Complete Thermodynamic Description Research Articles

Towards Complete Kinetic and Thermodynamic Description of the Degradation of Persistent Organic Pollutants in Soil Ecosystems on the Basis of the Multi-phase Pseudo-zero Order Rate Law: A case Study of DDE in Philippine Soil

Towards Complete Kinetic and Thermodynamic Description of the Degradation of Persistent Organic Pollutants in Soil Ecosystems on the Basis of the Multi-phase Pseudo-zero Order Rate Law: A case Study of DDE in Philippine Soil

Denaturant- or ligand-induced changes in protein volume by pressure shift assay.

A complete thermodynamic description of protein-ligand binding includes parameters related to pressure and temperature. The changes in the protein volume and compressibility upon binding a ligand are pressure-related parameters that are often neglected due to the lack of routine methods for their determination. Fluorescent pressure shift assay (FPSA) is based on pressure-induced protein unfolding and its stabilization by a ligand and offers a universal approach to determine protein-ligand binding volumes. Extremely high pressures are required to unfold most proteins and protein-ligand complexes. Thus, guanidinium hydrochloride (GdmHCl) is used as a protein-destabilizing agent. We determined that GdmHCl unfolds carbonic anhydrase isoforms in a different pathway, but the destabilization effect is linear in a particular concentration range. We developed a concept for the FPSA experiment, where both - the ligand and GdmHCl - concentrations are varied. This approach enabled us to determine protein-ligand binding volumes that otherwise would be impossible due to the equipment-unreachable pressures of protein unfolding.

Native Mass Spectrometry and Nucleic Acid G-Quadruplex Biophysics: Advancing Hand in Hand.

While studying nucleic acids to reveal the weak interactions responsible for their three-dimensional structure and for their interactions with drugs, we also contributed to the field of biomolecular mass spectrometry, both in terms of fundamental understanding and with new methodological developments. A first goal was to develop mass spectrometry approaches to detect noncovalent interactions between antitumor drugs and their DNA target. Twenty years ago, our attention turned toward specific DNA structures such as the G-quadruplex (a structure formed by guanine-rich strands). Mass spectrometry allows one to discern which molecules interact with one another by measuring the masses of the complexes, and quantify the affinities by measuring their abundance. The most important findings came from unexpected masses. For example, we showed the formation of higher- or lower-order structures by G-quadruplexes used in traditional biophysical assays. We also derived complete thermodynamic and kinetic description of G-quadruplex folding pathways by measuring cation binding, one at a time. Getting quantitative information requires accounting for nonspecific adduct formation and for the response factors of the different molecular forms. With these caveats in mind, the approach is now mature enough for routine biophysical characterization of nucleic acids. A second goal is to obtain more detailed structural information on each of the complexes separated by the mass spectrometer. One such approach is ion mobility spectrometry, and even today the challenge lies in the structural interpretation of the measurements. We showed that, although structures such as G-quadruplexes are well-preserved in the MS conditions, double helices actually get more compact in the gas phase. These major rearrangements forced us to challenge comfortable assumptions. Further work is still needed to generalize how to deduce structures in solution from ion mobility spectrometry data and, in particular, how to account for the electrospray charging mechanisms and for ion internal energy effects. These studies also called for complementary approaches to ion mobility spectrometry. Recently, we applied isotope exchange labeling mass spectrometry to characterize nucleic acid structures for the first time, and we reported the first ever circular dichroism ion spectroscopy measurement on mass-selected trapped ions. Circular dichroism plays a key role in assigning the stacking topology, and our new method now opens the door to characterizing a wide variety of chiral molecules by mass spectrometry. In summary, advanced mass spectrometry approaches to characterize gas-phase structures work well for G-quadruplexes because they are stiffened by inner cations. The next objective will be to generalize these methodologies to a wider range of nucleic acid structures.

Charting the Complete Thermodynamic Landscape of Gas Adsorption for a Responsive Metal-Organic Framework.

