Thermodynamic Characterization Research Articles

Thermodynamic Characterization of Volatile Alkylamine Boranes as Precursors for the Formation of BCxNy Films

Thermodynamic Characterization of Volatile Alkylamine Boranes as Precursors for the Formation of BCxNy Films

Carbon dioxide and acetone mixtures as refrigerants for industry heat pumps to supply temperature in the range 150–220 oC

Industry decarbonization is a key a challenge towards the transition to climate neutrality. Indeed, there is a need to satisfy heat at temperatures higher than 150 °C in relevant industrial sectors by upgrading lower temperature heat flows, such as heat from renewable heat sources, ambient heat or industrial waste heat. High temperature heat pumps (HTHP) can upgrade such heat flows enabling great savings in carbon emissions. New refrigerants are needed to develop HTHPs achieving high performances at high temperatures. This paper proposes the use of a new zeotropic mixture composed of carbon dioxide and acetone as the refrigerant of HTHPs working in the temperature range of 150–220 °C. The new fluid is compared with existing pure refrigerants currently used. The thermodynamic characterization of the CO2/acetone mixtures shows temperature glides below 50 K for CO2 mass fractions up to 10%. The best HTHP performance is shown for the mixture 5% CO2/95% acetone in mass fraction. For instance, such a mixture obtains a COP of 5.63 when the target outlet sink temperature is 200 °C and the temperature difference between the outlet heat sink and the inlet heat source is 70 K, showing an improvement of 46% compared to pure acetone.

Torr-level, seedless, non-resonant velocity distribution function measurement with a dual-color, single-shot coherent Rayleigh–Brillouin scattering scheme

A two order of magnitude spectral acquisition improvement in velocity distribution function measurement is demonstrated with a novel single-shot, dual-color coherent Rayleigh–Brillouin scattering (CRBS) scheme. By performing this non-resonant and seedless spectral diagnostic technique, capable of obtaining a spectrum in ns, we demonstrate accurate temperature (ranging from 300 K to 500 K) and pressure (ranging from 760 Torr down to 1 Torr) measurement capabilities, for a variety of atomic, molecular and multispecies gases. This demonstrated gas thermodynamic characterization capability of the dual-color CRBS scheme over broad ranges of pressure and temperature for a variety of gases is anticipated to be of great interest to a plethora of fields, ranging from aerospace applications to low-temperature plasmas, providing with an accurate measurement of physical properties of neutral particles, for a range of gases.

Unexpected thermodynamic signature for the interaction of hydroxymethylated DNA with MeCP2

Hydroxymethylated cytosine (5hmC) is a stable DNA epigenetic mark recognized by methyl-CpG binding protein 2 (MeCP2), which acts as a transcriptional regulator and a global chromatin-remodeling element. Because 5hmC triggers a gene regulation response markedly different from that produced by methylated cytosine (5mC), both modifications must affect DNA structure and/or DNA interaction with MeCP2 differently. MeCP2 is a six-domain intrinsically disordered protein (IDP) with two domains responsible for dsDNA binding: methyl-CpG binding domain (MBD) and intervening domain (ID). Here we report the detailed thermodynamic characterization of the interaction of hmCpG-DNA with MeCP2. We find that hmCpG-DNA interacts with MeCP2 in a distinctly different mode with a particular thermodynamic signature, compared to methylated or unmethylated DNA. In addition, we find evidence for Rett syndrome-associated mutations altering the interaction of MeCP2 with dsDNA in a cytosine modification-specific manner which may correlate with disease onset time and clinical severity score.

