Evaluation of electronic and biological interactions between N-[4-(Ethylsulfamoyl)phenyl]acetamide and some polar liquids (IEFPCM solvation model) with Fukui function and molecular docking analysis

Binding Affinity and Mechanism of Six PFAS with Human Serum Albumin: Insights from Multi-Spectroscopy, DFT and Molecular Dynamics Approaches

Per- and Polyfluoroalkyl Substances (PFAS) bioaccumulate in the human body, presenting potential health risks and cellular toxicity. Their transport mechanisms and interactions with tissues and the circulatory system require further investigation. This study investigates the interaction mechanisms of six PFAS with Human Serum Albumin (HSA) using multi-spectroscopy, DFT and a molecular dynamics approach. Multi-spectral analysis shows that perfluorononanoic acid (PFNA) has the best binding capabilities with HSA. The order of binding constants (298 K) is as follows: "Perfluorononanoic Acid (PFNA, 7.81 × 106 L·mol-1) > Perfluoro-2,5-dimethyl-3,6-dioxanonanoic Acid (HFPO-TA, 3.70 × 106 L·mol-1) > Perfluorooctanoic Acid (PFOA, 2.27 × 105 L·mol-1) > Perfluoro-3,6,9-trioxadecanoic Acid (PFO3DA, 1.59 × 105 L·mol-1) > Perfluoroheptanoic Acid (PFHpA, 4.53 × 103 L·mol-1) > Dodecafluorosuberic Acid (DFSA, 1.52 × 103 L·mol-1)". Thermodynamic analysis suggests that PFNA and PFO3DA's interactions with HSA are exothermic, driven primarily by hydrogen bonds or van der Waals interactions. PFHpA, DFSA, PFOA, and HFPO-TA's interactions with HSA, on the other hand, are endothermic processes primarily driven by hydrophobic interactions. Competitive probe results show that the main HSA-PFAS binding site is in the HSA structure's subdomain IIA. These findings are also consistent with the findings of molecular docking. Molecular dynamics simulation (MD) analysis further shows that the lowest binding energy (-38.83 kcal/mol) is fund in the HSA-PFNA complex, indicating that PFNA binds more readily with HSA. Energy decomposition analysis also indicates that van der Waals and electrostatic interactions are the main forces for the HSA-PFAS complexes. Correlation analysis reveals that DFT quantum chemical descriptors related to electrostatic distribution and characteristics like ESP and ALIE are more representative in characterizing HSA-PFAS binding. This study sheds light on the interactions between HSA and PFAS. It guides health risk assessments and control strategies against PFAS, serving as a critical starting point for further public health research.

Design and Exploration of Benzene Like Azobis Triazoles for Long-range Push-Pull Photo-Switching Attributes

This research paper presents a comprehensive study on the design and photovoltaic parameters of azobenzene type 24 photo switches (PSs) of triazole by density functional theory (DFT). The focus was on investigating how to create a long-range push-pull effect of different substituents on the PS properties for their application in photovoltaics by further substituent decoration. Their range of values for the maximum wavelength (λmax) ranged 315-556 nm while their HOMO-LUMO energies (Egaps) were 0.57-6.35eV. The stability of the PS was evaluated by measuring hardness (η) and softness (σ) values. Additionally, photovoltaic parameters such as open-circuit voltage (Voc), short-circuit current density (Jsc), fill factor (FF), and maximum power (Pmax) were calculated to assess the performance of the PS as photovoltaic materials. The results revealed that PSs 6 exhibited promising photovoltaic parameters to include Voc values ranging from 0.4-1.63eV, FF values ranging from 0.5438-0.929, Jsc values ranging from 19.27-50.75 mA/cm2, and Pmax values ranging from 14.72-75.91W. This indicates its potential as an efficient light-harvesting material for photovoltaic applications. Moreover, this study presents a pioneering investigation on the correlation between rotational velocity (R) and Mayer bond index (MBI) for the first time. The findings revealed a significant correlation between R and MBI, providing valuable insights into the structural dynamics of the PS. This novel finding opens up new avenues for understanding the structural dynamics of PS and their potential applications in various fields, including photovoltaics. The study provides valuable insights into the structure-property relationships of azobenzene-based PS and their suitability for photovoltaic devices. Further investigations are warranted to optimize the design of the PS, enhance their photovoltaic performance, and explore the underlying mechanisms of the correlation between R and MBIs.

