Critical assessment of popular biomolecular force fields for molecular dynamics simulations of folding and enzymatic activity of main protease of coronavirus SARS-CoV-2.

The main cysteine protease (M) of coronavirus SARS-CoV-2 has become a promising target for computational development in anti-COVID-19 treatments. Here, we benchmarked the performance of six biomolecular molecular dynamics (MD) force fields (OPLS-AA, CHARMM27, CHARMM36, AMBER03, AMBER14SB and GROMOS G54A7) and three water models (TIP3P, TIP4P and SPC) for reproducing the native fold and the enzymatic activity of M as monomeric and dimeric units. The MD sampling up to 1 μs suggested that the proper choice of the force fields and water models plays an essential role in reproducing the tertiary structure and the inter-residue distance between the catalytic dyad His41-Cys145.

Main and papain-like proteases as prospective targets for pharmacological treatment of coronavirus SARS-CoV-2.

The pandemic caused by the coronavirus SARS-CoV-2 led to a global crisis in the world healthcare system. Despite some progress in the creation of antiviral vaccines and mass vaccination of the population, the number of patients continues to grow because of the spread of new SARS-CoV-2 mutations. There is an urgent need for direct-acting drugs capable of suppressing or stopping the main mechanisms of reproduction of the coronavirus SARS-CoV-2.

Voronoi Polyhedra as a Tool for the Characterization of Inhomogeneous Distribution in 1-Butyl-3-methylimidazolium Cation-Based Ionic Liquids.

The inhomogeneity distribution in four imidazolium-based ionic liquids (ILs) containing the 1-butyl-3-methylimidazolium (Cmim) cation, coupled with tetrafluoroborate (BF), hexafluorophosphate (PF), bis(trifluoromethanesulfonyl)amide (TFSA), and trifluoromethanesulfonate (TfO) anions, was characterized using Voronoi polyhedra. For this purpose, molecular dynamic simulations have been performed on the isothermal-isobaric () ensemble. We checked the ability of the potential models to reproduce the experimental density, heat of vaporization, and transport properties (diffusion and viscosity) of these ionic liquids.

Distance Angle Descriptors of the Interionic and Ion-Solvent Interactions in Imidazolium-Based Ionic Liquid Mixtures with Aprotic Solvents: A Molecular Dynamics Simulation Study.

The aim of this paper is to quantify the changes of the interionic and ion-solvent interactions in mixtures of imidazolium-based ionic liquids, having tetrafluoroborate (BmimBF), hexafluorophosphate (BmimPF), trifluoromethylsulfonate (BmimTFO), or bis(trifluoromethanesulfonyl)imide (BmimTFSI), anions, and polar aprotic molecular solvents, such as acetonitrile (AN), γ-butyrolactone (GBL), and propylene carbonate (PC). For this purpose, we calculate, using the nearest-neighbor approach, the average distance between the imidazolium ring H atom in positions 2, 4, and 5 (H) and the nearest high-electronegativity atom of the solvent or anion (X) as distance descriptors, and the mean angle formed by the C-H bond and the H···X axis around the H atom as angular descriptors of the cation-anion and cation-solvent interactions around the ring C-H groups. The behavior of these descriptors as a function of the ionic liquid mole fraction is analyzed in detail.

The local structure in the BmimPF/acetonitrile mixture: the charge distribution effect.

The changes of the local structure in the binary mixture of 1-butyl-3-methylimidazolium hexafluorophosphate (BmimPF6) ionic liquid and acetonitrile are investigated over the entire composition range. Two charge distribution models of the ions are considered: in the first one, the atomic fractional charges of the cations and anions are kept equal with those in the neat ionic liquid, and hence they are independent from the mole fraction of the ionic liquid, while in the second one the charge distribution is scaled up by a mole fraction dependent factor. The sum of these charges converge to +1e and -1e on the cation and anion, respectively, at infinite dilution.

