We present a complete force field for liquid-state simulations on ionic liquids containing 1-ethyl-3methylimidazolium and 1-n-butyl-3-methylimidazolium cations and the tetrachloroaluminate and tetrafluoroborate anions. The force field is compatible with the AMBER methodology and is easily extendable to other dialkylimidazolium salts. On the basis of the general AMBER procedures to develop lacking intramolecular parameters and the RESP approach to calculate the atomic point charges, we obtained an all-atom force field which was validated against the experimental density, diffusion coefficient, vibrational frequencies, as well as X-ray (crystal state) and neutron (liquid state) diffraction structural data. Moreover, molecular mechanics calculations for the developed force field produce the cation's structures and dipole moments in very good agreement with quantum mechanical ab initio calculations. In addition, a basic study concerning the simulated liquid structure in terms of the radial distribution functions has been undertaken using molecular dynamics simulation. In summary, we achieved a very consistent picture in the computed data for the four room-temperature molten salts.

A classical force field for the room temperature molten salt 1-ethyl-3-methylimidazolium tetrachloroaluminate has been developed and successfully tested against experimental data (neutron diffraction, diffusion constants) by molecular dynamics computer simulation corresponding to a temperature of 298 K. The force field parameters for the cation have been derived from the AMBER description for the protonated amino acid histidine, whereas the AlCl4 - parameters have been achieved by parametrization of intramolecular terms with van der Waals parameters taken from the literature. All atomic partial charges have been obtained from ab initio calculations using the RESP methodology.

The SARS‐CoV‐2 pandemic is the biggest health concern today, but until now there is no treatment. One possible drug target is the receptor binding domain (RBD) of the coronavirus’ spike protein, which recognizes the human angiotensin‐converting enzyme 2 (hACE2). Our in silico study discusses crucial structural and thermodynamic aspects of the interactions involving RBDs from the SARS‐CoV and SARS‐CoV‐2 with the hACE2. Molecular docking and molecular dynamics simulations explain why the chemical affinity of the new SARS‐CoV‐2 for hACE2 is much higher than in the case of SARS‐CoV, revealing an intricate pattern of hydrogen bonds and hydrophobic interactions and estimating a free energy of binding, which is consistently much more negative in the case of SARS‐CoV‐2. This work presents a chemical reason for the difficulty in treating the SARS‐CoV‐2 virus with drugs targeting its spike protein and helps to explain its infectiousness.

We present a detailed computational study of the structure of ionic liquids based on the imidazolium cation. Both imidazolium-ring stacking and hydrogen bonding behavior are investigated from radial and spatial orientational distribution functions, as well as orientational correlation functions. The alkyl chain size and anion effect on the liquid structure are provided and discussed. Our results support models for liquid organization comparable to those formulated on the basis of experimental observations.

The redistribution of O and N during the final, thermal oxidation in dry O2 step in the formation of ultrathin silicon oxide/nitride/oxide dielectric films (ONO) was investigated using isotopic tracing and depth profiling with nanometer resolution. The results show that the final oxidation step induces atomic transport of O and N species in the system, such that the formed ONO structures are not stacked layer structures, but rather a silicon oxynitride ultrathin film, having moderate concentrations of N in the near-surface and near-interface regions, and a high N concentration in the bulk.