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PubMed2004

Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in a evolution reactor, I.

A theory for describing evolution as adaptive walks by a finite population with M walkers (M > or = 1) on an anisotropic Mt. Fuji-type fitness landscape is presented, from a thermodynamical point of view. Introducing the 'free fitness' as the sum of a fitness term and an entropy term and 'evolutionary force' as the gradient of free fitness on a fitness coordinate, we demonstrate that the behavior of these theoretical walkers is almost consistent with the thermodynamical schemes. The major conclusions are as follows: (1) an adaptive walk (=evolution) is driven by an evolutionary force in the direction in which free fitness increases; (2) the expectation of the climbing rate obeys an equation analogous to the Einstein relation in Brownian motion; (3) the standard deviation of the climbing rate is a quantity analogous to the mean thermal energy of a particle, kT (x constant). In addition, on the interpretation that the walkers climb the landscape by absorbing 'fitness information' from the surroundings, we succeeded in quantifying the fitness information and formulating a macroscopic scheme from an informational point of view.

Adaptation, Biological↗
PubMed2005

Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in an evolution reactor, II.

In our previous report [Aita, T., Morinaga, S., Hosimi, Y., 2004. Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in an evolution reactor I. Bull. Math. Biol. 66, 1371-1403], an analogy between thermodynamics and adaptive walks on a Mt. Fuji-type fitness landscape in an artificial selection system was presented. Introducing the 'free fitness' as the sum of a fitness term and an entropy term and 'evolutionary force' as the gradient of free fitness on a fitness coordinate, we demonstrated that the adaptive walk (=evolution) is driven by the evolutionary force in the direction in which free fitness increases. In this report, we examine the effect of various modifications of the original model on the properties of the adaptive walk. The modifications were as follows: first, mutation distance d was distributed obeying binomial distribution; second, the selection process obeyed the natural selection protocol; third, ruggedness was introduced to the landscape according to the NK model; fourth, a noise was included in the fitness measurement. The effect of each modification was described in the same theoretical framework as the original model by introducing 'effective' quantities such as the effective mutation distance or the effective screening size.

Algorithms↗
PubMed2005

Thermodynamic study of beta-N-acetylhexosaminidase enzyme heterogeneity in human seminal plasma.

BACKGROUND: It has been suggested that the activity of beta-N-acetylhexosaminidase (Hex) in seminal plasma may be used as a biochemical marker of azoospermia. The purpose of our study was to evaluate this hypothesis using a thermodynamic procedure developed to determine total Hex activity and that of its isoenzymes in this biological fluid. METHODS: Using the substrate 3,3'-dichlorophenolsulphoftaleinil N-acetyl-beta-D-glucosaminide, a highly significant difference (p<0.001) is found between the activation energy of Hex A (41.5 kJ/mol) and of Hex B (72.3 kJ/mol), making it possible to determine the activity of these isoenzymes from the apparent activation energy of the total Hex in seminal plasma. RESULTS: A significant difference between the normozoospermic and azoospermic groups was only found for Hex A isoenzyme activity (p<0.05), although with considerable overlapping between the values of both groups. Significant partial correlations were found for the total Hex, Hex A and Hex B activities with the immobile spermatozoa count (p<0.01) and for total Hex and Hex B with the dead spermatozoa count (p<0.05). In turn, Hex A had a significant partial correlation with the live spermatozoa count (p<0.05); however, Hex activity in seminal plasma of acromosomal origin appears to be of little importance in quantitative terms. CONCLUSIONS: It was not possible to confirm that total Hex activity in seminal plasma, or even of its isoenzymes Hex A and Hex B, is a suitable biochemical marker of azoospermia (efficiency< or =67%). The thermodynamic procedure described may be a useful alternative for the study of the Hex enzyme heterogeneity in spermatozoa.

Adult↗
PubMed2004

Thermodynamics and kinetics of solute transfer in reversed-phase liquid chromatography. Effect of annelation in polycyclic aromatic hydrocarbons.

