Current Physical Chemistry - Volume 13, Issue 2, 2023

Background: Here, the inverse protein folding problem is approached from the viewpoint of the entropic index q. We present a brief overview of the problem. Further, we provide general information about the three-dimensional structure of proteins and the universal characteristics of the folding process. Methods: We explain how the stereochemical model was conceived. Our main objective is to change how Monte Carlo (MC) simulations are performed. We replace the Boltzmann weight with the Tsallis weight in order to achieve better sampling. This change leads to the q Monte Carlo method (MCq). There are two main ways to employ the index q: one is to set it as a fixed parameter (MCq*), and the other is to set it as an autonomous variable associated with the instantaneous molecular radius of gyration, a feature that is allowed by the Beck-Cohen superstatistics. In addition, we propose a meaningful physical interpretation for the index q. Furthermore, we explain how to assemble amino acid sequences for the inverse problem. Results: We present several results and discuss the implications associated with the MC and MCq methods. The latter method is an efficient approach to tracking down folding intermediate conformations, which can enable us to better find and define folding pathways for successive configurations of a polymeric chain kept in solution at the same macroscale temperature, T. Conclusion: We have explained how and why protein kinetics becomes significantly more advantageous when we employ q ≠ 1. However, this is only possible if we set the correct upper value of qmax.

Background: This paper reports the thermal decomposition mechanisms of five pure honey samples of Indian origin using Differential Scanning Calorimetry (DSC) and Euro Vector Elemental Analyzer (EVEA) techniques. Methods: We have identified three transition temperatures along with a change in specific heat capacity (ΔCp), change in enthalpy (ΔH), and Gibbs free energy (ΔG) of these samples. Finally, samples were subjected to thermal elemental analyses to quantify the released amount of O, N, C, and H. Since glucose, fructose, and sucrose are the principal ingredients, they are present in the honey sample, along with good numbers of other organic molecules in small quantities. In addition, we have also recorded the C, H, and O percentages of pure glucose, fructose, and sucrose powders and correlated the ratio of C/H and C/O with honey samples. Results: The decomposition temperature for honey samples lies between 113.83°C and 127.07°C range. The ratios of these elements help us to ascertain the purity of these samples as well as to identify the dominating percentage of principal ingredients present in the given honey sample. Conclusion: The obtained experimental results were further used to identify the source of origin and medicinal quality and stability of honey samples.

Background: Additions of water monomer (H2O) to simplest ketene, i.e., H2C=C=O (mentioned as ketene, henceforth) in the Earth's atmosphere results in the formation of acetic acid. However, this reaction is not feasible under tropospheric conditions due to the high reaction barrier amounting to nearly 40 kcal mol^-1. A Significant reduction of the barrier height (below 20 kcal mol^-1) is achieved upon addition of another H2O molecule as a catalyst. It is worth mentioning that like H2O and ammonia (NH3), H2S could also play an important role in the “loss mechanism” of various atmospherically important species such as ketones and aldehydes. Aims: This study aims to get insight into the energetics and kinetics of a reaction between ketene and H2S in the troposphere which has not been done before. Objective: Due to close similarity of H2O and H2S, studying the sulfolysis reaction between ketene and H2S could provide some interesting insights into the nature of various hydrogen bonded complexes of ketene as well as the impact on the products formed under the atmospheric conditions. Methods: The water and ammonia catalyzed gas-phase addition reactions of ketene with H2S has been investigated using CCSD(T)-F12a/cc-pVTZ-F12a//M06-2X/6-311++G** level of theory. In this study, rate constants for all possible reaction channels are calculated using transition state theory. Results: It is found that, under tropospheric conditions at 298 K and 1 atm, the rates via catalyzed reaction channels are significantly faster than those via uncatalyzed reactions. Between the two catalysts, ammonia acts as far better catalyst than water for this reaction. However, since the concentration of water is significantly larger than ammonia, the effective rate of water catalyzed reaction becomes higher than that of ammonia catalyzed reaction. Combustion is a major source of ketene in atmosphere. Under combustion conditions such as in the presence of air and at or above ignition temperature, the ammonia catalyzed channel is faster below 1500 K, while the uncatalyzed reaction channel becomes faster above that temperature. Conclusion: Results from the present study show that the barrier for thioacetic acid formation through uncatalyzed sulfolysis of ketene via faster C=O addition pathway is substantially high as 40.6 kcal mol^-1. The barrier height of the two transition states TS1 and TS2 are 19.7 and 13.8 kcal mol^-1 for water catalyzed reaction and 14.4 and 7.2 kcal mol^-1 for ammonia catalyzed reaction. Thus, ammonia has appreciably lowered the barrier height compared to water as catalyst. It has been observed that the hydrolysis reaction is more probable than the sulfolysis reaction under atmospheric conditions in the troposphere, but the ammonia catalysed sulfolysis is the fastest one at 298 K. The effective rate constant of the water catalysed hydrolysis reaction is found to be more than the ammonia catalysed reaction due to the higher monomer concentration of water than ammonia. Ammonia catalyzed reaction rate increases monotonously with increasing temperature. Further rate coefficient for uncatalyzed reaction is found to be dominant under combustion conditions, i.e., above 1500 K.

