I optimized 02 structures containing NO2 group by Gaussian at 6 311G (d,p) level. In the output file i observed that the NO2 is not connected to the structure and appears as O=N=O .
Q1: When i to use this output as a starting structure for a TS search; should i reconnect the NO2 group to the structure by single bond or i have to keep the output structure as it is ?
i tried so many Keywords such as opt=(calcfc,ts,noeigen), opt=(calcall,ts,noeigen), # opt=(calcfc,tight,ts,noeigentest)... and many guesses but the irc showed that the TSs is not connecting the reagents and products!
Q2: is there any other option tofind the right TS of this pathway!
Any help is much appreciated
Hello,
Don't worry too much about the "NO2 is not connected to the structure". Gaussview shows bonds based on some pre-defined parameters so, it's quite common that in the output file some bonds are missing. However, that does not mean the atoms are not bonded. In your output file, the distance between N-C is reasonable and that means they are bonded.
Your freq calculation shows no imaginary frequency hence that structure is definitely not a TS. So, no point to run IRC calculations. TS search is not easy and may require a few trials before finding the correct one. Check this post where I have shared a few tips regarding TS search in Gaussian: https://www.researchgate.net/post/How_can_I_calculate_the_Transition_state_on_gaussian_and_construct_the_energy_profile
Dear Messaadia Saber ,
Apart from what Turbasu Sengupta said about GaussView not drawing the bond and the number of imaginary frequencies, it is also important to know which kind of reaction are you trying to study. My guess is the addition of NO2, so you want to study the bond formation between atoms C8 and N25 in your structure. That way, you can try to do a relaxed scan from that optimized structure: Tools → Redundant coordinates → Add → Bond → Coordinate 8 25 → Scan coordinate → 10 steps of 0.15 angstrom, for instance. And the keyword route should be as simple as opt=modredundant b3lyp/6-31g(d,p) (use the smaller but faster double-zeta basis set, there should be no problem and will still provide a nice guess for the transition state).
Something important you need to consider is that, due to the limitations of DFT, this bond dissociation will end up with the formation of [NO2]+ and the organic molecule as an anion. If you are interested in the homolytic cleavage to form two radicals, then it becomes much trickier.
Hope you find it helpful
Mr. Saber,
The correlative analysis between theory and experiment has show that BOMD and ADMP methods addressed correctly, amongst other theoretical methods, your question.
The TS is checked by frequency analysis. When there is only one negative frequency, then this represents your saddle point.
Please, consider work:
1. Ivanova, B., Spiteller, M. Electrospray ionization mass spectrometric solvate cluster and multiply charged ions: a stochastic dynamic approach to 3D structural analysis. SN Appl. Sci. 2, 731 (2020). https://doi.org/10.1007/s42452-020-2555-0.
In particular, consider Figure B2 and Table B2 (supporting information file, Appendix B,) therein.
Turbasu Sengupta thanks for your valuable suggestion
as i understand i keep the molecule as it is without reconnecting the NO2 group.
Enrique Manuel Arpa i am studying a cycloaddition reaction and this is one of the meta pathways (meta endo).
the new formed bonds are C8-N11 & C7-C13.
i will try your suggestion
thank you all
Dear Messaadia Saber,
After seeing your output file it seems that the structure optimized is not a true transition state instead the optimized structure is in global minimum. It is mandatory that TS is verified by one imaginary frequency that frequency is responsible for bond breaking and bond forming process. I advice you to optimize the reactant and products and verify whether it is in local minima by frequency calculation. Then you search the transition state structure by using QST2 approach. If you are getting the results in QST2 method then you will get the true TS for the reaction. If not then you can use QST3 method in which you have to guess the transition state correctly.
Thanks in advance!
In general, you should combine two methods: imaginary frequency analysis of transition state (TS) structure and the calculation of IRC, respectively. On the other hand, you could check doubly by the calculation of QST2 and QST3. Best regards.
Hi Dr Messaadia Saber . I hope the following link could help you:
https://sites.google.com/site/rangsiman1993/comp-chem/techniques/gaussian-trick-find-ts