Depth-First: Tag flatworld

The Aesthetics of Chemical Structure Diagrams

Rich Apodaca — Fri, 30 Mar 2007 10:21:00 +0000

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 (Chemical Information) World is Flat

Rich Apodaca — Wed, 27 Dec 2006 16:24:00 +0000

Certainly the need to extract chemical and physical data from the literature, as contrasted with bibliographic information, will increase. The new breed of chemical information specialists will not only have to be trained in information storage and retrieval but also in writing and digesting information - what is otherwise called reviewing. ...

Where are all the new chemical information specialists going to come from? Many of them will be people who start out in a career path in information science. But most will be Ph.D. chemists who will turn to information science as an alternative career in a tough job market. They will be no different than the many chemists who wound up as chemical marketing specialists back in the depression.

-Eugene Garfield, J. Chem. Inf. Comput. Sci. 1978, 18, 1-4

Thirty years may have passed, but the situation described by Garfield rings eerily familiar today. What could not have been anticipated is the degree to which the playing field for information producers is being flattened. Today's scientist-reviewer employs many of the same tools, accesses the same distribution channels, and eventually will compete for the same readers as established journals, databases, and other services.

For example, consider the sharp increase in the number of chemistry-related blogs within the last year. Although the underlying technologies are woefully ill-suited to the job, a groundswell of both writers and readers for this type of scientific communication has been exposed.

How far out can this trend be extrapolated? Garfield has argued that "in the future, it would be more and more difficult to distinguish (ordinary) laboratory scientists from information specialists." Looking back at the last thirty years, there is ample evidence to support this claim for information consumers and producers alike. How well are you and your organization positioned to thrive in the flat chemical information world that lies ahead?