We use molecular dynamics simulations to study the structure, dynamics, and transport properties of nano-confined water between parallel graphite plates with separation distances (H) from 7 to 20 Å at different water densities with an emphasis on anisotropies generated by confinement. The behavior of the confined water phase is compared to non-confined bulk water under similar pressure and temperature conditions. Our simulations show anisotropic structure and dynamics of the confined water phase in directions parallel and perpendicular to the graphite plate. The magnitude of these anisotropies depends on the slit width H. Confined water shows "solid-like" structure and slow dynamics for the water layers near the plates. The mean square displacements (MSDs) and velocity autocorrelation functions (VACFs) for directions parallel and perpendicular to the graphite plates are calculated. By increasing the confinement distance from H = 7 Å to H = 20 Å, the MSD increases and the behavior of the VACF indicates that the confined water changes from solid-like to liquid-like dynamics. If the initial density of the water phase is set up using geometric criteria (i.e., distance between the graphite plates), large pressures (in the order of ~10 katm), and large pressure anisotropies are established within the water. By decreasing the density of the water between the confined plates to about 0.9 g cm(-3), bubble formation and restructuring of the water layers are observed.

COVID-19, a newly discovered type of coronavirus, is the cause of the pandemic infection that was first reported in Wuhan, China, in December 2019. One of the most critical problems in this regard is to identify innovative drugs that may reduce or manage this global health concern. Nanoparticles have shown a pivotal role in drug delivery systems in recent decades. The surface of nanoparticles could be covered by a layer composed of different biomolecules (e.g., proteins and macromolecules) following the incubation with a biological fluid. This protein-rich layer is called “Protein Corona.” In this study, an all-atom molecular dynamics simulation was used for investigating the monomeric B domain of the spike glycoprotein due to its role in the accessibility of the spike glycoprotein to single-wall carbon nanotubes (SWCNTs). The interaction energy values between the carbon nanotube and B domain of the viral spike glycoprotein were evaluated. The obtained results, based on Lennard-Jones potentials, demonstrated that SWCNTs had an affinity to the B domain of the S1 subunit in the spike glycoprotein. The adsorption of SWCNTs on the B domain surface led to a significant change in solvent-accessible surface, internal hydrogen bonds, and finally in the tertiary structure, which could provide a reasonable method to impede the interaction between the angiotensin-converting enzyme II and SARS-CoV-2 spike glycoprotein. A decrease in the mean square displacement of the B domain was shown after the adsorption of SWCNTs as a result of increasing the hydrophobic-hydrophilic properties of the B domain. The arrangement of SWCNTs on the B domain surface and their interaction using the 2-acetamido-2-deoxy-β-D-glucopyranose group (988, 991, and 992) demonstrated that a change in the affinity of the S1 subunit could be used as a barrier to viral replication. The analysis of the SWCNT-B domain complex indicated that the presence of SWCNTs is able to cause alterations in the S1 subunit of the spike protein, and these nanotubes could be employed for further in-vitro and in-vivo antiviral studies. Also, SWCNTs are able to be utilized in drug delivery systems.

Molecular dynamics simulations are used to investigate microscopic structures and dynamics of methanol and methanol-water binary mixture films confined between hydrophobic infinite parallel graphite plate slits with widths, H, in the range of 7–20 Å at 300 K. The initial geometric densities of the liquids were chosen to be the same as bulk methanol at the same temperature. For the two narrowest slit widths, two smaller initial densities were also considered. For the nano-confined system with H = 7 Å and high pressure, a solid-like hexagonal arrangement of methanol molecules arranged perpendicular to the plates is observed which reflects the closest packing of the molecules and partially mirrors the structure of the underlying graphite structure. At lower pressures and for larger slit widths, in the contact layer, the methanol molecules prefer having the C–O bond oriented parallel to the walls. Layered structures of methanol parallel to the wall were observed, with contact layers and additional numbers of central layers depending on the particular slit width. For methanol–water mixtures, simulations of solutions with different composition were performed between infinite graphite slits with H = 10 and 20 Å at 300 K. For the nanoslit with H = 10 Å, in the solution mixtures, three layers of molecules form, but for all mole fractions of methanol, methanol molecules are excluded from the central fluid layer. In the nanopore with H = 20 Å, more than three fluid layers are formed and methanol concentrations are enhanced near the confining plates walls compared to the average solution stoichiometry. The self-diffusion coefficients of methanol and water molecules in the solution show strong dependence on the solution concentration. The solution mole fractions with minimal diffusivity are the same in confined and non-confined bulk methanol-water mixtures.

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