Thermodynamic characterization of LF, H, and mineral soil layers from oak forest ecosystems: Exploring the role of proximate analysis

Studying the thermodynamic properties of soil organic matter is a developing field that involves the measurement of the energy stored by the soil. Quantifying soil energy content is still challenging despite different methodological approaches are available to calculate that value. One of the options is the proximate analysis following the guidelines for the energetic characterization of biomass. However, proximate analyses are still unexplored for soils. In this paper, we investigate the potential of this analysis to contribute to study soil from a thermodynamic perspective. With that goal, 31 soil samples collected in mature oak forests following a depth transect were used for elemental, thermal and proximate analysis. Proximate analyses and energetic characterization were performed by simultaneous thermogravimetry and differential scanning calorimetry.These methods allowed fragmentation of the soil organic matter in water content, volatile matter, fixed carbon, and ash, as well as the quantification of the soil organic matter and energy content. Pearson's correlation showed significant relations among the proximate, the elemental components of soils and the energy. The equations relating all of these variables were calculated for soils from oak forests by partial least squares analysis. Equations representing the relationship between energy and the proximate fractions provide an additional alternative to calculate the heat of combustion of the soil organic matter. This value is the essential step for the thermodynamic characterization of soils.

Purification and thermodynamic characterization of acid protease with novel properties from Melilotus indicus leaves

A thermostable acid protease from M. indicus leaves was purified 10-fold using a 4-step protocol. We were able to isolate a purified protease fraction with a molecular weight of 50 kDa and exhibited maximal protease activity at pH 4.0 and 40 °C. Structural analysis revealed that the protease is monomeric and non-glycosylated. The addition of epoxy monocarboxylic acid, iodoacetic acid, and dimethyl sulfoxide significantly reduced protease activity while dramatically increasing the inhibition of Mn2+, Fe2+, and Cu2+. The activation energy of the hydrolysis reaction (33.33 kJ mol−1) and activation energy (Ed = 105 kJ mol−1), the standard enthalpy variation of reversible protease unfolding (2.58 kJ/mol) were calculated after activity measurements at various temperatures. Thermal inactivation of the pure enzyme followed first-order kinetics. The half-life (t1/2) of the pure enzyme at 50 °C, 60 °C, and 70 °C was 385, 231, and 154 min, respectively. Thermodynamic parameters (entropy and enthalpy) suggested that the protease was highly thermostable. This is the first report on the thermodynamic parameters of proteases produced by M. indicus. The novel protease appears to be particularly thermostable and may be important for industrial applications based on these thermodynamic properties.

The characteristics of methane adsorption capacity and behavior of tectonic coal

The research of methane adsorption on tectonic coal is an important content to gas disaster prevention and coalbed methane (CBM) exploration in outburst coal seams. Many projects of methane adsorption capacity and behavior of tectonic coal, such as adsorption difference between tectonic coal and its untectonic coal, adsorption evaluation of tectonic coal, factors for adsorption capacity of tectonic coal, gas-solid coupling feature in tectonic coal and supercritical adsorption phenomena of tectonic coal, were carried out by scientists. Combined with a long-term study on organic matter structure and methane adsorption of tectonic coal, the author summarized recent-years’ researches on adsorption capacity and behavior of tectonic coal-methane at home and abroad from the dispute of adsorption ability determination, the thermodynamic characterization of methane adsorption capacity, and the methane adsorption behavior of quantum chemical calculation of the adsorption and the gas content calculation based on loss compensation, respectively. It is believed that the coal structure controls the methane adsorption capacity and behavior characteristics of different tectonic coals, and from the perspective of thermodynamics, the adsorption capacity of different types of coals can be better distinguished. In the future, a more scientific and complete quantum chemical calculation of methane adsorption by tectonic coal and a compensation method based on instantaneous emission loss should be established, so as to better reveal the methane adsorption behavior of tectonic coal and the mechanism of coal and gas outburst. The research has a reference to fine research of coal adsorption and CBM exploration practices.

Bipyridil-based chelators for Gd(III) complexation: kinetic, structural and relaxation properties.

