Hydrogen bonding — again, again

I’ve been thinking about hydrogen bonding ever since my senior thesis in 1959. Although its’ role in the protein alpha helix had been known since ’51 and in the DNA double helix since ’53, little did we realize at the time just how important it would be for the workings of the cell. So I was lucky Dr. Schleyer put me at an IR spectrometer and had me make a bunch of compounds, to look for hydrogen bonding of OH, NH and SH to the pi electrons of the benzene ring. I had to make a few of them, which involved getting a (CH2)n chain between the benzene ring and the hydrogen donor. Just imagine the benzene as the body of a scorpion and the (CH2) groups as the length of the tail.  The SH compounds were particularly nasty, and people would look at their shoes when I’d walk into the eating club. Naturally the college yearbook screwed things up and titled my thesis “Studies in Hydrogen Bombing”, to which my parents’ friends would say — he looks like such a nice young man, why was he doing that?

At any rate I’m going to talk about a recent paper [ Science vol. 371 pp. 160 – 164 ’21 ] on the nature of the bond in the F H F – anion.  It’s going to be pretty hard core stuff with relatively little explanatory material. You’ve either been previously exposed to this stuff or you haven’t.  So this post is for the cognoscenti.  Hold on, it’s going to be wild ride.

In conventional hydrogen bonds, the donor (D) atom is separated from the Acceptor atom (A) by 2.7 Angstroms or more, and the hydrogen nucleus is found closer to A where the potential energy minimum is found.

So it looks like this D – H . .. A

The D-H bond isn’t normal, but is stretched  and weakened.  This means that it takes less energy to stretch it meaning that it absorbs infrared radiation at a lower frequency (higher wavelength) — red shift if you will. 

Such is what we were looking for and we found it comparing 

Benzene (CH2)n OH vibrations to butanol, pentanol, hexanol, etc etc. cyclohexane (CH2)n OH.

As the D – A distance shrinks there is ultimately a flat bottomed single well potential, where H becomes a confined particle (but still delocalized) betwen D and A.

The vibrations of protons in hydrogen bonds deviate markedly from the classic quantum harmonic oscillator beloved by physicists.  Here the energy levels on solving the classic H psi = E psi equation of quantum mechanics are evenly spaced (see Lancaster & Blundell “Quantum Field Theory” p. 20.)

However in real molecules, as you ascend the vibrational ladder, conventional hydrogen bonds show a decrease in the difference between energy levels (positive anharmonicity).  By contrast, when proton confinement dictates the potential shape in short hydrogen bonds (when D and A are close together, mimicking the particle in a box model in quantum mechanics) the spacing between states increases (negative anharmonicity).

The present work shows that in FHF- the proton motion is superharmonic — https://en.wikipedia.org/wiki/Subharmonic_function — which they don’t describe very well. 

When the F F distance gets below 2.4 Angstroms, covalent bonding starts to become a notable contributor to the short hydrogen bond, and the authors actually have evidence that there is overlap in FHF- between the 3s orbital of H and the 2 Pz orbitals of the donor and the acceptor atoms, yielding a stabilization of the resulting molecular orbital. 

Is that cool or what.  The bond sits right on the borderland between a covalent bond and a hydrogen bond, taking on aspects of both. 


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  • John Wayne  On January 15, 2021 at 3:12 pm

    That makes a ton of sense. Molecular orbitals aren’t really confined to individual molecules.

  • luysii  On January 15, 2021 at 3:44 pm

    Think you mean molecular orbitals aren’t really confined to individual atoms

  • Peter Shenkin  On January 16, 2021 at 1:48 pm

    Sounds something like the 3-center bonds in diborane….

    • luysii  On January 16, 2021 at 4:24 pm

      Yes. I wondered why the paper didn’t mention diborane, but they didn’t

      • Peter Shenkin  On January 17, 2021 at 4:09 am

        Maybe they thought it would be too borane…. (Sorry….)

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