Issue Date: September 5, 2016
Crystallography in the classroom
Joseph Tanski still remembers the first time he figured out a molecule’s structure using X-ray crystallography. It was the early 1990s, and he was a sophomore at Vassar College. It took more than a week, but at the end of the analysis he had deduced his compound’s atomic arrangement—an accomplishment that brought him more than a small measure of scientific satisfaction. That feeling was one he hoped to bring to more chemistry majors when he returned to Vassar as a faculty member in 2003.
In the two decades since Tanski solved his first X-ray structure, crystallography’s tools have advanced dramatically. Diffractometers have become more affordable; benchtop models are even available. Computers have become more powerful and crystallography software has become easier to use. An analysis that might have once required a cluster of Silicon Graphics machines, a dedicated server, and some programming know-how can now be done on a modern laptop with an easy-to-use program. Solving a crystal structure now takes hours or even minutes, not days. All these advances have made crystallography much more accessible to undergraduates.
“It’s a fundamental technique, right alongside nuclear magnetic resonance for determining a molecular structure,” Tanski said. And yet, he pointed out, it’s rarely taught to undergraduates.
Seeking to spark a discussion of how chemistry educators are trying to bring X-ray crystallography into the classroom and give ideas to his fellow educators, Tanski co-organized a symposium called “Engaging Undergraduates with X-ray Crystallography” in the Division of Chemical Education at last month’s American Chemical Society national meeting in Philadelphia.
“A lot of the information we teach our students in sophomore organic chemistry has origins in crystallography even though we don’t teach it from that perspective,” said symposium co-organizer Kraig Wheeler, a chemistry professor at Eastern Illinois University. “If we actually tied crystallography together with that part of science, I think our students would be better off.”
“I think that crystallography is sort of whitewashed in chemistry curricula these days,” added symposium co-organizer Amy Sarjeant, outreach and education manager at the Cambridge Crystallographic Data Centre and next year’s president of the American Crystallographic Association. “It’s seen as an expensive and time-consuming technique that’s difficult to understand. A lot of chemistry professors don’t have hands-on experience with crystallography, so they don’t tend to teach it.”
But, Sarjeant said, crystallography brings a three-dimensional perspective to chemistry that students simply can’t get from the two-dimensional drawings chemistry professors usually use. “When you see a student look at a crystal structure, their eyes light up and they get excited,” she said.
At the symposium, Sarjeant spoke about the teaching subset of the Cambridge Structural Database, a repository of more than 840,000 small-molecule organic and metal-organic crystal structures. The teaching subset contains about 700 structures that are free for educators to use.
For example, the subset includes a crystal structure of benzoic acid. In the solid state, this molecule forms a hydrogen-bonded dimer. Seeing that crystal structure, Sarjeant explained, can help students understand why the infrared spectrum of solid benzoic acid is different from what they’d predict just looking at a drawing of the molecule.
Sarjeant is currently developing the teaching subset to make it easier for educators to use. She hopes that her efforts will encourage educators to pick up these examples and run with them.
Tim Royappa, a chemistry professor at the University of West Florida, already uses the database’s teaching subset in his curriculum. It provides an excellent opportunity, he said, to give students a feel for what X-ray crystallography can tell chemists about molecules, even when they’re at a school that, like UWF, doesn’t have a diffractometer.
Royappa has developed an afternoon-long teaching module in which he uses the database’s teaching subset to illustrate chemical concepts such as hydrogen bonding, aromaticity, and valence-shell electron-pair repulsion theory. “It’s a very affordable exercise,” Royappa said. “It’s something that can be done easily by universities across the country and around the world. Educators anywhere can do the exercise for free as long as they have an internet connection.”
Other educators, such as the University of Minnesota’s Jane Wissinger and Albright College’s Christian Hamann, spoke about how they use X-ray crystal structures to help students understand what they’ve made in the lab. Both educators have their students do reactions that could lead to different products. In Wissinger’s case, the reaction could theoretically lead to either an endo- or an exo-substituted product. Hamann’s students are trying to determine whether they’ve made a 1,2- or a 1,4-disubstituted aromatic compound. In both cases, students don’t actually do the X-ray experiment. Instead, their instructor gives them the database crystal structure.
“It’s unambiguously clear what product is formed from the X-ray crystal structure,” Wissinger said. “There’s no other tool that can do that.”
“X-ray crystallography is the right tool to solve a problem of regiochemistry that you can’t solve with NMR, the workhorse of organic chemistry,” Hamann added.
Yan Kung, a chemistry professor at Bryn Mawr College, weaves much of the history of X-ray crystallography of proteins and other biological molecules through his biochemistry course. Upper-level students who take his research methodology course get to grow their own crystals of the enzyme ABL-kinase. Although Kung gives them the structure of this enzyme, instead of making them solve the structure themselves, the students learn how a drug binds to this target by looking at various crystal structures.
Some professors already have incorporated hands-on X-ray crystallography into their classrooms. Tanksi, for example, requires chemistry majors in their junior year to grow crystals of a compound, solve the compound’s structure using Vassar’s diffractometer, and then write up their results in the form of an article for Acta Crystallographica Section E, a popular journal for crystal structures. It’s not uncommon, he said, for these reports to actually get published, giving students a publication to add to their CVs.
“Our students that get hands-on experience with crystallography have a leg up on others,” Wheeler said. In one of his upper-level courses, students get a dozen eggs, from which they isolate cholesterol. They cocrystallize this with oxalic acid and solve the structure using X-ray diffraction.
The symposium organizers hope the event inspires more chemistry educators to incorporate crystallography into their classrooms, and coaxes crystallographers to help them do so. The crystallographic community has to show chemistry educators where they can use crystallography and how it can be effective, Wheeler said. “This is one of the areas we definitely need to develop—providing resources and assistance for using crystallography in lab and lecture courses.”
“If we can educate a generation of chemists who are familiar with crystallography, who know what it is and know what it does,” Sarjeant added, “that will make the next generation of professors that much more comfortable teaching crystallography.”
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