In the last 20 years, research in the field of MRI (magnetic resonance imaging) contrast agents (CAs) has been intensified due to the emergence of a disease called nephrogenic systemic fibrosis (NSF). NSF has been linked to the in vivo dissociation of certain Gd(III)-based compounds applied in MRI as CAs. To prevent the dechelation of the probes after intravenous injection, the improvement of their in vivo stability is highly desired. The inertness of the Gd(III) chelates can be increased through the rigidification of the ligand structure. One of the potential ligands is (2,2',2'',2'''-(([2,2'-bipyridine]-6,6'-diylbis(methylene))bis(azanetriyl))tetraacetic acid) (H4DIPTA), which has been successfully used as a fluorescent probe for lanthanides; however, it has never been considered as a potential chelator for Gd(III) ions. In this paper, we report the thermodynamic, kinetic and structural features of the complex formed between Gd(III) and DIPTA. Since the solubility of the [Gd(DIPTA)]- chelate is very low under acidic conditions, hampering its thermodynamic characterization, we can only assume that its stability is close to that determined for the structural analogue [Gd(FENTA)]- (H4FENTA: (1,10-phenanthroline-2,9-diyl)bis(methyliminodiacetic acid)), which is similar to that determined for the agent [Gd(DTPA)]2- routinely used in clinical practice. Unfortunately, the inertness of [Gd(DIPTA)]- is significantly lower (t1/2 = 1.34 h) than that observed for [Gd(EGTA)]- and [Gd(DTPA)]2- as a result of its spontaneous dissociation pathway during dechelation. The relaxivity values of [Gd(DIPTA)]- are comparable with those of [Gd(FENTA)]- and somewhat higher than the values characterizing [Gd(DTPA)]2-. Luminescence lifetime measurements indicate the presence of one water molecule (q = 1) in the inner sphere of the complex with a relatively high water exchange rate (k298ex = 43(5) × 106 s-1). DFT calculations suggest a rigid distorted tricapped trigonal prismatic polyhedron for the Gd(III) complex. On the basis of these results, we can conclude that the bipyridine backbone is not favourable with respect to the inertness of the chelate.

Membrane interactions of apoptotic inhibitor Bcl-xL: What can be learned using fluorescence spectroscopy

Permeabilization of the mitochondrial outer membrane–a point of no return in apoptotic regulation–is tightly controlled by proteins of the Bcl-2 family. Apoptotic inhibitor Bcl-xL is an important member of this family, responsible for blocking the permeabilization, and is also a promising target for anti-cancer drugs. Bcl-xL exists in the following conformations, each believed to play a role in the inhibition of apoptosis: (i) a soluble folded conformation, (ii) a membrane-anchored (by its C-terminal α8 helix) form, which retains the same fold as in solution and (iii) refolded membrane-inserted conformations, for which no structural data are available. In this review, we present the summary of the application of various methods of fluorescence spectroscopy for studying membrane interaction of Bcl-xL, and specifically the formation of the refolded inserted conformation. We discuss the application of environment-sensitive probes, Förster resonance energy transfer, fluorescence correlation spectroscopy, and fluorescent quenching for structural, thermodynamic, and functional characterization of protein-lipid interactions, which can benefit studies of other members of Bcl-2 (e.g., Bax, BAK, Bid). The conformational switching between various conformations of Bcl-xL depends on the presence of divalent cations, pH and lipid composition. This insertion-refolding transition also results in the release of the BH4 regulatory domain from the folded structure of Bcl-xL, which is relevant to the lipid-regulated conversion between canonical and non-canonical modes of apoptotic inhibition.

Thermodynamic Characterization of Nucleic Acid Nanoparticles Hybridization by UV Melting.

The advances in nucleic acid nanotechnology have given rise to various elegantly designed structural complexes fabricated from DNA, RNA, chemically modified RNA strands, and their mixtures. The structural properties of NA nanoparticles (NANP) generally dictate and significantly impact biological function; and thus, it is critical to extract information regarding relative stabilities of the different structural forms. The adequate stability assessment requires knowledge of thermodynamic parameters that can be empirically derived using conventional UV-melting technique. The focus of this chapter is to describe methodology to evaluate thermodynamic data of NANPs complexation based on DNA 12 base-pair (bp) duplex formation as an example.

Insights into crystal structure, elasticity, lattice dynamics, and thermodynamics of ternary magnesium alloy MgZn2Ce

We performed first-principles investigations on ternary magnesium alloy MgZn2Ce at high pressure to explore the pressure effect on the crystal structure, elastic property, lattice dynamics, and thermodynamic characterization. The calculated high-pressure single-crystal elastic constants manifested that MgZn2Ce is mechanically stable up to 20 GPa. We found not that the phonon dispersion curves throughout the entire Brillouin region and phonon density of states of MgZn2Ce show any instability or anomaly, hence the dynamical stability is strong under compression up to 20 GPa. Concurrently, the Raman and infrared-active phonon modes at Г point of the Brillouin zone are classified by factor group theory. Combining the quasi-harmonic approximation and Debye model, we further predict the thermal-physical properties of MgZn2Ce. It is hoped that physical properties predicted by this study will inspire researchers to synthesize new-type multiple magnesium alloys.

