Accurate Specification of Molecular Structures: The Case for Zero-Order Bonds and Explicit Hydrogen Counting

  • Alex M. Clark
  • Journal of Chemical Information and Computer Sciences, December 2011, American Chemical Society (ACS)
  • DOI: 10.1021/ci200488k

Representing chemical structures other than just organic molecules

What is it about?

Chemical informatics software is all but exclusively designed to represent simple organic molecules (i.e. most drugs). Any molecule that has bonds which do not fall into the single/double/triple categories, or has nontrivial valence states, cannot be handled with current software. This includes most chemistry. It can be solved with very modest additions to the working file format: bond orders of zero, and explicit control over automatic addition of hydrogen atoms.

Why is it important?

With these minor, easy-to-implement additions, which can be bolted onto the industry standard MDL Molfile format, it is possible to work with all kinds of inorganic & organometallic compounds. These structures can now be drawn and stored without ruining the information content (i.e. implying the wrong molecular formula, among other things). Adoption of these extensions means that all kinds of molecules are applicable to cheminformatics, instead of just simple drug-like organic molecules.

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The following have contributed to this page: Alex Michael Clark