Depth-First: The Aesthetics of Chemical Structure Diagrams

The Aesthetics of Chemical Structure Diagrams

Rich Apodaca — Fri, 30 Mar 2007 10:21:00 -0400

Quick - name your favorite tool for thinking and talking about chemistry. Many of them have become so refined and integral to the practice of chemistry that they no longer seem like mere tools. The atomic model, the periodic table, octet theory, and electronegativity all fall into this category. So do chemical structure diagrams.

Two-dimensional chemical structure diagrams are a language with both grammar and aesthetics. For example, if you draw pentavalent carbon, you've probably made a grammatical mistake. Aesthetics come into play when a grammatically-correct structure doesn't readily make sense because it uses unfamiliar drawing conventions such as strange bond angles, random bond lengths, unusual orientations, or atom labels that are too small. If you've ever worked in an interdisciplinary environment where non-chemists draw structures (god bless 'em for trying), you've probably experienced the importance of structure aesthetics.

Two recent publications attempt to formalize the aesthetic qualities of good chemical structure diagrams. One deals with chemical structures in general, and the other focuses specifically on stereochemistry. The first document is a draft recommendation on which comments will be accepted until June 30, 2007.

Two long-term trends are raising the importance of standards in this area: (1) structures are increasingly being generated by software without any human guidance, as in the case of chemical nomenclature translation; and (2) in a flat chemical information world in which new scientific publishing models come into being, journal editors will no longer have the final say in how structures are rendered.

The best tools don't just solve a technical problem - they make their users happy. Although aesthetic qualities can be difficult to define, they matter at least as much as technical correctness. Chemical structure diagrams are no exception.

Image Credit: Marshlight

"The Aesthetics of Chemical Structure Diagrams" by Geoff

Mon, 09 Apr 2007 11:37:54 -0400

Now if someone would just publish such a force field method, the rest of us would benefit. :-)

"The Aesthetics of Chemical Structure Diagrams" by Marco

Sat, 07 Apr 2007 07:56:35 -0400

Folks from CCG have used such a 2D forcefield to make their automatic active site 3D to 2D depiction tool. It doesnt even need to be a very fancy forcefield for it to work quite well, I suppose : )

"The Aesthetics of Chemical Structure Diagrams" by Geoff

Fri, 30 Mar 2007 16:35:22 -0400

It's interesting that both of these appear to be written by one of the ChemDraw developers. If anything, they package a variety of template "style sheets."

The program certainly tries to ensure you draw "good" diagrams, but the style can vary considerably.

One interesting thought about the structure layout -- some of these rules could be codified by something like a force field. For example, bond lengths shouldn't be too long. Except in cases where there's a lot of atoms which would bump -- then stretch one bond as needed. See, it seems like a constrained force field of some type.