Molecular Dynamics Simulation Study of Interaction between Model Rough Hydrophobic Surfaces

We study some aspects of hydrophobic interaction between molecular rough and flexible model surfaces. The model we use in this work is based on a model we used previously (Eun, C.; Berkowitz, M. L. J. Phys. Chem. B 2009, 113, 13222-13228), when we studied the interaction between model patches of lipid membranes. Our original model consisted of two graphene plates with attached polar headgroups; the plates were immersed in a water bath. The interaction between such plates can be considered as an example of a hydrophilic interaction. In the present work we modify our previous model by removing the charge from the zwitterionic headgroups. As a result of this procedure, the plate character changes; it becomes hydrophobic. By separating the total interaction (or potential of mean force, PMF) between plates into the direct and the water-mediated interactions we observe that the latter changes from repulsive to attractive, clearly emphasizing the important role of water as a medium. We also investigate the effect of roughness and flexibility of the headgroups on the interaction between plates and observe that roughness enhances the character of the hydrophobic interaction. The presence of a dewetting transition in a confined space between charge-removed plates confirms that the interaction between plates is strongly hydrophobic. In addition, we notice that there is a shallow local minimum in the PMF in case of charge-removed plates. We find that this minimum is associated with the configurational changes that flexible headgroups undergo, as the two plates are brought together.Comment: 27 pages, 9 figure

Semiempirical self-consistent polarization description of bulk water, the liquid-vapor interface, and cubic ice

We have applied an efficient electronic structure approach, the semiempirical self-consistent polarization neglect of diatomic differential overlap (SCP-NDDO) method, previously parametrized to reproduce properties of water clusters by Chang, Schenter, and Garrett J. Chem. Phys. 2008, 128, 164111] and now implemented in the CP2K package, to model ambient liquid water at 300 K (both the bulk and the liquid-vapor interface) and cubic ice at 15 and 250 K The SCP-NDDO potential retains its transferability and good performance across the full range of conditions encountered in the clusters and the bulk phases of water. In particular, we obtain good results for the density, radial distribution functions, enthalpy of vaporization, self-diffusion coefficient, molecular dipole moment distribution, and hydrogen bond populations, in comparison to experimental measurements

Dielectric and Thermal Effects on the Optical Properties of Natural Dyes: A Case Study on Solvated Cyanin

The optical properties of the flavylium state of the cyanin dye are simulated numerically by combining Car-Parrinello molecular dynamics and linear-response time-dependent density functional theory calculations. The spectrum of the dye calculated in the gas phase is characterized by two peaks in the yellow and in the blue (green and violet), using a GGA-PBE (hybrid-B3LYP) DFT functional, which would bring about a greenish (bright orange) color incompatible with the dark purple hue observed in nature. Describing the effect of the water solvent through a polarizable continuum model does not modify qualitatively the resulting picture. An explicit simulation of both solvent and thermal effects using ab initio molecular dynamics results instead in a spectrum that is compatible with the observed coloration. This result is analyzed in terms of the spectroscopic effects of the molecular distortions induced by thermal fluctuations