See you at the 3rd EuCheMS Chemistry Congress,

David

Well, take hope. You may remember the snapshots taken of pentacene molecules a while ago by atomic force microscopy that, surprisingly, looked exactly like pentacene? The ones where you could see that the rings at the ends were slightly lifted up, because the interactions with the surface were stronger in the middle of the molecule?

The group that did those images is at it again, and this time they tried something a little more complicated this time. The target molecule, cephalandole A, already hat it’s structure determined – wrongly, as it turned out, as the first structure had to be corrected.

Source: Gross, L. et al., Organic structure determination using atomic-resolution scanning probe microscopy. Nature Chemistry 10.1038/nchem.765, 2010.

The result is of course not as intuitive as that of pentacene, where electron density closely follows the molecular scaffold. A molecule with several different functional groups has a far greater variation in electron density and it shows in the image. Nevertheless you can still see parts of the actual structure.

Even better, the researchers could use this representation to identify the correct molecular structure from the four possible variants that the original NMR Data could not distinguish. So even at this early stage, the technique can be used to solve actual structure determination problems. Expect the technique to improve quickly, as NMR did. This may well change the way we determine molecular structures forever.

Speaking of change, the image had me thinking: What will this do to our perception of chemical molecules, and to the way we draw them? Chemists never had images of molecules, so they had to devise ways to show their important characteristics from scratch. That’s how we arrived at lines linking balls or letters, or, on a slightly more sophisticated level, bulgy van-der-Waals surfaces and the like.

But the molecules created by this technique don’t look like that. What comes out of the atomic force microscopy is far more real, in a chemical sense, because the tip of the cantilever measures something that actually determines chemical behavior. So the cephalandole A published by Gross et al. looks weird and unfamiliar at first, but maybe this is because we used to draw them in the wrong way. Maybe this is how chemists should draw such molecules, at least in some way.

I believe as the technique progresses and becomes more commonplace, the power of images alone will make it happen.

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Gross, L., Mohn, F., Moll, N., Meyer, G., Ebel, R., Abdel-Mageed, W., & Jaspars, M. (2010). Organic structure determination using atomic-resolution scanning probe microscopy Nature Chemistry DOI: 10.1038/nchem.765

Here’s his advice for young scientists who want to follow in his footsteps:

This is especially true for superhydrophobic coatings, which cause the Lotus Effect and hence are very promising not only for self-cleaning items, but also for anti-corrosion or anti-adhesive coatings. Everyone who ever scratched barnacles from the bottom of a ship knows how useful this could be. Since a superhydrophobic coating also reduces drag on surfaces, painting commercial ships with such a formulation would be a billion-dollar business.

The problem is of course, that superhydrophobic coatings do poorly out in the real world and tend to lose their unique properties due to sun bleaching or mechanical actions. Plants get around this by actively regenerating the coating from a reservoir within, an option not yet available to artificial materials.

This is about to change. In a current paper from Angewandte, Junqi Sun et al describe the creation of a coating based on a porous polymer layer made of polyelectrolyte complexes, which is made superhydrophobic by deposition of a fluoroalkylsilane layer. The polymer undercoat consists of layers of preformed complexes of polyallylamine hydrochloride and sulfonated PEEK which alternate with polyacrylic acid to an oveall thickness of about three microns. Those compounds were thermally cross-linked to form a durable layer that, according to the scientists, forms a foli that can be removed as a whole and transferred to other surfaces. Afterwards the fluoroalkylsilanes were deposited by CVD.

The resulting surface is superhydrophobic with a contact angle of about 160 degrees, which means that water sits as round droplets on such a surface without really interacting with the material. The trick however is that the fluoroalkylsilanes don’t just sit on the surface, but permeate the whole coating, thanks to the porosity of the matrix. That means that even severe damage to the coating can be undone, as long as there is any coating left.

Thisw is not just due to the presence of the perfluorated chains in the matrix. There is actually active repair happening, because the fluoroalkylsilanes migrate to the surface after damage. The effect is rather simple: The matrix is made out of hydrophilic hydrogels that tend to incorporate water into their structure. The hydrophobic perfluorated molecules thus get expelled from the watery matrix and migrate to the surface, restoring the superhydrophobicity.

In their experiment Junqi Sun et al. destroyed the surface repeatedly by etching with oxygen plasma, which not only destroys the surface but also makes it more hydrophilic by adding oxygen-containing functional groups. Nevertheless, within four hours after plasma etching a humid environment restores the superhydrophobicity of the surface completely. This process apparently can be repeated multiple times without the coating losing its properties.

