Tag Archives: Barnase

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.