Transition state theory

It is a pleasure to get back to science.  “The World Is Too Much With Us” is certainly true for me, with worries about family in Hong Kong and Taiwan, and whether our elites will send our young off to die in the Ukraine (said by someone who spent 1968 – 1970 as an Air Force Officer caring for the wounded and maimed from another misadventure).

But what could be purer to a chemist than transition state theory and the Eyring equation.  When I was an undergraduate, the Chemistry department brought Henry Eyring in for a lecture.  Although I didn’t realize it at the time, it was my first exposure to the Western zeitgeist.  Henry was a Mormon raised all over the west.  Here was this guy with his own equation, constantly talking about how dense he was, and how long it took him to see this and that.  The one unforgivable sin in the West is to brag about yourself — All hat and no cattle comes to mind.

Eyring would have been fascinated by a recent paper [ Proc. Natl. Acad. Sci. vol. 118 e2102006118 ’21 ] where the passage of a molecule back and forth across the free energy maximum was measured again and again.

A polyNucleotide hairpin of DNA  was connected to double stranded DNA handles in optical traps where it could fluctuate between folded (hairpin) and unfolded (no hairpin) states.  They could measure just how far apart the handles were and in the hairpin state the length appears to be 100 Angstroms (10 nanoMeters) shorter than the unfolded state.

So they could follow the length vs. time and measure the 50 microSeconds or so it took to make the journey across the free energy maximum (e.g. the transition state). A mere 323,495 different transition paths were studied.

The times to traverse between the two states were variable, and 40% of the time there was a pause during the passage where length didn’t change at all.  They could measure the height of microBarriers causing the pauses by their length. The average pause lifetime was 3 – 7 microSeconds implying a barrier height of 1 – 2 kT.

They didn’t find what they expected — e.g. two sizes of barrier — one for GC to break 3 hydrogen bonds and a smaller one for AT (to break two bonds).  Even when they looked at pure AT and GC hairpins they didn’t find just one size of pause, implying that more than 1 dimensional zippering is going on.

The pauses were best explained by something called the microscopic kinetic model from polymer chemistry — which implies that the pauses are due to the fact that each nucleotide residue must search through multiple nonNative conformations to find the correct structure for base pairing.

So unlike the stuff from gas phase kinetics which I grew up with, there are many different pathways up and down from the transition state.  Eyring would have loved this paper.    So do I.  It is pure and beautiful.


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