I am not a pro, but I have some experience with gaussian. For example, I can optimize a structure, calculate the frequency and rotational energies.

In the lab I made a nucleophilic substitution reaction where the Nucleophile $\ce{X}$ reacted with $\ce{R-\text{alkyl}-CH2-I}$ to form $\ce{R-\text{alkyl}-CH2-X}$ (iodide was eliminated). However, my molecule has on another position a benzylic bond "$\ce{R-Ph-CH2-O-R}$" as well and I noticed that a side reaction can occur at that position (depends on the nucleophile $\ce{X}$) where the nucleophile $\ce{X}$ reacted with "$\ce{R-Ph-CH2-O-R}$" to form "$\ce{R-Ph-X}$".

So there are two reactions: (1) The normal reaction with the alkyl $\ce{R-\text{alkyl}-CH2-I}$ to form $\ce{R-\text{alkyl}-CH2-X}$ and the side reaction (2) where the benzylic position in $\ce{R-Ph-CH2-O-R}$ is cleaved by the nucleophile $\ce{X}$ to form $\ce{R-Ph-X}$.

I am now trying to understand why the nucleophile $\ce{X}$ reacted with a benzylic $\ce{CH2}$ group at all even when its just a 15% conversion rather than the $\ce{R-\text{alkyl}-CH2-\text{Halogen}}$ group which is the favoured reaction. I think this could be illustrated by MOs, what do you think?

I already optimized the structure of my molecule and generated the formatted checkpoint file to display the molecular orbitals with GaussView. When I actually look at the HOMO and LUMO I don't get any useful information. At the benzylic position there is not really a high coefficient (no big MO) and at the $\ce{CH2}$ atom of "$\ce{R-CH2-I}$" there is even a smaller coefficient. I had expected to see at least a big MO at the carbon atom of the alkyl $\ce{R-CH2-I}$ - where the nucleophilic reaction is favoured - but thats not the case.

So my question is, how can I analyze the reaction behaviour with DFT calculations, especially with Gaussian? I think calculating transition states is to much. It would be nice to just get some useful information about the molecules reactive sides (electrophilic sides where nucleophiles can react). How can I do that? Which calculation should I make?

By the way I used this B3LYP basis set: b3lyp/6-31g(d,p) nosymm geom=connectivity



closed as too broad by LordStryker, tschoppi, Klaus-Dieter Warzecha, Philipp, user4076 Feb 28 '14 at 18:54

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  • 4
    $\begingroup$ "So my question is, how can I analyze the reaction behaviour with DFT calculations, especially with Gaussian?" -- To truly do this, you would have to map out the reaction pathway which involves characterizing transition states and computing the intrinsic reaction coordinate. This would require a huge amount of effort than you would be willing to commit. Try looking up how to compute "Electrostatic Potentials" in G09. I think this is what you are looking for judging by your post. What integration grid are you using? (don't say 'default'). Also Cartesian or spherical harmonic functions? $\endgroup$ – LordStryker Jan 27 '14 at 18:31
  • $\begingroup$ Have you tried to calculate Fukui function for your molecules? It may help, and it is relatively little effort. $\endgroup$ – Greg Jun 14 '17 at 16:03