New nanoporous materials have the ability to revolutionize adsorption and separation processes. In particular, materials with adaptive cavities have high selectivity and may display previously undiscovered phenomena, such as negative gas adsorption (NGA), in which gas is released from the framework upon an increase in pressure. Although the thermodynamic driving force behind this and many other counterintuitive adsorption phenomena have been thoroughly investigated in recent years, several experimental observations remain difficult to explain. This necessitates a comprehensive analysis of gas adsorption akin to the conformational free energy landscapes used to understand the function of proteins. We have constructed the complete thermodynamic landscape of methane adsorption on DUT-49. Traversing this complex landscape reproduces the experimentally observed structural transitions, temperature dependence, and the hysteresis between adsorption and desorption. The complete thermodynamic description presented here provides unparalleled insight into adsorption and provides a framework to understand other adsorbents that challenge our preconceptions.

Prediction of activities of all components in Sn-Ag-Cu and Sn-Ag-Cu-Zn lead-free solders using modified molecular interaction volume model

In this study, the activities of binary alloys (Sn-Ag, Sn-Cu, Sn-Zn, Ag-Cu, Ag-Zn, Cu-Zn) and ternary alloys (Sn-Ag-Cu, Sn-Ag-Zn, Sn-Cu-Zn) were predicted using molecular interaction volume model (MIVM), modified MIVM (M-MIVM), Wilson equation, and nonrandom two-liquid model. The prediction deviations of the M-MIVM were the smallest among the four thermodynamic models, indicating that the M-MIVM is reliable for predicting the activity of these multicomponent lead-free solders. On this premise, the activities of all components in ternary Sn-Ag-Cu solders at 1300 K were predicted using the M-MIVM. We found that the activities of Sn, Ag and Cu exhibit negative deviations from Raoult’s law and that these deviations eventually transform into positive deviations. The activities of all components in quaternary Sn-Ag-Cu-Zn solders at 1000 K were also predicted using the M-MIVM when Zn contents were 0.1 and 0.2. This study provides a complete thermodynamic description of Sn-Ag-Cu ternary and Sn-Ag-Cu-Zn quaternary alloys.

Decoupling gravitational sources by MGD approach in Rastall gravity

In the present work, we investigate the possibility of obtaining stellar interiors for static self-gravitating systems describing an anisotropic matter distribution in the framework of Rastall gravity through gravitational decoupling by means of minimal geometric deformation approach. Due to Rastall gravity breaks down the minimal coupling matter principle, we have provided an exhaustive explanation about how Israel-Darmois junction conditions work in this scenario. Furthermore, to obtain the deformed space-time, the mimic constraint procedure has been used. In order to check the viability of this proposal, we have applied it to the well known Tolman IV solution. A complete thermodynamic description of the effects introduced by the additional source is given. Additionally, the results have been compared with their similes in the picture of pure general relativity, pure Rastall gravity and within the framework of general relativity including gravitational decoupling. To perform the mathematical and graphical analysis we have taken the gravitational decoupling constant $\alpha$ and the Rastall's parameter $\lambda$ as free parameters and the compactness factor describing the general relativity sector to be $0.2$. Besides, to provide a more realistic picture we have bounded both parameters $\alpha$ and $\lambda$ by using real observational data to explore the limits of the theory under this particular model. Applications to study neutron or quark stars are suggested by using this methodology.

Thermodynamic modelling of the Ca–O system including 3rd generation description of CaO and CaO2

A complete thermodynamic description of the Ca–O system is proposed including 3rd generation modelling of crystalline CaO, liquid and amorphous CaO, and crystalline CaO2. Compared to previous modellings, a more robust description of the thermodynamic properties of the binary phases is achieved using data recently obtained by density functional theory calculations and molecular dynamics simulations. The heat capacity of crystalline CaO is reassessed, leading to a noticeably higher value below the melting point compared to previous modellings and resulting in a slightly higher standard entropy. It is highlighted that the parameters given in terms of polynomial functions of temperature that were employed so far in 3rd generation models to describe anharmonic contributions in the heat capacity of compounds were not suited to satisfactorily describe the thermodynamic properties of crystalline CaO. It is suggested that this observation can be generalized to most refractory oxides. Alternative terms are proposed in the Gibbs energy function that give more flexibility in fitting the experimental data and lead to more numerically reasonable values for the parameters. The liquid and amorphous CaO phase is described using the two-state model, leading to a significant improvement in the description of its heat capacity. The description of crystalline CaO2 is also improved as only estimates of the thermodynamic properties of the compound were available in previous modellings of the system. Finally, phase equilibria data on the Ca–CaO liquidus is reviewed, and it is highlighted that slight discrepancies in the relatively low temperature measurements can lead to significantly different descriptions of the liquid phase.

