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Wednesday, 15. January 2020

To Do:

  • Read up on SAPT
  • Figure out how to extract useful NBO data from calcs
  • Check output from ethene molclus calcs
  • Check SAPT output from Ethyne-NTF2
  • Check HF NBO calcs
  • Check NTF2 molclus calcs
    • Then get ethene HF calcs on
    • Check ethene energy calcs
  • Try optimising palladium with ligands (\(\ce{Pd(II)Cl4^{2-}}\)) since the ligands themselves would play a role in the interaction, this just isn’t viable.
  • Perhaps ruthenium might be another option (\(\ce{Ru(III)Cl3}\)) peter doesn’t like to fragment periodic systems

What I Did

I didn’t have the most productive day, It was mostly spent chatting and waiting. I got the rest of the molclus jobs running, so there’s currently a massive queue on monarch ATM.

I also started the ethyne SAPT jobs, using a smaller aug-cc-pVDZ basis set (aug-cc-pVTZ-DK/aug-cc-pVTZ for Pd and Ni respectively). These are also running without CCD and with a frozen core to try and decrease job time.

The PD ethyne/ethene jobs have been put on hold for the time being. Will discuss this further with Katya.

In the evening

I actually had a pretty decent night and wrote up a jupyter notebook script to process the homo-lumo data and autogenerate some plots for it as well.

It makes me feel a little bit more competent that my coding skills are vaguely transferable and that I even remember some python syntax stuff.

Progress Matrix

(1=Single Opt, 2=Pair opt, 3=HF, 4=SAPT )

Anions

BF2(CF3)2 BF4 C(CN)3 Cl NTF2 N(CN)2
Ethane 2-IP 2-IP 2-IP 2-IP 2-IP 2-IP
Ethene 3-done 3-done 3-done 3-done 3-done 3-done
Ethyne 4-IP 4-IP 4-IP 4-IP 4-IP 4-IP
Benzen 2-IP 2-IP 2-IP 2-IP 2-IP 2-IP
Furan 2-IP 2-IP 2-IP 2-IP 2-IP 2-IP
Pyrrole 2-IP 2-IP 2-IP 2-IP 2-IP 2-IP

Cations

Na C1MPyr ImidMe2 NMe4 PMe4
Ethane 2-IP 2-IP 2-IP 2-IP 2-IP
Ethene 3-done 3-done 3-done 3-done 3-done
Ethyne 4-IP 4-IP 4-IP 4-IP 4-IP
Benzen 2-IP 2-IP 2-IP 2-IP 2-IP
Furan 2-IP 2-IP 2-IP 2-IP 2-IP
Pyrrole 2-IP 2-IP 2-IP 2-IP 2-IP

Metals

Ni Pd
Ethane 2-IP 2-IP
Ethene 3-done 2-FAIL1
Ethyne 4-IP 2-FAIL1
Benzen 2-IP 2-IP
Furan 2-IP 2-IP
Pyrrole 2-IP 2-IP

  1. Can’t be optimised to a minimum without it’s tearing the ethyne apart and attempts to obtain useful information from a single point calculation on an assumed geometry present results that cannot be trusted. ↩↩