless, this path is used to guide the design of a practical and efficient path producing correct sampling. The convergence with this practical path is evaluated on test cases, and compares favorably with that of other methods such as power or polynomial path, soft-core van der Waals, and some other approaches presented in the literature.

Journal Article↗
PubMed1998

Thermodynamic Approaches to Microemulsions.

The thermodynamics of microemulsions is treated by decomposing the Helmholtz free energy into a sum of a free energy F0 of a dispersion in a continuous medium containing fixed, noninteracting globules and a free energy DeltaF due to the entropy of dispersion of globules in the continuous medium and to the interactions among them. The pressure p1 in the continuous medium of the system involving fixed, noninteracting globules is determined in two different ways. In one of them, it is calculated by minimizing the total free energy with respect to the volume fraction phi of the dispersed medium, while in the other it is considered equal to the external pressure. The equivalence between the conventional thermodynamics of a multicomponent mixture and a thermodynamics based on modeling a microemulsion as a dispersion is used to derive the basic equations. Equations are obtained for single microemulsions as well as microemulsions coexisting with an excess dispersed phase and with both excess phases. One demonstrates that the conventional Laplace equation is not valid for a microemulsion, and new equations are derived. One concludes that the approach involving the determination of p1 via the optimization of the total free energy is the proper one. Considering that DeltaF is dominated by the entropy of dispersion of globules in the continuous medium, equations are established relating the interfacial free energy at the surface of the globules to the radius of the globules and phi, for the case in which a microemulsion coexists with an excess dispersed phase. These equations reveal that for phi approximately 0.5 the above state cannot be stable and that a transition to another state involving a microemulsion coexisting with both excess phases is likely to occur. Copyright 1998 Academic Press.

Journal Article↗
PubMed2000

Thermodynamic Approach to the Wetting of Solids by Surface-Active Agents: A Supplementary Approach to the Gibbs Formalism.

The adsorption of a solute on a solid can be followed by contact angle measurements of a drop of the solution on the solid. The Gibbs isotherm model can be used for quantitative interpretation of wettability variations. Its use in linking the wettability to the adsorption isotherm involves assimilating the Gibbs' planes to the surfaces themselves. Within this framework, these interpretations lead to the conclusion that adsorption of surface-active agents is greater on solid-vapor interfaces than on solid-liquid interfaces, for hydrophilic solids. This is not the only approach. Thermodynamics allows other formalisms, the conclusions of which can be completely different. We present a thermodynamic approach which explicitly reveals relationships between surface tensions and contents of surfaces, without referring to the Gibbs' plane. This permits us to explain the behavior of a drop of surfactant solution put on hydrophilic or hydrophobic solids with conclusions different from those reached using the Gibbs approach. We show that all these thermodynamic approaches are linked; they do not dismiss one another but give different views of the same phenomenon. Copyright 2000 Academic Press.

Journal Article↗
PubMed2001

Analysis of Light Scattering Data on the Calcium Ion Sensitivity of Caseinate Solution Thermodynamics: Relationship to Emulsion Flocculation.

