Computational Study on the Inhibitory Effect of Natural Compounds against the SARS-CoV-2 Proteins

COVID-19 is more virulent and challenging to human life. In India, the Ministry of AYUSH recommended some strategies through Siddha, homeopathy, and other methods to effectively manage COVID-19 (Guidelines for AYUSH Clinical Studies in COVID-19, 2020). Kabasura Kudineer and homeopathy medicines are in use for the prevention and treatment of COVID-19 infection; however, the mechanism of action is less explored. This study aims to understand the antagonist activity of natural compounds found in Kabasura Kudineer and homeopathy medicines against the SARS-CoV-2 using computational methods. Potential compounds were screened against NSP-12, NSP-13, NSP-14, NSP-15, main protease, and spike proteins. Structure-based virtual screening results shows that, out of 14,682 Kabasura Kudineer compounds, the 250395, 129677029, 44259583, 44259584, and 88583189 compounds and, out of 3,112 homeopathy compounds, the 3802778, 320361, 5315832, 14590080, and 74029795 compounds have good scoring function against the SARS-CoV-2 structural and nonstructural proteins. As a result of docking, homeopathy compounds have a docking score ranging from −5.636 to 13.631 kcal/mol, while Kabasura Kudineer compounds have a docking score varying from −8.290 to −13.759 kcal/mol. It has been found that the selected compounds bind well to the active site of SARS-CoV-2 proteins and form hydrogen bonds. The molecular dynamics simulation study shows that the selected compounds have maintained stable conformation in the simulation period and interact with the target. This study supports the antagonist activity of natural compounds from Kabasura Kudineer and homeopathy against SARS-CoV-2’s structural and nonstructural proteins.</p

Design and fabrication of dioxyphenylcoumarin substituted cyclotriphosphazene compounds photodiodes

The present study introduces cyclotriphosphazene compounds substituted by dioxyphenylcoumarin as a photodiode application. Firstly, 7,8-dihydroxy-3-(3-methylphenyl)coumarin (1b) has been obtained by conventional as well as microwave assisted methods. Novel optoelectronic device characteristics for both mono and disubstituted dioxyphenylcoumarin bearing cyclotriphosphazene compounds (HCP-2 and HCP-4) have been synthesized from the reactions of cyclotriphosphazene containing dioxybiphenyl (HCP-1 and HCP-3) with compound 1b, respectively. The structures of compounds HCP 1–4 were identified by using elemental analysis, 1H, 13C-APT, 31P NMR and 2D HETCOR NMR and FT-IR spectroscopy methods. The Al/HCP-2/p-Si/Al and Al/HCP-4/-p-Si/Al photodiodes properties have been investigated from current-voltage (I−V) and capacitance-voltage (C−V) measurements. The electrical parameters of the prepared diodes such as ideality factor n and series resistance Rs were investigated in dark and at room temperature from (I−V) curve and Nord's method. As can be seen, the Al/HCP-2/p-Si/Al diode of high rectification ratio RR and with ideality factor greater than unity. The influence of light illuminations on the diode shows that the device can be used as photodiode with good efficiency. The barrier height ϕb and series resistance Rs have been calculated from the capacitance-voltage (C−V)and conductance-voltage (G−V) measurements under various applied frequencies from 10 kHz to 1 MHz. the high difference in the results of barrier height obtained from I-V and C-V calculations confirm the influence of series resistance and localized states on transport of charge carriers and the photodiode performance.TUBITAK-110T652 Fırat University, FÜBAP-FF.161

DFT investigations of the ground and excited state geometries of the benzothiazine and benzisothiazol based anticancer drugs

Density-functional theory (DFT) is a prevailing method for predicting the geometry of organic compounds. The ground state geometries have been calculated at the B3LYP/6-31G∗∗ and PBE0/6-31G∗∗ levels of theories. The excited state geometries have been computed at time dependent DFT (TD-DFT) by using TD-B3LYP/6-31G∗∗ and TD-PBE0/6-31G∗∗ levels of theories. It has been revealed that the PBE0 functional is better than B3LYP to predict the S–O and S–C bond lengths. Both of the functionals could not reproduce the S–N bond lengths. The B3LYP is good to imitate the C–N and C–O bond lengths. The C–C and C–Cl bond lengths have been impersonated by both the functionals. Moreover, it has also been revealed that the S–N bond length elongated while the C–N bond length shortened from ground to excited state

