Volume Free Energy Research Articles

Structural insights into the toxicity of type II ribosome inactivating proteins (RIPs): a molecular dynamics study

Ribosome Inactivating Proteins (RIPs) act by irreversibly depurinating the 28S rRNA ricin-sarcin loop (SRL) of the eukaryotic ribosome resulting in protein synthesis inhibition. In general, they consist of two variants: Type I which is single chained (∼30 kDa), and Type II, a more toxic variant which is a Type I N-glycosidase chain covalently linked to a lectin chain. These proteins are believed to play a pivotal role in defence mechanisms. Intriguingly, non-toxic variants of such toxic proteins do exist in nature. To explore their mode of action, in the present study we have selected three toxic (Ricin, Ebulin and HmRIP) as well as two non-toxic (BGSL and SGSL) RIPs and performed molecular docking and molecular dynamic simulations with the SRL loop. This study throws light on the structural stability and plasticity of the toxic and non-toxic RIP complexes. Furthermore, analysis of the active site cavity volume and binding free energy calculations reveal that the SRL, particularly the specific adenine (A4605), is relatively unstable in the case of non-toxic RIPs which is also supported by the free binding energy calculations, and the pocket size analysis indicates the abnormal increase in active site cavity volume of non-toxic RIPs with time. This first-of-its-kind comprehensive study of toxic and non-toxic RIPs gives insights about the mode of action and the dynamic nature of their interaction with the SRL loop. These observations will be helpful in the development of toxoids against RIPs and also in designing novel therapeutic approaches against human diseases.

Exploring molecular interactions in active amyl alcohol-haloalkane systems through thermodynamic properties and Jouyban–Acree correlation

ABSTRACT A comprehensive study on the thermodynamic and transport properties of binary mixtures composed of active amyl alcohol (AAA) and haloalkane’s was conducted within a temperature range of 303.15 K to 313.15 K. Experimental data on densities (ρ), viscosities (η), and speeds of sound (u) were employed to calculate excess molar volume (V E ), isentropic compressibility (K s E ), viscosity deviation (Δη), and excess Gibbs free energy for viscous flow (∆G* E ). The impact of dipole moment on these excess properties was investigated to gain insights into the prevailing intermolecular interactions within the mixtures. The Prigogine – Flory – Patterson (PFP) theory is applied to identify the predominant molecular interaction. The accuracy of the Jouyban–Acree model in correlating densities (ρ), viscosities (η), and speeds of sound (u) with composition were evaluated, demonstrating satisfactory agreement with experimental data.

THERMODYNAMIC PROPERTIES OF TERNARY LIQUID MIXTURE OF TOCOPHEROL ACETATE WITH CHLOROFORM AND DIETHYL ETHER AT 293 K

The reported study, measured the ultrasonic velocity (u), density (ρ) and viscosity (η) of ternary liquid mixtures of α-Tocopherol acetate with chloroform and diethyl ether in the concentration range (0 to 0.1 M) at 293K. These experimental parameters can be used to calculate various thermodynamic parameters like free volume (Vf), internal pressure (πin), Vander-Wall Constant (b) and Gibbs free energy (∆G*) etc. to identify the strength of molecular interaction. The results so obtained support the formation of complex structure and molecular aggregation through intermolecular hydrogen bonding in the ternary liquid system of α -Tocopherol acetate with chloroform and diethyl ether.

