Playing With Pyridines
During the past summer and current academic year, I’ve been working in Professor Dharni Vasudevan’s environmental chemistry lab at Bowdoin College. For those in the Chemistry Department, this means that I’m part of “Team Dirt”: My senior research project is all about soil. Sometimes, when I’m explaining my research to non-scientists, saying “My research is about soil” is as far as I get. Sometimes this is all my audience really cares to hear, and a more in-depth description would be wasted. In more receptive company, I find myself grappling with the level of chemistry background of my audience as I try to explain what about soil I am actually researching—an interesting dilemma to find myself in considering that barely a year ago I was still struggling to understand my own project as I applied for summer fellowship to do research with Prof. Vasudevan. I was recently chided by a professor at my college for briefly explaining my research to him using the term “cationic pyridine”—an inaccessible concept for a non-chemist—and instructed to work on my elevator pitch. While I appreciate the professor’s concern that I should be able to make my project accessible to non-scientists—in that regard, we’re on the same page—I cringed at the idea of entering the time in my life when I have to have an elevator pitch at the ready. I recognize that there’s a time and place for elevator pitches, but I can’t like them: My research is not something that I want to sell to someone using a couple of reductionist catchphrases, but something I want to be able to help others to understand. That’s what I hope to use this space to do.
So what are cationic pyridines?
My research is about soil. More specifically, it’s about how a certain group of chemical compounds, called organic cations, stick onto soils. The term “organic cation” might sound scary, but it’s really not: In a chemistry sense, the “organic” part just means that the compound has carbons and hydrogens in it. “Organic” in this context doesn’t have anything to do with its everyday usage, which associates the word with “natural-ness,” as in “organic apples”. Both natural compounds, such as cholesterol and nicotine, and synthetic compounds, such as pesticides and industrial chemicals, can be “organic” in the chemical sense if they contain carbons and hydrogens. The “cation” part of “organic cation” means that the compound has a positive charge. In the pictogram language of organic chemistry, organic cations look like this:
Loratadine (antihistamine) Ciprofloxacin (antibiotic)
You can see the positive charges on the hydrogen atoms represented by “H”.
Our lab is looking at organic cations because many “emerging contaminants”—that is, contaminants that have been recently detected in the environment—are either cationic or contain cationic substructures. You’re probably a whole lot more familiar with organic cations than you realize. Lots of pharmaceuticals that we take, or that are used on crops and livestock in agriculture, are organic cations or can turn into organic cations when they’re let out in the environment1-4. Loratadine and ciprofloxacin, shown above, are just a couple of examples. These compounds and others like them get released into the environment in human waste (they aren’t effectively filtered out by waste water treatment plants), in manure from treated farm animals, and in runoff from agricultural fields4-6.
The impact of emerging contaminants, such as pharmaceuticals, isn’t well understood4. We don’t have a strong understanding of the human and environmental health effects of constant, low-level exposure to these compounds in our water. Synthetic estrogens, such as those found in the birth control pill, are known to be able to feminize male fish even at almost indetectable concentrations, causing profound ecological effects6. The consequences of other pharmaceuticals are more hazy, partly because it’s possible that mixtures of different pharmaceuticals could have a more pronounced effect than the individual components4. Increased concentrations of antibiotics in the environment are one possible contributor to the observed rise in antibiotic resistance of various disease-causing bacteria5.
My research, in particular, is about a subset of organic cations called—now infamously, I guess—”cationic pyridines”. Cationic pyridines are just organic cations that contain a pyridine substructure, shown here: Pyridine
You can see the pyridine substructure in loratadine highlighted in blue in the first image above.
Cationic pyridine substructures are present in chemicals used in manufacturing, some of which are carcinogenic7. They are also present in the pesticide paraquat, which is banned for use in the EU but not in the United States (click here for a recent New York Times article on this compound), and in medications such as loratadine, which is the antihistamine in Claritin. Nicotine is a pyridine-containing compound. So is trigonelline, a compound present in coffee that gives the drink its bitter taste8.
Back to soils …
So, now that we know what compounds we’re looking at, what’s all this about interactions with soils? It might seem weird to think about chemicals “sticking” to soil (or, rather, “soils”, because it turns out that there are lots of different types of soil). We don’t usually think about soil being a “sticky” material. In fact, most of us, including chemistry students, don’t usually think about what exactly soil is at all: When my advisor, Prof. Vasudevan, teaches about soil in her environmental chemistry classes, she starts by asking the class, “What is soil?”, and she seems to expect to receive a couple of blank stares, and maybe the reply, “dirt”.
