Appendix A: The Chemistry of ChemDraw

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Overview

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ChemDraw automatically converts lines, characters, and other symbols into chemically meaningful figures as you work. This work occurs in the background, but you can choose to view this chemical data using Check Structure, Analyze Structure, and Expand Atom Labels. ChemDraw also uses this chemical data when exporting to file formats that support only a subset of the notations that ChemDraw does.

This appendix describes how ChemDraw interprets what you draw and how you can help ChemDraw better interpret what you mean.

Chemical Intelligence in ChemDraw

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ChemDraw was designed as a tool to aid in chemical communication. Most chemists would understand AcOo-C₆H₄COOH immediately, whether or not they recognized it as aspirin. Most computer programs, however, require what is known as a "complete connection table," in this case, a collection of 21 atoms connected by 5 double bonds and 16 single bonds in a specific pattern. ChemDraw takes what makes sense to a chemist and converts it into what makes sense to another application.

This chemical intelligence can be used as a sophisticated "spelling" checker for chemical compounds. For example, if you're investigating organic acids, a compound with the structural formula CH3COO would probably represent acetic acid. Present the same formula in a paper on transition metal chemistry, and you might be describing a novel methylated cobalt oxide. If you had asked ChemDraw to interpret it beforehand, you would have received a message reporting a valence error, and you might have been prompted either to add a negative charge or to change the capitalization.

ChemDraw can offer only suggestions. If you and your audience understand what you are trying to depict, then you can ignore these suggestions. In many cases, you can teach ChemDraw to understand the notation you're using. For more information, see "Applying Nicknames".