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A tale of three xylenes

27 April 2012 - General chemisty

And why would you try to separate the xylenes? The boiling points of the three isomers are separated by just 6°C so distillation is not an option unless you carry a lot of plates. Lusi & Barbour venture ahead anyway (DOI) and draw inspiration from an 50 year article on xylene separation by clathration (DOI). Key is a so-called Werner complex based on octahedral nickel with 4 phenylpyridine and two isothiocyanate ligands. This compound forms an host-guest compound with each of the xylenes and what matters to Lusi & Barbour is how selective this process is. When a xylene vapor is exposed to the nickel compound, the ortho isomer gets caught first (o/m=34.2, o/p=40.5). With this isomer out of the way meta is then preferred over para (m/p= 12.7). Interestingly the trend in thermal stability and sorption kinetics for the isolated compounds display the opposite trend. With respect to guest-accessible volume the trend is meta < para < ortho. The next quote is noteworthy: in the selectivity trends in terms of packing interactions, any such evaluation would be merely speculative; we recognize that many subtle factors may influence selectivity and that any simplistic approach based on comparing densities, interactions, and so on would be inadequate in providing a holistic explanation for the observed trend in guest preferences.
And why again would you try to separate the xylenes? Pure meta-xylene is used as an anti-knocking agent in gasoline. Big business assured.

Ester amidation the sodium methoxide way

22 April 2012 - Orgo

amidation of ester Ohshima 2012  Amides are important in organic chemistry but their synthesis involves more than a simple reaction between a carboxylic acid and an amine due to the unfavourable chemical equilibrium. In a variation called the Schotten-Baumann reaction the acid is activated as an acid chloride. You will not find esters in any list of amide precursors but a report by Ohshima et al. suggests esters and amines can react directly although with an unlikely catalyst: sodium methoxide ( DOI).
In one exploit the reagents are methyl benzoate and benzylamine and in dioxane the yield with just 5% NaOMe is 90%. The only catch is that the protocol requires absolute exclusion of water because otherwise the only thing that happens is ester saponification. Other bases that work are sodium tert-butoxide and NaHMDS. Bases that do not work are lithium tert-butoxide or lithium bis(trimethylsilyl)amide

Whats new in fingerprinting

20 April 2012 - CSI Norwich

So what is new in fingerprinting? Hazarika and Russel bring you up to speed in a Angewandte mini review (DOI). We have already seen in a previous episode of this blog how fingerprints can reveal the owners smoking or chewing gum habits with the use of coated gold nanoparticles.
In a similar vein magnetic particles coated with the right antibodies not only reveal the fingerprint pattern but by a specific colouration (amplified by fluorescence) also cannabis, cocaine or heroin use. Quantum dots QD's apparently have superior luminescence making them popular in fingerprint visualization. CeTe QD's have been shown to uncover a print left from a bloody finger.
With its ever increasing detection capabilities, liquid chromatography-mass spectrometry (LC-MS) is also making modest contributions to the field. The detection of methadone and lorazepam has been demonstrated in a laboratory setting.
And why stop there, if you have the funds you can equip your forensics lab with a SALDI/MS or desorption electrospray ionization/MS unit. On the other hand all these techniques basically destroy the evidence so moving on to non-invasive methods ATR infrared spectroscopy is also capable of images fingerprints. In one demonstration it was possible to detect particles of explosive residue in between the ridges.
But why all this focus on drugs and explosives? In many advanced societies (one this blog pretends to live in) there are bigger worries than drug abuse or terrorism, like say theft, robbery and random violence. You may want to focus instead on the detection of pharmaceuticals in general or legal vices such as the nicotine already mentioned or alcohol. That would be more helpful in preselecting the suspects.

Breslow on homochirality

15 April 2012 - Never mind the dinosaurs

Ronald Breslow has been taking some flack from the bloggosphere (here,here,here) not to mention twitter, for him mentioning dinosaurs in his JACS article on homochirality (DOI). Apparently dinosaurs sell. According to Breslow somewhere in the universe a planet exists inhabited by a life form with reversed stereochemistry but Breslow should have written that it could well be an advanced breed of grumpy bloggists and not dino's. A more serious offence according to the twitter mob is that Breslow in 2010 published a very similar article in Tetrahedron Letters but since we are boycotting Elsevier publications in this blog we are going to be lenient on this one. Never mind the dinosaurs or self-plagiarism, what point is Breslow trying to make? Here is the quick summary.
Starting point is the well-known Murchison meteorite which famously contains a collection of 5 alpha methyl amino acids enriched in the S enantiomer. Interstellar space has all the building blocks to make amino acids (ammonia, ketones, acetylenes etc.) and when concentrated on a meteorite the Strecker reaction could do the trick. Enantiomeric enrichment then could result from selective destruction of one enantiomer by circularly polarized light. The astronomers still argue what type of star could generate this type of radiation (neutron star? dwarf?) and with what energy.
In phase two, having arrived on planet earth the amino acid passengers disembark the meteorite and start an ambitious program of chirality transfer (make new chiral molecules) and chiral amplification (increasing enantiomeric excess).
With respect to the first objective Breslow explains his group has already demonstrated it is possible to remove the methyl group from an amino acid with some preservation of chirality by simply exposing it to an alpha keto-acid with a copper salt as catalyst. D-sugars such as ribose can be synthesised from formaldehyde in the Formose reaction and an intermediate step to glyceraldehyde catalysed by chiral amino acids is enantioselective.
With respect to amplification Breslow mentions that when amino acid solutions containing a small excess of one enantiomer are concentrated, racemic crystals form more easily than homochiral crystals and are thus removed from the system. Same story with glyceraldehyde where the racemic crystalline form has poor water solubility. Ribose on its own does not do this trick but when combined with a purine to a uridine (en route to RNA) again the racemic crystals stand out.
Is this a solid theory for the origin of homochirality? No, Breslow is quick to point out the theory is plausible at best but the hunt is on for the remaining missing links.