We describe the quantitative interrelation between the thermodynamic parameters of caseinate submicelles in the presence of calcium ions (0-14 mM) in aqueous medium and the capacity of the protein to induce depletion flocculation in oil-in-water emulsions at pH 7.0 and ionic strength 0.05 mol dm(-3). Measurements have been made by static and dynamic multiangle laser light scattering of the weight-average molecular weight, the radius of gyration, the hydrodynamic radius, and the second virial coefficient of caseinate submicelles in aqueous solution. Successive thermodynamic approximations with and without consideration of correlations between caseinate submicelles have been used to calculate the osmotic pressure in caseinate aqueous solutions and the free energy of the depletion interaction between droplets in oil-in-water emulsions stabilized by caseinate. Numerical results from both thermodynamic approximations are in reasonably good agreement with experiment, predicting a pronounced decrease in the strength of the depletion attraction at concentrations of Ca(2+) in the range 4-8 mM (with a minimum value at 8 mM). This correlates well with the great enhancement of stability of these emulsions with respect to flocculation in comparison with systems having no added ionic calcium and emulsions with lower (2 mM) or higher (10 mM) Ca(2+) contents. Nevertheless, the allowance for interactive correlations between caseinate submicelles seems to lead to a better prediction of emulsion flocculation on a qualitative level over the whole range of Ca(2+) concentrations studied (2-14 mM). The calculated pronounced decrease in depletion interaction strength is attributable to marked changes in weight-average molecular weight and mean size of aggregates, and to more positive values of the second virial coefficient of caseinate submicelles with increasing Ca(2+) content. Finally, we discuss the part played by the electrical charge on the protein in determining the overall strength of the flocculation-inducing attractive interactions between droplets. Copyright 2001 Academic Press.

Journal Article↗
PubMed1995

Enhanced stability in vivo of a thermodynamically stable mutant form of yeast iso-1-cytochrome c.

Previous work has established that the N57I amino acid replacement in iso-1-cytochrome c from the yeast Saccharomyces cerevisiae causes an unprecedented increase in thermodynamic stability of the protein in vitro, whereas the N57G replacement diminishes stability. Spectrophotometric measurements of intact cells revealed that the N57I iso-1-cytochrome c is present at higher than normal levels in vivo. Although iso-1-cytochrome c turnover is negligible during aerobic growth, transfer of fully derepressed, aerobically grown cells to anaerobic growth conditions leads to reduction in the levels of all of the cytochromes. Pulse-chase experiments carried out under these anaerobic conditions demonstrated that the N57I iso-1-cytochrome c has a longer half-life than the normal protein. This is the first report of enhanced stability in vivo of a mutant form of a protein that has an enhanced thermodynamic stability in vitro. Although the N57I protein concentration is higher than the normal level, reduced growth in lactate medium indicated that the specific activity of this iso-1-cytochrome c in vivo is diminished relative to wild-type. On the other hand, the level of the thermodynamically labile N57G iso-1-cytochrome c was below normal. The in vivo levels of the N57I and N57G iso-1-cytochrome c suggest that proteins in the mitochondrial intermembrane space can be subjected to degradation, and that this degradation may play a role in controlling their normal levels.

Aerobiosis↗
PubMed2001

Measurement uncertainty of thermodynamic data.

Thermodynamic quantities of chemical reactions are commonly derived from experimental data obtained by chemical analysis. The accuracy of the evaluated thermodynamic quantities is limited by the measurement uncertainty of the analytical techniques applied. Straightforward transfer of metrological rules established for determination of single analytes to the more complex process of evaluating values of thermodynamic quantities is not possible. Computer-intensive statistical methods and Monte Carlo techniques are shown to enable integration of existing metrological concepts. An initial stage of the integration of both concepts is presented, taking solubility data for Am(III) in carbonate media as an illustrative example. A cause and effect diagram is created as a means of identification of sources of uncertainty. The uncertainties are used in a resampling-based Monte Carlo study to produce a probability distribution of the value of a quantity.

Journal Article↗
PubMed2004

Solvent-based deuterium isotope effects on the redox thermodynamics of cytochrome c.

The reduction thermodynamics of cytochrome c (cytc), determined electrochemically, are found to be sensitive to solvent H/D isotope effects. Reduction of cytochrome c is enthalpically more favored in D(2)O with respect to H(2)O, but is disfavored on entropic grounds. This is consistent with a reduction-induced strengthening of the H-bonding network within the hydration sphere of the protein. No significant changes in E degrees ' occur, since the above variations are compensative. As a main result, this work shows that the oxidation-state-dependent differences in protein solvation, including electrostatics and solvent reorganization effects, play an important role in determining the individual enthalpy and entropy changes of the reduction process. It is conceivable that this is a common thermodynamic feature of all electron transport metalloproteins. The isotope effects turn out to be sensitive to buffer anions which specifically bind to cytc. Evidence is gained that the solvation thermodynamics of both redox forms of cytc are sensibly affected by strongly hydrated anions.

