Re: ORGLIST: a question on stereochemical nomenclature

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From: Jacob Zabicky (zabicky$##$bgumail.bgu.ac.il)
Date: Sun Jan 23 2005 - 11:02:37 EST


Hello again,

Thank you. Sorry for insisting, but I am still missing something. Would
not the chlorine atoms, as the heaviest of the the atoms attached to
the asymmetric center, be the one determining the highest ranking
group, in which case the cis priority rule will make for an S
configuration?

All the best,

Jacob

On Jan 22, 2005, at 6:50, Jonathan Brecher wrote:

> 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
>
> see:
> 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
> jsb$##$cambridgesoft.com
>
>
>
>
>
>> 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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