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Stereochemistry in structure and reaction searching

Stereochemistry in structure and reaction searching. SciFinder-hbz meeting 2012. Agenda. What is stereochemistry? How to add stereochemistry to structure queries? Type of stereospecific structure answers in SciFinder Absolute stereo Relative stereo Stereo that doesn’t match the query

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Stereochemistry in structure and reaction searching

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  1. Stereochemistry in structure and reaction searching SciFinder-hbz meeting 2012

  2. Agenda • What is stereochemistry? • How to add stereochemistry to structure queries? • Type of stereospecific structure answers in SciFinder • Absolute stereo • Relative stereo • Stereo that doesn’t match the query • No stereo in the structure • How to conduct a reaction search for stereo-specific compounds?

  3. What is stereochemistry? • Stereochemistry involves the study of the relative spatial arrangement of atoms within molecules • Chiral or asymmetric molecules cannot be superimposed by their mirror image

  4. Stereochemistry in the CAS REGISTRY File in SciFinder • Unique chemical substances are assigned unique CAS RNs. This is also true for different stereo-chemical isomers. The main definition of stereochemistry is in the name of the compound. • Until 1992 stereochemistry could only be searched by name. Then stereochemistry was added to structures in REGISTRY including the back-file • Stereochemistry may be implied by the name of the compound • A smaller percentage of stereospecific compounds don’t have defined stereo bonds. Coordination compounds and stereobonds between rings normally cannot be searched

  5. Considerations for stereochemistry in SciFinder • In older literature the stereochemistry of the molecules was not known (by the author) • REGISTRY would have unique CAS RNs for the stereo specific isomers and for a compound with no stereochemistry • this latter one also includes the literature to racemic (50-50%) mixtures of the stereoisomers • Stereo-bonds and geometric double bonds can be specified in SciFinder • Question is which stereo-compounds are relevant for the search?

  6. Stereochemistry in the structure drawing Clicking again on a stereo bond in the structure will switch the direction of the stereo bond

  7. Example: trans-Limonene oxide has 3 stereo-centers

  8. Analyze by stereo: various options • SciFinder’s stereo candidates show different classes of stereochemistry in the substance definition

  9. Absolute stereochemistry result • Stereochemistry is well known for each stereo-center • (1R, 4R, 6S) • Optical rotation is determined • 146 literature references associated to this CAS RN (1965-2011)

  10. Absolute stereochemistry mirror image result • Stereochemistry is well known for each stereo-center • (1S, 4S, 6R) • Optical rotation is determined • 50 literature references associated to this CAS RN (1970-2011)

  11. Relative stereochemistry result • Stereochemistry is relative to other stereo-centers • (1R, 4R, 6S)-rel • Optical rotation is unknown • 505 literature references associated to this CAS RN (1964-2011)

  12. No stereochemistry result • Stereochemistry is unknown or it is the racemic mixture • 819 literature references associated to this CAS RN (1910-2012) • 17 references in Medline

  13. Unmatched stereochemistry result - 1 • Stereochemistry matches only in the positions 1 and 6 • (1R, 4S, 6S)-rel • 475 literature references associated to this CAS RN (1959-2012)

  14. Unmatched stereochemistry result - 2 • Stereochemistry is unknown on positions 1 and 6, but it is known at position 4 • (4R) • 94 literature references associated to this CAS RN (1998-2011)

  15. Unmatched stereochemistry result - 3 • Stereochemistry is unknown in our structure, but there is stereochemistry somewhere else in the compound (in the other component) • 1 literature reference associated to this CAS RN (2008)

  16. What about stereochemistry in reaction searches?

  17. How to maintain the precision for stereo-bonds in reaction searches • Start with one of the reaction participants in the structure search • Identify all relevant stereo or non-stereo hits • Get all reactions with the appropriate role • Refine the results with a full reaction query

  18. Start with the earlier structure search result

  19. First reaction result with stereo-specific educt

  20. Refine using the full (flat) reaction query

  21. Review the results: not fully stereo-specific

  22. Other results are fully stereo-specific

  23. Stereo in structure and reaction search • Stereochemistry can be complex and incompletely defined • SciFinder allows structure queries to be well defined in terms of their stereochemistry • SciFinder offers a convenient overview of the groups of stereo results in the answer set • The power of stereo specific structure queries can be worked into reaction searching

  24. Stereochemistry instructure and reaction searching Questions? Comments?

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