A series of four-ring polycyclic aromatic hydrocarbons (PAHs) with varying annelation structure was studied by reversed-phase liquid chromatography. Using a polymeric octadecylsilica stationary phase over a temperature range from 273 to 303 K and an average pressure range from 585 to 3585 psi (1 psi = 6894.76 Pa), the thermodynamic and kinetic aspects of the retention mechanism were examined. Thermodynamic behavior was characterized by the retention factor, together with the associated changes in molar enthalpy and molar volume, whereas kinetic behavior was characterized by the rate constants, together with the associated activation enthalpies and activation volumes. The data indicate that pyrene, with a more condensed annelation structure, exhibits smaller changes in molar enthalpy and molar volume (delta Hsm = -4.4 kcal/mol, delta Vsm = -1.9 ml/mol; 1 cal = 4.184J) than PAHs with a more linear structure such as chrysene (delta Hsm = -8.2 kcal/mol, delta Vsm = - 11.7 ml/mol). The kinetic data indicate that pyrene undergoes faster rates of transport than chrysene (k(ms) = 313 and 14 s(-1), respectively), but the non-planar benzo[c]phenanthrene undergoes the fastest transport (k(ms) = 330 s(-1)). The activation enthalpies and activation volumes are similarly affected by the annelation structure. It is noteworthy that deviations from the exponentially modified Gaussian (EMG) model are observed for some PAH zone profiles at the lowest temperature, which suggests a possible change in retention mechanism. In order to characterize these deviations, the non-linear chromatography (NLC) model and a new bi-exponentially modified Gaussian (E2MG) model were examined. The regression results indicate that neither the NLC nor E2MG model offer significant improvements in the statistical quality of fit or provide a better description of the observed retention behavior.

Chromatography, Liquid↗
PubMed2004

Thermodynamic studies of pressure-induced retention of peptides in reversed-phase liquid chromatography.

The pressure-induced retention of peptides on reversed-phase HPLC was studied by systematically changing organic solvent composition and temperature at both low (19 bar) and high (318 bar) pressures using a homologous series of hydrophobic poly-L-phenylalanine (n = 2-7) as the model compound. Based on van' t Hoff plots under different organic solvent compositions and pressures, the enthalpy change for the solute (deltaH) was determined. Moreover, both the enthalpy and entropy change for each phenylalanine residue (deltadeltaH and deltadeltaS), which corresponds to solute retention on a microenvironment along the depth of C18 chain, were also calculated by direct subtractions. Results indicate that under acetonitrile (ACN) compositions above 35%, the pressure caused deltadeltaS value to change from a negative to a positive value and both deltaH and deltadeltaH to change from a negative to a less negative value, all leading to a thermodynamic state closer to those under 35% acetonitrile composition. This implies that the pressure-induced retention observed in this study was an entropy-favored but enthalpy-unfavored process and was explained by pressure-induced desorption of solvent molecules that were associated with the stationary phase or with the peptide solute. Under 35% acetonitrile composition, however, it was found that neither deltadeltaH nor deltadeltaS value was significantly changed by the pressure. Whereas, both deltaH value and the intercept of van't Hoff plots under 35% acetonitrile composition were increased by pressure. This indicates that under low organic solvent composition, 35%, most of the acetonitrile molecules adsorbed on the surface of the stationary phase and only little solvent molecules were dissolved in the bulk stationary phase where the phenylalanine residues were partitioned. This study has provided new thermodynamic insights to the pressure-induced retention for peptides and proteins.

Chromatography, High Pressure Liquid↗
PubMed2004

Determination of thermodynamic properties by supercritical fluid chromatography.

This survey attempts to summarise thermodynamic applications of supercritical fluid chromatography (SFC) with an emphasis on the results published during the last 10 years. In addition to a review of thermodynamic measurements by SFC, it contains brief sections on instrumental considerations and on the sources of auxiliary information needed when processing the retention data.

Chemical Phenomena↗
PubMed2004

Application of capillary gas chromatography to studies on solvation thermodynamics.

