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How to know if the following chemical structure of morphine is an R or S? What I basically need to know is: which chirality center do we use to make the decision?

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The structure that you are showing is neither R nor S.

As it has five chirality centers you need to look at all of them.

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You can see in the above figure that there are three R and two S centers in the configuration of morphine that you posted.

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