Wetting and dewetting of a (6,6) carbon nanotube in presence of an orthogonal electric field of varying strengths are studied by means of molecular dynamics simulations using seven different models of water. We have looked at filling of the channel, occupancy and structure of water inside it, associated free energy profiles, and also dynamical properties like the time scales of collective dipole flipping and residence dynamics. For the current systems where the entire simulation box is under the electric field, the nanotube is found to undergo electrodrying, i.e., transition from filled to empty states on increase of the electric field. The free energy calculations show that the empty state is the most stable one at higher electric field as it raptures the hydrogen bond environment inside the carbon nanotube by reorienting water molecules to its direction leading to a depletion of water molecules inside the channel. We investigated the collective flipping of water dipoles inside the channel and found that it follows a fast stepwise mechanism. On the dynamical side, the dipole flipping is found to occur at a faster rate with increase of the electric field. Also, the rate of water flow is found to decrease dramatically as the field strength is increased. The residence time of water molecules inside the channel is also found to decrease with increasing electric field. Although the effects of electric field on different water models are found to be qualitatively similar, the quantitative details can be different for different models. In particular, the dynamics of water molecules inside the channel can vary significantly for different water models. However, the general behavior of wetting and dewetting transitions, enhanced dipole flips, and shorter residence times on application of an orthogonal electric field hold true for all water models considered in the current work.

Structural and dynamical properties of interfacial water molecules near a hexagonal boron nitride sheet (h-BN) are investigated by means of Born-Oppenheimer molecular dynamics simulations. Orientational profiles in the interfacial regions reveal two distinct types of water molecules near the BN surface. Depending on the positions of the water molecules, on top of either N or B atoms, one type contains water molecules that are oriented with one OH bond pointing toward the N atoms and the other type contains water molecules that remain parallel to the BN sheet. Distinct hydrogen bonding and stabilization energies of these two types of water molecules are found from our calculations. In order to see the effects of dispersion interactions, simulations are performed with the BLYP (Becke-Lee-Yang-Parr) functional and also BLYP with Grimme's D3 corrections (BLYP-D3). An enhancement of water ordering near the surface is observed with the inclusion of dispersion corrections. Further analysis of the diffusion coefficients, rotational time correlation functions, and hydrogen bond dynamics shows that water molecules near the h-BN sheet move faster compared to bulk water molecules both translationally and rotationally. The water molecules in the first layer are found to show substantial lateral diffusion. The escape dynamics of water from the solvation layer at the BN surface is also looked at in the current study. We have also investigated some of the electronic properties of interfacial water such as the charge density and dipole moment. It is found that the water molecules at the surface of the BN sheet have a lower dipole moment than bulk molecules.

A novel coronavirus (SARS-CoV-2; COVID-19) that initially originates from Wuhan province in China has emerged as a global pandemic, an outbreak that started at the end of 2019 which claims 431,192 (Date: 15 th June 2020 (https://covid19.who.in) life till now. Since then scientists all over the world are engaged in developing new vaccines, antibodies, or drug molecules to combat this new threat. Here in this work, we performed an in-silico analysis on the protein-protein interactions between the receptor-binding (RBD) domain of viral SPIKE protein and human angiotensinconverting enzyme 2 (hACE2) receptor to highlight the key alteration that happened from SARS-CoV to SARS-CoV-2. We analyzed and compared the molecular differences between these two viruses by using various computational approaches such as binding affinity calculations, computational alanine, and molecular dynamics simulations. The binding affinity calculations show SARS-CoV-2 binds little more firmly to the hACE2 receptor than that of SARS-CoV. Analysis of simulation trajectories reveals that enhanced hydrophobic contacts or the van derWaals interaction play a major role in stabilizing the protein-protein interface. The major finding obtained from molecular dynamics simulations is that the RBD-ACE2 interface is populated with water molecules and interacts strongly with both RBD and ACE2 interfacial residues during the simulation periods. We also emphasize that the interfacial water molecules play a critical role in binding and maintaining the stability of the RBD/hACE2 complex. The water-mediated hydrogen bond by the bridge water molecules is crucial for stabilizing the RBD and ACE2 domains. The structural and dynamical features presented here may serve as a guide for developing new drug molecules, vaccines, or antibodies to combat the COVID-19 pandemic.