Parts per Million of Propanol and Arsine as Responsible for the Poisoning of the Propylene Polymerization Reaction

Polypropylene synthesis is a critical process in the plastics industry, where control of catalytic activity is essential to ensure the quality and performance of the final product. In this study, the effect of two inhibitors, propanol and arsine, on the properties of synthesized polypropylene was investigated. Experiments were conducted using a conventional catalyst to polymerize propylene, and different concentrations of propanol and arsine were incorporated into the process. The results revealed that the addition of propanol led to a significant decrease in the Melt Flow Index (MFI) of the resulting polypropylene. The reduction in the MFI was most notable at a concentration of 62.33 ppm propanol, suggesting that propanol acts as an effective inhibitor by slowing down the polymerization rate and thus reducing the fluidity of the molten polypropylene. On the other hand, introducing arsine as an inhibitor increased the MFI of polypropylene. The maximum increase in the MFI was observed at a concentration of 0.035 ppm arsine. This suggests that small amounts of arsine affect the MFI and Mw of the produced PP. Regarding the catalyst productivity, it was found that as the concentration of propanol in the sample increased (approximately seven ppm), there was a decrease in productivity from 45 TM/kg to 44 TM/kg. Starting from 10 ppm, productivity continued to decline, reaching its lowest point at 52 ppm, with only 35 MT/kg. In the case of arsine, changes in catalyst productivity were observed at lower concentrations than with propanol. Starting from about 0.006 ppm, productivity decreased, reaching 39 MT/kg at a concentration of 0.024 ppm and further decreasing to 36 TM/kg with 0.0036 ppm. Computational analysis supported the experimental findings, indicating that arsine adsorbs more stably to the catalyst with an energy of -60.8 Kcal/mol, compared to propanol (-46.17 Kcal/mol) and isobutyl (-33.13 Kcal/mol). Analyses of HOMO and LUMO orbitals, as well as reactivity descriptors, such as electronegativity, chemical potential, and nucleophilicity, shed light on the potential interactions and chemical reactions involving inhibitors. Generated maps of molecular electrostatic potential (MEP) illustrated the charge distribution within the studied molecules, further contributing to the understanding of their reactivity. The computational results supported the experimental findings and provided additional information on the molecular interactions between the inhibitors and the catalyst, shedding light on the possible modes of inhibition. Solubles in xylene values indicate that both propanol and arsine affect the polymer's morphology, which may have significant implications for its properties and final applications.

Structural, electronic, intermolecular interaction, reactivity, vibrational spectroscopy, charge transfer, Hirshfeld surface analysis, pharmacological and hydropathy plot on 5-Bromo nicotinic acid - Antiviral study (Hepatitis A, B, and C)

The therapeutic properties of 5-Bromonicotinatic acid (5BNA) were studied for antiviral illnesses like Hepatitis A, Hepatitis B and Hepatitis C and the influence of electron-donating and electron-withdrawing properties of functional groups on the nicotinic acid was evaluated and represented in this study using the DFT approach. The molecular parameters were determined for both gases as well as for various solvent phases. The reactive areas in the compound are examined utilising Fukui analysis. The molecular interactions are accomplished by recognising the different types of bonding found in the compound using the AIM, ELF, LOL, RDG and IRI. Solvation investigations were demonstrated to have an influence on molecular orbital energy, ESP, UV-Vis and NLO analyses. Electron-hole, NBO and Hirshfeld investigations are used to investigate the transfer of charges and interactions inside the molecule. The method of vibrational spectroscopy (IR and Raman) is used to differentiate and identify the various types of vibrations displayed by the compound. The hydropathy plots for the proteins 2A4O, 6CWD and 2OC8 associated with Hepatitis A, Hepatitis B and Hepatitis C illustrate the disquiet and attraction of the amino acids towards the water.

