Molecular capsules
enabling clarifying stories for organic chemistry?

How might the stories used to teach organic chemistry be improved? Here is one speculative idea - tell stories with molecular encapsulation (little box with a few molecules in it).

Teaching organic chemistry is hard, in part, because the molecular systems described have complex behavior (hydrated, transient, population aggregated, high-dimensional conformation spaces, etc). Molecular encapsulation simplifies that behavior, by isolating and constraining a few molecules. I speculate this might enable nice stories for introductory content.

Normally when teaching orgo, descriptive abstraction is used to separate out underlying behaviors. What if instead, you could use systems that physically suppress obscuring behaviors? That provide concrete, motivating, explorable model systems.

Systems that push around electrons. Change energy levels. Force bending. Impose chirality. Prevent rotation. Slow tumbling. Mash together reactants. Think protein active site.

As a quick illustration, if some ground state requires a molecule to have a particular shape, you can make that state and associated transitions go away, by putting the molecule in a cage, and physically preventing it from bending that way.

All this is simply the engineering of good introductory examples for chemistry education, by looking for nanometer-size environments with pedagogically helpful properties. Protein active sites, and surface chemistry, are other reservoirs of stories.

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Clarifying insight... from better experts.
Are you tired of seeing wonderful insights in research talks, and knowing they won't reach introductory content for years? I suggest the importance of direct research expertise, in creating accessible and powerful introductory content, is pervasively underestimated.


Julius Rebek, Jr [flash] at Scripts.

Molecular Close-Up: Images show motions of single, confined molecule. Blury videos of a molecule in a nanotube. Based on (DOI: 10.1126/science.1138690).


From 2008. Used without permission.


Key question: as molecule manipulative educational simulation software improves, do physically-inspired isolation stories become superfluous?

The Rebek group site [flash] has some old chime files. My fuzzy recollection is they need a bit of hand editing to use. Now that there are good javascript molecule viewers, it would be nice to extract them. And to replace the "used without permission" images here with interactive fun.

I wish there were videos of Rebek talking chemistry. It's notably fun. It might be worth trying to find someone to encourage it.

Mention nice properties. Separability of E & B. Physically constrain away energy states.

Sketch an example story. Work backward from papers. Rebek [flash] under "Publications". ggl.

Find stories which notably escape the usual obscuring fuzz.

Give credit: idea prompted by Rebek's talk at MIT in May 2012.

Related topics not up yet: teaching with micro&nano-fluidics; teaching atoms-up; using protein active site examples when teaching intro chem; sysbio compartmentalization.

Misc. Was 'cage", now "capsule", to match literature... but I still like cage. It has size implication capsule lacks, no? Box? Rephrase intro, with consistent "behavior" vs "mess of behaviors". Explain "descriptive abstraction". Point at molecules in small spaces paper... if it's online.

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