Correlated ab initio and density functional calculations on small model molecules for the unit cell of polyparaphenylene in its aromatic and quinoidal forms: equilibrium geometries and vibrational spectra

The role of herbal plants in the inhibition of SARS-CoV-2 main protease: A computational approach

COVID-19 has quickly spread across the globe, becoming a pandemic. This disease has a variable impact in different countries depending on their cultural norms, mitigation efforts and health infrastructure. This study aims to assess the herbal plants in the pursuit of potential SARS-CoV-2 M^pro inhibitors using in silico approaches. We have considered 16 extracted compounds of 10 different species of these plants. In order to explain their inhibition properties and chemical reactivity pattern, we have performed the density functional theory based calculations of frontier molecular orbitals, molecular electrostatic potential surface and chemical reactivity descriptors. Our calculated lipophilicity, aqueous solubility and binding affinity of the extracted compounds suggest that the inhibition potentials in the order; harsingar > aloe vera > giloy > turmeric > neem > ginger > red onion > tulsi > cannabis > black pepper. On comparing the binding affinity with hydroxychloroquine, we note that the inhibition potentials of the extracts of harsingar, aloe vera and giloy are very promising. In order to validate this, we have also performed MD simulation and MM-PBSA binding free energy analysis. Therefore, we believe that these findings will open further possibilities and accelerate the works towards finding an antidote for this malady.

Exploration of natural compounds with anti-SARS-CoV-2 activity via inhibition of SARS-CoV-2 Mpro

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a dreaded pandemic in lack of specific therapeutic agent. SARS-CoV-2 Mpro, an essential factor in viral pathogenesis, is recognized as a prospective therapeutic target in drug discovery against SARS-CoV-2. To tackle this pandemic, Food and Drug Administration-approved drugs are being screened against SARS-CoV-2 Mpro via in silico and in vitro methods to detect the best conceivable drug candidates. However, identification of natural compounds with anti-SARS-CoV-2 Mpro potential have been recommended as rapid and effective alternative for anti-SARS-CoV-2 therapeutic development. Thereof, a total of 653 natural compounds were identified against SARS-CoV-2 Mpro from NP-lib database at MTi-OpenScreen webserver using virtual screening approach. Subsequently, top four potential compounds, i.e. 2,3-Dihydroamentoflavone (ZINC000043552589), Podocarpusflavon-B (ZINC000003594862), Rutin (ZINC000003947429) and Quercimeritrin 6"-O-L-arabinopyranoside (ZINC000070691536), and co-crystallized N3 inhibitor as reference ligand were considered for stringent molecular docking after geometry optimization by DFT method. Each compound exhibited substantial docking energy >-12 kcal/mol and molecular contacts with essential residues, including catalytic dyad (His41 and Cys145) and substrate binding residues, in the active pocket of SARS-CoV-2 Mpro against N3 inhibitor. The screened compounds were further scrutinized via absorption, distribution, metabolism, and excretion - toxicity (ADMET), quantum chemical calculations, combinatorial molecular simulations and hybrid QM/MM approaches. Convincingly, collected results support the potent compounds for druglikeness and strong binding affinity with the catalytic pocket of SARS-CoV-2 Mpro. Hence, selected compounds are advocated as potential inhibitors of SARS-CoV-2 Mpro and can be utilized in drug development against SARS-CoV-2 infection.

Towards unsupervised polyaromatic hydrocarbons structural assignment from SA-TIMS-FTMS data

With the advent of high resolution ion mobility analyzers and their coupling to ultrahigh resolution mass spectrometers, there is a need to further develop a theoretical workflow capable of correlating experimental accurate mass and mobility measurements with tridimensional candidate structures. In the present work, a general workflow is described for unsupervised tridimensional structural assignment based on accurate mass measurements, mobility measurements, in silico 2D-3D structure generation, and theoretical mobility calculations. In particular, the potential of this workflow will be shown for the analysis of polyaromatic hydrocarbons from Coal Tar SRM 1597a using selected accumulation - trapped ion mobility spectrometry (SA-TIMS) coupled to Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). The proposed workflow can be adapted to different IMS scenarios, can utilize different collisional cross-section calculators and has the potential to include MSⁿ and IMSⁿ measurements for faster and more accurate tridimensional structural assignment.

Theoretical study of phenylene-thiophene oligomers: structure-properties relationship

Theoretical results including geometrical characteristics, electronic structures, photophysical parameters (lowest excitation energies, electron affinities (EAs), ionization potentials (IPs), maximum of absorption and emission) and vibrational modes of some new oligomers, based on phenylene-thiophene motives, are investigated using Density Functional Theory DFT/B3LYP/6-31G(d) approach. The electronic and optical properties of phenylene-based derivatives can be tuned through the insertion of thiophene in the main oligomers backbone as well as the addition of alkoxy-substituent groups on 2 and 5 positions on phenylene groups. It can be noticed, that different conformational behaviors and steric effects take place. Then, an increase in conjugation length induces a decrease in the gaps energy and a bathochromic shift of absorption/emission spectra. Based on these computed results, which are consistent with the available experimental data, the correlation structure-properties is better understood, where these nanostructures show a great potential for opto-electronic devices.

A DFT ANALYSIS OF THE MOLECULAR STRUCTURES AND VIBRATIONAL SPECTRA OF 4,4′-SULFONYLDIPHENOL

We have studied the structural properties and vibrational spectra of Bisphenol S (4,4′-sulfonyldi-phenol) with the help of Density Functional Calculations using a 6-311G∗∗ basis set. In addition we recorded experimental spectra in our laboratory. With the help of the GaussView program we could provide a complete assignment of the vibrational lines to the calculated normal modes of the molecule. The calculated and experimental vibrational spectra agree rather well with each other and we found the properties of Bisphenol S to be rather similar to the sulfa drug dapsone studied earlier. Interestingly, the electron donating power of an OH aubstituent at a phenyl ring seems to be less effective than that of an NH2 (in dapsone) substituent, because in Bisphenol S the relative intensity of the ring breathing line in the Raman spectrum appears to be much larger than in dapsone. We reach this conclusion about the electron donating powers of susbtituents, because in an early study on chlorine substituted anilines we have found that the larger the electron density in the ring becomes, the more the relative intensity of that line diminishes.