Subject: saddle calculations-summary

From: Ramesh Gopalaswamy <[email-masked]>
Date: Thu, 30 May 1996 17:21:11 -0400 (EDT)

My sincere thanks to all who helped me with their valuable suggestions
on 'saddle' routine and TS optimzation. Here's a summary of replies.......

******************************************************************************
> Hello CCLers,
> 	Could someone give me some pointers on SADDLE calculations
> to locate TS and what to do further on it - refining the TS and force
> calculations etc. Any tips on useful keywords are welcome.
> Thanks so much.
> 
> Ramesh

From [email-masked] May 23 16:51:33 1996 Date: Thu, 23 May 1996 11:46:58 -0700
(PDT) From: Kimberley Cousins <[email-masked]> To:
[email-masked] Subject: saddle calcs

Hi.  You didn't mention if you were using AMPAC/MOPAC or what (although I 
asssume that you are). I've used SADDLE in the past in these programs to 
search for a TS with mixed success.  I now usually make a guess at a TS 
structure instead of using this command.  I then use something like NLLSQ 
or SIGMA to locate the closest stationary point.  If I've guessed well 
that point is the TS(exactly one negative eigenvalue in the resulting 
force matrix).  If you insist on using SADDLE, depending on the 
coordinates chosen for starting material(s) and product(s) you may find 
an approximate TS geometry that you will then use with NLLSQ or SIGMA (or 
another routine depending on which version of which program you are using!)

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

(909)880-5391
[email-masked]

From [email-masked] May 23 16:53:06 1996
Date: Thu, 23 May 1996 14:46:40 -0400 (EDT)
From: Chretien Steeve <[email-masked]>
To: [email-masked]
Cc: Chretien Steeve <[email-masked]>
Subject: Transition state determination

Hi,

	I am a graduate student in theoritical chemistry in the researh
group of Dr Dennis R. Salahub at Universite de Montreal. You can take a look
at the articles below which talk about many methods.

(1) Klaus Muller, Angewandte chemie, vol. 19, 1980, p.1-13

(2) Y. Abashkin and Nino Russo, J. Chem. Phys., vol. 100, 1994, p.4477-83

	I hope that this references will help you.

			Best regard

				Steeve Chretien

From [email-masked] May 23 16:56:51 1996
Date: Thu, 23 May 1996 15:37:22 EDT
From: [email-masked]
To: [email-masked]
Subject: CCL:Saddle calculations

Ramesh, you don't specifically mention that you are using MOPAC, but I
suspect you are. If this is the case, then, take the geometry of the
output from the saddle (best guess of TS geometry) as the input to a job
with the keyword NLLSQ or TS or SIGMA. Each of these is slightly
different, but allows optimization of stationary points that are not
minima. It is possible that the optimizer will "find" one of the minima,
rather than the TS. Compare the output geometry and energy to see if it
stayed "near" the saddle output. If it has, then you MUST run FORCE
calculation on that refined geometry (not on the output of the SADDLE
calculation). If all is well, you will find that 1) the gradient is
small enough for a FORCE calculation, and bfgs optimizer will not be
invoked and 2) that there is one and only one "negative" (actually
imaginary) frequency, corresponding to one and only one negative
eigenvalue of the Hessian (force constant matrix). If this is the case,
then you have indeed found a 1st order saddle point, or transition
state. In my experience, it is important to then follow this up with two
more runs. Both start at the refined TS geometry, but use the keyword
IRC=1 in one and IRC=-1 in the other. You should also use the keywords
LARGE and X-PRIO for these runs. The output should show the energy and
the geometry proceding from the TS to the reactant, and the product. If
the endpoints of the IRC runs are in fact your intended reactant and
product, then you have found a transition state connecting the two.

What you don't know yet is whether this is the lowest energy TS between
these two points on the potential energy surface. For that, you get to
keep searching, using the same techniques, but testing out different
potential reactant geometries, etc.

