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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Effect of multidomain structure on the field dependences of magnetization and forced striction in easy-plane antiferromagnets

The forced magnetostriction and magnetization are measured in the easy-plane-type two-sublattice NiCl₂ antiferromagnet (AFM) in the case where this AFM passes from the multidomain to a single-domain state. It is shown that, in accordance with the magnetoelastic nature of the multidomain state, the field dependences of the forced magnetostriction and magnetization are interrelated and affected by the transition from the multidomain to the single-domain state. The character of these dependences corresponds to the case where the magnetization and striction are proportional to the number of domains with an energetically favored orientation with respect to the external magnetic field.     

Influence of branch length asymmetry on the electrophoretic mobility of rigid rod-like DNA

The electrophoretic mobility of three-arm asymmetric star DNA molecules, produced by incorporating a short DNA branch at the midpoint of rigid-rod linear DNA fragments, is investigated in polyacrylamide gels. We determine how long the added branch must be to separate asymmetric star DNA from linear DNA with the same total molecular weight. This work focuses on two different geometric progressions of small DNA molecules. First, branches of increasing length were introduced at the center of a linear DNA fragment of constant length. At a given gel concentration, we find that relatively small branch lengths are enough to cause a detectable reduction in electrophoretic mobility. The second geometric progression starts with a small branch on a linear DNA fragment. As the length of this branch is increased, the DNA backbone length is decreased such that the total molar mass of the molecule remains constant. The branch length was then increased until the asymmetric branched molecule becomes a symmetric three-arm star polymer, allowing the effect of molecular topology on mobility to be studied independent of size effects. DNA molecules with very short branches have a mobility smaller than linear DNA of identical molar mass. The reason for this change in mobility when branching is introduced is not known, however, we explore two possible explanations in this article. (i) The branched DNA could have a greater interaction with the gel than linear DNA, causing it to move slower; (ii) the linear DNA could have modes of motion or access to pores that are unavailable to the branched DNA.     

Study of approximate coupled cluster methods for first-order static properties

In this paper, we analyse the algebraic structure of the equations for calculating the first order static properties using several approximate versions of Coupled Cluster (CC) methods. In particular, the non-variational and the variational method using a CC wavefunction corresponding to an appropriately defined perturbed Hamiltonian as well as the simple expectation value expression using a CC stationary state are studied under different approximations. Two different models are proposed: (a) use of maximum overlap orbitals where the pertinent approximations are TT ₂, T ⁽¹⁾ T ₂ ⁽¹⁾, (b) use of Hartree-Fock orbitals and T(T ₁+T ₂), T ⁽¹⁾(T ₁ ⁽¹⁾ +T ₂ ⁽¹⁾ ) approximations. It is analytically shown that in both these models certain approximate versions of the methods under purview yield identical results for first order static properties.NCL Communication No. 3725     

A variational coupled cluster theory for closed shells using a propagator modification procedure

A general partial summation method for including arbitrary classes of diagrams to all orders in the coupled cluster based size consistent energy functional for closed shell states is developed. Since the various reduced density matrices which appear in the energy functional are essentially the time-independent analogues of the corresponding many body Green functions, it is possible to derive Dyson-like equations for these quantities. By expanding the associated proper self energy parts in terms of the T-amplitudes, one can carry out partial summations in the reduced density matrices and thus in energy. At a higher level, higher order terms in a proper self energy can also be generated by renormalizing the internal propagators in it, and considering only the irreducible self-energy terms.     

Solid phase extraction and analysis of horse urine for aminocaproic acid

Summary A rapid and efficient procedure is described for extraction and determination of aminocaproic acid in horse urine. Urine was extracted by passing through a bonded silica column (Bond-Elut). The adsorbed drug was washed free of endogenous materials before being eluted. The extract was then examined by thin-layer chromatography and HPLC. The purity of the extract was determined by gas chromatography-mass spectrometry.     

