The purpose of a chemical structure diagram is to convey information - typically the identity of a molecule - to another human reader or as input to a computer program. Any form of communication, however, requires that all participants understand each other. Recommendations are provided for the display of two-dimensional chemical structure diagrams in ways that avoid ambiguity and are likely to be understood correctly by all viewers. Examples are provided in many areas, ranging from issues of typography and color selection to the relative positioning of portions of a diagram and the rotational alignment of the diagram as a whole. Explanations describe which styles are preferred and which should be avoided. Principal recommendations include: 1) Know your audience: Diagrams that have a wide audience should be drawn as simply as possible; 2) Avoid ambiguous drawing styles; 3) Avoid inconsistent drawing styles.

The interpretation (automatic or otherwise) of chemical names is complicated by the poor quality of such names in common usage. A practical interpretation system for chemical names must consider not only the published rules for chemical nomenclature but also their misinterpretations, corruptions, and popular extensions. This paper describes the design of Name=Struct, an automated system for the conversion of chemical names to their corresponding structures, and discusses the nomenclature interpretation problems addressed in its development. The comprehensiveness and accuracy of Name=Struct are analyzed in several contexts.

Stereochemical configuration is determined by the relationship of atoms in three-dimensional space, yet remains most commonly represented in two-dimensional media such as printed publications or computer screens. Recommendations are provided for the display of three-dimensional stereochemical information in two-dimensional diagrams in ways that avoid ambiguity and are likely to be understood correctly by all viewers. Examples are provided for all types of stereochemical configuration, with explanation of which styles are preferred and which should be avoided. Principal recommendations include:Know your audience: Diagrams that have a wide audience should be drawn as simply as possible.Avoid ambiguous drawing styles.Avoid the use of perspective diagrams and class-specific drawing styles (Fischer projections, Haworth projections, etc.) when structures are to be interpreted by computers.Use solid wedges to indicate bonds that project above the plane of the paper and hashed wedges to indicate bonds that project below the plane of the paper; in both cases, the bonds must be oriented with the narrow end at the stereogenic center.Avoid connecting stereogenic centers with a stereobond.

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