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SARS-CoV-2, which causes COVID-19 disease, has proven to be a disastrous pandemic due to its contagious nature. This study has been planned to theoretically explore some antidotes against this virus from natural compounds. A total of 150 compounds from the shogaol class and shogaol derivatives (SDs) have been screened whereas 50 among those, which obeyed Lipinski's Rule of Five (Ro5), have further been investigated using molecular docking techniques. Furthermore, reference antiviral drug chloroquine (ChQ) and Co-Crystallized inhibitor have also been studied against Mpro of SARS-CoV-2 for comparing the potential of our docked ligands. Surprisingly, 78% of our docked ligands have shown binding energies and inhibition constants lower than ChQ and all ligands showed these values lower than an inhibitor. We further visualized the nature of intermolecular interactions for the best docked six ligands, which have shown higher binding affinities. We have also assessed ADMET properties for three ligands that displayed visually the best intermolecular interactions. Quantum analysis of three selected ligands L4, L5, and L9 has proved their reactivity and kinetic stability. Moreover, molecular dynamic simulations over 60 ns have been run for free Mpro and its selected three ligand-protein complexes for evaluating conformational stability and residual flexibility of docked complexes. Furthermore, 100 ns the MD simulations have been performed for two ligand complexes L4, L5 (with negative binding free energy), and inhibitor. Available parameters suggest stable complexes for our ligands and could be active drugs against SARS-CoV-2 in near future. A total of 50 shogaol derivatives (SDs) which obeyed Lipinski's rule of five (Ro5) have been investigated using molecular docking and dynamic techniques. We have also assessed intermolecular interactions, ADMET properties, quantum chemical analysis for the best complexes. [ABSTRACT FROM AUTHOR]

The ongoing eruption of the COVID-19 pandemic instigated by severe-acute-respiratory-syndrome-coronavirus 2 (SARS-CoV-2) has produce enormous damage to the world. The need of the hour is to stop this pandemic by inhibiting the main protease (MPro) of SARS-CoV-2, which is primarily involved in viral replication. Our study aims to find potential inhibitors for MPro by docking marine fungi-based 90 antiviral compounds against SARS-CoV-2. Among these, 11 antiviral compounds (obeying Lipinski RO5) are selected from 90 docked antiviral compounds on the basis of binding energy range (− 6.4 kcal/mol to − 9 kcal/mol) and low inhibition constant values (0.23 μ M to 2.5 μ M) as compared with remdesivir (reference compound) toward MPro of SARS-CoV-2. Tryptoquivaline F, arisugacin B, and arisugacin A antiviral compounds exhibited effective hydrogen and hydrophobic (alkyl, π -alkyl, and π -anion) interactions and are expected to be potential protease inhibitors. Drug-likeness of these lead compounds are elaborated by boiled-egg and bioavailability radar map. The toxicity profile showed that the lead compounds L1, L2, and L3 have no AMES toxicity, skin sensitization, and cardiac toxicity. The RMSD graph proposed that all the complexes, i.e. L1, L2, and L3 are in the adequate RMSD range with the average value of 2.1 Å. All the complex systems of L1, L2, and L3 showed fluctuations in the acceptable RMSF range of 1.5 Å to 3 Å. The molecular dynamics simulation proved the stability of docked complexes L1, L2, and L3 in the binding pocket of main protease. The average hydrogen count of all complexes is L1 = 6 9. 5 , L2 = 6 7. 7 , and L3 = 6 8. 6 H-bonds. The complexes L1-MPro, L2-MPro, and L3-MPro have an average value of R g as 22.44 Å, 22.63 Å, and 22.50 Å, respectively. The lead compounds L1 (tryptoquivaline F), L2 (arisugacin b), and l3 (arisugacin A) in this study are the most promising inhibitors of SARS-CoV-2 main protease MPro, which are not reported in ealier studies. Our findings will evoke the scientific interest for their further in vitro and in vivo experimental studies. The marine fungi-based 90 antiviral agents from different chemical classes were screened against MPro of SARS-CoV-2. The lead compounds L1 (Tryptoquivaline F), L2 (Arisugacin B), L3 (Arisugacin A) in current study are the most promising inhibitors of SARS-CoV-2 main protease MPro. [ABSTRACT FROM AUTHOR]

