title: Cavitation free energy for organic molecules having various sizes and shapes.
abstract: Cavitation free energy DeltaG(cav), corresponding to the formation of an excluded volume cavity in water, is calculated for a large set of organic molecules employing the thermodynamic integration procedure, which is realized as the original two-step algorithm for growing the interaction potential between the hard cavity wall and the water molecules. A large variety of solute systems is considered. Their characteristic radii change in the range 3-7 A; spherical cavities with radii 3-6 A are also studied. The interaction between water molecules is described by the four-site nonpolarizable TIP4P model. The diversity of the trial molecular set is provided by using a specially formulated nonspherical criterion classifying the cavity shapes according to their deviation from a sphere. Molecular objects were partly taken from the data base NCI Diversity with the aid of this criterion. The so-computed free energies are approximated by the linear volume dependence DeltaG(cav)V = XiV, where V is the cavity volume. This relation works fairly well until the cavity size becomes very large (the effective radius larger than 7 A). The volume dependence valid for solutes of arbitrary shapes can be included in a calculation of the nonpolar free energy component as required in the implicit water model.
authors.affiliation: Research Computing Center M.V. Lomonosov, Moscow State University, Vorobjovi Gory, MGU NIVC, 119992 Moscow, Russia. fedor.grigoriev@gmail.com
authors.forename: F V
authors.initials: FV
authors.lastname: Grigoriev
authors.forename: M V
authors.initials: MV
authors.lastname: Basilevsky
authors.forename: S N
authors.initials: SN
authors.lastname: Gabin
authors.forename: A N
authors.initials: AN
authors.lastname: Romanov
authors.forename: V B
authors.initials: VB
authors.lastname: Sulimov