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

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Alex M. Clark

Molecular Materials Informatics, Inc., 1900 rue St. Jacques #302, Montréal, Québec, Canada H3J2S1

J. Chem. Inf. Model., 2011, 51 (12), pp 3149–3157

DOI: 10.1021/ci200488k

Publication Date (Web): November 23, 2011

Section:

History, Education, and Documentation

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.

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History

Published In Issue December 27, 2011
Article ASAPDecember 08, 2011
Just Accepted ManuscriptNovember 23, 2011
Received: October 13, 2011

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

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NAOMI: On the Almost Trivial Task of Reading Molecules from Different File formats

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