We’ll never be able to really understand chemistry

We’ll never be able to really understand chemistry. That’s my take on the first Chemistry article of 2014 in PNAS (vol. 111 pp. 15 – 20). The article is actually titled “Is the simplest chemical reaction really so simple?” The first heading in the article reads “H + D2 Collision Looks Like Playing Molecular Pool on a Warped Table”

Oy Vey.

Chemistry doesn’t get simpler than that. We’re talking about a reaction with 3 protons, 2 neutrons and 3 electrons. After a bit of back-patting about how much computational chemistry studying this (and similar) reactions has taught us, they throw up figure #2 — a potential energy surface for the reaction, which is identical to what I studied in grad school 50+ years ago.

Theory works well for collisions of H with D2 when all 3 nuclei are linear (180 degrees). Experiments were carried out in the gas phase. No solvent. The D2 was in the lowest vibrational state, and one of the first few of the rotational levels (j = 0, 1, 2). They used D2 to tell products from reactants. Theory and experiment agree and the results look our mental picture of the reaction e.g. it looks like what happens with billiard balls on a good table.

So far so good. Then “We did one experiment too many”.

A rather amazing statement.

What they did was to examine the differential cross-sections of the HD products that were produced with more vibrational excitation (ν′ = 4). They find that the potential energy surface isn’t purely repulsive at higher vibrational levels (which occur in every reaction occurring in living tissue).

As they put it “Warped Billiard Table Changes as the Pool Balls Move and Is Weirder than First Imagined” I’ll let them continue — they’re funny and write well. “So far, we have been fortunate to consider only one potential energy surface (PES) as governing the motion of the nuclei. However, the H3 system is a Jahn–Teller system having a second PES connected to the first at a conical intersection seam whose minimum is located about 2.7 eV (64 kcal/mol) above the asymptotes of the ground state. Once this is energetically accessed, we can expect electronic nonadiabatic transitions to occur in which we must consider motion of the nuclei on both PESs at the same time. This hurts the classical mind (my highlighting). We will need to consider playing molecular pool on interconnected warped billiard tables whose shapes change with the motion of the pool balls. Well, no one ever promised us that chemical reactions would be simple, even for what is called the simplest chemical reaction of them all.”

No solvent, very little internal energy of the D2 and all this is going on. This will give drug chemists trying to dock ligands into a protein cavity nightmares.

Happy New Year, I guess.

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