CCL: Summary: Drawing TS for QST2 calculations

 Sent to CCL by: "Adil R Zhugralin" [zhugrali]_[bc.edu]
 Thanks to everyone who's answered my previous question.
 QUESTION:
 I'm trying to get 2 molecules to react to give me an adduct. Unfortunately, the
 molecules are big (overall ~100 atoms). In GaussView, I find, it is practically
 impossible to draw them such that the proper trajectory is maintained and at the
 same time get the labeling to be consistent. Any suggestions about how to do it?
 Any software that could assist in creating starting material MolGroups? Thanks
 in advance.
 ANSWERS:
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 You may try to combine the coordinates of the two reactants together and then
 use chemoffice(chem3d) to display and manipulate them.
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 I will often start from the adduct and work my way back. Build the adduct
 and then sever bonds to form the two reactants. GaussView allows you to move
 the entire "group" upon lengthening the bonds between the two
 reactants.
 Atom labeling may be a little more difficult if you want the software to
 automatically number. The times that I've set up QST2 calculations I've
 manually written the input files and then manually pasted in the atom
 coordinates (to correspond to the product) after running a simple AM1
 calculation on the "transition state" to obtain the atom coordinates.
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     The simplest approach to this is to take one of the structures and
 transform it into the other without deleting any atoms. This will keep
 the atom ordering the same as OPT=QST2/3 requires. Then delete bonds and
 move atoms to get products or an estimate of the TS starting from the
 reactants.
     Read in the first structure. Then select New/Add to MolGroup to
 generate a connected view. Select the molecule and Copy from the Edit
 menu and paste it in the new view. Repeat for QST3.
     There is also a tool in GaussView which attempts to help you re-organize
 the atoms, looks like a chain on the icon. It have not tried it with 100
 atoms so I would start the the mechanism above if possible and use chain
 if something gets confused, starting with 95+ of the atoms in the right
 order should make this easier.
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