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Why ChemWriter Doesn't Follow IUPAC's Recommendations on Depicting Unknown Double Bond Stereochemistry

The language of chemical structure diagrams has been in use for many decades. Although most of this language is well-documented and well-understood, many dark corners can be found.

Stereochemistry is a particularly thorny area. For example, if a chemist makes an olefin that's known to be a mixture of (E) and (Z) forms, how should that information be conveyed graphically?

The good news is that IUPAC considered this case in their excellent Graphical Representation of Stereochemical Configuration. Section ST-4.4 deals specifically with the question of unspecified double bond geometry and notes three options in common use.

Cutting to the chase, IUPAC does not consider a crossed double bond representation acceptable. Nevertheless, that's what exactly what ChemWriter uses. Read on to find out why.

Option 1: Linear Substituent Geometry

The simplest option is to draw the double bond and its substituents linearly. This depiction style should only be used when the double bond has exactly two substituents, one on each end. When possible, the double bond itself should be arranged horizontally. If the entire structure is linear, it may be represented in textual form instead, without any explicit bonds. In practice, linear styles are primarily used for small molecules, although they are acceptable for structures of any size.

Although this form may be acceptable in some cases, there are simply too many cases where it fails (e.g. any tri- or tetrasubstituted bond) for it to be generally useful. Additionally, this form requires that chemists are aware of the convention. In other words, there's no convenient way for a drawing program to convey this rule to a user.

Option 2: Wavy Substituent Bonds

The most common convention for depicting double bonds with unspecified configuration in molecules of all sizes uses a wavy bond (ST-0.4) adjacent to the double bond. Under no circumstances, however, should the wavy bond join the double bond to another stereogenic center.

When possible, use only one wavy line:

Wavy lines to stereocenters are not allowed:

However, two wavy lines are preferred when the double bond terminus has two atoms:


In rare cases, it is impossible to depict an unspecified double bond configuration either by draw- ing the substituents linearly or by using wavy bonds. In those cases, it is clearest to depict the two con- figurations as two separate molecular entities separated by the text “and/or”.

The main problem with this recommendation is that it provides no single convention that will work across all possible cases. This presents a real problem for maintainers of databases and other informatics systems. It also poses a serious problem for users of these systems, who would need to be aware of all of these conventions while using any software implementing them.

Another problem with the use of wavy lines is that many chemists view them as being appropriate only in the context of tetrahedral stereochemistry.

The complexity of the rules for this recommendation make it extremely difficult to reduce to working code. This applies both to the development of user interfaces for creating and editing structures, as well as tools to display structures given a double bond stereo type of "cis or trans" (e.g.: molfile).

Option 3: Crossed Double Bond

A crossed double bond has sometimes been used to indicate unspecified double bond configuration or a mixture of configurations. This type of bond is not considered acceptable for general use, although it may still be required by some computer software.

Unfortunately, no rationale for the rejection of this style is given. Perhaps at the time of writing, this convention was not in wide use. However, it appears that the creators of at least some large, public-facing databases are using exactly this convention now.

Now, consider the crossed bond style from the perspective of consistency. There's just one rule to remember: if the double bond stereochemistry is unknown, use a crossed bond. Similarly, if you don't see a crossed double bond, you can assume that defined stereochemistry is being depicted.

It turns out that this convention makes it also quite easy to create (and use) a drawing tool to indicate unknown and/or undefined configuration.


Our default position at Metamolecular is to follow the recommendations of standards bodies whenever possible. But when those recommendations clash with practicality or user experience, we err on the side of good user experience and being practical.

The recently-released ChemWriter 2.10.0 renderer disregards the IUPAC recommendations on depicting unknown double bond stereochemistry, but as I hope I've been able to convince you, we do so with good reason.