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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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December 9, 2013

Low Energy Records

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Posted by Derek

Pick an empirical formula. Now, what's the most stable compound that fits it? Not an easy question, for sure, and it's the topic of this paper in Angewandte Chemie. Most chemists will immediately realize that the first problem is the sheer number of possibilities, and the second one is figuring out their energies. A nonscientist might think that this is the sort of thing that would have been worked out a long time ago, but that definitely isn't the case. Why think about these things?

What is this “Guinness” molecule isomer search good for? Some astrochemists think in such terms when they look for molecules in interstellar space. A rule with exceptions says that the most stable isomers have a higher abundance (Astrophys. J.­ 2009, 696, L133), although kinetic control undoubtedly has a say in this. Pyrolysis or biotechnology processes, for example, in anaerobic biomass-to-fuel conversions, may be classified on the energy scale of their products. The fate of organic aerosols upon excitation with highly energetic radiation appears to be strongly influenced by such sequences because of ion-catalyzed chain reactions (Phys. Chem. Chem. Phys.­ 2013, 15, 940). The magic of protein folding is tied to the most stable atomic arrangement, although one must keep in mind that this is a minimum-energy search with hardly any chemical-bond rearrangement. We should rather not think about what happens to our proteins in a global search for their minimum-energy structure, although the peptide bond is not so bad in globally minimizing interatomic energy. Regularity can help and ab initio crystal structure prediction for organic compounds is slowly coming into reach. Again, the integrity of the underlying molecule is usually preserved in such searches.

Things get even trickier when you don't restrict yourself to single compounds. It's pointed out that the low-energy form of the hexose empirical formula (C6H12O6) might well be a mixture of methane and carbon dioxide (which sounds like the inside of a comet to me). That brings up another reason this sort of thinking is useful: if you want to sequester carbon dioxide, what's the best way to do it? What molecular assemblies are most energetically favorable, and at what temperatures do they exist, and what level of complexity? At larger scales, we'll also need to think about such things in the making of supramolecular assemblies for nanotechnology.

The author, Martin Suhm of Göttingen, calls for a database of the lowest-energy species for each given formula as an invitation for people to break the records. I'd like to see someone give it a try. It would provide challenges for synthesis, spectroscopy and (especially) modeling and computational chemistry.

Comments (13) + TrackBacks (0) | Category: Chemical News | In Silico


COMMENTS

1. Curious Wavefunction on December 9, 2013 10:33 AM writes...

Broken link.

Permalink to Comment

2. Anonymous on December 9, 2013 10:35 AM writes...

"It's pointed out that the low-energy form of the hexose empirical formula (C6H12O6) might well be a mixture of methane and carbon dioxide."

So why does methane burn in CO2 to give CO and H2O?

Permalink to Comment

3. Eric on December 9, 2013 11:40 AM writes...

#2 - I assume the answer is that at STP, your reaction proceeds; at near absolute-zero, the methane-CO2 mixture is the thermodynamic winner.

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4. Paul on December 9, 2013 11:58 AM writes...

So why does methane burn in CO2 to give CO and H2O?

That has more (gas) molecules, so at high temperature/low pressure the equilibrium shifts to that side.

Permalink to Comment

5. Anonymous on December 9, 2013 12:23 PM writes...

I think this is like the "napsack problem" (see Wikipedia), but where you have to distribute all the atoms between simple low energy gas molecules, in order to minimize overall energy?

Permalink to Comment

6. barry on December 9, 2013 1:59 PM writes...

the question goes back at least to Perkin. He hoped that he could get quinine just by cooking together C,H,N,O to match the empiric formula. I.e. he assumed that because quinine was naturally occurring and crystaline, it must be the minimum energy cmpd, and should be accessible. Of course, he got mauve instead, and became quite wealthy on it.

Permalink to Comment

7. gippgig on December 9, 2013 4:29 PM writes...

If there is an accurate way to predict energy from structure this might make a good crowdsourcing game like Foldit.

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8. Nick K on December 9, 2013 7:31 PM writes...

Surely the question is meaningless unless we specify the conditions (temperature and pressure) as alluded to in posts 2-4.

Permalink to Comment

9. Sam Adams The Dog on December 10, 2013 2:34 AM writes...

Seems to me this idea goes back at least to Margaret Dayhoff. @8, not only T and P, but also elemental abundance. IIRC, it was noted in the '50s that if you take the element abundance characteristic of life (on earth, at least), then, at STP, the equilibrium mixture is going to be mainly CO2, H2O, N2, with insignificant amounts of anything else. But elemental abundance matters. More H2, and you start to get CH4. I don't recall whether there's enough in the "life empirical formula" to give you much. But I do know that if you take away the H, O and N, you get graphite. :-) But only at STP, of course.

Permalink to Comment

10. Sam Adams The Dog on December 10, 2013 2:34 AM writes...

Seems to me this idea goes back at least to Margaret Dayhoff. @8, not only T and P, but also elemental abundance. IIRC, it was noted in the '50s that if you take the elemental abundance characteristic of life (on earth, at least), then, at STP, the equilibrium mixture is going to be mainly CO2, H2O, N2, with insignificant amounts of anything else. But elemental abundance matters. More H2, and you start to get CH4. I don't recall whether there's enough in the "life empirical formula" to give you much. But I do know that if you take away the H, O and N, you get graphite. :-) But only at STP, of course.

Permalink to Comment

11. Henry Rzepa on December 10, 2013 6:46 AM writes...

This stochastic search at a high quantum level for a given collection of atoms was reported some time ago: doi 10.1021/jp057107z. It carried the delightful title Mindless chemistry

Permalink to Comment

12. Paul on December 10, 2013 12:57 PM writes...

One place this sort of thing shows up is in the engineering of rocket engines. The gas in an engine is at high temperature and pressure, and it's a good approximation to consider it to be in local chemical equilibrium, at least before it expands too much down the nozzle.

Permalink to Comment

13. nwl on December 11, 2013 9:22 AM writes...

Methane and carbon dioxide can be beat by 100kj/mol by liquid water and carbon (16 kj/mol if the water is gasous). Since both options have two moles of gas, entropy shouldn't matter much.

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