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. 

 

At the 55th

This is a mostly nonscientific post concerning the 55th reunion of the Princeton Class of 1960 last weekend. First the Science. Nick Cozzarelli was one of the most distinguished members of our class — great work on Topoisomerase, editor of PNAS for 10 years which established a prize named for him for the best paper each year. No one I’ve ever talked to in the class knew of him or his work. Shirley Tilghman, president of Princeton certainly did, and was shocked to hear of his untimely passing from Burkitt’s lymphoma when I told her of it at our 50th, saying he was a great scientist. However, he’s one of the reasons Princeton back then was a great institution (and hopefully still is). The son of an immigrant shoemaker in Newark NJ, he was taken in, given a scholarship, and worked his way through, serving meals in commons etc. etc. I made sure the undergraduates picking up a little cash by pouring drinks and serving meals at reunions heard about him. He was a good friend.  R. I. P. Nick.

Another friend, an emeritus prof of chemical engineering, referees a lot of papers. He estimates that 80% of the papers in his field, quantum chemistry, coming from China are absolute trash. According to him China gives bonuses to people getting published in high impact journals. What he finds particularly appalling is that he writes up a detailed list of corrections and improvements for the paper, and then finds it published totally unchanged in another journal.

He and I reminisced about our great undergraduate advisor Paul Schleyer with the department chair (who of course knew of him since he is one of the most cited and prolific (1,400 papers) chemists of the 20th century). He’s another reason Princeton was such a great institution back then (and hopefully still is). For details please see https://luysii.wordpress.com/2014/12/15/paul-schleyer-1930-2014-a-remembrance/ and https://luysii.wordpress.com/2014/12/14/paul-schleyer-1930-2014-r-i-p/

I finally saw the new Chemistry building (under construction at the 50th) and it is gorgeous. The NMR set up is particularly impressive, with the megaHertz of the machinery a factor of 15 greater than those we first started using in the 60s. Alas Varian is no more. It was bought a few years ago by another company which terminated the business. For where the money came from see https://luysii.wordpress.com/2011/05/16/princeton-chemistry-department-the-new-oberlin/.

In a remarkable coincidence, my wife an I were able to chat with the son of a neurologist in my call group, just finishing up his PhD in Chemistry there. How improbable is that?

Now for the nonScientific part.

For those undergraduates reading this at similar institutions, some advice — get to know as many of your classmates as you can. Premeds at Princeton back then had to take a lot of the same courses — biology, basic chemistry, organic chemistry, calculus, physics etc. etc. So we got to know each other. The rest of the class, not so much unless we were in other organizations (in my case, the marching band, Triangle club, and the eating club). At reunions I always meet classmates that I wish I knew back then and form new friendships.

Sometimes that isn’t always easy, with everyone working out the various important issues present from 18 to 22. A classmate’s wife described the men of the class at their 25th reunion as ‘roosters’, crowing and impressing each other. Not the case 30 years later. Everyone glad just to be there and catch up.

Princeton was all male back then. The current wives (some being #2, #3, #5) are an impressive bunch. They were uniformly intelligent and interesting. Not a bimbo in the lot of them, although most were very attractive physically. So the class may have slept with bimbos, but they were no longer in evidence.

Various seminars were held. I went to one about America’s relation to food. The panelists were 6 trim females with a fair amount of pseudoscience and touchy feely crap emitted, but at least the cautionary tale of the trash in the popular press about diet was mentioned (e.g. the paper about eat chocolate lose weight). What was fascinating was that the incidence of obesity (BMI over 29) in the group of several hundred listeners was at most 5%, proving, once again, that obesity in the USA is largely a class phenomenon. Also noted, is that I only saw one or two undergraduates and graduates smoking, again a class phenomenon, something Americans don’t like to talk about, but there nonetheless.

A memorial service for classmates was held in the chapel (built in 1929 but designed to appear that it was built in 1299). The organ is magnificent as were the acoustics, the sound surrounding you rather than coming at you. Bach and Vidor were performed by the organist. Apparently there was quite a battle about which to do first — refurbish the organ or the chapel acoustics. The stone had roughened distorting the sound so it didn’t echo properly. Clear plastic was applied to smooth the stone and then the organ was fixed. If you can hear a concert there please do so. Great composers write for the space their music will be performed in as well as the instruments it will be performed on, certainly true of Gabrielli, Bach and Vidor.

On a sadder note. I know of 4 suicides of class members (we started with around 725). Probably there are more. Also a good friend and classmate’s wife and daughter appeared to accept an award in his name. Although still alive he is incontinent, unable to walk and demented from Alzheimer’s. Despite degrees from Princeton, Harvard and Penn, Board examiner in Neurology blah blah blah, I was totally unable to help him. All I could do was offer emotional chicken soup to his wife, something my immigrant grandmother did with her 4th grade education in the dry goods store she ran. That’s why it’s good to be retired from neurology and not see this day after day.

