Modeling the DFT structural and reactivity studies of a pyrimidine -6-carboxylate derivative with reference to its wavefunction-dependent, MD simulations and evaluation for potential antimicrobial activity

Synthesis, Characterization and Assessment of Antioxidant and Melanogenic Inhibitory Properties of Edaravone Derivatives

A series of edaravone derivatives and the corresponding Cu(II) complexes were synthesized and characterized using spectroscopic and analytical techniques such as IR, UV, NMR and elemental analysis. Antioxidant activities of all compounds were examined using free radical scavenging methods such as hydrogen peroxide scavenging activity (HPSA), 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2-2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) assays. All of the tested compounds exhibited good antioxidant activity. Further, the frontier orbital energy levels, as well as various chemical properties, were determined using the density functional theory (DFT) calculations. The MEP maps of all of the derivatives were plotted to identify the nucleophilic and electrophilic reactive sites. Further, binding energies of all of the organic compounds with the protein tyrosinase was investigated to determine their potential anti-melanogenic applications. The selected ligand, L6 was subjected to molecular dynamics simulation analysis to determine the stability of the ligand-protein complex. The MD simulation was performed (150 ns) to estimate the stability of the tyrosinase-L6 complex. Other key parameters, such as, RMSD, RMSF, Rg, hydrogen bonds, SASA and MMPBSA were also analyzed to understand the interaction of L6 with the tyrosinase protein.

Engineering of the Central Core on DBD-Based Materials with Improved Power-Conversion Efficiency by Using the DFT Approach

Developing proficient organic solar cells with improved optoelectronic properties is still a matter of concern. In the current study, with an aspiration to boost the optoelectronic properties and proficiency of organic solar cells, seven new small-molecule acceptors (Db1-Db7) are presented by altering the central core of the reference molecule (DBD-4F). The optoelectronic aspects of DBD-4F and Db1-Db7 molecules were explored using the density functional theory (DFT) approach, and solvent-state calculations were assessed utilizing TD-SCF simulations. It was noted that improvement in photovoltaic features was achieved by designing these molecules. The results revealed a bathochromic shift in absorption maxima (λmax) of designed molecules reaching up to 776 nm compared to 736 nm of DBD-4F. Similarly, a narrow band gap, low excitation energy, and reduced binding energy were also observed in newly developed molecules in comparison with the pre-existing DBD-4F molecule. Performance improvement can be indicated by the high light-harvesting efficiency (LHE) of designed molecules (ranging from 0.9992 to 0.9996 eV) compared to the reference having a 0.9991 eV LHE. Db4 and Db5 exhibited surprisingly improved open-circuit voltage (V OC) values up to 1.64 and 1.67 eV and a fill factor of 0.9198 and 0.9210, respectively. Consequently, these newly designed molecules can be considered in the future for practical use in manufacturing OSCs with improved optoelectronic and photovoltaic attributes.

Evidences of noncovalent interactions between indole and dichloromethane under different solvent conditions

CONTEXT

Theoretical investigation of indole (IND) and its binary combination with dichloromethane (DC) in various solvents were computed to track the impact of molecular interactions on spectral characteristics. When transitioning from plain drug to complexes, different modes of IND display a substantial shift in peak location. The 3561.26 cm^-1 band shows (~15.58 cm^-1) red shift upon dilution. The geometry in various solvents was calculated using quantum chemical calculation utilizing density functional theory (DFT). The highest ALIE values are located at the indole skeleton and on complexation with DC, and the ring atoms become more electron rich. The atom-centered density matrix propagation (ADMP) molecular dynamic (MD) calculation shows that the geometries optimized through the DFT calculation match the global minima effectively. MD simulations indicate that indole is more stable in water and methanol.

