FT-IR and FT-Raman spectra, thermo dynamical behavior, HOMO and LUMO, UV, NLO properties, computed frequency estimation analysis and electronic structure calculations on α-bromotoluene

Bioactive O^N^O^ Schiff base appended homoleptic titanium(iv) complexes: DFT, BSA/CT-DNA interactions, molecular docking and antitumor activity against HeLa and A549 cell lines

Five new homoleptic derivatives of titanium(iv) have been developed and characterized by physicochemical techniques. Metal complexes, TiH2L1 [(C38H26N6O4)Ti], TiH2L2 [(C38H24F2N6O4)Ti], TiH2L3 [(C38H24Cl2N6O4)Ti], TiH2L4 [(C38H24Br2N6O4)Ti] and TiH2L5 [(C38H24N8O8)Ti], were obtained by treating Ti(OPri)4 with appropriate ONO ligands (H2L1-H2L5) in anhydrous THF as solvent. The electronic structures and properties of titanium(iv) complexes (TiH2L1-TiH2L5) and ligands (H2L1-H2L5) were examined by DFT studies. The stability of all synthesized derivatives was assessed by a UV-visible technique using 10% DMSO, GSH medium and n-octanol/water systems. The binding interactions of BSA and CT-DNA with respective titanium(iv) complexes were successfully evaluated by employing UV-visible absorption, fluorescence, circular dichroism (CD) techniques and docking studies. The in vitro cytotoxicity of TiH2L2, TiH2L3 and TiH2L4 complexes was assessed against HeLa (human epithelioid cervical cancer cells) and A549 (lung carcinoma) cell lines. The IC50 values of TiH2L2, TiH2L3 and TiH2L4 were observed to be 28.8, 14.7 and 31.2 μg mL-1 for the HeLa cell line and 38.2, 32.9 and 67.78 μg mL-1 for A549 cells, respectively. Complex TiH2L3 exhibited remarkably induced cell cycle arrest in the G1 phase and 77.99% ROS production selectivity in the HeLa cell line.

A theoretical and electrochemical impedance spectroscopy study of the adsorption and sensing of selected metal ions by 4-morpholino-7-nitrobenzofuran

The selectivity of a novel chemosensor, based on a modified nitrobenzofurazan referred to as NBD-Morph, has been investigated for the detection of heavy metal cations (Co2+, Pb2+, Mg2+, Ag+, Cu2+, Hg2+, Ni2+, and Zn2+). The ligand, 4-morpholino-7-nitrobenzofurazan (NBD-Morph), was characterized using spectroscopic techniques including FT-IR and 1H NMR. Vibrational frequencies obtained from FT-IR and proton NMR (1H) chemical shifts were accurately predicted employing the density functional theory (DFT) at the B3LYP level of theory. Furthermore, an examination of the structural, electronic, and quantum chemical properties was conducted and discussed. DFT calculations were employed to explore the complex formation ability of the NBD-Morph ligand with Co2+, Pb2+, Mg2+, Ag+, Cu2+, Hg2+, Ni2+, and Zn2+ metal cations. The comparison of adsorption energies for all possible conformations reveals that NBD-Morph exhibits sensitivity and selectivity towards metal ions, including Pb2+, Cu2+, Ag+, and Ni2+. However, an assessment of their reactivity using QTAIM topological parameters demonstrated the ligand's greater complexation ability toward Cu2+ or Ni2+ than those formed by Pb2+ or Ag+. Additionally, molecular electrostatic potential (MEP), Hirshfeld surfaces, and their associated 2D-fingerprint plots were applied to a detailed study of the inter-molecular interactions in NBD-Morph-X (X = Pb2+, Cu2+, Ag+, Ni2+) complexes. The electron localization function (ELF) and the localized-orbital locator (LOL) were generated to investigate the charge transfer and donor-acceptor interactions within the complexes. Electrochemical analysis further corroborates the theoretical findings, supporting the prediction of NBD-Morph's sensory ability towards Ni2+ metal cations. In conclusion, NBD-Morph stands out as a promising sensor for Ni2+.

