Thermodynamic Characterization Research Articles

SARS-CoV-2 strain wars continues: Chemical and thermodynamic characterization of live matter and biosynthesis of Omicron BN.1, CH.1.1 and XBC variants

SARS-CoV-2 has during the last 3 years mutated several dozen times. Most mutations in the newly formed variants have been chemically and thermodynamically characterized. New variants have been declared as variants under monitoring. The European Centre for Disease Prevention and Control has suggested the hypothesis that the new BN.1, CH.1.1 and XBC variants could have properties similar to those of VOC. Thermodynamic properties of new variants have been reported in this manuscript for the first time. Gibbs energy of biosynthesis, as the driving force for viral multiplication, is less negative for the new variants than for the earlier variants. This indicates that the virus has evolved towards decrease in pathogenicity, which leads to less severe forms of COVID-19.

Partitioning the Two-Leg Spin Ladder in Ba2Cu1-x Zn x TeO6: From Magnetic Order through Spin-Freezing to Paramagnetism.

Ba2CuTeO6 has attracted significant attention as it contains a two-leg spin ladder of Cu2+ cations that lies in close proximity to a quantum critical point. Recently, Ba2CuTeO6 has been shown to accommodate chemical substitutions, which can significantly tune its magnetic behavior. Here, we investigate the effects of substitution for non-magnetic Zn2+ impurities at the Cu2+ site, partitioning the spin ladders. Results from bulk thermodynamic and local muon magnetic characterization on the Ba2Cu1-x Zn x TeO6 solid solution (0 ≤ x ≤ 0.6) indicate that Zn2+ partitions the Cu2+ spin ladders into clusters and can be considered using the percolation theory. As the average cluster size decreases with increasing Zn2+ substitution, there is an evolving transition from long-range order to spin-freezing as the critical cluster size is reached between x = 0.1 to x = 0.2, beyond which the behavior became paramagnetic. This demonstrates well-controlled tuning of the magnetic disorder, which is highly topical across a range of low-dimensional Cu2+-based materials. However, in many of these cases, the chemical disorder is also relatively strong in contrast to Ba2CuTeO6 and its derivatives. Therefore, Ba2Cu1-x Zn x TeO6 provides an ideal model system for isolating the effect of defects and segmentation in low-dimensional quantum magnets.

Solid state synthesis, thermal, spectral, optical, crystal structure and atomic packing studies of 2-(3-Hydroxyphenyl)-2,3-dihydroquinazolin-4(1H)-one

The environment friendly solid state synthesis is adopted for the synthesis of molecular complex, 2-(3-Hydroxyphenyl)-2,3-dihydroquinazolin-4(1H)-one, (ANHB) with utmost yield. The phase diagram (PD) of anthranilamide (AN) ─ 3-hydroxybenzaldehyde (HB) system gives the compositional behavior of composites in the entire range, and has identified the formation of two eutectics and a molecular complex. The novelty and structural behavior of ANHB was studied using FTIR, NMR, UV–vis, fluorescence, DSC and PXRD techniques. The various thermodynamic characterizations of eutectics and complex are done using the heat of fusion values obtained from DSC. The single crystal XRD (SCXRD) and atomic packing studies of grown ANHB crystal infer that ANHB crystallizes in centro-symmetric triclinic space group P 1¯ with two molecules in the asymmetric unit and four molecules in the unit cell. The synthesized complex shows fluorescence emission in visible region.

Thermodynamic analysis, synthesis, characterization, and evaluation of 1-ethyl-3-methylimidazolium chloride: Study of its effect on pretreated rice husk

This work is focused on the determination of the optimal reaction conditions to synthesize the ionic liquid 1-ethyl-3-methylimidazolium chloride ([EMIM][Cl]) and assess its suitability for the pretreatment of rice husk. The modified UNIFAC (UNIversal quasi-chemical Functional-group Activity Coefficients) approach for ionic liquids is used to develop a thermodynamic model that describes the reactive system methylimidazole (MIM), chloroethane (C2H5Cl) and [EMIM][Cl]. The model allows to study the phase equilibria coexistence (vapor–liquid equilibria and solid–liquid equilibria) and yields the theoretically optimal conditions to synthesize the ionic liquid. The model predictions are validated with the available experimental and reported data. By implementing the developed model, a simple way to synthesize ionic liquid [EMIM][Cl] was found allowing to study its influence on the structure and morphology of pretreated rice husk. The lignocellulosic materials involved in this study are characterized by their composition, enzymatic digestibility, scanning electron microscopy, and crystallinity. Compared to untreated material, [EMIM][Cl]-pretreated rice husk produces cellulose that can be efficiently enzymatic hydrolyzed with high sugar yields. This work offers a suitable methodology to include the synthesis and thermodynamics of the solvent media within the design of low-cost ionic liquids for lignocellulosic biomass pretreatment.