The potentiality of capillary gas chromatography (GC) as a means for research on solubility phenomena is focused. Basic thermodynamic information can be obtained in a simple and direct way from this technique relying on few parameters with their associated errors tightly controlled. An unexplored field of solvation phenomenology inaccessible to other techniques is revealed by the accuracy of capillary GC, provided that relevant chromatographic variables are utilized and an adequate treatment of the experimental information performed. The present article reviews different approaches for the attainment of basic thermodynamic information through capillary GC. Some traditional concepts on the treatment of chromatographic data for physicochemical measurement are questioned. Applications of the technique to research on solubility phenomena are depicted.

Chemical Phenomena↗
PubMed2004

Thermodynamic equilibrium of the solute distribution in size-exclusion chromatography.

Our understanding of the nature of solute retention in size-exclusion chromatography (SEC) is predicated upon an equilibrium, entropy-controlled, size-exclusion mechanism. The entropic nature of the separation depends, in turn, upon the solute distribution coefficient (K(SEC) being at (or close to) thermodynamic equilibrium. Classic experiments to confirm this assumption were performed over thirty years ago. Here, we combine information obtained from both flow and static mixing SEC experiments to show that the solute distribution in SEC is in thermodynamic equilibrium over a molar mass range extending one order of magnitude higher than previously measured (from 2 x 10(3) to 1.1 x 10(6) Da) using crosslinked polystyrene packing material of identical pore size (10(4) A). The differences between our observations and previous ones conducted over three decades ago are ascribed, principally, to advances in stationary phase synthesis and column technology for SEC in particular and, secondarily, to improvements in the performance of the various instrumental components of liquid chromatographic systems in general.

Chromatography, Gel↗
PubMed2005

Thermodynamic and kinetic characterization of nitrogen-containing polycyclic aromatic hydrocarbons in reversed-phase liquid chromatography.

A series of five nitrogen-containing polycyclic aromatic hydrocarbons (NPAHs) was studied on polymeric octadecylsilica using methanol and acetonitrile as the mobile phase. The thermodynamic and kinetic behavior was examined as a function of ring number, annelation structure, and position of the nitrogen atom. The retention factors for the NPAHs are smaller than those for the parent PAHs in methanol, while the converse is true in acetonitrile. The changes in molar enthalpy are relatively comparable in both mobile phases with 1-aminopyrene having values of -5.0 +/- 0.2 kcal/mol in methanol and -6.3 +/- 0.7 kcal/mol in acetonitrile (1 cal = 4.184 J). However, the rate constants from mobile to stationary phase (k(sm)) and from stationary to mobile phase (k(ms)) demonstrate large differences as a function of mobile phase. For example, the rate constants k(ms) for 1-aminopyrene and 4-azapyrene are 675 and 62 s(-1), respectively, in methanol at 303 K. In contrast, the same solutes demonstrate rate constants of 3.47 and 3.9 x 10(-3) s(-1), respectively, in acetonitrile. The activation energies for transfer from mobile phase to transition state (deltaE(double dagger(m)) and from stationary phase to transition state (deltaE(double dagger(s)) also differ as a function of mobile phase. For example, the activation energies deltaE(double dagger(s)), for 1-aminopyrene are 21 and approximately 0 kcal/mol, whereas those for 4-azapyrene are 19 and 23 kcal/mol, in methanol and acetonitrile, respectively. Based on these thermodynamic and kinetic results, the relative contributions from the partition and adsorption mechanisms are discussed.

Adsorption↗
PubMed2005

Thermodynamic study of N-trifluoroacetyl-O-alkyl nipecotic acid ester enantiomers on diluted permethylated beta-cyclodextrin stationary phase.

