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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

Thanks.

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

Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. Avoid asking multiple distinct questions at once. See the How to Ask page for help clarifying this question. If this question can be reworded to fit the rules in the help center, please edit the question.

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    $\begingroup$ "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