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Chemistry LibreTexts

2.2: Chemical Representations on Computer: Part II

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    CHEM3351: Cheminformatics

    Spring 2018: Bucholtz



    Learning Objectives

    • Understand the principles behind connection table representation of chemical structures
    • Translate structural formulas into simplified connection tables and vice-versa
    • Recognize the parts of a MOL file, a common connection table file format
    • Map the correspondence between features of a structural formula and entries in a MOL file
    • Adjust connection tables to make simple modifications to chemical structures
    • Track how changes in a chemical sketch program and the underlying connection table data relate to each other.

    Like structural formulas, connection tables represent the basic building blocks of structural organic chemistry: atoms and bonds. They encode information and rules about chemical structures in the form of a table that a computer algorithm can parse. A program can then use this information in many ways, to present a visual image to a user, to compare structural features among many compounds and associated data, to provide a link between chemical records in different databases, and much more. Connection tables enable chemical structure information to be programmatically accessible and are the key to most cheminformatics applications.