Thermodynamic studies were performed on 12 pairs of N-trifluoroacetyl-O-alkyl nipecotic acid ester enantiomers on diluted permethylated beta-cyclodextrin stationary phase (CP Chirasil-Dex CB). The influence of ester alkyl group structure on interaction with permethylated beta-cyclodextrin (Me-CD) and enantioselectivity was studied. The types of alkyl groups studied included n-alkyl (C1-C5) and groups containing branching at differing locations relative to the chiral center of the molecule. The results show that for a given molecular weight, the n-alkyl esters have stronger interactions with Me-CD than esters containing branched alkyl groups. However, although having weaker interactions with Me-CD, esters containing alpha-branched alkyl groups exhibit higher enantioselectivity than the corresponding n-alkyl or beta-branched isobutyl esters. From the retention data, thermodynamic parameters were estimated using the retention increment method and enthalpy-entropy compensation plots (ln R' versus deltaH) were constructed. The results suggest that ester enantiomers with branching at the alpha-carbon of the ester alkyl group have additional and/or different types of enantioselective interactions with Me-CD than the C1-C5 n-alkyl esters or beta-branched isobutyl ester. In order to obtain a qualitative sense of the interaction with Me-CD, structures of the diastereomeric complexes formed between Me-CD and some of the ester enantiomers were modeled using simulated annealing molecular dynamics.

Indicators and Reagents↗
PubMed2005

Determination of thermodynamic properties of isotactic poly(1-butene) at infinite dilution using density and inverse gas chromatography.

The partial molar volumes, V1(M), and the molar volume of isotactic crystalline low-molecular-weight poly(1-butene), iPBu-1, V1, have been calculated from the measured density of {iPBu-1 + solvent (n-hexane, n-heptane, n-nonane, n-decane, p-xylene, cyclohexane and chloroform)} systems. Some of the thermodynamic quantities were also obtained for the iPBu-1 with eight hydrocarbons (n-octane, n-decane, n-undecane, n-dodecane, n-tridecane, o-xylene, m-xylene, p-xylene) by the method of inverse gas chromatography at various temperatures. The weight fraction activity coefficients of the solvent at infinite dilution, omega2(infinity) and the Flory-Huggins thermodynamic interaction parameters, chi21(infinity), between polymer and solvents were determined. The partial molar free energy, deltaG2(infinity), the partial molar heat of mixing, deltaH2(infinity), at infinite dilution and the polymer solubility parameter, delta1, were calculated. Additionally, the (solid + liquid) binary mixtures equilibria, SLE, of iPBu-1 with three hydrocarbons (n-octane, n-decane and m-xylene) were studied by a dynamic method. By performing these experiments over a large concentration range, the T-x phase diagrams of the polymer-solvent systems were constructed. The excess Gibbs energy models were used to describe the nonideal behaviour of the liquid phase. The omega2(infinity) were determined from the solubility measurements and were predicted by using the UNIFAC FV model.

Butanes↗
PubMed2005

Thermodynamic studies of complexation and enantiorecognition processes of monoterpenoids by alpha- and beta-cyclodextrin in gas chromatography.

Gas-liquid chromatography was applied in thermodynamic investigations of processes of complexation and enantioseparation by alpha- and [-cyclodextrins of chiral monoterpenoids. The distribution constants, stability constants and thermodynamic parameters enthalpy, entropy and free energy of the complexation processes were determined. It has been found that enantioseparation of monoterpenes by alpha- and beta-cyclodextrins is the result of formation of 1:2 stoichiometric complexes. When 1:1 stoichiometric complexes are formed, enantioselectivity is not observed. All investigated processes of complexation are enthalpy-driven regardless of the stoichiometry of the formed complexes. -deltaH, -TdeltaS and -deltaG of complexation process have higher values for bicyclic than for monocyclic monoterpenoids as well as for alpha-CD than for beta-CD. The first or second step of complexation may be responsible for enantioselectivity.

Chromatography, Gas↗
PubMed2005

Thermodynamic functions and intra-particle mass transfer kinetics of structural analogues of a template on molecularly imprinted polymers in liquid chromatography.

The parameters of the thermodynamics and mass transfer kinetics of the structural analogues (L-enantiomers) of the template were measured on an Fmoc-L-tryptophan (Fmoc-L-Trp) imprinted polymer, at different temperatures. The equilibrium isotherm data and the overloaded band profiles of these compounds were measured at temperatures of 298, 313, 323, and 333 K. The isotherm data were modeled. The thermodynamic functions of the different adsorption sites were derived from the isotherm parameters, using van't Hoff plots. The mass transfer parameters were derived by comparing the experimental peak profiles and profiles calculated using the lumped pore diffusion (POR) model for chromatography. These data show that (1) the strength between the substrate molecules and the MIP increases with increasing number of functional groups on the substrates; (2) enthalpy is the driving force for the affinity of the substrates for the MIP; (3) surface diffusion is the dominant mass transfer mechanism of the substrates through the porous MIP. For those substrate molecules that have the same stereochemistry as the template, the energetic surface heterogeneity needs to be incorporated into the surface diffusion coefficients. Heterogeneous surface diffusivities decrease with increasing affinity of the substrates for the MIP.

