While using ChemDraw Professional to construct some cyclic allenes and rotationally restricted biphenyls, I came across anomalous assignments of stereochemistry. [For the latest version of the 2013 IUPAC BlueBook go here and for errata look here.]

The major issue is the assignment of a stereodescriptor (R/S) to the hydroxyl carbons in the allenes 1/2 and biphenyls 3/4. By the CD analysis allenes 1 and 2 are diastereomers as are biphenyls 3 and 4 when, in fact, allenes 1 and 2 are identical as are biphenyls 3 and 4! Because the pairs are not diastereomers but identical, a stereochemical assignment [non-stereogenic] is not warranted.

Rotate the structures 180° about the horizontal axis. Allene 1 superimposes on 2; biphenyl 3 superimposes on 4. These two structures are no different from the case of cycloheptanols 5/6 rotated about the horizontal axis or ᴅ-arabitols 7/8 about a vertical axis. Structures 5 through 8 are handled properly; structures 1 through 4 are not. Is it just me or is there something wrong with the CD algorithm that doesn't address this issue?

A minor issue is the use of the terms R/S when the intent is Ra/Sa. Indeed, IUPAC prefers the descriptors M/P. In this instance, the allenic component of 1/2 and the biphenyl entity in 3/4 would be designated as ‘P’ rather than ‘S’.

Rule P- (PDF):

The helicity rule can also be applied to the stereogenic axis in allenes and biphenyls. Looking along the chirality axis the ligands are arranged in pairs. When proceeding from the nearer ligand having priority in the pair to the further away atom or group having priority in the pair, the chirality is described by the symbols ‘M’ if the path is anticlockwise; the symbol is ‘P’ if the path is clockwise. Stereodescriptors ‘M’ and ‘P’ are used in preferred IUPAC names. The lowest locant on the axis is cited before the stereodescriptor.

  • $\begingroup$ It looks inconsistent. For (5P)-cyclodeca-5,6-dien-1-ol 1/2, "Show Stereochemistry" shows a label at the -OH group, but "Analysis -> Name" only gives "(6S)-cyclodeca-5,6-dien-1-ol". $\endgroup$
    – Loong
    May 14 at 12:27
  • $\begingroup$ @Loong: Well, at least one section of CD gets it right. I have contacted Perkin-Elmer about this issue. Hopefully, they will take corrective action. $\endgroup$
    – user55119
    May 14 at 13:28
  • 1
    $\begingroup$ @Loong: Perkin-Elmer (ChemDraw) has acknowledged the error. Presumably it will be corrected in a future version. $\endgroup$
    – user55119
    May 17 at 12:41


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