Electron transfer-mediated synergistic nonlinear optical response in the Agn@C18 (n = 4-6) complexes: A DFT study on the electronic structures and optical characteristics

Seeking highly efficient and stable non-linear optical (NLO) materials is crucial yet challenging, given their promising applications in laser diodes and photovoltaics. In this study, we employ the excess electron and charge transfer strategies to theoretically design three novel complexes, namely Agn@C18 (n = 4-6), by adsorbing silver clusters onto the cyclo[18]carbon ring (C18). Our aim is to investigate the NLO characteristics of these complexes using density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations. The results reveal that the adsorption of Ag clusters onto C18 leads to a decrease in excitation energy and an increase in dipole moment and oscillator strengths, thereby significantly enhancing the hyperpolarizability of the complexes. Strikingly, among all these complexes, Ag6@C18 exhibits the highest first hyperpolarizability value of approximately 109496.2620 au calculated at the B3LYP/cc-PVDZ-pp level of theory, which is about 1.3 × 106 times higher than that of pure C18. This finding validates the effectiveness of the proposed strategies in enhancing the NLO response of the species. Moreover, the calculated UV-Vis absorption spectrum demonstrates that the Agn@C18 complexes with excess electrons exhibit absorption at longer wavelengths (ranging from 385 to 731 nm) compared to C18. In addition, the stability, chemical bonding, and charge transfer characteristics of the Agn@C18 (n = 4-6) complexes were also discussed. These findings highlight the potential of these complexes for the development of highly efficient NLO devices.

Rational design of thiazolidine-4-one-gallic acid hybrid derivatives as selective partial PPARγ modulators: an in-silico approach for type 2 diabetes treatment

Type 2 diabetes mellitus is a bipolar metabolic disorder characterized by abnormalities in insulin production from β-cells and insulin resistance. Thiazolidinediones are potent anti-diabetic agents that act through the modulation of the peroxisome proliferator-activated receptor γ (PPARγ), a nuclear receptor. However, their full agonistic activity leads to severe side effects by stabilizing Helix12 through strong hydrogen bonding with the TYR473 residue. Partial and selective PPARγ modulators (GW0072, GQ16, VSP-51, MRL-20, MBX-213, INT131) have demonstrated superior results compared to full agonists without causing adverse effects, as reported in existing data. To address this uncertainty and advance therapeutic options, we identified and designed a novel class of compounds (A1-A23) based on a hybrid structure combining phenolic and Thiazolidine-4-one's moieties. Our rational drug design strategy incorporated structural-activity relationship principle, and validated the docking studies through calculated the root mean square deviation. Additionally, we conducted molecular docking, binding energy, molecular dynamics simulations, and post-molecular dynamics calculations to evaluate the dynamics behavior between the ligands and protein. The selected ligands demonstrated highly favorable docking scores and binding energies, comparable to the co-crystal (rosiglitazone) such as A12 (-13.9 kcal/mol and -86.2 kcal/mol), A1 (-11.1 kcal/mol and -79.5 kcal/mol), A13 (-11.3 kcal/mol and -91.4 kcal/mol), and the co-crystal itself (-9.8 kcal/mol and -76 kcal/mol), respectively. Finally, the MD revealed that, the selected ligands were equally contributed for stabilization of Helix12 and β-sheets. It was concluded, the designed ligands (A12, A1, and A13) exhibited weaker hydrogen-bond interactions with specific residue TYR473 which partially modulated the PPARγ protein.Communicated by Ramaswamy H. Sarma.