3-(N,N-Diacylamino)quinazolin-4(3H)-ones : preparation, stereostructure and application in kinetic resolution of amines

3-Amino-2-[(S)-1-tert-butyldimethylsilyloxy-2-methylpropyl)quinazolin-4(3 H)-one was prepared from L-valine in six steps without the requirement for chromatography and used to prepare a number of 3-monoacylaminoquinazolinones (MAQs) by reaction with acid chlorides. The barrier to rotation around the N-N bond in these MAQs (~16 kcal/mol) is sufficient for it to constitute a chiral axis on the NMR timescale though not on the real timescale in solution.;N,N-Diacylation of 3-aminoquinazolinones results in the formation of 3-diacylaminoquinazolinones (DAQs). When the two N-acyl groups of the imide in the DAQs are not identical, the N--N bond becomes a chiral axis with the two planes containing the quinazolinone and imide moieties orthogonal to one another as shown by X-ray crystal structures for twelve of these DAQs. The barrier to N--N bond rotation is sufficiently high to allow separation of diastereoisomers (atropisomers) when there is an additional chiral centre present either in an acyl group or in the Q-C2 substituent of the DAQ.;These DAQs are highly selective acylating agents for the less sterically hindered of two secondary amines and, in enantiopure form, are highly enantioselective acylating agents for racemic amines, even under conditions of stoichiometry (1 eq. DAQ: 2 eq. amine) thus allowing recovery of the derivatised amine enantiomer and unreacted amine enantiomer. In these kinetic resolutions the presence of the N--N chiral axis was shown to be mandatory for high enantioselectivity to result. Where competitive attack of the racemic amine on both N-acyl groups of the DAQ occurred, it was found that each enantiomer reacted with a different N-acyl group (parallel kinetic resolution).;Of particular interest were DAQs bearing homochiral N-acyl substituents [(S)-2-acetoxypropanoyl] for which separation of diastereoisomers was not required. The N-N bond in these DAQs is still a chiral axis because the most stable conformation of the imide moiety has an exo/endo orientation of the carbonyl groups which is much preferred over the alternative endo/exo as revealed by NMR spectroscopy. Consequently these DAQs are also enantioselective acylating agent for amines.;For 3-(N-2-acetoxypropanoyl-N-acyl)aminoquinazolinones a single exo/endo conformation is present in solution in some cases but an interconverting exo/endo &lrhar2; endo/exo mixture in others.;The imide conformational preferences in both classes of 2-acetoxypropanoyl-containing DAQs above were ascribed to the presence of a high conformational preference within the 2-acetoxypropanoyl group itself.;In their reaction with amines, the rates of reaction of 3 sets of 2-acetoxypropanoyl-containing DAQs were correlated with the orientation of the (2-acetoxypropanoyl) methyl group in their crystal structures. It was concluded that the stereostructures in the crystal and in solution were essentially the same. This result should allow an understanding of the origin of the high enantioselectivity in these acylations with the prospect of increasing it to even higher levels by rational means

Tuning the Electronic and Charge Transport Properties of Schiff Base Compounds by Electron Donor and/or Acceptor Groups

Organic semiconductors have gained substantial interest as active materials in electronic devices due to their advantages over conventional semiconductors. We first designed four Schiff base compounds, then the effect of electron donor/acceptor groups (methyl/nitro) was studied on the compounds’ electronic and transport nature. The absorption spectra (λabs) were computed by time-dependent DFT at TD-B3LYP/6-31+G** level. The effect of different solvents (ethanol, DMF, DMSO, and acetone) was investigated on the λabs. The substitution of the -NO2 group to the furan moiety at the 5th position in Compound 3 leads to a red-shift in the absorption spectrum. A smaller hole reorganization energy value in Compound 3 would be beneficial to get the hole’s intrinsic mobility. In contrast, a reduced-electron reorganization energy value of Compound 4 than hole may result in enhanced electron charge transfer capabilities. The reorganization energies of compounds 1 and 2 exposed balanced hole/electron transport probability. The optical, electronic, and charge transport properties at the molecular level indicate that Compound 3 is suitable for organic electronic device applications