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Li, Y., Li, L., & Sun, J. (2010). Bioinspired Self-Healing Superhydrophobic Coatings Angewandte Chemie International Edition DOI: 10.1002/anie.201001258

Helium is, essentially a non-renewable resource that is, while being the second-most abundant element in the universe, comparatively scarce on earth. The main source is alpha decay of certain unstable isotopes in minerals, and as you might imagine, that’s a rather slow process. There are several cryogenic applications like high-end NMR spectrometers that won’t run without Helium, so there is no easy replacement. On the other hand, there are huge amounts of helium wasted every day because the gas is kept artificially cheap.

I met Professor Richardson at the Lindau conference and he was kind enough to answer a few questions about the looming resource crisis, it’s causes and possible solutions.

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Professor Richardson, when did you first recognize Helium as a resource issue?

Richardson: About 15 or 20 years ago, because there is only so much Helium in the world. There are two sources of helium in the world. One is the sun. Helium was first discovered in the sun. The flux of alpha particles from the sun results in an equilibrium saturation of five parts per million in the atmosphere, and the recovery of helium from the atmosphere will be very difficult and expensive because of the low concentration. Another source, and indeed the primary source of helium is rocks, granite. It contains uranium and Radium that produce helium by alpha decay. In the 19th century the alpha decay was the principal evidence for the age of the earth, and the exact age of the earth is 4.7 billion years. And the helium in natural gas formations accumulated through alpha decay over those 4.7 billion years. And the problem is, we will soon dissipate our helium.

By using it up?

Well, there are two issues: The rich wells are in the USA, they contain up to 2 % helium within the natural gas. But the United States decided to sell their strategic helium reserve five years ago, driving prices down. And second, the rest of the helium in the U.S. will last only 25 years at current usage.

Is there any replacement?

For cryogenic instruments that need liquid helium that boils at four degrees Kelvin there is no replacement. Superconducting magnets, MRI machines, high-field magnets in nuclear magnetic resonance in about every chemistry department depend on a reliable source of liquid helium. And there is no replacement. There are other uses of helium for which there are replacements. In the U.S. helium is used for welding metals, whereas in Europe argon is used. Argon is roughly one percent of the atmosphere rather than 5 ppm. But the government policy in the US has fixed helium at a price that is ridiculously cheap. Frequently it’s less expensive to use helium than argon, and that is insane.

What you are saying is that helium should be far more expensive.

Yes. It should be treated as a precious commodity rather like just another gas that will last forever. There is no chemical process available to produce Helium.

And nuclear fusion?

Well, maybe in a thousand years or something. It is at least 50 years away. I don’t hold my breath.

Are there resource management strategies in place?

Helium is just too cheap. For instance, NASA uses about 30 percent of the helium for purging rocket engines. They use liquid helium to wash out the fuel, hydrogen and oxygen, out of the rocket engines, and they don’t bother to recover it, because it is too cheap. If helium became a hundred times more expensive, they would use shrouds to recover it.

Wouldn’t far higher helium prices hurt scientists that use cryogenic equipment?

Yes, it would. But they will be able to do their science only for the next 25 years otherwise. The clock is already ticking. The strategy I propose is treat it as a rare gas, a precious gas and have it forever.

As it happens the trans-azobenzene fits snugly in the cyclodextrine cavity, while the bent cis-form doesn’t. This offers a number of interesting possibilities, ranging from the inevitable switchable hydrogels to rather more amazing structures, such as switchable ion channels and functionalized surfaces.

The latest invention, just published in Angewandte Chemie by the Münster-based chemists Nalluri and Ravoo, uses this principle to influence the collective behavior of vesicles in solution. It is possible to make micelles and vesicles from cyclodextrines. I didn’t know that, but it’s fairly obvious: The sugars of the cyclodextrine ring are water-soluble, so if you just attach some long-chained hydrocarbon to each sugar moiety you get amphiphilic building blocs for vesicles or bilayers.

What the researchers did then is rather straightforward: They connected two azobenzene moieties with a PEG linker and added the resulting molecule to a solution of monodisperse cyclodextrine vesicles, which coagulate nore or less immediately, since the trans-azobenzenes find a suitable resting place in the cyclodextrine cavity. This shows as an increase in optical density of about an order of magnitude. This macroscopic change can, of course be reversed by irradiation with light at a suitable wavelength. There are two interesting aspects here. For one, this reminds me of certain biological Systems, like certain sponges that can be separated into their component cells which then re-aggregate into a fully functional animal.

The other, probably far more significant issue is the fact that this degree of control over a macroscopic system fits snugly into the general pattern of progress made in this area of science. Self-organising macromolecular systems may well be the next Really Big Thing in materials technology – incremental steps slowly adding up to a level of knowledge that enables, at one point, a really huge leap in technology. We may be closing in on that point.

