Physical Chemistry Research
Volume:11 Issue: 4, Autumn 2023

The interaction of the three planar porphyrins (L1), 5,10,15,20-tetrakis (1-ethyl-1-λ4-pyridine-4-yl) porphyrin (L2), and 5,10,15,20-tetrakis (1-methyl-1-λ4-pyridine-4-yl) porphyrin (L3), with G-quadruplex in the presence of Li+, Na+ , K+ , Rb+ ,Cs+ ,Ca2+ ,Mg2+ ions was studied by density functional theory and molecular dynamics simulation. Single point energy calculations were performed on sampled structures from molecular dynamics simulations. Sampling was performed by free energy landscape (FEL) method. Quantum calculations were performed by B3LYP density functional method and 6-31G basis function. Quantum descriptors frontier orbital energies, ionization energy, chemical species hardness, chemical potential and the number of transferred electrons were calculated. The results show that loops and sheets of G-quadruplex are involved in interaction with ligands. The stability of the complex between ligands and G-quadruplex in the presence of K+ and Na+ ions is greater than the stability of the complex in the presence of Cs+ and Mg2+ ions.

Molecular docking is applied to investigate interactions between 1638 approved drugs and the COVID-19 virus proteins (Spike, non-structural proteins NSP3, NSP7, NSP8, NSP9, NSP10, NSP12 (two binding sites), NSP15, NSP16, and NSP10-NSP16 complex), and the human angiotensin converting enzyme 2, ACE2 protein, and its Spike@ACE2 complex. Structures of these approved drugs are fully optimized with the universal force field (UFF) and their lowest energy conformations are used for docking on the (co)crystallized structures of the target proteins taken from the protein data bank (PDB). The docking procedure is performed in two stages and the results are evaluated based on four ranking indices or docking scores which measure comparative affinities of the studied drugs towards the COVID-19 virus proteins. Details of the positions, orientations and interactions of the first three highest-rank drugs in the binding pocket of the COVID-19 Spike, NSP7 and the human ACE2 proteins (as representatives) are visualized, analyzed and discussed. Based on the results of this molecular docking study, Vazegepant, Dasabuvir, Vitamin E, Fosamprenavir, Raltegravir, Canagliflozin, Biliverdin and Imatinib drugs can be considered promising for further molecular mechanics/dynamics simulations and then clinical studies, to accomplish the screening task.

SARS-CoV-2 has ravaged numerous in the world and it is at present a subject of research. In this study, we present two potential antiviral compounds for the treatment of this disease compared with the current reference drug. The objective of this work is geared at investigating two antiviral compounds as a promising therapy for the treatment of COVID-19. Molecular dynamics simulation and quantum theory of atoms in molecules (QTAIM) were employed to study the host-guest interaction and dynamics between the nCov protein and inhibitors. Results obtained after a triplicate run of 100 ns for each compound revealed that compound B2 showed better inhibitory potential with MMGBSA binding energy of -40.05 kcal/mol compared to the referenced drug. It is fascinating to note that B1 had a comparable binding potential with B2 suggesting some similarity in their inhibitory features. The QTAIM results showed that Laplacian 𝛻2ρ(r) and ellipticity (ε) are positive indicating a stable protein-ligand interaction. The order of stability agrees with the MM-GBSA energies trend obtained. The results show that B1 and B2 might arise as a hopeful therapeutic for the cure of Covid-19. Though, a crucial trial can be showed to authenticate this conclusion.

A perturbed hard-sphere chain equation of state (PHSC) is employed to predict the volumetric properties of some nanofluids containing Co3O4 in ethylene glycol (EG), SnO2 in EG, TiO2-anatase (-A) in EG, TiO2-rutile (-R) in EG, Al2O3 in EG/H2O, Sb2O5-SnO2 in EG/H2O, ZnO in polyethylene glycol (PEG)/H2O and CuO in H2O. Two temperature-dependent parameters in the proposed EoS were expressed in terms of molecular scaling constants  effective hard-sphere diameter, and ε; non-bonded interaction energy. The mentioned scaling constants were correlated with melting temperatures and densities which show the rationality of them. It is also indicated in this study without knowledge of potential energy function can able to illustrate the volumetric properties of nanofluids. Comparisons between the calculated liquid densities and the experimental values over the temperature range from 273.15 to 363.15 K and the pressure range from 0.1 to 45 MPa show that the average absolute deviation is 1.49%.

