The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.

Among the alternative host materials for solid polymer electrolytes (SPEs), polycarbonates have recently shown promising functionality in all-solid-state lithium batteries from ambient to elevated temperatures. While the computational and experimental investigations of ion conduction in conventional polyethers have been extensive, the ion transport in polycarbonates has been much less studied. The present work investigates the ionic transport behavior in SPEs based on poly(trimethylene carbonate) (PTMC) and its co-polymer with ε-caprolactone (CL) via both experimental and computational approaches. FTIR spectra indicated a preferential local coordination between Li(+) and ester carbonyl oxygen atoms in the P(TMC20CL80) co-polymer SPE. Diffusion NMR revealed that the co-polymer SPE also displays higher ion mobilities than PTMC. For both systems, locally oriented polymer domains, a few hundred nanometers in size and with limited connections between them, were inferred from the NMR spin relaxation and diffusion data. Potentiostatic polarization experiments revealed notably higher cationic transference numbers in the polycarbonate based SPEs as compared to conventional polyether based SPEs. In addition, MD simulations provided atomic-scale insight into the structure-dynamics properties, including confirmation of a preferential Li(+)-carbonyl oxygen atom coordination, with a preference in coordination to the ester based monomers. A coupling of the Li-ion dynamics to the polymer chain dynamics was indicated by both simulations and experiments.

Herein, molecular modeling techniques were used with the main goal to obtain candidates from a drug database as potential targets to be used against SARS-CoV-2. This novel coronavirus, responsible by the COVID-19 outbreak since the end of 2019, became a challenge since there is not vaccine for this disease. The first step in this investigation was to solvate the isolated S-protein in water for molecular dynamics (MD) simulation, being observed a transition from "up" to "down" conformation of receptor-binding domain (RBD) of the S-protein with angle of 54.3 and 43.0 degrees, respectively. The RBD region was more exposed to the solvent and to the possible drugs due to its enhanced surface area. From the equilibrated MD structure, virtual screening by docking calculations were performed using a library contained 9091 FDA approved drugs. Among them, 24 best-scored ligands (14 traditional herbal isolate and 10 approved drugs) with the binding energy below -8.1 kcal/mol were selected as potential candidates to inhibit the SARS-CoV-2 S-protein, preventing the human cell infection and their replication. For instance, the ivermectin drug (present in our list of promise candidates) was recently used successful to control viral replication in vitro. MD simulations were performed for the three best ligands@S-protein complexes and the binding energies were calculated using the MM/ PBSA approach. Overall, it is highlighted an important strategy, some key residues, and chemical groups which may be considered on clinical trials for COVID-19 outbreak.

This paper presents atomistic molecular dynamics simulation studies of lithium bis(trifluoromethane)sulfonylimide (LiTFSI) in a blend of 1-ethyl-3-methylimidazolium (EMIm)-TFSI and poly(ethylene oxide) (PEO), which is a promising electrolyte material for Li- and Li-ion batteries. Simulations of 100 ns were performed for temperatures between 303 K and 423 K, for a Li:ether oxygen ratio of 1:16, and for PEO chains with 26 EO repeating units. Li(+) coordination and transportation were studied in the ternary electrolyte system, i.e., PEO16LiTFSI⋅1.0 EMImTFSI, by applying three different force field models and are here compared to relevant simulation and experimental data. The force fields generated significantly different results, where a scaled charge model displayed the most reasonable comparisons with previous work and overall consistency. It is generally seen that the Li cations are primarily coordinated to polymer chains and less coupled to TFSI anion. The addition of EMImTFSI in the electrolyte system enhances Li diffusion, associated to the enhanced TFSI dynamics observed when increasing the overall TFSI anion concentration in the polymer matrix.

