Group Additivity Analysis of the Heat Capacity Changes Associated with the Dissolution into Water of Different Organic Compounds

Structural Order in the Hydration Shell of Nonpolar Groups versus that in Bulk Water

The poor solubility of nonpolar compounds in water around room temperature is governed by a large and negative entropy change, whose molecular cause is still debated. Since the Frank and Evans original proposal in 1945, the large and negative entropy change is usually attributed to the formation of ordered structures in the hydration shell of nonpolar groups. However, the existence of such ordered structures has never been proven. The present study is aimed at providing available structural results and thermodynamic arguments disproving the existence of ordered structures in the hydration shell of nonpolar groups.

Shedding light on the extra thermal stability of thermophilic proteins

An entropic stabilization mechanism has recently gained attention and credibility as the physical ground for the extra thermal stability of globular proteins from thermophilic microorganisms. An empirical result, obtained from the analysis of thermodynamic data for a large set of proteins, strengthens the general reliability of the theoretical approach originally devised to rationalize the occurrence of cold denaturation [Graziano, PCCP 2014, 16, 21755-21767]. It is shown that this theoretical approach can readily account for the entropic stabilization mechanism. On decreasing the conformational entropy gain associated with denaturation, the thermal stability of a model globular protein increases markedly.

Liquid Polyamorphous Transition and Self-Organization in Aqueous Solutions of Ionic Surfactants

Polyamorphous transitions in supercooled water, porous substances, solutions of polyols, and proteins are studied intensively. They accompany the self-organization of hydrocarbons and surfactants. In this study, the methods of polyamorphous transition identification are proposed, and their dependence on hydrocarbons and surfactant concentration and sizes is investigated. The place of polyamorphous transitions in the general theory of phase separation is determined, and their bistability, self-oscillations, hysteresis, fluctuations, cooperative effect, enthalpy, and entropy are described. Surface, volume, and diffusion instabilities of polyamorphous transitions are analyzed. Technologies based on the properties of polyamorphous transitions are proposed.

Universality of thermodynamic constants governing biological growth rates

Background

Mathematical models exist that quantify the effect of temperature on poikilotherm growth rate. One family of such models assumes a single rate-limiting ‘master reaction’ using terms describing the temperature-dependent denaturation of the reaction's enzyme. We consider whether such a model can describe growth in each domain of life.

Methodology/Principal Findings

A new model based on this assumption and using a hierarchical Bayesian approach fits simultaneously 95 data sets for temperature-related growth rates of diverse microorganisms from all three domains of life, Bacteria, Archaea and Eukarya. Remarkably, the model produces credible estimates of fundamental thermodynamic parameters describing protein thermal stability predicted over 20 years ago.

Conclusions/Significance

The analysis lends support to the concept of universal thermodynamic limits to microbial growth rate dictated by protein thermal stability that in turn govern biological rates. This suggests that the thermal stability of proteins is a unifying property in the evolution and adaptation of life on earth. The fundamental nature of this conclusion has importance for many fields of study including microbiology, protein chemistry, thermal biology, and ecological theory including, for example, the influence of the vast microbial biomass and activity in the biosphere that is poorly described in current climate models.

On the heat-capacity change of pairwise hydrophobic interactions

Computer simulations [S. Shimizu and H. S. Chan, J. Am. Chem. Soc. 123, 2083 (2001); D. Paschek, J. Chem. Phys. 120, 10605 (2004)] have demonstrated that the heat-capacity change associated with the interaction of two nonpolar spherical particles, at room temperature, shows a complex behavior with a significant maximum at the distance corresponding to the desolvation barrier configuration and a small minimum at the distance corresponding to the contact configuration. Taking advantage of the detailed analysis performed by Paschek, the two-state model of Muller is applied to estimate the energetic strength and the intactness of the H bonds in the hydration shell of a xenon atom and in the concave part of the joint Xe-Xe hydration shell. In both hydration shell regions the H bonds are energetically stronger but more broken than those in bulk water. In addition, those in the concave part of the joint Xe-Xe hydration shell are, in absolute, stronger and more broken. These thermodynamic features coupled to simple geometric arguments allow the calculation of heat-capacity values that are in agreement with those provided by computer simulations for the pairwise Xe-Xe interaction.

On the hydration heat capacity change of benzene

The heat capacity change associated with the hydration of benzene is a large and positive quantity, but it is significantly smaller than that associated with the hydration of an alkane having the same accessible surface area of benzene, the corresponding alkane. This large difference merits attention and should be rationalized. This task is performed by means of the two-state Muller's model for the reorganization of H-bonds. It results that: (a) the hydration shell of both hydrocarbons consists of H-bonds that are enthalpically stronger but slightly more broken than those in bulk water; (b) the hydration shell of benzene consists, on average, of enthalpically slightly weaker H-bonds with respect to the corresponding alkane. The latter feature, due to the presence of the weak benzene-water H-bonds, is the physical cause of the large difference in the hydration heat capacity change, according to the two-state Muller's model.

