Summary: Loacting a transition state

[Genzo.Tanaka;at;netaspx.com]

Hi all,
 
 
I would like to thank those who responded my
 questions on locating a transition state.  All of them are quite
 instructive for me. Special thanks go to  David Gallagher and James J.P.
 Stewart who actually located the transition state for my system (See below). I
 could also locate a transition state.
 
 
Responses exhibited wide spectra of
 perception of the transition state search:
 
 
|---- Easy          
                      
              David Gallagher, James J.P.
 Stewart, David Close
 
|
 
|---- Accurate methods      
              Valentine Ananikov, Alexander
 Martins
 
|
 
|---- Difficult        
                      
            Irene Newhouse, Bin Shan
 
|
 
|---- Black art        
                      
        Markus Dittrich
 
|
 
|----More than one TS      
               Stephen Bowlus
 
|
 
|---- Existence of TS      
                  David Shobe
 
 
 David Gallagher did find the transition
 state for the hydrolysis reaction of acetylcholine with water using PM5 method
 in CAChe version of MOPAC 2002. Using PM3 in MOPAC, James Stewart proved that
 the structure derived from the above PM5 method has only one negative frequency.
 I used the PM5 TS structure with PM3 in Gaussin98 [#P RHF/PM3 opt=(TS,CalcFC)],
 however, the job stopped yielding two negative frequencies (Optimization
 stopped.   -- Wrong number of Negative eigenvalues: Desired=  1
 Actual=  2 ). The suggestion by Valentine Ananikov, Alexander Martins and
 Bin Shan  [opt=(modredundant,TS,noeigen)] solved this problem. 
 
 
In the above, we assume that there is a
 transition state for a given reaction. David Shobe raised a question whether or
 not the transition structure exists, pointing out a no barrier reaction for
 TiCl4 + H2O -->
 TiCl4(H2O). The existence of a TS may be
 considered from the free energies for the reactants and the products. If the
 products are higher in free energy than the reactants, there must be a barrier.
 However, for the opposite case, there is no grantee that the barrier exists. Are
 anyone aware of any criteria for the existence of the transition state?
 
 
Regards,
 
 
 
Genzo
 
 
 
 
My posting was
 
 
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 
 
 
 
Here are the responses for my
 questions
 
 
***
 
This should be easy, but what exactly is
 R-C-O-C-R meant to be?
 
 An ether (R-CH2-0-CH2-R) or an anhydride (R-CO-O-CO-R) or what?
 
 If you send me the exact structures, I'll try and run it for you.
 
 David Gallagher   <dgallagher;at;cachesoftware.com>
 
***
 
 
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   <dgallagher;at;cachesoftware.com>
 ***
 
Attached are two MOPAC data sets.  In
 the first, bug.mop, I used David's 
 geometry from his PM5 result.  I changed PM5 to PM3, and ran the TS.
  This 
 runs without problem.
 
  From the ARC file, I made bug1.mop.  This runs the FORCE calculation and
 
 confirms that there is exactly 1 imaginary frequency.
 
 So, in summary, both PM3 and PM5 (and, I assume, all the other methods) 
 give more-or-less the same transition state.
 
 As far as the system being difficult, my apologies, but what was difficult?
 
 (I use MOPAC as stand alone, because I'm more comfortable with that.)
 
 Best wishes,
 
 Jimmy   <jstewart;at;fujitsu.com>
 
***
 
 
I'm not really an expert on TS
 optimizations, although I was willing to help
 someone who was even further back on the learning curve than I was.
  And
 I've never had much luck with opt=qst2.  You've checked that the atoms
 correspond properly between reactant and product, which is good.  I
 think
 sometimes opt=qst2 has trouble if the path from reactants to products is
 indirect: opt=qst2 will try to find a path that takes the reagent *through*
 the other molecule, instead of going *around* it. 
  
 I don't even know what signal 11 error is.  It sounds like a Unix
 message.
 Two possibilities that come to mind are that there was a time limit for the
 job which ran out, or that the system administrator "killed" it for
 some
 reason.
  
 Given what you've told me, I would try the opt=modredundant again, after I
 found out what Signal 11 error means and had done whatever was necessary to
 avoid it.  Oh, and you may want to send your question to the CCL list,
 since
 someone else may have a better idea!
  
 --Dave S.   <dshobe;at;sud-chemieinc.com>
 
***
 
I think of these as being multi-step
 reactions.  Maybe you're trying to find
 a TS that doesn't exist, because you skipped a step?  
 
 > 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'
 >
 
 It turns out that in one of the examples that poisoned my mind against
 opt=qst2, the transition state was not found for an equally good reason: the
 reaction was an association reaction TiCl4 + H2O --> TiCl4(H2O), and as
 it
 turns out the energy is monotonic from reactants to product: there is no
 activation barrier.
 
 Anyway, I wish you luck in solving your transition state puzzles.
 