Finally the P-rade. It is a great emotional lift for the psyche to march a mile or so to the reviewing stand being cheered by probably 1,000 – 2,000 younger graduates the whole time. The younger they got the louder the cheers and the drunker they were. It’s pretty hard not to feel good after that. I have heard that the only weekend event where more beer is consumed than Princeton reunions is the Indianapolis 500.  Along those lines, I only saw one truly drunk individuals among the 250 or so classmates and significant others although just about everyone had alcohol.  The alcoholics are no longer around for the 55th.

Paul Schleyer 1930 – 2014, A remembrance

Thanks Peter for your stories and thoughts about Dr. Schleyer (I never had the temerity to even think of him as Paul). Hopefully budding chemists will read it, so they realize that even department chairs and full profs were once cowed undergraduates.

He was a marvelous undergraduate advisor, only 7 years out from his own Princeton degree when we first came in contact with him and a formidable physical and intellectual presence even then. His favorite opera recording, which he somehow found a way to get into the lab, was don Giovanni’s scream as he realized he was to descend into Hell. I never had the courage to ask him if the scars on his face were from dueling.

We’d work late in the lab, then go out for pizza. In later years, I ran into a few Merck chemists who found him a marvelous consultant. However, back in the 50’s, we’d be working late, and he’d make some crack about industrial chemists being at home while we were working, the high point of their day being mowing their lawn.

I particularly enjoyed reading his papers when they came out in Science. To my mind he finally settled things about the nonclassical nature of the norbornyl cation — here it is, with the crusher being the very long C – C bond lengths

Science vol. 341 pp. 62 – 64 ’13 contains a truly definitive answer (hopefully) along with a lot of historical background should you be interested. An Xray crystallographic structure of a norbornyl cation (complexed with a Al2Br7- anion) at 40 Kelvin shows symmetrical disposition of the 3 carbons of the nonclassical cation. It was tricky, because the cation is so symmetric that it rotates within crystals at higher temperatures. The bond lengths between the 3 carbons are 1.78 to 1.83 Angstroms — far longer than the classic length of 1.54 Angstroms of a C – C single bond.

I earlier wrote a post on why I don’t read novels, the coincidences being so extreme that if you put them in a novel, no one would believe them and throw away the book — it involves the Princeton chemistry department and my later field of neurology — here’s the link https://luysii.wordpress.com/2014/11/13/its-why-i-dont-read-novels/

Here’s yet another. Who would have thought, that years later I’d be using a molecule Paul had synthesized to treat Parkinson’s disease as a neurologist. He did an incredibly elegant synthesis of adamantane using only the product of a Diels Alder reaction, hydrogenating it with a palladium catalyst and adding AlCl3. An amazing synthesis and an amazing coincidence.

As Peter noted, he was an extremely productive chemist and theoretician. He should have been elected to the National Academy of Sciences, but never was. It has been speculated that his wars with H. C. Brown made him some powerful enemies. I’ve heard through the grapevine that it rankled him greatly. But virtue is its own reward, and he had plenty of that.

R. I. P. Dr. Schleyer

Keep on truckin’ Dr. Schleyer

My undergraduate advisor (Paul Schleyer) has a new paper out in the 15 July ’14 PNAS pp. 10067 – 10072 at age 84+. Bravo ! He upends what we were always taught about electrophilic aromatic addition of halogens. The Arenium ion is out (at least in this example). Anyone with a smattering of physical organic chemistry can easily follow his mechanistic arguments for a different mechanism.

However, I wonder if any but the hardiest computational chemistry jock can understand the following (which is how he got his results) and decide if the conclusions follow.

Our Gaussian 09 (54) computations used the 6-311+G(2d,2p) basis set (55, 56) with the B3LYP hybrid functional (57⇓–59) and the Perdew–Burke–Ernzerhof (PBE) functional (60, 61) augmented with Grimme et al.’s (62) density functional theory with added Grimme’s D3 dispersion corrections (DFT-D3). Single-point energies of all optimized structures were obtained with the B2-PLYP [double-hybrid density functional of Grimme (63)] and applying the D3 dispersion corrections.

This may be similar to what happened with functional MRI in neuroscience, where you never saw the raw data, just the end product of the manipulations on the data (e.g. how the matrix was inverted and what manipulations of the inverted matrix was required to produce the pretty pictures shown). At least here, you have the tools used laid out explicitly.

For some very interesting work he did last year please see https://luysii.wordpress.com/2013/07/08/schleyer-is-still-pumping-out-papers-crystallization-of-a-nonclassical-norbornyl-cation/

Hitler’s gifts (and Russia’s gift)

In the summer of 1984 Barack Obama was at Harvard Law, his future wife was a Princeton undergraduate, and Edward Frenkel a 16 year old mathematical prodigy was being examined for admission to Moscow State University. He didn’t get in because he was Jewish. His blow by blow description of the 5 hour exam on pp. 28 – 38 of his book “Love & Math” is as painful to read as it must have been for him to write.

