Talk:Mod:00636773Organic

1.1 Part 1 (13/45%)'

1.1.1 Formation and Hydrogenation of Cyclopentadiene Dimer (1/10%)

In your table you are referring to the total electronic energy E(RB3LYP) in Hartrees. However, you are supposed to compare the thermodynamical energies obtained using Molecular Mechanics. These energies are in Kcal/mol.

You can read clearly in the the chem wiki what you are supposed to do in this exercise:

The objective of this part of the module is to establish on the basis of the results obtained from the molecular mechanics technique whether the cyclodimerisation of cyclopentadiene and the hydrogenation of the dimer is kinetically or thermodynamically controlled.

Why have you decided to do this exercise with 6-31G(d,p) basis sets instead of using molecular mechanics as you were asked? You could have done both and compared them, but not ignore what you are supposed to do here.

Also, the energy values you report obtained with ChemBio are too high for these molecules…

Anyways, you could have included the .log file, maybe I was able to subtract the correct themodynamical energies, but the energy in your table is not the correct energy for this exercise.

Even though, you haven´t done what you were asked to do in this exercise and you report the incorrect energy, the ranking of the energies of the molecules is incorrect. The exo is thermodynamically more stable than the endo, therefore the equilibrium is kinetically controlled as the endo product is the only one produced when the dimerisation occurs at room temperature. However, your guess about the hydrogenation product is correct. In addition, you haven´t written anything about the thermodynamic/kinetic control of this reaction as you are asked to do (read again the objective of this exercise).

You should read carefully what you are asked to do and write your report consistently with the objectives!

1.1.2 Atropisomerism in an Intermediate related to the Synthesis of Taxol (0/10%)

I quote from Chemwiki what you are asked to do here:

The objective is to explore which of the two atropisomers is the more stable.

Procedure

Using MMFF94s force-field to determine the most stable isomer 9 or 10, and to rationalise why the alkene reacts slowly (hint: read the literature on hyperstable alkenes![6]. Pay particular attention to the conformation of the resulting optimised structure, to see if any aspect of this structure could be improved by further minimisations (preceeded if necessary by a manual edit of the structure to move atoms into more correct orientations).

(https://wiki.ch.ic.ac.uk/wiki/index.php title=Mod:organic#Objectives_for_Set_exercises:_Part_1)

Again, incorrect energy! Secondly, each of the intermediates has 4 possible conformations, you have only represented one, how do you know that it is the most stable of the 4?

And where is the discussion about the hyperstability of the alkenes?

1.1.3 Taxol NMR - Spectroscopic Simulation using Quantum Mechanics (12/25%)

Again, there is a ciclohexane motif in the molecules, that means that there are at least 2 configurations for each of them, a chair an a twist boat. You don´t even mention this. (0/5%)

Well done at least, comparing the results of two different data sets, but maybe you could have done some statistical analysis to obtain a better description of the comparison. (12/20%)

It is clear that your results are not satisfactory, as you only modeled one of the possible conformations, and your missed the lower energy conformations of both!

1.2 Part 2 (49/55%)

1.2.1 The Crystal Structures of the Shi Catalyst and the Jacobsen Catalyst (5/5%)

Well done finding the crystal structures of both catalysts.

1.2.2 The Calculated NMR Properties of the Epoxides (3/5%)

You present the HNMR and CNMR for dihydronapthalene, but only literature values for the HNMR. For than-stilbene you only present the HNMR.

1.2.3 The Assignment of the Absolute Configurations for Alkenes 2 and 4 (35/35%)

OR: (15/15%)

Dihydronapthalene: well done finding literature values and you obtained good agreement with the literature

Tran-stilbene: again, good work.

Good job with the enantiomeric excess and including so many references in the discussion. (20/20%)

1.2.4 NCI and QTAIM Analysis for the Transition State (4/6%)

Trans-beta-metyl-styrene: Nice animations in the QTAIM analysis and good but brief discussion for the NCI analysis.

Dihydronaphtalene: I can only find the NCI analysis, very brief discussion….

1.2.6 New Candidates (2/4%)

A bit more of discussion about it would have resulted in a better mark...

'General Comments

You haven´t done what you were asked to do...Also, the way of presenting the results is a bit messy and not very clear.

Total mark: 62%