The structural and dynamical changes in the solvation shell surrounding Li+ in a multianion environment are studied by Raman spectroscopy and molecular dynamics (MD) simulations. The ternary electrolyte is composed of a mixture of two ionic liquids (ILs), n-methyl-n-propylpyrrolidinium bis­(trifluoromethanesulfonyl)­imide ([PYR13]­[TFSI]) and 1-ethyl-3-methylimidazolium dicyanamide ([EMIM]­[DCA]), and a lithium bis­(trifluoromethanesulfonyl)­imide ([Li]­[TFSI]) salt (0–1 M). A 1:9 volumetric mixture of [PYR13]­[TFSI]/[EMIM]­[DCA] formed an eutectic that exhibited a lower melting point than that of either parent IL. The local structure of Li+ in this eutectic is found to be heterogenous and preferentially solvated by [DCA], which is the smaller and more abundant anion. Whereas [TFSI] is able to bridge multiple Li+ at high salt concentrations and form both monodentate and bidentate conformations through its oxygen atoms, [DCA] is capable of forming only monodentate coordination with Li+ through either of its end nitrogen atoms. The Raman and MD analyses suggest a wide distribution of solvation structures in the form of [Li­(TFSI) m (DCA) n ](m+n−1)– where m = 0–1 and n = 3–4. The computations showed increased ion pair lifetime for Li+–[DCA] and decreased lifetimes for Li+–[TFSI] in the ternary mixture with the increase in the [Li]­[TFSI] concentration. These results show that the solvation and transport properties of charge carriers in ILs can be modified via the presence of multiple ions with varying degree of coordination, which provides an approach to impact the performance in electrochemical processes.

Molecular dynamics (MD) simulations have been performed for prototype models of polymer electrolytes in which the salt is an ionic liquid based on 1-alkyl-3-methylimidazolium cations and the polymer is poly(ethylene oxide), PEO. The MD simulations were performed by combining the previously proposed models for pure ionic liquids and polymer electrolytes containing simple inorganic ions. A systematic investigation of ionic liquid concentration, temperature, and the 1-alkyl- chain length, [1,3-dimethylimidazolium]PF6, and [1-butyl-3-methylimidazolium]PF6, effects on resulting equilibrium structure is provided. It is shown that the ionic liquid is dispersed in the polymeric matrix, but ionic pairs remain in the polymer electrolyte. Imidazolium cations are coordinated by both the anions and the oxygen atoms of PEO chains. Probability density maps of occurrences of nearest neighbors around imidazolium cations give a detailed physical picture of the environment experienced by cations. Conformational changes on PEO chains upon addition of the ionic liquid are identified. The equilibrium structure of simulated systems is also analyzed in reciprocal space by using the static structure factor, S(k). Calculated S(k) display a low wave-vector peak, indicating that spatial correlation in an extended-range order prevail in the ionic liquid polymer electrolytes. Long-range correlations are assigned to nonuniform distribution of ionic species within the simulation box.

In recent years, the global climate change is in evidence and it is almost a consensus that it is caused by the greenhouse gases emissions. An alternative to reduce these emissions is carbon capture and storage (CCS), which employs solvents based on amine compounds. In this scene, ionic liquids (IL) have been investigated to a greater extent for this application. In this work, we make an evaluation of interactions between gases (CO2, SO2, and H2S) and anion/cation from IL, as well as cation-anion interactions. For this, quantum calculations under vacuum were performed at the B3LYP/6-311+G** level of theory and using the M06-2X functional, where dispersion effects are considered. Among the well-studied systems based on imidazolium cations and fluorinated anions, we also studied the tetraalkylammonium, tetraalkylphosphonium, ether-functionalized imidazolium based systems, and tetrahexylammonium bis(trifluoromethanesulfonyl)imide, [THA][Tf2N], as a potential prototype. The ion pairs evaluated include [Tf2N](-)-based IL, with alkyl chain varying from [C1mim](+) to [C8mim](+) and [C1mim](+)-based IL. We found that the anion becomes more available to interact with gas with the weakening of the cation-anion interaction. [THA][Tf2N] has a binding energy of -274.89 kJ/mol at the B3LYP/6-311+G** level of theory, which is considered energetically interesting to gas capture applications.

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