Gibbs Energy Contribution Research Articles

Insights on the comparative affinity of ribonucleic acids with plant-based beta carboline alkaloid, harmine: Spectroscopic, calorimetric and computational evaluation

Small molecules as ligands target multifunctional ribonucleic acids (RNA) for therapeutic engagement. This study explores how the anticancer DNA intercalator harmine interacts various motifs of RNAs, including the single-stranded A-form poly (rA), the clover leaf tRNAphe, and the double-stranded A-form poly (rC)-poly (rG). Harmine showed the affinity to the polynucleotides in the order, poly (rA) > tRNAphe > poly (rC)·poly (rG). While no induced circular dichroism change was detected with poly (rC)poly (rG), significant structural alterations of poly (rA) followed by tRNAphe and occurrence of concurrent initiation of optical activity in the attached achiral molecule of alkaloid was reported. At 25 °C, the affinity further showed exothermic and entropy-driven binding. The interaction also highlighted heat capacity (ΔCop) and Gibbs energy contribution from the hydrophobic transfer (ΔGhyd) of binding with harmine. Molecular docking calculations indicated that harmine exhibits higher affinity for poly (rA) compared to tRNAphe and poly (rC)·poly (rG). Subsequent molecular dynamics simulations were conducted to investigate the binding mode and stability of harmine with poly(A), tRNAphe, and poly (rC)·poly (rG). The results revealed that harmine adopts a partial intercalative binding with poly (rA) and tRNAphe, characterized by pronounced stacking forces and stronger binding free energy observed with poly (rA), while a comparatively weaker binding free energy was observed with tRNAphe. In contrast, the stacking forces with poly (rC)·poly (rG) were comparatively less pronounced and adopts a groove binding mode. It was also supported by ferrocyanide quenching analysis. All these findings univocally provide detailed insight into the binding specificity of harmine, to single stranded poly (rA) over other RNA motifs, probably suggesting a self-structure formation in poly (rA) with harmine and its potential as a lead compound for RNA based drug targeting.

Determining the Gibbs Energy Contributions of Ion and Electron Transfer for Proton Insertion in ϵ-MnO2.

Electrochemically active ϵ-MnO2 and ɣ-MnO2 as tunnel-type host-guest structures have been extensively studied by crystallography and electrochemical techniques for application in battery cathode materials. However, the Gibbs energies of the underlying ion and electron transfer processes across the electrode interfaces have not yet been determined. Here we report for the first time these data for ϵ-MnO2 . This was possible by measuring the mid-peak potentials in cyclic voltammetry and the open-circuit potentials under electrochemically reversible conditions.

Determination of Individual Gibbs Energies of Ion and Electron Transfer in Electrochemical Insertion Processes

Based on three-phase electrode models, we study to access the Gibbs energy contributions for the transfer of ions and electrons in Prussian blue analogs since they have long life cycles and high energy efficiency. Ni[Fe(CN)6] (HCFNi) and Cu[Fe(CN)6] (HCFCu) were preliminarily synthesized by a hydrothermal process. The obtained HCFNi powders were supported on a paraffin-impregnated graphite electrode in contact with an organic electrolyte, producing solid-state oxidation-reduction electrochemical reactions, which have been monitored by cyclic voltammetry and open circuit potential measurements in the presence of potassium as intercalating ion. The results show a behavior according to the Nernst equation as the potassium ion concentration varies, with a slope of 61.2 mV/dec. These experiments make it possible to access Gibbs free energy values for both transfers separately and replicate them for different insertion ions, such as Na+ and Li+.Figure: (Left) Open circuit potential measurements; (center) mid-peak potential measurements; and (right) cyclic voltammetry for Ni[Fe(CN)6] in potassium media. Figure 1