Study of the intermolecular interaction in hydrophobic deep eutectic solvent of (2-n-octyl-4-isothiazolin-3-one + 1-decanol) from the density, viscosity, thermodynamic, spectroscopic and quantum chemical calculations

Hydrophobic deep eutectic solvents (HDESs) are considered as green solvents and have been developed rapidly in recent years, which are widely used in diverse applications. In this study, we introduce a binary system composed of 2-n-octyl-4-isothiazolin-3-one (OIT) as a novel hydrogen bond acceptor (HBA) and 1-decanol as a hydrogen bond donor (HBD) under atmospheric pressure. The fundamental physicochemical properties, including density and dynamic viscosity, of the binary systems with various mole ratios were measured at temperatures of 293.15 K, 303.15 K, 313.15 K, 323.15 K, and 333.15 K. The excess molar volume (VmE), viscosity deviation (Δη) and excess Gibbs free energy (ΔG∗E) for activation of viscous flow were calculated and fitted according to the Redlich-Kister type polynomial equation. Furthermore, the spectral analysis (FTIR, UV–vis and 1H NMR) confirmed the presence of intermolecular hydrogen bonding in the binary systems. In addition, quantum chemical calculations revealed that there may be multiple modes of hydrogen bond formation between OIT molecule and 1-decanol molecule. However, selecting the most energetically favorable point, the most prominent hydrogen bond was found to be between the amide O atom of OIT and the hydroxyl H atom of 1-decanol.

Effects of the new type of extended uncertainty principle on Van der Waals black hole thermodynamics: A theoretical and deep learning approach

In this paper, we study the Van der Waals black holes (the case [Formula: see text]) in the anti-de Sitter space under the effect of the linear extended uncertainty principle (EUP). The analysis was undertaken using deep learning by employing physics-informed neural networks in addition to the semi-classical approach, we have calculated the thermal quantities, including mass, volume, temperature, entropy, and Gibbs free energy. Additionally, we visually depict the effects of the EUP-term on the thermodynamic properties of the studied black holes.

Density, viscosity, excess properties, and intermolecular interaction of propylene glycol methyl ether + 1,2-propylenediamine binary system

In this work, the systematic measurements of physicochemical properties, viz., density (ρ) and viscosity (η) values of propylene glycol methyl ether (PGME) + 1,2-propylenediamine (1,2-PDA) binary system, including pure substances, over the entire mole fraction range at the temperatures of T/K = (298.15 to 318.15) under atmospheric pressure of P = 100.5 kPa. The fundamental data were used to calculate several excess properties, including excess molar volume (VmE), viscosity deviation (Δη), and excess activation Gibbs free energy (ΔG∗E). Meanwhile, the work further investigated the values of thermal expansion coefficient (αp), partial molar volume (V¯) and apparent molar volume (Vφ), thereby offering a comprehensive understanding on non-ideal behavior of the binary system. Furthermore, the variations in ρ values with various molar ratios and temperatures were evaluated through Jouyban-Acree model and nonlinear least squares method. Simultaneously, Grunberg-Nissan model, Eyring-Margules model, Heric model, and McAllister model, were used to fit the dependence of η values on the molar ratio. Arrhenius equation was employed to fit the temperature dependency of η values. In addition, Redlich-Kister (R-K) equation was utilized to fit the VmE, Δη, and ΔG∗E values of binary system. Based on spectral analyses of Raman, ultra-violet (UV), and 1H Nuclear Magnetic Resonance (NMR) and density functional theory (DFT) calculation, the intermolecular hydrogen bond (IHB) of PGME with 1,2-PDA was discussed in depth.

Viscosity Studies of Binary Liquid Mixture of Methyl Acrylate and Benzene and Substituted Halo Benzenes at 313.15k

Studied the binary liquid mixtures of Methyl Acrylate with Benzene (B), and Substituted Halo Benzene molecules like Chloro Benzene (CB) and Bromo Benzene (BB) at 313.15K. Initially, the density and viscosities of the mixtures are measured and this data is utilized to calculate excess properties like excess molar volume (VE), excess viscosity (ηE), and excess Gibbs free energy (ΔG*E). These excess parameter values are fitted in the Redlich–Kister Polynomial equation and the intermolecular interaction is discussed.