Structural characterization of a cytosine-rich potential quadruplex forming sequence in the EGFR promoter

I-motifs are tetra-helixes that may form in cytosine-rich strands. They are based on cytosine–cytosine+ base pairs that require the N3 hemi-protonation of the nucleobases, and therefore, the stability of these non-canonical DNA arrangements depends on pH. These structures are promising targets for the development of new cancer therapies since they are enriched in the promoters of oncogenes where they can play a role in the regulation of transcription. The proximal promoter of the EGFR oncogene has multiple regions with a significant potential to form such a tetra-helix arrangement. Here, we present the thermodynamic characterization of a C-rich sequence located 37 nucleotides upstream of the transcription starting site of EGFR. We confirmed the ability of this sequence to fold into an I-motif. By applying a global analysis of calorimetric and spectroscopic data, we derived the dependency of the apparent standard Gibbs free energy change associated with the I-motif folding upon temperature and pH. The results showed that, in contrast to in silico prediction, only 4 CC+ base pairs formed while additional GC and TT base pairings were detected in the I-motif. Noteworthy, a single residue mutation at G14 largely shifts the equilibrium toward the formation of multimeric species.

Pseudouridimycin-A Potent Nucleoside Inhibitor of the RNA Polymerase Beta Prime Subunit of Streptococcus pyogenes.

Streptococcus pyogenes (group A streptococcus, GAS), a Gram-positive bacterium, is a major cause of mild to severe life-threatening infections. Antibacterial resistance to penicillin and macrolides poses a major threat in the treatment of GAS and necessitates alternate drugs and newer antibiotics. In this direction, nucleotide-analog inhibitors (NIAs) have emerged as important antiviral, antibacterial, and antifungal agents. Pseudouridimycin (PUM), a nucleoside analogue inhibitor discovered from the soil bacterium Streptomyces sp., has proven to be effective against multidrug-resistant S. pyogenes. However, the mechanism of its activity remains elusive. In this study, subunits of the RNA polymerase of GAS have been identified as targets for PUM inhibition and the binding regions have been mapped to the N-terminal domain of the β' subunit, using computational methods. The antibacterial activity of PUM against macrolide-resistant GAS was evaluated. PUM showed effective inhibition at 0.1-1 μg/mL concentration, which was higher when compared to earlier reports. The molecular interaction between PUM and the RNA polymerase β'-N terminal subunit was investigated using isothermal titration calorimetry (ITC), circular dichorism (CD), and intrinsic fluorescence spectroscopy. The thermodynamic characterization by ITC showed an affinity constant of 6.175 × 105 M-1 denoting a moderate affinity. Fluorescence studies revealed that the interaction of protein-PUM was spontaneous in nature and follows a static quenching of tyrosine signals from the protein. The near- and far-UV CD spectral analysis concluded that PUM induced local tertiary structural changes in the protein, predominantly contributed by aromatic amino acids rather than notable changes in the secondary structure. Hence PUM could be a promising lead drug target for macrolide-resistant strains of S. pyogenes and enable eradication of pathogen in the host system.

Discerning perturbed assembly of lipids in a model membrane in presence of violacein: Effects of membrane hydrophobicity

For the lack of effective antibiotics towards antibiotic resisting bacteria, it is required to discover new antibiotics and to understand their antimicrobial mechanism. Violacein is a violet pigment found in several gram-negative bacteria possessing antimicrobial properties to gram-positive bacteria. This present article investigates the insertion ability of this molecule into a model membrane composed of zwitterionic phospholipids. Thermodynamic characterization of lipid monolayers in the presence of violacein was carried out using a single lipid layer formed at air-water interface. The molecule inserts into the layer altering the area occupied by each lipid and the in-plane compressibility of the film. This insertion increases with the hydrophobic chain length of the lipid. The perturbed self-assembly of lipids in a bilayer is quantified using a lipid multilayer system applying the X-ray reflectivity technique. The electron density profile from the reflectivity data shows that the molecule inserts into the fluid phase creating a relatively ordered chain conformation. Further, the insertion into the gel phase is observed to increase with the increased thickness of the hydrophobic core of a bilayer.

The SARS-CoV-2 Hydra, a tiny monster from the 21st century: Thermodynamics of the BA.5.2 and BF.7 variants

SARS-CoV-2 resembles the ancient mythical creature Hydra. Just like with the Hydra, when one head is cut, it is followed by appearance of two more heads, suppression of one SARS-CoV-2 variant causes appearance of newer variants. Unlike Hydra that grows identical heads, newer SARS-CoV-2 variants are usually more infective, which can be observed as time evolution of the virus at hand, which occurs through acquisition of mutations during time. The appearance of new variants is followed by appearance of new COVID-19 pandemic waves. With the appearance of new pandemic waves and determining of sequences, in the scientific community and general public the question is always raised of whether the new variant will be more virulent and more pathogenic. The two variants characterized in this paper, BA.5.2 and BF.7, have caused a pandemic wave during the late 2022. This paper gives full chemical and thermodynamic characterization of the BA.5.2 and BF.7 variants of SARS-CoV-2. Having in mind that Gibbs energy of binding and biosynthesis represent the driving forces for the viral life cycle, based on the calculated thermodynamic properties we can conclude that the newer variants are more infective than earlier ones, but that their pathogenicity has not changed.

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.