Subject: Re:Locating a transition state - Success!

From: David Gallagher <[email-masked]>
Date: Wed, 01 May 2002 15:20:09 -0700

Hi Genzo,

Although, the old MOPAC PM3 hamiltonian seems to have difficulty in 
locating a transition state for your reaction, the latest PM5 method in 
MOPAC 2002 nailed it first go with a saddle calculation.

The attached Zip file includes pictures and the MOPAC output of the gas 
phase transition state for your hydrolysis reaction. In the picture, the 
bond thickness indicates the relative bond order and the numbers are the 
atom distances in Angstroms. The force calculation shows a single negative 
vibration and the IRCs verify that this is the only transition state along 
this particular reaction path for the concerted reaction. The new PM5 
method has been re-parameterized for higher accuracy and MOPAC 2002 
includes new algorithms. It seems to be much faster and more reliable for 
finding transition states than the older MOPAC methods such as PM3 and AM1. 
Also, I was able to model the transition state with the COSMO water solvent 
field. As expected, the energy was much lower.

Although, the old PM3 seems to work fine for a simple ester hydrolysis, the 
charged quaternary ammonium group seems to confuse it. The best transition 
state structure I got out of PM3 had a second negative vibration due to a 
methyl rotation. However, the bond orders, atom distances and negative 
vibration all indicated a proton transfer only (not the C-O bond break), so 
I don't think that this was the correct transition state for the reaction.

If you need more information about MOPAC 2002 you can view the manual at 
http://www.cachesoftware.com/techsupport/mopac/  The pictures and 
calculations were done with the CAChe version of MOPAC 2002.

I hope this helps
Regards
David Gallagher, Fujitsu

At 03:51 PM 4/26/2002 -0400, [email-masked] wrote:

>Hi,
>
>I am trying to locate a transition state for a system about 30 atoms using 
>an empirical
>method. So far I haven't had any success. I would appreciate if you could
>give me any suggestions.
>
>I am interested in a hydrolysis reaction pathway, using PM3 in Gaussian 98:
>
>R-C-O-C-R' + H*-O'H ---> R-C-O-H*  + H-O'-C-R'
>
>I have done the following:
>1) opt=Ts ; This always failed due to incorrect number of negative
>frequencies.
>2) Scan  ; I have not tried much.
>3) opt=ModRedundant: Scanning succeeded, but the population analysis after
>the scanning seemed failed. The output did not indicate why it failed, but
>the heading of population analysis appeared, followed by signal 11 error.
>4) opt=qst2; There is (are) one or two statement(s) "stationary point was
>found" (the distances were the same for all, but the angles and torsions 
>were slightly different in the two stationary points) in the output, but 
>the optimization (?) kept going and failed; Optimization aborted
>--- No acceptable step or Inconsistency: ModMin=   2.
>
>I optimized two reactant molecules individually and moved them close to make
>a reaction. The products were also optimized. The order of the atoms are
>exactly the same.
>
>
>Thanks,
>
>Genzo Tanaka
>Network Computing Services, Inc./
>Army High Performance Computing Research Center at FAMU
>