•Amorphous SiO2,ZrO2,HfO2 are obtained by DFT melt-quench for various melt T.•Melt threshold T is found for a given heat/cool rate separating types of structures.•Little known two edge sharing ...SiO4-tetrahedra are easily formed in some structures.•A sharp drop in density as a function of melt T is found for a-ZrO2 and a-HfO2.•The drop is a result of atom coordination numbers decrease in amorphous states.
Ab initio molecular dynamics modeling in the NPT ensemble is used to obtain amorphous states by melting SiO2, ZrO2 and HfO2 crystals. A wide range of melt stabilization temperatures are used. Two types of SiO2 amorphous states are obtained. For melt temperatures below 4500 K, a perfect silica glass is obtained without any point defects. For melt temperatures above 4500 K, silica point defects such as threefold coordinated oxygen atoms, edge-sharing SiO4-tetrahedra, and others together with a wide range of Si-O-Si rings including 3-, and 4-membered rings appear. When the temperature of the melt exceeds the ZrO2 and HfO2 crystal melting point by 100 – 400 K, a sharp drop in the density of amorphous states is observed, accompanied by a decrease in atomic coordination, but this does not lead to the formation of defect states in the depth of the band gap of hafnium and zirconium dioxides.
The previously developed high-performance parallel method of the atomistic simulation of the ion beam sputtering deposition process is applied to the SiO2 thin films. Structural properties of ...deposited films such as density, concentration of point defects, ring statistics, as well as effects arising from the interaction of high energy sputtered Si atoms with the growing film are discussed.
•DESIL force field reproduces structure of glassy silica.•Deposited film density exceeds the density of glassy silica.•Concentration of the point defects decreases with thickness of film.•Film density increases with energy of the deposited atoms.
The use of computer simulation methods has become an indispensable component in identifying drugs against the SARS-CoV-2 coronavirus. There is a huge body of literature on application of molecular ...modelling to predict inhibitors against target proteins of SARS-CoV-2. To keep our review clear and readable, we limited ourselves primarily to works that use computational methods to find inhibitors and test the predicted compounds experimentally either in target protein assays or in cell culture with live SARS-CoV-2. Some works containing results of experimental discovery of corresponding inhibitors without using computer modelling are included as examples of a success. Also, some computational works without experimental confirmations are also included if they attract our attention either by simulation methods or by databases used. This review collects studies that use various molecular modelling methods: docking, molecular dynamics, quantum mechanics, machine learning, and others. Most of these studies are based on docking, and other methods are used mainly for post-processing to select the best compounds among those found through docking. Simulation methods are presented concisely, information is also provided on databases of organic compounds that can be useful for virtual screening, and the review itself is structured in accordance with coronavirus target proteins.
Display omitted
•Low melting siloxane- and phosphate-bridged phthalonitrile monomers are reported.•Computational model aimed to predict monomers Tg is developed.•Cured resins demonstrate excellent ...thermal performance featured to phthalonitriles.
The series of low-melting siloxane- and phosphate-bridged phthalonitriles are studied. The monomers of this type possess glass transition temperatures more than 100°C lower than for common phthalonitriles. Based on the collected experimental data molecular dynamics simulations aimed to predict glass-transition temperatures of the considered types of low-melting phthalonitriles are reported. The validity of computational model is confirmed by successful synthesis of the new monomers, e.g. phosphate- and phosphonate-bridged phthalonitriles are introduced for a first time. Cured Bis(3-(3,4-dicyanophenoxy)phenyl) phenyl phosphate demonstrates thermal performance featured to phthalonitriles (HDT∼450°C, T5%=524°C, Yc, (Ar)=80%) along with increased thermo-oxidative stability. In aggregate with convenient processing the considered phthalonitriles can be used as high-temperature matrices for fiber-reinforced plastics production by vacuum infusion or RTM techniques.
Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand ...into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.
The kinetics of oxidation of allyl alcohol to glycidol in the presence of extruded titanium silicalite was investigated. Based on the experimental data obtained, a kinetic model of the process was ...developed and the activation energies of the target and side reactions, the rate constants and the adsorption equilibrium were determined. Testing of the process of allyl alcohol epoxidation was carried out and the adequacy of the proposed kinetic model was evaluated at the bench laboratory installation of continuous action.
Graphic Abstract
A virtual structure-oriented screening of candidates for inhibitors of blood coagulation factor XIIa was carried out. This coagulation factor is one of the most promising therapeutic targets for the ...development of anticoagulants without disturbing normal hemostasis. The screening was carried out in the database of organic compounds of the Voronezh State University, consisting of more than 19 thousand molecules. At the first stage of virtual screening, ligands were positioned in the active center of factor XIIa using the SOL docking program. At the second stage, for the best ligands, the protein-ligand binding enthalpy was calculated using the MOPAC program and the PM7 quantum-chemical method, taking into account the solvent in the COSMO continuum model. All calculations were carried out using the supercomputing resources at Lomonosov Moscow State University. In total, more than 30 thousand ligand conformers are docked, and for more than 400 of the best of them, the protein-ligand binding enthalpy was calculated. 16 compounds are selected as the most promising candidates for subsequent in vitro testing of their ability to inhibit factor XIIa.
Docking represents one of the most popular computational approaches in drug design. It has reached popularity owing to capability of identifying correct conformations of a ligand within an active ...site of the target-protein and of estimating the binding affinity of a ligand that is immensely helpful in prediction of compound activity. Despite many success stories, there are challenges, in particular, handling with a large number of degrees of freedom in solving the docking problem. Here, we show that SOL-P, the docking program based on the new Tensor Train algorithm, is capable to dock successfully oligopeptides having up to 25 torsions. To make the study comparative we have performed docking of the same oligopeptides with the SOL program which uses the same force field as that utilized by SOL-P and has common features of many docking programs: the genetic algorithm of the global optimization and the grid approximation. SOL has managed to dock only one oligopeptide. Moreover, we present the results of docking with SOL-P ligands into proteins with moveable atoms. Relying on visual observations we have determined the common protein atom groups displaced after docking which seem to be crucial for successful prediction of experimental conformations of ligands.
Lomonosov-2 supercomputer is used to search for new organic compounds that can suppress the replication of the SARS-CoV-2 coronavirus. The latter is responsible for the COVID-19 pandemic. Docking and ...a quantum-chemical semiempirical atomistic modeling method are used to find inhibitors of the SARS-CoV-2 papain-like protease, which is one of the key coronavirus enzymes responsible for its replication. The atomistic model of the papain-like protease of this coronavirus is based on the high-resolution structure deposited in the Protein Data Bank. The SOL docking program has been used for virtual screening of more than
low molecular weight molecules (ligands). Ligands with the highest protein-ligand binding energy, selected using the docking results, were subjected to quantum-chemical calculations. The latters are performed by the PM7 semiempirical method with the COSMO implicit solvent model using the MOPAC program. The enthalpy of protein-ligand binding is calculated for the best position of the ligand in the protein.
ligands were selected for experimental in vitro testing as candidates for papain-like protease inhibitors base on docking and quantum-chemical results. In case of experimental confirmation, these compounds may become the basis for direct-acting antiviral drugs for the SARS-CoV-2 coronavirus.
PDF
