From smithja -x- at -x- ucarb.com  Wed Aug  5 17:20:57 1998
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From: "Smith JA (Jack)" <smithja _-at-_)ucarb.com>
To: "'chemistry[ AT ]www.ccl.net'" <chemistry[ AT ]www.ccl.net>,
        "'Gurp'"
	 <gurp "-at-" pml.tno.nl>
Subject: RE: Molecular area of adsorbates
Date: Wed, 5 Aug 1998 16:44:20 -0400
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Ronald A van Gurp wrote:

> 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
> 
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
 Catalyst Skill Center     || FAX:    (304) 747-4672
 P.O. Box 8361             || 
 S. Charleston, WV  25303  || smithja[ AT ]ucarb.com
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