Absorption wavelength (TD-DFT) and adsorption of metal chalcogen clusters with methyl nicotinate: Structural, electronic, IRI, SERS, pharmacological and antiviral studies (HIV and omicron)

The DFT B3LYP-LAND2DZ technique is used to examine interactions of Methyl nicotinate with copper selenide and zinc selenide clusters. The existence of reactive sites is determined using ESP maps and Fukui data. The energy variations between HOMO and LUMO are utilised to calculate various energy parameters. The Atoms in Molecules and ELF (Electron Localisation Function) maps are employed to investigate the topology of the molecule. The Interaction Region Indicator is used to determine the existence of non-covalent zones in the molecule. The UV-Vis spectrum using the TD-DFT method and DOS graphs are used to obtain the theoretical determination of electronic transition and properties. Structural analysis of the compound is obtained using theoretical IR spectra. To explore the adsorption of copper selenide and zinc selenide clusters on the Methyl nicotinate, the adsorption energy and theoretical SERS spectra are employed. Furthermore, pharmacological investigations are carried out to confirm the drug's non-toxicity. The compound's antiviral efficacy against HIV and Omicron is demonstrated via protein-ligand docking.

Insight into the Mechanism of Cobalt-Nickel Separation Using DFT Calculations on Ethylenediamine-Modified Silica Gel

The separation of Co(II) and Ni(II) from leaching solution is gaining interest because Co(II) and Ni(II) are increasingly used in emerging strategic areas, such as power batteries. Herein, the surface of silica gel is functionalized with 1,2-ethylenediamine and used for the separation of Co(II) and Ni(II). The Co(II) removal efficiency of the modified silica is 80.2%, with a 4-fold improvement in the separation factor. The geometry, frequency, and electrostatic potential of the ethylenediamine modified silica gel (en/SG) are calculated. The corresponding properties of M²⁺ (M-Co, Ni) adsorbed on en/SG in an aqueous solution are simulated and analyzed. The results show that ethylenediamine tends to form [Men(H₂O)₄]²⁺ after binding to M²⁺, and the binding ability of Co(II) to ethylenediamine is stronger. Besides, the thermodynamic calculations show that en/SG has a more negative Gibbs free energy when absorbing Co(II) in aqueous solution, so en/SG is more inclined to bind with Co(II) preferentially. It is the difference in complexation ability between Ni, Co, and ethylenediamine that enlarges the difference in the original physical adsorption, thus strengthening the separation performance. This work will provide guidance for a rational design of high-performance nickel-cobalt adsorption materials.

DFT investigations and molecular docking as potent inhibitors of SARS-CoV-2 main protease of 4-phenylpyrimidine

In this work, quantum chemical descriptors and a vibrational analysis of 4-Phenylpyrimidine (4-PPy) were also investigated. Through conformational analysis, the most stable conformer can be determined. The geometry of the molecular structure was optimized by using the density functional theory (DFT) at the B3LYP/6-311++G(d,p) level. The theoretically obtained FT-IR and FT-Raman spectral data agree with the experimental results. UV-Vis was done in the gas phase along with different solvents by the TD-DFT method and the PCM solvent model. Molecular electrostatic potential, natural bond orbital analysis, nonlinear optical properties, and global chemical reactivity parameters were described through the DFT method. Besides, the chemical implications of a molecule were explained using an electron localization function and a local orbital locator. We attempted to detect the antiviral activity of the 4-PPy compound by predicting molecular docking into coronavirus 2 (SARS-n-CoV-2) protein structures (6LU7, 6M03, and 6W63), because COVID-19 is known to have serious adverse effects in all areas of human life worldwide, and possible drugs need to be investigated for this. The results of the docking simulation demonstrate good affinities for binding to the receptors.

Modular and Computational Access to Innocuous Multistep Metal-Free Synthesis of 1,3,4-Oxadiazoles as Enzyme Inhibitors

An array of 1,3,4-oxadiazole hybrids, 7a-s, structurally intriguing cores with potential in natural product synthesis and drug discovery, have been synthesized using innovative comparable conventional and microwave-assisted protocols. The synthesis was performed by the reaction of secondary amine-based acetamides, 6a-s, as the electrophile and piperidine-based oxadiazoles as the nucleophile, 3, under the metal-free reaction conditions. High yield in minimum time with highest purity was obtained by the microwave-irradiated method instead of the conventional one. The structural elucidations were made through infrared, 1H NMR, 13C NMR, and elemental analysis studies. The whole array of synthesized compounds, 7a-s, was evaluated for their potential against α-glucosidase and butyryl cholinesterase (BChE) enzymes. Natural bond orbital and structural optimizations were made by using the B3LYP method and the basis set of 6-311++G(d,p). Frontier molecular orbitals and molecular electrostatic potential were calculated at the same level of selected compounds as potential candidates against BChE and α-glucosidase enzymes utilizing the time-dependent density functional theory. Fifteen compounds out of 19 were observed to be active against α-glucosidase enzyme in comparison with acarbose as the reference standard and 7 against the BChE enzyme compared to eserine as the reference standard. The highest potential of compound 7j against BChE is well correlated by the higher binding interaction with target protein as -10.2, calculated by docking studies. The recruited compounds against both enzymes could be the best anti-enzymatic drugs and part of drugs discovery programs after further analysis.

