Identification of phytocompounds from Houttuynia cordata Thunb. as potential inhibitors for SARS-CoV-2 replication proteins through GC–MS/LC–MS characterization,molecular docking and molecular dynamics simulation

The COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a massive viral disease outbreak of international concerns. The present study is mainly intended to identify the bioactive phytocompounds from traditional antiviral herb Houttuynia cordata Thunb. as potential inhibitors for three main replication proteins of SARS-CoV-2, namely Main protease (Mpro), Papain-Like protease (PLpro) and ADP ribose phosphatase (ADRP) which control the replication process. A total of 177 phytocompounds were characterized from H. cordata using GC–MS/LC–MS and they were docked against three SARS-CoV-2 proteins (receptors), namely Mpro, PLpro and ADRP using Epic, LigPrep and Glide module of Schrödinger suite 2020-3. During docking studies, phytocompounds (ligand) 6-Hydroxyondansetron (A104) have demonstrated strong binding affinity toward receptors Mpro (PDB ID 6LU7) and PLpro (PDB ID 7JRN) with G-score of???7.274 and???5.672, respectively, while Quercitrin (A166) also showed strong binding affinity toward ADRP (PDB ID 6W02) with G-score -6.788. Molecular Dynamics Simulation (MDS) performed using Desmond module of Schrödinger suite 2020–3 has demonstrated better stability in the ligand–receptor complexes A104-6LU7 and A166-6W02 within 100 ns than the A104-7JRN complex. The ADME-Tox study performed using SwissADMEserver for pharmacokinetics of the selected phytocompounds 6-Hydroxyondansetron (A104) and Quercitrin (A166) demonstrated that 6-Hydroxyondansetron passes all the required drug discovery rules which can potentially inhibit Mpro and PLpro of SARS-CoV-2 without causing toxicity while Quercitrin demonstrated less drug-like properties but also demonstrated as potential inhibitor for ADRP. Present findings confer opportunities for 6-Hydroxyondansetron and Quercitrin to be developed as new therapeutic drug against COVID-19.

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Control over Kinetic and Thermodynamically Driven Pathways of Crystallization to Yield Cofacial and Slipped-Stack Dimers in Single Crystals

Control over the molecular packing in the solid state is of utmost importance in regulating the bulk optical properties of organic semiconductors. The electronic coupling between the molecules makes it possible to improve the properties of the bulk materials. This work reports an example of control over the selective formation of polymorphic single crystals of donor–acceptor-type small-molecule compound 25TR by 1) kinetic or 2) thermodynamic course of crystallisation to yield slipped stack (S) and cofacial (C) dimers in the single crystals. The distinct optical characteristics of the C-dimer and S-dimer are summarised. Both forms show significant excitonic interactions in the solid state, and the S-dimeric form has strong yellowish orange fluorescence, whereas the C-dimeric form is non-fluorescent in the crystalline state. DFT calculations and differential scanning calorimetric experiments revealed that the C-dimer polymorph is the thermodynamically stable form with a free energy offset of 0.43 eV in comparison with the S-dimer. Interestingly, the thermodynamically driven non-fluorescent single crystal was found to be convertible to its fluorescent form irreversibly by thermal trigger. The charge-carrier-transport characteristics of these two polymorphs were computed by using the Marcus–Hush formalism. The computations of the charge-carrier-transport behaviour revealed that the S-dimer ( 25TR_(R) ) is ambipolar, whereas the C-dimer ( 25TR_(Y) ) is predominantly n-type.     

Lauricella hypergeometric series $$F_A^{(n)}$$ F A ( n ) over finite fields

The Ramanujan Journal - In this paper, we develop a finite field analogue for one of the Lauricella series, $$F^{(n)}_A$$ . Extending results of Greene, a finite field analogue for the multinomial...     

Evolution of the calcium hydroxyapatite crystal structure under plasma deposition and subsequent reducing treatment

The structure of hydroxyapatite plasma coatings on a titanium substrate has been investigated by the X-ray Rietveld method. The hydroxyapatite crystal structure in plasma-deposited samples is characterized by strong distortions of its main element (tetrahedral PO₄ cluster) and coordination calcium polyhedra, as well as calcium deficit in the Ca2 site; however, these features do not change the main motif of the hydroxyapatite structure. The bond distortions in PO₄ clusters are estimated by the Bauer method. It is shown that hydrothermal treatment leads to the almost complete recovery of the hydroxyapatite structure.     

