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.
Coronaviruses (CoVs) have been responsible for three major outbreaks since the
beginning of the 21st century, and the emergence of the recent COVID-19 pandemic has
resulted in considerable efforts to design new therapies against coronaviruses. Thus, it
is crucial to understand the structural features of their major proteins related to the
virus–host interaction. Several studies have shown that from the seven known CoV
human pathogens, three of them use the human Angiotensin-Converting Enzyme 2 (hACE-2) to
mediate their host’s cell entry: SARS-CoV-2, SARS-CoV, and HCoV-NL63. Therefore,
we employed quantum biochemistry techniques within the density function theory (DFT)
framework and the molecular fragmentation with conjugate caps (MFCC) approach to analyze
the interactions between the hACE-2 and the spike protein-RBD of the three CoVs in order
to map the hot-spot residues that form the recognition surface for these complexes and
define the similarities and differences in the interaction scenario. The total
interaction energy evaluated showed a good agreement with the experimental binding
affinity order: SARS-2 > SARS > NL63. A detailed investigation revealed the
energetically most relevant regions of hACE-2 and the spike protein for each complex, as
well as the key residue–residue interactions. Our results provide valuable
information to deeply understand the structural behavior and binding site
characteristics that could help to develop antiviral therapeutics that inhibit
protein–protein interactions between CoVs S protein and hACE-2.
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