Investigation of J-Aggregates of 2,3,7,8,12,13,17,18-Octabromo-5,10,15,20-tetrakis(4-sulfonatophenyl) Porphyrin in Aqueous Solutions

The highly distorted water-soluble 2,3,7,8,12,13,17,18-octabromo-5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin (Br8TPPS44-) is readily protonated under acidic pH, forming the diacid H2Br8TPPS42- and subsequently the zwitterionic H4Br8TPPS4, which eventually evolves into J-aggregates. These latter species exhibit a relevant bathochromic shift with respect to the monomer with a quite sharp band due to motional narrowing. The depolarization ratio measured in resonant light scattering spectra allows estimating a tilt angle of ~20° of the porphyrins in the J-aggregate. The kinetic parameters are obtained by applying a model based on the initial slow nucleation step, leading to a nucleus containing m monomers, followed by fast autocatalytic growth. The kc values for this latter step increase on decreasing the acid concentration and on increasing the porphyrin concentration, with a strong power-law dependence. No spontaneous symmetry breaking or transfer of chirality from chiral inducers is observed. Both Atomic Force Microscopy (AFM) and Dynamic Light Scattering (DLS) point to the presence, in both the solid and solution phases, of globular-shaped aggregates with sizes close to 130 nm. Density functional theory (DFT) calculations performed on simplified models show that (i) upon protonation, the saddled conformation of the porphyrin ring is slightly altered, and a further rotation of the aryl rings occurs, and (ii) the diacid species is more stable than the parent unprotonated porphyrin. Time-dependent DFT analysis allows comparing the UV/Vis spectra for the two species, showing a consistent red shift upon protonation, even if larger than the experimental one. The simulated Raman spectrum agrees with the experimental spectrum acquired on solid samples.

Simple dihydropyridine-based colorimetric chemosensors for heavy metal ion detection, biological evaluation, molecular docking, and ADMET profiling

In this study, two novel chemosensors containing dihydropyridine fragment namely; (2E, 2E')-1,1'-(2,6-dimethyl-1,4-dihydropyridine-3,5-diyl)bis(3-(4-(dimethylamino)phenyl)prop-2-en-1-one) (1), (2E,2E',4E,4E')-1,1' -(2,6-dimethyl-1,4-dihydropyridine-3,5-diyl)bis(5-(4-(dimethylamino)phenyl)penta-2,4-dien-1-one) (2) have been synthesized and characterized. The solvatochromic behavior was explored in different solvents of various polarities. The visual detection, as well as UV-Vis and fluorescence measurements were carried out to explore the colorimetric and optical sensing properties of the investigated chemosensors towards various metal ions such as Al3+, Cr3+, Mn2+, Fe3+, Co2+, Ni2+, Cu2+, Mg2+, Hg2+ and Zn2+. The chemosensors 1 and 2 have strong detecting abilities, with excellent sensitivity and selectivity for Cu2+ and Fe3+, respectively, over the other metal ions. The chemosensors were totally reversible upon addition of EDTA to the formed complexes and displayed a turn on-off-on fluorescence response based on an effect of chelation-quenching fluorescence. The antioxidant activities of the investigated chemosensors were assessed. They were examined in-silico for their capacity to block the Akt signaling pathway, which is involved in cancer proliferation with interpreting their pharmacokinetics aspects. Furthermore, in-vitro antitumor evaluation against a panel of cancer cell lines for the investigated chemosensors has been examined. Conclusively, chemosensor 1 was more effective at scavenging free radicals and as an anticancer agent and could be exploited as a therapeutic candidate for cancer therapy than chemosensor 2 due to its potential inhibition of Akt protein.

Theoretical, antioxidant, antidiabetic and in silico molecular docking and pharmacokinetics studies of heteroleptic oxovanadium(IV) complexes of thiosemicarbazone-based ligands and diclofenac