Animals↗
PubMed1991

Thermodynamics of the disproportionation of adenosine 5'-diphosphate to adenosine 5'-triphosphate and adenosine 5'-monophosphate, II. Experimental data.

High-pressure liquid-chromatography and microcalorimetry have been used to determine equilibrium constants and enthalpies of reaction for the disproportionation reaction of adenosine 5'-diphosphate (ADP) to adenosine 5'-triphosphate (ATP) and adenosine 5'-monophosphate (AMP). Adenylate kinase was used to catalyze this reaction. The measurements were carried out over the temperature range 286 to 311 K, at ionic strengths varying from 0.06 to 0.33 mol kg(-1), over the pH range 6.04 to 8.87, and over the pMg range 2.22 to 7.16, where pMg = -log a(Mg2+). The equilibrium model developed by Goldberg and Tewari (see the previous paper in this issue) was used for the analysis of the measurements. Thus, for the reference reaction: 2 ADp(3-) (ao) AMp(2-) (ao)+ ATp- (ao), K degrees = 0.225 +/- 0.010, DeltaG degrees = 3.70 +- 0.11 kJ mol (-1), DeltaH degrees = -1.5 +/- 1. 5 kJ mol (-1), degrees S degrees = -17 +/- 5 J mol(-1)K(-1), and ACP(p) degrees approximately = -46 J mo1l(-1)K(-1) at 298.15 K and 0.1 MPa. These results and the thermodynamic parameters for the auxiliary equilibria in solution have been used to model the thermodynamics of the disproportionation reaction over a wide range of temperature, pH, ionic strength, and magnesium ion morality. Under approximately physiological conditions (311.15 K, pH 6.94, [Mg2+] = 1.35 x 10(-3) mol kg(-1), and I = 0.23 mol kg(-1)) the apparent equilibrium constant (KA' = m(SigmaAMP)m(SigmaATP)/[ m(SigmaADP)]2) for the overall disproportionation reaction is equal to 0.93 +/- 0.02. Thermodynamic data on the disproportionation reaction and literature values for this apparent equilibrium constant in human red blood cells are used to calculate a morality of 1.94 x 10(-4) mol kg(-1) for free magnesium ion in human red blood cells. The results are also discussed in relation to thermochemical cycles and compared with data on the hydrolysis of the guanosine phosphates.

Journal Article↗
PubMed2004

Thermodynamic consideration on single oil in water emulsion film stabilized by cationic surfactant.

The emulsion film has become the focus of the study of emulsion because the film stability and structure play a crucial role on the whole stability and structure of emulsions. In this study, the single emulsion film stabilized by tetradecyltrimethylammonium bromide (C14TAB) in dodecane phase has been investigated thermodynamically. In order to make clear the theoretical treatment, it has been reviewed how the thermodynamic quantities of extremely thin films are defined and how it is related to the experimental variables such as temperature, pressure, and concentrations of solutes. By using the equations demonstrated here, the film tension and film surface tension, which were evaluated from the measurement of contact angle between the emulsion film and the surrounding bulk meniscus, have been inspected thermodynamically from the viewpoint of the influence of added salt (KBr) concentration on the structure of thin emulsion film. In addition, the comparison of the results obtained has also been made between the foam and emulsion films to reveal the effect of an ambient dodecane phase on the properties of the film.

Journal Article↗
PubMed2001

Combining solvent engineering and thermodynamic modeling to enhance selectivity during monoglyceride synthesis by lipase-catalyzed esterification.

