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According to my understanding, the filled orbital (lone pair electron for this) is more nucleophilic (higher energy) if:

  1. it has more $\mathrm p$ character (since p orbital is the furthest from the nucleus, which has the lowest stabilizing effect between $\mathrm s$, $\mathrm{sp}$, $\mathrm{sp^2}$, $\mathrm{sp^3}$, and $\mathrm{p}$)
  2. the atom has a negative charge

Drawing the resonance formulae about an ester group

enter image description here

and according to the internet, the oxygen in C=O bond is much more nucleophilic than another oxygen since:

  1. it has $\mathrm{sp^3}$ character
  2. it is negatively charged

However, what I am thinking is:

  1. another oxygen also bears $\mathrm{sp^3}$ character (left resonance structure)
  2. the resonance structure on the right is minor compared to that on the left (according to what I have been taught, more charges means less major resonance structure), so the magnitude of partial-positive in that oxygen should not be high

Therefore, won't both oxygens in the ester group comparably nucleophilic?

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Because of the depicted resonance structure, you rightly stated, that the carbonyl group is more nucleophilic (since no negative charge can be "resonanced" on the non-carbonyl oxygen). The other thing is, non-carbonyl oxygen has $\mathrm{sp}^2$ hybridization - with its $\mathrm{sp}^2$ lone pair it can stabilize antibonding sigma orbital of the carbonyl (on the carbon) and with its lone pair in p orbital it can stabilize antibonding pi orbital of the carbonyl (again on the carbon) - and that is why it can even donate the lone pair to this antibonding orbital in the resonance structure you are showing.

So, because of the resonance structure plus donation of electrons from non-carbonyl oxygen (thus lacking the $\mathrm{sp}^3$ character), the carbonyl oxygen should be more nucleophilic.

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