Thermodynamic characterization of the (H2 + C3H8) system significant for the hydrogen economy: Experimental (p, ρ, T) determination and equation-of-state modelling

For the gradual introduction of hydrogen in the energy market, the study of the properties of mixtures of hydrogen with typical components of natural gas (NG) and liquefied petroleum gas (LPG) is of great importance. This work aims to provide accurate experimental (p, ρ, T) data for three hydrogen-propane mixtures with nominal compositions (amount of substance, mol/mol) of (0.95H2 + 0.05C3H8), (0.90H2 + 0.10C3H8), and (0.83H2 + 0.17C3H8), at temperatures of 250, 275, 300, 325, 350, and 375 K, and pressures up to 20 MPa. A single-sinker densimeter was used to determine the density of the mixtures. Experimental density data were compared to the densities calculated from two reference equations of state: the GERG-2008 and the AGA8-DC92. Relative deviations from the GERG-2008 EoS are systematically larger than those from the AGA8-DC92. They are within the ±0.5% band for the mixture with 5% of propane, but deviations are higher than 0.5% for the mixtures with 10% and 17% of propane, especially at low temperatures and high pressures. Finally, the sets of new experimental data have been processed by the application of two different statistical equations of state: the virial equation of state, through the second and third virial coefficients, B(T, x) and C(T, x), and the PC-SAFT equation of state.

Thermodynamic characterization of a macrocyclic Zika virus NS2B/NS3 protease inhibitor and its acyclic analogs.

Cyclization of small molecules is a widely applied strategy in drug design for ligand optimization to improve affinity, as it eliminates the putative need for structural preorganization of the ligand before binding, or to improve pharmacokinetic properties. In this work, we provide a deeper insight into the binding thermodynamics of a macrocyclic Zika virus NS2B/NS3 protease inhibitor and its linear analogs. Characterization of the thermodynamic binding profiles by isothermal titration calorimetry experiments revealed an unfavorable entropy of the macrocycle compared to the open linear reference ligands. Molecular dynamic simulations and X-ray crystal structure analysis indicated only minor benefits from macrocyclization to fixate a favorable conformation, while linear ligands retained some flexibility even in the protein-bound complex structure, possibly explaining the initially surprising effect of a higher entropic penalty for the macrocyclic ligand.

Investigation of the Roasting Behavior of Mixtures of Molybdenum Trioxide and Molybdenum Concentrates

In this paper, a new process of roasting molybdenum concentrates with the addition of molybdenum trioxide (MoO3) was proposed. Using molybdenum disulfide (MoS2) to represent molybdenum concentrates and based on theoretical studies and experimental investigations, the roasting behavior and reaction routes were identified by thermodynamic calculations, thermogravimetric analysis, and characterization of the reaction process and reaction products. The effects of the MoO3/MoS2 ratio, reaction time, and temperature as well as the forming pressure of pellets on the solid–solid reaction of MoO3 and MoS2 were investigated, and the products were characterized using X-ray diffraction, scanning electron microscopy, and carbon–sulfur analysis. The optimum MoO3/MoS2 ratio was determined as 6.5, and the optimum reaction conditions were a temperature of 650 °C and a holding time of 60 min. The particle size of MoO2 increased gradually with the extension of the holding time, and finally, MoO2 particles with a particle size of 1.1 μm could be obtained. The sulfur content of the product MoO2 decreased significantly with the increase in the MoO3/MoS2 ratio or reaction temperature, and after this desulfuration process, the minimum sulfur content of the products was 98 ppm. Comparing powder samples with molded samples formed at 50 MPa revealed that a certain pressure promoted the reaction with an efficiency increase of about 14.6%.