In the present work nanocomposite thin films have been prepared from poly(vinyl alcohol) (PVA) mixed with carbon nanotube (CNT) and carbon nano particles (CN) by casted method. The aim of this work produce texture of PVA with CNT and CN, the effect of CNT and CN content in thin films nanocomposite were measured by utilizing reflectance and absorbance data. The contents of CNT and CN reinforcement in the PVA matrix increase the optical properties such as reflectance, absorption coefficient, refractive index, extinction factor. But the transmittance and reflectance of thin films nanocomposite (PVA-0.05CNT, PVA-0.05CN, and PVA-0.025CNT-0.025CN) decreased, on anther hand the conductivity and dielectric constant were increased. The direct allowed transition of energy gap decreased from 4.0 eV to 2.9 eV, the indirect allowed transition of energy gap decreased from 4.4 eV to 2.8 eV, respectively. Urbach energy was increased from 1.238 eV to 2.711 eV after added the CNT and CN to PVA texture. The scanning electron microscope was used to evaluate the particle sizes of CNT and CN after preparation from the experimental method, which used in the PVA lattice to constitute the thin films nanocomposite (PVA-0.05CNT, PVA-0.05CN, and PVA-0.025CNT-0.025CN). The AFM test used to exhibit the roughness.

In this paper, the deactivation of the iron-based catalyst was assessed in the presence of Zr, Mn, and Cr promoters at two different loadings (5 and 10%). ANN/GPLE hybrid technique was applied for model determination and parameter estimation, as well as calculation of catalyst stability in the following conditions: temperature=280℃, H2/CO=2, and pressure=1.8 atm. The results showed that the promoter loading could change the deactivation behavior of the iron catalyst such that the first-order GPLE model well fitted the results at a promoter loading of 5%. For the case of 10% loading, the second-order GPLE model well fitted the results. A decline in the promoter loading on the iron catalysts enhanced the catalyst stability while decreasing its deactivation constant (kd). The promoter loadings of 5% and 10% indicated coking and sintering mechanisms, respectively. Among the different promoters at various loadings, Mn promoter at the loading of 5% could significantly prolong the catalyst life and enhance the stability of the iron catalyst. Zr increased the deactivation constant of Fe catalyst (kd) more than other promoters. ANN/GPLE technique is a promising method for the catalytic deactivation investigation, model determination, and parameter estimation.

TiO2-NPs were proven to be effective antibacterial agents.In this work,hydrothermal processing was used to synthesize TiO2-NPs and their photocatalytic, antibacterial activities were investigated.In addition, this research is explored the effects of magnetic field in the hydrothermal synthesis of TiO2-NPs.FE-SEM,UV-VIS,EDX andXRD were used to analyze the TiO2-NPs.The use of a magnetic field in the hydrothermal synthesis of TiO2-NPs (Treated) has led to the successful formation of TiO2 nano rode in shape compared with untreated particles (No magnetic field) which exhibit no definite shape.Antibacterial activities were performed against two of the most important bacteria strains that cause disease in humans: S. aureus and E. coli.The treated TiO2-NPs exhibited enhanced antibacterial activity when compared with untreated TiO2-NPs samples.The treated TiO2-NPs show a greater efficacy on antibacterial properties compared to the untreated TiO2 NPs. In addition, the photocatalytic activity of TiO2-NPs has been investigated by applying the photodegradation of the methylene blue (MB) method using UV light under neutral conditions.The findings have proved that the degradation efficiency of MB dye in an aqueous solution has been affected by the irradiation time.Also, treated TiO2-NPs had a high photodegradation efficiency of 96% of the dye after 3 hours compared with untreated samples recorded at only 21%

