Subject: summary - transition state search

From: "Dr. Ibrahim Noorbatcha" <[email-masked]>
Date: Mon, 10 May 1999 18:12:55 +0800 (MYT)

Dear All,

I received several replies regarding my query on stand-alone programs 
for transition state search.  I am planning to start from Victor's 
"navigator".  Thank you very much for the replies.  Summary 
follows:

-----------------------------------------------------------------
From: Frank Jensen <[email-masked]>

        the ICC book does not have computer codes, but it does have
references to the most common algorithms for TS searches. There are no
general methods for TS searches, and a lot of different methods
have been proposed. I don't think there are any 'stand-alone' programs,
most are build into mics. computational chemistry codes. Most are
based on the Newton-Raphson approach, and if you have that available
as a stand-alone, then it is fairly easy to modify it to do TS
as well. The other main alternative for locating TSs is variations
of LST/QST, look up some of the recent work of Schlegel, as they
have done a good job implementing a version in G98.

ICC:    http://bogense.chem.ou.dk  

--------------------------------------------------
From: Victor Lua~na <[email-masked]>

   Check the code 'navigator' available at

           http://www3.uniovi.es/~quimica.fisica/qcg/navigator.html
                                                                     
------------------------------------------------------------
From: "Przemyslaw G. Czyryca" <[email-masked]>

I, personally, don't know about a separate
_program_ doing TS search using a given energy function. Usually TS search
algorithms are included in QM software (like Gaussian, Mopac and so on).

The algorithms themselves are not particulary sophisticated. A good
review you can find in a book:  
"Theoretical Aspects of Physical Organic Chemistry: the SN2 mechanism"
Shaik S.S., Shlegel H.B., Wolfe S.   Wiley, New York 1992

The chapter about locating minima and TS structures is exceptionally
useful when you are preparing lectures: algorithms are illustrated with
nice 3D pictures of energy surface.  

-----------------------------------------------
[email-masked]

I've the book by F.Jensen. As far as I know there's no program or
algorithm given except for the description of the theory and
its application based on Molecular Orbital Theory.
           
-----------------------------------------------------------
 "Noertemann, Fr. Folke" <[email-masked]>

 1.) No, the Jensen-Book does not give the algorithm together with
      a program listing for a geometry-optimizer/transition state searcher.
      However, it is an excellent textbook, providing a broad overview.
  2.) Only a couple of days ago (it may be two weeks now), there was
       a similar request and I replied to one of them. Unfortunately, I
       forgot who it was.
       During my thesis I wrote such a program. Given the total energy,
       the energy gradients and the molecular geometry, it will either
   During my thesis I wrote such a program. Given the total energy,
       the energy gradients and the molecular geometry, it will 
either
       - optimize the geometry
       - look for a transition state
       However, I am out of my former research group and I have no 
idea whether my professor is willing to distribute the program 
or not.  In order to find out, you will have to contact either:
Markus [email-masked]   
He wrote large parts of the code,
including the frequency analysis
       OR
       Sven Krueger
       [email-masked]   He should be able to say
       something about the availability
                                                
--------------------------------------------------
Tucker Carrington <[email-masked]>

I know almost nothing about finding transition states but I remember a method
by
Cerjan and Miller.  It was published about 15 years ago.  In JPC I think.
There
are probably newer and maybe better methods.
                                             
-------------------------------------------------
Andreas Goeller <[email-masked]>

There is a website with examples from F. Jensen. Have a look at
http://bogense.chem.ou.dk/~icc/

---------------------------------------
Jose Carlos Corchado <[email-masked]> 

Polyrate ( http://comp.chem.umn.edu/polyrate/ ) can do that. You can
interface your potential energy function with Polyrate and find stationary
points and perform normal mode analysis.  The main goal of Polyrate is the
calculation of rate constants by means of several transition-state based
methods with semiclassical tunneling contributions, but you can use it
only for analyzing the stationary points. However, it has the problem that
the implemented optimizers are not very efficient.

-------------------------------------
TOPPER ROBERT <[email-masked]>  

Have a look at 
comp.chem.umn.edu/WWW/Truhlar/Truhlar.html
and look in "Computer Programs."
The program is free to academic users, but
you must sign and fax or mail a license agreement
before downloading the code. The distrubution 
includes a very detailed manual and source code
in addition to lots of test cases.