Structural, dynamical, and dipolar properties of water molecules in nanoconfinement between either two hexagonal boron nitride (h-BN) or two graphene sheets are investigated by means of ab initio and classical molecular dynamics simulations. In particular, we have focused on the perturbation of water properties caused by the two confining h-BN and graphene sheets when they are separated by a distance in the nanodomain. The structure of water near h-BN sheets is found to be noticeably different from that for graphene sheets because of the presence of polar bonds in the BN sheets. The density profiles show that water is more structured near the h-BN sheets than near graphene. The orientational profiles of water molecules near the h-BN and graphene surfaces also reveal differences in water orientational structure near the two surfaces. Various dynamical quantities such as the rotational relaxation, diffusion, hydrogen bond dynamics, and the escape dynamics from the solvation layers near the surfaces reveal a slower relaxation for the interfacial water near h-BN sheets. The slowdown of the dynamics can be attributed to the interactions of water with polar B–N bonds. The partial charges on the B and N atoms are found to make the water–surface interactions more favorable for the BN sheets than for the nonpolar graphene surfaces. The force-field-based classical simulation results are found to be qualitatively similar to those of ab initio simulations for the structural behavior, although some differences are found in the dynamical properties. The ab initio simulations reveal a faster rotational dynamics of the interfacial water molecules than that of bulk, whereas an opposite behavior is predicted by the empirical force fields used in the current study.

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The severity of global pandemic due to severe acute respiratory syndrome coronavirus-2 (SARS–CoV-2) has engaged the researchers and clinicians to find the key features triggering the viral infection to lung cells. By utilizing such crucial information, researchers and scientists try to combat the spread of the virus. Here, in this work, we performed in silico analysis of the protein–protein interactions between the receptor-binding domain (RBD) of the viral spike protein and the human angiotensin-converting enzyme 2 (hACE2) receptor to highlight the key alteration that happened from SARS-CoV to SARS-CoV-2. We analyzed and compared the molecular differences between spike proteins of the two viruses using various computational approaches such as binding affinity calculations, computational alanine, and molecular dynamics simulations. The binding affinity calculations showed that SARS-CoV-2 binds a little more firmly to the hACE2 receptor than SARS-CoV. The major finding obtained from molecular dynamics simulations was that the RBD–ACE2 interface is populated with water molecules and interacts strongly with both RBD and ACE2 interfacial residues during the simulation periods. The water-mediated hydrogen bond by the bridge water molecules is crucial for stabilizing the RBD and ACE2 domains. Near-ambient pressure X-ray photoelectron spectroscopy (NAP-XPS) confirmed the presence of vapor and molecular water phases in the protein–protein interfacial domain, further validating the computationally predicted interfacial water molecules. In addition, we examined the role of interfacial water molecules in virus uptake by lung cell A549 by binding and maintaining the RBD/hACE2 complex at varying temperatures using nanourchins coated with spike proteins as pseudoviruses and fluorescence-activated cell sorting (FACS) as a quantitative approach. The structural and dynamical features presented here may serve as a guide for developing new drug molecules, vaccines, or antibodies to combat the COVID-19 pandemic.

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In this work, we have studied the behavior of water molecules confined in nanobubbles at the hybrid interfaces of graphene and diamond surfaces at varying temperatures. We have performed molecular dynamics simulations to investigate different spectral and dynamical properties of the confined water. The confined water molecules are characterized through calculations of their vibrational spectral properties. The spectral features are found to change significantly with variation of temperature and density of the nanobubbles. The calculated vibrational spectral results are found to be in reasonably good agreement with available experiments. Furthermore, we have looked at the dynamical properties of water molecules in the graphene nanobubbles. The current results reveal the presence of strong heterogeneity in the dynamical properties in nanobubbles at supercritical temperature. Water molecules that are confined in small nanobubbles at high density are found to possess very slow relaxation time scales because of stronger hydrogen bonding and spatial constraints. These water molecules can be considered as essentially irrotational water molecules. In other cases, water molecules confined in nanobubbles at lower density at supercritical temperature are found to show very fast relaxation time scales as the thermal energy dominates the dynamics of water molecules in these cases.