Week n+13¶
Monday 27/9¶
What I did today:¶
- I decided that I want charged of each of the derivatives, so I’m optimising them in ORCA and and will use Multiwfn to get their charges
- In this porcess I realised that the geometry for the \(\ce{NO2-NH2}\) geometry was actually just \(\ce{NO2-H}\), so I guess I have to re-do that :/
Tuesday 28/9¶
What I did today:¶
- After chatting with Michael, I’ve started to re-structure my thesis a bit, so that I can write more of a combined methods and results section.
- Since all the TS geometry have been completed, I’ve rendered out those as a pretty figure
- Woo! I’m making progress on my writing!!! I’mma make a writing matrix to keep track of how I’m going
- I’ve gotten my results from the ba21t job, and I have a sneaky negative frequency in there… normally I wouldn’t care too much, but my transmission coefficient is at 13.4, so the reaction is pretty much instantaneous. I’m not particularly happy with that assessment, so I’m doing a full hessian guided optimisation to see if it comes down a bit
- I’m getting a bit desperate, so I’m running a crest job to see if I can find a more stable configuration of ba22r as well
Wednesday 29/9¶
What I did today:¶
- Second dose AZ
- Finished the first draft of \(F_Z\)
- Put a lot of work into figuring out the Wigner transmission coefficient approximation, only to find that it didn’t fix my problem anyway
Thursday 30/9¶
What I did today:¶
- Since the benchmarks are all done, I’m removing that matrix from my notes
- Working on the CPCM section was interesting, as all of the figures that I had used ended up being replaced by new ones that served the narrative a bit better
- I’ve completed the field scans sections, but I’m not sure that I’m saying enough there. I just don’t really know what I have to say to say about it. I think that In general I should consider this primarily a methods writeup and I can come back to flesh out the discussion components a bit later.
- I’ve been trying to understand the mechanisms behind the derivatives, and I’ve reached a point where I think I know what’s going on, but I’m creating some EDDs to try and double check the logic.
Friday 1/10¶
What I did today:¶
- EDDs finished last night at like 10pm, so I’ve left them till this morning to interpret. Preliminary results seems to support my theories about how they’re working though!
- I got pretty distracted getting PyMOL running with openVR…
- Trying to figure out these derivatives…
- I think I got them sorted in the notes below, and have made some generalisations about how they work.
Notes table¶
| System | Effect on S relative to H-H | Effect on R relative to H-H | S | R |
|---|---|---|---|---|
| \(\ce{R1 = H, R2 = H}\) | - | - | - helps hybridisation (\(\ce{N->\beta}\)) | - prevents hybridisation |
| \(\ce{R1 = H, R2 = NH2}\) | ⬇︎ | ⬇︎ | - makes C more electrophilic (\(\ce{\beta->\pi}\)) | - makes C more electrophilic (\(\ce{\pi->\beta}\)) - makes N more nucleophilic (\(\ce{\pi->N}\)) |
| \(\ce{R1 = H, R2 = NO2}\) | ⬆︎ | ⬆︎ | - Helps hybridisation (\(\ce{N->\beta}\)) - makes C less electrophilic (systematic) (\(\ce{\beta->NO2}\)) |
- makes C less electrophilic (systematic) (\(\ce{\beta->NO2}\)) - prevents hybridisation |
| \(\ce{R1 = NH2, R2 = H}\) (reversed) | ⬆︎ | ⬆︎ | - flipped - Pushes electron density back onto the cyclising amine |
- flipped - makes C less electrophilic (\(\ce{O->\pi->\beta}\)) |
| \(\ce{R1 = NH2, R2 = NH2}\) | ⬆︎ | ⬆︎ | - flipped - Pushes electron density back onto the cyclising amine (more available than in NH-H) |
- makes C less electrophilic (\(\ce{O->\pi->\beta}\)) |
| \(\ce{R1 = NH2, R2 = NO2}\) | ⬆︎ | ⬆︎ | - Helps hybridisation (\(\ce{N->\beta}\)) | - prevents hybridisation |
| \(\ce{R1 = NO2, R2 = H}\) | ⬇︎ | ⬆︎ | - Helps hybridisation (\(\ce{N->\beta}\)) |
- prevents hybridisation - Negative charge accentuates OEEF |
| \(\ce{R1 = NO2, R2 = NH2}\) | ⬇︎ | ⬆︎ | - Helps hybridisation (\(\ce{N->\beta}\)) |
- prevents hybridisation - Negative charge accentuates OEEF |
| \(\ce{R1 = NO2, R2 = NO2}\) | ⬇︎ | ⬆︎ | - Helps hybridisation (\(\ce{N->\beta}\)) makes C less electrophilic (systematic) (\(\ce{\beta->NO2}\)) |
- prevents hybridisation - Negative charge accentuates OEEF - makes C less electrophilic (systematic) (\(\ce{\beta->NO2}\))makes C less electrophilic (systematic) (\(\ce{\beta->NO2}\)) |
- General trends:
- \(\ce{R2}\) has more effect on the R isomer than the S
- Effects in the order of \(\ce{NH2<H<NO2}\)
- \(\ce{R1}\) has more effect on the S isomer than the R
- Effects also in the order of \(\ce{NH2<H<NO2}\)
- Both \(\ce{R1}\) and \(\ce{R2}\) on their own, with normal \(F=Z/-Z\) (where the other \(\ce{=H}\)) causes splitting to occur with S decreasing in energy and R increasing
- \(\ce{R2}\) has more effect on the R isomer than the S
- General mechanisms:
- S
- Helps hybridisation (\(\ce{N->\beta}\))
- Makes C more electrophilic (\(\ce{\beta->\pi}\))
- When OEEF flipped, Pushes electron density back onto the cyclising amine
- R
- Prevents hybridisation
- Makes N more nucleophilic (\(\ce{\pi->N}\))
- When \(\ce{R2=NO2}\), makes C less electrophilic (systematic) (\(\ce{\beta->NO2}\))
- When \(\ce{R1=NO2}\), engative charge accentuates OEEF
- When OEEF flipped, makes C less electrophilic (\(\ce{O->\pi->\beta}\))
- S
Writing Matrix¶
| Section | Status | Notes | In Progress |
|---|---|---|---|
| Abbreviations | Later | ||
| Abstract | Later | ||
| Intro | Second draft done | ||
| Computational details | First draft done | ||
| Reaction benchmarking | To do | ||
| Static \(F_Y\) | First draft done | ||
| Static \(F_Z\) | First draft done | ||
| Static \(\varepsilon_r\) | First draft done | ||
| Efield Scans | First draft done | I’m not sure what else to add here, but it feels weak. | |
| EDD maps | First draft done | perhaps needs a discussion of the implication of these mechanisms? | |
| Relaxed \(\vec F\) | To do |  |
|
| Derivatives | First draft done | ||
| Conclusion | Later | ||
| Acknowledgements | Later | ||
| Appendices | Later/WIP |