Demos > Stereochemistry

Stereochemistry is an important concept in chemisty and is essential for understanding chemical structure. However, stereochemistry is not an easy concept to communicate, and much of chemistry education involves trying to master the topic, especially when it comes to the representation of stereochemical information in 2D and 3D. To make things even more difficult, CIP rules have long been the standard for assinging parity to stereochemical features, but such instruction is often greatly simplified so students can more easily understand it, as the CIP algorithm is incredibly complex, tedious and not without flaws. CIP rules have seen many revisions over the decades and more recently with the work of Paulina Mata and from Hanson et. al. References may be found at the bottom of the page.

ChemDoodle has an expert system to recognize and resolve stereochemical configurations in 2D and 3D. This demo focuses on drawn 2D structures using the ChemDoodle 2D algorithms. Simply draw your stereochemical feature in the sketcher below and press the Resolve Stereochemistry button. The ChemDoodle stereochemistry system is incredibly thorough and can even resolve drawn projections, examples below.

Resolve Stereochemistry

Click on a template to load it into the sketcher.

Examples

  • CIP Validation

    The CIP rules have long been the standard for describing configurations of stereochemical features in a molecule. While flawed, they have seen many revisions over the decades and were clarified by the work of Paulina Mata. These rules were adopted by IUPAC for naming standards and fully described in the Blue books. The most recent CIP rules from IUPAC were then algorithmically analyzed and standarized by Hanson et al. to remove any ambiguities and describe a completely consistent system for CIP assignments.

    ChemDoodle 2D implements all 6 current CIP rules as well as auxilliary desciptors and mancude ring support. The CIP algorithm in ChemDoodle is validated against the test suite provided by Hanson et. al. and is 100% accurate in all 300 test cases provided. A sample of the variety and scope of the Hanson validation suite is provided here for your verification. See if you can determine how many stereochemical features are present and what their configurations are (hint: just because an atom has a wedge bond attached does not mean it is a stereochemical feature). Then click on the molecule to see the answer. These stereochemical features are resolved in real time by ChemDoodle.

  • Projections

    ChemDoodle 2D can automatically detect drawn stereochemical projections and assign configurations to projection centers. Fischer, Haworth and chair projections are currently supported.

    See if you can determine how many stereochemical features are present and what their configurations are. Then click on the molecule to see the answer. These stereochemical features are resolved in real time by ChemDoodle 2D.

  • Edge Cases

    These are the complex CIP edge case tests from NextMove Software.

    See if you can determine how many stereochemical features are present and what their configurations are. Then click on the molecule to see the answer. These stereochemical features are resolved in real time by ChemDoodle 2D, and are 100% accurate.

References

  1. Cahn, R. S.; Ingold, C. K. Specifcation of Configuration about Quadricovalent Asymmetric Atoms. J. Chem. Soc. 1951, 612-622.
  2. Cahn, R. S.; Ingold, C.; Prelog, V. Specification of Molecular Chirality. Angew. Chem., Int. Ed. 1966, 5, 385-415.
  3. Prelog, V.; Helmchen, G. Basic Principles of the CIP-System and Proposals for a Revision. Angew. Chem., Int. Ed. 1982, 21, 567-583.
  4. Mata, P.; Lobo, A. M. The CIP Sequence Rules: Analysis and Proposal for a Revision. Tetrahedron: Asymmetry 1993, 4, 657-668.
  5. Mata, P.; Lobo, A. M. Implementation of the Cahn-Ingold-Prelog System for Stereochemical Perception in the LHASA Program. J. Chem. Inf. Comput. Sci. 1994, 34, 491-504.
  6. Mata, P.; Lobo, A. M. Comparison of Constitutional Properties in the CIP System: The CIP Sequence Rule 1. Tetrahedron: Asymmetry 1995, 6, 693-696.
  7. Mata, P. The CIP System Again: Respecting Hierarchies Is Always a Must. J. Chem. Inf. Comput. Sci. 1999, 39, 1117-1118.
  8. May, J. W. CHEMINFORMATICS FOR GENOME-SCALE METABOLIC RECONSTRUCTIONS. Doctor of Philosophy, University of Cambridge, June 2014.
  9. Hanson, R. M.; Musacchio, S.; Mayfield, J. W.; Vainio, M. J.; Yerin, A.; Redkin, D. Algorithmic Analysis of Cahn−Ingold−Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation. J. Chem. Inf. Model. 2018, 58, 1755-1765.
  10. Brecher, J. Graphical Representation of Stereochemical configuration. Pure Appl. Chem. 2006, 78, 1897-1970.

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