Subject: Re: CCL:van der walls radius

From: "Tamas E. Gunda" <[email-masked]>
Date: Tue, 18 Apr 2000 15:18:57 +0200

Chinapong wrote:
> Dear all,
> What's program that can calculate van der walls radius of
> functional groups such as CH3, i-Pr, t-Bu group? How can I find van der
> walls radius of functional from expermental data?
> Sincerely Your,
> Chinapong

As with the exception of the most simple groups, the exact shape depends
on the conformation of the moiety in question, I think that no simple answer
exists on the vdW radius of a group,

However, something similar called to Verloops's Sterimol parameters was
developed in the
seventies. Maybe it could be interesting to you:

Verloop's steric parameters for QSAR (L and B1 to B5), originally were
calculated by the program Sterimol. These parameters characterize the shape
of a molecule or substituent, the geometrical features which might
significantly influence the biological activity. L is the length of the
molecule/substituent, B1-B4 is the measure of the width in four rectangular
directions, B5 is the maximum width perdendicular to L (taking into account
the vdW radii of the atoms)(see the attached sterimol.gif image).
The farthest extension in the X direction of the group is calculated as L,
the atoms are represented as spheres with their van der Waals radii. Next
the group is rotated around the X axis (atoms #1-#2). During the rotation
the minimum and maximum distances to the X axis in the XY and YZ planes are
calculated. When the absolute minimum is found, it will be B1, and the
corresponding other three distance values, in ascending order, B2 - B3; the
absolute maximum is taken as B5.

For a detailed description of these parameters consult :

Verloop, A., Hoogenstraaten, W., Tipker, J.: Development and Application of
New Steric Substituent Parameters in Drug Design in: Drug Design (E.J.
Äriens, ed), vol VII., chapter 4, Academic Press, N.Y.,1976.

The program Mol2Mol can calculate these sterimol parameters

Dr Tamas E. Gunda
Research Group for Antibiotics of the Hungarian Acad. Sci.
University of Debrecen, POBox 36
H-4010 Debrecen, Hungary
tel.: (+36-52) 316666/2472
fax: (+36-52) 512914