Thermodynamic descriptors of sensible heat driven liquid-liquid phase separation

• Solvent (Water/alcohol) provides the principal contribution in governing the solution thermoresponsive behavior. • Analytical derivation of temperature and concentration dependent gradient of the scaled Gibbs energy of mixing. • Scaled Gibbs energy gradient derived as a function of the Gibbs stability criterion and also in activity coefficient terms. • Scaled/Reduced activity coefficient can delineate LCST/UCST regimes without computing the Gibbs energy of mixing. • All the above parameters successfully characterize LCST/UCST behavior with literature/experimental corroboration. Separation of a homogeneous solution into its constituent liquids through sensible heating obviates the need for vaporization/distillation and the associated latent heat of phase change. Therefore, it could enable alternative more energy efficient cycles in many applications that involve the separation of miscible liquids. This can be achieved by utilizing Lower and Upper Critical Solution Temperature (LCST/UCST) driven phase separation. This study identifies the thermodynamic descriptors for predicting LCST/UCST exhibiting ionic liquid (IL) - water/alcohol (solvent) solutions, and therefore provides a fundamental insight into the underlying energetics responsible for temperature and concentration dependent miscibility of multicomponent solutions. Excess Gibbs energy analysis of 50 solutions revealed that the solvent (water/alcohol) played a pivotal role in phase separation and exhibited contrasting excess Gibbs energy contributions in the LCST and UCST regimes. Furthermore, analysis of scaled Gibbs energy was carried out to elucidate the energetics of phase separation and differentiate between LCST and UCST thermodynamically. Consequently, we introduce the solvent Reduced Activity Coefficient (RAC) which was used to successfully predict the phase separation behavior without evaluating the Gibbs energy function, thus saving significant computation time.

Thermodynamic assessment of the C[sbnd]Cr[sbnd]Ti system—Supported by DFT calculations

The thermodynamic description of the CCrTi ternary system has been reassessed. The main reason was to adjust the solubility limit of Cr in MC (M = Cr, Ti), but also to take the solubility of Ti in M3C2 and M7C3 into account. Another reason was that the thermodynamic descriptions of all the three constituent binary systems (CCr, CTi and CrTi) had been revised after the previously published description of the CCrTi system. Important metastable end-members and interaction parameters were calculated using Density Functional Theory (DFT). For fcc-CrC and Ti3C2, DFT was used together with a recently published method to calculate the molar Gibbs energy as a function of temperature (Gm(T)). For fcc-CrC also the magnetic contribution and the magnetic transition temperature, i.e. the Curie temperature (TC), were included. DFT was also used to calculate Gibbs energy of formation at 0 K for Ti7C3 and to calculate the molar excess Gibbs energy contribution, and TC, as a function of Ti composition in MC. DFT calculated parameters were compared with experiments or previous assessments. Selected experimental information from literature was then used to optimize parameters that are difficult to calculate with DFT, e.g. interaction parameters for the liquid phase and temperature dependence for interaction parameters in the solid phases. The resulting thermodynamic description, which is based on critically reviewed binary descriptions, reproduces the experimental solidification sequence, found in literature, equally well as the previous description of the CCrTi system. Furthermore, in contrast to the previous description, the new description also reproduces the most recent experimentally determined solubility of Cr in MC and takes the solubility of Ti in M3C2 and M7C3 into account. Finally the new description uses DFT calculated metastable end-members and interaction parameters, which gives more reliable predictions, especially at low temperatures.

Gibbs energies of activation for reacting systems with multiple reactant‐state and transition‐state conformations

AbstractThree distinct procedures for obtaining the effective Gibbs energies of activation from computed energies for a reaction involving multiple reactant‐state (RS) and transition‐state (TS) conformers are shown to be equivalent. If Boltzmann‐weighted average Gibbs energies for RS and TS are evaluated, then the Gibbs energy contribution from entropy of mixing of both RS and TS conformers must also be included in order to obtain the correct value for the effective Gibbs energy of activation. Application to a solvolytic reaction of 4,4′‐dimethoxybenzhydrylpyridinium cation, which is shown to satisfy the Curtin‐Hammett principle with rapid interconversion of RS conformers, demonstrates the use of each procedure for evaluation of the effective Gibbs energy of activation.