METHODS

DFT studies have been employed to study the interaction between indole and dichloromethane. CAM-B3LYP/6-311++G(d)(6D,7F) level of theory was employed using Gaussian 16 W suite. Quantum topological descriptors were discussed using quantum theory of atoms in molecules (QTAIM) with the help of Multiwfn software. Reduced density gradient (RDG) plot describes the nature of the interaction, while average local ionization energy (ALIE) explained the variation in local ionization energy of the molecular surface before and after complexation.

Modeling the structure and reactivity landscapes of a pyrazole-ammonium ionic derivative using wavefunction-dependent characteristics and screening for potential anti-inflammatory activity

Spectroscopic investigations of 1-phenyl -2,3-dimethyl-5-oxo-1,2-dihydro-1H-pyrazol-4-ammonium 2[(2-carboxyphenyl) disulfanyl]benzoate (PACB) reported experimentally and theoretically. NH-O interaction is observed and there is a very large downshift for NH-O stretching frequency. Reactive sites are identified from the chemical and electronic properties. For PACB the maximum repulsion was around H33, H55 and H57 atom. LOL shows red regions between C-C and blue around C atoms are surrounded by a delocalized electron cloud. The red ring is a hallmark of electron density depletion from the NCI plot due to electrostatic repulsion and its existences suggests that coordination sphere for PACB is minimally strained around the central ion. Atomic contact energy values and high score of the docking results obtained propose that, PACB may have inhibitory properties and have a significant function in pharmacological chemistry. Molecular dynamics simulation was performed to validate the stability of the title compound with the Bovine thrombin-activatable fibrinolysis inhibitor protein.Communicated by Ramaswamy H. Sarma.

DFT investigations on conformational analysis, solvation effects, reactivity studies, chemical descriptors and docking of two anti‐cancerous drugs, Lenvatinib and Regorafenib

Two anticancer drugs, lenvatinib (LNTB) and regorafenib (RGFB) are evaluated for their solvent effects, wavefunction reactivity properties and different chemical descriptors by means of theoretical methods. Potential energy surface scan studies about all possible rotable bonds are performed and lowest energy conformations of LNTB and RGFB are for the torsion angles C25‐C24‐C29‐N9 and C25‐N10‐C15‐C21. Reactive sites are O and N, H atoms, giving nucleophilic and electrophilic attacks for both the molecules. Solvation free energies are calculated in different solvents and all solvents are suitble except heptane. Electron densities of LNTB and RGFB show that closed‐shell interactions are in different regions. The intramolecular hydrogen bonds of the compounds LNTB and RGFB are found at O2‐H38, Cl1‐H37 & O5‐H47 and F2‐H38, N11‐H45, O7‐H35 & O7‐H37, respectively. Due to anticancer activities, LNTB and RGFB are docked with different proteins which give binding affinities from ‐8.4 to ‐10.5 for RGFB and ‐7.9 to ‐10.1 kcal/mol for LNTB.

DFT and MD simulation investigation of favipiravir as an emerging antiviral option against viral protease (3CLpro) of SARS-CoV-2

As per date, around 20 million COVID-19 cases reported from across the globe due to a tiny 125 nm sized virus: SARS-CoV-2 which has created a pandemic and left an unforgettable impact on our world. Besides vaccine, medical community is in a race to identify an effective drug, which can fight against this disease effectively. Favipiravir (F) has recently attracted too much attention as an effective repurposed drug against COVID-19. In the present study, the pertinency of F has been tested as an antiviral option against viral protease (3CLpro) of SARS-CoV-2 with the help of density functional theory (DFT) and MD Simulation. Different electronic properties of F such as atomic charges, molecular electrostatic properties (MEP), chemical reactivity and absorption analysis have been studied by DFT. In order to understand the interaction and stability of inhibitor F against viral protease, molecular docking and MD simulation have been performed. Various output like interaction energies, number of intermolecular hydrogen bonding, binding energy etc. have established the elucidate role of F for the management of CoV-2 virus for which there is no approved therapies till now. Our findings highlighted the need to further evaluate F as a potential antiviral against SARS-CoV-2.