Subject: Summary-Transition States

From: "Hodgkin, Ed" <[email-masked]>
Date: Thu, 04 Aug 1994 09:10:22 -0500 (EST)

From: Hodgkin, Ed
Date: Thu, Aug 4, 1994 9:10 AM
Subject: Summary-Transition States
To: [email-masked]
Dear All

Thanks for your replies to my question about modelling transition states and 
reaction pathways. Here is a summary.

The original question was:

> I am hoping to model a reaction mechanism using either MOPAC or Gaussian80 
and 
> need some help with constructing transition states or following the reaction 
> coordinate. I understand it is possible to do this in both packages.
> 
> My reaction shows unusual selectivity between two products. Each of the 
> products is formed by a concerted intramolecular mechanism, which I imagine 
is 
> the most straightforward case to model. Furthermore reactants and products 
are 
> conformationally constrained so there is no problem with flexibility.
> 
> I would be very grateful for any hints you can offer.

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Message for Hodgkin, Ed

From:   DR. LIOTTA
Date:   Thu, Jul 28, 1994 3:40 pm
Subject:        Re: MOPAC and GAUSSIAN80
To:     Hodgkin, Ed
File(s):        Attach.Txt1

Regarding Message ID : 40245182704991/414481@MAIL1

From: NAME: DR. LIOTTA <MAIL1::PMDF::emrycc.cc.emory.edu::chemdcl3>

To: NAME: hodgkine <PRIN1::MRAM_PRIN1::hodgkine>

Date      : 28-JUL-1994 15:40:00.00
I have recently being studying transition states using MOPAC, 
but have not been happy with the results so I'm also trying
to study them using Gaussian92. I can give you a few pointers
for MOPAC and would be interested in hearing what other people
tell you about Gaussian80.

Firstly you need to create a reaction surface by taking the 
product and systematically increasing the bond lengths of the
bonds which form during your reaction. This should give you a
rough estimate of the saddle point. Use the saddle point for 
further calculations, removing the constraints and using the
keywords NNLSQ GRADIENTS CYCLES=100 (or 50-300) AM1 (or PM3 etc.).
Repeat this until your gradient is <3 and then use the keyword
SIGMA instead of NNLSQ. When a stationary point is found, test
if it is a transition structure by using the keywords FORCE and
LARGE instead of SIGMA and GRADIENTS. If one negative force 
constant is obtained, and the bonds which are forming or breaking
are in the first vibration, you have a transition state.

Hope this helps. I was not sure how much you have already done.
V.Cornel (Emory University)

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Message for Hodgkin, Ed

From:   kcousins
Date:   Thu, Jul 28, 1994 12:38 pm
Subject:        Modeling TS's
To:     Hodgkin, Ed
File(s):        Attach.Txt1

Regarding Message ID : 22633182704991/414258@MAIL1

From: NAME: kcousins <MAIL1::PMDF::wiley.csusb.edu::kcousins>

To: NAME: hodgkine <PRIN1::MRAM_PRIN1::hodgkine>

Date      : 28-JUL-1994 12:38:51.00
Edward,

I have some experience modeling TS's using AMPAC and MOPAC, and will share
my wealth with you.  There are several papers and reviews on this subject,
although I don't have the references.  You might try searching the CCL
archives as these kinds of questions come up frequently.  You might also
check out the five (or six) volumes of "Reviews in Computational
Chemistry" edited by Lipkowitz and Boyd.

I've modeled several 3,3 sigmatropic rearrangement TS's with eventual
success.  I had an idea what the TS might look like to start with, a
somewhat dangerous position that also makes the job alot easier.  I
defined both the product and starting geometries (Z-matrices) so that all
atoms corresponded in number and attachement (e.g. carbon atom 1 in the
starting material was also carbon atom 1 in the product, and in both cases
the carbon atom is bound to hydrogen atoms 10 and 11).  This is not a
trivial process, but is sometimes simplified by deriving both geometries
in cartesian coordinates, then reordering the atoms so that both are in
the same order, then running 1 SCF in Mopac to obtain the Z-Matrix.  The
correspondance of the two geometries must, however, still be varified.

In addition, both Z-Matrices must have the same changing bond length,
angle, or dihedral.  This variable must be one that changes significantly
during the reaction, and can be used to determine the reaction path.  In
my reaction, the 1 and 6 atoms in the 1,5 unsaturated system undergoing a
3,3-sigmatropic rearrangement are defined such that the sixth atom has a
bond length relative to the first atom.  This enables me to progressively
shortent the atom1-atom6 bond distance to create an approximate reaction
path.  The reaction path calculation itself is built into MOPAC, and the
input consists of the starting geometry with the reaction coordinate
indicated with -1, the product geometry likewise, and step-wise values of
the reaction coordinates.  I vary the 1-6 bond length by .2 angstroms
normally.

