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Consider [(1⁠S,2⁠S,4⁠S)-bicyclo[2.2.1]hept-5-en-2-yl]acetic acid:

[(1S,2S,4S)-bicyclo[2.2.1]hept-5-en-2-yl]acetic acid

(Source: http://www.chemspider.com/Chemical-Structure.22823922.html)

According to the chemspider nomenclature, this has three S stereocenters. However, when I perform the CIP both manually and computationally, the center labeled ? comes up as R. I am trying to figure out if I am misunderstanding CIP (particularly the expansion part for handling double-bonds) or if the literature is wrong in this case. I would greatly appreciate if some chemist here could work out this example to give me another data point.

confused chemist
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1 Answers1

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According to the Cahn–Ingold–Prelog priority rules, a double bond considered as ($\ce{CCX}$), where $\ce{X}$ depends on the substitution on the double bond. In your case, $\ce{X}$ is hydrogen ($\ce{H}$). Thus, I arranged the priority as depicted in following diagram (chiral carbon in consideration is marked with asterisk):

(1S,2S,4S)-Bicyclo[2.2.1]hept-5-en-2-ylacetic acid

Hydrogen is the least priority group on the chiral carbon. Among other three groups, the bridgehead carbon is a $\ce{-CH2 -}$ group, hence can be marked as ($\ce{CHH}$) on priority checking. The final two groups can be marked as ($\ce{CCH}$). I used red and blue color on one group (methine on the ring), and black on the other (double bond) to distinguish these two group. Since both has identical substitutions on first carbon, we need to moved to second carbon. On double bond, it is again ($\ce{CCH}$), but bothe red and blue carbon give ($\ce{CHH}$) priority checking. Thus, double bond has the highest priority as indicated. Therefore, assignment for this chiral center is ($S$)- as given in chemspider website.

Mathew Mahindaratne
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  • Thank you very much! I was misunderstanding the algorithm. I thought that the idea was to merge the atoms at each successive level away from the chiral center, so that in the second round we would be comparing CCH vs CHH + CHH = CCHHHH. Now a followup question is, in a hypothetical case where we have something like CCH vs CCH + CHH, does the second group take priority due to having an extra branch, or do we move to the next level of comparison? I assume the former. – confused chemist Nov 11 '19 at 17:39
  • It's not clear to me what your question on hypothetical question. Yet, for your question in hand, I think you still confused how to go by carbon to carbon (since it is a ring). Well, first carbons from chiral atom here have: CCH, CHH, CCH, therefore, $\ce{CH2}$ group is the priority #3. Between other two, we have to look at second carbons: carbon with double bond still has CCH (twice) while other carbon has CCH twice. Therefore, carbon with double bond has the highest priority between them so, chiral center has a ($S$)-nomenclature.. – Mathew Mahindaratne Nov 11 '19 at 18:04
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    Thanks again. I understand how this works now. Can't upvote you since I don't have the points but much appreciated! – confused chemist Nov 11 '19 at 18:29
  • I appreciate your concern. Just for your info, since it's your own question, you are allowed to upvote or downvote, and even accept any answer as you wish. :-) – Mathew Mahindaratne Nov 11 '19 at 18:45