Perturbing π-clouds with Substituents to Study the Effects on Reaction Dynamics of gauche-1,3-Butadiene to Bicyclobutane Electrocyclization

The conical intersection (CI) governs the ultra-fast relaxation of excited states in a radiationless manner and are observed mainly in photochemical processes. In the current work, we investigated the effects of substituents on the reaction dynamics for the conversion of gauche-1,3-butadiene to bicyclobutane via photochemical electrocyclization. We incorporated both electron withdrawing (−F) and donating (−CH₃) groups in the conjugated system. In our study, we optimized the minimum energy conical intersection (MECI) geometries using the multi-configurational state-averaged CASSCF approach, whereas, to study the ground state reaction pathways for the substituted derivatives, dispersion corrected, B3LYP-D3 functional was used. The non-adiabatic surface hopping molecular dynamics simulations were performed to observe the behaviour of electronic states involved throughout the photoconversion process. The results obtained from the multi-reference second-order perturbation correction of energy at the XMS-CASPT2 level of theory, topography analysis, and non-adiabatic dynamics suggest that the −CH₃ substituted derivatives can undergo faster thermal conversion to the product in the ground state with a smaller activation energy barrier compared to −F substituted derivative. Our study also reveals that the GBUT to BIBUT conversion follows both conrotatory and disrotatory pathways, whereas, on substitution with −F or −CH₃, the conversion proceeds via the conrotatory pathway.     

Hetero-Polar Sextuple Bond: A Relativistic Quantum Chemical Study**

Number of bonds formed by sharing an electron pair between two atoms is not restricted to one, it can go beyond four and six is the maximum. While homopolar sextuple bond in Mo₂ and W₂ has been reported, such a high bond order in heteropolar diatomics has remained elusive. In the pursuit of the sextuple bond in polar diatomics, the present study depicts the existence of such multiple bonds in Rhodium-Scandium hetero-diatom based on relativistic quantum chemical calculations. The bonding comprises of three normal electron sharing covalent bonds and three dative covalent bonds.     

A theoretical investigation of Zn?Zn and Be?Be one electron bond

Attachment of one electron to 1,2-diBeX-benzene and 1,2-diZnX-benzene derivatives leads to the formation of stronger Be Be and Zn Zn interaction compared to the neutral one. This is reflected in the dramatic shortening of the Be Be and Zn Zn distance. The formation of these 2-center-1-electron bonds have also been confirmed by topological survey of electron density using quantum theory of atoms in molecules and electron localization function. The formation of these bonds is expected to render stability to these radical anions. These radical anions are stable toward electron detachment and computed bond dissociation energy values are also significant.     

Elucidating the therapeutic activity of selective curcumin analogues: DFT-based reactivity analysis

Structural Chemistry - Density functional theory (DFT) has been employed to study the structure, stability and reactivity of curcumin and some of its important analogues by computing HOMO-LUMO...     

A class of finite difference schemes for interface problems with an HOC approach

In this paper, we propose a new methodology for numerically solving elliptic and parabolic equations with discontinuous coefficients and singular source terms. This new scheme is obtained by clubbing a recently developed higher‐order compact methodology with special interface treatment for the points just next to the points of discontinuity. The overall order of accuracy of the scheme is at least second. We first formulate the scheme for one‐dimensional (1D) problems, and then extend it directly to two‐dimensional (2D) problems in polar coordinates. In the process, we also perform convergence and related analysis for both the cases. Finally, we show a new direction of implementing the methodology to 2D problems in cartesian coordinates. We then conduct numerous numerical studies on a number of problems, both for 1D and 2D cases, including the flow past circular cylinder governed by the incompressible Navier–Stokes equations. We compare our results with existing numerical and experimental results. In all the cases, our formulation is found to produce better results on coarser grids. For the circular cylinder problem, the scheme used is seen to capture all the flow characteristics including the famous von Kármán vortex street. Copyright © 2016 John Wiley & Sons, Ltd.