Does the release of hydration water come with a Gibbs energy contribution?

Hydration is a major force driving molecular recognition events involving biopolymers. Such events are generally accompanied by release or uptake of water molecules from the hydration shells of participating biomolecular solutes. The exchange of water molecules between the hydration and bulk populations is known to proceed with changes in volume, enthalpy, and entropy. It is less clear if the water exchange also contributes to free energy. The thermodynamic analysis performed in this study suggests that the release or uptake of individual water molecules may contribute not only to enthalpy and entropy but also to free energy. While water molecules solvating a particular solute or an atomic group may exhibit a near exact enthalpy–entropy compensation resulting in a zero contribution to free energy, this tendency is not universal to all solutes. Another level of complexity stems from the modulation of Gibbs energy contributions of released water molecules by pressure and temperature. We emphasize the need for further studies to quantify the thermodynamics of hydration and understand how pressure and temperature modulate the energetics of water release from the hydration shells of various atomic groups and, hence, to elucidate the contribution of hydration as a driving force in biomolecular events as a function of temperature and pressure.

Effect of water—ethanol solvent on the stability of copper(ii) coordination compound with the nicotinate ion

The stability constants of copper(II) complexes with nicotinate ion in water—ethanol solvent were determined by the potentiometric method at 25.0±0.1 °C and ionic strength of 0.25 (NaClO4) in the range XEtOH = 0—0.7 mole fractions. The stability constant of copper(II) nicotinate complex considerably increases with increasing ethanol concentration in the solvent. The contributions of reactants to the Gibbs energy of the complex formation reaction on going from water to aqueous ethanol were analyzed. The results of thermodynamic analysis of solvation effects were used to evaluate the ratio of the ion and ligand transfer Gibbs energy contributions to the change in the reaction Gibbs energy in the water—ethanol system.

Partitioning of Cr and Si between cementite and ferrite derived from first-principles thermodynamics

Partitioning of Cr and Si between cementite and ferrite was investigated by first-principles thermodynamics taking into account vibrational, electronic, and magnetic Gibbs energy contributions. At finite temperatures, these contributions lower the partitioning Gibbs energy and compete with the configurational entropy, which favors impurity segregation to ferrite due to its larger volume fraction compared to cementite. Due to the large positive partitioning enthalpy contribution of Si at T = 0 K, partitioning of Si to cementite is virtually absent in agreement with experiment. The situation is drastically different for Cr impurities. Incorporation of finite-temperature effects resolves the discrepancy between experimental observations and previous T = 0 K first-principles calculations. Cr strongly segregates to cementite due to the enhanced magnetic entropy of cementite above 400 K, i.e., near the Curie temperature of cementite. The increasing magnetic fluctuations in ferrite cause a strong reduction of the partitioning coefficient in the temperature range from 773 to 973 K in qualitative agreement with experiment. Quantitative agreement with calphad data and experimental data for equilibrium Cr concentrations in a wide range of alloy compositions is achieved by renormalizing the theoretical magnetic partitioning Gibbs energy by a constant scaling factor.

Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: Predictive thermodynamic model

Cyanine dyes are important chemical modifications of oligonucleotides exhibiting intensive and stable fluorescence at visible light wavelengths. When Cy3 or Cy5 dye is attached to 5′ end of a DNA duplex, the dye stacks on the terminal base pair and stabilizes the duplex. Using optical melting experiments, we have determined thermodynamic parameters that can predict the effects of the dyes on duplex stability quantitatively (ΔG°, Tm). Both Cy dyes enhance duplex formation by 1.2kcal/mol on average, however, this Gibbs energy contribution is sequence-dependent. If the Cy5 is attached to a pyrimidine nucleotide of pyrimidine–purine base pair, the stabilization is larger compared to the attachment to a purine nucleotide. This is likely due to increased stacking interactions of the dye to the purine of the complementary strand. Dangling (unpaired) nucleotides at duplex terminus are also known to enhance duplex stability. Stabilization originated from the Cy dyes is significantly larger than the stabilization due to the presence of dangling nucleotides. If both the dangling base and Cy3 are present, their thermodynamic contributions are approximately additive. New thermodynamic parameters improve predictions of duplex folding, which will help design oligonucleotide sequences for biophysical, biological, engineering, and nanotechnology applications.