In fact, soil is actually incredibly complex: A lot of soil is made up of broken rocks, in the form of sand, clay minerals, and metal oxides9. The other part of soils is made up of organic matter9, which is chemistry code talk for dead stuff and poop. When plants and animals die, they get decomposed by microbes living in the soil into organic (carbon containing!) compounds. Poop also gets decomposed and adds nutrients to the soil, so much so that manure is added to agricultural fields as fertilizer. Soil is the great equalizer, the place where dead stuff, excrement, and crushed-up rocks get broken down and mixed up, the place where they stop being something ugly or disgusting and turn into the material that feeds new life, in the form of plants, and so feeds all of us as well. To borrow from Hamlet’s ominous warning to his uncle, soil is the means by which a beggar can end up eating, indirectly, a king (IV, iii).
Soil does a lot more for us besides break down our trash and turn it into food: Because soil is “sticky” to certain kinds of compounds, it can trap environmental pollutants and keep them from getting into groundwater and surface water systems, where they could get into our drinking water sources or affect the health of aquatic organisms4, 10-11. In the case of what we call “legacy” contaminants from industrial activities and large-scale pesticide use, exposure in drinking water can pose serious risks to human health—think chromium VI, the Erin Brockovich chemical; lead in Flint, Michigan; MTBE (methyl tert butyl ether), the now-banned carcinogenic gasoline additive which was recently and inexplicably detected in drinking well water on Long Island; or those carcinogenic pyridine compounds used in industry. Soil is doing us a big favor if it can filter compounds like this these out of our water.
As I mentioned above, the human and environmental impacts of emerging contaminants such as pharmaceuticals are less well understood and may be more subtle; in this case, just understanding where these compounds accumulate in the environment and how much of them are present in our waters and soils would be a major step forward. Quantifying the “stickiness” of individual contaminants can help us do exactly that. If we know how “sticky” a specific compound is, then we can calculate how much of the compound is present in ground and surface waters. We can then shift the focus of our research to determining whether the concentrations of individual compounds present in waters are high enough to cause human or ecological health risks. If a compound is very “sticky” to soils, we can then figure out how retention on soils affects the “residence time” of the compound in the environment—that is, how long it takes the compound degrade and be removed from the environmental system. Although we typically think about the retention of contaminants on soils as a good thing (because it means the contaminants aren’t in water), it can also slow the degradation of contaminants, so that they linger longer in the environment and can be re-released into water at a later date.
Even better than being able to quantify the amounts of emerging contaminants like pyridine-containing compounds in waters and soils would be the ability to predict the amounts of these compounds in waters and soils. Prediction is preferable to direct measurement because it’s cheaper and quicker. The US Environmental Protection Agency (EPA) currently has a predictive model that predicts the partitioning of neutral compounds between waters and soils, but it doesn’t work for organic cations, like pyridine-containing compounds1, 3, 11-14. Other, newly developed predictive models have significant limitations13, 15. So our lab is working on the development of a stronger predictive model that would help us predict the “stickiness” of organic cations to soils.
Measuring pyridine sorption (“stickiness”)
My role in the project of predictive model development is to experimentally measure the “stickiness” of simple cationic pyridine compounds on aluminosilicate clays. Aluminosilicate clays are part of the “crushed-rock” portion of soils, and we know from previous research that cationic pyridines mainly interact with this part of soils (along with negatively charged sites on organic matter)1, 3. Aluminosilicate clays have a permanent negative charge, so positively-charged pyridines can “stick” onto the clays by electrostatic attraction (positive and negative electric charges attract). The official term for the sticking process is “sorption”.
In lab, I measure the sorption of simple pyridine compounds using a high-performance liquid chromatography instrument (HPLC). The instrument is a little complicated to explain: To use it, I first have to prepare samples of the pyridine compound in water. Then the HPLC injects the sample into a metal column that I previously filled up with an aluminosilicate clay16. The HPLC tells me how long it takes the sample to come out of the column, which is really a measurement of how strongly the pyridine interacts with the clay. I can use the amount of time it takes the sample to come out to calculate the stickiness, or “sorption affinity”, of the compound.
