Week n+12¶

Sunday 19/9¶

lots of bench jobs have been finishing, so I’ve been extracting data to be able to process them
I submitted the LB -2 jobs as well, since I have a TS for that, but I am genuinely suspecting that the LB is going to be acting as a base as well

Meeting with Katya
Kept just trying to push these jobs out
Re-wrote all of my benchmarking pathway code to be more generalised and responsive, and as a result I found a whole bunch of little bigs that I squashed.

Still trying to slam out these jobs
It looks like the Lb detaches as soon as it takes the proton, activating the Brønsted base pathway, which is quite fast. I’m running an opt to now to see if the Lb stabilises the TS somehow

Pushing jobs through still
I’m suspecting that all the processes to get from lb2r to lb2t are barrierless, but that doesn’t make sense, since the proton transfer is only favourable where the reaction coordinate is < 2Å, and I’m not entirely sure how to find that energy, as there doesn’t seem to be a saddle point that I can optimise to.
Okay, I’m running a whole stack of scans atm
- Discovery
  - Scanning the reaction coordinate with the LB stabilising the TS
  - Scanning the proton transfer from the amine to LB at a distance from the reaction coordinate
  - To do: Scanning the proton transfer from the amine to the LB at a distance in to the reaction coordinate
  - Scanning the abstraction of the proton from the lb2r by pip- as a non-coordinating base
- Production
  - Scanning the reaction coordinate with the proton fixed on the LB
  - Scanning the reaction coordinate with the proton fixed on the amine
  - Scanning the protonated pip leaving the molecule

Wrote figure captions
Kept pushing jobs through
Counselled friends that have been struggling through lockdown
Kept writing… I actually got a decent chunk done, all things considered, but I’m still really not sure how to go about discussing the efield sections since a lot of it is just saying “yup, it matches the theory” and “yup, a dielectric stabilised the polarised species”.
I did make a decision to stop looking for the elusive lb2t TS. Seeing that the deprotonation of the amine by the LB is barrierless, it really only seems logical that the reaction is the more simple, stabilised Brønsted pathway.

Pathway	Pre -Transition State	Reactant	Transition state	Product
Non-activated		done	done	done
Brønsted Acid 1	queued	done	done	done
Brønsted Acid 2	queued	done	scan - done	done
Brønsted Base	queued	done	done	done
Lewis Acid	scan - done	done	done	done
Lewis Base adding in		done	cyc-proton-up-scan - done cyc-proton-down-scan - done lb detaching scan - done	done
Lewis base as Brønsted base	scan - done	queued	queued	done