Hybrid QM/MM simulation of the hydration phenomena of dipalmitoylphosphatidylcholine headgroup

Pressure-dependent flow enhancement in carbon nanotubes

It is a known and experimentally verified fact that the flow of pressure-driven nanoconfined fluids cannot be accurately described by the Navier-Stokes (NS) equations with non-slip boundary conditions, and the measured volumetric flow rates are much higher than those predicted by macroscopical continuum models. In particular, the flow enhancement factors (the ratio between the flow rates directly measured by experiments or simulations and those predicted by the non-slip NS equation) reported by previous studies have more than five orders of magnitude differences. We showcased an anomalous phenomenon in which the flow enhancement exhibits a non-monotonic correlation with fluid pressure within the carbon nanotube with a diameter of 2 nm. Molecular dynamics simulations indicate that the inconsistency of flow behaviors is attributed to the phase transition of nanoconfined fluid induced by fluid pressures. The nanomechanical mechanisms are contributed by complex hydrogen-bonding interactions and regulated water orientations. This study suggests a method for explaining the inconsistency of flow enhancements by considering the pressure-dependent molecular structures.

Influence of Substrate Hydrophilicity on Structural Properties of Supported Lipid Systems on Graphene, Graphene Oxides, and Silica

Pristine graphene, a range of graphene oxides, and silica substrates were used to investigate the effect of surface hydrophilicity on supported lipid bilayers by means of all-atom molecular dynamics simulations. Supported 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid bilayers were found in close-contact conformations with hydrophilic substrates with as low as 5% oxidation level, while self-assembled monolayers occur on pure hydrophobic graphene only. Lipids and water at the surface undergo large redistribution to maintain the stability of the supported bilayers. Deposition of bicelles on increasingly hydrophilic substrates shows the continuous process of reshaping of the supported system and makes intermediate stages between self-assembled monolayers and supported bilayers. The bilayer thickness changes with hydrophilicity in a complex manner, while the number of water molecules per lipid in the hydration layer increases together with hydrophilicity.

Hybrid QM/MM Molecular Dynamics Study of Benzocaine in a Membrane Environment: How Does a Quantum Mechanical Treatment of Both Anesthetic and Lipids Affect Their Interaction

Biomolecular dynamics studies using a QM/MM approach have been largely used especially to study enzymatic reactions. However, to the best of our knowledge, the very same approach has not been used to study the water/membrane interface using a quantum mechanical treatment for the lipids. Since a plethora of biochemical processes take place in this region, we believe that it is of primary importance to understand, at the level of molecular orbitals, the behavior of a drug in such an odd environment. In this work, we take advantage of an integration of the CPMD and the GROMACS code, using the Car-Parrinello method, to treat the benzocaine local anesthetic as well as two of the membrane lipids and the GROMOS force field to treat the remaining lipids and the water molecules.

Molecular dynamics study of the electric and dielectric properties of model DPPC and dicaprin insoluble monolayers: size effect

Atomistic modeling of insoluble monolayers is currently used to inspect their organization and electric characteristics, providing a link between theory and experiment. Extensive molecular dynamics simulations at 300 K were carried out for model films of the lipids dipalmitoylphosphatidylcholine (DPPC) and dicaprin (DC) at the air/water interface. Surface concentrations corresponding to a set of points along the surface pressure/area isotherms of the surfactants were considered. The models contained 25 or 81 lipid molecules in hexagonal arrangement and explicit aqueous media (TIP3P) treated in periodic boundary conditions. Molecular dynamics simulations based on a classical force field (CHARMM27) were carried out and key characteristics of the studied films were estimated. The dielectric properties of the films in normal and tangential direction were quantified by means of dipole moment magnitude and orientation analysis and by monolayer dielectric permittivity. The contributions of lipids and interfacial water to each component of the considered characteristics were assessed and their variations upon film compression were discussed and compared for the two monolayers and to earlier results. The dielectric permittivity tensors were analyzed. Electrostatic potential profiles across the layers and surface pressure values were used for more detailed clarification of experimental measurements. The results show dissimilar behavior of the two lipids at the air-water interface. While the average electric and dielectric properties of DPPC monolayers result from opposite surfactant and water contributions, the two subsystems are synergetic in the DC films. The anisotropy of the monolayer dipole moment and dielectric permittivity is explained by domination of a different subsystem in the various components. Tangential characteristics turn out to be more sensitive to the size of the model and to the degree of film compression.

Structural aspects of lipid monolayers: computer simulation analyses

Extensive molecular dynamics simulations at room temperature were carried out for model films of two dissimilar lipids (DPPC and dicaprin) at the air/water interface. To study the peculiarities of the organization patterns at different average areas per molecule, surface concentrations corresponding to five almost equally spaced points along the isotherms of the two surfactants were considered. A variable of prime interest was the density distribution in a direction normal to the interface of the monolayer components: interfacial water and surfactant on one hand and the separate moieties of the lipids on the other hand. The packing pattern and cluster size dispersion were studied by means of Voronoi tessellation and radial distribution functions. Speculations regarding structural changes upon phase-state changes during film compression were made. Individual characteristics for surfactant heads and tails as well as for interfacial water were outlined and related to the available experimental data. An analysis of the diffusion coefficients revealed the limiting factors for lipid lateral and normal diffusion. Structural arguments in support of changes in monolayer dielectric properties with the area per molecule were provided.