The role of the envelope protein in the stability of a coronavirus model membrane against an ethanolic disinfectant.

Ethanol is highly effective against various enveloped viruses and can disable the virus by disintegrating the protective envelope surrounding it. The interactions between the coronavirus envelope (E) protein and its membrane environment play key roles in the stability and function of the viral envelope. By using molecular dynamics simulation, we explore the underlying mechanism of ethanol-induced disruption of a model coronavirus membrane and, in detail, interactions of the E-protein and lipids. We model the membrane bilayer as N-palmitoyl-sphingomyelin and 1-palmitoyl-2-oleoylphosphatidylcholine lipids and the coronavirus E-protein. The study reveals that ethanol causes an increase in the lateral area of the bilayer along with thinning of the bilayer membrane and orientational disordering of lipid tails. Ethanol resides at the head-tail region of the membrane and enhances bilayer permeability. We found an envelope-protein-mediated increase in the ordering of lipid tails. Our simulations also provide important insights into the orientation of the envelope protein in a model membrane environment. At ∼25 mol. % of ethanol in the surrounding ethanol-water phase, we observe disintegration of the lipid bilayer and dislocation of the E-protein from the membrane environment.

Sequence-Engineering Polyethylene-Polypropylene Copolymers with High Thermal Conductivity Using a Molecular-Dynamics-Based Genetic Algorithm.

Polymer sequence engineering is emerging as a potential tool to modulate material properties. Here, we employ a combination of a genetic algorithm (GA) and atomistic molecular dynamics (MD) simulation to design polyethylene-polypropylene (PE-PP) copolymers with the aim of identifying a specific sequence with high thermal conductivity. PE-PP copolymers with various sequences at the same monomer ratio are found to have a broad distribution of thermal conductivities. This indicates that the monomer sequence has a crucial effect on thermal energy transport of the copolymers. A non-periodic and non-intuitive optimal sequence is indeed identified by the GA, which gives the highest thermal conductivity compared with any regular block copolymers, for example, diblock, triblock, and hexablock. In comparison to the bulk density, chain conformations, and vibrational density of states, the monomer sequence has the strongest impact on the efficiency of thermal energy transport via inter- and intra-molecular interactions. Our work highlights polymer sequence engineering as a promising approach for tuning the thermal conductivity of copolymers, and it provides an example application of integrating atomistic MD modeling with the GA for computational material design.

Solubility of Carbon Dioxide in Pentaerythritol Hexanoate: Molecular Dynamics Simulation of a Refrigerant-Lubricant Oil System.

We have investigated the solubility and the solvation structure between a refrigerant (carbon dioxide, CO2) and a lubricant oil (pentaerythritol hexanoate, PEC6) by molecular dynamics simulations. First, to investigate the solubility, we calculated the vapor-liquid equilibrium pressure. The chemical potential of the liquid phase and the gas phase were calculated, and the equilibrium state was obtained from the crossing point of these chemical potentials. The equilibrium pressures agreed well with experimental data over a wide range of temperatures and mole fractions of CO2. Second, the solvation structure was also investigated on a molecular scale. We found the following characteristics. First, the tails of the lubricant oil are relatively rigid inside the ester groups but flexible beyond. Second, CO2 molecules barely enter the lubricant core as delimited by the ester groups. Third, the double-bonded oxygen atoms of the ester groups are good sorption sites for CO2. Fourth, only a few CO2 molecules are attached to more than one carbonyl oxygen simultaneously. Finally, there is also significant unspecific sorption of CO2 in the alkane tail region. These results indicate that increasing the size of the rigid lubricant core would probably decrease the solubility, whereas increasing the number of polar groups would increase it.

Azobenzene switch with a long-lived cis-state to photocontrol the enzyme activity of a histone deacetylase-like amidohydrolase.

The control of enzymes by use of an external stimulus such as light enables the temporal and spatial regulation of defined chemical reactions in a highly precise manner. In this work we investigated and characterized the reversible photocontrol of a bacterial histone deacetylase-like amidohydrolase (HDAH) from Bordetella/Alcaligenes strain FB188, which holds great potential to control deacetylation reactions of a broad spectrum of substrates in biotechnological and biomedical applications. Several HDAH variants with a single surface accessible cysteine close to the active site were developed and covalently modified by a monofunctional azobenzene-based photoswitch [4-phenylazomaleinanil (4-PAM)]. The enzymatic activity of three HDAH variants (M30C, S20C and M150C) were shown to be controlled by light. The thermal cis-to-trans relaxation of azobenzene conjugated to HDAH was up to 50-fold retarded compared to unbound 4-PAM allowing light pulse switching rather than continuing irradiation to maintain the thermodynamically less stable cis-state of covalently attached 4-PAM.