A series of new heteroleptic oxovanadium(IV) complexes with the general formula [VOL1-6(Dcf)] (1-6), where L1-6 = thiosemicarbazone (TSC)-based ligands and Dcf = diclofenac have been synthesized and characterized. The spectral studies along with the density functional theory calculations evidenced the distorted square-pyramidal geometry around oxovanadium(IV) ion through imine nitrogen and thione sulfur atoms of TSC moiety, and two asymmetric carboxylate oxygen atoms of diclofenac drug. The complexes were evaluated for in vitro antioxidant activity using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), 2,2'-diphenyl-1-picrylhydrazyl (DPPH), hydrogen peroxide (H2O2) and superoxide radical scavenging assays with respect to the standard antioxidant drugs butylated hydroxyanisole (BHA) and rutin. The in vitro antidiabetic activity of the complexes was tested with enzymes such as α-amylase, α-glucosidase and glucose-6-phosphatase. The complexes containing methyl substituent showed higher activity than that containing the nitro substituent due to the electron-donating effect of methyl group. The in silico molecular docking studies of the oxovanadium(IV) complexes with α-amylase and α-glucosidase enzymes showed strong interaction via hydrogen bonding and hydrophobic interactions. The dynamic behavior of the proposed complexes was analyzed by molecular dynamics (MDs) simulations, which revealed the stability of docked structures with α-amylase and α-glucosidase enzymes. The in silico physicochemical and pharmacokinetics parameters, such as Lipinski's 'rule of five', Veber's rule and absorption, distribution, metabolism and excretion (ADME) properties predicted non-toxic, non-carcinogenic and safe oral administration of the synthesized complexes.Communicated by Ramaswamy H. Sarma.

Experimental and computational studies of silver(I) dibenzoylmethane-based complexes, interaction with DNA/RNA/BSA biomolecules, and in vitro cytotoxic activity

Two silver(I) complexes of composition [Ag₂(L)₂] (1) and [Ag(L)(PPh₃)₂](2) (HL = dibenzoyl- methane, PPh₃ = triphenylphosphine) were synthesized and characterized by elemental analysis, FTIR, NMR, XRPD, and UV-visible spectra. The molecular structures of the studied ligands and Ag(I) complexes have been characterized using Density Function Theory (DFT) calculations. This analysis has enabled us to determine the reactivity and the coordination site(s) for each ligand. Ag(I) ion is found to be coordinated with the ligand's oxygens in almost a linear fashion in complex (1), while in complex (2) it adopts a tetrahedral geometry. The interaction compounds with biomolecules; calf thymus (ct DNA), yeast-tRNA, and bovine serum albumin (BSA) were investigated using both absorption and fluorescence spectroscopy. The in vitro cytotoxic studies of the complexes against normal human lung fibroblast (WI38), cancerous breast (MDA-MB-231), mammary gland breast (MCF7), hepatocellular (HePG2), and prostate (PC3) cell lines indicated that the complexes are highly toxic to the cancer cells but less toxic towards the normal one when compared with the ligand. Flow cytometric results showed that complex (1) induced cell cycle arrest at the G2/M phase, and complex (2) at G2/M and S phases. Moreover, the results of apoptotic genes (caspase3 and p53) and anti-apoptotic (Bcl2) led us to suggest an apoptotic killing mechanism of cells rather than a necrotic one.

Density functional modeling, and molecular docking with SARS-CoV-2 spike protein (Wuhan) and omicron S protein (variant) studies of new heterocyclic compounds including a pyrazoline nucleus

Nowadays, different vaccines and antiviral drugs have been developed and their effectiveness has been proven against SARS-CoV-2. Pyrazoline derivatives are biologically active molecules and exhibit broad-spectrum biological activity properties. In this scope, four new molecules (4a-d) including a pyrazoline core were synthesized in order to predict their antiviral properties theoretically. Compounds 4a-d were purified by the crystallization method. The structures of 4a-d were completely characterized by NMR, IR, and elemental analysis. The molecular structures of the compounds in the ground state have been optimized using density functional theory with the B3LYP/6-31++G(d,p) level. The quantum chemical parameters were predicted by density functional theory calculations. Moreover, the molecular docking studies of 4a-d with SARS-CoV-2 Spike protein (Wuhan) and omicron S protein (variant) were presented to investigate and predict potential interactions. The binding sites, binding types and energies, bond distances of the non-covalent interactions and calculated inhibition constants (calc. Ki) as a consequence of molecular docking for 4a-d were presented in this study. Furthermore, the stability of the protein-4a complex obtained from the docking was investigated through molecular dynamics simulation.Communicated by Ramaswamy H. Sarma.

