I have a TS, the vibration of the negative frequency looks very promising. However, my first few efforts to perform an IRC have resulted in both forward and reverse directions producing *almost* (off by a tiny energy value as you will see) identical structures rather than unique ones. I've never seen this before. The IRC command I have used is:
irc=(LQA, forward,recorrect=never,recalc=-5,MaxPoints=200,rcfc,maxcycle=200)
Changing the forward to reverse and running in a separate file.
I've attached the vector displacements of my TS search, I'm interested in the nucleophilic attack of the charged nitrogen on the carbonyl group. I've also attached what the energy decent in reverse and forward look like (even those the end structure are virtually identical to the human eye).
Any ideas?
I am trying a standard irc=rcfc,forward,maxstep=3) just to see if a small step will take them in the right direction.
I went back to the TS search output file and despite returning all the frequencies and thermochemistry, I found this at the very end of the file:
Error termination request processed by link 9999.
Error termination via Lnk1e in /software/chemistry/gaussian09-c01/AVX//g09/l9999.exe at Tue Feb 28 10:27:17 2017.
Job cpu time: 0 days 2 hours 6 minutes 56.3 seconds.
I wonder (1) why did the TS calculation crash despite returning what I wanted and (2) has this had any effect on the IRC calculation. I am think of trying the IRC but asking it to calculate the FCs from scratch and only loading the geometry from the TS checkpoint file.
Dear Anthony,
I have faced the same problem a few times and found that the considered TS structure was wrong with a little bit difference in my case. There is a possibility to get a good result by modifying your TS structure or please see the another answers for my question that may help you.
Manwhile, I am wondering what is happening if you save and opt imaginary frequency of your TS structure from +0.25 and -0.25 sides?
https://www.researchgate.net/post/Problem_The_optimized_TS_structure_connects_same_intermediate_from_both_side_of_IRC_reverse_and_forward
Many thanks,
Cem
After a bit of a discussion with the Gaussian support team, I *kind of* understand what went wrong. The problem has nothing to do with my IRC. It si as simple as an incorrect TS. Looking carefully at my Opt it never converged. As I was not using Opt=noeigentest my first optimisation step returned:
Optimization stopped.
-- Wrong number of Negative eigenvalues: Desired= 1 Actual= 2
-- Flag reset to prevent archiving.
The calculation stopped as there were more than one negative eigenvalues of the full Hessian. A transition state should have only one large negative eigenvalue for the second derivative matrix, which is associated with the reaction coordinate. But here I had 2, so the program stopped with "Wrong number of Negative eigenvalues: Desired= 1 Actual= 2".
Eigenvalues --- -0.01087 -0.00094 0.00037 0.00054 0.00085
Eigenvalues --- 0.00108 0.00156 0.00191 0.00223 0.00236
Gaussian immediately followed through to FREQ and gave me a single negative eigen value. I wasn't careful enough and I assumed that that was my transition state. It was not.
Since yesterday, I've gone back to the 3-21G transition state and used those FCs to read into a 4-31G calculation. I have since found the same TS, now I am loading it into my final 6-31G(d). Hopefully, this stepwise approach will work. I found that using the FCs from the 3-21G into a 6-31G(d) were too different and the calculation failed to find the TS minimum.
You can retry it by fixing the phase (be it bond length, bond angle or dihedral angle). Follow the imaginary frequency in transition state output, any of the three above parameters are having maximum change in Transition State. This vector will increase in a particular direction and decrease in the opposite direction. Then, specify that parameter through the atom sequence. The commands are available in gaussian website. It's simple. Just after the keyword forward/reverse, write => phase = (atom number, atom number ...)
Another suggestion, try to read the geometry as well as frequencies from checkpoint file
Cem Burak Yildiz, Please can you tell me if it is sufficient to use this method when you save and opt imaginary frequency of your TS structure from +0.25 and -0.25 sides which will correspond to the forward and reverse intermediates, then should we perform an IRC again or not ?
Dear Meriem Almi
This method may give right result for the desinged reaction mechanism. Of course, however, it is not sufficient to provide a reaction mechanism without IRC calculations. This method is just to have an idea about the optimized transition state structure. In my case, to the best of my memory, the optimized TS structure looks fine by modifying +0.25 and -0.25 sides. However, the IRC could not result in the desired minimas. Then, I realized that the TS structure was wong. After many attempts the conrrect TS structure was found and approved by IRC. So, I strongly suggest to perform IRC calculations to confirm your TS structure!
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