The Tensions of Scientific Storytelling
Science depends on compelling narratives.
Capturing Benzene Dimers
Often the reader is unaware of what lurks beneath the surface of a journal article. There is a prehistory to what is reported. In the course of the work, the authors make decisions that influence how the narrative unfolds. Just as one is interested in how Thomas Mann wrote Death in Venice and, as one reads the novella, what the feelings of the boy Tadzio really are, so one wants to know the story behind the story of a scientific narrative. I only truly know this about my own work, so with the permission of my coauthors, I will tell you the story behind one of my recent papers in the Journal of the American Chemical Society. This may not be the best choice, because I’m a writer too. Like a mild disease, poetry and theater have infected my science writing. So have the strategies of storytelling.
The article is “Jailbreaking Benzene Dimers,” published in 2012 with two colleagues, Andrey Rogachev and Xiao-Dong Wen. At the time they were postdoctoral researchers in my group; each has now embarked on an independent career. Our paper found its home in an excellent journal, after, incidentally, rejection from another excellent journal. That rejection too can be construed as part of the journey. It made us improve the underlying proofs for our suggested structures, and so made the story stronger.
The story begins with a reference to our previous theoretical work on the behavior of benzene under pressure, which led to the questions we had about benzene dimerization: “In the course of thinking about benzene under gigapascal pressure, we decided we might learn something from the dimers of benzene, as signposts to the pressure-induced polymerization of the compound.”
What we didn’t relate is that there is another, preceding record of chemists experimentally compressing benzene and getting amorphous, hard-to-characterize polymers rather than the nice, orderly structures our group had predicted. Those studies suggested to us that perhaps we should study the first step in any polymerization, and that is the reaction of just two benzene molecules with each other, the dimers. We didn’t rehash the prehistory because it would have taxed the patience of the readers, presumably chemists already familiar with it. As it was, we had a good enough story to tell. The article has hardly the quality of Mann’s novella, but he also chose what to omit, for instance not to tell the reader the previous life of the young boy Tadzio.
After that hint of previous work, we jump right into the current study:
To induce the benzenes to dimerize, we brought two benzene molecules to an uncomfortably close contact, and then let loose the geometry optimization of a quantum chemical program… The molecules reacted to this torture by moving apart, or by forming dimers.
Why did we do that? Because that’s what high pressure does—it forces molecules closer to each other than they “normally” would like to be, much as people do in a subway car at rush hour.
We did not tell our readers that our “explosion” method of finding structures (meaning we put the molecules too close to each other in the simulation, then let them “blow apart,” expand, and in the process explore new bonding arrangements of their component atoms) was already in the literature to study possible arrangements of a given number of atoms. We simply didn’t know that our method was not new; we were led to this procedure for sampling all kinds of bonding by our noses (or rather, Dr. Wen’s nose).
Wen showed me the set of dimers he got from his calculations. Because of my organic chemistry background, I saw that some of his dimers were known, but two were new to me (5 and 6 in the figure above). I said the equivalent of “Play it again, Sam,” and off we went, first continuing the “explosive” way of looking for new benzene dimer structures, and eventually substituting a more systematic exploration as we spotted the essential molecular characteristics of the new molecules.
Where is the dramatic tension here? This work is theory; we predicted a total of four new benzene dimers, and we postdicted seven that are known (and one that people had suggested previously but hasn’t yet been made). The postdiction is actually a good check on our method. We tried very hard to estimate the stability of the predicted new guys. The drama (although I might be biased) is that no one had thought of these four molecules before. Once written down, they seem eminently makeable. But are the calculations behind our predictions good enough? Evidently the reviewers who first rejected our paper—good quantum chemists all, even if I found them illogical for some minutes—thought “no.” One real tension remains unresolved, the classic tension between theory and experiment: Will these molecules actually be made?
Where is the narrative? Before this paper, chemists had synthesized amorphous benzene polymers and seven known dimers. We (both the scrabbler and the writer sides of my coauthors and me) have woven the new structures into a narrative of how a simple dimer is not simple, but rather has 12 realizations (same number of atoms, connected up in a different way; chemists call these isomers of each other). If you saw the scattered pages and computer screen of the theorizing scrabbler’s calculations at the outset of this work, you would never find the story in it. Just numbers. The story behind the story took shape in conversations between my coauthors and me. As writers, we polished up the tale.
The article constructs an inner life for the molecules. We had to worry whether the isomers that we proposed were stable. The molecules’ persistence in the lab depends on the barriers to their falling apart or reacting with other molecules, which are created by bonds, energy levels, and so on. Those barriers are a kind of prison cell; we want the molecules imprisoned, so to speak, because we need time to study them. Ergo the title of the paper—my collaborators (perhaps cursing under their breath at the labor involved) had to look for all the ways in the world by which these dimers could break out of their bond-imposed jail to the greener pastures of lower free energy, a state that all molecules “prefer” to reach.