Subject: Molecular area of adsorbates

From: Gurp <[email-masked]>
Date: Wed, 5 Aug 1998 17:00:48 +0200

Dear Netters,

We are looking for a program that calculates the area of a molecule,
which is projected on a surface. The practical background is the
following: consider molecules that are adsorbed on a surface. What is
the average area they occupy on that surface ? This depends of course on
how a particular molecule adsorbs on a surface, i.e. its orientation
relative to the surface. As a first estimate one may take the average of
a certain number of projections (or cross sectional areas). Does anyone
know of a program that calculates such projected surfaces from a MOL,
XYZ, PDB or QUANTA MSF file input, or, even better, a program which also
takes into account the preferred orientations of a molecule on a surface
?

I will summarize your reactions.

Thanx, 

Ronald A. van Gurp
Prins Maurits Laboratory TNO
P.O. Box 45
2280 AA Rijswijk
The Netherlands

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From: "Smith JA (Jack)" <[email-masked]>
Date: Wed, 5 Aug 1998 16:44:20 -0400

> takes into account the preferred orientations of a molecule on a
Look at Craig Taverner's steric program
(ftp://hobbes.gh.wits.ac.za/pub/steric/) based on solid angles.  The
solid angle corresponds to a projection onto an enclosing sphere, but if
you set the origin far enough away from the molecule (effectively
increasing the radius of the enclosing sphere), the solid angle
projection will approach an orthogonal projection. The projected area
would be R*R*(Solid Angle), where R is the radius of the sphere (the
distance between the origin and the furthest atom).  The program will
read PDB format, and it will generate a GnuPlot plot of the angular
profile.  The program should be easily modified to give the othogonal
projection directly without resetting the origin.

- Jack

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 Jack A. Smith             ||
 Union Carbide             || Phone:  (304) 747-5797
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