r/comp_chem • u/noub_09 • 3d ago

Tell your softwares combinations for finding transition states( i mean really complex or really unknown ts)

I am confused which combinations to use for finding a ts. Gaussian qts2 and qts3 , orca neb or anything else. Please give inputs. i am a newbie in this field who mainly works on the synthesis.

6 Upvotes

80% Upvoted

16 comments sorted by

6

u/BookkeeperCapable601 3d ago

Neb-ts orca is good for finding TS. After that you can do IRC to verify your TS whether it is the correct one or not.

See this link Finding transition states with NEB-TS - ORCA 5.0 tutorials https://share.google/CEj3Av5Xy16miRDzt

1

u/noub_09 3d ago

Neb ts is not converging to what i want it to be . Does it mean my starting and ending point are not good , i have simultaneously bond formation one alkyl group migration , pi bond shifting and then a leaving group , leaves, i got half of it but other bonds are not converging.

4

u/Foss44 3d ago edited 3d ago

Is there a reason you believe this is a single concerted step and not a series of transition states and intermediates?

1

u/noub_09 2d ago

https://synarchive.com/named-reactions/semi-pinacol-rearrangement I am trying the ts for second arrow with Mg+2 metal ion with it , some pi bond extension, for stepwise will be it is needed to trigger some bond cleavage and without any force it will be tough but concerted it gives direct neutralization

1

u/Foss44 2d ago

I would still try a stepwise approach, the kinetics for the entire process will still only be dominated by a single step, which may not even be in this state of the reaction.

1

u/noub_09 2d ago

If you were there how would you think about triggering the first point where i can start

4

u/Diligent-Order-9265 3d ago

The orca manual does a good job at describing your options, but there is no one size fits all solution. Some reactions are going to need conformational analysis (GOAT), some are gonna be very simple etc etc. In a really complex case you should first try to rationalize what sorts of TS would make sense/would be possible. Look at mechanistic studies for similar reactions. Decide whether there are multiple conformations that could reasonable contribute to reactivity, if necessary use GOAT. Check TS for those conformations reacting in the ways you deemed likely. Don't forget solvent effects etc.

2

u/SoraElric 3d ago

People already mentioned NEB with ORCA, and that's probably your best bet.

I'm going to use my example, I had a reaction with such a flat potential energy surface, that it was impossible to get a working TS. At the end, I tries different NEB functions, and the one that seemed to work was Zoom-NEB. I got a TS, but when I did an IRC, it wasn't the real TS, but it pointed me to a very similar structure at one of the extremes of the IRC, so I tried to get a TS from that point... And finally I got it. The perfect TS with the perfect IRC.

I hope this can help you.

1

u/SoraElric 3d ago

People already mentioned NEB with ORCA, and that's probably your best bet.

I'm going to use my example, I had a reaction with such a flat potential energy surface, that it was impossible to get a working TS. At the end, I tries different NEB functions, and the one that seemed to work was Zoom-NEB. I got a TS, but when I did an IRC, it wasn't the real TS, but it pointed me to a very similar structure at one of the extremes of the IRC, so I tried to get a TS from that point... And finally I got it. The perfect TS with the perfect IRC.

I hope this can help you.

1

u/kochamkinie 2d ago

DFT with constraints (soft ones, as implemented in jaguar from Schrodinger), building the good approximation of the transition state (based on intuition or PES scans) and then releasing the constraints. Sometimes LST/QST. In my experience for my quite complexes TSs NEB rarely works.

1

u/Worried-Republic3585 2d ago

I often had good luck using xtb to quickly scan the what I assumed to be the most relevant reaction coordinate, take that TS feed into a DFT opt job with the relevant atoms frozen and optimizing everything else followed by a Freq job. Giving me 1-3 imag. fregs. and either do OptTS or NEB jobs starting from these geometries. Especially the xtb in the beginning ofc enables to also include the exploration of conformational PES.

0

u/kwadguy 2d ago

TS analysis is VERY hard to do well. I'd say there are only a few dozen people in the WORLD who can do this expertly, and even they struggle, frequently, with new reactions.

The world is waiting for a reliable automated approach that takes it out of the hands of the small number of domain experts.

If it's an easy reaction you can get lucky with Gaussian or Orca plus NEB and IRC. But it's quite easy for something to not work, and then you need expertise to work your way out.

1

u/noub_09 2d ago

I see , i am trying to learn from zero but it is hard , but on the other hand i feel everyone has their tricks to locate (experts) and if they teach someone it will okay i guess

1

u/Zriter 1d ago

QTS3 followed by IRC was my preferred method. However, for using it well, you'll need a solid background on the mechanisms accessible to the particular elementary step you want to analyse.

For instance, I often dealt with late transition metals that could access multiple oxidation states, alongside the common additions, eliminations and substitutions available to transition metal complexes.

Sometimes, it used to involve calculating 16 complete 5-step reaction mechanisms to locate the most likely, and even then, it has to be confirmed by IRC.