This article was published in Scientific American’s former blog network and reflects the views of the author, not necessarily those of Scientific American
Since 2011 is the International Year of Chemistry, the good folks at CENtral Science are organizing a blog carnival on the theme, "Your favorite chemical reaction".
My favorite chemical reaction is the chlorite-iodide reaction, and it's my favorite because of the life lessons it has taught me.
The reaction has overall stoichiometry:
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ClO2- + 4 I- + 4 H+ = 2 I2 + Cl- + H2O
Written out that way, as a simple set of reactants and products, it doesn't look that exciting, but when the reaction is run in a continuous flow stirred tank reactor (CSTR), where reactions are flowed in and products are removed, it can exhibit oscillatory behavior. The oscillations in the concentrations of iodine (I2) and iodide (I-) can be tracked experimentally, the former by measuring UV absorbance at 460 nm, the latter by measuring the potential of an ion-specific electrode.
An early study of the kinetics of this reaction determined that it “is catalyzed by the iodine product, and the autocatalysis is inhibited by iodide ion.” (Kern and Kim 1965, 5309) In 1985, Epstein and Kustin proposed the first mechanism for this reaction to account for the oscillatory behavior, one that includes 13 elementary steps and 12 chemical species. Two years later, Citri and Epstein proposed an improved model mechanism with 8 elementary mechanistic steps and 10 chemical species. The Citri-Epstein model proposes a different set of elementary steps to describe the oxidation of iodide by chlorite. In addition, it eliminates the intermediate IClO2-, “whose existence has been called into question elsewhere.” (Citri and Epstein 1987, 6035) The resulting model mechanism seemed to produce better agreement between predicted and measured concentrations of iodide and iodine than that given by the earlier model.
The chlorite-iodide reaction also happens to have been the reaction at the center of most of my research for my Ph.D. in chemistry.
Here are some of the lessons I learned working with the chlorite-iodide reaction:
Experimental tractability matters, at least when you're doing experiments. The general thrust of my research was to work out clever ways to perform empirical tests of proposed mechanisms for oscillating chemical reactions, but the chlorite-iodide reaction was not the first reaction I worked with. I started out trying to make some clever measurements on another reaction, the minimal bromate oscillator (MBO). However, after maybe six months of fighting to set up the conditions where the MBO would give me oscillations, I had to make my peace with the idea that its "small" region in phase-space with oscillatory behavior was really, really small. Luckily, in my reading of the relevant literature on the experimental and theoretical approaches we were taking, I had come across a similar inorganic chemical oscillator with an "ample" oscillatory region, one which promised to make my time in the lab exponentially less frustrating. That's right, the chlorite-iodide reaction was my rebound system, but we stayed together and made it work.
When your original research project gets stuck, it's good to have a detailed plan for how to move forward when you talk to the boss. My advisor was really keen for that minimal bromate oscillator that was making my life in the lab a nightmare. So, when I met with him to tell him I wanted to break up with the MBO and take up with the chlorite-iodide reaction, I had to make the case for the new system. I came armed with the articles that described its substantial oscillatory region, and the articles that described the MBO's tiny one. I prepared some calculations describing how much more precise our pump-rates would need to be to find MBO oscillations, and catalogues that listed the prices of the new equipment we would need. I brought the articles proposing mechanisms for the chlorite-iodide reaction so I could display the virtues of their elementary mechanistic steps from the point of view of the kind of experimental probing we had in mind. Because I did my homework and was able to make a persuasive case, the boss was happy to let me start working with the chlorite-iodide system right away, and to kiss the minimal bromate oscillator goodbye forever.