Monoglyceride synthesis by Rhyzomucor miehei lipase was investigated via direct esterification between glycerol (adsorbed onto silica gel) and oleic acid in organic solvents. The main difficulty is to avoid the unwanted production of di- and tri-glycerides. It was demonstrated that an increase in solvent polarity, using mixtures of n-hexane and 2-methyl-2-butanol (2M2B), improves drastically the selectivity toward monoglyceride formation. In pure n-hexane, the monoglyceride represents only 6 molar % of the total products at the thermodynamic equilibrium (34 and 60% for di- and tri-glyceride respectively). Use of an equivolume mixture of n-hexane/2M2B enables a product mixture to be obtained containing 94% of monoglyceride at equilibrium (2.4 and 0% for di- and tri-glyceride respectively). This positive effect is counterbalanced by a decrease both in initial velocities and in substrate conversion at thermodynamic equilibrium.A modeling, able to predict the three thermodynamic equilibria governing the 3 consecutive reactions, based on activity coefficient calculations using the UNIFAC model, is proposed. It takes into account both the partition of water between solvent and immobilized catalyst, and the partition of glycerol between solvent and silica gel. A good correlation with experimental data obtained in n-hexane/2M2B mixtures was observed.

Journal Article↗
PubMed2005

Comparison of the thermodynamic properties of particulate and monolithic columns of molecularly imprinted copolymers.

A variety of polymerization techniques can be used to prepare molecularly imprinted copolymers (MIPs) for the purpose of the separation of enantiomers by HPLC. Unfortunately, the lack of thermodynamic and kinetic data characterizing the imprinted polymers prepared by these different techniques prevents the rational choice of the one most suited for a specific application. We investigated and compared the thermodynamic properties of copolymers imprinted for Fmoc-L-tryptophan and prepared by two different methods. The first was an in situ polymerization method that gives monolithic columns (monolithic MIPs), the second, a traditional method giving bulk MIPs. Examination of the thermodynamic properties on these two different MIPs showed that three types of binding sites coexist on their surface. The highest energy sites adsorb only the imprinted molecule or template. Most of the intermediate energy sites adsorb both the template and its antipode, although part of them may adsorb only the template. Finally, the lowest energy sites provide nonselective interactions of both the template and its antipode. On the nonimprinted copolymer, there are only two types of sites. The high-energy sites have a slightly lower energy that the intermediate sites of the MIPs, and the low-energy sites have properties close to those of the lowest energy sites on the MIPs. The monolithic MIPs have fewer nonselective sites than the bulk MIPs. However, the polar porogen that is needed to prepare the monolithic MIPs negatively affects the enantiomeric separation.

Journal Article↗
PubMed2006

Molecular adsorption at silica/CH3CN interface probed by using evanescent wave cavity ring-down absorption spectroscopy: determination of thermodynamic properties.

Evanescent wave cavity ring-down absorption spectroscopy is applied to measure the thermodynamic properties of the surface adsorption for neutral trans-4-[4-(dibutylamino)styryl]-1-(3-sulfopropyl) pyridinium (DP) and charged trans-4-[4-(dibutylamino)styryl]-1-methylpyridinium iodide (DMP+ I-) at the silica/CH3CN interface, where the interfacial density is determined by measurement of absorbance. The bulk concentration dependence of the surface density may be characterized with a Langmuir isotherm model, which yields saturated surface density, equilibrium constant, and free energy of adsorption of (7.0 +/- 0.3) x 10(13) cm(-2), (1.3 +/- 0.2) x 10(4) M(-1), and -23.5 +/- 0.4 kJ/mol for DP and (8.9 +/- 0.3) x 10(12) cm(-2), (2.6 +/- 0.7) x 10(4) M(-1), and -25.2 +/- 0.6 kJ/mol for DMP+ I-, respectively. The surface density of the isolated silanol groups may then be estimated in terms of the molecular probe results. The absorption contribution from the bulk solution is a factor of approximately 10(1)-10(2) smaller than the total absorbance measured such that subtraction of the bulk contribution leads to negligible change of the thermodynamic properties. The DP is adsorbed to the SiOH sites by forming hydrogen bonds, while the DMP+ cation is bound to the SiO- sites by electrostatic attraction. Surface forces are also probed by addition of triethylamine (TEA), which is competitive with DP for the silanol sites. When the TEA concentration is increased, the DP surface density is found to decrease, whereas the DMP+ surface density increases. The obtained thermodynamic properties are generally consistent with those measured by second harmonic generation spectroscopy. However, when a tetramethylammonium ((CH3)4N+ Cl-) salt is added, the DMP+ cation behaves differently between these two methods. Formation of an electrical double layer may account for the difference.

