RE: Molecular area of adsorbates

 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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