 --David Shobe   <dshobe;at;sud-chemieinc.com>
 
***
 
Transition states are always a difficult
 problem.  You will have to be 
 pretty close to the actual state to get it to optimize.  Yes, that's as
 
 circular as it sounds!
 
 I would strongly urge you to search the literature for similar transition 
 states & use those structures to guide you in your initial guess.
 
 Irene Newhouse   <einew;at;hotmail.com>
 
 
***
 
The results of the first step are very
 common.  But this is not a problem.
 You must look at the output with software that will show the vibration
 frequencies.  Only one of them will involve motion along the
 coordinates
 of the reaction path you are trying to follow.  Look at the other
 negative
 frequencies.  You will see that they have nothing to do with your
 reaction
 coordinates.  It may be some low frequency involving the wagging of an
 exo-cyclic group.  Find the atoms involved in the unwanted motion.  Go
 to
 the Standard Orientation near the end of the output and disturb these 
 coordinates a little (maybe change them 0.1 A).  Run the OPT (TS) again
 with these new coordinates.  You will quickly come down off the local
 minimia you are stuck on and be at the true TS.
   Regards, Dave Close.   <closed;at;ACCESS.ETSU.EDU>
 
***
 
 
First, I would further research whether
 the (apparently) four center reaction that is being done here is really feasible
 (or is that the question you are trying to answer?)  I would guess there
 are two TS that are encountered in this reaction.  For example, addition of
 water to form RCO-  ... +H2O'CR' (tight) ion pair, followed by hydrogen
 transfer to form the two neutral species.
 
 
 
Regardless of the mechanism, I would
 use something like SADDLE in Mopac or CHAIN in Ampac to get an estimate of the
 possible TS, then refine the TS using eigenvector following or some gentle
 gradient reduction method.  The general idea is to come up with an
 approximate starting geometry that is somewhere on the reaction coordinate (not
 just two molecules in space; this is where some inference about the probable
 mechanism is needed); a final product geometry that is on the other side of the
 hump, and then work both ends against the middle to find an approximate TS.
  Then refine.  Then do IRC calculations to assure that you are
 actually doing the chemistry you think.  There is a section in the Mopac
 manual about all this, and it is included in an early JCAMD (around 1996, I
 think).
 
 
 
Sorry if this is redundant to what you
 know ... 
 
 
 
Stephen Bowlus  
  <stephen.bowlus;at;lionbioscience.com>
 
***
 
I can't tell you much concrete. Finding
 transition states aka
 looking for saddle point is a black art. I am currently
 doing something similar for a 20 atom system using ab initio methods and
 don't have much experience with semi-empirical ones.
 
 In general you have to start as close as possible to the true
 transitions state when starting a saddle point search. Otherwise
 you won't be able to get it. You could make an educated guess or
 first constrain some degrees of freedom you think are important
 while looking for saddle points. Comparing the energies can give
 you a hint in which direction you have to go.
 Just moving two optimized molecules close to each other won't
 do in 99.9% of the cases. Your transition state will be
 'something inbetween'. Maybe a partial transfer of your groups,
 partial bond formation... You will have to play around.
 If you have a good guess about a possible reaction coordinate
 contrain you system such that you mimick the reaction, monitoring
 the energies. That should allow you to position your system as
 close to the transition state as possible.
 
 In any case. Once you think you found the transition state you
 have to make sure that you have found a saddle point
 by recalculating your hessian matrix which has to have one and
 only one imaginary frequency. Otherwise you're back to where
 you were before.
 
 
 Good luck,
 
 
Markus Dittrich   <markus;at;ks.uiuc.edu>
 ***
 
opt(TS, noeigentest) should help.
 
 I suggest you HF/3-21G instead of PM3 for preliminary calculations
 and B3LYP/6-31G* for more accurate data.
 
 regards, Valentin Ananikov.   <val;at;cacr.ioc.ac.ru>
 
***
 
Hi,
 
         First of all, it's a good idea use DFT methods
 instead of 
 semiempirical ones. The results ara more reliable.
 
         You can use the keyword OPT=(TS, NoEigenTest) with a
 good guess 
 for the geometry. Futhermore, the keyword OPT=QST3 it's a good option 
 too. Don't forget use a good basis set, like 6-31G.
 
         Try these sugestions.
 
         Good luck,
 
         Alexander Martins.   <alex.msilva;at;uol.com.br>
 
***
 
Hi,
     Genzo,try something like this
 
 # opt(modredundant,TS,noeigen,CalcFC) rb3lyp/6-31g(d) nosymm
 
 CalcFC calculates the initial force constants be computed at the first point
 
 and helps to determine which direction the atoms are to to move.The keyword 
 noeigen and nosymm are also important.
    And it is also extremely important to specify a good initial 
 guess.Finding transition state is by no means an easy task...according to my
 
 experience.
    Good luck.
 
 Bin Shan   <philipbshan;at;hotmail.com>
 
***

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