# 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
• 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 ($$\ce{O->\pi->\beta}$$)

#### 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