Developing heterogeneous metal nanocatalysts is highly desirable since the catalyst can be easily separated and reused for several times. In this manuscript, we have immobilized gold nanoparticles (AuNPs) on the surface of mesoporous silica (SiO 2) using simple amino acid-based phenolic chelating molecules and utilized as highly reusable catalyst for nitroarene reduction. The synthesized nanocomposites (Au@SiO2-1 and Au@SiO2-2) have been unambiguously confirmed using powder X-ray diffraction (PXRD), Fourier transform infrared (FT-IR), high resolution-transmission electron microscopy (HR-TEM) and X-ray photoelectron spectroscopy (XPS). Interestingly, Au@SiO2-1 exhibited highly enhanced 4-nitrophenol reduction that was studied using absorption spectroscopy. Further catalytic activity of Au@SiO2-1 was also explored for 2-nitroaninline and 4-nitroaniline. The reusable studies demonstrated that the catalyst did not show significant change in the activity up to ten cycles. After catalytic reactions studies confirmed the strong attachment of AuNPs on the SiO2 matrix. Immobilization of AuNPs directly on the mesoporous SiO2 using L1/L2/MPTS organic surface functional molecule was performed. The integration of AuNPs on SiO2 matrix was confirmed using PXRD, FT-IR, HR-TEM and XPS analysis. Aromatic nitro to aromatic amine conversion catalytic studies showed good reusability and enhanced reduction activity for Au@SiO2-1. [ABSTRACT FROM AUTHOR]

New cytotoxic steroidal glycoside of methanol extract from Kochia prostrata (L.) Schrad was investigated in this study. Bio-guided isolation from ethylacetate fraction of whole plant afforded steroidal glycosides named as 5-ene-dimethylcholest3-O- β -D-glucoside (Kochioside 1A1), 5-ene-methylcholest3-O- β -D-glucoside (Kochioside 2A1) and 4-ene-dimethylcholest3-O- β -D-glucoside (Kochioside 3A1). Their structures were assigned by physical and spectroscopic methods. Kochiosides 1A1–3A1 showed inhibitory potential against brine shrimp lethality bioassay with etoposide standard drug. The new steroidal glycoside kochiosides 1A1–3A1 showed inhibition values of 8.3201, 8.8205 and 8.2310 μ g/mL, respectively with LD 5 0 compared to standard etoposide LD 5 0 (7.4625 μ g/mL) drug. Moreover, six new derivatives were designed by substituting the –NH2 and –OCH3 at R1, R2 and R3 positions in the isolated compounds. Herein, various molecular descriptors, frontier molecular orbitals (FMO), electron affinity, ionization potential and molecular electrostatic potential (MEP) were carried out to understand the active sites and biological active nature of the new cytotoxic steroidal glycoside kochiosides. The effect of electron donating groups (–NH2 and –OCH3) was also investigated on the structural parameters and electronic properties in gas and solvent (DMSO) phases. The energy gap, MEP and reactivity descriptors values demonstrate that the kochioside 3A1 retains good reactivity, which is in good agreement with current experimental studies. New cytotoxic steroidal glycoside of methanol extract from Kochia prostrata (L.) Schrad was investigated. Moreover, six new derivatives were designed by substituting the –NH2 and OCH3 at R1, R2 and R3 positions. The effect of electron donating groups (–NH2 and –OCH3) were also investigated on the structural parameters and electronic properties in gas and solvent (DMSO) phases. The energy gap, molecular electrostatic potential and reactivity descriptors values demonstrate that the kochioside 3A1 retains good reactivity, which is in good agreement with current experimental studies. [ABSTRACT FROM AUTHOR]

In the present investigation, for the first time, we have performed a thorough study about different functionals and basis sets for linear and nonlinear optical (NLO) properties of para-nitroaniline (p -NA), which is considered as proto-type NLO molecule, among organic NLO materials. There is a dire need of such data base for p -NA because many investigators are using such values of p -NA for comparative analysis. A range of different functionals including HF, BLYP, PW91, PBE, B3LYP, M06, M06-2X, PBE0, BHandHLYP, CAM-B3LYP, LC-BLYP, and B3LYP-D3 are applied in conjugation with several commonly basis sets such as 6-31G*, 6-311G*, 6-311G**, 6-311+G**, cc-pVDZ, and cc-pVTZ. A variety of functional and basis sets combinations are calculated and graphically compared with each other. The calculated total dipole moment for the p -NA is found to be 6.79 D which is quite closer to experimentally determined value. The lowest calculated value for linear isotropic polarizability at HF/6-31G* level of theory is 1 1. 7 4 × 1 0 − 2 4 esu while higher values observed with remaining all methods especially 14% polarizability increases in presence of basis set with diffuse functions and similar trend of variation is also observed in linear anisotropic polarizability. Similarly, the calculated value of frequency dependent second-order polarizability is found to be 9. 5 9 × 1 0 − 3 0 esu at PBE0/6-311+G** level of theory which is quite closer to experimental value of 9. 6 × 1 0 − 3 0 esu. A comparison between the calculated and experimental results shows good agreement among geometries, dipole moments and NLO polarizabilities for p -NA. Moreover, the frontier molecular orbital (FMO) and electron density difference map (EDDM) analysis along with density of state (DOS) plots are also presented to get more physical intuitions into the structure–property relationship and electronic communications between terminal accepter and donor groups through π -conjugation. The present investigation provides benchmark data including various commonly used functionals and basis sets for the calculation of NLO properties of p -NA. Thus, the present investigation will put straight several future studies when it comes to comparative NLO study of organic materials. • The present investigation provides benchmark data including various commonly used functionals and basis sets for the calculation of NLO properties of para-nitroaniline. • Additionally, we explore the electronic communications between terminal accepter and donor groups through π-conjugation in p-NA. [ABSTRACT FROM AUTHOR]

