0000000000328714
AUTHOR
Juan Luis Pascual-ahuir
Molecular surface calculations on organic compounds
Abstract The molecular surface area was calculated for 82 hydrocarbons, esters, ethers, alcohols and ketones including linear, branched and cyclic ones. The relationship between the aqueous solubility and the molecular surface area was determined for each family of compounds and for all the families together. The results show that solubility is mainly determined by molecular surface area and that the influence of functional group is the same for all the oxygen containing compounds studied.
The solvent-excluding surface as a descriptor of ionic channels: Gramicidin-A
Abstract We have set out a methodology for checking the performance of the methods used to compute the Solvent-Excluding Surface. The method consists of computing the area of the Solvent-Excluding Surface of a model of channel, with a fixed pore size, for several values of the solvent radius. The graphical representation of the value of the area versus the radius of the solvent sphere shows a sharp change just at the radius of the pore. With this model we may analyze the ability of each method to describe small changes of the surface. We made the study with GEPOL93, older versions of GEPOL and MSDOT. The study is applied to a natural protein channel, as is Gramicidin-A, showing that this ty…
GEPOL: An improved description of molecular surfaces. I. Building the spherical surface set
The algorithm used by the program GEPOL to compute the Molecular Surface (MS), as defined by Richards, is presented in detail. GEPOL starts like other algorithms from a set of spheres with van der Waals radii, centered on the atoms or group of atoms of the molecule. GEPOL computes the MS by first searching the spaces inaccessible to the solvent and consequently filling them with a new set of spheres. Here we study the behavior of the method with its parameters, presenting several examples of application.
GEPOL: An improved description of molecular surfaces II. Computing the molecular area and volume
The algorithm used by the program GEPOL for a finer description of molecular surface (for a fast calculation of molecular area and volume and for an efficient selection of sampling points) is presented in detail. Different types of surfaces such as van der Waals and Richard's molecular surfaces can be computed. As we described in the first article (J.L. Pascual-Ahuir and E. Silla, J. Comp. Chem., 11, 1047(1990)), GEPOL begins by building a set of spherical surfaces which fill the space which is not solvent accessible. In this second article, a triangular tessellation approach to select the parts of these spherical surfaces which form the molecular surface is described. By using a data coded…