Pentacene snapshot

28 August 2009 - AFM

You can no longer trust the Swiss to look after your money without interference from the tax collector but as always you can trust them to build high-precision instruments like clocks or lets say a high-definition atomic force microscope. Gross et al. (IBM) have produced intriguing ATM images of the molecule pentacene with unprecedented resolution (DOI).



In the images not only the carbon-carbon bonds are clearly visible but also the carbon-hydrogen bonds. Other notable features: the molecule actually resembles the ball-and-stick model that students of chemistry are supposed to ignore in favor of a space-filling model, the extremities appear to stand out and surprise: the molecules appear to cast a shadow?

For the experiment pentacene is deposited on a copper surface with a 2 atom thick layer of sodium chloride. To the end of the gold ATM tip is attached a carbon monoxide molecule (picked up along the way) and the tip is lowered to 4 Angstrom above the surface and the force exerted on it (at 4 K) is measured. Typically an attractive force of 110 picoNewton is measured inside one of the arene rings and this force decreases to 60-90 pN when the tip hovers above one of the carbon atoms. The researches assign the observed atomic contrast to Pauli repulsion (do not bother to read the pretty worthless Wikipedia article on this topic), the other forces (van der Waals force) and electrostatic forces are attractive but only create background noise, only explaining the observed dark halo.

Interestingly the result is presented as a new technique for molecular structure elucidation like NMR or crystallography.

Frustrated Lewis pairs save the planet

22 August 2009 - carbon dioxide sequestration

Stephan and partners have expanded their frustrated Lewis pair concept into carbon dioxide sequestration. Tris(pentafluorophenyl)boron and tri-tert-butylphosphine are mixed in bromobenzene and 1 bar carbon dioxide and the product -described as a phosphonium type of carbamic acid - forms immediately! (DOI). Heating this compound to 80° C releases the gas again.


More recent frustrated Lewis news: a B-N system tackling 1,3-dienes (DOI) or nitrous oxide ( DOI) and a N-B Lewis pair based on lutidine and B(C6F5)3 capable of THF ring-opening (DOI),

Old firefly problem solved

18 August 2009 - Bioluminescence

Fireflies are well known for their bioluminescence - glow-in-the-dark - properties. Although all fireflies use luciferin as the sole reagent for this to take place, the emitted color can vary from green to red among the different species, yellow-green for fireflies, green to orange for click beetles and green to red for railroad worms. This unsolved problem in chemistry however is about to be cracked as researchers from Osaka University have re-analysed the actual molecule responsible for the luminescence called oxyluciferin (DOI).

Here is what sets the luminescence in motion: with ATP and luciferase, luciferin is converted to luciferin-AMP which reacts with oxygen and then loses AMP and then carbon dioxide to form the excited oxyluciferin which then decays to the ground state with emission of a photon.
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The researchers synthesised oxyluciferin in the laboratory using a new work-up procedure (growing crystals by evaporating from isopropanol) that enabled them to side-track decomposition and enabled them to determine accurate crystal structures.

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First surprise: the compound is an enol and not a ketone. In (physiologically more relevant) solution, enolic oxyluciferin is found to equilibrate quickly with the mono- and diphenolate and second surprise: within a narrow pH range these species can account for the entire emission spectrum. So no longer need then to invoke any of the other theories that have been circulating: keto-enol mechanism (color variation due to keto-enol isomerism) , twisted intramolecular charge-transfer (TICT) mechanism (differences in rotational freedom excited state), or a microenvironment mechanism (color variation due to specific luciferin - luciferase interactions).

Melamine detector at 2 ppb

10 August 2009 - Melamine update

Less than a year ago this blog reported on the melamine milk scandal and why chemical testing apparently is not that straightforward. There obviously is room for improvement and the first innovation in melamine testing is just in (DOI).

Ai, Liu and Lu of the Chinese Academy of Science @ Changchun combine cyanuric acid with gold particles in colloidal gold via a ethylene mercapto spacer. The color of this water solution is wine-red but when melamine is added it turn blue. The melamine forms the well-known melamine cyanurate complex through extensive hydrogen bonding as a result of which the gold particles aggregate and it is well known that the color of colloidal gold solutions depend strongly on gold particle size.

The great news is that the researchers report melamine detection at the 2.5 ppb level and that within one minute which is three times below the melamine safety limit. Issue to solve: detection of melamine in raw milk at the 2 ppm level still requires extensive sample preparation (extraction, filtration, centrifuging) because many other milk components would otherwise interfere.

Molecular belts

01 August 2009 - Part II

Two succesfull attempts have been reported recently synthesising a new class of molecular belts, the so-called cycloparaphenylenes (carbon nanohoops in marketing speak) that are taking cyclophanes one step further. Jasti & Bertozzi et al. (DOI) beat Takaba & Itami et al. (DOI) by a good five months. The cycloparaphenylene molecule (C6H4)12 in question consists of 12 phenylene units linked together by para joints. It can be envisioned as cyclic poly(p-phenylene) and also as a carbon nanotube segment. Both methods rely at some point on a Suzuki reaction. In the Bertozzi method several oligomers have to be separated:


Not so in the Itami method:


Key strategic advantage for both: direct cyclization of phenylene units would increase ring strain by 50 kcal/mole (will fail) whereas same step with intermediates containing unsaturated rings adds only 5 kcal/mole strain.

Also see molecular belts part I