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Novel chiral Cp ligands

26 October 2012 - But coincidences do not exist

chiral cp ligands  Two fresh publications this week on the topic of chiral cyclopentadienyl ligands may be a coincidence. But tested on a very similar substrate set and published in the same journal (Science)? Something must be going on and it does not help that the one group is located in Basel and the other in Lausanne, two cities separated by a distance of only 134 kilometres.

The cyclopentadienyl (Cp) ligand is a very common ligand in catalysis but an asymmetric version is apparently problematic although they have been reported before (example here: DOI). In the Lausanne exploit (DOI) the Cp core is fused with a chiral cyclohexyl group and in the Basel work the appendage is based on biotin (DOI).

No common denominator was found, none of the groups members share a publication or a common employer. There is not even a common grant supplier. Both groups share a long tradition in the subject matter, the Basel group in all sorts of rhodium catalysed enantioselective transformations and the Lausanne group in artificial metalloenzymes and enantioselective catalysis. For both groups the invention seems almost inevitable.

Coincidently the test reaction both groups use (dihydroisoquinoline synthesis via ethylene insertion) was also independently reported by two groups in 2011, one located in Ottawa (DOI) and the other in Münster (DOI) and in the same journal (JACS). So who is the unknown puppeteer?, did the chiral Cp ligand start as a Swiss bar bet? All information volunteered to this blog will be handled confidentially or else there is Twitter.

Fun with Open Babel

04 October 2012 - The CRD

Last time on this blog's Chemical Reaction Database segment the absence of any InChi2svg tool was duly noted. But we have been looking the wrong way! Open Babel is an amazing chemical toolbox that can do lots of stuff, including (not InChi) but SMILES to svg conversion!.

Here is a quick summary of the installation procedure from the NNNS computer lab (server: x86_64 x86_64 x86_64 GNU/Linux centos Red Hat 4.1.2-48)
tar zxf openbabel-2.3.1.tar.gz
mkdir build
cd build
cmake ../openbabel-2.3.1
make
make install
whereis openbabel
openbabel: /usr/local/lib/openbabel
whereis obabel
obabel: /usr/local/bin/obabel


No complications whatsoever. This documentation gives you an overview of what is possible on the command line using the obabel tool.

For example, this command:

obabel -:"Cn1cnc2c1c(=O)n(c(=O)n2C)C" -:"n1c(c2c(nc1)ncn2)N" -ofpt
>
> Tanimoto from first mol = 0.4

gives you the similarity between caffeine and adenine as the Tanimoto coefficient.
Creating the .svg image is easy as well:

obabel -:"CN1C=NC2=C1C(=O)N(C(=O)N2C)C" -xu -O out.svg

svg image below (Firefox only):
CH 3 N N O N O N CH 3 H 3 C - OBDepict

Meanwhile in the Whitesides lab (III)

01 October 2012 - Nanotech

whitesides2012.jpgYes, it is Nobel season again and time for our annual George Whitesides plug, see earlier episodes here from 2011 and 2010. So what has his lab been up to this year?

We have already seen oil droplets traversing a liquid maze but what about a especially designed maze for air bubbles?( DOI). At each branch in a microchannel network a bubble makes a binary choice (left / right) opting for the channel with the largest volumetric flow rate of the carrier liquid. As each bubble affects the flow rate of the channel it is in, the travelling behaviour of a bunch of bubbles tends to get very complex. The project aims to simulate the behaviour of red blood cells in blood vessels or a car in inner-city traffic. Surprise: a single bubble does not necessarily travel along the shortest path.

2012 also brought a new method for separation of gold nanoparticles (DOI). Desired nanorods and undesired nanospheres have the same density and regular centrifugation of nanogold solutions would be pointless. On the other hand, in a layered multiphase system the nanorods could be isolated based on a difference in viscosity. One such multilayered system is water-based Brij35 / oxazoline polymer / ficcol. After centrifugation, simple visual inspection gives away the location of the nanorods: the brown top Brij layer.

In 2010 Maglev technology for some reason was used to accurately measure the density of various brands of peanut butter. This year the application range has been extended to forensic science. Several brands of gunpowder (Hercules Blue Dot, IMR Trail Boss) can be differentiated using maglev. Regular glitter (!?) (Alpha Jewels I, Crystalina #321) was also included in the study (DOI). So if in a future episode of one of the many CSI franchises you see somebody levitating a sample you know where the invention came form.

The Whitesides lab has a continuing interest in keeping nematode worms in a lab-on-a-chip. Latest exploit with drug-screening potential: record an electrocardiogram of the throat section as the worm is having its drug-laced dinner (DOI). It definitely chokes on antiparasitic drug Ivermectin.

The soft polymer gripper that was featured in this blog in 2011 has evolved into a creepy multigait soft robot (DOI) that looks remarkably like a headless guy in a swimsuit (MOVIE!). The device reversibly contracts by letting air in and out through microchannels. In a second evolutionary step the robot has been fitted with camouflage thanks to an outer layer with microfluidic channels (DOI). The channel pattern and also the color of the dyes can be customised for a wide range of surfaces (carpet, leaf litter , rocks). Other variations are glow-in-the-dark-robots and by controlling the temperature the robot can be stand out in the infrared or even disappear from the infrared.