Bench Press

I have a great deal of respect for the early pioneers of chemistry — not just because they were intelligent and inquisitive and spawned entire fields of research, but mainly because they were able to do this while never having the ability to see what they were studying. So, although the early experimenters could conduct experiments to indirectly validate or invalidate their hypotheses on a macro-scale (like shaking a tree to see what fruit fell out rather than actually looking up at the tree to see the individual fruit), the fact that they could never see or manipulate or count molecules meant that most of their work resided in the domain of thought experiments.

And, although the scientific community now take the existence of atoms and molecules for granted, I think the early Avogadros of chemistry would have been especially gratified by the recent work at IBM’s research facility in Zurich to use atomic force microscopy to actually see molecules of pentacene (five fused aromatic 6-carbon rings, pictured below)

The results are detailed both on IBM’s press page as well as in the Aug 28 issue of Science. But, in graphical terms, this is the scientific community’s current best picture of pentacene:

Amazing isn’t it? More of the technical details are presented in the video IBM put together in conjunction with the press release (below), but in a nutshell, atomic force microscopy uses a well-defined atomic tip to “feel” out the electronic surface of a molecule. The ability to do this and even be able to resolve the respective hydrogen atoms is a testament to IBM’s ability to put together an incredibly stable (both to mechanical and thermal fluctuations) and precise setup.

From IBM’s perspective, this breakthrough allows them to continue to push ahead on the advanced nanotechnology and semiconductor research which they depend on to churn out next-generation electronics, but for the scientific community, these advances could result not only in better atomic force microscopy experimental techniques, but potentially also a new way to understand and study the chemical reactions and structures which have such great influence over our lives.

Publication: Science 28 August 2009: Vol. 325. no. 5944, pp. 1110 – 1114; DOI: 10.1126/science.1176210

(Image credit – Pentacene chemical diagram) (Image credit – AFM picture)

One thing that biologists have learned quickly is that evolution can easily solve problems that we can only dream about understanding. A key part of the power of evolution comes from the fact that biological systems are self-replicating; cells divide and make copies of themselves, organisms give rise to offspring, and so on. Biochemists have been using so-called “directed” evolution in order to engineer really cool new proteins and molecules, such as a whole spectrum of new fluorescent proteins that Roger Tsien (2008 Nobel in Chemistry) made.

In the last decade or two, chemists have started to experiment with chemical, non-biological systems that are self-replicating, by using catalysts that make more of themselves. This autocatalysis, as it’s called, can lead to some surprising findings, such as the one published this week in Science magazine.

Some molecules can come in two mirror image forms called enantiomers that behave exactly the same way, except one is left-handed and the other is right-handed. Not all molecules have a “thumb” that makes them have the hand-like asymmetry, but by tweaking a symmetric molecule, one can add a thumb to make them have an enantiomer. The “thumb” that breaks the molecule’s symmetry can be anything from a huge cluster of atoms, in which asymmetries are easily detectable, to a tiny substitution for a different isotope, in which asymmetries are nearly undetectable.

The authors constructed a catalyst that makes more of itself from a pool of “fuel” molecules. The key thing here is that these fuel molecules are asymmetric; they each have on Carbon-12 isotope on one side, and one Carbon-13 isotope on the other side. There’s just slightly more of one enantiomer than the other. Surprisingly, the catalyst, because it makes more of itself, biases new copies of itself to one mirror form, which causes more bias in the newer generations of copies. At the end of the reaction, when all the fuel is spent, the catalyst is dramatically enriched in one mirror form over another, even though the system that started was only ever-so-slightly, almost undetectably biased in one form.

One of the big questions about the origins of life is about things like asymmetry. All organisms have bias in their molecules for one particular mirror version, but where this asymmetry came from is hard to analyze. One theory that’s growing in popularity is about autocatalytic systems: a small initial bias for one mirror form got amplified over time by self-replicating chemistry, until finally when life started, the molecules were all asymmetric in the same way. As a sort of modern confirmation of that theory, this study shows that even the smallest, most trivial of asymmetries can be amplified by self-replicating systems. Whatever the real history of life is, we do know that nature can pull off some amazing feats that still boggle our minds.