The isoxazole derivatives gained significant attention in our daily life from better biological activity to the semiconducting materials. This study deals in depth investigation of two isoxazole derivatives, i.e. 2-[(E)-(3,4-Dimethylisoxazol-5-yl)iminomethyl]phenol ( 1) and 1-[(E)-(3,4-Dimethylisoxazol-5-yl)iminomethyl]-2-naphthol ( 2) with respect to the geometric, charge transport, optoelectronic and nonlinear optical properties by density functional theory (DFT) and time-dependent DFT. The comprehensible intra-molecular charge transfer (ICT) was conceived from HOMOs to LUMOs. Strength of the electron donor groups was investigated on the absorption wavelengths, emission wavelengths, ionization potentials (IPs), electron affinities (EAs), total/partial densities of states and structure-property relationship. The smaller hole reorganization energies and superior transfer integrals of isoxazole derivatives ( 1 and 2) than the electron ones are leading to higher hole intrinsic mobility values as compared to the electron mobility exhibit that these systems would be good hole transport contenders. The first hyperpolarizability values are about 19 and 21 times larger than that of urea suggesting that 1 and 2 can also be considered as potential contestants for NLO applications as well. The FMO, MEP, IP, EA, NLO and SAR of isoxazole derivatives were studied by DFT and TDDFT. The effect of donor strength was discussed on optoelectronic and charge transport properties. The smaller hole reorganization energies and superior transfer integrals of both the derivatives is leading to higher hole intrinsic mobility values as compared to the electron mobility exhibit that these systems would be good hole transport contenders. [ABSTRACT FROM AUTHOR]

The triphenylamine (TPA), thiophene and pyrimidine are being used as efficient advanced functional semiconductor materials. In the present study, some new TPA donor–π–acceptor derivatives were designed where TPA moiety acts as donor, thiophene-pyrimidine π-bridge and acetic/cyanoacetic acid as acceptor. The ground-state geometries were optimized at B3LYP/6-31G** level of theory. The excitation energies and oscillator strengths were computed at TD-CAM-B3LYP/6-31G** (polarizable continuum model (PCM), in methanol) level of theory. The electronic, photophysical and charge transport properties were calculated wherever possible the computed values were compared with the available experimental as well as computational data. The electron injection (ΔGinject), relative electron injection (ΔGinjectr), electron coupling constants (∣VRP∣) and light harvesting efficiencies (LHE) have been calculated and compared with referenced compounds. The energies of the lowest unoccupied molecular orbitals (ELUMOs), diagonal bandgaps and energy level offsets were studied to shed light on the electron transport behavior. The effect of anchoring groups (acetic acid and cyanoacetic acid) was studied on the properties of interests in the dye and dye@Ti6O12. It was observed that after interaction of dye with the TiO2 cluster intra-molecular charge transport enhanced from HOMO of the dye to LUMO of the semiconductor cluster. The cyanoacetic acid anchoring group leads the superior LHE, ΔGinject and ∣VRP∣ which might improve the solar cell performance. [ABSTRACT FROM AUTHOR]

