Tag Archives: Henry Eyring

Why there’s more to chemistry than quantum mechanics

As juniors entering the Princeton Chemistry Department as majors in 1958 we were told to read “The Logic Of Modern Physics” by P. W. Bridgeman — https://en.wikipedia.org/wiki/The_Logic_of_Modern_Physics.   I don’t remember whether we ever got together to discuss the book with faculty, but I do remember that I found the book intensely irritating.  It was written in 1927, in early hay day of quantum mechanics.  It  said that all you could know was measurements (numbers on a dial if you wish) without any understanding of what went on in between them.

I thought chemists knew a lot more than that.  Here’s Henry Eyring — https://en.wikipedia.org/wiki/Henry_Eyring_(chemist)https://en.wikipedi developing transition state theory a few years later in 1935 in the department.  It was pure ideation based on thermodynamics, which was developed long before quantum mechanics and is still pretty much a quantum mechanics free zone of physics (although people are busy at work on the interface).

Henry would have loved 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.  You can find much more about the work here — https://luysii.wordpress.com/2022/02/15/transition-state-theory/

Does Bridgeman have the last laugh — remember all that is being measured are numbers (lengths) on a dial.

Here’s another recent paper Eyring would have loved — [ Proc. Natl. Acad. Sci. vol. 119 e2112372118 ’22  — ] https://www.pnas.org/doi/epdf/10.1073/pnas.2112382119  ]

The paper studied Barnase, a 110 amino acid protein which degrades RNA (so much like the original protein Anfinsen studied years ago).  Barnase is highly soluble and very stable making it one of the E. Coli’s of protein folding studies.

The new wrinkle of the paper is that they were able to study the folding and unfolding and the transition state of single molecules of Barnase at different temperatures (an experiment which would have been unlikely for Eyring to even think about doing in 1935 when he developed transition state theory, and yet this is exactly the sort of thing what he was thinking about but not about proteins whose structure was unknown back then).

This allowed them to determine not just the change in free energy (deltaG)  between the unfolded (U) and the transition state (TS) and the native state (N) of Barnase, but also the changes in enthalpy (delta H) and entropy (delta S) between U and TS and between N and TS.

Remember delta G = Delta H – T delta S.  A process will occur if deltaG is negative, which is why an increase in entropy is favorable, and why the decrease in entropy between U and TS is unfavorable.   You can find out more about this work here — https://luysii.wordpress.com/2022/03/25/new-light-on-protein-folding/

So the purely mental ideas of Eyring are being confirmed once again (but by numbers on a dial).  I doubt that Eyring would have thought such an experiment possible back in 1935.

Chemists know so much more than quantum mechanics says we can know.  But much of what we do know would be impossible without quantum mechanics.

However, Eyring certainly wasn’t averse to quantum mechanics, having written a text book Quantum Chemistry with Walter and Kimball on the very subject in 1944.

New light on protein folding

Henry Eyring would have loved this paper [ Proc. Natl. Acad. Sci. vol. 119 e2112372118 ’22  — https://www.pnas.org/doi/epdf/10.1073/pnas.2112382119  ] He developed transition state theory.  You can read about it and what Eyring was actually like here — https://luysii.wordpress.com/2022/02/15/transition-state-theory.

The paper also gives an excellent history of the intellectual twists and turns of the protein folding problem.  It starts with Anfinsen’s work on Ribonuclease (RNAase), which is a rather simple protein.  He noted that even when unfolded (denatured), RNAase would spontaneously fold to its native structure.  Thus was born the thermodynamic hypothesis of protein structure.  Because the native form occurred spontaneously it had to have the lowest free energy of all the possible conformations.   This was long before we knew about protein chaperones,.

This was followed by the molten globule idea.  It was modeled on solid formation from a gas in which a metastable liquid phase precedes solid formation during gas deposition.  The molten globule has a high degree of secondary structure (alpha helices, beta sheets), but no fixed arrangement of them relative to each other (e.g. no tertiary structure).  To be considered a molten globule, the protein must have an expanded structure relative to the native fully folded protein.

This was followed by the energy landscape theory of protein folding, something I never liked because I never saw a way to calculate the surface of the landscape.  Proteins fold by following the landscape to a lower potential energy, the way a skier follows the mountain down hill. It seems like a high falutin’ way of saying proteins fold, the same way docs say you have idiopathic something or other instead of saying we don’t know what caused what you have.  In the energy landscape theory molten globule intermediates are not necessary.

Then there is the foldon hypothesis — proteins fold following a unique pathway by the cooperative and sequential formation of native structure domains (e.g. the foldons).  Folding amounts to the productive tinkering of amino acids and foldons rather than the diffusion of a protein in a funnel-like energy landscape.

The paper studied Barnase, a 110 amino acid protein which degrades RNA (so much like the original protein Anfinsen studied years ago).  Barnase is highly soluble and very stable making it one of the E. Coli’s of protein folding studies.

The new wrinkle of the paper is that they were able to study the folding and unfolding and the transition state of single molecules of Barnase at different temperatures (an experiment which would have been unlikely for Eyring to even think about doing in 1935 when he developed transition state theory, and yet this is exactly the sort of thing what he was thinking about but not about proteins whose structure was unknown back then).

The work alluded to in the link to another post above, did something similar except that they used DNA instead of a protein.  Here is the relevant part of it.

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.

This allowed them to determine not just the change in free energy (deltaG)  between the unfolded (U) and the transition state (TS) and the native state (N) of Barnase, but also the changes in enthalpy (delta H) and entropy (delta S) between U and TS and between N and TS.

Remember delta G = Delta H – T delta S.  A process will occur if deltaG is negative, which is why an increase in entropy is favorable, and why the decrease in entropy between U and TS is unfavorable.

Almost all of the entropy decrease  between U and N occurs between U and TS.  Which makes sense as the transition state is a lot more ordered than than the unfolded state.  Most of the change in enthalpy occur on the TS –> N transition.

The results are most consistent with both the energy landscape of Wolynes and the molten globule  They describe the transition state as like a golf course, where there are many positions for the ball (the molten globule), but only one place to go down to the native state.  Once the hole is found the protein zooms down to the native state through the potential energy funnel.

Fascinating stuff.

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.