Experimental tractability is relative, not absolute (and Materials and Methods often leave stuff out). The chlorite-iodide reaction was certainly easier to work with -- within a week, I found oscillations where the literature said I would -- but it was not completely smooth sailing. There were pumps that didn't perform as they should, which meant I was taking them apart and swapping out components. There were days when I couldn't get any reliable measurements because the pH meter I used with my iodide-specific electrode had been left on for too many hours in a row. And, there were little details I discovered in setting up experimental runs day in and day out that were not fully discussed in the "materials and methods" section of the published papers describing the chlorite-iodide reaction. Reproducibility is hard
Reactions happen in three-dimensional space, not just in reaction space. One of the experimental challenges of the chlorite-iodide reaction is that, to find the dynamical behavior you're looking for, you have to stir the reactants in the tank reactor at the right speed. Stirring much faster or much slower will change the dynamics of the reaction, as will using a reactor with significantly different internal geometry. ("Dimples" protruding into the cylindrical space inside the reactor are supposed to help you mix the reactants more effectively, rather than giving them the opportunity to hang out unmixed by the walls.) Appropriate stirring speed was not one of the parameters spelled out by the papers whose descriptions of the reaction I was using to get started, nor was reactor geometry. I had to do experiments to work out the stirring speed that (with the geometry of the reaction vessel we had on hand) produced the same behavior as these other papers were reporting. Once I found that stir-speed, I kept that constant for my experimental runs. Also, I made detailed measurements of the reactor we were using, which turned out to be a really good thing when that reactor broke. I was able to take those measurements to the glass-blower's shop and get replacements (plural) made.
Time well spent in setting things up is frequently rewarded with good data. It was absolutely worth it to spend a couple hours at the beginning of each run calibrating pump flow-rates and checking out the iodide-selective electrode performance with standard solutions, since this let me apply the experimental conditions I wanted to and make accurate measurements. Did I mention that reproducibility is hard?
Qualitative measurements require patience, too. Among other things, I was interested in mapping the edges of regions in phase-space where the chlorite-iodide reaction displayed different kinds of behavior. On one edge, there was a bifurcation where you would find steady state behavior (i.e., stable concentrations of reaction species) that, coming up on the bifurcation point, became tiny-amplitude oscillations that grew. On the other edge, the oscillations had attained their maximum amplitude, but their period (that is, the lag between oscillatory peaks) grew longer and longer until there weren't any more peaks and the reaction settled into another steady state. The thing was, it was hard to know when you were set up with conditions where the period of oscillation was just really, really long (sometimes around 20 minutes between peaks, if memory serves) or when you had found the steady state. You had to be patient. While I was exploring that edge of the reaction in phase-space, I started thinking maybe that was a good metaphor for certain aspects of graduate school.
You probably can't measure everything you'd want to measure, but sometimes measuring one more thing can help a lot. As I mentioned above, the Citri-Epstein mechanism for the chlorite-iodide reaction posited ten chemical species in the various steps of the reaction. In a perfect world, you'd want to be able to measure each of those species simultaneously over time as the reaction proceeded. But, as one learns pretty quickly in grad school, this is not a perfect world. When I started with this reaction, published papers were reporting simultaneous dynamical measurements of only two of those species (iodide and iodine). Chloride is one of the hypothesized intermediates, and there are chloride-specific electrodes on the market. However, the membrane in a chloride-specific electrode also reacts with ... iodide. Other intermediate species might be measured by various chemical assays if the progress of the reaction could be halted in the samples being assayed. By the end of my graduate research, I had figured out a way to use a flow-through cuvette and a seat-of-the-pants spectral deconvolution technique to measure the time-series of one additional species in the reaction, the chlorite ion (ClO2-). This was enough to do some evaluation of the proposed mechanism that was not possible without it.
Later on, when I became a philosopher of science, this work gave me some insights into the circumstances in which chemists are happy to be instrumentalists (e.g., recognizing that the fact that a proposed reaction mechanism was consistent with the observed kinetics of the reaction was no guarantee that this was the actual mechanism by which the reaction proceeded) and the circumstances in which they lean towards being realists (by finding ways to distinguish better proposed mechanisms from worse ones). But back when I was actually getting glassware dirty running the chlorite-iodide reaction, this reaction helped me learn how to be a scientist.
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Works cited:
Citri, Ofra, and Irving R. Epstein (1987) “Dynamical Behavior in the Chlorite-Iodide Reaction: A Simplified Mechanism”, Journal of Physical Chemistry 91: 6034-6040.
Epstein, Irving R., and Kenneth Kustin (1985) “A Mechanism for Dynamical Behavior in the Oscillatory Chlorite-Iodide Reaction”, Journal of Physical Chemistry 89: 2275-2282.
Kern, David M., and Chang-Hwan Kim (1965) “Iodine Catalysis in the Chlorite-Iodide Reaction”, Journal of the American Chemical Society 87(23): 5309-5313.