Paper Citing NAMD - Abstract
Harris, Robert C.; Pettitt, B. Montgomery
Effects of geometry and chemistry on hydrophobic solvation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:14681-14686, OCT 14 2014
Inserting an uncharged van der Waals (vdw) cavity into water disrupts the distribution of water and creates attractive dispersion interactions between the solvent and solute. This free-energy change is the hydrophobic solvation energy (Delta G(vdw)). Frequently, it is assumed to be linear in the solvent-accessible surface area, with a positive surface tension (gamma) that is independent of the properties of the molecule. However, we found that gamma for a set of alkanes differed from that for four configurations of decaalanine, and gamma = -5 was negative for the decaalanines. These findings conflict with the notion that Delta G(vdw) favors smaller A. We broke Delta G(vdw) into the free energy required to exclude water from the vdw cavity (Delta G(rep)) and the free energy of forming the attractive interactions between the solute and solvent (Delta G(att)) and found that gamma < 0 for the decaalanines because -gamma(att) > gamma(rep) and gamma(att) < 0. Additionally, gamma(att) and gamma(rep) for the alkanes differed from those for the decaalanines, implying that none of Delta G(att), Delta G(rep), and Delta G(vdw) can be computed with a constant surface tension. We also showed that Delta G(att) could not be computed from either the initial or final water distributions, implying that this quantity is more difficult to compute than is sometimes assumed. Finally, we showed that each atom's contribution to gamma(rep) depended on multibody interactions with its surrounding atoms, implying that these contributions are not additive. These findings call into question some hydrophobic models.