Definition organocatalyst corrupted

08 April 2012 - Catalysis

asymmetric alkylation Xiao 2012  Jian Xiao does not get it. If you take an organocatalyst and combine it with a metal it no longer acts as an organocatalyst. It is just an organic co-catalyst. Look up the definition of an organocatalyst. The concept of merging organocatalysis with transition metal catalysis is silly. Unfortunately Xiao is not alone in his delusion. A quick literature scan reveals a bunch of cooperative organocatalytic/metal catalysis research by various groups (examples: DOI, DOI) notably that of McMillan who introduced the concept of cooperative catalysis in the first place (example DOI).
The Xiao publication in Organic Letters (DOI) deals with the enantioselective alpha-alkylation of aldehydes with a masked carbocation, a theme visited by researchers on many occasions since 2007. In this variation the aldehyde is propanal or butanal and the masked carbocation for example xanthydrol is activated by Lewis acid copper(I) chloride. The aldehyde is activated by a chiral secondary amine forming the enamine and is also the chiral auxiliary. This reaction is enantioselective allright but it comes at a price: the amine is huge (bad atom economy) and in contemporary chemistry, a metal loading of 20% is no longer considered catalysis. On the upside substrate scope is definitely extended.

The stomatocyte rocket

05 April 2012 - Making It move VIII

stomatocytes wilson 2012.gifThis blog by now has a fishtank full of autonomous moving chemical entities (see making-it-move part VII) and the latest creature making the splash has been designed by Wilson/Nolte/van Hest as reported in Nature Chemistry (DOI). It is all about a polymersome which is a hollow vesicle in the micron range with a membrane made from an amphiphilic synthetic block copolymer, usually investigated as a drug delivery agent. WNvH envisioned a polymersome rocket with a little opening allowing the entry of hydrogen peroxide as the fuel and filled with a platinum nanoparticle (PtNP) as the motor. The thrust is then provided by the catalytic conversion of hydrogen peroxide to water and oxygen which escapes as bubbles from the vesicle gap as the nozzle . But how to make one of those vesicles and how to trap Pt particles inside them?
A blockcopolymer composed of polystyrene and polyethylene glycol (PE(44)-PS(177)-PE(44)) was dissolved in THF/dioxane, then water was added and then the solution was dialysed against water. As water is pushed into the system the polymer strands self-organise into sheets which then fold first into bowls and and then into vesicles.
A solution of PVP capped PtNP was added as well. By a process of endocytosis these particles are trapped into the vesicle: a stomatocyte. Experimental control was tricky: the polystyrene content controls the folding of the vesicle, the THF content controls the final gap left open (80% leaves a 5 nm gap while 90% seals everything up) and the nanoparticle size controls the number of particles trapped. At 80 nanometers it is just one.
With the aid of a CCD camera it was then possible to track the stomatocyte movements. Without adding any fuel all that was observed is regular Brownian motion but with adding of hydrogen peroxide true to the intended design the stomatocytes turned into little rockets and both the speed increased as well as the the mean-square displacement.

The perfect samarium iodide recipe

01 April 2012 - Mythbusters

Szostak, Spain & Proctor have seriously investigated (11 JORG pages!) several procedures for the synthesis of samarium iodide, an important reagent in organic chemistry (DOI). A traditional method is reaction of 2-fold excess samarium metal with diiodoethane or iodine in THF with stringent exclusion of water and air in a Schlenk line. Prepare for some convictions smashed.
The onset of a blue colour is not really indicative of the completion of the reaction: it is not possible to distinguish a 0.005 from a 0.1 molar solution. The presence of water does not affect the overall yield of the reaction although it correlates with the induction time ranging from 10 minutes to up to 2 hours during which water eats away at the samarium metal. This is a time-saver for the front-line bench chemist. As surprise number two, against all conventional lore the reaction does not even suffer from the presence of oxygen. So get rid of that Schlenk line and quit degassing all the time! The only precaution that still makes sense is excluding oxygen from the finished product in storage because Sm(II) is easily oxidized to Sm(III). Ditto the peroxide content of THF was found to be irrelevant.
And then there is unusual case of the inactive batches of samarium metal that have plagued chemists for the past 30 years. Typically attributed to the formation of an oxide layer Szostak, Spain & Proctor did not find the corresponding evidence. The true explanation remains shrouded in mystery but at least an inactive batch can now be identified by measurement of its density. Again in the true spirit of alchemy an inactive batch can be activated by dry-rolling samarium in an inert atmosphere followed by oxidation with iodine but not with diiodoethane. Equally intriguing: the shelf-live of SmI2 derived from iodine is much shorter than that derived from diiodoethane.