Biophysical characterization and design of a minimal version of the Hoechst RNA aptamer

RNA aptamers are oligonucleotides, selected through Systematic Evolution of Ligands by EXponential Enrichment (SELEX), that can bind to specific target molecules with high affinity. One such molecule is the RNA aptamer that binds to a blue-fluorescent Hoechst dye that was modified with bulky t-Bu groups to prevent non-specific binding to DNA. This aptamer has potential for biosensor applications; however, limited information is available regarding its conformation, molecular interactions with the ligand, and binding mechanism. The study presented here aims to biophysically characterize the Hoechst RNA aptamer when complexed with the t-Bu Hoechst dye and to further optimize the RNA sequence by designing and synthesizing new sequence variants. Each variant aptamer-t-Bu Hoechst complex was evaluated through a combination of fluorescence emission, native polyacrylamide gel electrophoresis, fluorescence titration, and isothermal titration calorimetry experiments. The results were used to design a minimal version of the aptamer consisting of only 21 nucleotides. The performed study also describes a more efficient method for synthesizing the t-Bu Hoechst dye derivative. Understanding the biophysical properties of the t-Bu Hoechst dye-RNA complex lays the foundation for nuclear magnetic resonance spectroscopy studies and its potential development as a building block for an aptamer-based biosensor that can be used in medical, environmental or laboratory settings.

Probing pharmaceutically important amino acids L-isoleucine and L-tyrosine Solubilities: Unraveling the solvation thermodynamics in diverse mixed solvent systems

The study specifically investigates the solubilities of L-isoleucine and L-tyrosine in water-mixed solvent systems (DMF, DMSO, and ACN), exploring the behaviour of amino acids in complex environments. The experimental methods prioritize meticulous solvent purification to ensure reliable results. The work explores solubility data, uncovering temperature-dependent trends and intricate interactions influencing solubility in the chosen mixed solvent systems. The study emphasizes the impact of thermodynamic properties, solvent-solvent interactions, and amino acid structure on solubility patterns. The broader implications highlight the relevance of understanding amino acid behaviour in diverse solvent environments, offering potential applications in cosmetics and pharmaceutical industries. The distinct solubility patterns contribute valuable insights, enhancing on the understanding of the solution stability and interactions of L-isoleucine and L-tyrosine in different solvent systems. In conclusion, work suggests the enhanced utilization of L-isoleucine and L-tyrosine in various industries, driven by a profound understanding of their solubility in mixed solvent systems. The research expands our knowledge of amino acid behaviour, paving the way for advancements in industries relying on protein-based products and technologies.

Deep Earth Chronicles: High-Pressure Investigation of Phenakite Mineral Be2SiO4

Beryllium silicate, recognized as the mineral phenakite (Be2SiO4), is a prevalent constituent in Earth's upper mantle. This study employs density-functional theory (DFT) calculations to explore the structural, mechanical, dynamical, thermodynamic, and electronic characteristics of this compound under both ambient and high-pressure conditions. Under ideal conditions, the DFT calculations align closely with experimental findings, confirming the mechanical and dynamical stability of the crystalline structure. Phenakite is characterized as an indirect band gap insulator, possessing an estimated band gap of 7.83 eV. Remarkably, oxygen states make a substantial contribution to both the upper limit of the valence band and the lower limit of the conduction band. We delved into the thermodynamic properties of the compound, including coefficients of thermal expansion, free energy, entropy, heat capacity, and the Gruneisen parameter across different temperatures. Our findings suggest that Be2SiO4 displays an isotropic behavior based on estimated anisotropic factors. Interestingly, our investigation revealed that, under pressure, the compression of phenakite is not significantly affected by bond angle bending.

Influence of mudstone on coal spontaneous combustion characteristics and oxidation kinetics analysis

To explore the spontaneous combustion characteristics and hazards of the low-temperature oxidation (LTO) stage in the process of spontaneous combustion of coal and mudstone, the pore structure, spontaneous combustion characteristic parameters, and exothermic characteristics of coal and mudstone were tested and studied, and the oxidation kinetic parameters were calculated. The results show that mudstone has a larger specific surface area and pore volume than coal. From the fractal characteristics, the pore structure of mudstone is more complex than that of coal. According to the comparison of theoretical and actual gas generation and oxygen consumption rate curves, it is found that there is an interaction between coal and mudstone in the LTO process. With the increase of mudstone mass ratio, gas production, and its oxygen consumption rate increase. Among them, CM-4 (Coal:Mudstone = 1:1) has the highest exothermic intensity and the exothermic factor (A) and fire coefficient (K) increase with the increase of mudstone content. The apparent activation energy of the mudstone sample is lower than that of the raw coal, indicating that the sample after adding mudstone is more likely to have spontaneous combustion in the LTO stage.

Solubility and thermodynamics of mesalazine in aqueous mixtures of poly ethylene glycol 200/600 at 293.2-313.2K

In this study, the solubility of mesalazine was investigated in binary solvent mixtures of poly ethylene glycols 200/600 and water at temperatures ranging from 293.2K to 313.2K. The solubility of mesalazine was determined using a shake-flask method, and its concentrations were measured using a UV-Vis spectrophotometer. The obtained solubility data were analyzed using mathematical models including the van't Hoff, Jouyban-Acree, Jouyban-Acree-van't Hoff, mixture response surface, and modified Wilson models. The experimental data obtained for mesalazine dissolution encompassed various thermodynamic properties, including ΔG°, ΔH°, ΔS°, and TΔS°. These properties offer valuable insights into the energetic aspects of the dissolution process and were calculated based on the van't Hoff equation.

Determination of the role of specific amino acids in the binding of Zn(II), Ni(II), and Cu(II) to the active site of the M10 family metallopeptidase

Metallopeptidases are a group of metal-dependent enzymes that hydrolyze peptide bonds. These enzymes found in Streptococcus pneumoniae assist the pathogen in infecting the host by breaking down host tissues and extracellular matrix proteins. Considering metallopeptidases' significant role in bacterial virulence, inhibiting this enzyme represents a promising avenue for research. These enzymes are characterized by the presence of Zn(II) in the active site, proper coordination of which is essential for their catalytic function. This work aims to determine the significance of the specific amino acids in the metal binding domain of metallopeptidase from S. pneumoniae. For this purpose, we investigated the coordination chemistry of Zn(II), Ni(II), and Cu(II) ions with point-mutated peptide models of the metal-binding domain. Mutations were introduced at His-2 (L1) and Glu-1. Studies have shown that at pH 7.14 (pH of infected lungs by S. pneumoniae), point mutation on glutamic acid caused only minor effects on the binding of Zn(II) and Ni(II), while significantly improving Cu(II) binding. The stability of copper complexes is greater with the mutant Glu-1 → Gln-1 than with the original domain due to a hydrogen bonding network created by the Gln backbone with its side chain. Substituting histidine resulted in a significant reduction in metal binding for all metal ions, highlighting the crucial role of His-2 in metal coordination. Introduced mutations at neutral pH did not significantly affect the secondary structure of metal complexes. However, at alkaline pH, the peptides showed a higher percentage of antiparallel β-sheet structures upon the addition of Cu(II), Ni(II) and Zn(II).