A De Novo‐Designed Type 3 Copper Protein Tunes Catechol Substrate Recognition and Reactivity

AbstractDe novo metalloprotein design is a remarkable approach to shape protein scaffolds toward specific functions. Here, we report the design and characterization of Due Rame 1 (DR1), a de novo designed protein housing a di‐copper site and mimicking the Type 3 (T3) copper‐containing polyphenol oxidases (PPOs). To achieve this goal, we hierarchically designed the first and the second di‐metal coordination spheres to engineer the di‐copper site into a simple four‐helix bundle scaffold. Spectroscopic, thermodynamic, and functional characterization revealed that DR1 recapitulates the T3 copper site, supporting different copper redox states, and being active in the O2‐dependent oxidation of catechols to o‐quinones. Careful design of the residues lining the substrate access site endows DR1 with substrate recognition, as revealed by Hammet analysis and computational studies on substituted catechols. This study represents a premier example in the construction of a functional T3 copper site into a designed four‐helix bundle protein.

A De Novo-Designed Type 3 Copper Protein Tunes Catechol Substrate Recognition and Reactivity.

De novo metalloprotein design is a remarkable approach to shape protein scaffolds toward specific functions. Here, we report the design and characterization of Due Rame 1 (DR1), a de novo designed protein housing a di-copper site and mimicking the Type 3 (T3) copper-containing polyphenol oxidases (PPOs). To achieve this goal, we hierarchically designed the first and the second di-metal coordination spheres to engineer the di-copper site into a simple four-helix bundle scaffold. Spectroscopic, thermodynamic, and functional characterization revealed that DR1 recapitulates the T3 copper site, supporting different copper redox states, and being active in the O2 -dependent oxidation of catechols to o-quinones. Careful design of the residues lining the substrate access site endows DR1 with substrate recognition, as revealed by Hammet analysis and computational studies on substituted catechols. This study represents a premier example in the construction of a functional T3 copper site into a designed four-helix bundle protein.

Using thermodynamics to obtain geochemical information from genomes.

Thermodynamic characterization of the relative stabilities of chemical compounds is a pillar of conceptual models in various fields of geosciences. Analogous models applied to genomes can yield new information about the relationship between genomes and their geochemical environments. In this perspective article, we present a chemical and thermodynamic analysis of prokaryotic lineages that have been the target of previous phylogenomic studies of evolutionary adaptation to varying redox conditions. The thermodynamic model development begins by quantifying the effects of hydrogen activity (aH2 ) and temperature on the relative stabilities of organic compounds with different carbon oxidation state. When applied to proteins instead of metabolites, the same techniques can be used to identify combinations of aH2 and temperature at which reference proteomes for Class I or Class II methanogens are relatively stable. The calculated aH2 values are compatible with reported measurements for habitats of methanogens ranging from highly reducing submarine hydrothermal systems to less reducing environments including methanogenic sediments. In contrast to the transition between the two classes of methanogenic archaea, that between basal and terrestrial groups of Thaumarchaeota (denoting the origin of ammonia-oxidizing archaea) occurs at a less-reducing redox boundary. These examples reveal the consequences of energy minimization driving evolution and show how geochemical calculations involving biomolecules can be used to quantify and better understand the coevolution of the geosphere and biosphere.

Experimental Thermodynamic Characterization of the Chalcopyrite-Based Compounds in the Ag–In–Te System for a Potential Thermoelectric Application