Thermodynamics of dynamic transformation of hot deformed austenite in four steels of increasing carbon contents

Recent observations regarding the dynamic transformation of deformed austenite at temperatures above the Ae3 are reviewed for four different steels of increasing carbon contents. The structures observed are Widmanstätten in nature and appear to have formed displacively. The effect of deformation on the Gibbs energy of austenite in these steels is estimated by assuming that the austenite continues to work harden after initiation of the transformation and that its flow stress and dislocation density can be derived from the experimental flow curve. By further taking into account the inhomogeneity of the dislocation density, Gibbs energy contributions are derived that are sufficient to promote transformation as much as 100°C above the Ae3. The present calculations indicate that the dislocation densities in the regions that experience transformation are 2–15 times higher than the average values. It is also suggested that, at the lower carbon levels, plate growth is followed by C diffusion, while it is accompanied by C diffusion at the higher carbon contents.

Aggregation Thermodynamics of Sodium Octanoate Micelles Studied by Means of Molecular Dynamics Simulations

The present work is aimed at studying the computation of the thermodynamic potentials that describe the stability of anionic surfactant molecules in micellar aggregates. We report a set of molecular dynamics simulations of a sodium octanoate micelle in aqueous solution using the umbrella sampling method along with the Jarzynski equality in order to compute the potential of mean force for the dissociation process of one surfactant molecule from a previously assembled micellar aggregate. The Jarzynski average was computed at several different temperatures in order to estimate the Gibbs energy of association for the octanoate anion, which was split into its enthalpic and entropic contributions. We also estimated the contributions arising from the polar head and the apolar tail for each thermodynamic potential, and a detailed picture emerged from these simulations. The aggregation is driven mostly by the Gibbs energy contribution arising from the hydrophobic tail, which was large enough to cancel out the unfavorable contribution from the polar head. Although the association process may be ascribed mostly to the transfer of the apolar tail to the micellar core, it should be noted that the polar head also contributed with a favorable entropic term to the overall Gibbs energy. These findings were rationalized by comparing the energetic and structural patterns of the hydration process of a free monomer in solution to an aggregated molecule. The interaction energy distributions presented at least two discernible populations and each population was related to a different structural pattern, as characterized by the radial distribution functions. Altogether, the changes in both the energy and structure of the hydration layer are consistent with the entropy-driven association of the surfactant into the micellar aggregate.

The dynamic transformation of deformed austenite at temperatures above the Ae3

Recent observations regarding the dynamic transformation of deformed austenite at temperatures above the Ae3 are reviewed. Experimental results obtained on four different steels over the temperature range from 743 to 917°C and at strains up to ε=5 are described. It is shown that there is a critical strain for the formation of superequilibrium ferrite and that the volume fraction of transformed ferrite increases with the strain. The structures observed are Widmanstätten in form and appear to have nucleated displacively. The effect of deformation on the Gibbs energy of austenite is estimated by assuming that the austenite continues to work-harden after initiation of the transformation and that its flow stress and dislocation density can be derived from the experimental flow curve by making suitable assumptions about two-phase flow. By further taking into account the inhomogeneity of the dislocation density, Gibbs energy contributions (driving forces) are derived that are sufficient to promote transformation as much as 100°C above the Ae3. The C diffusion times required for the dynamic formation of the cementite particles observed are estimated. These range from ∼25 to 100μs and are therefore consistent with the times available during rolling. The Gibbs energy calculations suggest that growth of the Widmanstätten ferrite is followed by C diffusion at the lower carbon contents, while it is accompanied by C diffusion at the higher carbon levels.

