all blogs

Cyclobutadiene X-ray structure debate continues

22 March 2013 - Crystallography

dimethylcyclobutadieneXray  Opposition to the cyclobutadiene X-ray structure claimed by Yves-Marie Legrand in 2010 (DOI) continues. According to Legrand 1,3-dimethylcyclobutadiene formed by photolysis of a pyrone is stable when confined to a calixarene cavity and when analyzed at 175K displays two geometries, one square-planar and one rectangular-bent. Carbon dioxide is also present in the cavity as a reaction product but is hydrogen-bonded at the most. Rzepa in 2010 was quick to blog his doubts: cyclobutadiene when formed quickly recombines with CO2 to a Dewar benzene like compound (earlier blog here). The same opposition was aired by Scheschkewitz (DOI) and Alabugin et al. also in 2010 (DOI). Both opponents noted the CO2 molecule in the crystallographic data is unusually bent (111°C) something Legrand and the reviewers had apparently missed.
In their 2010 rebuttal Legrand et al. (DOI) argue that in many studies dealing with very unstable molecules the data tend to get messy and that in that respect our data are no worse than these studies, if not better. They also note that bent carbon dioxide has been observed in other systems.
In 2011 the Legrand team took a step further: they presented evidence (NMR, MS) that 1,3-dimethylcyclobutadiene (still carcerand confined) is stable in water at room temperature for several weeks and even up to 50 °C
This year Rzepa (DOI) presented more computational evidence against the Legrand model and also this year Shatruk and again Alabugin reinvestigated the original crystallographic data (DOI). Again no cyclobutadiene.

The 3 degrees of 3D printing

19 March 2013 - Tech

In a recent Nature Chemistry Michelle Francl is making a case for the good old molecular models. Increasingly in disuse with the steady progress of computer technology, Franck argues that they remain a powerful conceptual tool and we are reminded that Crick in his discovery of DNA relied heavily on physical models.

The article also mentions 3D printing of molecular models. That would present the best of both worlds and this blog's interest is generated. The internet uncovers several ventures into this area. The Scripps institute has a spin-off called the Scripps Physical Model Service dedicated to physical models. This institute also has experience in adding augmented reality for example by projecting a electron-density map on the physical model. It deals mostly with big biomolecules. The manufacturer of the 3D-printer also has a dedicated modeling page. Models are available on loan from the Center for BioMolecular Modeling. Models of simple molecules like caffeine or fullerene can apparently be purchased at shapeways. For the artistically inclined, 3D molecules can also be etched by laser in glass at commercial outlet

3D printing has also moved into nanotech. For reports in the popular press on nanoscale 3D printing not of molecules but nanostructures see here and here and here.

On an even smaller scale there is of course Leroy Cronin the man who in a recent TED promised he will eventually be able to actually print drug molecules on demand. (youtube here). If he is experimenting with SEM technology, building molecules atom by atom, he is either very patient or he owns a lot of SEM machines. Otherwise the promise is nonsensical. The TED talk was only three minutes but Cronin is not doing himself a favour by making these dubious claims. Only by browsing through his papers you can get clue what he really means: 3D printing of continuous microreactors that supplied with the right chemicals can make the drugs. Interesting concept but apparently too complex to fit into these 3 TED minutes. In the meanwhile the damage is done: hundreds of online publications are more than happy to inform you that drugs can be 3D printed.

Pd catalysed ketones from alkenes

13 March 2013 - CRD 114

Publication : Morandi / Wickens / Grubbs DOI
Substrate : internal alkene
Product: ketone
Active catalyst: Pd(MeCN)4(BF4)2
Oxidizing agent: Benzoquinone, can be replaced by oxygen balloon
Observations: DMA cosolvent suppresses isomerization, in 4-octene the cis isomer reacts faster.
Ketone synthesis Grubbs 2013.PNG

The jumping soft robot

05 March 2013 - Making it Jump I

In a spin-off to our Making-it-Move series it is now time for Making-it-Jump. Some time ago the Whitesides lab demonstrated how a soft robotic gripper can be used to lift eggs. This type of device is based on multilayered soft silicone rubber with microchannels that can be inflated and deflated by air pressure. Apparently pressurised air travels too slow so Shepherd et al. in a recent Whitesides lab contribution wondered what would happen when an explosive force is brought in. (DOI)

In a novel tripedal robot, oxygen and methane are combined in the center together with high-voltage wires for ignition. The exhaust valves are located at the extremities and each ignition results in a jump. Here are the numbers: jump height: 30 times height device. Speed: 3.6 m/s, maximum temperature increase at combustion center: 500°C after 3 ms (some plastic degradation takes place.). Some robot footage was posted on Youtube but not entirely convincing. A lot of spastic movement but not a clear jump. Not in this video anyway.

By the way: the article mentions the BostonDynamics Sand Flea as an example of technology the new jumping robot could be employed in. Now this flea can jump!