Excess properties, intermolecular interactions, and CO2 absorption property of ethylene glycol + diethylenetriamine binary solutions

In this work, the density (ρ) and viscosity (η) data of ethylene glycol (EG) + diethylenetriamine (DETA) binary solutions at T = 298.15 K–318.15 K and P = 100.5 kPa are reported. The basic physicochemical data of binary solutions were used to investigate their excess molar volume (VmE), viscosity deviation (Δη), and excess viscous flow activation Gibbs free energy (ΔG*E), which revealed that there was strong intermolecular interaction in the EG (1) + DETA (2) binary solutions. The density values, viscosity values, and excess properties of binary solutions were fitted by parametric models, such as Jouyban-Acree model, McAllister four-body model, and Redlich-Kister (R-K) equation. After that, the binary solutions were spectroscopically analyzed to further discuss their intermolecular interaction. Meanwhile, Raman, UV, and 1H NMR spectra jointly demonstrated the intermolecular hydrogen bonding of the binary solutions as the form of –OH···N(H2)–. Finally, CO2 absorption was carried out to investigate the CO2 absorption property of the binary solutions, which provided reference data for CO2 capture.

Methods to modify supersaturation rate in membrane distillation crystallisation: Control of nucleation and crystal growth kinetics (including scaling)

While water vapour flux is often regarded as the critical parameter in membrane distillation crystallisation (MDC), there are multiple factors that will determine the kinetics of nucleation and crystal growth. A Nývlt-like equation is therefore introduced that can relate how multiple conditional parameters (membrane area, flux, temperature difference, crystalliser volume, magma density) independently modify nucleation rate and supersaturation, enabling a normalising approach for the characterisation of nucleation and crystal growth kinetics within MDC. Each parameter can be modified to increase supersaturation rate, which reduced induction time and broadened the metastable zone width (MSZW) at induction. An increase in supersaturation mitigated scaling and favoured bulk nucleation. This is due to the increase in volume free energy provided by the elevated supersaturation that reduces the critical energy requirement for nucleation to favour a homogeneous primary nucleation mechanism. An increase in temperature difference or magma density narrowed the MSZW. For each parameter, either supersaturation rate, supersaturation or induction time were fixed, while the other two factors were amended. While higher supersaturation rates generally favoured larger crystal sizes with broader size distributions, a high level of supersaturation at a low supersaturation rate increased particle size and narrowed the size distribution. In practice, these factors may be applied collectively and synergistically to deliver strict control over crystal growth, which remains a challenge for current evaporative technology. This was illustrated when facilitating an increase in supersaturation rate with membrane area, where an identical nucleation order was identified between membrane systems, from which it can be implied that MDC affords an inherently scalable solution for crystallisation.

Effect of water or ethanol on the excess properties of deep eutectic solvents (tetrabutylammonium bromide + formic acid/propionic acid)

The density and viscosity of binary mixtures of [tetrabutylammonium bromide + formic acid/propionic acid] with water or ethanol were determined in the entire molar fraction range of 288.15–318.15 K. The influences of temperature, deep eutectic solvents (DESs) composition and molar fraction, as well as different solvents on the excess molar volume, apparent molar volume, partial molar volume, viscosity deviation and excess viscous flow activation Gibbs free energy of the binary mixed system were investigated in detail. The interaction of DESs with solvent molecules in binary system mixtures is discussed. It demonstrated the existence of hydrogen bonding between DESs and solvent molecules, and that the interaction between DESs and ethanol was stronger than DESs-water. By introducing the concepts of relative volume and relative viscosity, the viscosity values of the binary mixed system were predicted by combining the Redlich-Kister equation. This study is expected to provide a theoretical reference for the future application of DESs.