Prediction of vibrational spectrum and thermodynamic properties for phosphorus mononitride

In this work, an accurate potential energy curve (PEC) for the ground electronic state of phosphorus mononitride (PN) molecule has been determined from a variationally improved Hulburt-Hirschfelder (VIHH) oscillator model in conjunction with the experimental spectral constants (De,ωe,ωexe,Be,αe,re). We have numerically solved the Schrödinger equation for the VIHH potential using the LEVEL program, obtaining the pure vibrational spectrum that converges to the dissociation limit. In addition, the partition functions of PN molecule are calculated using the full rovibrational energies. Ultimately, thermodynamic properties like molar heat capacity, entropy, enthalpy, and Gibbs free energy were calculated for the PN molecule and show good agreement with those data from the NIST (National Institute of Standards and Technology) database.

Fundamental Equation of State for Fluid Tetrahydrofuran

An empirical fundamental equation of state in terms of the Helmholtz energy for tetrahydrofuran is presented. In the validity range from the triple-point temperature up to 550 K and pressures up to 600 MPa, the equation of state enables the calculation of all thermodynamic properties in the liquid, vapor, and super-critical regions including saturation states. Based on an extensive literature review, experimental data are represented within their experimental uncertainty. In the homogeneous liquid phase at atmospheric pressure, the uncertainty in density is 0.015 %, speed of sound is represented with an uncertainty of 0.03 %, and isobaric heat capacity has an uncertainty of 0.4 %. Isobaric heat capacities in the homogeneous vapor phase are described with an uncertainty of 0.2 %. Higher uncertainties occur above atmospheric pressure for all homogeneous properties. Depending on the temperature range, vapor pressure can be calculated with an uncertainty from 0.02 % to 3 %. The extrapolation behavior is evaluated, showing reasonable extrapolation behavior towards extreme conditions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10765-023-03258-3.

Information theory and thermodynamic properties of diatomic molecules using molecular potential

Owing to the devise applications of molecules in industries, the bound state solution of the non-relativistic wave equation with a molecular potential function has been obtained in a closed-form using the Nikiforov-Uvarov method. The solutions of the bound state are then applied to study the information-theoretic measures such as the one-dimensional Shannon and Renyi entropic densities. The expectation values for the position and momentum spaces were obtained to verify the Heisenberg's uncertainty principle. Utilizing the energy spectrum equation, the thermodynamic vibrational partition function is obtained via the Poisson summation. Other thermodynamic function variations with absolute temperature have been obtained numerically for four diatomic molecules (H2, N2, O2, and HF) using Maple 18 software. The Shannon global entropic sum inequality has also been verified. The Renyi sum for constrained index parameters satisfies the global entropic inequality. The thermodynamic properties of the four molecules are similar and conform to works reported in the existing literature. The obtained vibrational energies are in fair agreement with the ones obtained using other forms of potential energy. The result further indicates that the lowest bounds for the Shannon, Renyi, and Heisenberg inequalities are ground states phenomena.

Computational and theoretical chemistry of newly synthesized and characterized 2,2'-(5,5'-(1,4-phenylene)bis(1H-tetrazole-5,1-diyl))bis-N-acetamides

Energetic heterocycles, including pyridines, triazoles, and tetrazoles, exhibit greater density, heats of formation, and oxygen balance compared to their carbocyclic counterparts, making them a promising approach for synthesizing novel bis-tetrazole acetamides. Synthesized compounds A-F, some of which feature a chlorine atom attached to the phenyl ring, serve as valuable synthons for aryl coupling reactions. Analysis via 1H-NMR and 13C-NMR spectroscopy, as well as density functional considerations through B3LYP functional correlation with 6-311 +  + G(d) and 6-31G(d) basis set, revealed the observed LUMO/HOMO energies and charge transfer within the molecule. Additionally, the dipole moment, chemical hardness, softness, ionization potential, local reactivity potential via Fukui indices and thermodynamic properties (entropy, enthalpy, and Gibbs free energy) of the molecule were calculated through density functional theory studies. In addition, Molecular Docking studies were conducted to investigate the anti-cancer potential of synthesized heterocyclic compounds against caspase 3, NF-KAPPA-B and P53 protein. Molecular docking analysis demonstrated a potent interaction between 2,2'-(5,5'-(1,4-phenylene)bis(1H-tetrazole-5,1-diyl))bis-N-(2,4-dinitrophenyl) acetamides (6d) and TP53 and NF-KAPPA-B with binding energies of - 11.8 kJ/mol and - 10.9 kJ/mol for TP53 and NF-KAPPA-B, respectively. Similarly, 2,2'-(5,5'-(1,4-phenylene)bis(1H-tetrazole-5,1-diyl))bis-N-(2-chlorophenyl) acetamides (6f) exhibited a strong interaction with caspase-3 with binding energy of -10.0 kJ/mol, indicating their potential as therapeutic agents against these proteins. Furthermore, the findings of current study was further strengthen by 100 ns molecular dynamics (MD) simulations. Finally, theoretical studies of oxygen balance and nitrogen percentage suggest that these molecules can be utilized as energetic materials.

Highly efficient and stable lead-free cesium copper halide perovskites for optoelectronic applications: A DFT based study

Recently synthesized industrially significant perovskites C s 3 C u 2 X 5 (X = C l , B r , I ) are subjected to a density functional theory (DFT) investigation utilizing the CASTEP code. This study explores various physical features, including structural, optical, thermodynamic, elastic, mechanical, and electronic properties. There is a strong correlation between the optimized structure parameters and the existing experimental data, which demonstrates the reliability of our DFT-based computations. The band structure and density of states (TDOS and PDOS) analysis revealed that all the studied perovskites are direct band gap semiconductors, and C s 3 C u 2 B r 5 has the smallest band gap (2.092 eV). We also discussed the mechanical and cell stability using the Born stability criterion and formation energy, respectively. The mechanical and dynamic stability of each phase is confirmed by the analysis of the elastic constants. According to the computed values of Pugh's and Poisson's ratios as well as Cauchy's pressure, all of the studied compounds are ductile in nature. The study of density of states, total charge density, and Mulliken atomic populations reveal that all the compounds have complex bonding with both ionic and covalent properties. Finally, utilizing the elastic constant data, the Debye temperatures of C s 3 C u 2 C l 5 , C s 3 C u 2 B r 5 , and C s 3 C u 2 I 5 have been determined as 82.90 K, 100.00 K, and 80.70 K, respectively. The analysis of thermodynamics (relatively low values of both Θ D and K min ) as well as optical properties indicate that all the investigated materials have the potential to serve as thermal barrier coating (TBC) materials.

The effect of strain on hydrogen storage characteristics in K2NaAlH6 double perovskite hydride through first principle method

Today, hydrogen is one of the most credible options for a non-polluting, carbon-free energy carrier. Hydrogen can be obtained or produced by different means from different renewable energy sources and can be stored in solid, liquid, or gaseous form. Storing hydrogen in complex hydrides in solid form is one of the most efficient methods of storage because they are secure, offer high hydrogen capacity, and demand optimal functioning conditions. Complex hydrides give a large gravimetric capacity that allows large amounts of hydrogen to be stored. This study examined the effects of triaxial strains on hydrogen storage properties of the perovskite-type compound K₂NaAlH₆. The analysis was conducted through first principle calculations using the full potential linearized augmented plane wave (FP-LAPW) approach. Our results indicate that the formation energy and desorption temperature of K₂NaAlH₆ hydride were improved under a maximum triaxial compressive strains of ε ≈ - 5%. Specifically, the values of formation energy and desorption temperature were - 40.14 kJ/mol.H₂ and 308.72 K, respectively, compared to the original values of - 62.98 kJ/mol.H₂ and 484.52 K. In addition, the analysis of the densities of states showed that changes in the dehydrogenation and structural properties of K₂NaAlH₆ were closely linked to the Fermi level value of the total densities of states. These findings provide valuable insights into the potential of K₂NaAlH₆ as a hydrogen storage material.

