Summary: Loacting a transition state
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:
David Gallagher, James J.P.
Stewart, David Close
|---- Accurate methods
Valentine Ananikov, Alexander
Irene Newhouse, Bin Shan
|---- Black art
|----More than one TS
|---- Existence of TS
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?
My posting was
I am trying to locate a transition state for a system about 30 atoms using an
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
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
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
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.
Here are the responses for my
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
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
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
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.
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.)
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.
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
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
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
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,
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
turns out the energy is monotonic from reactants to product: there is no
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
of the reaction path you are trying to follow. Look at the other
frequencies. You will see that they have nothing to do with your
coordinates. It may be some low frequency involving the wagging of an
exo-cyclic group. Find the atoms involved in the unwanted motion. Go
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
Sorry if this is redundant to what you
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.
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>
First of all, it's a good idea use DFT methods
semiempirical ones. The results ara more reliable.
You can use the keyword OPT=(TS, NoEigenTest) with a
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.
Alexander Martins. <alex.msilva;at;uol.com.br>
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
Bin Shan <philipbshan;at;hotmail.com>
Description: Binary data
Description: Binary data