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Organicus liquor regius

24 October 2010 - Physicial organic chemistry

Aqua regia is an inorganic mixture of nitric acid and hydrochloric acid well known to dissolve noble metals like gold. A group of researchers from the Georgia Institute of Technology have now come up with an organic solvent - a mixture of pyridine and thionyl chloride that also dissolves gold, palladium and silver but not platinum (Lin et al. DOI). A typical dissolution rate is 0.3 mol/m2/hr. The authors call their own invention of unprecedented scientific significance and kindly suggest a name for the new solvent: Organicus liquor regius.

As with aqua regia, to state that the metal is dissolved is misleading, rather gold is oxidized to the Au(III)Cl4- ion. Thionyl chloride itself is unable to do this but the charge-transfer complex with pyridine can. The researchers struggle to identify the counterion. They do find 4-chloropyridine and then pyridine oligomers which also explains the viscosity increase but no experimental evidence for reduced sulfur. Only tucked away in the supporting information, a plausible almost-balanced equation is presented.

Dry solvent myths

19 October 2010 - In the laboratory

It is one of these chores in the organic chemistry laboratory: drying wet solvents. Now do not say solvents are supposed to be wet, chemists simply want to dry out the water present in the solvent because it interferes with whatever they intend to do with it. Williams and Lawson Lawton (University of Johannesburg) required some really dry solvents and decided to compare some trusted drying procedures with the aid of advanced calorimetric coulometric Karl Fischer titration (DOI).

THF (107 ppm water) is typically dried (to 43 ppm) using sodium wire and benzophenone (cumbersome and procedure not without danger, see ketyl) but chemists may be pleasantly surprised to learn that storage of THF with 20% by weight molecular sieves for three days is much better (4 ppm). As an alternative silica is disappointing but passing THF over a column of neutral alumina again gets you to 5 ppm and much quicker. Molsieves also beat conventional techniques for drying toluene dichloromethane acetonitrile or methanol. Sounds too much like a molsieve add? The paper was co-funded by industry but at first glance none of them is selling it.

Update: reader P. informs us it should be coulometric not calorimetric titration. So noted!
Update: Author name is not Lawson but Lawton (25 March 2014)

Chemistry teachers discover Wikipedia

18 October 2010 - About time

klik hier voor de afbeelding op ware grootteIn the November issue of the Journal of Chemical Education May et al. of the University of Michigan report on their experiences with a classroom project aimed at improving Wikipedia (DOI). Students were given topics with instructions and started or expanded the corresponding Wikipedia articles. Examples are asymmetric induction (see before and after ) and fire-safe polymers. Overall their experiences were positive. Luckily the article did not complain about the grumpy old men (myself included) that patrol the chemistry pages and demand that newbies publish proper licences with their images or include DOI's with their references.
Notable observation: the students are more motivated and critical in writing for wikipedia because the result is publicly visible and for eternity.

Helpful links:
Wikipedia:School and university projects
Wikipedia talk:WikiProject Chemistry

Newman-Kwart update

15 October 2010 - Mechanistically speaking

In a previous episode of this blog the Newman-Kwart rearrangement was introduced as the thermal conversion of a O-aryl N,N-dialkyl thiocarbamate to S-aryl N,N-dialkyl thiocarbamate. This reaction is known to proceed through the oxathietane intermediate A in a unimolecular reaction. In 2008 however Gilday (DOI) observed reaction rate increase with reaction concentration increase and subsequently proposed a partial bimolecular reaction though cyclic intermediate B. Recently Burns et al. stepped in to re-investigate and now reassure us it is A after all (DOI). The confusion is all about the difficulty of accurately measuring reaction rates of high temperature reactions. In contrast to the Gilday study , the Burns study did not find any variation of reaction rate with concentration. It did however notice peculiar cooling effects: a high reaction concentration involves less total reaction volume in the reaction tube leading to better exposure to the oil bath and less susceptible to cooling from the environment. Apparently the extent of fume hood sash opening already makes a difference.

When the reaction mode is changed to microwave irradiation the Gilday study and the Burns study are in agreement (conversion increase with concentration) but again the devil is in the details. Burns notes that in a typical microwave experimental setup the temperature fluctuates around the set temperature. But as a higher concentrated medium (solvent is dimethylformamide) has a higher relative permittivity energy transfer is more efficient (larger Loss tangent) leading to oscillatory overheating and an apparent higher reaction rate. So who it right? Some of the Gilday team already no longer need to be convinced: Jonathan D. Moseley is co-author in both studies.
Newman kwart burns 2010

Nobel Prize in Chemistry 2010

07 October 2010 - News

2010 has been a good Nobel Prize year for chemists with three solid organic chemists in the chemistry section Richard F. Heck, Ei-ichi Negishi and Akira Suzuki and two material scientists Andre Geim and Konstantin Novoselov in the physics section. The relevant Wikipedia pages have been prepared well in advance: the Heck reaction, Negishi reaction and the Suzuki reaction are all coupling reactions. Also see the very lengthy graphene article.