Solubility and thermodynamic study of deferiprone in propylene glycol and ethanol mixture

This work aims to obtain the solubility, density and thermodynamic parameters of deferiprone in propylene glycol and ethanol. For this purpose, a shake-flask technique was applied for solid-liquid equilibration and the spectrophotometry method was employed for solubility measurement. Solubility and density of deferiprone in non-aqueous mixtures of propylene glycol and ethanol were measured in the temperatures 293.2-313.2 K. Some equations including van't Hoff, the Jouyban-Acree, the Jouyban-Acree-van't Hoff, the mixture response surface and modified Wilson equations were used for the mathematical data modeling. The apparent thermodynamic parameters of the deferiprone dissolution process were computed and reported.

Structure and size-dependent vibrational and thermal properties of Ni clusters: A systematic ab initio approach

There is scarce information on the vibrational and thermal properties of small Ni clusters. Here, the outcomes of ab initio spin-polarized density functional theory calculations on the size and geometry effects upon the vibrational and thermal properties of Ni_n (n = 13 and 55) clusters, are discussed. For theses clusters a comparison is presented between the closed shell symmetric octahedral (O_h) and the icosahedral (I_h) geometries. The results indicate that the I_h isomers are lower in energy. Besides, ab initio molecular dynamics runs at T = 300K show that Ni₁₃ and Ni₅₅ clusters transform from their initial O_h geometries towards the corresponding I_h ones. For Ni₁₃, we also consider the lowest energy less symmetric layered 1-3-6-3 structure, and the cuboid, recently observed experimentally for Pt₁₃, which is competitive in energy but is unstable, as phonon analysis reveals. We calculate their vibrational density of states (νDOS) and heat capacity, and compare with the Ni FCC bulk counterpart. The characteristic features of the νDOS curves of these clusters are interpreted in terms of the clusters' sizes, the interatomic distance contractions, the bond order values as well as the internal pressure and strains of the clusters. We find that the softest possible frequency of the clusters is size and structure-dependent, being the smallest for the O_h ones. We identify mostly shear, tangential type displacements involving mainly surface atoms for the lowest frequency of the spectra of both I_h and O_h isomers. For the maximum frequencies of these clusters the central atom shows anti-phase movements against groups of nearest neighbor atoms. An excess of heat capacity at low temperatures with respect to the bulk is found, while at high temperatures a constant limiting value, close but lower to the Dulong and Petit value, is determined.

Complexation of anthocyanins, betalains and carotenoids with biopolymers: An approach to complexation techniques and evaluation of binding parameters

Natural pigments are bioactive compounds that can present health-promoting bioactivities in the human body. Due to their strong coloring properties, these compounds have been widely used as color additives as an alternative to artificial colorants. However, since these pigments are unstable under certain conditions, such as the presence of light, oxygen, and heat, the use of complexation and encapsulation techniques with biopolymers is in demand. Moreover, some functional properties can be achieved by using natural pigments-biopolymers complexes in food matrices. The complexation and encapsulation of natural pigments with biopolymers consist of forming a complex with the aim to make these compounds less susceptible to oxidative and degrading agents, and can also be used to improve their solubility in different media. This review aims to discuss different techniques that have been used over the last years to create natural pigment-biopolymers complexes, as well as the recent advances, limitations, effects, and possible applications of these complexes in foods. Moreover, the understanding of thermodynamic parameters between natural pigments and biopolymers is very important regarding the complex formation and their use in food systems. In this sense, thermodynamic techniques that can be used to determine binding parameters between natural pigments and potential wall materials, as well as their applications, advantages, and limitations are presented in this work. Several studies have shown an improvement in many aspects regarding the use of these complexes, including increased thermal and storage stability. Nonetheless, data regarding the biological effects on the human body and the sensory acceptance of natural pigments-biopolymers complexes in food systems are scarce in the literature.

Study of thermodynamics of a thermal electron in scattering

This work presents the study of the thermodynamic properties of thermal electrons participating in scattering events. This is necessary because scattering with a thermal electron in presence of a laser field was not studied yet and it reduces the complexity of event measurement (differential cross-section). To study thermodynamic properties, the authors model the thermal Hamiltonian in presence of a laser field and used it to study the thermodynamic properties using the partition function. The study shows thermodynamic energy, around the target with distance at field amplitude 0.1 a.u. to 0.9 a.u. has destructive interference, above field amplitude 1 a.u. to 2.5 a.u. has superposition and at field amplitude 2.5 a.u. and 3 a.u. have coulomb potential like nature. Also, thermodynamic energy with temperature was found constant except at field amplitude 2.5 a.u. and at field amplitude 2.5 a.u. destructive interference at 10 °C and 21 °C. The thermodynamical potential at field amplitude 0.1 to 3.5 a.u. found constant and above field amplitude 3.5 a.u. increased linearly when studied with respect to temperature at 10 Å . The thermal Hamiltonian increase sharply when thermal electrons enter in 1-5 Å , slowly in 5-10 Å and beyond 10 Å constant, and the thermal Hamiltonian nature is like coulomb potential.

Effectiveness and mechanisms of the adsorption of carbendazim from wastewater onto commercial activated carbon

The wide application of fungicides is becoming one of the main causes of water pollution. Activated carbon (AC) is a frequently-used adsorbent in water treatment. In this work, aiming to obtain a better understanding of fungicides on AC, carbendazim was selected as a model fungicide in water. The effects of AC dosage, adsorption temperature, adsorption time and pH value of solution on carbendazim adsorption by AC were investigated. When the initial concentration of carbendazim was 500 mg L^-1 and the volume of wastewater was 25 mL, the optimum dosage of AC and reaction time was determined to be 0.3 g and 150 min, respectively. The pH ranging from 3.0 to 10.0 exhibited little effect on the adsorption capability of AC. The higher the adsorption temperature was, the better adsorption capacity was. Adsorption capacity could reach 32.31 mg g^-1 under the optimal adsorption conditions. The kinetics study reveals that the adsorption of carbendazim occurred on the surface of adsorbent during initial stage. The adsorption data was well fitted by Langmuir adsorption isotherm, indicating that the adsorption process was monolayer adsorption. The thermodynamic experiments confirmed that the adsorption of carbendazim was an endothermic process with the coexistence of physical and chemical adsorption. Because the main components of AC used in this research work is amorphous carbon with low impurity and its surface has not been modified with additional functional groups, the conclusion of the study was easy to be replicated by repeated experiments. Therefore, the findings of this study could guide the adsorption of carbendazim onto the other kinds of AC with high specific surface area, and provide useful information for application of commercial AC in treatment of fungicides wastewater.

Physico-chemical parameters of phase separation of the mixture of BSA and triton X 100 in aqueous solutions of monohydroxy compounds

Clouding behavior and thermodynamic properties for the TX 100 + BSA mixture were investigated in aqueous and aq. alcoholic media. In an aqueous environment, the values of cloud point (CP), at which a clear solution becomes cloudy, for TX 100 decreases with augmentation of the concentration of BSA. The reverse result was obtained in the aq. alcoholic media. In this study, we have used ethanol (EtOH), 1-propanol (1-PrOH), and 2-butanol (2-BuOH) as alcohols. The changes of CP values in alcoholic media have been obtained in the following order: CP_H2O+EtOH > CP_H2O+2-BuOH > CP_H2O+1-PrOH. The standard free energy (∆G_c^o), standard enthalpy (∆H_c^o), and standard entropy (∆S_c^o) changes of clouding were derived at CP. The ΔG_c⁰ values of TX 100 + BSA decreases in the aqueous and alcoholic media with increasing the concentration of BSA and alcohol. This process becomes endothermic in the aq. alcoholic media. Different thermodynamic properties of transfer and entropy-enthalpy compensation parameters for the phase partitioning of the TX 100 + BSA mixture have been calculated and assessed properly.