Pat

From [email-masked] May 23 17:03:55 1996
Date: Thu, 23 May 1996 15:16:52 -0500
From: Irene Newhouse <[email-masked]>
To: [email-masked]
Subject: RE: SADDLE

These comments refer to SADDLE as implented in MOPAC:

It's a touchy routine & often crashes, even with small molecules.  I've had
MUCH better luck by starting from product & doing a reaction coordinate to
pull it apart into reactants.  Select out the structure with the highest 
energy & refine using keywords like NLLSQ.  If that doesn't work, freeze the
critical coordinates, optimize around them & then unfreeze & do NLLSQ.  Check
your results by doing a frequency computation & animating the frequencies to
see if the largest motion of the "negative" frequency [there should be only 1]
corresponds to the reaction.  You should also do a DRC, but that's tricky, too.

TS keyword in MOPAC is alleged to be the greatest thing since sliced bread.
Not so!  90% of the time it goes to a product with no negative eigenvalues in
the force constant matrix in spite of the fact that it's supposed to track 
along the reaction coordinate only.  Once it found a transition state for me,
but not for the reaction I wanted.  I never did figure out what reaction it
was for!

If these general things don't help enough, maybe you could write me more about
what you're trying to do & I could see if I could provide more concrete sug-
gestions.

Irene Newhouse

From [email-masked] May 24 11:50:36 1996
Date: Thu, 23 May 1996 21:24:14 EDT
From: [email-masked]
To: [email-masked]
Subject: Re: CCL:Saddle calculations

Generally, I look at the z-matrices and compare the geometric
parameters. Usually, if the optimizer has taken the system to one of the
minima, instead of the TS, there will be a VERY close match (less than
1% difference) between each corresponding value. There do exist in some
software packages "overlay" or "comparison" modules, but, there is
usually no need. If the nllsq or ts or sigma optimizer winds up
somewhere else (not one of the two minima) and the heat of formation is
more positive than either of the minima (may be close to the heat of
formation for the saddle point, or may be tens of kcal/mol away), I
would go ahead and do the force calculation to test for the one and only
imaginary frequency.

It may not be terribly scientific, but, then, my experience and the
teachings of those with even more experience says that finding TS's is
still something of an art. On the other hand, finding TS's and
corresponding estimates of Ea's is one of the more rewarding things to
do in this field, so keep on going!

Pat

From [email-masked] May 24 11:54:07 1996
Date: Fri, 24 May 1996 14:25:35 +0800 (SST)
From: Chin Wee Shong <[email-masked]>
To: [email-masked]
Cc: W S Chin <[email-masked]>
Subject: Saddle calculations

Hi Ramesh,

I have some experience before with SADDLE, it never worked - the 
optimized geometries did not give one and only one negative force 
constant.  We are now using Eigenvalue following (EF) procedure, it is 
much more promising.  All you need to do is to give a fair guess of the 
structure of the transition state - usually intermediate of your starting 
and end molecules.  

Wish you luck,
Chin W S

From [email-masked] May 24 11:57:58 1996
Date: Fri, 24 May 1996 11:41:38 BST
From: Jeffrey J Gosper <[email-masked]>
To: Ramesh Gopalaswamy <[email-masked]>
Subject: Re: CCL:Saddle calculations
Have a look at http://www.caos.kun.nl/~borkent/compcourse/comp.html
and http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm

for information on these topics.

Please summaries your responses for the CCL.

/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\
 Dr. Jeff Gosper                                         
 Dept. of Chemistry		                        
 BRUNEL University                                     
 Uxbridge Middx UB8 3PH, UK                            
 voice:  01895 274000 x2187                            
 facsim: 01895 256844                                  
 internet/email/work:   [email-masked]     
 internet/WWW: http://http1.brunel.ac.uk:8080/~castjjg 
Re_View's Home page (A molecular display/animation/analysis program):
   http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm
\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/

From [email-masked] May 24 11:58:37 1996
Date: Fri, 24 May 1996 10:09:35 -0400 (EDT)
From: Ryszard Czerminski <[email-masked]>
To: Ramesh Gopalaswamy <[email-masked]>
Subject: Re: CCL:Saddle calculations

Some time ago I have been using routines from GAMESS
for this purpose. I found them very robust and
well documented.

Ryszard

 ..................................
Ryszard Czerminski
Molecular Simulations Incorporated
16 New England Executive Park
Burlington, MA 01803-5297
tel: (617)229-8875 x 217
fax: (617)229-9899
e-mail: [email-masked]