Inside Informatics 19.3

Stereochemistry in ChemBioDraw

New stereochemical features in the latest version of ChemBioDraw 

Jesse Gordon, Jesse Gordon, Jesse Gordon


Outlined here are all of ChemBioDraw's version 12 tools for stereochemistry:

This article begins with how ChemBioDraw represents stereochemical bonds and then proceeds on to ChemDraw’s representation of chiral centers, finally finishing with more advanced topics for both absolute stereochemistry and relative stereochemistry. This article, and ChemDraw’s chiral representations in general, rely on the IUPAC recommendations in the paper entitled "Graphical Representation of Stereochemical Configuration" in: IUPAC Chemical Nomenclature and Structure Representation Division. Pure Appl. Chem. 78, 1897 (2006). (See:

Bond Drawing Conventions

The following table describes the chemical conventions ChemBioDraw recognizes:



Single bond, unspecified stereochemistry; unless in a special projection representation (discussed below).

Single bond, "down" stereochemistry (into the plane of the paper, away from the viewer). ChemDraw figures out the "down" direction from the context; see detailed note below.

Single bond, "up" stereochemistry (out of the plane of the paper, toward the viewer), from the narrow end to the wide end; for the heavy bar, ChemDraw figures out "up" direction from the context.

Single bond, mixture of "up" and "down" stereoisomers in an unspecified proportion, or unknown stereochemistry. In the context of other CambridgeSoft software, such as ChemBioFinder search tools, a wavy bond is interpreted the same as a single bond.

Double bond, with cis/trans stereochemistry as drawn.

Double bond, with cis/trans stereochemistry mixed or unknown. These three representations are chemically identical; ChemDraw recognizes the latter two because many people dislike the "crossed line" representation.

NOTE: With regards to the "down" direction of the hashed bond, as discussed in the IUPAC paper "Graphical Representation of Stereochemical Configuration" referenced above, the convention preferred by IUPAC is to interpret from a hashed bond as "down" from narrow-to-wide. IUPAC acknowledges, however, that another convention is wide-to-narrow. Because of that, ChemDraw uses the context instead of strict directionality, and will interpret either way from a diagram with a hashed bond. Contrast this method to the wedge bond, which does not have two different conventions, and hence, ChemDraw always interprets "up" as going from narrow-to-wide

Stereochemistry in Projection Representations

The single-bond representation can mean a stereocenter in various projections. ChemBioDraw interprets the single-bonds below as stereochemicals having chiral centers:

All three of the previous projections represent variations of glucose, a stereochemical molecule with multiple chiral centers. All three also use single bonds to indicate stereochemistry, with the projection itself implying the stereochemical configuration, rather than hash and wedge bonds. ChemDraw interprets the stereochemistry according to the established conventions of each projection. Below are the same three molecules with chiral centers identified.

ChemDraw can interpret mixed representations as well. In the Haworth projection of glucose (below left), the α-glucofuranose form, the projection representation on the ring is mixed with wedge and hash bonds on the side chain. ChemDraw interprets that accurately too, with the stereochemical centers shown on the right.

Absolute Stereochemistry

ChemBioDraw calculates the absolute stereochemistry according to the Cahn-Ingold-Prelog (CIP) priority rules (methodology is described in detail later). Use the "Show Stereochemistry" menu item, from the "Object" menu, to assign tetrahedral and double-bond stereochemistry labels.

Only tetrahedral and double-bond stereochemistry are supported, and only non-racemic stereochemistry is interpreted. Stereochemical indicators for aromatic bonds are not displayed.

The stereochemistry feature calculates and displays the following:

  • (R), (S): Standard tetrahedral stereochemistry. For example:

  • (r), (s): Tetrahedral stereochemistry determined by other stereochemical centers. Strictly, (r) and (s) are pseudoasymmetric centers, while (R) and (S) indicates an asymmetric center. For a fuller description of pseudoasymmetry, see: E. L. Eliel, S. H. Wilen. Stereochemistry of Organic Compounds. pp. 117–124. John Wiley, New York (1994). An example of pseudoasymmetric centers:
  • (E), (Z): Standard double-bond stereochemistry. For example:

Advanced Absolute Stereochemistry

ChemDraw interprets chirality in contexts well beyond the basics described previously. In the pair of molecules below, the molecule on the left has a pseudoasymmetric center, and hence is labeled (r), while the molecule on the right has an asymmetric center, and hence is labeled (R).

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