Adsorption↗
PubMed2005

Thermodynamic analysis of the heterogenous binding sites of molecularly imprinted polymers.

The thermodynamic interactions of two polymers, one Fmoc-L-Trp-imprinted (MIP), the other one an unimprinted reference (NIP), with the two Fmoc-tryptophan enantiomers were studied by frontal analysis, which allows accurate measurements of the adsorption isotherms. These isotherms were acquired at temperatures of 40, 50, 60, and 70 degrees C, for sample concentrations ranging between 0.005 and 40 mM. The mobile phase used was acetonitrile with one percent acetic acid as an organic modifier. Within the measured concentration ranges, the tri-Langmuir isotherm model accounts best for the isotherm data of both enantiomers on the MIP, the bi-Langmuir model for the isotherm data of Fmoc-L-Trp on the NIP. These isotherm models were selected using three independent processes: statistical tests on the results from regression of the isotherm data to different isotherm models; calculation of the affinity energy distribution from the raw isotherm data; comparison of the experimental and the calculated band profiles. The isotherm parameters obtained from these best selected isotherm models showed that the enantiomeric selectivity does not change significantly with temperature, while the affinity of the substrates for both the MIP and the NIP decrease considerably with increasing temperatures. These temperature effects on the binding performance of the MIP were clarified by considering the thermodynamic functions (i.e., the standard molar Gibbs free energy, the standard molar entropy of adsorption, and the standard molar enthalpy of adsorption) for each identified type of adsorption sites, derived from the Van't Hoff equation. This showed that the entropy of transfer of Fmoc-L-Trp from the mobile to the MIP stationary phase is the dominant driving force for the selective adsorption of Fmoc-L-Trp onto the enantioselective binding sites. This entropy does not change significantly with increasing temperatures from 40 to 70 degrees C.

Adsorption↗
PubMed2006

Investigation of thermodynamic properties of poly(methyl methacrylate-co-n-butylacrylate-co-cyclopentyl styryl-polyhedral oligomeric silsesquioxane) by inverse gas chromatography.

The thermodynamic properties of poly(methyl methacrylate-co-butyl acrylate-co-cyclo -pentylstyryl polyhedral oligomeric silsesquioxane) (poly(MMA-co-BA-co-styryl-POSS)) were investigated by means of inverse gas chromatography (IGC) using 20 different kinds of solvents as the probes. Some thermodynamic parameters, such as molar heats of sorption, weight fraction activity coefficient, Flory-Huggins interaction parameter, partial molar heats of mixing and solubility parameter were obtained to judge the interactions between POSS-contained polymers and solvents and the solubility of the polymers in these solvents. It was found that acetates, aromatic hydrocarbons and hydrocarbon halides were good solvents, n-hexane, ethanol, n-propanol, n-butanol and n-pentanol were moderate solvents, while n-heptane, n-octane, n-nonane, n-decane and methanol were poor solvents for all POSS-contained polymers within the experimental temperature range. Incorporation of POSS in polymer increased the solubility of polymers in solvents, and the more the POSS in polymer was, the better the solubility was and stronger the hydrogen bonding interaction was, but the POSS content in polymers seemed to have no obvious influence on the solubility parameter of polymers.

Chromatography, Gas↗
PubMed2005

Thermodynamic modeling of contact angles on rough, heterogeneous surfaces.

