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In organic chemistry , considering definitions of electrophilic and nucleophilic:

Electrophilic:having an affinity for electrons : being an electron acceptor.

nucleophilic : having an affinity for atomic neuclei (also can we say proton?) : being an electron donor.

So both being opposite to each, why dont we say nucleophilic as protophilic?

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Because not all "nucleophilic" agents react equally well with all types of relatively exposed nuclei. Phosphines are very unwilling to extract a proton but quite nucleophilic if the available electronic vacancy is in carbon or a transition metal.

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Nucleophile- nucleus loving . but it means the one which donates electron or has a negative charge on itself.

The name/ term is given as nucleophile because it would try to give away its electron pair to molecule which has less electron density possibly an electrophile. like in nucleophillic addition reactions the nucleophile attacks that part for example say in : carbonyl compounds on the carbon which has a less density of electron as the $\pi e^-$ land on oxygen . So was that a proton site or nucleus site or a site where electron density is less .

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