Nonrelativistic treatment of inversely quadratic Hellmann-Kratzer potential and thermodynamic properties

The study presents approximate analytical solutions of the Schrödinger equation with a newly proposed potential model called Inversely Quadratic Hellmann-Kratzer potential (IQHKP). This potential is a superposition of Inversely Quadratic Hellman potential and Kratzer potential. The energy eigenvalues and corresponding wavefunction are calculated via the formula method. We applied our results to evaluate thermodynamic functions such as vibrational free energy, F, vibrational internal energy, U, vibrational entropy, S, and vibrational specific heat, C. We also reported special cases of importance.

Dirac equation and thermodynamic properties with the Modified Kratzer potential

In this work, we present the analytical solutions of Dirac equation for modified Kratzer potential in the pseudospin and spin symmetry limits using the formula method. The energies of the pseudospin and spin symmetry limit are obtained analytically and numerically. The numerical values are compared with those obtained in literature. Furthermore, we study the thermodynamic properties of some diatomic molecules within the nonrelativistic spin symmetry limits.

Determination of kinetic triplet, thermal degradation behaviour and thermodynamic properties for pyrolysis of a lignocellulosic biomass

Kinetic triplet, thermal degradation behaviour and thermodynamic properties of peanut shells were determined on the basis of non-isothermal thermogravimetric experiments conducted at three different heating rates under N₂ atmosphere. A single differential peak was observed for the devolatilization stage. The kinetic triplet of devolatilization stage was determined using Coats-Redfern and a combined method consisting the utilization of isoconversional and Criado methods. Kinetic validation revealed that the kinetic triplet determined using the combined method described the experimental values more precisely. The reaction mechanism ascertained by the combined method was D5-D3 combination. The E_a value was strong function of conversion, and computed using isoconversional methods (Boswell, Flynn-Wall-Ozawa, Starink, Tang) between 169 and 268 kJ/mol. Entalphy, entrophy and Gibbs energy changes were computed in 164-259 kJ/mol, -37-141 J/(mol.K) and 173-187 kJ/mol ranges, respectively. The comprehensive pyrolysis index values were also calculated, and shown to increase with increasing heating rate.

DFT study of new organic materials based on PEDOT and 4-[2-(2-N, N-dihydroxy amino thiophene) vinyl] benzenamine

In the present study, we theoretically determine the optoelectronic, electronic, nonlinear optical (NLO) and thermodynamic properties of new materials from the conjugated organic polymer poly (3,4-ethylenedioxythiophene) (PEDOT) doped with halogens (fluorine and chlorine), combined with the organic semiconductor 4-[2-(2-N, N-dihydroxy amino thiophene) vinyl] benzenamine (DATVB). The molecular geometry of the ground state, the optoelectronics and electronic parameters have been calculated by combining the 6-311++G (d, p) basis set with various functionals of the density functional theory (DFT). The functionals B3LYP and CAM-B3LYP have been used for NLO parameters. The energy gaps obtained for all the compounds are less than 3.0 eV. These results clearly show that PEDOT and its derivatives can be considered as good semiconductors. They can be tested for use in the manufacture of organic solar cells (OSC) and organic light-emitting diodes (OLED). The first order hyperpolarizabilities of these PEDOT hybrid compounds are much higher than those of the reference compound for NLO applications, namely para-nitroaniline (p-NA), which opens up a new field of application for PEDOT in NLO devices. The thermodynamic parameters such as the zero-point vibrational energy (ZPVE), the enthalpy (H), the heat capacity at constant volume (c_v), the entropy (S) and the free energy (G) have been calculated and are reported herein.

Quantum mechanical investigations of mechanical and thermodynamic properties of SiC and ZrO2 ceramics

The mechanical and thermodynamic properties of β and α structures of SiC and also monoclinic and cubic structures of ZrO₂ have been considered via first-principles investigations based on the ultrasoft pseudopotential plane-wave DFT method. The calculated lattice constants, elastic constants, and mechanical properties of all the structures are in agreement with earlier DFT works and experimental reports, which show that the applied method is applicable. Also, the pressure-dependency performances of thermodynamic and mechanical properties of cubic structures of ZrO₂ and SiC, from 0 to 50 Gpa pressure, have been studied. The obtained elastic constants and mechanical properties of both structures increase with the enhancement of pressure. These results show that SiC is more difficult to be compacted as pressure increases. The thermodynamic properties of these structures show that variations of thermodynamic properties with temperature and pressure for ZrO₂ are slightly higher than SiC.

The study of spectroscopy and vibrational assignments of high nitrogen material 1,1'-azobis-1,2,3-triazole

Benefiting from the new strategy of oxidative azo coupling of the N-NH₂ moiety, a series of energetic nitrogen-rich molecules with long catenated nitrogen chains have been successfully synthesized. As one of them, the synthesized 1,1'-azobis-1,2,3-triazole shows excellent thermal stability, great explosive performance, and special photochromic properties, which has caused widespread concern. To further characterize its performance, the structural, electronic, vibrational, mechanical, and thermodynamic properties of 1,1'-azobis-1,2,3-triazole were investigated based on the first-principles density functional theory calculations. The obtained structural parameters are consistent with previous results. We used the band structure, density of states, Mulliken charges, bond populations, and electron density to analyze the electronic properties and chemical bonding. The vibrational frequency regions (396.51-3210.12 cm^-1) were assigned to the corresponding vibrational modes. Furthermore, mechanical properties of 1,1'-azobis-1,2,3-triazole are also calculated. Finally, the thermodynamic properties of 1,1'-azobis-1,2,3-triazole were calculated, including the specific heat at constant volume C_v, temperature*entropy TS, enthalpy H, Gibbs free energy G, and Debye temperature Θ_D.

Thermodynamic properties and hysteresis loops in a hexagonal core-shell nanoparticle

We applied Monte Carlo simulation to investigate the thermodynamic properties and hysteresis loops of the hexagonal core-shell nanoparticle described by a ferrimagnetic mixed-spin (3/2, 5/2) Ising model. The results revealed the significance of the single-ion anisotropy, exchange coupling, external magnetic field in dominating various thermodynamic quantities and hysteresis loops. We obtained the variation of the critical temperature with various parameters. Under certain parameter conditions, the system may exhibit rich multiple-loop hysteresis behaviors, depending on the competition among the physical parameters.

Theoretical study of the chemical reactivity of a class of trivalent phosphorus derivatives towards polyhaloalkanes: DFT study

In the current work, the chemical reactivity of some trivalent phosphorus derivatives R₂PR^' towards polyhaloalkanes CCl₃POR ' '₂ was studied by the quantum method DFT/B3LYP/6-311G(d,p). The introduction of substituents for the trivalent phosphorus derivative and polyhaloalkane allowed us to have more information on these reactions. On the one hand, the calculation of reactivity indices derived from the DFT/B3LYP/6-311G(d,p) method and the gap_{LUMO - HOMO} show that trivalent organophosphorus derivatives behave as nucleophiles, while polyhaloalkanes act as electrophiles. On the other hand, the calculation of the activation barrier and the determination of the free enthalpy variation prove that the kinetic and thermodynamic products of these reactions result from the nucleophilic attack of the phosphorus atom on the chlorine halogen. All these theoretical predictions are in very good agreement with the experimental results.

