Structures that InChI and SMILES can't represent

Even in organic chemistry there are lots of strucures that cannot be represented by InChIs and currently cannot be communicated without structure diagrams. I’ve gone randomly to Beilstein Journal of Organic Chemistry (as it’s Open Access) and found three consecutive abstracts. They contain ideas of variable locants, spatial arrangements, non-atomic species (balls), reactions, ion pairs, organometallic coordination. It would be an act of scientific barbarism to copyright anything below.

Novel base catalysed rearrangement of sultone oximes to 1,2-benzisoxazole-3-methane sulfonate derivatives
Veera Reddy Arava, Udaya Bhaskara Rao Siripalli, Vaishali Nadkarni, Rajendiran Chinnapillai
Beilstein Journal of Organic Chemistry 2007, 3:20 (8 June 2007)
[Full Text] [PDF] [Album] [PubMed] [Related articles]

m-Iodosylbenzoic acid – a convenient recyclable reagent for highly efficient aromatic iodinations
Andreas Kirschning, Mekhman S Yusubov, Roza Y Yusubova, Ki-Whan Chi, Joo Y Park
Beilstein Journal of Organic Chemistry 2007, 3:19 (4 June 2007)[Abstract] [Full Text] [PDF] [Album] [PubMed] [Related articles]

A convenient catalyst system for microwave accelerated cross-coupling of a range of aryl boronic acids with aryl chlorides
Matthew L Clarke, Marcia B France, Jose A Fuentes, Edward J Milton, Geoffrey J Roff
Beilstein Journal of Organic Chemistry 2007, 3:18 (30 May 2007)
[Abstract] [Full Text] [PDF] [Album] [PubMed] [Related articles]

FWIW: CML can manage much of the uncertainty above, but although it is a work of breathtaking beauty it also shouldn’t be copyrighted.

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One Response to Structures that InChI and SMILES can't represent

  1. These are all acknowledged limitations
    What Can InChI Currently Not Represent?
    InChI currently does not support the representation of:
    * Polymers
    * Conformers
    * Complex organometallics
    * Cluster molecules
    * Polymorphs
    * Excited state and spin isomers
    * Non-local stereochemistry/chirality
    * Topological isomers
    * Mixtures
    * Reactions
    * Unspecific isotopic enrichment
    * Markush Structures
    based on what I’ve heard Markush IS under consideration byt the team as are a number of the other issues above…

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