Dihydroorotate dehydrogenase (DHODH) is a rate-limiting enzyme in the biosynthesis of pyrimidone that catalyzes the oxidation of dihydro-orotate to orotate. Uridine-monophosphate is biosynthesized using orotate. DHODH inhibitors have demonstrated antiviral activity against Cytomegalovirus, Ebola, Influenza, Epstein-Barr virus, and Picornavirus. DHODH inhibitors' anti-SARS-CoV-2 activity is also being investigated. DHODH inhibitors (leflunomide and its metabolite teriflunomide) have been demonstrated to have anti-SARS-CoV-2 activity. In relation with the importance of this enzyme in drug designing, in present analysis, we have developed statistically robust and interpretable 2D- and 3D- Quantitative structure-activity relationship (QSAR) models based on a dataset of 92 molecules of biologically active 2-aryl-4-quinoline carboxylic acid analogues reported as DHODH inhibitors. The correlation coefficient R2 values of training set of the PLS and all five KPLS models for the respective fingerprints were obtained as 0.7091, 0.8336 (linear), 0.7586 (radial), 0.8606 (dendritic), 0.6832 (desc) and 0.7670 (molprint2D) respectively (R2 ≈ 0.9 but > 0.6), while the external validation coefficient Q2 values (Q2 > 0.6) of the test set are 0.7009, 0.7503 (linear), 0.7737 (radial), 0.8250 (dendritic), 0.6756 (desc) and 0.7533 (molprint2D) with lower values of uncertainties.

Geniposidic acid is an iridoid glycoside. Iridoid glycosides showed antitumor, anti-inflammatory, cardiovascular, anti-hepatotoxic, choleretic, hypoglycaemic, hypolipidemic, antispasmodic, antiviral, immunomodulatory, and purgative activities. In this study, we focused on an iridoid glycoside geniposidic acid and computationally established the molecule as an anticancer drug.By doing so, we performed molecular docking, molecular dynamic simulation, DFT calculation, and OSIRIS-MOLINSPIRATION profiling targeting various oncogenic receptors. Outcomes suggested that geniposidic acid showed good interactions with 4DRH, 4AG8 and 4HJO. As these receptors showed anticancer activity by interacting with peptidylprolyl isomerase, VEGFR2, and EGFR tyrosine kinase, it might be possible that geniposidic shows its activity in the same way. RMSD , RMSF , Rg , and SASA values of docked conformers create a positive impact on receptor interaction. DFT calculation stated that HOMO orbital of geniposidic acid mainly delocalized on total aglycone part, and in the case of LUMO orbital image showed that total electron cloud focused on C-O-C=C-COOH group of aglycone part. In-silico profiling of geniposidic acid showed that the molecule positively interacted with G-protein coupled receptor and nuclear receptors. This information collectively confirms that if we relaunch geniposidic acid in a pharmacologically established manner, then it will be a boon for mankind to treat cancer.

Corrosion is a phenomenon wherein metal gets degraded when it gets exposed to the environment. This deterioration of the metal leads to many impacts such as structure damage and material failure, leakage, environmental contamination, economic loss etc. This has made to find the solution so as to protect the material and corrosion inhibitor is one among several corrosion control strategies. These are typically molecules which adsorb onto the surface of the substrate and avoid its interaction with the environment thereby inhibiting the corrosion. These inhibitors are applied in many systems such as heat exchangers, storage tanks, boilers, cooling towers, pipes etc. Chromate being such a type of inhibitor is discriminated due to its non-environmentally friendly nature. Instead, scientific community is in search of highly performing green inhibitors for mostly employed industrially important steel materials. Curcumin and its derivatives satisfy this primary criterion along with the added advantages like economical, easy to obtain and non-toxic nature. This review covers the application of curcumin and its derivatives in corrosion inhibition of industrially important materials in different corrosive environments.

The kinetics of elementary reactions of H, H2, and H2O species with electronically excited CO(triplet Π state) is theoretically studied using the multireference second-order perturbation theory. The corresponding thermodynamically and kinetically favored reaction pathways are identified. It has been revealed that the reactivity of CO(a3Πr) to these small H-containing species is much higher than that of the ground state CO(X1Σ+) molecule. Appropriate thermal rate constants for specified reaction channels with CO(a3Πr) are calculated using the Rice–Ramsperger–Kassel–Marcus theory-based master equation approach and the capture approximation. The obtained temperature-dependent rate coefficients can be incorporated into the future kinetic submechanisms aimed to describe the CO(a3Πr−X1Σ+) ultraviolet flame chemiluminescence. The corresponding Arrhenius-type expressions are reported for a wide temperature range (T=200−3000 K), relevant to atmospheric and combustion chemistry.

