On Fri, Apr 2, 2010 at 1:04 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> what does the data look like?
>
Here's a typical example:
http://chem.wayne.edu/~hbs/chm6440/PES.html
In this there is an implied function E(x,y) where x and y are two
geometrical coordinates. They are not normally simple bond lengths and
angles but combinations of them. Examples are "symmetry coordinates" which
often map onto vibrations and "reaction coordinate(s)" the variation of
geometry during the reaction. There are normally many dimensions (e.g. 3N-6
for non-linear molecule) but the diagrams are normally restricted to 1,2, or
3 geometrical coordinates so they can be pictorially displayed.
Each point (x,y,z,p,q...) corresponds to a configuration of atoms which
could be displayed in Jmol. So moving the mouse over the surface would show
the variation of the structure coupled to the variation in energy.
A typical example of a 2D PES is the variation of energy with 2 torsion
angles such as in the "alanine dipeptide" (actually acetyl alanyl
methylamide). This is a classic introduction to molecular mechanics. Here's
a small bad picture:
http://ats.vimeo.com/241/156/24115602_200.jpg
the two axes are the two main torsion angles phi and psi
>
>
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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