CCL:G: IRC-TS-PES

Dear Prof Dan
 Thank you for your kind reply and I will remember not to hit button twice next time sending message to CCL. I am glad that you have explain me a lot. I learned a lot from your email but i have already figured it out what to do next, i performed the calculation and also finalize my TS.
1) Earlier, I was interested to extract every geometry of IRC path to evaluate the ring delocalization of the ligand molecule. I found out that whole IRC pathway the ligand(heterocylce moleule) will have different delocalization and ring delocalization can be measured to predict the critical bonding stage...bong formation at the product side.
 
2) Also I figured it out about looking at the TS and of course noeigen test Gaussian will keep
searching/optimizing even if no imaginary frequency was found or the Hessian has two or more imaginary negative eigenvalues. I learned my mistake and I checked the negative hessian eigen values. Now i have confirmed my TS with imaginary frequency. No problem at all. Thanks for your advice.
 
3) I hope i will be able to perform the scan and i look into the link. Thanks once again.
 
Sujit
 
 
 
 
 
On Wed, Oct 26, 2011 at 5:28 AM, Dan Maftei http://dan.maftei---uaic.ro">dan.maftei---uaic.ro <owner-chemistry,,ccl.net> wrote:

Sent to CCL by: Dan Maftei [dan.maftei:uaic.ro]
Dear Sujit,

First, I'd recommend not to double-click the send button when writing to
CCL. Your message will appear twice.

1) Second, why optimizing the IRC geometries? It's pointless, really.
Starting from those 21 geometries found after a significant
computational effort for locating the TS then for performing the IRC,
you'll end up with 2 final geometries, one corresponding to the
reactants and the other to the products. To verify that TS corresponds
to THAT reaction pathway, a visual inspection of the IRC geometries is
usually enough. Even in the TS, after a frequency run, you should be
able to predict the reaction course by inspecting the displacement
vector which is the Hessian eigenvector corresponding to the Hessian
negative eigenvalue (imaginary frequency).

To extract, however, the geometries for each IRC step, you may find
useful the GAUSSTOOL package (a pack of C-shell scripts written by Cu G.
Phung,
http://www.ccl.net/cca/software/UNIX/gaussian-utilities/README.shtml) on
Linux/UNIX or, if using Windows, GaussView.

2) Third (I mean second), if the job for finding the TS yielded ONE (and
ONLY one) imaginary frequency, the final geometry calculated IS a
transition state, at the level or theory you are doing the computations.
I suggest to check you output file carefully, as the noeigentest
parameter for the OPT keyword will make Gaussian to keep
searching/optimizing even if no imaginary frequency (oe negative Hessian
eigenvalue) was found or the Hessian has two or more imaginary negative
eigenvalues. However, if you've been able to perform IRC calculations,
the TS may be the one of interest...
Also it is not uncommon after a geometry optimization to obtain a
different geometry with respect to the initial one. Otherwise, why
running geometry optimization?
What did you mean by delocalization inside a ring? Your TS geometry does
not display "aromatic" bonds inside the ring? This doesn't mean the
chemistry of your geometry has changed! That's why I hate visualization
software which displays multiple bonds. Any visualization program will
display single, aromatic, double or triple bonds based on some values
and tolerances hardcoded. If you give a ethane molecule as input, with
about 2.0 angstroms between the carbon atoms, it will display as two CH3
groups. It doesn't mean it's chemistry has changed. You've only
elongated a bond. It will be displayed broken as the bond length is
sufficiently larger than the one the program knows or has been told.

Finally, I don't know if that's the case in your TS geometry, but if it
is, you may use the above considerations.

3) If looking towards PES scans and use Gaussian for that, first
identify your coordinates of interest (those beings scanned) and
"freeze" them to some equidistant values while optimizing (relaxing) the
rest of the structure. The Gaussian keyword(s) for that is
opt(z-matrix,...) or opt(modredundant,...). Both are well documented in
the user guide (online, http://www.gaussian.com/g_tech/g_ur/k_opt.htm).

Regards,
Dan


On 10/25/2011 10:43 PM, Sujit Kumar Mondal sujitharvard|,|gmail.com wrote:
> Hi
> I am working on Intrinsic Reaction Co-ordinate for hetero cycle organic
> molecules and transition metal system. I performed IRC calculation which
> produced 21 step of a reaction profile path, I would like to optimized
> all the 21 structures obtained in IRC path including the transition
> state individually.
> 1) Can any one tell me the keywords for optimizing all the structures
> obtained in IRC? I do not know how to do that, please help me out.
>
> 2) secondly, I tried to optimize my transition state using keywords
> opt=(Calcfc,TS,noeigentest,maxcycle=200) Scf=(conver=5,maxcycle=200)
> but I found that my optimized transition state has changed all the
> atomic property including delocalization inside the 5membered ring
> compare to the transition state I build up (as input file). Can anyone
> tell me what should be done here?
> i need help......
>
> 3) I would like to perform a potential energy scan, could someone tell
> me the keywords for a potential energy scan of a particular system?
>
> Looking forward for your reply
> Sujit
>
>


--
Dan Maftei,
Assistant Professor,
Faculty of Chemistry/Department of Chemistry
University Alexandru Ioan Cuza Iasi
Bd. Carol 1, Nr. 11, 700506 Iasi, Romania

Tel: +40 232 201307
E-mail(s):
dan.maftei]![chem.uaic.ro
dan.maftei]![uaic.ro



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