Molecular docking and simulation studies against nucleoside diphosphate kinase (NDK) of Pseudomonas aeruginosa with secondary metabolite identified by genome mining from paenibacillusehimensis

Pseudomonas aeruginosa is one of the leading opportunistic pathogens that causes nosocomial pneumonia and mostly in people with cystic fibrosis. In the present study, an in-silicoapproach was adopted to identify the novel drug target against Pseudomonas aeruginosa by employing subtractive genomics and molecular docking studies. Each step in the subtractive genomics scrutinized the bacterial proteome and determined a potential drug target against Pseudomonas aeruginosa. 71 essential proteins were obtained from the subcellular localization method that resides in the extracellular region. Metabolic pathways were studied to elucidate the unique pathways where the involvement of proteins present in the pathogen was predicted and a total of 6 unique pathways were determined. By, Genome mining of the source organism Paenibacillusehimensis, 9 ligands were obtained. The molecular docking analysis between the binding site of target protein NDK and ligands was carried out by employing the AutoDock Vina tool. Based on the highest binding affinity, Paenibactin, AnabaenopeptinNZ857 and Nostamide A complex with NDK protein with a lower binding energy of -7.5 kcal/mol, -7.4and -7.2 kcal/molrespectively were considered for the simulation studies. Molecular dynamics simulation studies showed the ligand in complex with protein was highly stable and rigid for a duration of 150 ns. For Paenibactin, AnabaenopeptinNZ857 and Nostamide Acomplex with protein, RMSD plot showed a deviation of ∼0.2-0.3 nm till ∼30ns/50 ns-110ns and further stabilized. The radius of the gyration plot clearly showed that the values stayed at ∼1.45 nm- 1.55 nm showing compactness and stability. The SASA stayed at the range ∼80nm2 and at least one total number of hydrogen bonds was shown throughout the 150 ns simulation for all three possible ligand-protein complexes. In the RMSF plot, the maximum fluctuation was ranged from ∼0.4-0.42 nm at the range between ∼57ns-60ns.The Paenibactin, AnabaenopeptinNZ857 and Nostamide A complex with NDK protein showed a stable, rigid and compact interaction throughout the simulation of duration 150 ns.Communicated by Ramaswamy H. Sarma.

DFT, hirshfeld and molecular docking studies of a hybrid compound - 2,4-Diamino-6-methyl-1,3,5-triazin-1-ium hydrogen oxalate as a promising anti -breast cancer agent

The six-membered heterocyclic ring - 1,3,5-triazine and its derivatives have garnered a lot of attention because they're good bioactive herbicides, cancer agents, and other things. One such triazine derivative, 2,4-diamino-6-methyl-1,3,5-triazin-1-ium hydrogen oxalate (DMTHO), was produced in this work, and the structure was optimised using density functional theory's B3LYP functional and the basis set 6–31++G (d,p). Additionally, the chemical underwent in-depth research using molecular docking analysis, Hirshfeld, and density functional theory. The electron densities distribution in the atoms is provided by natural orbital analysis, which also characterises the chemical bonding and reaction behaviour of the compound. The calculated HOMO and LUMO energies indicate that charge transfer occurs inside the molecule. Chemical reactivity traits including HOMO-LUMO energy gaps, softness, total energy, chemical hardness, electronic chemical potential, and electrophilicity of bioactive substances have all been subjected to analytical investigation. Total dipole moment (μ) and first-order hyperpolarizability (β) measurements for the investigated chemical indicate that DMTHO may exhibit microscopic nonlinear optical (NLO) behaviour with nonzero values. A quantitative description about intermolecular interactions in the produced crystal is provided by the Hirshfeld surface analysis. Further docking studies of the compound have been performed and the results reveals that the compound inhibit the breast cancer related protein - casein kinase (CK2) – and the possibility of developing as a potential anti breast cancer lead.