Use of isothermal titration calorimetry to study various systems

Isothermal titration calorimetry (ITC) is a technique that allows precise measurements and a complete thermodynamic description of association, interaction or binding processes. This review will address uses of ITC in studies of self-assemble of monocomponent systems and interacting systems in broad spectrum. It also focuses on use of ITC on conformational study, thermodynamic study, reaction kinetics, adsorption phenomena, etc. ITC studies on the association of different monocomponents such as surfactants and polymers to provide quantitative information on different thermodynamic functions associated with micellization / association (Gibbs energy, enthalpy and entropy). Studies on binding isotherm by ITC provide a comprehensive description of the interaction process. Emphasis will be given to analyze the rapid reaction kinetics with new models. This review stresses the importance of using direct calorimetric measurements to obtain and report accurate thermodynamic data, even in complex systems. These data, whenever possible, should be confirmed and verified with other techniques

Quantum ion thermodynamics in liquid interiors of white dwarfs

ABSTRACT We present an accurate analytic approximation for the energy of a quantum one-component Coulomb liquid of ions in a uniform electron background that has been recently calculated from first principles. The approximation enables us to develop in an analytic form a complete thermodynamic description of quantum ions in a practically important range of mass densities at temperatures above crystallization. We show that ionic quantum effects in liquid cores of white dwarfs (WDs) affect heat capacity, cooling, thermal compressibility, pulsation frequencies, and radii of sufficiently cold WDs, especially with relatively massive helium and carbon cores.

Status of free-energy representations for the homogeneous electron gas

Renewed interest in the homogeneous electron gas (HEG) has been stimulated by recent accurate simulations of it over a wide range of densities and temperatures. Those data, combined with known theoretical limits, have led to analytical representations of the free energy. Such a representation is, at least in principle, the complete HEG equation of state. The initial objective here is to establish that the two best representations [``corrKSDT,'' Phys. Rev. Lett. 112, 076403 (2014), Phys. Rev. Lett. 120, 076401 (2018), and ``GDB'' Phys. Rev. Lett. 119, 135001 (2017)] of the simulation data and constraints are effectively the same in both functional form and accuracy of representation. The second objective is to disclose and delineate a significant difficulty. Despite their expected accuracy for the free energy, the underlying functional form is not adequate for derived thermodynamic properties. As an example, the specific heats obtained from the representations exhibit anomalies suggesting the need first for additional simulation data in critical regimes, then for refined fitting functions. The existing representations are, however, almost certainly adequate for applications based on the free energy alone (e.g., density-functional theory for warm dense matter). The third objective is to show that, despite their inability to provide a complete thermodynamic description of the HEG, the best analytical representations do provide a fully adequate exchange-correlation local density approximation for free-energy density-functional calculations.

A generalized Finch\u2013Skea class one static solution

In the present article, we discuss relativistic anisotropic solutions of Einstein field equations for the spherically symmetric line element under the class I condition. To do so we apply the embedding class one technique using Eisland condition. Within this approach, one arrives at a particular differential equation that links the two metric components e^{nu } and e^{lambda }. In order to obtain the full space–time description inside the stellar configuration we ansatz the generalized form of metric component g_{rr} corresponding to the Finch–Skea solution. Once the space–time geometry is specified we obtain the complete thermodynamic description i.e. the matter density rho , the radial, and tangential pressures p_r and p_t, respectively. Graphical analysis shows that the obtained model respects the physical and mathematical requirements that all ultra-high dense collapsed structures must obey. The M–R diagram suggests that the solution yields stiffer EoS as parameter n increases. The M–I graph is in agreement with the concepts of Bejgar et al. (Mon Not R Astron Soc 364:635, 2005) that the mass at I_{max} is lesser by few percent (for this solution sim 3%) from M_{max}. This suggests that the EoSs is without any strong high-density softening due to hyperonization or phase transition to an exotic state.

Thermodynamic modeling of the chromium-yttrium-oxygen system

Based on the CALPHAD (CALculation of PHAse Diagrams) method, a complete thermodynamic description of the Cr-Y-O ternary system is obtained in the present work. The thermodynamic properties of YCrO3 phase are critically assessed and the experimentally determined Cr2O3-Y2O3 quasi-binary section is reproduced. The current optimization results agree well with most of the experimental data in literature. The thermodynamic description of Cr-Y-O is then used to calculate the phase relations under different temperatures or oxygen partial pressures. The stability of the YCrO3 phase is discussed based on the calculation results.