Solvation enthalpies and heat capacities ofn-alkanes in four polymer phases by capillary gas chromatography

Molar solvation enthalpy (deltasol H(o)298) and molar heat capacity changes (deltasol C(o)p) were determined by gas chromatography for the C6-C12 n-alkanes on four preferred stationary phases (100% polydimethyl siloxane, 50% diphenyl-50% dimethyl polysiloxane, 50% trifluoropropyl methylsiloxane, and polyethylene glycol) in commercial FSOT. Statistical evaluation indicated the temperature independence of deltasol C(o)p in the range 303-393 K. Deltasol H(o)298 depends linearly on the number of carbon atoms in the n-alkanes, but no linearity could be established for deltasol C(o)p of higher homologues on polar columns, which may be due to a more ordered state on the liquid phase. The homologues for which a linear temperature dependence exists demonstrated that deltasol C(o)p is related linearly to the van der Waals volume and the temperature derivative of the density of the stationary phase. The results are consistent with a simple physical explanation at the molecular level.

Unifying temperature effects on the growth rate of bacteria and the stability of globular proteins

The specific growth rate constant for bacterial growth does not obey the Arrhenius-type kinetics displayed by simple chemical reactions. Instead, for bacteria, steep convex curves are observed on an Arrhenius plot at the low- and high-temperature ends of the biokinetic range, with a region towards the middle of the growth range loosely approximating linearity. This central region has been considered by microbiologists to be the "normal physiological range" for bacterial growth, a concept whose meaningfulness we now question. We employ a kinetic model incorporating thermodynamic terms for temperature-induced enzyme denaturation, central to which is a term to account for the large positive heat capacity change during unfolding of the proteins within the bacteria. It is now widely believed by biophysicists that denaturation of complex proteins and/or other macromolecules is due to hydrophobic hydration of non-polar compounds. Denaturation is seen as the process by which enthalpic and entropic forces becomes imbalanced both at high and at low temperatures resulting in conformational changes in the enzyme structure that expose hydrophobic amino acid groups to the surrounding water molecules. The "thermodynamic" rate model, incorporating the heat capacity change and its effect on the enthalpy and entropy of the system, fitted 35 sets of data for psychrophilic, psychrotrophic, mesophilic and thermophilic bacteria well, resulting in biologically meaningful estimates for the important thermodynamic parameters. As these results mirror those obtained by biophysicists for globular proteins, it appears that the same or a similar mechanism applies to bacteria as applies to proteins.

On the Intactness of Hydrogen Bonds around Nonpolar Solutes Dissolved in Water

Angell developed a simple two-state model of hydrogen bonds with the aim to describe some properties of pure water. Muller extended the two-state model description to treat the unusual thermodynamics of hydrophobic hydration. We show here that, to correctly reproduce a qualitative feature of the temperature dependence of the hydration heat capacity change of nonpolar solutes by means of the two-state Muller's model, the hydrogen bonds in the hydration shell have to be more broken than those in bulk water. This contrasts with the suggestion in the literature that more hydrogen bonds form around a nonpolar solute in water.

Group additivity schemes for the calculation of the partial molar heat capacities and volumes of unfolded proteins in aqueous solution

A critical review is given of the present state of group additivity schemes for the calculation of partial molar volumes and heat capacities of unfolded proteins. The comparison between the experimental values and the predictions based on the different models shows clearly that only the peptide-based additivity scheme represents properly both the absolute values and the temperature dependence of these thermodynamic quantities.

The basis of the hydrophobic effect

The property of a molecule that most reliably determines the magnitude of the hydrophobic effect that it will experience is the number of hydrogen-carbon bonds it contains not the accessible surface area of its nonpolar portions. This conclusion follows from an examination of the standard free energies of transfer of alkanes, alkenes, alkadienes, and arenes from water to hexadecane. When the standard free energies of transfer for hydrocarbons in these different classes are plotted as a function of the number of hydrogen-carbon bonds they contain, all of the data fall upon the same line. These standard free energies of transfer are also directly proportional to the number of hydrogen-carbon bonds the hydrocarbons contain. When the same standard free energies of transfer are plotted as a function of the accessible surface areas of the hydrocarbons, the data do not fall upon the same line nor are the standard free energies of transfer directly proportional to the accessible surface areas. An examination of the standard free energies of transfer for the different classes of hydrocarbons from the gas phase to water and from the gas phase to hexadecane reinforces the conclusion that the number of hydrogen-carbon bonds in a molecule rather than its accessible surface area is the basis of the hydrophobic effect. Consequently, estimates of the contribution of different functional groups to the hydrophobic effect providing the free energy of folding of a molecule of protein or providing the free energy of dissociation for the association of two proteins or the association of a ligand with a protein should be made by counting the number of hydrogen-carbon bonds excluded from water rather than computing the accessible surface areas excluded from water.

