title: Accurate specification of molecular structures: the case for zero-order bonds and explicit hydrogen counting.
abstract: Most data structures used to represent molecular entities for cheminformatics are underspecified for purposes of representing nonorganic chemical species. Two extensions are proposed: allowing bond orders of 0 and adding an atom property to control the number of inferred attached hydrogen atoms. The case for these two extensions is made by demonstrating the effective representation of a number of unconventional bonding types that cannot be effectively represented by data structures currently in common use. A set of enhancements to the industry standard MDL CTfile format is proposed, which includes a backward compatibility mechanism to maximize interpretability by software that has not been updated to make use of the extensions.
authors: Molecular Materials Informatics, Inc., 1900 rue St. Jacques #302, Montréal, Québec, Canada H3J2S1. aclark@molmatinf.com
authors: Alex M
authors: AM
authors: Clark
mesh_terms: D000465:Algorithms; D006859:Hydrogen / Q000737:chemistry*; D006860:Hydrogen Bonding; D048088:Informatics / Q000379:methods; D015394:Molecular Structure; D004364:Pharmaceutical Preparations / Q000737:chemistry*; D012984:Software
chemical_list: D004364:Pharmaceutical Preparations; D006859:Hydrogen