title: Potential of mean force of hydrophobic association: dependence on solute size.
abstract: The potentials of mean force (PMFs) were determined for systems involving formation of nonpolar dimers composed of methane, ethane, propane, isobutane, and neopentane, respectively, in water, using the TIP3P water model, and in vacuo. A series of umbrella-sampling molecular dynamics simulations with the AMBER force field was carried out for each pair in either water or in vacuo. The PMFs were calculated by using the weighted histogram analysis method (WHAM). The shape of the PMFs for dimers of all five nonpolar molecules is characteristic of hydrophobic interactions with contact and solvent-separated minima and desolvation maxima. The positions of all these minima and maxima change with the size of the nonpolar molecule, that is, for larger molecules they shift toward larger distances. The PMF of the neopentane dimer is similar to those of other small nonpolar molecules studied in this work, and hence the neopentane dimer is too small to be treated as a nanoscale hydrophobic object. The solvent contribution to the PMF was also computed by subtracting the PMF determined in vacuo from the PMF in explicit solvent. The molecular surface area model correctly describes the solvent contribution to the PMF together with the changes of the height and positions of the desolvation barrier for all dimers investigated. The water molecules in the first solvation sphere of the dimer are more ordered compared to bulk water, with their dipole moments pointing away from the surface of the dimer. The average number of hydrogen bonds per water molecule in this first hydration shell is smaller compared to that in bulk water, which can be explained by coordination of water molecules to the hydrocarbon surface. In the second hydration shell, the average number of hydrogen bonds is greater compared to bulk water, which can be explained by increased ordering of water from the first hydration shell; the net effect is more efficient hydrogen bonding between the water molecules in the first and second hydration shells.
authors: Faculty of Chemistry, University of Gdańsk, ul. Sobieskiego 18, 80-952 Gdańsk, Poland.
authors: Emil
authors: E
authors: Sobolewski
authors: Mariusz
authors: M
authors: Makowski
authors: Cezary
authors: C
authors: Czaplewski
authors: Adam
authors: A
authors: Liwo
authors: Stanisław
authors: S
authors: Ołdziej
authors: Harold A
authors: HA
authors: Scheraga
mesh_terms: D000473:Alkanes / Q000737:chemistry*; D002073:Butanes / Q000737:chemistry; D019281:Dimerization; D057927:Hydrophobic and Hydrophilic Interactions; D008697:Methane / Q000737:chemistry; D008956:Models, Chemical; D015394:Molecular Structure; D010420:Pentanes / Q000737:chemistry; D011407:Propane / Q000737:chemistry; D012996:Solutions / Q000737:chemistry; D014867:Water / Q000737:chemistry*
chemical_list: D000473:Alkanes; D002073:Butanes; D010420:Pentanes; D012996:Solutions; D014867:Water; C039752:neopentane; D008697:Methane; D011407:Propane