Minimum in the temperature dependence of the Kováts retention indices of nitroalkanes and alkanenitriles on an apolar phase

The Kováts retention indices (I) of 1-nitroalkanes and alkanenitriles were determined on polydimethylsiloxane and Innowax (polyethylene glycol) columns in a wide temperature range. The temperature dependence of the retention indices exhibits a definite minimum for the early members of the homologous series. The position of the minimum shifts to lower temperatures with increasing carbon atom number of the solute. The thermodynamic explanation of an extreme in the I vs. T function is the higher solvation heat capacities of nitroalkanes and alkanenitriles relative to those of the reference n-alkanes, owing to the deviation from the ideal state in the solution. A novel equation was derived which describes the minimum in the I vs. T function, too.

Temperature dependence of Henry's law constant in an extended temperature range

The Henry's law constants H for chloroform, 1,1-dichloroethane, 1,2-dichloropropane, trichloroethene, chlorobenzene, benzene and toluene were determined by the EPICS-SPME technique (equilibrium partitioning in closed systems--solid phase microextraction) in the temperature range 275-343 K. The curvature observed in the ln H vs. 1/T plot was due to the temperature dependence of the change in enthalpy delta H0 during the transfer of 1 mol solute from the aqueous solution to the gas phase. The nonlinearity of the plot was explained by means of a thermodynamic model which involves the temperature dependence of delta H0 of the compounds and the thermal expansion of water in the three-parameter equation ln (H rho TT) = A2/T + BTB + C2, where rho T is the density of water at temperature T, TB = ln(T/298) + (298-T)/T, A2 = -delta H298(0)/R, delta H298(0) is the delta H0 value at 298 K, B = delta Cp0/R, and C2 is a constant. delta Cp0 is the molar heat capacity change in volatilization from the aqueous solution. A statistical comparison of the two models demonstrates the superiority of the three-parameter equation over the two-parameter one ln H vs. 1/T). The new, three-parameter equation allows a more accurate description of the temperature dependence of H, and of the solubility of volatile organic compounds in water at higher temperatures.

An analysis of the hydration thermodynamics of the CONH group

The hydration thermodynamics of the CONH group play a fundamental role for the stability of the native conformation of globular proteins, but cannot be measured in a direct manner. The values of the thermodynamic functions have to be extracted from experimental measurements on model compounds using group additivity approaches. The estimates determined by Makhatadze and Privalov in the temperature range 5–100°C are used in the present study in view of their qualitative reliability. They are analyzed by means of a suitable approach that couples scaled particle theory calculations with the application of the modified Muller's model. It results that the negative entropy change is caused by the excluded volume effect for cavity creation, exaggerated in liquid water by the small size of water molecules themselves; the negative enthalpy change is determined by the H-bond energetics, formation of CONH–water H-bonds, and reorganization of water–water H-bonds. The negative heat capacity change, a striking feature of CONH hydration thermodynamics, is because the H-bonds in the hydration shell of the CONH group are less broken than those in bulk water in the temperature range examined.Key words: peptide group, hydration, excluded volume effect, H-bonds, two-state model, negative heat capacity change.

A study on the enthalpy-entropy compensation in protein unfolding

A large number of thermodynamic data including the free energy, enthalpy, entropy, and heat capacity changes were collected for the denaturation of various proteins. Regression indicated that remarkable enthalpy-entropy compensation occurred in protein unfolding, which meant that the change in enthalpy was almost compensated by a corresponding change in entropy resulting in a smaller net free energy change. This behavior was proposed to result from the water molecule reorganization, which contributed significantly to the enthalpy and entropy changes but little to the free energy change in protein unfolding. It turned out that the enthalpy-entropy compensation could provide novel insights into the problem of enthalpy and entropy convergence in protein unfolding.

On the temperature-induced coil to globule transition of poly-N-isopropylacrylamide in dilute aqueous solutions

Poly-N-isopropylacrylamide (PNIPAM) is a chemical isomer of poly-leucine, having the polar peptide group in the side-chain rather than in the backbone. It has been demonstrated experimentally that PNIPAM dissolved in aqueous solution undergoes a collapse transition from coil to globule on increasing temperature above the θ-point. By a careful reviewing of existing experimental data, we emphasize that such coil to globule collapse has to be considered an intramolecular first-order transition, analogous to the cold renaturation of small globular proteins. The main theoretical approaches to the coil to globule collapse in homopolymers are discussed briefly, and a critical comparison between the existing models is performed. We point out that, as a general result, the coil to globule collapse is expected to be a first-order transition for rigid and semi-rigid macromolecules. Finally, taking advantage of the analogy between the coil to globule collapse of PNIPAM and the cold renaturation of small globular proteins, we try to clarify some important and intriguing aspects of protein thermodynamics. This leads to the conclusion that the amphiphilic nature of polypeptide chain plays the fundamental role for the existence of two temperature-induced conformational transitions.