First-principles calculation of electronic, vibrational, and thermodynamic properties of triaminoguanidinium nitrate

In recent years, the important energetic material triaminoguanidinium nitrate (TAGN) has been widely used, and the process of synthesizing TAGN has become more and more perfect. However, there are relatively few theoretical studies on TAGN. This paper uses first-principles calculations to more systematically study the crystal structure, and electronic, vibrational, and thermodynamic properties of TAGN. The calculation results show that the calculated unit cell parameters are relatively consistent with the values obtained through X-ray diffraction experiments. This article describes in detail the state density of the valence electrons of each atom. By analyzing the vibrational properties of TAGN crystal, the vibration mode corresponding to each optical wave is obtained. At the same time, the vibration mode of each peak in the Raman spectrum and the infrared spectrum is described in detail. Then, the calculated value is compared with the experimental value; it can be seen that the error is relatively small. According to the vibration characteristics, a series of thermodynamic functions such as enthalpy (H), Debye temperature (Θ), free energy (F), and entropy (S) are calculated. These thermodynamic functions can provide a certain reference for future research.

Study of Bohr Mottelson Hamiltonian with minimal length effect for Woods-Saxon potential and its thermodynamic properties

The Bohr Mottelson Hamiltonian with the variable of β collective shape for the Woods-Saxon potential in the rigid deformed nucleus for γ=0 and the X(3) model was investigated in the presence of the minimal length formalism. The Bohr Mottelson Hamiltonian was solved approximately by proposing a new wave function. The q-deformed hyperbolic potential concept such that the rigid deformed nucleus of the Bohr Mottelson equation in the minimal length formalism for Woods-Saxon potential was used, so that the equation was reduced to the form of Schrodinger-like equation with cotangent hyperbolic potential. The hypergeometric method was used to obtain the energy spectra equation and the unnormalized wave function of the system. The results showed that the energy spectra were affected by the quantum number, the minimal length parameter, and the atomic mass. The larger mass of the atom affected the energy spectra to decrease, the increase of the values of the minimal length affected the increase of the energy spectra of all atoms. The energy spectra were used to determine the thermodynamic properties including the partition function, mean energy, specific heat, free energy, and entropy of the quantum system with the help of the imaginary error function.

The structural, electronic, and optical properties of hydrofluorinated germanene (GeH1-xFx): a first-principles study

The structural, electronic, and optical properties of hydrofluorinated germanene have been studied with different occupancy ratios of fluorine and hydrogen. The hybridization of H-1 s and Ge-4p orbitals in hydrogenated germanene and F-2p and Ge-4p orbitals in fluorinated germanene plays a significant role in creating an energy bandgap. The binding energy and phonon calculations confirm the stability of hydrofluorinated germanene decreases with the increase of the F to H ratio. The value of the energy bandgap decreased by increasing the ratio of F and H. The optical properties have been studied in the energy range of 0-25 eV. Six essential parameters such as energy bandgap (E_g), binding energy (E_b), dielectric constant ε(0), refractive index n(0), plasmon energy (ћω_p), and heat capacity (C_p) have been calculated for different occupancies of H and F in hydrofluorinated germanene for the first time. The calculated values of structural parameters agree well with the reported values.

Solutions of the Schrödinger equation and thermodynamic properties of a combined potential

The solution of the radial Schrödinger equation was obtained using the methodology of supersymmetric approach with a combination of modified generalized Pöschl-Teller potential and inversely quadratic Yukawa potential model. The non-relativistic ro-vibrational energy spectra and the corresponding wave functions were obtained and numerical results were generated for some states. The variation of energy of the combined potential and the subsets potentials with the screening parameter for various quantum number were graphically studied. The effect of the potential parameters on the energy for different states was also studied numerically. For more usefulness and applications of the work, the vibrational partition function and the various thermal properties like mean energy, Helmholtz energy, heat capacity and entropy were calculated. The behaviour of the thermodynamic properties with respect to temperature change for various quantum number and maximum quantum states were examined in detail. The temperature has positive effect on all the thermal properties except the free energy.

The Change Mechanism of Structural Characterization and Thermodynamic Properties of Tannase from Aspergillus niger NL112 Under High Temperature

Tannase from Aspergillus niger NL112 was purified 5.1-fold with a yield of 50.44% via ultrafiltration, DEAE-Sepharose Fast Flow column chromatography, and Sephadex G-100 column chromatography. The molecular weight of the purified tannase was estimated as 45 kDa. The optimum temperature and pH for its activity were 45 °C and 5.0, respectively. The results of circular dichroism, FT-IR (Fourier transform infrared) spectroscopy, and fluorescence spectra indicated that high temperature could lead to the change of tannase secondary and tertiary structures. Tannase had a greater affinity for tannic acid at 40 °C with a K_m value of 2.12 mM and the greatest efficiency hydrolysis (K_cat/K_m) at 45 °C. The rate of inactivation (k) increased with the increase of temperature and the half-life (t_1/2) gradually decreased. It was found to be 1.0 of the temperature quotient (Q₁₀) value for tannic acid hydrolysis by tannase. The thermodynamic parameters of the interaction system were calculated at various temperatures. The positive enthalpy (ΔH) values and decreasing ΔH values with the increase of temperature indicated that the hydrolysis of tannase was an endothermic process. Our results indicated that elevated temperature could change the tertiary structure of tannase and reduce its thermostability, which caused a gradual decrease of tannase activity with an increase in temperature.

Density functional theory for the thermodynamic gas-phase investigation of butanol biofuel and its isomers mixed with gasoline and ethanol

Herein, we present the results of our study on the thermodynamic properties of the isomers of butanol (n-butanol, 2-butanol, i-butanol, and t-butanol) to evaluate their thermodynamic potential as a complementary biofuel and/or substitute for ethanol and gasoline. The Gaussian09W software was used to perform molecular geometry optimization calculations using density functional theory with the B3lyp hybrid function using the base set 6-311++g(d,p) and the compound methods G3, G4, and CBS-QB3. Calculations of the fundamental frequency of the molecules were performed to obtain the molecular vibration modes for the respective frequencies. These calculations provided thermodynamic parameters such as the entropy, enthalpy, and specific molar heat at constant pressure, all as a function of the temperature. The parameter values obtained by each method were compared to the experimental values available in the literature. The results showed good accuracy, especially those obtained at the B3lyp/6-311++g(d,p) level for n-butanol. The error between the theoretical and experimental values for the combustion enthalpy of n-butanol was less than 4% at 298.15 K; due to the good prediction of its thermodynamic properties, we used n-butanol as a model for the prediction of other thermodynamic properties. We started a molecular docking study of four ligands, namely, n-butanol, ethanol, propanol, heptane, isooctane, and methanol interacting with butanol isomers. The highest values of affinity energy found were for N-butanol. The possible formation of hydrogen bonds, associations by means of London forces, hydrogen, and alkyl interactions were analyzed. n-Butanol was added to ethanol-gasoline mixtures in the temperature range of 298.15 to 600 K and the results suggest that n-butanol has a higher calorific value than gasoline-ethanol mixtures in G30E, G40E, G50E, G60E, G70E, G80E, G90E, and E100 blends. As such, n-butanol releases greater amounts of heat during combustion and is thus a viable alternative to biofuels.

