View source for Talk:Title=Mod:mvs243

= Comments =

== Cyclopentadiene  (0.20) 75% ==
For your exo and endo products you're missing the energy breakdown for strectchin/bending/etc, so the claim of "reduced amount of steric congestion" needs some data backing it up.


"stabilised by in phase secondary orbital interactions between the secondary non bonding orbitals of the diene and dienophile. "
Just a small thing, but you could have added an illustration for the bonding or one of those energy reaction diagrams.


"It has been experimentally determined that the actual product of the dimerisation is the higher energy endo isomer. "
Literature reference?


"Dihydro dicyclopentadiene molecules"
Giving just one energy (kcal or kJ) is sufficient.


"hydrogen bond in the C5" "norborene part of the molecule"
All of that is right, but the text needs some tidying up. Please refer to molecule 3 and 4 and try to structure the text a bit more.


Do refer to your own tables when you're saying things like: 
"There is a large amount of ring strain relief when the double bond is hydrogentated in the norborene part of the molecule."
Rather say something along the lines of: "Molecule 4 has a much lower energy . This is a result of the much bigger release in ring strain energy, as compared to molecule 3. Theis can be shown by our computations, where molecule 4 has a much lower total bending contribution..."



" This can be explained by the possible greater amount of ring strain present in 1,2-dihydrodicyclopentadiene which means there is a greater deviation from the normal bond angle of 120o for an sp2 carbon."
You didn't mention the angles anywhere or draw them into your molecular structure. It's important that you mention those values and discuss them in more detail - especially comparing how much more they differ from sp2 or sp3.

By the way, a neat little trick to get the correct degree sign (°)  is to type "Alt + 0176" under Windows.

== Taxol (0.25) 91 % ==



Good introduction and good use of graphics!

But you didn't mention which method you used - was that MM or DFT. Which forecfield, which basis set did you use?

"It can be seen that molecule atropisomer 2 is the more stable isomer of the taxol intermediate..."
...because of it's lower overall energy.
Just a minor quibble, but makes it easier to read without having to refer to the picture and look yourself.


"This can be rationalised by looking at the orbital overlap in atropisomer 2" "stabilising anti peri-planar between the stabilising interaction between the σ*C-O orbital and the σC-H orbital "

Good discussion.



"This can be illustrated when the energies of atropisomer 1 and its hydrogenated counterpart are compared: "

Nice explanation, good use of the different angles! That's what I would have liked in the dimerisation reaction above! Good effort on calculating the parent alkane!




It's good that you linked your computation. However, please mention in the text which method you used for the computation - DFT calculation is sufficient, freq keyword and solvent-correlation are added bonuses. Ideally when reading the text you would give all the relevant information without having the reader go and double-check what calculation you actually talking about.

That's also part of any discussion - writing it in a nice-to-read way. It may be obvious to you what you're talking about but someone else might have no clue whatsoever. :)


"Further optimisation of the molecule was attempted by moving the positions of the atoms in the cyclohexane ring structure. However a chair conformation was not obtained and consequently this is the lowest energy conformer that I was able to analyse. "

Good extra effort!

Nice work on the 13C table. I especially like the visualisation.


Your conclusion that the method is "not completely accurate" is a tad general. If you had a closer look at your file (or the wiki) you'd have found out, that carbons can be predicted quite reliably, actually.

However, if a carbon has a neighboring heteroatom they seem off - one then has to apply a correction factor. 
A bit more in-depth discussion or googling please. ;)


"In the case of hydrogen "

In the case of the proton NMR / 1HNMR...


"The shifts that were computed also did not give any information about coupling "

You could have calculated the shifts with gNMR - but that is an optional task. 
So, there were no coupling constants because you didn't measure them. It is okay not to calculate (because optional) but then don't mention it at all. 
That's the kind of thing professors will prey upon in a viva, or your peers will ask about in a paper you submit. It basically shows that you found out that there's a "problem" but didn't bother looking further into it. ;)


"As it is possible to compute coupled NMR spectrums, a further extension of this experiment could be to do the analysis in this way once it becomes cheaper in computational terms. "

Ah, okay, now that makes sense. Disregard the above section. :)
But how then do you think shifts and coupling are related? You're not being very precise on either.


A shift is not linearly dependent on the coupling. 
Of course they're interconnected. But the shift basically gives you information about the neighboring environment, while the coupling, or better: the multipicity would give you info on the neighboring protons (3J coupling).

So, the multiplicity doesn't explain the deviations in shift, but the fact that in experiment you have movement and different conformations does.

Can you try to differentiate more clearly next time? Break it down into several points and try to explain each point step by step, then your discussion will become much clearer and much more precise.

== Epoxide (0.05)  65% ==


The intro is way too short.


What's the geometry of the Manganese complex? Does this contribute to the reactivity of the system? 




"shield the aryl rings"

shield them from what exactly?


"selectivity"

What selectivity would that be and how does it work?

Please elaborate:
Disfavourable interaction with the substrate only allows the substrate to approach in one way (bulky groups pointing away) so that the substrate can be epoxidised from one side only (, leading to enantiomeric selectivity.
Ever heard of enantiotop half spaces? ;)



"The anomeric centres"

You keep mentioning the anomeric centres - but which ones are they? aton number?
And what is the definition of an anomeric centre?


"This can happen to all of the C-O bonds"

Well, there's a lot that CAN happen - but does it happen and does it happen to all of them? 

Why don't you show the bond lengths of your molecule? The different bonds differ a lot from each other.

== NMR  (0.05) 85% ==

Please order by molecule not by method.

"Overall the computed NMR agrees to a reasonable extent with the experimentally determined values. "

The 13C doesn't. Why is that? Influence of heteroatoms maybe? Any other reasons?

The proton spectra is in very good agreement, that's true.


"There is a general over approximation of all the shifts which occurs for the same reasons as described previously."

Please refer to the section your speaking of



"There is a closer resemblance to literature with the hydrogen NMR values for these epoxides than was seen in the previous molecule"

Yes. But that's mainly due to less methyl groups (which you should average) and a more rigid ring system - the latter is in agreement with your observation of a decreased ring system.

"and consequently the greater likelihood of attaining a global energy minimum"
Well, yes and no. You're sort of right, because you're phrasing it general enough. ;) A bit more specific please.

== Optical Rotation and TS  (0.35) 100% ==

Good, but this section needs a quick intro on how reliable the method for alpha<=100°.
So for trans-b-methylstyrene it's actually not 100% reliable.


"so it is not surprising that the computed value is also different"

well, the compputation could theoretically be the same as one of the two...


Very good section on the VCD analysis ! :)


Excellent discussion on the 'ee' and 'k' task. Very nice graphic, too!


Your findings on enantiomeric excess might also help explain why the OR values in literature are a bit off. 


Very good work on this section!

== QTAIM and NCI (0.10) 100% ==


Cool, good section!

== Final notes==

Generally many typos, especially in the beginning.
Try to clean up your text and make it more readable next time.

In places you need to be a bit more specific and quite generally discuss things more in-depth. 

Overall good report! 90%