DFT and canonical ensemble investigations on the thermodynamic properties of Syngas and natural gas/Syngas mixtures

Abstract Density Functional Theory and canonical ensemble were used to investigate thermodynamic properties of Syngas and its mixture with natural gas. The following thermodynamic potentials were obtained: internal energy, enthalpy, entropy and Gibbs free energy for temperatures ranging from 0.5 K to 1500 K. It was observed that CO and H2 were the most stable Syngas components, possessing the ability to render Syngas less favorable to the temperature increase. Also, we verified that Syngas presents properties similar to an antiknock agent for natural gas, raising its resistance to temperature increases. Were determined the Poisson coefficients and Bulk modulus for Natural gas/Syngas mixtures and Shomate equation coefficients for some Syngas types, providing a more complete thermodynamic description for these gases. Additionally, thermodynamic potentials of combustion for Natural gas/Syngas mixtures were predicted, showing that this biofuel can reduce the calorific power of natural gas and makes its combustion less favorable due its antiknock behavior. However, a mixture with 30% of Syngas may be useful for natural gas combustion, since it present a calorific power between 73.41% and 79.49% of that of natural gas, which is a substantial fraction of energy released during combustion, showing good future prospects to the Natural gas/Syngas mixture to the renewable energy generation.

Complete thermodynamic description of the Mg-Ca-O phase diagram including the Ca-O, Mg-O and CaO-MgO subsystems

A complete thermodynamic description of the Mg-Ca-O system and phase diagrams is developed. It is based on our extensive thermodynamic analysis of solid CaO and MgO data and validation of the low-temperature Mg-Ca-O phase diagram up to 1050 K. This work presents the high- temperature oxygen solubilities and revisions of calculated melting points of the oxides. An extension of the empirical schemes for predicting the activity coefficient of oxygen in liquid elements is proposed to predict data for the Mg-O system. Consistent thermodynamic descriptions of the complete binary Ca-O and Mg-O systems are developed. It is shown that this framework is crucial to understand recently measured significantly different melting points of CaO under oxidizing versus reducing conditions. The revised description of the MgO-CaO quasibinary oxide system considers all experimental data, revealing significantly different melting equilibria compared to all previous publications.

Field-Directed Self-Assembly of Mutually Polarizable Nanoparticles.

Directed assembly of dielectric and paramagnetic nanoparticles can be used to synthesize diverse functional materials that polarize in response to an externally applied electric or magnetic field. However, theories capable of predicting the self-assembled states are lacking. In the proposed work, we develop a complete thermodynamic description of such assemblies for spherical nanoparticles. We show how an important physical feature of these types of particles, mutual polarization, sculpts the free energy landscape and has a remarkably strong influence on the nature of the self-assembled states. Modeling the mutual polarization among nanoparticles requires solving a many-bodied problem for the particle dipole moments. Typically, this computationally expensive task is avoided by neglecting mutual polarization and assuming that each particle in a concentrated dispersion acquires the same dipole moment as a single, isolated particle. Although valid in the limit of small dielectric or permeability contrasts between particles and solvent, this constant dipole assumption leads to qualitatively incorrect predictions for coexisting phases in equilibrium at large dielectric or permeability contrasts. Correctly accounting for mutual polarization enables a thermodynamic theory that describes the equilibrium phase diagram of polarizable dispersions in terms of experimentally controllable variables. Our theoretical predictions agree with the phase behavior we observe in dynamic simulations of these dispersions as well as that in experiments of field-directed structural transitions. In contrast to predictions of a constant dipole model, we find that dispersions of particles with different dielectric constants or magnetic permeabilities exhibit qualitatively different phase behavior. This new model also predicts the existence of a eutectic point at which two crystalline phases and a disordered phase of nanoparticles all simultaneously coexist.