When I started this research project, I didn’t think it would be nearly as complicated as it has turned out to be: For much of the summer and fall semester I measured and re-measured pyridine sorption affinities, trying to understand why I wasn’t getting the results I had hypothesized. The sorption affinities I calculated for the pyridines were changing in ways that my advisor, Prof. Vasudevan, and I, hadn’t expected. We still don’t know exactly why this is, and I spent a lot of time this fall trying to prove that what I was seeing was wrong—that it was the effect of a faulty experimental design or instrumentation error. Now, though, we think we might actually be seeing something more exciting: an indication that the sorption process for pyridines isn’t as simple as we thought it was. Understanding what is actually going on with the pyridines in lab could give us a much better handle on what they’re doing when they’re out in the environment!
Author Bio: Danielle is a senior at Bowdoin College majoring in Chemistry and Hispanic Studies. She is currently completing an NSF-funded research with Professor Dharni Vasudevan on the interactions between emerging environmental contaminants and aluminosilicate clays, which are a major component of soils. Besides studying chemistry, Danielle enjoys working as a writing assistant at the Bowdoin Center for Learning and Teaching (CLT) and singing in the Bowdoin Chorus.
- MacKay, A. A.; Vasudevan, D., Polyfunctional ionogenic compound sorption: challenges and new approaches to advance predictive models. Environ Sci Technol 2012, 46 (17), 9209-23.
- Aaryn D. Jones, G. L. B., Sheela G. Agrawal, and Dharni Vasudevan, Factors Influencing the Sorption of Oxytetracycline to Soils. Environmental Toxicology and Chemistry 2005, 24 (4), 761-770.
- Droge, S. T.; Goss, K. U., Sorption of organic cations to phyllosilicate clay minerals: CEC-normalization, salt dependency, and the role of electrostatic and hydrophobic effects. Environ Sci Technol 2013, 47 (24), 14224-32.
- Kolpin, D. W. F., E.T.; Meyer, M. T.; Thurman, E. M; Zaugg, S. D.; Barber, L. B.; Buxton, H. T., Pharmaceuticals, Hormones, and Other Organic Wastewater Contaminants in U.S. Streams, 1999-2000: A National Reconnaissance. Environ Sci Technol 2002, 36 (6), 1202-1211.
- Kümmerer, K., Pharmaceuticals in the Environment: sources, fate, effects, and risks. . Springer-Verlag: 2009.
- Ankley, G. T. B., B.W.; Huggett, D.B.; Sumpter, J.P., Repeating History: Pharmaceuticals in the Environment. Environmental Science & Technology 2007, 8211-8217.
- Bi, E. S., T.C.; Haderlein, S.B. , Environmental factors influencing sorption of heterocyclic aromatic compounds to soil. Environmental Science and Technology 2007, 41 (9), 3172-3178.
- Cho, J.-S.; Bae, H.-J.; Cho, B.-K.; Moon, K.-D., Qualitative properties of roasting defect beans and development of its classification methods by hyperspectral imaging technology. Food Chemistry 2017, 220, 505-509.
- Brady, N. C. W., Ray. R, The Nature and Properties of Soils. 13 ed.; Prentice Hall: New Jersey, USA, 2002.
- Vasudevan, D.; Bruland, G. L.; Torrance, B. S.; Upchurch, V. G.; MacKay, A. A., pH-dependent ciprofloxacin sorption to soils: Interaction mechanisms and soil factors influencing sorption. Geoderma 2009, 151 (3-4), 68-76.
- Droge, S.; Goss, K. U., Effect of sodium and calcium cations on the ion-exchange affinity of organic cations for soil organic matter. Environ Sci Technol 2012, 46 (11), 5894-901.
- Jolin, W. C.; Sullivan, J.; Vasudevan, D.; MacKay, A. A., Column Chromatography To Obtain Organic Cation Sorption Isotherms. Environ Sci Technol 2016, 50 (15), 8196-204.
- Droge, S. T.; Goss, K. U., Development and evaluation of a new sorption model for organic cations in soil: contributions from organic matter and clay minerals. Environ Sci Technol 2013, 47 (24), 14233-41.
- Droge, S. T.; Goss, K. U., Ion-exchange affinity of organic cations to natural organic matter: influence of amine type and nonionic interactions at two different pHs. Environ Sci Technol 2013, 47 (2), 798-806.
- Jolin, W. C. G. R. C., K.; Medina, J.; Vasudevan, D.; MacKay, A., Predicting organic cation sorption coefficients: Accounting for affinity and abundance of exchange ions using a simple probe molecule. In Review.
- Jolin, W. C. Sorption of organic cations to soils and soil minerals. University of Connecticut, 2016.