Theoretical modelling for contact angle hysteresis carried out to date has been mostly limited to several idealized surface configurations, either rough or heterogeneous surfaces. This paper presents a preliminary study on the thermodynamics of contact angles on rough and heterogeneous surfaces by employing the principle of minimum free energy and the concept of liquid front. Based on a two-dimensional regular model surface, a set of relations were obtained, which correlate advancing, receding and system equilibrium contact angles to surface topography, roughness and heterogeneity. It was found that system equilibrium contact angles (theta(ES)) can be expressed as a function of surface roughness factor (delta) and the Cassie contact angle (theta(C)): costheta(ES) = deltacostheta(C). This expression can be reduced to the classical Wenzel equation.: theta(ES) = theta(W) for rough but homogeneous surfaces, and the classical Cassie equation theta(ES) = theta(C) for heterogeneous but smooth surfaces. A non-dimensional parameter called surface feature factor (omega) was proposed to classify surfaces into three categories (types): roughness-dominated, heterogeneity-dominated and mixed-rough-heterogeneous. The prediction of advancing and receding contact angles of a surface is dependent on which category the surface belongs to. The thermodynamic analysis of contact angle hysteresis was further extended from the regular model surface to irregular surfaces; consistent results were obtained. The current model not only agrees well with the models previously studied by other researchers for idealized surfaces, but also explores more possibilities to explain the reported experimental results/observations that most existing theories could not explain.

Colloids↗
PubMed2005

The thermodynamic principles of isochoric cryopreservation.

The goal of this study is to introduce the fundamental thermodynamic principles of isochoric (constant volume) cryopreservation for low temperature preservation of biological materials. Traditionally, cryopreservation is performed in an isobaric process (constant pressure) at 1 atm, because this is our natural environment and it is most convenient experimentally. More than half a century of studies on cryopreservation shows that the major mechanism of damage during isobaric cryopreservation is the increase in intracellular ionic concentration during freezing, which presumably causes chemical damage to the components of cells. Cryoprotectants as well as hyperbaric pressures have been developed as methods to reduce the extent of chemical damage during freezing. The theoretical studies in this paper show that in isochoric cryopreservation, the increase in solution concentration during freezing is lower at each temperature by almost an order of magnitude from that in isobaric cryopreservation. This suggests that isochoric cryopreservation could be a preferential alternative to isobaric cryopreservation. The technology for isochoric cryopreservation is very simple; freezing in a constant volume chamber. Using a simple isochoric cryopreservation device, we confirm the theoretical thermodynamic predictions.

Cryopreservation↗
PubMed2005

Thermodynamics of solubility, sublimation and solvation processes of parabens.

Saturated vapor pressures for a number of parabens (methyl- (MePB); ethyl- (EtPB), n-propyl- (PrPB) and n-butyl- (BuPB)) were obtained and from their respective temperature dependences the sublimation enthalpy, DeltaH(sub)( degrees ), and sublimation entropy, DeltaS(sub)(degrees), as well as their respective relative fractions in the process calculated. The sublimation enthalpies are: DeltaH(sub)(degrees)(MePB)=98.8+/-0.8; DeltaH(sub)(degrees)(EtPB)=100.9+/-0.7; DeltaH(sub)(degrees)(PrPB)=123.7+/-0.6; DeltaH(sub)(degrees)(BuPB)=108.4+/-0.8 kJmol(-1). The obtained values are discussed with regard to X-ray data from the literature. Theoretical calculations of the respective crystal lattice energies were carried out and compared to the experimental data. The following parameters were analyzed: (a) energetic contribution of van der Waals forces and hydrogen bonding to the total packing energy of the crystals; (b) contributions of the different fragments of the paraben molecules to the packing energy; (c) influence of bias of the supposed C-H distances on the result of the calculation procedure. Enthalpies of evaporation were estimated from the measured enthalpies of sublimation and enthalpies of fusion, and compared with literature data. Moreover, the thermodynamic functions of solvation of the molecules in water and in a number of n-alcohols were evaluated. The thermodynamic terms (Gibbs energy, enthalpy and entropy) of the solvation process were split up in their respective specific and nonspecific fraction, and these values compared for all combinations of parabens and solvents. The influence of mutual saturation of the phases in the water-octanol system on the partitioning process of the molecules is also discussed.

Entropy↗