Excess properties, computational chemistry and spectroscopic analyses of 1,2-propanediamine + n-propanol/isopropanol binary mixtures

To understand excess properties and intermolecular interactions of 1,2-propanediamine and n-propanol/isopropanol binary mixtures, their density and viscosity were systemically measured at T = (298.15–318.15) K under atmospheric pressure (1005 hectopascals in Tianjin, China), and their excess molar volume (VmE), viscosity deviation (Δη) and excess viscous activation free energy (ΔG*E) were also calculated. From the results of VmE, it can be inferred that two n-propanol/isopropanol molecules and one 1,2-propanediamine molecule have the strongest binding capacity and form the most stable intermolecular hydrogen bonds. The experimental density and kinematic viscosity were correlated and predicted by several semi-empirical models, among which the Jouyban-Acree model had a better fit for the density and the McAllister four-body equation had a better fit for the kinematic viscosity, and the calculated results of VmE, Δη and ΔG*E were analyzed using the R-K equation. Meanwhile, the apparent molar volume, partial molar volume, thermal expansion coefficient and viscous activation parameters of 1,2-propanediamine and n-propanol/isopropanol solutions were calculated and analyzed. After that, the existence of intermolecular hydrogen bonds (IHBs) between 1,2-propanediamine and n-propanol/isopropanol binary mixtures was demonstrated on the basis of computational chemistry. And then, the IHBs between 1,2-propanediamine and n-propanol/isopropanol binary mixtures with the form of –OH···NH2– were further confirmed based on Raman, ultraviolet (UV), fluorescence (FLS) and nuclear magnetic resonance (1H NMR) spectral technologies.

Density functional study of thermodynamic properties, thermal expansion and lattice thermal conductivity of Fe2VAl in the high-temperature region

Here, we present the phonon calculations for thermodynamic properties, thermal expansion and lattice thermal conductivity of Fe2VAl in the temperature range of and compare them with existing experiment. Phonon dispersion is computed using the finite displacement method and supercell approach. The positive frequencies of all the phonon modes indicate the mechanical stability of the compound. The specific heat at constant volume and Helmholtz free energy are calculated under harmonic approximation, while calculation of thermal expansion is done under quasi-harmonic approximation. Lattice thermal conductivity is calculated using first-principle anharmonic lattice dynamics calculations. The zero-point energy and Debye temperature are computed as and 638 K, respectively. The calculated thermal expansions are found to be and at 300 and 800 K, respectively. A significant deviation between calculated () and experimental () values of are observed at 300 K. But, as the temperature increases, the calculated and experimental come closer with the corresponding values of and at 800 K. The possible reasons for the deviation of are addressed. The temperature dependence of phonon lifetime is computed in order to understand the feature of . The present study suggests that DFT-based phononic calculations provide reasonably good explanations of available experimental phonon-related properties of Fe2VAl in the high-temperature range of .

The general class of accelerating, rotating and charged Plebanski-Demianski black holes as heat engine

We first review the general class of accelerating, rotating and charged Plebanski-Demianski (PD) black holes in the presence of cosmological constant, which includes the Kerr-Newman rotating black hole and the Taub-NUT spacetime. We assume that the thermodynamical pressure may be described by the negative cosmological constant, and so the black hole represents anti-de Sitter (AdS) PD black hole. The thermodynamic quantities like surface area, entropy, volume, temperature, Gibb's and Helmholtz's free energies of the AdS PD black hole are obtained due to the thermodynamic system. Next, we find the critical point and corresponding critical pressure, critical temperature and critical volume for the AdS PD black hole. Due to the study of specific heat capacity, we obtain the specific heat capacity (with constant volume) CV=0 and the specific heat capacity (with constant pressure) CP≥0. From this result, we conclude that the AdS PD black hole may be stable. We examine the Joule-Thomson expansion of the PD black hole, and by evaluating the sign of the Joule-Thomson coefficient μ, we determine the heating and cooling nature of the PD black hole. Putting μ=0, we find the inversion temperature. Next, we study the heat engine for the AdS PD black hole. In the Carnot cycle, we obtain the work done and its maximum efficiency. Also, we describe the work done and its efficiency for a new engine. Finally, we analyze the efficiency of the Rankine cycle in the PD black hole heat engine.