Hydrophobicity of benzene

The present work tries to clarify the molecular origin of the poor solubility of benzene in water. The transfer of benzene from pure liquid phase into water is dissected in two processes: transfer from gas phase to pure liquid benzene; and transfer from gas phase to liquid water. The two solvation processes are analyzed in the temperature range 5-100 degrees C according to Lee's Theory. The solvation Gibbs energy change is determined by the balance between the work of cavity creation in the solvent, and the dispersive interactions of the inserted benzene molecule with the surrounding solvent molecules. The purely structural solvent reorganization upon solute insertion proves to be a compensating process. The analysis shows that the work of cavity creation is larger in water than in benzene, whereas the attractive energetic interactions are stronger in benzene than in water; this scenario is true at any temperature. Therefore, both terms act in the same direction, contrasting the transfer of benzene from pure liquid phase into water and determining its hydrophobicity.

Differential scanning calorimetry study of the thermodynamic stability of some mutants of Sso7d from Sulfolobus solfataricus

Sso7d from the thermoacidophilic archaebacterium Sulfolobus solfataricus is a small globular protein with a known three-dimensional structure. Inspection of the structure reveals that Phe31 is a member of the aromatic cluster forming the protein hydrophobic core, whereas Trp23 is located on the protein surface and its side chain exposed to the solvent. The thermodynamic consequences of the substitution of these two residues in Sso7d have been investigated by comparing the temperature-induced denaturation of Sso7d with that of three mutants: F31A-Sso7d, F31Y-Sso7d, and W23A-Sso7d. The denaturation processes proved to be reversible for all proteins, and represented well by the two-state N if D transition model in a wide range of pH. All three mutants are less thermally stable than the parent protein; in particular, in the pH range of 5.0-7.0, the F31A substitution leads to a decrease of 24 degreesC in the denaturation temperature, the F31Y substitution to a decrease of 10 degreesC, and the W23A substitution to a decrease of 6 degreesC. A careful thermodynamic analysis of such experimental data is carried out.

Thermodynamics of dissolving gaseous argon in different solvents

The solvation of argon in 10 different solvents at room temperature is analysed in terms of the theoretical framework developed by Lee. In order to perform calculations, we used the approach devised by Pierotti and firmly validated by Lee's theory. The fair agreement between the experimental and the calculated values of Δ G. Δ H. , and Δ S. is carefully analysed. It proves that the excluded volume effect, due to cavity creation in the solvent, opposes the solubility process. This effect in water is exaggerated by the small size of the water molecules and is the cause of hydrophobicity. The qualitative difference between water and hydrazine with regard to the solvation enthalpy and entropy changes is rationalized on the basis of the contributions arising from the structural reorganization in the two solvents on solute insertion.Key words: hydrophobic hydration, cavity creation, structural solvent reorganization.

Thermodynamic analysis of the effect of selective monodeamidation at asparagine 67 in ribonuclease A

Selective deamidation of proteins and peptides is a reaction of great interest, both because it has a physiological role and because it can cause alteration in the biological activity, local folding, and overall stability of the protein. In order to evaluate the thermodynamic effects of this reaction in proteins, we investigated the temperature-induced denaturation of ribonuclease A derivatives in which asparagine 67 was selectively replaced by an aspartyl residue or an isoaspartyl residue, as a consequence of an in vitro deamidation reaction. Differential scanning calorimetry measurements were performed in the pH range 3.0-6.0, where the unfolding process is reversible, according to the reheating criterion used. It resulted that the monodeamidated forms have a different thermal stability with respect to the parent enzyme. In particular, the replacement of asparagine 67 with an isoaspartyl residue leads to a decrease of 6.3 degrees C of denaturation temperature and 65 kJ mol-1 of denaturation enthalpy at pH 5.0. These results are discussed and correlated to the X-ray three-dimensional structure of this derivative. The analysis leads to the conclusion that the difference in thermal stability between RNase A and (N67isoD)RNase A is due to enthalpic effects arising from the loss of two important hydrogen bonds in the loop containing residue 67, partially counterbalanced by entropic effects. Finally, the influence of cytidine-2'-monophosphate on the stability of the three ribonucleases at pH 5.0 is studied and explained in terms of its binding on the active site of ribonucleases. The analysis makes it possible to estimate the apparent binding constant and binding enthalpy for the three proteins.