Structural, spectroscopic, in silico, in vitro and DNA binding evaluations of tyrosyl-lysyl-threonine

The main objective of the present study is to investigate the molecular structure and DNA binding interaction of the tyrosyl-lysyl-threonine (YKT) tripeptide, which has anticancer, antioxidant and analgesic properties, using various in silico (MD, QM, molecular docking), spectroscopic (UV, FT-IR, FTIR-ATR, Raman, gel electrophoresis) and in vitro (MCF-7 and HeLa cancer cell lines and BEAS-2B cell line) methods. The optimized geometry, vibrational wavenumbers, molecular electrostatic potential (MEP), natural bond orbital (NBO) and HOMO-LUMO (highest occupied molecular orbital- lowest unoccupied molecular orbital) calculations were carried out with Density Functional Theory (DFT) using B3LYP/6-311++G(d,p) basis set to indicate conformational, vibrational and intramolecular charge transfer characteristics. The assignment of all fundamental theoretical vibration wavenumbers was performed using potential energy distribution analysis (PED). DNA is a significant pharmacological target of drugs in several diseases such as cancer. For this reason, molecular docking calculation was used to elucidate the binding and interaction between YKT tripeptide and DNA at the atomic level. Also, the dynamic behaviors of YKT and DNA was examined using MD simulations. Besides, the interaction of YKT with DNA was experimentally examined by UV titration method and agarose gel electrophoresis method. Experimental results showed that YKT was intercalatively and electrostatically bound to CT-DNA (Calf thymus DNA) and cleavage pBR322 DNA in the presence of H₂O₂. The pharmacokinetic profile of YKT was also obtained. Cytotoxic effect of YKT was evaluated on MCF-7, HeLa and BEAS-2B cell lines. Hence, these studies about YKT tripeptide may pave the way for the development of various cancer drugs. Communicated by Ramaswamy H. Sarma.

Investigation of reactive properties, adsorption on fullerene, DFT, molecular dynamics simulation of an anthracene derivative targeting dihydrofolate reductase and human dUTPase

Anthracenes are aromatic compounds with flexible structure and reactivity which are of great interest to theoretical and experimental chemists. Theoretical investigations of 1,4-dihydroxy-5,8-bis[2-(2-hydroxyethylamino)ethylamino]anthracene-9,10-dione (Mitoxantrone) (DDEA) based on density functional theory, molecular dynamics and adsorption on fullerene are reported in the present research. The suitable situation for adsorption with fullerene (C60) is the cyclohex-2-ene-1,4-dione ring of DDEA. Selected quantum-molecular descriptors have been calculated to predict the most reactive sites of the DDEA molecule. Interactions of DDEA with water have been studied using MD simulations. MD simulations were also used to study solubility parameter, a significant quantity for the development of pharmaceutical formulations. The affinity of DDEA on human dihydrofolate reductase and deoxyuridine triphosphatase enzymes was investigated by MD simulation of the protein-ligand complex obtained by molecular docking study.Communicated by Ramaswamy H. Sarma.

New Schiff base ligand and its novel Cr(III), Mn(II), Co(II), Ni(II), Cu(II), Zn(II) complexes: spectral investigation, biological applications, and semiconducting properties

New Schiff base ligand, derived from antiviral valacyclovir, and its novel Cr(III), Mn(II), Co(II), Ni(II), Cu(II), Zn(II) complexes have been synthesized. By using a variety of analytical and spectroscopic techniques, the type of bonding between the ligand and the metal ions in the recently formed complexes was clarified. The Schiff base ligand act as a bidentate and coordinated with the metal ions through the azomethine-N and the phenolic-O centers, in a mono-deprotonated form. Except for the Zn(II) complex, which displayed a tetrahedral geometry, all complexes displayed octahedral geometry. The TGA findings supported that the stability and decomposition properties of the metal complexes were entirely distinct from one another. The thermogram showed decomposition of all investigated metal complexes above 200 °C in three, four or five steps, and indicated the high thermal stability of these complexes. According to XRD patterns, the particles of these complexes were located at the nanoscale. Moreover, for all the samples analyzed, the TEM images showed uniform and homogeneous surface morphology. The biological activity revealing the high efficiencies of the screened complexes as antibacterial and antitumor agents. The antimicrobial activity of the ligand and its complexes was examined against a variety of pathogenic bacteria and fungi including Escherichia coli, Staphylococcus aureus and Candida albicans. The data obtained revealed that the metal ion in the complexes enhanced the antimicrobial activity compared to the free ligand. The high efficiencies toward S. aureus, E. coli, and C. albicans appeared by Cu(II) complex 23, Ni(II) complex 20, and Ni(II) complex 19, respectively. The antitumor activity of the ligand and its complexes was tested against Hepatocellular carcinoma cell line (HepG-2 cells), the residue 28 which produced after heating the Cu(II) complex 25 at 200 °C for 1 h, exhibited strong inhibition of HepG-2 cell growth. The results of the DNA cleavage investigation demonstrated the ability of investigated Cu(II) complex to degrade DNA. The docking findings showed strong interactions of both the ligand and its examined Cu(II) complex, revealing their ability to cleavage DNA and their potent inhibitory effects on tumor cells. The electrical conductivity study confirmed that the ligand and its investigated complexes had semiconducting properties.