Background: Studies on the thermal decomposition of synthesized complexes have great importance for calculating the thermal stability and characterization of copper (II) soap complexes, and represent new investigations on the solution of environmental problems. Aim: The present research work aims to report new findings in the field of thermogravimetric analysis and biocidal studies for copper (II) groundnut complexes with urea and thiourea ligands. Objective: The objective of this study was to conduct the kinetic analysis of copper (II) soap complexes of nitrogen and sulphur-containing ligands with the help of a thermogravimetric analyser (TGA), as this technique is commonly applied for thermal analysis. Methods: In relevance of aforesaid applications, the present work deals with determining the different thermal degradation steps of newly synthesized copper (II) groundnut urea complex (CGU) and copper (II) groundnut thiourea complex (CGT) by using Coats- Redfern, Horowitz-Metzger, Broido, and Piloyan-Novikova equations for determining kinetic parameters, i.e., the energy of activation (E), rate constant, order of decomposition reaction, and pre-exponential factor (Z). Results: The results obtained from kinetic parameters were used to evaluate the thermodynamic parameters, i.e., entropy of activation (ΔS), enthalpy of activation (ΔH), and Gibbs free energy of activation (ΔG), corresponding to the activation by using previously mentioned equations. Kinetics of degradation for the synthesized complexes in solid state were studied using thermogravimetric analysis technique (TGA) in nitrogen atmosphere. Conclusion: The present study has discussed the biocidal activities of these complexes against Staphylococcus aureus and an explicit correlation between structure and biological activity has also been provided.

Background: The structural features allow cyclodextrins to form solid inclusion complexes (host–guest complexes) with wide variety of solid, liquid, and gaseous compounds as a guest. It is the utmost an astounding property of the cyclodextrins, and is commonly termed as molecular recognition. The process of formation of an inclusion complex of the cyclodextrins has been associated with the substitution of the water inside the hydrophobic cavity and the non–covalent bonding interactions of the guest in the hydrophobic host cavity. Objective: To study the thermal gravimetry analysis behaviour for α–cyclodextrin–clove oil, α–cyclodextrin–neem oil and β–cyclodextrin–clove oil adducts using TGA–DSC. To compute specific heat capacity at constant pressure, as a function of temperature for the studied systems. Methods: The thermal gravimetry analysis and differential scanning calorimetry techniques are used. Results: It is observed that the calculated Cp values from DSC curves are of low magnitude for α–CD–neem oil adduct as compared to that of individual constituents over the temperature range studied. An interesting pattern for the Cp values is found to emerge in case of α– CD–clove oil and β–CD–clove oil adducts wherein the calculated Cp values are higher in magnitude than for pure clove oil but are lower than that of the pure cyclodextrins. Conclusion: Using thermal methods, the attempt to understand the possibilities of molecular complex formation between cyclodextrins and medicinally important neem oil and clove oil is described. The crystals of inclusion compounds for clove oil and neem oil with α–CD and β–CD are synthesized. The results of TGA–DSC for the crystals are presented and analysed. Other: The results of neem oil–adducts have been explained in terms of binding of part of tri–glyceride linkages by 2–3 cyclodextrin molecules as neem oil is tri–glyceride and the adduct is having lower stability.