Understanding the physical and thermodynamic properties of monoethanolamine‐ionic liquids for solvent screening in CO2 capture process

AbstractThe physical properties such as density, surface tension, and viscosity of monoethanolamine (MEA)‐ionic liquids (ILs) solvent mixtures were studied experimentally in this work. The ILs namely, tetrabutylammonium acetate TBAAc, tetrabutylammonium bromide TBABr, and tetrabutylammonium hydroxide TBAOH were used. All the above parameters were measured at atmospheric pressure and various temperatures from 283 to 313 K with a 10 K interval. From the measured experimental data, thermodynamic properties such as thermal expansion, excess molar volume, viscosity deviation, and excess Gibbs free energy were also calculated. The physical and thermodynamic properties are more important to understand the solvent behavior during solvent screening in solvent‐based CO2 capture process. The 30 wt% solvent mixture composition was prepared as 28, 25, and 20 wt% MEA mixed with 2, 5, and 10 wt% ILs. Furthermore, a single empirical model was developed from the measured experimental data and the results are correlated. A good agreement was obtained between correlated and experimental data.

A Cluster Expansion Free Method for Computing Higher Derivatives of the Free Energy and Estimating the Error between the Finite and Infinite Volume Free Energy

The theory of phase transitions is one of the branches of statistical physics in which smoothness and continuity play an important role. In fact, phase transitions are characterized mathematically by the degree of non-analyticity of the thermodynamic potentials associated with the given system. In this paper, we propose a method that is not based on cluster expansions for computing the higher derivatives of the free energy and estimating the error between the finite and infinite volume free energy in certain continuum gas models. Our approach is suitable for a direct proof of the analyticity of the pressure or free energy in certain models of Kac-type. The methods known up to now strongly rely on the validity of the cluster expansion. An extension of the method to classical lattice gas models is also discussed.

Studies on excess molar volumes and viscosity deviations of binary mixtures of household kerosene and premium motor spirit at 303K

Density and viscosity of binary liquid mixtures of household kerosene (HHK) and premium motor spirit (PMS) were determined over the entire range of mole fraction at 303K. Excess molar volume (VE), molar volume (Vm), Excess Viscosity (ηE), Viscosity deviations (Δη) and excess Gibbs free energies of activation of viscous flow (ΔGE) were calculated. The results obtained shows that excess free energy of activation were all positive over the entire mole fraction. The viscosity deviation shows both negative and positive values. The positive VE obtained in this study shows increase in volume in the binary mixture. This work will help in effective monitoring, detection of adulterated kerosene and subsequent enforcement of severe penalty on such adulteration.

VOLUMETRIC AND VISCOMETRIC DETERMINATION OF BINARY LIQUID MIXTURES OF 2-ETHOXYETHANOL AND AMYL ACETATE AT TEMPERATURES OF (298.15 AND 303.15) K

Densities and viscosities have been determined at temperatures of (298.15 and 303.15) K for binary liquid mixtures of 2-ethoxyethanol with amyl acetate over the entire range of solvent composition. From the experimentally determined values, excess molar volume, VE, excess viscosity, ηE and excess Gibbs free energy of activation of viscous flow, G*E have been calculated. These calculated excess thermodynamic functions were fitted to Redlich-Kister polynomial equation to obtain the fitting coefficients and standard deviations. The values of excess molar volume, VE were negative and that of the excess viscosities, ηE were found to be positive, while excess Gibbs free energy of activation of viscous flow, ΔG*E were negative over the whole range of solvent composition for the binary systems at the studied temperatures. The behavior of these excess functions with composition of the mixtures have been discussed in respect of molecular interactions between the components of liquid systems. The mixture viscosities were correlated using empirical relations like Grunberg-Nissan, Frenkel, Hind, Wijk and Kendall-Monroe model equations. Comparison of these interaction parameters have been engaged to explain the intermolecular interactions between the alkoxy alcohol and the ester.

