Re: ORGLIST: a question on stereochemical nomenclature

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From: Jonathan Brecher (jsb$##$
Date: Fri Jan 21 2005 - 23:50:13 EST

At 1:40 AM -0500 1/21/05, Jacob Zabicky wrote:
>Hello everybody,
>An interesting problem for a molecule with a C2 axis of symmetry, where
>its girality is conferred by the E configuration of the chlorine atoms
>attached to the unsaturated exo-double bonds. I would like to ask
>Jonathan what was the ranking given to the substituents, in order to
>ascribe the R configuration to positions 1 and 3 of the cyclobutane
>ring of the left-hand side formula.

Well, the ranking was given "clockwise" in both cases, since that's
pretty much the definition of an (R) stereodescriptor when a
stereocenter is viewed so that the lowest-ranking substituent (the
hydrogen) is behind the other three.

I imagine the real question is really "why". Relative to each
tetrahedral stereocenter, one double bond is oriented cis and one is
oriented trans. Rule 3 of the CIP rules says "seqcis precedes
seqtrans" -- that is, a double bond that is cis relative to the
stereocenter being analyzed gets a higher priority than one oriented
trans relative to that same stereocenter.

Gotta always keep in mind that "the CIP rules" are the ones
formulated in the original CIP papers, and *not* necessarily the
fraction of them that you were taught. Few textbooks cover even Rule
1 completely, and there are 5 parts to the full rules:

The Rules

R.S. Cahn, C.K. Ingold, and V. Prelog, "Specification of Molecular
     Chirality", _Angew. Chem., Int. Ed. Engl._ 1966, 5, 385-414
     (errata: 1966, 5, 511);
     _Angew. Chem._ 1966, 78, 413-447.
V. Prelog and G. Helmchen, "Basic principals of the CIP-System and
     Proposals for a Revision", _Angew Chem._ 1982, 94, 614-631;
     _Angew. Chem., Int. Ed. Engl._ 1982, 21, 567-583.

1. Higher atomic number precedes lower
2. Higher atomic mass number precedes lower
3. _Seqcis_ precedes _seqtrans_
4. Like pair R,R or R,S precedes unlike pair R,S or S,R
5. R precedes S

also see:

P. Mata, A.M. Lobo, C. Marshall, and A.P. Johnson, "The CIP Sequence
     Rules: Analysis and Proposal for a Revision." _Tetrahedron:
     Asymmetry._ 1993, 4, 657-668.

1 - a) Higher atomic number precedes lower
     b) A duplicated atom, with its predecessor node having the same
        label closer to the root, ranks higher than a duplicated atom,
        with its predecessor node having the same label farther from the
        root, which ranks higher than any non-duplicated-atom-node.
2 - Higher atomic mass number precedes lower
3 - seqcis stereogenic units precede seqtrans stereogenic units and those
     precede non-stereogenic units (seqcis ? seqtrans > non-stereogenic.
     The domain of application of this rule is restricted to geometrically
     diastereomorphic planar tetraligant atoms and double bonds. All
     cases involving geometrically enantiomorphic two-dimensional
     stereogenic units are considered in Rules 4 and 5.
4 - a) Chiral stereogenic units precede pseudoasymmetric units and these
        Precede non-stereogenic units. Geometrically enantiomorphic two-
        dimensional stereogenic units precede two-dimensional
        non-stereogenic units.
     b) When two ligands have different descriptor pairs, then the one
        with the first-chosen _like_ descriptor-pair has priority over
        the one with a corresponding _unlike_ descriptor-pair. _Like_
        descriptor pairs are: RR, SS, MM, PP, seqCisseqCis,
        seqTransseqTrans, RseqCis, SseqTrans, MseqCis and PseqTrans,
        RM, SP. _Unlike_ pairs are: RS, MP, RP, SM, seqcisseqTrans,
        RseqTrans, SseqCis, PseqCis and MseqTrans.
        Methodology for pairing descriptors:
          The descriptor assigned to geometrically enantiomorphic double
        bonds should be associated in the digraph with the first node
        corresponding to the atoms involved in the double bond.
          For each ligand the descriptor chosen as first (highest ranked
        descriptor) is paired with all the remaining descriptors.
        The following characteristics determine the hierarchical rank of
        the pairs of descriptors:
         i) Higher rank of the second descriptor in the pair
        ii) Lower rank of the least common ancestor in the graph.
     c) r precedes s and p precedes m
5 - A ligand with descriptor R, M, or seqCis has priority over its
     enantiomorph with descriptor S, P or seqTrans.

The rules are pretty concise, but there's a LOT of subtlety in there!

Jonathan Brecher
CambridgeSoft Corporation

>On Jan 19, 2005, at 19:43, Jonathan Brecher wrote:
>> At 12:20 PM -0500 1/19/05, Luis Salvatella wrote:
>>> Dear all,
>>> Can anybody name both enantiomers for
>>> [2(4)E]-1r,3c-dichloro-2,4-bis(chloromethylidene)cyclobutane ?
>> Your name sounds fine. If you're looking for the CIP stereochemistry
>> assignments, it would be (1R,2E,3R,4E)-1,3-dichloro... for your left
> > structure and (1S,2E,3S,4E)-1,3-dichloro... for your right.
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