Poly(vinyl alcohol) as a water protecting agent for silver nanoparticles: the role of polymer size and structure.

Chemical modification of silver nanoparticles (AgNPs) with a stabilizing agent, such as poly(vinyl alcohol) (PVA), plays an important role in shape-controlled seeded-growth and colloidal stability. However, theoretical aspects of the stabilizing mechanism of PVA are still poorly understood. To gain a better understanding of the role of PVA in water protecting effects for silver nanoparticles, we developed an atomistic model of a AgNP grafted with single-chain PVA of various lengths.

Competition between Cation-Solvent and Cation-Anion Interactions in Imidazolium Ionic Liquids with Polar Aprotic Solvents.

The subtle interplay between ion solvation and association was analyzed in mixtures of imidazolium-based ionic liquids (ILs) with polar aprotic solvents. A site-specific pattern of cation-solvent and cation-anion interactions was disclosed by a careful analysis of the H and C NMR chemical shift dependence of the mixture composition. It was established that the less polar but more donating γ-butyrolactone is more prone to establish H-bonds with the imidazolium-ring hydrogen atoms of the IL cations than propylene carbonate, particularly at the H site and at high dilutions x <0.

Local Structure in Terms of Nearest-Neighbor Approach in 1-Butyl-3-methylimidazolium-Based Ionic Liquids: MD Simulations.

Description of the local microscopic structure in ionic liquids (ILs) is a prerequisite to obtain a comprehensive understanding of the influence of the nature of ions on the properties of ILs. The local structure is mainly determined by the spatial arrangement of the nearest neighboring ions. Therefore, the main interaction patterns in ILs, such as cation-anion H-bond-like motifs, cation-cation alkyl tail aggregation, and ring stacking, were considered within the framework of the nearest-neighbor approach with respect to each particular interaction site.

Control of Carbon Nanotube Electronic Properties by Lithium Cation Intercalation.

We show that the electronic properties of single walled carbon nanotubes (SWCNTs) can be tuned continuously from semiconducting to metallic by varying the location of ions inside the tubes. Focusing on the Li(+) cation inside the (26,0) zigzag semiconducting and (15,15) armchair metallic SWCNTs, we found that the Li(+)-SWCNT interaction is attractive. The interaction is stronger for the metallic SWCNT, indicating in particular that metallic tubes can enhance performance of lithium-ion batteries.

Probing structural patterns of ion association and solvation in mixtures of imidazolium ionic liquids with acetonitrile by means of relative (1)H and (13)C NMR chemical shifts.

Mixtures of ionic liquids (ILs) with polar aprotic solvents in different combinations and under different conditions (concentration, temperature etc.) are used widely in electrochemistry. However, little is known about the key intermolecular interactions in such mixtures depending on the nature of the constituents and mixture composition.

Non-covalent interactions in ionic liquid ion pairs and ion pair dimers: a quantum chemical calculation analysis.

Ionic liquids (ILs) being composed of bulky multiatomic ions reveal a plethora of non-covalent interactions which determine their microscopic structure. In order to establish the main peculiarities of these interactions in an IL-environment, we have performed quantum chemical calculations for a set of representative model molecular clusters. These calculations were coupled with advanced methods of analysis of the electron density distribution, namely, the quantum theory of atoms in molecules (QTAIM) and the non-covalent interaction (NCI; J.

Complexation of Ni(ClO4)2 and Mg(ClO4)2 with 3-hydroxyflavone in acetonitrile medium: conductometric, spectroscopic, and quantum chemical investigation.

The complex formation of Ni(ClO4)2 and Mg(ClO4)2 with 3-hydroxyflavone (HL, flavonol) in acetonitrile was studied using conductometric and spectroscopic methods. It was found that interaction of nickel cation with HL leads to formation of the doubly charged [Ni(HL)](2+) complex, whereas in solutions of magnesium perchlorate the complex with anion [MgClO4(HL)](+) is formed. Using the extended Lee-Wheaton equation, the limiting equivalent conductivities of [Ni(HL)](2+) and [MgClO4(HL)](+) and thermodynamic constants of their formation were obtained at 288, 298, 308, 318, and 328 K.

