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Chemically orthogonal means that two functional groups or molecules do not engage in similar/identical chemical reactions or exhibit significant differences in their chemical reactivities. An amino and a nitro are chemically orthogonal nitrogen-functions. On the other hand, an aldehyde and a ketone can be considered chemically very similar with respect to most reaction conditions.

I have to admit that this terminology is rather general and does apply to many functions. It is probably not of too much use.

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