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Nalluri, S., & Ravoo, B. (2010). Lichtgesteuerte molekulare Erkennung und Adhäsion von Vesikeln Angewandte Chemie DOI: 10.1002/ange.201001442

Volunteer for the Organiser

This way, you will be registered for free and though you have to work during the congress, you still will have the chance to visit lectures. But there are also some catches, of course: You have to wear a “Volunteer-Shirt” so everybody knows that you can help, and you have to speak at least English (fluent). As always, additional languages are an asset.

In case you’re interested, please contact
euchems-congress2010@gdch.de

See you in Nürnberg!

See you in Nürnberg

However, it seems that I’m wrong and that there is a way. Recently a group around Jeffrey L. Gustafson from Yale made some interesting progress in that direction. They report a tripeptide catalyst that mediates highly enantioselective electrophilic bromination of aromatic rings. The significance for atropisomerism stems from the fact that bromine atoms next to a biaryl single bond effectively prevent rotation around this bond if another functional group is present at the other ring.

So what they do is, they start with a substituted biphenyl that in principle exhibits axial chirality, but has such a low rotation barrier that it rapidly interconverts. Such a product was triple-brominated with NBS, which led to an axial-chiral compound with a rotation barrier of about 30 kJ/mol, enough to prevent racemisation at room temperature.

Of course just using NBS yields a racemic mixture so what’s needed to promote one enantiomer over the other is a chiral catalyst. There are few things as proudly chiral as peptides, and since lewis bases are known to catalyse bromination reactions, that’s where Gustafson et al. started. The first peptide turned out encouraging. It needs mentioning that they cheated a little, that is, they didn’t just tune the catalyst for maximum efficiency, but in between modified the substrate to fit the reaction best. However, in the end they came up with a combination of substrate and catalyst that produced a 97:3 enantiomeric ratio. I find that rather impressive, especially for a proof of concept.

There are a few limits to this reaction scheme, but all in all it turns out to be rather versatile. As the authors show it tolerates several different (and synthetically important) substituents like nitro groups or fluorine, and of course this is just the start. I for one wait expectantly for the first atropisomer-selective total synthesis of a natural product.

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Gustafson, J., Lim, D., & Miller, S. (2010). Dynamic Kinetic Resolution of Biaryl Atropisomers via Peptide-Catalyzed Asymmetric Bromination Science, 328 (5983), 1251-1255 DOI: 10.1126/science.1188403

The material is a molecule crystal with nanometer-sized channels that are lined with metal centers, which absorb several small gases like oxygen, ammonia, hydrogen or ethylene. Everything larger than the pore diameter is excluded, for example propylene. A gas that enters the structure coordinates the iridium centers, changing the overall color: Red for ammonia, dark green for oxygen. As transition metals do, the Iridium also works as a catalyst: Treating the crystal with ethylene and hydrogen at 75 °C yields ethane at 99% conversion.

The researchers proved that the reaction happens within the crystal by trying the same with a mixture of ethylene and propylene, the latter being excluded from the pores and the former being hydrogenated with a selectivity of 25:1. That’s not bad for a start.

Of course, setting out by separating gases by chemical means promises even more selectivity than mere molecule size. That’s where things get interesting, and mathching the Nature paper there was a publication in Nature Chemistry that fits the bill. It is also about a metal-organic crystal with nanometer-sized channels, albeit in this case it’s a polymer, and the metal ions seem to have only a structural function. The magic is happening in the ligands.

The monomer that forms the material, [Zn(TCNQ)₄bpy₂], has a flexible three-dimensional structure constructed from Zn(II) centres and the organic ligands 4,4’-bipyridyl (bpy) and 7,7,8,8-tetracyano-p-quinodimethane (TCNQ). Polymerisation happens via dimerisation of TCNQ-units, interconnecting the monomers and setting the stage for what happens next.

According to the researchers it’s this dimer that causes the selectivity. The material ignores all small molecules, independent of size, except O₂ and the isoelectronic NO. Both are good electron acceptors and form reversible charge-transfer-complexes with the TCNQ dimer in the pore wall. The electronic configuration of the dimers that form the walls of the nanometer-sized channels enables the material to capture larger molecules as well: aromatic hydrocarbons that are caught by π-stacking.

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Shimomura, S., Higuchi, M., Matsuda, R., Yoneda, K., Hijikata, Y., Kubota, Y., Mita, Y., Kim, J., Takata, M., & Kitagawa, S. (2010). Selective sorption of oxygen and nitric oxide by an electron-donating flexible porous coordination polymer Nature Chemistry DOI: 10.1038/nchem.684

Huang, Z., White, P., & Brookhart, M. (2010). Ligand exchanges and selective catalytic hydrogenation in molecular single crystals Nature, 465 (7298), 598-601 DOI: 10.1038/nature09085