Polymorphism of benzylthiouracil, an active pharmaceutical ingredient against hyperthyroidism

The crystal structures of dimorphic benzylthiouracil, a drug against hyperthyroidism, have been redetermined and the atom coordinates of the two independent molecules of form I have been obtained for the first time. The dimorphism convincingly demonstrates the conformational versatility of the benzylthiouracil molecule. It has been established through calorimetric studies that the low-temperature form II transforms endothermically (Δ_II→IH = 5.6(1.5) J g^-1) into form I at 405.4(1.0) K. The high-temperature form I melts at 496.8(1.0) K (Δ_I→LH = 152.6(4.0) J g^-1). Crystallographic and thermal expansion studies show that form II is denser than form I, leading to the conclusion that the slope of the II-I equilibrium curve in the pressure-temperature phase diagram is positive. It follows that this dimorphism corresponds to a case of overall enantiotropic behaviour, which implies that both solid phases possess their own stable phase region irrespective of the pressure. Moreover, form II is clearly the stable polymorph under ambient conditions.

Cubane and cubanoid: Structural, optoelectronic and thermodynamic properties from DFT and TD-DFT method

In this paper, we report structural, electronic and optical properties of cubane (C₈H₈) and cubanoids (cubane-like molecules) using Density Functional Theory (DFT). The cubanoids are cubanes for which Carbon atoms have been substituted by Nitrogen (N), Phosphorus (P), Boron (B), Silicon (Si), Arsenic (As), Antimony (Sb) or Bismuth (Bi) atoms. These molecules presented exceptional stability with several different symmetry point groups, being the majority T_d. All calculated vibrational frequencies are positive for any studied molecules indicating that all these structures are in a stable state. The HOMO-LUMO gaps and DOS were calculated converged towards to values between 1.87 eV and 5.61 eV, actually showing promising electronic properties (Just for comparison, the cubane energy gap is 7.50 eV). The optical absorptions were also calculated for the cubanoid structure using the Time-Dependent Density Functional Theory (TD-DFT). Their dependence on the wavelength is analyzed, where five of theses structures absorb on the visible region. Finally, the extrapolation of thermodynamic properties indicates that these cubanoid could be potentially synthesized spontaneously, where four structures, the synthesis would occur for temperatures below 400 K, while for Si₄Bi₄H₄ structure, the synthesis would occur at room temperature.

Sono-hydro priming process (ultrasound modulated hydration): Modelling hydration kinetic during paddy germination

Application of ultrasound technology in modulating the hydration process during paddy germination was analyzed in this study. The effect of hydropriming (24 h) and sono-hydro priming (ultrasound priming, 12 h) on the hydration behaviour of paddies was determined at different temperatures (25-40 °C). Ultrasound pulse was applied for 10 min after every one hour for sono-hydro priming. Germination potential and microstructure analysis of treated paddies were also performed. Downward concave curve observed in hydration process of paddies indicates initial high-water absorptionthrough diffusion process. Sono-hydro priming process showed higher hydration rate compared to hydropriming. The changes in moisture content during hydration processes fitted to theoretical (Fick's model) and empirical model (Peleg model) exhibited high regression coefficient (R² > 0.95) indicating suitability for predicting hydration behaviour in both paddies for germination. The Peleg model adequately predicted saturation moisture content and sono-hydro priming efficiently increased the water absorption rate. Effective moisture diffusivity determined from Fick's diffusion model increased for sono-hydro priming. Activation energy estimated from effective moisture diffusivity required in sono-hydro priming (E_a = 20.32 and 19.19 KJ/mol respectively) for pigmented rice and non-pigmented rice was lower than hydropriming (E_a = 27.11 and 32.15 KJ/mol respectively). Both hydration processes were endothermic and non-spontaneous inferred from thermodynamic properties. Sono-hydro priming exhibited < 95% germination potential with shorter soaking time (12 h) owing to the high mass transfer rate. SEM micrograph revealed water absorption through various micro-cavities during sono-hydro priming. Thus, sono-hydro priming potentially reduced the soaking process (approximately 50%) with higher germination rate in paddies beneficial for commercial malting of grains.

Gaseous complex hydrides NaMH4 and Na2MH5 (M = B, Al) as hydrogen storage materials: a quantum chemical study

Metal hydrides are feasible for energy storage applications as they are able to decompose with hydrogen gas release. In this work, gaseous complex sodium hydrides, NaMH₄ and Na₂MH₅ (M = B or Al), have been investigated using DFT/B3P86 and MP2 methods with 6-311++G(d,p) basis set; the optimized geometry, vibrational spectra and thermodynamic (TD) properties have been determined. Based on TD approach, a stability of the hydrides to different dissociation channels is analysed; the enthalpies of formation ∆_fH°(0) of gaseous species have been obtained: - 1 ± 17 kJ mol^-1 (NaBH₄), 91 ± 14 kJ mol^-1 (NaAlH₄), - 13 ± 16 kJ mol^-1 (Na₂BH₅), and 71 ± 16 kJ mol^-1 (Na₂AlH₅). The complex hydrides are confirmed to produce gaseous products with hydrogen gas release at elevated temperature, whereas heterophase reactions, with NaH and B/Al products in condensed state, are predicted to occur spontaneously at lower temperature. Graphical abstract.

Crystal structure, chemical reactivity, kinetic and thermodynamic studies of new ligand derived from 4-hydroxycoumarin: Interaction with SARS-CoV-2

Currently, Covid-19 pandemic infects staggering number of people around the globe and causes a high rate of mortality. In order to fight this disease, a new coumarin derivative ligand (4-[(pyridin-3-ylmethyl) amino]-2H-chromen-2-one) (LTA) has been synthesized and characterized by single-crystal X-ray diffraction, NMR, ATR, UV-Visible and cyclic voltammetry. Chemical reactivity, kinetic and thermodynamic studies were investigated using DFT method. The possible binding mode between LTA and Main protease (Mpro) of SARS-CoV-2 and their reactivity were studied using molecular docking simulation. Single crystal X-ray diffraction showed that LTA crystallizes in a monoclinic system with P2 1  space group. The reactivity descriptors such as nucleophilic index confirm that LTA is more nucleophile, inducing complexation with binding species like biomolecules. The kinetic and thermodynamic parameters showed that the mechanism of crystal formation is moderately exothermic. The binding energy of the SARS-CoV-2/Mpro-LTA complex and the calculated inhibition constant using docking simulation showed that the active LTA molecule has the ability to inhibit SARS-CoV-2.

An analysis of structural phase transition and allied properties of cubic ReN and MoN compounds

The present work aims at the study of structural, elastic, electronic, and thermodynamic properties of transition metal nitrides: ReN and MoN in the zinc-blende (B3) phase. The plane wave pseudopotential and norm-conserving pseudopotential have been applied in Quantum-Espresso code based on density-functional theory (DFT). The results show a first-order phase transition from B3 to B1 (rock-salt) structure at 42 GPa and 2.5 GPa for ReN and MoN respectively. The elastic behaviors of these compounds are also unfolded in this work. The brittleness of the ReN and ductility of MoN is identified with the help of Pugh's index and Poisson's ratio. The strong anisotropic behaviors of both compounds are detected under the influence of pressure. The electronic and bonding features of proposed compounds are evaluated by means of band structures, the density of states (DOS), Fermi surface, and charge density plots. The obtained results forecast the metallic behavior and ionic bonding of ReN and MoN in both phases: B3 and B1. Additionally, various thermodynamic properties are also investigated under high pressures and temperatures (from 0 to 2000 K). Conceivably, these properties are reported for the first time in the B3 structure of these compounds and will be useful for many applications in modern technologies as well.