Push–pull effect on the geometries, electronic and optical properties of thiophene based dye-sensitized solar cell materials

Geometries, electronic structure and electronic absorption spectra of thiophene based dye-sensitized solar cells were performed using Density Functional Theory (DFT) and time dependent density functional theory (TD-DFT). Different electron donating and electron withdrawing groups have been substituted. Geometries and electronic properties have been computed at B3LYP/6-31G∗∗ and absorption spectra at TD-B3LYP/6-31G∗∗ level of theory. Major change in bond lengths and bond angles occurs in the system where there is electron withdrawing or electron donating groups have been substituted. In SYSTEM-2 and SYSTEM-3 intra charge transfer has been observed. HOMO of SYSTEM-2 and SYSTEM-3 is delocalized on left side while LUMO on right side of the molecule. In SYSTEM-1, HOMO is on left side while LUMO is in the center. The designed systems show two absorption peaks for each of the system. In short, choice of appropriate electron withdrawing and donating groups is very important for improving the performance of dye-sensitized solar cells

Selectivities in acylation of primary and secondary amine with diacylaminoquinazolinones and diacylanilines

1115-1121The diacylaminoquinazolinones are highly selective acylating agents for primary amines in the presence of secondary amines. The chemoselective N-acetylation reagents have been investigated using 2-substituted N,N-diacylaminoquinazolinones (DAQs) and 2-substitued-N-diacylanilines (DAAs). Determination of the selectivity ratios have been made by comparison of the crude product in each case with authentic samples of the amide products using NMR spectroscopy. The control experiments in which pairs of amines compete for acetyl chloride show some selectivity but not comparable with that of DAQs and DAAs selectivity. When the DAQs, DAAs and acetyl chloride react with mixtures of pyrrolidine and piperidine, they give amides in the corresponding ratios. The DAQs 1 and 2 react entirely with diethylamine without any competitive reaction with diphenylamine. The high level of chemoselectivity has also been observed when the 1 and 2 react exclusively with the ethanolamine without any competitive reaction with diethanolamine. Moreover, 1 and 2 react with succinimide without any competitive reaction with phthalimide. </span

First principles investigations of electronic, photoluminescence and charge transfer properties of the Naphtho[2,1-b:6,5-b′]difuran and its derivatives for OFET

We have designed new derivatives of naphtha [2,1-b:6,5-b′] difuran as DPNDF-CN1 and DPNDF-CN2. The molecular structures of DPNDF, its derivatives DPNDF-CN1 and DPNDF-CN2 have been optimized at the ground (S0) and first excited (S1) states using density functional theory (DFT) and time-dependent density functional theory (TD-DFT), respectively. Then the highest occupied molecular orbitals (HOMOs), the lowest unoccupied molecular orbitals (LUMOs), photoluminescence properties, electron affinities (EAs), reorganization energies (λs) and ionization potentials (IPs) have been investigated. The balanced λ(h) and λ(e) showed that DPNDF, DPNDF-CN1 and DPNDF-CN2 would be better charge transport materials for both hole and electron. The effect of attached acceptors on the geometrical parameters, electronic, optical and charge transfer properties have also been investigated

Investigation of the Effect of Substituents on Electronic and Charge Transport Properties of Benzothiazole Derivatives

A series of new benzothiazole-derived donor–acceptor-based compounds (Comp1–4) were synthesized and characterized with the objective of tuning their multifunctional properties, i.e., charge transport, electronic, and optical. All the proposed structural formulations (Comp1–4) were commensurate using FTIR, 1H NMR, 13C NMR, ESI-mass, UV–vis, and elemental analysis techniques. The effects of the electron-donating group (-CH3) and electron-withdrawing group (-NO2) on the optoelectronic and charge transfer properties were studied. The substituent effect on absorption was calculated at the TD-B3LYP/6-31+G** level in the gas and solvent phases. The effect of solvent polarity on the absorption spectra using various polar and nonpolar solvents, i.e., ethanol, acetone, DMF, and DMSO was investigated. Light was shed on the charge transport in benzothiazole compounds by calculating electron affinity, ionization potential, and reorganization energies. Furthermore, the synthesized compounds were used to prepare thin films on the FTO substrate to evaluate the charge carrier mobility and other related device parameters with the help of I-V characteristic measurements