Once the reaction path calculation is complete, the highest energy point
is assumed to be an approximate TS and is optimized further using one of
the routines to locate saddle points.  When a stationary point is reached,
a force calculation is performed to verify that that point is indeed a TS.

There is also a routine in MOPAC called SADDLE that supposedly does alot
of this for you--but you still have to define the two geometries
consistantly.  I've had more luck with SADDLE when I've used geometries
close to the transition state, say two points obtained during the reaction
path calculations.

Finally, its sometimes difficult to locate a TS structure because the
calculation get's "stuck" going around a peak.  One way I handle this is
to "tweek" one or two atoms (move them a little in the calculation
geometry) in an effort to move away from the problem area.

Hope these experiences are helpful.  If you require further assistance,
please ask.  Best wishes!

Kimberley Cousins
Department of Chemistry
California State University, San Bernardino
5500 University Parkway
San Bernardino, CA  92407

(909)880-5391
[email-masked]

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Message for Hodgkin, Ed

From:   m10!frisch
Date:   Fri, Jul 29, 1994 8:33 am
Subject:        Re: CCL:Modelling Transition States
To:     Hodgkin, Ed
File(s):        Attach.Txt1

Regarding Message ID : 01139092704991/415125@MAIL1

From: NAME: m10!frisch <MAIL1::PMDF::uunet.uu.net::m10!frisch>

To: NAME: Hodgkin, Ed 
<MAIL1::PMDF::uunet.uu.net::uunet!prince.mm.wyeth.com!HODGKINE>

Date      : 29-JUL-1994 08:33:46.00
    From: Hodgkin, Ed
    Date: Thu, Jul 28, 1994 3:38 PM
    Subject: Modelling Transition States
    To: [email-masked]
    Dear All
    
    I am hoping to model a reaction mechanism using either MOPAC or
    Gaussian80 and need some help with constructing transition states or
    following the reaction coordinate. I understand it is possible to do
    this in both packages.
    
If this is not a typo and you're really running Gaussian 80, you might want
to consider Gaussian 92.  It's only $600 for a Windows PC and most things
should be faster in G92 on a 486 PC than in Gaussian 80 on any platform.
Gaussian 92 does follow the intrisic reaction coordinate path down from
a transition state to the reactants and products connected by that transition
state.  Gaussian 80 cannot do this, and neither can most versions of MOPAC
(I don't think the latest ones can, either, but I'm not positive).

There is advice on finding transition structures in our book "Exploring
Chemistry Using Electronic Structure Theory", also available from Gaussian,
Inc.  While the examples are for Gaussian 92, the general principles are
applicable with any package.

If you'd like more information, you can send email to [email-masked]

Mike Frisch
[email-masked]

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Message for Hodgkin, Ed

From:   E. Lewars
Date:   Mon, Aug 1, 1994 4:19 pm
Subject:        modelling transition states
To:     Hodgkin, Ed
File(s):        Attach.Txt1

Regarding Message ID : 74127110804991/418217@MAIL1

From: NAME: E. Lewars <MAIL1::PMDF::alchemy.chem.utoronto.ca::elewars>

To: NAME: hodgkine <PRIN1::MRAM_PRIN1::hodgkine>

Date      :  1-AUG-1994 16:19:16.00
You asked about finding TS's with MOPAC and G80.  First, these are not the 
easiest programs to use, especially G80.  Get hold of Spartan if you
possibly can.  It's made by Wavefunction, Inc, 18401 Von Karman, Suite 210,
Irvine, CA 92715;  (714)955-2120.  If you must use MOPAC or G80, I hope you
have a visualizing program like, e.g. PcModel (Serena Software, Box 3076,
Bloomington, IN 47402-3076; (812)333-0823).
  Helpful books on your problem are 
   A Spartan Tutorial  (Wavefunction)
   Experiments in Computational Chemistry,  Hehre, Burke, Shusterman, Pietro
   (Wavefunction)
   Practical Strategies for Electronic Structure Calculations  Wavefunction
  Evaluation of Modern Electronic Structure Models  (Wavefunction)
  (the above books are oriented to Spartan, but are likely to be useful
with MOPAC & G80 too.
  Also:  Exploring Chemistry with Electronic Structure Methods,  J. B.
   Foresman and A. Frisch (Gaussian, Inc., 4415 Fifth Ave., Pittsburgh,
   PA 15213; ([email-masked]).
Good Luck
===
By the way, the Gaussian TS algorithm is particularly a nuisance to use.
It is not very robust, and frequently fails.  if you must use it, try to
get your TS first using a semiemp program like MOPAC, them use that TS
as input for G80.
Errol Lewars
===
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