Hydrophobicity within the three-dimensional Mercedes-Benz model: Potential of mean force

Abstract

Articles you may be interested inThe hydrophobic effect in a simple isotropic water-like model: Monte Carlo study J. Chem. Phys. 140, 144904 (2014) We use the three-dimensional Mercedes-Benz model for water and Monte Carlo simulations to study the structure and thermodynamics of the hydrophobic interaction. Radial distribution functions are used to classify different cases of the interaction, namely, contact configurations, solvent separated configurations, and desolvation configurations. The temperature dependence of these cases is shown to be in qualitative agreement with atomistic models of water. In particular, while the energy for the formation of contact configurations is favored by entropy, its strengthening with increasing temperature is accounted for by enthalpy. This is consistent with our simulated heat capacity. An important feature of the model is that it can be used to account for well-converged thermodynamics quantities, e.g., the heat capacity of transfer. Microscopic mechanisms for the temperature dependence of the hydrophobic interaction are discussed at the molecular level based on the conceptual simplicity of the model.

The application of the integral equation theory to study the hydrophobic interaction

“…First, we examined the water structure around hydrophobic particles. It has been shown previously 25,45 that water molecules around hydrophobic solutes are more ordered than bulk water. We therefore examined the description of the hydration shells as given by the solute-water PDFs.…”

“…(5) was chosen to be 0.085 as in other studies of this model. 25,35,37 The nonpolar solutes are modeled as Lennard-Jones particles without hydrogen-bonding arms, interacting with the water molecule through the potential described by Eq. (2).…”

“…Urbic et al 24 applied the Wertheim integral equation theory (IET) to the same model to obtain the solute-solute pair distribution functions (PDFs), which are directly related to the PMFs via: PMF(r) = −k B Tln g(r). More recently, Dias et al 25 used the three-dimensional (3D MB) and slightly modified version of the model, as well as 2D MB and TIP4P water model 26 to study the PMF between two hydrophobic solutes.…”

Hydrophobic interactions in the formation of secondary structures in small peptides

“…As illustrated by the simulated PMF in Fig. 3(b), the hydrophobic potential is expected to have a desolvation barrier (db) and a solvent-separated minimum (ssm), in addition to the contact minimum (cm) [34,35]. The difference between the cm and ssm positions ∼d w , where d w is the diameter of a water molecule.…”

“…Based on explicit-water simulations of a pair of methanes in water, we argue that a realistic range is ∼5.0Å and show that this favors β sheets. We also considered desolvation barrier (db) effects as they are critical in protein energetics [33][34][35][36][37][38][39][40][41][42][43]. db effects were neglected in many implicit-water potential functions [31,32] despite studies showing its importance for protein structure prediction [44].…”