Abstract: MATH/CHEM/COMP 2002, Dubrovnik, June 24-29, 2002
Quantitative Treatment of Steric Effects With the Aid of Molecular van der Waals Descriptors for
Size and Shape of Substituents
Marius Olah1, Dan Ciubotariu2, Ciprian Ciubotariu3,
Corina Seiman1, Dan Dragos2, Marian Pasere2, and Mihai Medeleanu4
1West University of Timisoara, Faculty of Chemistry-Biology-Geography, Department of Organic Chemistry, St. Pestalozzi No.16, 1900 Timisoara
2 University of Medicine and Pharmacy, Faculty of Pharmacy, Department of Organic Chemistry, P-ţa Eftimie Murgu No.2, 1900 Timisoara, Romania
3 “Politehnica” Technical University, Faculty of Automation and Computer Sciences, Department of Computer Sciences, 1900 Timisoara, Romania
4 Faculty of Chemical Engineering, “Politehnica” Technical University, St. Bocsa 6, 1900 Timisoara, Romania
Developing faster algorithms for calculating van der Waals (vdW) surface area and volume of molecules, and new structural descriptors based on them, is still an active area of research in computational chemistry. Using the hard-spheres model we have developed a series of vdW indicators of molecular size and shape.
In this paper we present the steric parameters, which measure various directions within the molecular vdW space. Thus, we assimilated the substituents with an ellipsoid, with a cylinder, and a with sphere, and we introduced the following steric parameters:
(i) the axes of the ellipsoid (a, b, c),
(ii) the (d, G) indicators, where G is the maximal dimension of an axis linking the contact point between the given substituent and its parent structure with vdW center of gravity of that substituent, and d represents the radius of a cylinder having an equivalent volume with the vdW volume of the substituent,
(iii) the radii derived from the concept of packing density and from the values of vdW volumes (u’V) and surfaces (u’S), and
(iv) the globularity measure (GM) defined as the ratio VW/VS, where VW represents the vdW volume and SW is the vdW surface.
The algorithms by which these vdW steric parameters have been calculated are presented. The application of the above vdW descriptors for quantifying the steric effects for organic reactions and biological interactions is also discussed.