Re-evaluation of the thermodynamic equilibria on the zirconia-rich side of the ZrO2-YO1.5 system

The thermodynamic database of ZrO2-YO1.5 system, which has been extensively studied by many groups, was re-assessed and improved particularly on the ZrO2-rich side of the system. Due to sluggish kinetics and diffusionless transformations in the ZrO2-rich side of ZrO2-YO1.5 system, providing accurate phase diagram and thermochemical data had become problematic. The newly developed thermodynamic database shows well agreement with the related experimental data, which were wisely evaluated and carefully selected to ensure the accuracy of the developed database. Applying the CALPHAD (CALculation of PHAse Diagrams) approach, the interaction parameters of the cubic, tetragonal, monoclinic, and liquid phases were optimized to develop a complete and self-consistent thermodynamic description of the ZrO2-YO1.5 system. The Gibbs energy model for the monoclinic phase was also modified to a regular solution. The improved thermodynamic database of the ZrO2-YO1.5 system can give more accurate modeling results, especially for the ZrO2-rich side of the system, which has critical applications.

Thermodynamic modeling of the La-Te system aided by first-principles calculations

A complete thermodynamic description of the La-Te binary system is developed by means of CALculation of PHAse Diagram (CALPHAD) method in combination with available experimental data in the literature and the present first-principles calculations based on density functional theory. The intermetallic phases with homogeneity ranges, La3-xTe4 and LaTe2-x, are modeled using a two-sublattice (La,Va)3(Te)4 model and a three-sublattice (La)1(Te)1(Te,Va)1 model based on their structure features, respectively. The intermetallic phases, LaTe and LaTe3, are treated as stoichiometric compounds. The thermodynamic properties of the intermetallic compounds and their corresponding end members at finite temperatures are predicted using first-principles quasi-harmonic approach. The associate solution model is used to describe the short-range ordering behavior of the liquid phase. The calculated phase diagram agrees well with the available phase equilibrium data in the literature.

The Thermodynamic Database Database

This paper describes an effort to organize the condensed phases thermodynamic data freely available in electronic form within the scientific literature through the design of a special-purpose search engine indexingdata electronically available in the “thermodynamic database” (TDB) format. This focus is motivated by the fact that it is widely used and can be readily read or imported into most thermodynamic modeling software. This form of data also provides a rather complete thermodynamic description of a given system and thus enables researchers to generate any phase diagram cross-section of interest, a capability typically not available in traditional phase diagram handbooks. For convenience, users can quickly preview selected cross sections directly online. In designing this system, special emphasis was devoted to ensuring that the bibliographic references of the original data sources are transparently reported and to providing links to the original data sources, rather than the data itself, in order to enforce access rights. This effort was made possible by combining and building upon a number of key components, such as the CALPHAD journal's supplementary information section, the NIMS database, the NISTmaterials data repository, the Crossref bibliographic service, and various thermodynamic (OpenCalphad, ATAT) and graphical (gnuplot, XTK) software.

Thermodynamic assessment of the niobium-fluorine system by coupling density functional theory and CALPHAD approach

The complete thermodynamic description of the niobium-fluorine system is presented for the first time in this work. It results from a critical evaluation of the available experimental data and new thermodynamic calculations. In total, three niobium fluoride solid phases (NbF3, NbF4 and NbF5) and seven gaseous species (NbF, NbF2, NbF3, NbF4, NbF5, Nb2F10 and Nb3F15) have been considered during the assessment. Novel data for all the gaseous species were calculated combining density functional theory (DFT), for the prediction of the molecular parameters, and statistical mechanical calculations, for the determination of the thermal functions (i.e. standard entropy and heat capacity). The developed thermodynamic model was found to correctly reproduce all the available experimental data and was used to calculate the Nb-F phase diagram, which is presented in this work as well.

First-principles calculations and thermodynamic modeling of the Yb-Ni binary system

A complete thermodynamic description of the Yb-Ni binary system is developed by means of the CALculation of PHAse Diagram (CALPHAD) method in combination with first-principles calculations based on density functional theory (DFT) and available experimental data in the literature. Finite temperature thermodynamic properties of the Yb-Ni intermetallic compounds are predicted using the quasi-harmonic approach, where first-principles phonon calculations are performed to calculate the lattice vibrational entropy. The associate solution model is used to describe the complex thermodynamic behavior of the liquid phase. The calculated phase diagram agrees well the experimental phase equilibrium data in the literature. By the coupling of CALPHAD modeling with first-principles calculations, the present work provides a more thermodynamically accurate model of the Yb-Ni system when compared to previous models.