A quantum chemical investigation has been performed to spotlight the structure–property relationship among methoxybenzeylidene-based humidity sensor and water molecules. The chemical interactions among (E)-2-(4-(2-(3,4-dimethoxybenzeylidene)hydrazinyl)phenyl) ethane-1,1,2-tricarbonitrile (DMBHPET) sensor and water molecules have been studied using density functional theory (DFT) methods. The molecular structural parameters, binding energies and Infrared (IR) spectroscopic analyses have been performed to assess the nature of intermolecular interactions. Three different positions have been identified for possible attachments of H2O molecules through hydrogen bonding interactions. These positions include NH (complex 1a), p-OCH3 (complex 1b) and N=N (complex 1c) group in sensor molecule (1) for the chemical adsorption of water molecules. While, the complex 1abc includes all three sites with simultaneously three H2O molecules attached to it through hydrogen bonding. The binding energies calculated for complex 1a(NH…H2O), complex 1b(CH3O…H2O), complex 1c(N=N…H2O) and complex 1abc are -30.97, -18.41, -13.80 and -65.36 kcal/mol, respectively. The counterpoise (CP) scheme has been used to correct the basis set superposition error (BSSE) in calculation of binding energies of sensor and H2O complexes. The higher binding energy of -65.36 kcal/mol for complex 1abc represents that the present methoxybenzeylidene-based sensor has significant potential through hydrogen bonding formation for sensing humidity as indicated in our previous experimental investigation. The evidence of hydrogen bonding interactions between sensor 1 and H2O molecules has been traced through structural parameters, red shift in IR spectra as well as molecular electrostatic maps. Thus the present investigation highlights the first computational framework for a molecular level structure-binding activity of a methoxybenzeylidene-based sensor and water molecules. [ABSTRACT FROM AUTHOR]

The structures of 5,5′-bis(naphth-2-yl)- 2,2′-bithiophene (NaT2), 5,5″-bis(naphth-2-yl)-2,2′:5′,2′-terthiophene (NaT3), 5,5‴-bis(naphth-2-yl)-2,2′:5′,2″:5″,2‴-tetrathiophene (NaT4), 5,5″″-bis(naphth-2-yl)-2,2′:5′,2″:5″,2‴:5‴,2″″-quinquethiophene (NaT5) and 5,5′″″-bis(naphth-2-yl)-2,2′:5′,2″:5″,2‴:5‴,2″″:5″″,2′″″-sexithiophene (NaT6) have been optimized at PBE1PBE/6-31G* level of theory. By increasing the chain length (thiophene units) energy gap decreases. The hole reorganization energy also decreases from NaT2-NaT6. We have observed that mobility of NaT5 and NaT6 can be enhanced by minimizing the polarization and relaxation. The end-capped naphthyl groups have been rotated from 0°-60° in the case study of NaT2, it was found that hole reorganization energy increases with the increment in angle. Furthermore the charge transport properties of 5,5′-bis(thionaphth-2-yl)-2,2′-bithiophene (TNT2), 5,5″-bis(thionaphth-2-yl)-2,2′:5′,2″-terthiophene (TNT3), and 5,5‴-bis(thionaphth-2-yl)-2,2′:5′,2″:5″,2‴-quaterthiophene (TNT4) have been investigated at the same level of theory. It has been studied that cis isomers have higher hole reorganization energies as compared to trans ones thus these isomers would diminish the mobility. [ABSTRACT FROM AUTHOR]

The triphenylamine (TPA), thiophene and pyrimidine are being used as efficient advanced functional semiconductor materials. In the present study, some new TPA donor–π–acceptor derivatives were designed where TPA moiety acts as donor, thiophene-pyrimidine π-bridge and acetic/cyanoacetic acid as acceptor. The ground-state geometries were optimized at B3LYP/6-31G** level of theory. The excitation energies and oscillator strengths were computed at TD-CAM-B3LYP/6-31G** (polarizable continuum model (PCM), in methanol) level of theory. The electronic, photophysical and charge transport properties were calculated wherever possible the computed values were compared with the available experimental as well as computational data. The electron injection (ΔGinject), relative electron injection (ΔGinjectr), electron coupling constants (∣VRP∣) and light harvesting efficiencies (LHE) have been calculated and compared with referenced compounds. The energies of the lowest unoccupied molecular orbitals (ELUMOs), diagonal bandgaps and energy level offsets were studied to shed light on the electron transport behavior. The effect of anchoring groups (acetic acid and cyanoacetic acid) was studied on the properties of interests in the dye and dye@Ti6O12. It was observed that after interaction of dye with the TiO2 cluster intra-molecular charge transport enhanced from HOMO of the dye to LUMO of the semiconductor cluster. The cyanoacetic acid anchoring group leads the superior LHE, ΔGinject and ∣VRP∣ which might improve the solar cell performance. [ABSTRACT FROM AUTHOR]