Water permeability of poly(ethylene terephthalate): a grand canonical ensemble molecular dynamics simulation study.

In this work, our previous simulation method on the calculation of solubility of nonpolar solutes in nonpolar polymers [H. Eslami and F. Müller-Plathe, Macromolecules 40, 6413 (2007)] has been extended to the case of solubility calculation for water, as a polar penetrant, in poly(ethylene terephthalate), as a polar polymer. The chemical potentials of water in the polymer phase and in the gas phase have been calculated by employing our grand canonical ensemble molecular dynamics simulation method [H. Eslami and F. Müller-Plathe, J. Comput. Chem. 28, 1763 (2007)]. In this paper it is shown that performing just two independent simulations, one in the polymer phase and one in the vapor phase, in the grand canonical ensemble, is sufficient to calculate the phase coexistence point. The calculated solubilities, diffusion coefficients, and permeability coefficients are in good agreement with experimental data. Also the calculated glass transition temperature of the wet polymer is shown to be in a very good agreement with experiment.

Reverse nonequilibrium molecular dynamics calculation of the Soret coefficient in liquid heptane/benzene mixtures.

We studied the thermal diffusion behavior of mixtures of benzene and heptane isomers by reverse nonequilibrium molecular dynamics. For n-heptane/benzene mixtures, we investigated the concentration dependence of the Soret coefficient. The Soret coefficient for equimolar mixtures of the three heptane isomers 3-methylhexane, 2,3-dimethylpentane, and 2,4-dimethylpentane in benzene has been calculated. Compared to the experimental data, the simulation results show the same trend in dependence of the mole fraction and degree of branching. The negative Soret coefficient indicates the enrichment of alkanes in the warm side. In the case of the heptane isomers in benzene, we could study the influence of the difference in shape and size on the thermal diffusion behavior at constant mass. In the simulation as well as in the experiment, we found that the Soret coefficients become higher with increasing degree of branching. Such behavior cannot be explained only by mass and size effects. The effect of the molecular shape needs to be considered additionally.

Interface between platinum(111) and liquid isopropanol (2-propanol): a model for molecular dynamics studies.

A molecular dynamics model and its parametrization procedure are devised and used to study adsorption of isopropanol on platinum(111) (Pt(111)) surface in unsaturated and oversaturated coverages regimes. Static and dynamic properties of the interface between Pt(111) and liquid isopropanol are also investigated. The magnitude of the adsorption energy at unsaturated level increases at higher coverages. At the oversaturated coverage (multilayer adsorption) the adsorption energy reduces, which coincides with findings by Panja et al. in their temperature-programed desorption experiment [Surf. Sci. 395, 248 (1998)]. The density analysis showed a strong packing of molecules at the interface followed by a depletion layer and then by an oscillating density profile up to 3 nm. The distribution of individual atom types showed that the first adsorbed layer forms a hydrophobic methyl "brush." This brush then determines the distributions further from the surface. In the second layer methyl and methine groups are closer to the surface and followed by the hydroxyl groups; the third layer has exactly the inverted distribution. The alternating pattern extends up to about 2 nm from the surface. The orientational structure of molecules as a function of distance of molecules is determined by the atom distribution and surprisingly does not depend on the electrostatic or chemical interactions of isopropanol with the metal surface. However, possible formation of hydrogen bonds in the first layer is notably influenced by these interactions. The surface-adsorbate interactions influence the mobility of isopropanol molecules only in the first layer. Mobility in the higher layers is independent of these interactions.

Reverse nonequilibrium molecular-dynamics calculation of the Soret coefficient in liquid benzene/cyclohexane mixtures.

Reverse nonequilibrium molecular dynamics is the method applied here for the investigation of thermal diffusion in realistic molecular fluids. The Soret coefficients of benzene/cyclohexane mixtures are calculated using an all-atom model. The autocorrelation functions indicate that the mole fraction gradient converges much slower than the temperature gradient. Compared to experimental data, the results show the same tendency of the Soret coefficient variation versus the mole fraction. Although a systematic error exists for the magnitude of the Soret coefficient, a meanwhile systematic error for both the mutual diffusion and thermal diffusion coefficients provides some explanation of it; and the calculation with different force field parameters indicates a possibility to annihilate the systematic error. The influences of algorithm variables such as cutoff lengths and perturbation intensities are tested. Furthermore the temperature dependence of the Soret effect is observed, yielding the same trend as previous studies.