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I am a little bit confused between charge distribution and HOMO/LUMO site in determining chemical reactivity. In charge distribution, the sites which are deficient and abundant in electrons are localized (e.g. in carbonyl molecules, we would expect that the carbonyl carbon to be partially positive and we would predict that a nucleophile would attack into that deficient carbon) but in HOMO/LUMO orbitals the site for reactivity differs on the orientation and sign of the orbitals. It may be in HOMO this carbon has an orbital for an overlap but in LUMO a node may appear in that site. My question is where would the nucleophile react in a species, by charge distribution or HOMO/LUMO orbital?

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You need both an empty LUMO for the electrophile with an in phase HOMO for the nucleophile at the site of attack AND the proper charge distributions.

The LUMOs are critical; you can't shove electron density into more electron density, and LUMOs represent a lack of electron density. However, the electron density for a nucleophile will be attracted to the partial positive charges.

Organic chemistry normally requires you make judgments about the relative impacts of various phenomena, and this is another example.

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