Structure, solvation, and dynamics of Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺ complexes with 3-hydroxyflavone and perchlorate anion in acetonitrile medium: a molecular dynamics simulation study.

Molecular dynamics simulations of complexes of Mg(2+), Ca(2+), Sr(2+), and Ba(2+) with 3-hydroxyflavone (flavonol, 3HF) and ClO₄⁻ in acetonitrile were performed. The united atoms force field model was proposed for the 3HF molecule using the results of DFT quantum chemical calculations. 3HF was interpreted as a rigid molecule with two internal degrees of freedom, i.

Translational diffusion in mixtures of imidazolium ILs with polar aprotic molecular solvents.

Self-diffusion coefficients of cations and solvent molecules were determined with (1)H NMR in mixtures of 1-n-butyl-3-methylimidazolium (Bmim(+)) tetrafluoroborate (BF4(-)), hexafluorophosphate (PF6(-)), trifluoromethanesulfonate (TfO(-)), and bis(trifluoromethylsulfonyl)imide (TFSI(-)) with acetonitrile (AN), γ-butyrolactone (γ-BL), and propylene carbonate (PC) over the entire composition range at 300 K. The relative diffusivities of solvent molecules to cations as a function of concentration were found to depend on the solvent but not on the anion (i.e.

Acetonitrile boosts conductivity of imidazolium ionic liquids.

We apply a new methodology in the force field generation (Phys. Chem. Chem.

A new force field model for the simulation of transport properties of imidazolium-based ionic liquids.

A new, non-polarizable force field model (FFM) for imidazolium-based, room-temperature ionic liquids (RTILs), 1-ethyl-3-methyl-imidazolium tetrafluoroborate and 1-butyl-3-methyl-imidazolium tetrafluoroborate, has been developed. Modifying the FFM originally designed by Liu et al. (J.

Vibrational energy transfer between carbon nanotubes and liquid water: a molecular dynamics study.

The rates and magnitudes of vibrational energy transfer between single-wall carbon nanotubes (CNTs) and water are investigated by classical molecular dynamics. The interactions between the CNT and solvent confined inside of the tube, the CNT and solvent surrounding the tube, as well as the solvent inside and outside of the tube are considered for the (11,11), (15,15), and (19,19) armchair CNTs. The vibrational energy transfer exhibits two time scales, subpicosecond and picosecond, of roughly equal importance.

Ab initio study of phonon-induced dephasing of electronic excitations in narrow graphene nanoribbons.

Vibrational dephasing of the lowest energy electronic excitations in the perfect (16,16) graphene nanoribbon (GNR) and those with the C2-bond insertion and rotation defects is studied with ab initio molecular dynamics. Compared to single-walled carbon nanotubes (SWCNTs) of similar size, GNRs shows very different properties. The dephasing in the ideal GNR occurs twice faster than that in the SWCNTs.

Uniform diffusion of acetonitrile inside carbon nanotubes favors supercapacitor performance.

An unusual behavior of liquid acetonitrile (AN) confined inside carbon nanotubes (CNTs) is predicted by molecular dynamics simulation. In contrast to water, which shows inhomogeneous variation of both translational and rotational diffusion with CNT diameter [ Nano Lett. 2003, 3, 589; 2004, 4, 619], the diffusion coefficient of AN changes uniformly and can be described by a simple analytic model.

Dynamics and structure of nickel chloride-methanol solutions: quasi-elastic neutron scattering and molecular dynamics simulations.

The high-resolution quasi-elastic neutron scattering (QENS) technique has been applied to study the translational diffusion of methanol protons in pure methanol (MeOH) at 223 and 297 K, and in 0.3 and 1.3 molal non-aqueous electrolyte solutions (NAESs) of NiCl in methanol at 297 K.