Design and selection of high energy materials based on 4,8-dihydrodifurazano[3,4-b,e]pyrazine

In order to search for high energy density materials, various 4,8-dihydrodifurazano[3,4-b,e]pyrazine based energetic materials were designed. Density functional theory was employed to investigate the relationships between the structures and properties. The calculated results indicated that the properties of these designed compounds were influenced by the energetic groups and heterocyclic substituents. The -N3 energetic group was found to be the most effective substituent to improve the heats of formation of the designed compounds while the tetrazole ring/-C(NO2)3 group contributed much to the values of detonation properties. The analysis of bond orders and bond dissociation energies showed that the addition of -NHNH2, -NHNO2, -CH(NO2)3 and -C(NO2)3 groups would decrease the bond dissociation energies remarkably. Compounds A8, B8, C8, D8, E8, and F8 were finally screened as the potential candidates for high energy density materials since these compounds possess excellent detonation properties and acceptable thermal stabilities. Additionally, the electronic structures of the screened compounds were calculated.

Theoretical investigation of some 1,2,4-triazole-based molecules synthetized

In this study, theoretical calculations were made and interpreted to obtain chemical, nonlinear optical properties and antibacterial activity parameters of 14 registered heterocyclic 4, 5-dihydro-1H-1, 2, 4-triazole-5-one derivatives in the literature. For this purpose, first of all, 14 compounds registered in the literature and two main structures were optimized to find the minimum energy and the most stable structure by using the “B3LYP/6-311++G (d, p)” methods. HOMO–LUMO energies calculated from these optimized structures, energy differences and chemical parameters derived from HOMO–LUMO energies (I; Ionization potential, A; electron affinity, ΔE; Energy Gap, χ; electronegative σ; molecular softness, ω; Electrophilic Index, ε; Nucleophilic Index, μ; Chemical Potential) values were determined. In addition to chemical parameters, polar calculations were made for nonlinear optical properties, and it was evaluated whether the compounds could be optical materials. Finally, the antimicrobial properties of the molecules were calculated theoretically and compared with the experimental results by calculating the volume.

Computational investigation of the alkaloids of Pilocarpus microphyllus species as phytopharmaceuticals for the inhibition of sterol 14α-demethylase protease of Trypanosoma cruzi

Trypanosoma cruzi is a protozoan transmitted by the insect Triatoma infestans, popularly known as kissing bug. This protozoan causes the Chagas disease, a Neglected Tropical Disease. This study aimed to investigate, through DFT method and B3LYP hybrid functional, the physicochemical, pharmacokinetic, and pharmacodynamic properties of the alkaloids present in the leaves of the species Pilocarpus microphyllus (jaborandi) as a potential inhibitory activity on the protease sterol 14α-demethylase of T. cruzi associated with the techniques of molecular docking, molecular dynamics, MM-PBSA and ADMET predictions. The molecules of isopilosine, epiisopiloturine, epiisopilosine, and pilosine showed up the lowest binding energies by molecular docking, good human intestinal absorption, low penetration in the blood-brain barrier, antiprotozoal and anticarcinogenic activities in ADMET studies. It has been observed a better binding affinity of the sterol 14α-demethylase protease with isopilosine in molecular dynamics and MM-PBSA studies, which indicates it as a potential drug candidate for Chagas disease.Communicated by Ramaswamy H. Sarma.