Congratulations are registered from totallysynthetic, In The Pipeline, everydayscientist and Lamentations on Chemistry. Chemjobber notes that a Nobel Prize for coupling reactions has long been awaited but that it took this long because of the three-limit rule. Contributions to the field have been made by many but if you wait long enough only three of them are left. Not entirely true, of the reactions listed on the coupling reaction page 4 inventors are very much alive and as of this week in a foul mood. Perhaps as a consolation for one of them, everydayscientist reported that in a recent episode of the Simpsons, Lisa Simpson predicted as a winner Kenkichi Sonogashira of Sonogashira reaction fame.

Speaking of predictive powers, in the h-index alluded to in a previous blog the only newly appointed Nobel winner listed is Negishi at position 379 (!) out of 550 entries. For comparison Buchwald (Buchwald-Hartwig amination) holds position 41 and Trost (allylic asymmetric substitution) number 18 with related reactions based on palladium. The Thompson list turned out equally non-predictive. The journal Chemical & Engineering News on the other hand appears to have a good nose for news. In May of this year their blog started a search for Richard Heck who had apparently disappeared from the radar but was tracked down in the Philippines. Chembark in his prediction had positioned Suzuki/Heck/Sonogashira/Tsuji (not Negishi) at number three.

More on coupling reactions in this blog: Palladium_cycle_in_Suzuki_reaction_made_visible, a Negishi coupling in action, Copper-free_Sonogashira_coupling and the Gold-catalysed_Sonogashira reaction

More on graphene-related blogs: Nanotubes_unzipped, Invisible Ink and Chemical_graphiti

Meanwhile in the Whitesides lab

01 October 2010 - Multidisciplinary research

Whitesides peanutbutter research 2010.jpgWith George M. Whitesides leading the h-index for chemists and the count-down to NPIC day underway, lets find out what is going on in his Harvard lab these days. It is all about miniaturization.

The stretchable antenna (Kubo, Li 2010 DOI) can be used in wearable technology and in biomedical engineering because it can be applied to any nonplanar surface. Made from a liquid metal (a gallium / indium alloy, see Galinstan) and encased in elastomeric microfluidic channels it can stretch to more than twice its original length, a new record in this particular field. The trick: use two not just one type of PDMS elastomer with variation in stiffness.

In infochemistry alphanumerical information is transmitted by chemistry (Kim et al. 2010 DOI). In one manifestation called the infofuse, a strip of nitrocellulose is ignited and as the flame-front moves forward with a speed of 3 centimeter per second it encounters metal-salt containing spots in an information pattern. By using 4 different metals, 7 distinct optical pulses are created. Problem to solve: slow down flame-front speed to allow uninterrupted 24-hour transmission of information. Solution: create a slowfuse pattern connecting information-carrying fastfuse strands. Implementation: apply slow match technology (invented 15th century), a cigarette will also do.

Wax printing is proposed as an inexpensive way to produce microfluidic patterns (channels & reservoirs) in a paper-based analytical device (PAD) based on a commercial printer , wax of course and a hot plate. The printer delivers the wax on a paper sheet and the hot plate melts the wax into the paper forming hydrophobic barriers. The aim is zero-cost medical diagnostics for for example the measurement of glucose and cholesterol levels. Another example is ELISA testing with again paper now replacing a regular microtiter plate (Cheng et al. DOI). HIV antibody test results can be scanned and quantisised using a cheap scanner or cell phone.

The Whitesides lab has also tackled the critical issue of measuring reduced-fat content in peanut butter. Mirica et al. (DOI) did so by measuring peanut butter density by magnetic levitation , a technique ordinarily used to suspend trains or lab animals. Skippy's reduced fat peanut butter clearly stands out from the regular one.

Moving on from the unusual to the bizarre: how about confining the miniature worm C. elegans (length: 1 mm) to a lab-on-a-chip (Hulme et al. DOI). The chip houses 16 worms, each in their individual chamber with a channel for delivering a constant supply of food (E. Coli) and a channel for removal of bacterial waste and progeny and for clamping down the worm. Compared to the old-fashioned petri-dish, the chip allows the continuous monitoring (a microscope) of a single worm throughout its lifetime inside its chamber. The worms live for about 9 days. The main conclusions: the longer it takes for the worm to grow to maximum volume the longer it will live and the longer the worm is able to swim above a certain stroke frequency the longer it will live. Main cause of death after the 9 days: eggs hatching inside the worm instead outside of the worm (not-so intelligent design).

More fun with Whitesides in the making it move blog.

Watch George Whitesides at TED@youtube and what exactly is simplicity?.