In this paper, activated carbon (AC) was utilized to eliminate formaldehyde from synthetic sewage. To this end, three kinds of activated carbon were utilized including commercial AC (CAC), AC derived from walnut shell (ACWS), and AC derived from lotus leaves (ACLL). Also, the influence of sorption time, formaldehyde concentration, and adsorbent dose on formaldehyde removal was investigated. The surface properties of the adsorbents were determined by SEM, FTIR and BET analyses. The outcomes showed that CAC has a higher specific surface area (978.4 m2/g) than other adsorbents. Also, the highest adsorption efficiency of formaldehyde using CAC, ACWS, and ACLL adsorbents was 99.2%, 88.2%, and 54%, respectively, indicating significant adsorption capacity of CAC compared to other adsorbents. Also, the Langmuir isotherm model was fitted better with the laboratory data due to the higher R2 compared to the Freundlich model. Moreover, the experimental data follows the pseudo-second order kinetic model. What is more, the utmost adsorption capacity of formaldehyde was 48.5 mg/g. The reusability of adsorbents displayed that CAC has a remarkable recyclability and can be utilized in seven cycles with high sorption efficiency (>90%).

The comparative kinetic study of the oxidation process of ambroxol hydrochloride (AMH) by potassium permanganate (KMnO4) in an alkaline aqueous environment in the presence and absence of palladium (II) catalyst has been analyzed at 25oC. The reaction shows the dependence of the first order on KMnO4 and fractional order with respect to AMH, sodium hydroxide medium. The addition of the salt component has no effect on the reaction. Dependence of temperature, dielectric constant and intervention of free radicals had been also studied. The reaction stoichiometry was found to be 1:1 relative to the substrate and oxidant respectively. The obtained oxidation products are identified as 2-amino-3,5-dibromobenzaldehyde hydrochloride and 4-aminocyclohexanone by liquid chromatography-mass spectra. Thermodynamic parameters such as, change in entropy, enthalpy and free energy, and activation energy regarding the slow step of the mechanism are calculated and included in the table. Moreover, a suitable mechanism for the reaction is proposed and rate laws are derived and verified.

The adsorptions of some mono and polyatomic gases on graphene nanoflake surfaces are investigated. Graphene nanoflake surface has been modeled and a suitable model for the graphene surface is found among a set of 2, 4, 7, and 19 hexagonal rings. State-of-the-art methods of density functional theory have been used in the present work. The adsorption energies and equilibrium distances have been calculated for a variety of mono and polyatomic gases such as Ar, O2, CO2, and CS2 gases for all possible orientations. Three highly symmetric adsorption sites on the surface are studied in the present work: atom-site, hollow-site, and bridge-site. For the monoatomic gases, the hollow-site and for polyatomic gases of CO2 and CS2, bridge-site are found to be more favorable than other sites. The best orientation for the studied polyatomic gases is found to be parallel. Results are compared with the available experimental data.

In this research, some thermophysical properties of ethylene glycol with water (H2O) and two solvent mixtures dimethylformamide/ water (DMF + H2O) were studied. The densities (ρ) and viscosities (η) of ethylene glycol in water and a mixed solvent dimethylformamide (DMF + H2O) were determined at 298.15 K, t and a range of concentrations from 0.1 to1.0 molar. The ρ and η values were subsequently used to calculate the thermodynamics of mixing including the apparent molar volume (ϕv), partial molar volume (ϕvo) at infinite dilution. The solute-solute interaction is presented by Sv results from the equation ∅_v=ϕ_v^o+S_v √m. The values of viscosity (B) coefficients and Falkenhagen coefficient(A) of the Jone-Dole equation and Gibbs free energy of activation (∆G*) for viscous flow of solution were estimated. The positive values of ϕ_v^o between 35.58 and 49.908 and Sv values from 12.54 to 8.83 indicate strong solute-solvent interactions.

We reported a numerical investigation of the thermal transport properties of argon (Ar) + hydrogen (H2) plasma working gases such as the dynamic viscosity and thermal conductivity under the presence of various titania (TiO2) precursors. Titanium nitride (TiN), titanium isopropoxide (TIP), and titanium butoxide (TB) mixed with water or ethanol having molar concentrations of 0.5M, 0.75M, and 1M were used. Results showed that the dynamic viscosity value of the plasma jet was decreased by the presence of TB and TIP precursor solution, notably for high concentration and feed rate, indicating a decrease in the momentum of particles inside the plasma jet. On the other hand, the thermal conductivity increased when TB and TIP solutions were injected and were influenced by the solution concentration and feed rate. This was attributed to the additional hydrogen ions from TIP and TB precursors, which are absent in the TiN precursor, that increase the number of mobile atomic species. From these transport properties, the modified ability of heating factor of Ar+H2 plasma was calculated. The highest values were obtained for the compositions, including the TB precursor solution, which is 2 to 3.5 times higher than pure Ar+H2 plasma working gases.