A year earlier the left in Europe had mobilized against the placement of Pershing missiles in Europe by president Reagan, already known there as a crude and witless former actor, but, unfortunately possessed of nuclear weapons. Tens of thousands marched. He had even called the Soviet Union an Evil Empire that year. Leftists the world over were outraged. How unsophisticated to even admit the possibility of evil. Articles such as “Reagan’s image in Europe does not help Allies in deploying American missiles” appeared in the liberal press.

The hatred of America is nothing new for the left.

Reset the clock to ’60 – ’62 when I was a grad student in the Harvard Chemistry department. The best place to meet women was the International house. It had a piano, and a Polish guy who played Chopin better than I did. It had a ping pong table, and another Polish guy who beat me regularly. The zeitgeist at Harvard back then, was that America was rather crude (the Ugly American was quite popular), boorish and unappreciative of the arts, culture etc. etc.

One woman I met was going on and on about this, particularly the condition of the artist in America, and how much better things were in Europe. I brought up Solzhenitzen, and the imprisonment of dissidents over there. Without missing a beat, she replied that this just showed how important the Russian government thought writers and artists were. This was long before Vietnam.

It was definitely a Saul on the road to Damascus moment for me. When the left began spelling America, Amerika in the 60s and 70s, I just ignored it.

Fast forward to this fall, and the Nobels. The 7th Chemistry Nobel bestowed on a department member when I was there went to Marty Karplus. The others were Woodward, Corey, Lipscomb, Gilbert, Hoffman, Bloch. While Bill Lipscomb was a Kentucky gentleman to a T (and a great guy), Hoffman spent World War II hiding out in an attic, his father being in a concentration camp (guess why). Konrad Bloch (who looked as teutonic as they come) also got out of Europe due to his birth. Lastly Karplus got out of Euruope as a child for the same reason. Don Voet, a fellow grad student, whose parents got out of Europe for (I’ll make you guess), used to say that the Universal Scientific Language was — broken English.

So 3/7 of the Harvard Chemistry Nobels are Hitler and Europe’s gifts to America.

Russia, not to be outdone, gave us Frenkel. Harvard recognized his talent, and made him a visiting professorship at age 21, later enrolling him in grad school so he could get a PhD. He’s now a Stanford prof.

So the next time, someone touts the “European model” of anything, ask them about Kosovo, or any of this.

—

Those of you in training should consider the following. You really won’t know how good what you are getting really is until 50 years or so have passed. That’s not to say Harvard Chemistry’s reputation wasn’t very good back then. Schleyer said ‘now you’re going to Mecca’ when he heard I’d gotten in.

Also to be noted, is that all 7 future Nobelists in the early 60s weren’t resting on their laurels, but actively creating them. The Nobels all came later

Where has all the chemistry gone?

Devoted readers of this blog (assuming there are any) must be wondering where all the chemistry has gone.  Willock’s book convinced me of the importance of group theory in understand what solutions we have of the Schrodinger equation.  Fortunately (or unfortunately) I have the mathematical background to understand group characters and group representations, but I found Willock’s  presentation of just the mathematical  results unsatisfying.

So I’m delving into a few math books on the subject. One is  “Representations and Characters of Groups” by James and Liebeck (which provides an application to molecular vibration in the last chapter starting on p. 367).  It’s clear, and for the person studying this on their own, does have solutions to all the problems. Another is “Elements of Molecular Symmetry” by Ohrn, which I liked quite a bit.  But unfortunately I got stymied by the notation M(g)alpha(g) on p. 28. In particular, it’s not clear to me if the A in equation (4.12) and (4.13) are the same thing.

I’m also concurrently reading two books on Computational Chemistry, but the stuff in there is pretty cut and dried and I doubt that anyone would be interested in comments as I read them.  One is “Essential Computational Chemistry” by Cramer (2nd edition).  The other is “Computational Organic Chemistry” by Bachrach.  The subject is a festival of acronyms (and I thought the army was bad) and Cramer has a list of a mere 284 of them starting on p. 549. On p. 24 of Bachrach there appears the following “It is at this point that the form of the functionals  begins to cause the eyes to glaze over and the acronyms appear to be random samplings from an alphabet soup.”  I was pleased to see that Cramer still thinks 40 pages or so of Tom Lowry and Cathy Richardson’s book is still worth reading on molecular orbital theory, even though it was 24 years old at the time Cramer referred to it.  They’re old friends from grad school.   I’m also pleased to see that Bachrach’s book contains interviews with Paul Schleyer (my undergraduate mentor).  He wasn’t doing anything remotely approaching computational chemistry in the late 50s (who could?).  Also there’s an interview with Ken Houk, who was already impressive as an undergraduate in the early 60s.

Maybe no one knows how all of the above applies to transition metal organic chemistry, which has clearly revolutionized synthetic organic chemistry since the 60’s, but it’s time to know one way or the other before tackling books like Hartwig.

Another (personal) reason for studying computational chemistry, is so I can understand if the protein folding people are blowing smoke or not.  Also it appears to be important in drug discovery, or at least is supporting Ashutosh in his path through life.  I hope to be able to talk intelligently to him about the programs he’s using.

So stay tuned.