Cold unfolding of β‐hairpins: A molecular‐level rationalization

Isolated β-hairpins in water have a temperature dependence of their conformational stability qualitatively resembling that of globular proteins, showing both cold and hot unfolding transitions. It is shown that a molecular-level rationalization of this cold unfolding can be provided extending the approach devised for globular proteins (Graziano G. Phys Chem Chem Phys 2010; 12:14245-14252). The decrease in the solvent-excluded volume upon folding, measured by the decrease in the solvent accessible surface area, produces a gain in configurational/translational entropy of water molecules that is the main stabilizing contribution of the folded conformation. This always stabilizing Gibbs energy contribution has a parabolic-like temperature dependence in water and is exactly counterbalanced at two temperatures (i.e., the cold and hot unfolding temperatures) by the always destabilizing Gibbs energy contribution due to the loss in conformational degrees of freedom of the peptide chain.

Effect of ethylene glycol on micellization and micellar-catalyzed alkaline hydrolysis reaction of a cationic surfactant at 293–313 K

Changes in critical micellar concentrations (CMC’s) of gemini surfactant, α, ω-ethane bis(dimethyl cetyl ammonium bromide) (C16-2-C16) with different concentrations of ethylene glycol (EG) addition have been investigated by electrical conductivity method. Subsequently, alkaline hydrolysis of ethyl acetate (EA) in the presence of C16-2-C16 and C16-2-C16-EG has been studied conductometrically at 303.2 and 313.2 K, respectively. It was found that an increase in concentrations of EG added to C16-2-C16 aqueous solutions caused an increase in CMC’s of C16-2-C16, provoked by the decrease in the interfacial Gibbs energy contribution to GM∘. The hydrolysis of EA showed catalytic and restrained dual behavior in the presence of surfactant, it may be related to higher microviscosity and change of morphology with increased surfactant for C16-2-C16 at higher concentration. Addition of EG did not change microenvironment in micellar interfacial region significantly, which had less effect on gemini C16-2-C16 micellar catalytic efficiency.

Effects of Organic Solvent Addition on the Aggregation and Micellar Growth of Cationic Dimeric Surfactant 12-3-12,2Br-

The micellization and micellar growth of cationic dimeric surfactant propanediyl-alpha-omega-bis(dodecyldimethylammonium) bromide, 12-3-12,2Br-, have been studied in several water-organic solvent mixtures. The organic solvents were ethylene glycol, glycerol, 1,2-propylene glycol, 1,3-propylene glycol, acetonitrile, dioxane, formamide, and N,N-dimethylformamide. Results showed that the aggregation process was less favored in the binary mixtures than in pure water, which was explained by considering the influence of the solvophobic effect on micellization. The addition of organic solvents was accompanied by a diminution in the average aggregation number, Nagg, of the dimeric micelles. This diminution was due to the decrease in the interfacial Gibbs energy contribution, Delta G0interfacial, to the Gibbs energy of micellization caused by the decrease in the hydrocarbon/bulk-phase interfacial tension. As a result of the micelle size diminution, the concentration at which the sphere-to-rod transition occurred, C*, was higher in the mixtures than in pure water. Micelle size reduction is accompanied by a decrease in the ionic interactions and in the extra packing contribution to the deformation of the surfactants tails, making the formation of cylindrical micelles less favorable.

Effects of head group size on micellization of cetyltrialkylammonium bromide surfactants in water–ethylene glycol mixtures

Micellization of cetyltrialkylammonium bromide (alkyl = methyl, ethyl, propyl, and butyl) surfactants has been studied in various water–ethylene glycol, EG, mixtures. This study provided the opportunity of investigating how, for a given hydrophobic tail length, the head group size determines the effect of the addition of EG on the micellization process. Conductivity, surface tension, spectroscopic and steady-state fluorescence measurements were carried out. The influence of additional methylenes in the headgroups on the Gibbs energy of micellization, Δ G M ° , was found to derive from changes in the solvophobic Gibbs energy contribution and from variations in the electrostatic headgroups interaction contribution.