Journal Article↗
PubMed1996

Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three Fv mutants complexed with lysozyme.

Using site-directed mutagenesis, X-ray crystallography, and titration calorimetry, we have examined the structural and thermodynamic consequences of removing specific hydrogen bonds in an antigen-antibody interface. Crystal structures of three antibody FvD1.3 mutants, VLTyr50Ser (VLY50S), VHTyr32Ala (VHY32A), and VHTyr101Phe (VHY101F), bound to hen egg white lysozyme (HEL) have been determined at resolutions ranging from 1.85 to 2.10 A. In the wild-type (WT) FvD1.3-HEL complex, the hydroxyl groups of VLTyr50, VHTyr32, and VHTyr101 each form at least one hydrogen bond with the lysozyme antigen. Thermodynamic parameters for antibody-antigen association have been measured using isothermal titration calorimetry, giving equilibrium binding constants Kb (M-1) of 2.6 x 10(7) (VLY50S), 7.0 x 10(7) (VHY32A), and 4.0 x 10(6) (VHY101F). For the WT complex, Kb is 2.7 x 10(8) M-1; thus, the affinities of the mutant Fv fragments for HEL are 10-, 4-, and 70-fold lower than that of the original antibody, respectively. In all three cases entropy compensation results in an affinity loss that would otherwise be larger. Comparison of the three mutant crystal structures with the WT structure demonstrates that the removal of direct antigen-antibody hydrogen bonds results in minimal shifts in the positions of the remaining protein atoms. These observations show that this complex is considerably tolerant, both structurally and thermodynamically, to the truncation of antibody side chains that form hydrogen bonds with the antigen. Alterations in interface solvent structure for two of the mutant complexes (VLY50S and VHY32A) appear to compensate for the unfavorable enthalpy changes when protein-protein interactions are removed. These changes in solvent structure, along with the increased mobility of side chains near the mutation site, probably contribute to the observed entropy compensation. For the VHY101F complex, the nature of the large entropy compensation is not evident from a structural comparison of the WT and mutant complexes. Differences in the local structure and dynamics of the uncomplexed Fv molecules may account for the entropic discrepancy in this case.

Antigen-Antibody Complex↗
PubMed2004

Structural and thermodynamic properties of group 13 imidometallanes and their heavier analogues.

Systematic theoretical studies of the [XMYH](n) inorganic rings and clusters (M = Al, Ga, In; Y = N, P, As; X = H, F, Cl, Br, I; n = 1-6) have been carried out using hybrid Hartree-Fock density functional theory. A consistent set of the structural and thermodynamic properties has been obtained. The stability of the MY bond decreases in the order Al > Ga >or= In; N >> P > As. Terminal groups X have a minor influence on the subsequent elimination enthalpies of the clusters. In the case of X = H, hydrogen elimination makes formation of the [HMYH](6) oligomers from MH(3) and YH(3) thermodynamically favorable; while in the case of halide substituents, formation of [XMYH](6) is thermodynamically unfavorable, except for the system with the strongest MY bond (AlN). Substitution of the acidic hydrogen by X is favorable energetically for all [HMYH](6) clusters, but is complicated by the processes of cluster destruction to form the [X(2)MYH(2)](2) dimers. The high stability of the [HMNH](6) clusters makes them attractive single-source precursors for the production of 13-15 composites.

Journal Article↗