Potentials of mean force for hydrophobic interactions between hydrocarbons in water solution: dependence on temperature, solute shape, and solute size

Abstract

We carried out molecular dynamics (MD) simulations with the AMBER force field for four pairs of spherical dimers of different size (neopentane, bicyclooctane, adamantane, and fullerene‐C60) using the TIP3P model of water as solvent. For comparison, we performed MD simulations for a linear molecule of n‐pentane at the same conditions. To assess the entropy contribution to the Gibbs free energy, MD simulations were run at three different temperatures of 273 K, 323 K, and 348 K, respectively, using umbrella‐sampling/the WHAM method. The stability of dimers is described by a potential of mean force (PMF). The shape of PMF curves for hydrophobic interactions is characteristic, and entails a contact minimum, a solvent‐separated minimum, and a desolvation maximum. The depth and position of the contact minimum for each pair change with the size of the nonpolar particle, and are consequently shifted to a larger distance for larger molecules. Additionally, the Lennard–Jones contribution to the PMF increases simultaneously with an increase in particle size. For a linear dimer, the contact minimum is shifted to a shorter distance than it is for spherical systems with the same number of carbon atoms. The contact minima on PMF curves increase with temperature, suggesting that the association entropy is positive. Dimensionless PMF curves showed a low dependency (near contact minima regions) on temperature, as the association entropy is low. Copyright © 2014 John Wiley & Sons, Ltd.

Water around fullerene shape amphiphiles: A molecular dynamics simulation study of hydrophobic hydration

“…This model has been successfully used in recent MD simulations of hydrating properties of pristine fullerenes/fullerene derivatives in aqueous medium or in binary water-containing solvents 36,[79][80][81][82][83][84][85][86][87] and in simulations of C 60complexes with biomacromolecules. 10,64,88,89 To obtain a start configuration, bare fullerene or amphiphilic molecule (and counterion if needed) in optimized geometry is placed in a cubic box and then solvated with n = 1000 or 3000 water molecules, which are uniformly and randomly distributed over the simulation box.…”

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged–Hydrophobic/Polar and Polar–Hydrophobic/Polar Side Chains

“…The PMF is one of the free-energy properties with which to calculate the physicochemical properties of the systems studied. The calculated PMFs can subsequently be used to compute measurable physicochemical characteristics of the systems studied, such as, for example, association constants, 23–25 and are also suitable when direct experiment is inapplicable (for example to study hydrophobic association 26,27 ) or to lower the cost of experiment. 28–30 The PMFs can also be used to determine the preferred mode of interaction of the molecules or groups under study in water.…”

Experimental (FT‐IR) and theoretical (DFT) studies on prototropy and H‐bond formation for pyrazine‐2‐amidoxime

“… with the force constant k = 2 kcal/mol/Å 2 and the “ equilibrium ” distance ( d 0 ) for a given window equal to 3.0, 4.0, … , 13.0 Å for a dimer studied in this work, for windows from 1 to 11. Snapshots from MD simulations were saved after every 0.2 fs; as a result, 15,000 trajectory frames were written (i.e., every 100th frame was written) for each window at 298 K. It was shown previously that this procedure was sufficient, and a PMF plot convergenced …”