Nucleation kinetics, Williamson-Hall analysis, hardness and dielectric properties of pyridine-2-carboxylictrichloroacetate single crystals

The single crystals of pyridine-2-carboxylictrichloroacetate (P2CT) were synthesized using standard method at room temperature. Nucleation parameters such as, radius of critical nucleus, nucleation rate, and interfacial and volume free energy has been estimated. The solubility of the crystal at different temperatures is analyzed. Thermodynamic parameters from vibration analysis are compared with the enthalpy obtained from solubility to predict the stability of the crystal. X-ray diffraction investigating the structural aspects establishes the crystal structure belonging to crystal system as monoclinic nature. Williamson–Hall approach assesses the structural characteristics of the grown crystal: average crystallite size along with lattice strain. In between 220 and 1000 nm wavelength range, the optical absorption spectra of P2CT are recorded. Based on derivation of absorption spectrum fitting method, optical energy band gap and nature of optical transitions in the crystal is determined. Vickers microhardness test estimates the hardness parameters and elastic stiffness is evaluated through Wooster's empirical relation.

Ab initio study of the phonon and thermodynamic properties of the scheelite MWO4 (M = Ba, Sr or Ca) compounds

In this work, we performed the calculations based on density functional theory with different exchange and correlation energy approximations and employed the method of the constant force within the harmonic approximation, to study the phonon and thermodynamic properties of the three MWO4 (M = Ca, Sr or Ba) compounds with scheelite-type structure. In the first part of the work, we carried out an analysis of the performance of the local density approximation (LDA) and generalized gradient approximation of the Perdew-Burke-Ernzerhof revised for solids (GGA-PBEsol) on the computed phonon density of states, specific heat at constant volume, entropy and Gibbs free energy of the scheelite BaWO4 compound. Comparisons between calculated and experimental data showed that the GGA-PBEsol approach exhibited better performance. In the second part of the work, we extended the study of the thermodynamic properties to the SrWO4 and CaWO4 compounds, which are not presented in the literature, using the GGA-PBEsol approximation. It was found that the magnitude of the specific heat at the constant volume at high temperature respects the following order: BaWO4 > CaWO4 > SrWO4. Moreover, it was verified a relation between M2+ ionic radius in the scheelite MWO4 (M = Ba, Sr or Ca) and their entropy, Gibbs energy, and Helmholtz free energy.

Newly synthesized MAX phase Zr2SeC: DFT insights into physical properties towards possible applications.

A DFT study of the synthesized MAX phase Zr2SeC has been carried out for the first time to explore its physical properties for possible applications in many sectors. The studied properties are compared with prior known MAX phase Zr2SC. The structural parameters (lattice constants, volume, and atomic positions) are observed to be consistent with earlier results. The band structure and density of states (DOS) are used to explore the metallic conductivity, anisotropic electrical conductivity, and the dominant role of Zr-d states to the electrical conductivity at the Fermi level. Analysis of the peaks in the DOS and charge density mapping (CDM) of Zr2SeC and Zr2SC revealed the possible variation of the mechanical properties and hardness among them. The mechanical stability has been checked using elastic constants. The values of the elastic constants, elastic moduli and hardness parameters of Zr2SeC are found to be lowered than those of Zr2SC. The anisotropic behavior of the mechanical properties has been studied and analyzed. Technologically important thermodynamic properties such as the thermal expansion coefficient (TEC), Debye temperature (ΘD), entropy (S), heat capacity at constant volume (Cv), Grüneisen parameter (γ) along with volume (V) and Gibbs free energy (G) are investigated as a function of both temperature (from 0 to 1600 K) and pressure (from 0 to 50 GPa). Besides, the ΘD, minimum thermal conductivity (Kmin), melting point (Tm), and γ have also been calculated at room temperature and found to be lowered for Zr2SeC compared to Zr2SC owing to their close relationship with the mechanical parameters. The value of the ΘD, Kmin, Tm, and TEC suggest Zr2SeC as a thermal barrier coating material. The optical properties such as dielectric constant (real and imaginary part), refractive index, extinction coefficient, absorption coefficient, photoconductivity, reflectivity, and loss function of Zr2SeC are computed and analyzed to reveal its possible applications.