Electrophoretic dynamics of large DNA stars in polymer solutions and gels

We have developed a procedure for synthesizing large stable branched DNA structures that enables visualization via fluorescence microscopy. Using this procedure we have synthesized large DNA stars and observed their electrophoretic behavior in polymer solutions and gels. In dilute polyacrylamide solutions, the DNA stars move as random coils and appear to experience only brief collisions with the polymer chains in solution. The effect of polymer solution concentration on the electrophoretic mobility of stars in the dilute regime is found to be in good accord with predictions of the transient entanglement coupling (TEC) model. In semidilute polymer solutions, the star arms extend in the field direction and drag the core through the matrix. The star arms form several U-shaped conformations as they collide and engage with polyacrylamide chains. The U-shaped conformations occasionally evolve into J-shaped conformations as the star arms slide off the matrix chains they engage during electrophoretic migration. In concentrated polymer solutions, the arms of the star extend and form V-shaped structures with the core as the apex. The arms then pull the core through the matrix. These V-shaped conformations are much longer-lived than U-shaped ones and, unlike the latter, do not transform to J-shaped conformations. In polyacrylamide and agarose gels, where matrix entanglements are fixed, DNA stars become trapped when entanglements with matrix molecules prevent the core from being pulled through the matrix by the extended arms. This trapping was observed at all gel concentrations and electric fields studied.     

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.     

Observation of Slow Relaxation and Single‐Molecule Toroidal Behavior in a Family of Butterfly‐Shaped Ln4 Complexes

A family of five isostructural butterfly complexes with a tetranuclear [Ln₄] core of the general formula [Ln₄(LH)₂(μ₂‐η¹η¹Piv)(η²‐Piv)(μ₃‐OH)₂]?x H₂O?y MeOH?z CHCl₃ ( 1 : Ln=Dy^III, x=2, y=2, z=0; 2 : Ln=Tb^III, x=0, y=0, z=6; 3 : Ln=Er^III, x=2, y=2, z=0; 4 : Ln=Ho^III, x=2, y=2, z=0; 5 : Ln=Yb^III, x=2, y=2, z=0; LH₄=6‐{[bis(2‐hydroxyethyl)amino]methyl}‐N′‐(2‐hydroxy‐3‐methoxybenzylidene)picolinohydrazide; PivH=pivalic acid) was isolated and characterized both structurally and magnetically. Complexes 1 – 5 were probed by direct and alternating current (dc and ac) magnetic susceptibility measurements and, except for 1 , they did not display single‐molecule magnetism (SMM) behavior. The ac magnetic susceptibility measurements show frequency‐dependent out‐of‐phase signals with one relaxation process for complex 1 and the estimated effective energy barrier for the relaxation process was found to be 49 K. We have carried out extensive ab initio (CASSCF+RASSI‐SO+SINGLE_ANISO+POLY_ANISO) calculations on all the five complexes to gain deeper insights into the nature of magnetic anisotropy and the presence and absence of slow relaxation in these complexes. Our calculations yield three different exchange coupling for these Ln₄ complexes and all the extracted J values are found to be weakly ferro/antiferromagentic in nature (J₁=+2.35, J₂=?0.58, and J₃=?0.29 cm^?1 for 1 ; J₁=+0.45, J₂=?0.68, and J₃=?0.29 cm^?1 for 2 ; J₁=+0.03, J₂=?0.98, and J₃=?0.19 cm^?1 for 3 ; J₁=+4.15, J₂=?0.23, and J₃=?0.54 cm^?1 for 4 and J₁=+0.15, J₂=?0.28, and J₃=?1.18 cm^?1 for 5 ). Our calculations reveal the presence of very large mixed toroidal moment in complex 1 and this is essentially due to the specific exchange topology present in this cluster. Our calculations also suggest presence of single‐molecule toroics (SMTs) in complex 2 . For complexes 3 – 5 on the other hand, the transverse anisotropy was computed to be large, leading to the absence of slow relaxation of magnetization. As the magnetic field produced by SMTs decays faster than the normal spin moments, the concept of SMTs can be exploited to build qubits in which less interference and dense packing are possible. Our systematic study on these series of Ln₄ complexes suggest how the ligand design can help to bring forth such SMT characteristics in lanthanide complexes.