Effects of Ethylene Glycol Addition on the Aggregation and Micellar Growth of Gemini Surfactants

Micellization of three didodecyl dicationic dibromide gemini surfactants with different methylene spacer lengths, 12-s-12,2Br- where s = 3-5 methylene groups, has been investigated in water-ethylene glycol, EG, mixtures with weight percentages of EG up to 50%. Subsequently, effects of the addition of the organic solvent on the micellar growth of these surfactants and on the surfactant concentration range where sphere-to-rod transitions occur were studied by means of steady-state and time-resolved fluorescence quenching and spectroscopic measurements. Results show that an increase in the weight percentage of ethylene glycol added to aqueous 12-s-12,2Br- (s = 3-5) micellar solutions causes the sphere-to-rod transition to occur at higher surfactant concentrations than in pure water. The diminution in the average aggregation number, N(agg), when wt % EG increases, provoked by the decrease in the interfacial Gibbs energy contribution to DeltaG degrees M, is the main factor responsible for this observation. The decrease in N(agg) is accompanied by a decrease in the ionic interactions and the extra packing contribution to the deformation of the surfactants tails, making formation of cylindrical micelles less favorable. Besides, an increase in the solvent content and polarity of the interfacial region does not favor formation of direct ion pairs, decreasing the tendency of micelles to grow.

Prediction of Diffusion Coefficients in Liquid Systems

On the basis of Eyring's absolute reaction rate theory, a new model for the Maxwell−Stefan diffusivity has been developed. This model, an extension of the Vignes equation, describes the concentration dependence of the diffusion coefficient in terms of the diffusivities at infinite dilution and an additional excess Gibbs energy contribution. This energy part allows the explicit consideration of thermodynamic nonidealities within the modeling of this transport property. If the same set of interaction parameters, which has been derived from vapor−liquid equilibrium (VLE) data, is applied for this part and for the thermodynamic correction, a theoretically sound modeling of VLE and diffusion can be achieved. The influence of viscosity and thermodynamics on the model accuracy is thoroughly investigated. For this purpose, diffusivities of 85 binary mixtures consisting of alkanes, cycloalkanes, halogenated alkanes, aromatics, ketones, and alcohols are computed. The average relative deviation between experimental ...

Study on Molecular Aggregates of N-(1,1-Dihydroperfluoroalkyl)-N,N,N-trimethylammonium Chloride

Dissolution into water of solid fluorinated cationic amphiphiles was investigated in detail for four amphiphiles with different alkyl chain lengths: N-(1,1-dihydroperfluorooctyl)-, N-(1,1-dihydroperfluoro-decyl)-, N-(1,1-dihydroperfluorododecyl)-, and N-( 1,1-dihydroperfluorotetradecyl)-N,N,N-trimethylammonium chloride. The dissolution seemed quite fast just from appearance, but it took a very long time to reach thermodynamic dissolution equilibrium, where a specific conductance of the solution steadily increased with time even after the solid particles perfectly disappeared from the solution. Change in sizes of molecular aggregates with time was confirmed by dynamic light scattering, and the distribution of sizes decreased with time and with increasing temperature. The critical micelle concentrations (cmc's) were determined from the specific conductivity change against concentration, after the dissolution equilibrium was reached. The cmc of the latter two amphiphiles monotonically increased with temperature, and the Gibbs energy contribution per CF 2 group to micellization was 1.54 times as large as that per CH 2 group from the slope of the plots of ln(cmc) against the carbon number of the alkyl chain. The rate of dissociation of micellar aggregates to monomers was traced by electric conductivity on an oscilloscope screen, and the activation energy obtained from its temperature dependence was found to decrease with increasing alkyl chain length. Taking all experimental results into consideration, the processes from the solid state to aggregates in the dissolved state in thermodynamic equilibrium were proposed.