[MMTK] coordinates

D. Joe Anderson deejoe@iastate.edu
Fri, 22 Nov 2002 12:47:37 -0600


On Fri, Nov 22, 2002 at 06:03:14PM +0100, Konrad Hinsen wrote:
> > PRO R and PRO S
> > supose we have a polymer chain of pentane.
> > then the hydrogen atoms placed the third carbon atom from either side are
> > said to possess pro R and pro S dihedral angle type.
> > this pro R and pro S is valid for all other hydrogen atoms except two i.e
> > on the first and last state which are in trans state with respect to
> > backbone ..
> 
> I can't say that I understand the difference between R and S... Anyway,
> it seems to be irrelevant for the purpose of finding Cartesian coordinates.
> What MMTK requires is a Z Matrix. In the Z Matrix, you specify precisely
> what each dihedral angle means, and any arrangement can be covered.

R and S are part of the international standard chemical nomenclature for
refering to the absolute configuration about a chiral center.

"prochiral" just means that the atom in question is not a center of
chirality, but were an addition or substitution made at that atom, it would
become a chiral center.  If a reaction happening on one side of the molecule
would produce an absolute configuration of "S" then that side of the
molecule is the "pro S" side, if "R" then that is the "pro R" side.

This could be important especially in the context of modeling interactions
with small chiral molecules, or reactions that recognize chiral substrates
or produce chiral products.

See, for instance:

xrefer - (R-S) system (Cahn-Ingold-Prelog system)
http://www.xrefer.com/entry/644439

http://www.wikipedia.org/wiki/Cahn_Ingold_Prelog_priority_rules

--Joe