In silico studies on phytochemicals to combat the emerging COVID-19 infection

The current COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its variants, remains a serious health hazard globally. The SARS-CoV-2 Mpro and spike proteins, as well as the human ACE2 receptor, have previously been reported as good targets for the development of new drug leads to combat COVID-19. Various ligands, including synthetic and plant-derived small molecules, can interact with the aforementioned proteins. In this study, we investigated the interaction of eight phytochemicals, from selected medicinal plants (Aegle marmelos, Azadirachta indica, and Ocimum sanctum) commonly used in Indian traditional medicine, with SARS-CoV-2 Mpro (PDBID: 6LU7), SARS-CoV-2S spike protein (PDB ID: 6M0J) and the human ACE2 receptor (PDB ID: 6M18). All compounds were subjected to density functional theory (DFT) and frontier molecular orbitals (FMO) analysis to determine their geometry, and key electronic and energetic properties. Upon examining the interactions of the phytochemicals with the human ACE2 receptor and the SARS-CoV-2 Mpro, spike protein targets, two compounds (C-5 and C-8) were identified as the best binding ligands. These were further examined in MD simulation studies to determine the stability of the ligand–protein interactions. QSAR, pharmacokinetic and drug-likeness properties studies revealed that C-5 may be the best candidate to serve as a template for the design and development of new drugs to combat COVID-19.

Synthesis, antimicrobial activity, density functional modelling and molecular docking with COVID-19 main protease studies of benzoxazole derivative: 2-(p-chloro-benzyl)-5-[3-(4-ethly-1-piperazynl) propionamido]-benzoxazole

This study contains synthesis, antimicrobial activity, density functional modelling and molecular docking studies of benzoxazole derivative: 2-(p-chloro-benzyl)-5-[3-(4-ethly-1-piperazynl) propionamido]-benzoxazole. The synthetic procedure of investigated compound is given in detail. The newly synthesized benzoxazole compound and standard drugs were evaluated for their antimicrobial activity against some Gram-positive, Gram-negative bacteria and fungus C. albicans and their drug-resistant isolates. The benzoxazole compound has been characterized by using ¹H-NMR, IR and MASS spectrometry and elemental analysis techniques. The molecular structure of the compound in the ground state has been modelling using density functional theory (DFT) with B3LYP/6-311++g(d,p) level. The molecular docking of 2-(p-chloro-benzyl)-5-[3-(4-ethly-1-piperazynl) propionamido]-benzoxazole with COVID-19 main protease has been also performed by using optimized geometry and the experimentally determined dimensional structure of the main protease (M-pro) of COVID-19.

Computational investigations of three main drugs and their comparison with synthesized compounds as potent inhibitors of SARS-CoV-2 main protease (Mpro): DFT, QSAR, molecular docking, and in silico toxicity analysis

In this study, we examined five previously synthesized compounds and checked their binding affinity towards the SARS-CoV-2 main protease (M^pro) by molecular docking study, and compared the data with three FDA approved drugs, i.e., Remdesivir, Ivermectine and Hydroxychlorochine. In addition, we have investigated the docking study against the main protease of SARS-CoV-2 (M^pro) by using Autodock 4.2 software package. The results suggested that the investigated compounds have property to bind the active position of the protein as reported in approved drugs. Hence, further experimental studies are required. The formation of intermolecular interactions, negative values of scoring functions, free binding energy and the calculated binding constants confirmed that the studied compounds have significant affinity for the specified biotarget. These studied compounds were passed the drug-likeness criteria as suggested by calculating ADME data by SwissADME server. Moreover, the ADMET properties suggested that the investigated compounds to be orally active compounds in human. Furthermore, density functional computations (DFT) were executed by applying GAUSSIAN 09 suit program. In addition, Quantitative Structure-Activity Relationship (QSAR) was studied by applying HyperChem Professional 8.0.3 program.