The equilibrium concentration space of the Ag–In–Te system in the part AgInTe2–Te–In2Te3 was studied through the modified solid-state electromotive force (EMF) method by dividing In2Te3–In2Te5–Ag3In97Te147 (I), In2Te5–Te–Ag3In97Te147 (II), Ag3In97Te147–Te–AgIn5Te8 (III), AgIn5Te8–Te–AgIn3Te5 (IV), and AgIn3Te5–Te–AgInTe2 (V), into separate phase regions at T ≤ 500 K. The formation of a thermodynamically stable combination of the binary and ternary phases in the (I)–(V) phase regions from a metastable phase mixture of substances was carried out at T ≤ 500 K in the R(Ag+) part of the positive electrode (PE) of the galvanic cells (GCs) of the structure: (−) C |∙| Ag |∙| SE |∙| R(Ag+) |∙| PE |∙| C (+), where C is the graphite (inert electrode), SE is the solid-state electrolyte (Ag3GeS3Br glass), and Ag is the left (negative) electrode. The Ag+ ions in the R(Ag+) region functioned as small nucleation centers for the formation of the stable phases. The spatial position of the (I)–(V) phase regions in the concentration space of the Ag–In–Te system relative to the position of silver was used to express the overall potential-forming reactions with the participation of the substances Ag, Te, In2Te5, Ag3In97Te147, AgIn5Te8, AgIn3Te5, and AgInTe2. The subsequent EMF measurements were carried out by applying the same GCs. The temperature dependences of the EMF of GCs with PE of the (I)–(V) phase regions were here used to determine, for the first time, the values of standard thermodynamic functions of the binary and ternary compounds. The determined values of the Gibbs energies of the formation of compounds are equal: GIn2Te5○=(182.7±1.9) kJ·mol−1, GAgInTe2○=(115.0±3.1) kJ·mol−1, GAgIn3Te5○=(301.5±6.5) kJ·mol−1, GAgIn5Te8○=(487.6±11.3) kJ·mol−1, and GAg3In97Te147○=(8594±189) kJ·mol−1 The correctness of the division of the equilibrium phase space of the Ag–In–Te system in the part AgInTe2–Te–In2Te3 involving the AgInTe2, AgIn3Te5, AgIn5Te8, and Ag3In97Te147 compounds was confirmed by the agreement of the calculated and literature-based thermodynamic data for In2Te5 compound. Compositions of pairs of the ternary compounds for their subsequent practical application were proposed.

Evidence for charge and spin density waves in single crystals of La3Ni2O7 and La3Ni2O6

Charge and spin order is intimately related to superconductivity in copper oxide superconductors. To elucidate the competing orders in various nickel oxide compounds are crucial given the fact that superconductivity has been discovered in Nd$_{0.8}$Sr$_{0.2}$NiO$_2$ films. Herein, we report structural, electronic transport, magnetic, and thermodynamic characterizations on single crystals of La$_3$Ni$_2$O$_7$ and La$_3$Ni$_2$O$_6$. La$_3$Ni$_2$O$_7$ is metallic with mixed Ni$^{2+}$ and Ni$^{3+}$ valent states. Resistivity measurements yield two transition-like kinks at $\sim$110 and 153 K, respectively. The kink at 153 K is further revealed from magnetization and specific heat measurements, indicative of the formation of charge and spin order. La$_3$Ni$_2$O$_6$ single crystals obtained from topochemical reduction of La$_3$Ni$_2$O$_7$ are insulating and show an anomaly at $\sim$176 K on magnetic susceptibility. The transition-like behaviors of La$_3$Ni$_2$O$_7$ and La$_3$Ni$_2$O$_6$ are analogous to the charge and spin order observed in La$_4$Ni$_3$O$_{10}$ and La$_4$Ni$_3$O$_8$, suggesting charge and spin order is a common feature in the ternary La-Ni-O system with mixed-valent states of nickel.

Prediction of equations of state of molecular liquids by an artificial neural network.

In this work an artificial neural network (ANN) was used to determine the pressure and internal energy equations of state of noble gases and some molecular liquids by predicting thermodynamic state variables like density and temperature encoded in the radial distribution function. The ANN is trained to predict the thermodynamic state variables using only the structural data. Then, predicted values are used to compute equations of state of real liquids such as argon, neon, krypton and xenon as well as some molecular liquids like nitrogen, carbon dioxide, methane and ethylene. In order to assess the ANN predictions the relative percentage error with the exact values were determined, showing that its magnitude is less than 1%. Thus, the comparison between equations of state computed with the predicted variables and experimental results exhibits a very good agreement for most of the liquids studied here. Since our ANN implementation only requires the microscopic structure as an input, data incoming from experiments, theoretical frameworks or simulations are suitable to perform predictions of state variables and with that complement the thermodynamic characterisation of liquids through the determination of equations of state. Moreover, further improvements or extensions related with the microscopic structure database can be safely addressed without changing the neural network architecture presented here.