Hello, everyone. I have been working with Gaussian and Reaction Plus Pro to study the reaction mechanism of our synthesis result. We have proposed a mechanism, and one of the intermediates requires an ion species. Unfortunately, I can't figure out how to add a proton to a specific atom in Gaussian. I would appreciate any ideas you may have. Thanks in advance!
You should be able to add a hydrogen atom to your system by using the molecular editor of your choice (such as Gaussview, which seems included in the Reaction Plus Pro package, but there are more). You can visually see the reacting molecules and add the proton where the reaction needs it. As it will change the charge of the system (if you don't consider additional molecules, such as the acid molecule that will give the proton) you will need to add it to the input file of Gaussian. Gaussian input file has this layout:
(nº of processors, memory, etc)
# (task)
(blank line)
calculation_name
(blank line)
(charge) (multiplicity)
Coordinates
(blank line)
When your system is protonated, and if you don't include the conjugate base that will form after the proton transfer in the calculation, it will alter the formal charge of the overall system and the spin multiplicity as well. Check your structure and set them accordingly.
Keep in mind that the protonation process will add another calculation step in which the "acid" (whichever you are using) will give the proton to the "base" (your product), a process that might have an additional reaction barrier and reagent/product geometries.
Hope this helps!
Pablo García-Aznar thank you very much. It helped me a lot. I used TfOH as the acid, and the side product is H₂O. I tried this method, and it seems to work — the charges change. However, during the simulation, I could only observe the Mulliken charges, not the NBO charges, because Reaction Plus Pro didn’t run properly when I set it to use NBO. But thank you very much once again.
- Badges
- Science method
- Similar topics
- Biological Science
- Ecology