Influence of phenylpropanoid units of lignin and its oxidized derivatives on the stability and βO4 binding properties: DFT and QTAIM approach

Obtaining lignin products is currently one of the great challenges, mainly because of its stable and poorly reactive structure. This work used a DFT and QTAIM approach, seeking to understand the influence of lignin structure on the reactivity and βO4 binding properties of 18 model structures. The computational modeling used confirmed that lignins derived from more oxygenated monomers have a smaller HOMO-LUMO gap, and therefore are less stable. In the developed study, the replacement of alpha hydroxyl with a carbonyl was able to abruptly change the electron topology, reducing binding energy in βO4 indicating which SHOX model is more susceptible to breakage.

Identification of some novel oxazine substituted 9-anilinoacridines as SARS-CoV-2 inhibitors for COVID-19 by molecular docking, free energy calculation and molecular dynamics studies

Coronavirus disease (COVID-19), a life-threatening disease, is caused by SARS-CoV-2. The targeted therapeutics of small molecules helps the scientific community to fight against SARS-CoV-2. In this article, some oxazine substituted 9-anilinoacridines (A1-A48) was designed by docking, MM-GBSA and molecular dynamics (MD) simulation studies for their COVID-19 inhibitory activity. The docking of ligands A1-A48 against SARS-CoV-2 (PDB ID: 5R82) are performed by using Glide module, in silico ADMET screening by QikProp module, binding energy using Prime MM-GB/SA module, MD simulation by Desmond module and atomic charges were derived by Jaguar module of Schrodinger suit 2019-4. Compound A38 has the highest G-score (-7.83) when compared to all the standard compounds which are proposed for COVID-19 treatment such as ritonavir (-7.48), lopinavir (-6.94), nelfinavir (-5.93), hydroxychloroquine (-5.47) and mataquine (-5.37). Compounds A13, A23, A18, A7, A48, A46, A32, A20, A1 and A47 are significantly active against SARS-CoV-2 main protease when compared with hydroxychloroquine and mataquine. The residues GLN19, THR24, THR25, THR26, LEU27, HIE41, SER46, MET49, ASN119, ASN142, HIE164, MET165, ASP187, ARG188 and GLN189 of SARS-CoV-2 main protease play a crucial role in binding with ligands. The in silico ADMET properties of the molecules are within the recommended values. The binding free energy was calculated using PRIME MM-GB/SA studies. From the ligands A38, A13, A23, A18, A7, A48 and A46 with significant Glide scores may produce significant COVID-19 activity for further development. Compound A38 was subjected to MD simulation at 100 ns to study the dynamic behaviour of protein-ligand complex.Communicated by Ramaswamy H. Sarma.

A theoretical study on cyclometalated iridium (III) complexes by using a density functional theory

Cyclometalated iridium (III) complexes (Ir1–Ir4) are calculated in detail with computational chemistry methods. The calculated structural parameters of Ir3 are compared with experimental values and a good fit is obtained. IR spectra are calculated at B3LYP/LANL2DZ/6-31G(d) level in the gases phase. Calculated 1H-NMR chemical shift values of the mentioned complexes are compared with the experimental data and all chemical shifts are assigned to the respective atoms. The quantum chemical parameters such as absolute hardness ([Formula: see text]), absolute softness ([Formula: see text]) electronegativity ([Formula: see text]), chemical potential ([Formula: see text]) and electronic charges ([Formula: see text]) are calculated and are associated with the experimental anti-cancer properties of the related complexes. Nonlinear optic properties of the Ir1–Ir4 were investigated with the average linear polarizability ([Formula: see text]), the anisotropy of the polarizability ([Formula: see text]), first hyperpolarizability ([Formula: see text]) values. Hole transfer ([Formula: see text]), electron transfer integrals ([Formula: see text]), hole reorganization energies ([Formula: see text]) and electron reorganization energies ([Formula: see text]) are examined. In addition, molecular docking study was performed. It was found that the molecular docking results are similar to the experimental anti-cancer trend.