Characterization of the ergometric properties of commercial bioactive dairy peptides

The thermodynamic properties of bioactive peptides provide insights into their functional behavior and their biological efficacy. We conducted precise analyses of the density, the ultrasonic velocity and the relative attenuation of serial dilutions of three commercial dairy peptides prepared by enzymatic methods. From these we determined the partial specific volume and the partial specific adiabatic compressibility coefficient for the peptides. At concentrations greater than ~2.5 ​mg ​mL⁻¹, the apparent values for specific volume and adiabatic compressibility were constant, differing between the three peptides at ±3% for specific volume and ±70% for compressibility. Both specific volume and adiabatic compressibility were highly dependent on concentration, indicating the importance of precise low concentration measurements to obtain correct values for these thermodynamic parameters. From these parameters it was apparent that restructuring of water molecules around the peptides (and their associated counterions) led to compact solutes that were also incompressible. These thermodynamic analyses are critical for understanding how the properties and the beneficial effects of bioactive peptides are influenced by their chemical environment.

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Dissolved dairy peptide properties distinguishable from ergometric analyses.

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Specific volume and adiabatic compressibility evaluate bioactive peptide hydration.

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Commercial bioactive dairy peptides are compact and incompressible.

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Compactness and incompressibility of peptide affected by hydrogen-bonding amino acids.

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Solution concentration affects values of measured thermodynamic parameters.

Thermal and hydrodynamic properties of coronavirus at various temperature and pressure via molecular dynamics approach

COVID-19 is an epidemic virus arising from a freshly discovered coronavirus. Most people involved with the coronavirus will experience slight to moderate respiratory disease and recover without needing particular therapy. In this work, the atomic stability of the coronavirus at different thermodynamic properties such as temperature and pressure, was studied. For this purpose, the manner of this virus by atomic precession was described with a molecular dynamics approach. For the atomic stability of coronavirus description, physical properties such as temperature, total energy, volume variation, and atomic force of this structure were reported. In molecular dynamics approach, coronavirus is precisely simulated via S, O, N, and C atoms and performed Dreiding force field to describe these atoms interaction in the virus. Simulation results show that coronavirus stability has reciprocal relation with atomic temperature and pressure. Numerically, after 2.5 ns simulation, the potential energy varies from - 31,163 to - 26,041 eV by temperature changes from 300 to 400 K. Furthermore, this physical parameter decreases to - 28,045 eV rate at 300 K and 2 bar pressure. The volume of coronavirus is another crucial parameter to the stability description of this structure. The simulation shows that coronavirus volume 92% and 14% increases by 100 K and 2 bar variation of simulation temperature and pressure, respectively.

Effect of sodium chloride on the thermodynamic, rheological, and microstructural properties of field pea protein isolate/chitosan complex coacervates

The effect of increasing sodium chloride concentration (c_NaCl, 0-0.4 M) on the formation and rheological and microstructural properties of field pea protein isolate (FPPI)/chitosan (Ch) complex coacervates was investigated. The maximum turbidity and zeta potential of FPPI/Ch mixtures consistently decreased with the increasing c_NaCl. The tertiary conformation of FPPI was altered to facilitate the aggregation of FPPI/Ch complexes via hydrophobic interactions. Changes in thermodynamic parameters during the titration of FPPI with Ch confirmed the addition of NaCl could cause the inhibition of electrostatic complexation and the induction of non-Coulombic interactions. FPPI/Ch complex coacervates exhibited first enhanced and then weakened viscoelastic properties and an initially tightened and then a loosened microstructure as the c_NaCl increased. In summary, appropriate c_NaCl favors the formation of FPPI/Ch complex coacervates with improved functionalities via the coordination of promoted hydrophobic interactions and inhibited electrostatic attractions, facilitating the application of this protein ingredient in food development.

Determination of the structural, electronic, optoelectronic and thermodynamic properties of the methylxanthine molecules theophylline and theobromine

RHF and DFT (wB97XD and B3LYP) methods with the 6-31++G** basis set have been used to study structural, optoelectronic and thermodynamic properties of Theophylline and Theobromine. Dipole moment, average polarizability, anisotropy, first-order molecular hyperpolarizability, second-order molecular polarizability, HOMO and LOMO energy gap, molar refractivity, chemical hardness, chemical softness, electronic chemical potential, electronegativity, electrophilicity index, dielectric constant, electric susceptibility, refractive index and their thermodynamic properties have equally been calculated. To understand the vibrational analysis of our system, IR and RAMAN frequencies were calculated and described. Results reveal that molecules can have applications in linear and nonlinear optical devices, photonic devices and in molecular electronics. Equally, from dipole moment, average polarizability, anisotropy, first-order molecular hyperpolarizability, second-order molecular polarizability, HOMO and LOMO energy gap, molar refractivity, chemical hardness, chemical softness, electronic chemical potential, electronegativity, electrophilicity index and literature we suggest that Theophylline and Theobromine be consider as candidates for the treatment of COVID-19 and other respiratory diseases.

A molecular dynamics study on the thermal properties of carbon-based gold nanoparticles

Due to unique features in surface activity, thermal stability, electrical and thermal conductivity, and compatibility with biomolecules such as DNA and proteins, carbon-based nanoparticles are raised potential as a candidate for various applications such as catalytic processes, drug delivery, light, and electrical engineering. Based on this premise, thermodynamic features of pure, graphene, and carbon nanotube (CNT)-based gold nanoparticles (AuNPs) are investigated using molecular dynamics approach. Melting, heat capacity, thermal conductivity, contact angle of molten AuNPs, and phase transition are calculated as indicators of thermodynamic properties of pure and carbon-based AuNPs. Simulation results indicate that the presence of a carbon platform and its contact surface area has a significant role in the thermodynamic properties of AuNPs and leads the phononic heat capacity and thermal conductivity to decrease for AuNPs. The platform also causes the melting point temperature of AuNPs to increase. The melting of gold on the carbon base is of the first-order type. In addition, contact angle for molten AuNPs on the Graphene is significantly higher than the one on the CNT due to more contact area on the Graphene substrate.Graphical abstract .

Molecular characterization, catalytic, kinetic and thermodynamic properties of protease produced by a mutant of Bacillus cereus-S6-3

The proteolytic strain Bacillus cereus-S6-3 was subjected to mutagenic treatments viz. UV irradiations and methyl methane sulfonate (MMS). The obtained mutant strain, B. cereus-S6-3/UM90 showed 1.34 fold over the parent strain. Molecular characterization of proteases from the parent (PP/S6-3) and mutant (PM/UM90) strains indicated that they were consisted of two domains and binds a zinc ion and 4 calcium ions in the active site. Amino acid sequence alignment of PM/UM90 protease showed 19 amino acid residues were substituted compared to that of the wild-type enzyme. However, both proteases contained equal number of aromatic and hydrophobic amino acids. Protease from PM/UM90 showed an effective improvement in thermal properties in terms of reaction temperature, t_1/2, the values of k_d, activation energy (E_a), and decimal reduction time (D) within the temperature range from 60 to 80 °C. In addition, the kinetic and thermodynamic parameters for substrate hydrolysis (i.e., K_m, V_max, ΔH*, ΔG*, ΔS*, k_cat, V_max/K_m, k_cat/K_m, ΔG*_E-T and ΔG*_E-S) showed a significant improvement of the catalytic efficiency for PM/UM90 protease. Furthermore, the correlation between thermodynamic properties and the patterns of amino acid substitution of wild-type enzyme to has been discussed.