This study used the cation exchange approach to carry out significant chemical modifications in Moroccan Rhassoul clay by inserting a cationic surfactant (N-Methyl-N,N,N-trioctylammonium chloride) through the void between the leaves. In order to investigate the chemical composition and surface characteristics of clay as it was being treated, Fourier transform infrared spectroscopy (FTIR), X-ray fluorescence (XRF), X-ray diffraction (XRD), and thermogravimetric analysis (TGA) were explored as physical approaches.. The treatment of a textile effluent (blue reagent 19 RB19) using this modified clay as an adsorbent has demonstrated a substantial removal efficiency of the pollutant load.The experiments were carried out under static conditions to optimize certain parameters such as the pH value, the adsorbent concentration, as well as the characteristic time of contact. The maximum adsorption capacity was 80% with a mass-volume ratio of 0.6 g / l at pH = 5. The kinetic study has revealed that the second-order model is better suited for a contact time of about 60 min. The study of adsorption isotherms shows that the Langmuir model correctly describes the adsorption process with an extreme adsorbed amount up to 204 mg/g at 25 ° C.

The current study was aimed at elucidation of the adsorption properties of Amberlite IRA-68 resin for vanadium ions in aqueous media. We investigated the effect of different parameters such as contact time, pH, initial concentration, temperature and adsorbent dosage on the uptake rate of vanadium. The findings showed that equilibrium data were best fitted by the Freundlich isotherm, and maximum adsorption capacity of the resin was 211.5 mg g-1 at 50 ◦C. The best possible pH for adsorption was 4.5. The first, and second-order reaction models and the Weber–Morris model were applied on the kinetics data. Among them, the best fitting was obtained by the second-order model. The rate controlling step at onset of the uptake was liquid film resistance, which gradually changed to intraparticle diffusion. Thermodynamic study revealed that adsorption was endothermic and spontaneous. The Amberlite IRA-68 resin could preserve more than 95% of its capacity after 8 cycles of adsorption/desorption.

This work reports the recycling of waste polystyrene that was expanded by homgeneous sulfonation reactions using different methods. The obtained sulfonates polystyrenes (PSS) were identified using various techniques such as FTIR spectrometry, Thermogravimetric Analysis (TGA), and X-ray diffraction (XRD). The FTIR spectrometry showed the appearance of the S-O band at 1050 cm-1 and S=O at 1180 cm-1 of the sulfur trioxide, which confirmed the polystyrene’s modification. It is important to note that great thermal stability happened for the material which was modified at T=445°C, compared with the starting one T=400°C. In addition, the average macromolecular masses (Mv) were obtained by viscosity. The polymer exhibited polyelectrolyte behavior. The results showed an increase up to 69% in the degree of sulfonation due to the essentially higher time, beside a positive correlation between the degree and the color during synthesis. This outcome ultimately indicated a high percentage of changing benzene rings and the results were confirmed by the potentiometric dosage method.

Cyclin-dependent kinase 2 (CDK2) has appeared as a promising healing goal for anticancer treatments. Thus, this work seeks to predict new nominee drugs against cancer. In the present paper, a three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, and molecular dynamic simulation (MD) were put in to search the binding between CDK2 and Styrylquinoline inhibitor to design novel anticancer agents. The best 3D-QSAR models were performed via Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) with elevated values of Q2of 0.580, and 0.68, as well as values of R2= 0.90 and 0.91, sequentially. The forecasting ability of the models was tested by Y-randomization and external validation employing a test set of 9 molecules with a predicted determination coefficient Rtest2 of 0.99 and 0.94 for CoMFA and CoMSIA respectively. The molecular docking approach with Sybyl X.2 is conducted in this study to enhance the analysis taken out from CoMFA and CoMSIA contour maps and to afford an in silico search for the best appropriate method of inhibitor interaction within its enzyme .Furthermore, the dynamic performance and strength of the high-activity molecules were tested by performing MD simulations. This study provides leadership in to design of new potent molecules.