Subject: Transition States & Unichem (Summary)

From: [email-masked]
Date: Wed, 20 Mar 1996 12:19:46 -0400 (EDT)

Many thanks to all who responded to my question about using unichem
in the search for transition states.  The responses fell into two 
categories: 1) don't use unichem for this (at least not without help
from some other program), and 2) look at url xxx for information on
general features of ts searching.  The urls were quite helpful....

The original post was:

I would like to learn about using unichem (initially just the semi-empirical
methods, but later dgauss and/or gaussian) to model transition states. I
thought a simple case to start with would be the keto-enol transition state
for 2-butanone.  In MOPAC and gaussian there are methods to help get close
to the transition state (saddle and lst or qst) that start with initial state
and final state geometries.  Unichem does have an option to optimize to
a transistion state, but seems to lack the tools needed to find an 
approximate structure that is close enough for the optimizer to take over.
I have made several unsucessful attempts at "guessing" what this ts might
look like, but so far have not found a good enough guess.  I am using 
unichem's implementation of am1, and so far have only found structures whose
gradients are too large for computation of frequencies, and so I have no
confidence that I have found the ts.

Any suggestions?

********************************************************************

Just a simple suggestion based on my own limited experience:  if the
reaction coordinate can be expressed in a realatively simple way in terms
of the length of a single interatomic distance (eg, H---O), then a reaction
coordinate driving process, which constrains and optimizes the structure at
successively smaller (or larger) distances can often be a quick and easy
way to find the approximate TS.  Why not give it a try.

 Eilert Ofstead

**************************************************************************

I am also using programs such as MOPAC and Gaussian to calculate 
transition states (hetero Diels-Alder) and have found very quickly 
that manuals and other peoples experience in the area is very 
limited.  I would be greatful if you could share and answers that are 
passed to you directly, avoiding CCL.  If you have any problems in 
the future with Gaussian, try [email-masked] as he has been 
very helpful to me.

Yours
Carl Windsor

*********************************************************************

Please do not use my name or my affiliation if you happen 
to summarize the answers to your question. The 
straightforward answer to your question about doing 
transition state optimizations in the Unichem package is 
 ... don't do it! Use Mopac if you wish for semiempirical 
methods or use Gaussian for molecular orbital and DFT 
methods. Experience has shown me that the transition 
state optimizer is NOT robust at all in the Unichem 
package for either the semiempirical or DFT methods. 
Someday this will change, I'm sure.

********************************************************************

Re the query about finding the 2-butanone keto/enol TS: one possibility is to 
find the keto/enol TS for the _simplest_ keto/enol tautomerization, ethanal/
ethenol (acetaldehyde/ vinyl alcohol), then replace the appropriate H's by
CH3 groups, and subject this new structure to a TS optimization.
Errol Lewars

*******************************************************************

Yes, it's true UniChem lacks multi-structure input routines.  Given that
semiempirical methods that have them require a half-guess at the structure
to not thrash [or at least they have in my cases!]  You might be best off
doing a reaction coordinate.  If you absolutely insist on having Unichem
do your z-matrix, instead of doing it by hand, get Babel to let you convert
to a z-matrix you can manipulate to vary the reaction coordinate.  Using
the structure closest to the TS in UniChem [use Babel to convert it to PDB
so UniChem can read it] may work.

Another approach is to use a known TS as a guess for yours.  I believe that
Warren Hehre & co-workers give such a structure in some of the books they've
written for use with the Spartan code - you can do most of the exercises
they give with UniChem, & they give LOTS of examples of TS's for organic
reactions.     If you don't have access to the books, I recommend a lit.
search for an analogous TS to use as an initial guess.

Good luck!
Irene Newhouse

*********************************************************************

I don't know exactly about Unichem, but why use it
if MOPAC itself has provisions to locate a TS?
You can do grid search by varying two variables,
which could be C--H and O--H distances in this case.
Gnuplot will even make a plot of the output, if
the grid of numbers isn't enough.
This procedure will allow you to get very close
to the TS, from you can apply the TS keyword.
Exactly this procedure is the subject of a
www course I composed:
http://www.caos.kun.nl/~borkent/compcourse/comp.html
Best regards,

  *****    J.H. (Hens) Borkent, CAOS/CAMM Center,

*****************************************************************

Why not have a look at the WWW pages I have setup that include a number of TSs
 (fully optimized 
and characterized) from PM3 and AM1 calculations. These should give you a good
 starting point for 
experimentation on a number of derivatives or alternative parameter sets. If
 you (or anyone else for 
that matter) has TSs that there willing to share with others I would welcome
 them being deposited 
at this location. The URL is:
http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm

Addtionally, if you (or anyone else) generates TSs via semi-empirical methods
 I would be prepared to 
help generate an animation sequence and multi-structure file of the reaction
 being simulated. 

Please contact me if your interested.

 Dr. Jeff Gosper                                         

***********************************************************************

Hi 

I'm using Dgauss for TS, but my way to obtain TS structure is via MOPAC . 
First of all I prepare the approximation of TS by AM1 or PM3 method than 
I do calculation using DGauss or Gamess. I send you the TS state for this 
reactinon obtained by MOPAC. 

Stanislaw Oldziej

am1 results snipped out.....

************************END of SUMMARY*************************

So, I tried some of the listed ts structures in the web pages and found that
unichem's semi-empirical methods would verify that these were in fact ts
structures, when I asked unichem to optimize to a transition state (starting
from a structure that was very, very close..) the semi-empirical code
converged to a quite different, energy minimum structure.  The ts optimizer
for DGAUSS was more robust and would optimize to a ts, given a good initial
guess and a semi-empirical hessian...

The web pages of Borkent and Gosper referred to above were particularly
helpful.

I will stick to MOPAC and Gaussian (and perhaps DGAUSS) for this sort of work.

Steve Williams
Chemistry
ASU
Boone, NC 28608