Molecular dynamics simulation of polystyrene copolymer with octyl short-chain branches in toluene

In this study, dimensional, conformational and dynamic behaviors of a short-chain branched styrene/1-octene copolymer chain with different 1-octene percentages, i.e., 0, 2, 4 and 6%, in toluene are investigated at the temperature of 298.15 K via molecular dynamics simulation. The chain dimensions and flexibility in the solvent are evaluated by calculating the radius of gyration (R_g), end-to-end distance (<r₀>), surface area (A_ch), and volume (V_ch) of the copolymer chain. The mean square displacement (MSD) and diffusivity coefficient for each copolymer chain are measured to determine its dynamic behavior and mobility in aromatic media. To consider the effect of increasing the 1-octene co-monomer percentage on the copolymer chain affinity to the solvent molecules, the interaction energy (E_int) and Flory-Huggins (FH) interaction parameter are calculated for each equilibrated solution model. The simulation results indicate that the co-monomer level increment in the copolymer structure reduces the chain R_g amount and its interaction with the solvent. The <r₀> of the chain increases up to 4% co-monomer content, while further co-monomer content decreases the <r₀> value. Additionally, the viscosity of the equilibrated dilute solutions is calculated via non-equilibrium molecular dynamics simulation (NEMD). Moreover, the steric hindrance of the copolymers and the solvent molecules capturing in the dilute solution is determined via radial distribution function (RDF) analysis. Helmholtz free energy and the system entropy changes are calculated to evaluate the tendency of the copolymer to the solvent molecules and its dilute solution irregularity, respectively. Graphical abstract The figure shows the variations trend of the poly(styrene-co-1-octene) chain dimensions in toluene aromatic solvent by increasing the 1-octene content (x), after the equilibration state. Red and blue colors represent the carbon atoms of the copolymer chain backbone and 1-octene side chains, respectively. The styrene rings and the hydrogen atoms of the chains were removed for better view.

Vibrational, thermodynamic, and dielectric properties of ε-CL-20: first-principles calculations

The DFT theory is used to investigate the vibration forms of ε-CL-20 by discussing the phonon DOS and infrared and Raman spectra. By observing them, the detailed vibration forms can be obtained, and the vibrations are different in the different regions. Our calculated vibrational results are consistent with previous data. In order to deeply comprehend CL-20, we also investigate the thermodynamic properties, finding that entropy, enthalpy, Debye temperature, and heat capacity are increased with the rising temperature and the vibrational free energy decreases with the increasing temperature. The ε_xx, ε_yy, and ε_zz are similar, which reflects the small anisotropy among [100], [010], and [001]. Moreover, it can be noticed that the major contribution for static dielectric constants originates from the electronic contribution.

A first principle study of the structural, electronic, and temperature-dependent thermodynamic properties of graphene/MoS2 heterostructure

After an initial assessment of the structural and electronic properties of graphene, monolayer MoS₂, and graphene/MoS₂ bilayer hetero-structure, the temperature-dependent thermodynamic properties of graphene/MoS₂ bilayer hetero-structure are examined by using density functional theory calculations. The structure, bandgap, partial density of states, and thermodynamic properties of graphene, monolayer MoS₂ and graphene/MoS₂ system are investigated and analyzed. Findings from the present study are in good agreement with the previously reported theoretical and experimental studies. Monolayer MoS₂ and graphene form a stable Van der Waals heterostructure owing to their negative binding energy, and the system acts as a zero-bandgap semiconductor. Debye temperature and the heat capacity of graphene, MoS₂ monolayer, and graphene/MoS₂ system are calculated from phonon dispersion relations to be 2100 K, 600 K, and 1400 K, and 0.7 J/g.K, 0.218 J/g.K, and 0.46 J/g.K, respectively. Introduction of graphene into the MoS₂ semiconductor is, therefore, found to improve the overall thermodynamic properties of the composite as graphene preserved its superior thermal properties. The findings will be beneficial to calculate thermal conductivity of the graphene/MoS₂ heterostructure for minimizing the temperature effect in electronic or optoelectronic devices.

Equation of state and thermodynamic properties for mixtures of H 2 O , O 2 , N 2 , and CO 2 from ambient up to 1000 K and 280 MPa

Supercritical water oxidation (SCWO) is an effective technique to treat wet organic wastes. Its modeling requires an accurate calculation of thermodynamic properties. In this work an equation of state (EOS) is proposed which accurately predicts the thermodynamic state of mixtures of water, oxygen, nitrogen, and carbon dioxide for a wide range of compositions, temperatures, and pressures including supercritical conditions. The EOS includes a volume translation, an evolved α -function and non-quadratic mixing rules. The introduced parameters are regressed to experimental data. From the pressure-explicit EOS, enthalpy, specific heats at constant volume and constant pressure, and fugacity coefficients are derived and calculated. The binary mixtures H 2 O / O 2 , H 2 O / N 2 , H 2 O / CO 2 , N 2 / CO 2 as well as the ternary mixture H 2 O / O 2 / N 2 are well predicted by the proposed EOS with relative errors below 10% and 15%, respectively. The region of low temperature and high pressure is most difficult to predict with relative errors up to 20%.

First-principles study of structural, electronic, magnetic, thermodynamic and mechanical properties of ferromagnetic Mn2MoAl Heuslar alloy

The Mn-based Mn₂MoAl type ternary Heusler alloy is of particular interest due to its potential ferromagnetic properties and high spin-polarization. The present paper aims to explore the physical properties of this new alloy for its possible technological applications and also provide theoretical basis to the future experiments. The electronic structure, magnetism, and elastic properties of the alloy are studied by using first-principles calculations based on density functional theory (DFT), along with calculation of thermodynamic properties within quasi-harmonic approximation. The structural analysis predicts the optimized lattice constant of 5.90 Å and the ferromagnetic stable state. The electronic band structure calculations at GGA-level reveal that present alloy is nearly half-metal with spin-polarization up to 94% at the Fermi level, whereas, GGA + U calculations reveal Mn₂MoAl alloy to be a quite spin polarized metal. The calculated total magnetic moment M_t of the unit-cell is found to be 1.04 μ_B, which nearly obeys M_t = │Z_t-24│formula. The individual Mn, Mo and Al atoms carry magnetic moment of 0.70 μ_B, -0.28 μ_B, -0.01μ_B, respectively. Employing quasi-harmonic approximation, interesting thermodynamic properties of the alloy have been investigated. Furthermore, the elastic and mechanical properties have been investigated. The results confirm that Mn₂MoAl alloy is mechanically stable, ductile, anisotropic, with metallic inter-atomic bonding and is expected to be beneficial for the spintronic technology.

Structural, electronic, optical, and thermodynamic properties of hydrochlorinated Janus graphene: a first-principle study

The structural, electronic, optical, and thermodynamic properties of hydrochlorinated Janus graphene (J-GN) have been studied using first-principle DFT calculations. The band structure and density of states have been discussed. The values of 16 parameters have been calculated for the most stable chair (C) structure of hydrochlorinated J-GN. Out of sixteen, 12 parameters such as static dielectric constant ε(0), refractive index n(0), birefringence Δn(0), threshold conductivity σ(ω), plasmon energy (ћω_p), binding energy (E_b), cohesive energy (E_c), enthalpy (E), entropy (S), free energy (F), heat capacity (C_p), and Debye temperature (Θ_D) have been calculated for the first time. The structural and electronic properties have also been studied at 0-GPa, 25-GPa, 35-GPa, 50-GPa, 90-GPa, 100-GPa, 150-GPa, 200-GPa, and 220-GPa external pressures. The hydrochlorinated J-GN shows the direct band gap behavior up to 35 GPa and becomes indirect band gap after 35 GPa. Further, it shows a stable structure up to 90 GPa and becomes unstable at 100-GPa external pressure. The calculated values of all parameters agree well with the available reported values of some parameters at 0 GPa.