all blogs

Wikibooks: Functional groups

31 March 2010 - Wikipedia curation project

In the third part of our wikibook chemistry curation project again hundreds of Wikipedia editors have contributed to bring you the ultimate wikibook this time on functional groups. To keep it simple the 30 or so of the most important functional groups (amines, alcohols, alkenes) are listed alphabetically. Topics covered: nomenclature, properties and reactivity.

Open here: Wikibooks/Isomerism.pdf (8.5 MB, 120 pages)
Open here: Wikibooks/Organic_Reactions.pdf (10 MB, 184 pages)
Open here: Wikibooks/Functional_groups.pdf (12 MB, 167 pages)


Chemical molecular gastronomy

30 March 2010 -A review reviewed

When a chemist and a cook get together you get molecular gastronomy (MG) but thus far the cooks have brought the bulk into the marriage. A recent UK/SA/Danish Chemical Reviews addition (public access!) should bring in the chemist's perspective. MG: the scientific study of why some food tastes terrible, some is mediocre, some good, and occasionally some absolutely delicious (DOI). At the onset the reviewers are critical: MG contains little new science and little work has appeared in the scientific literature.

A collection of under appreciated facts: stressing the importance of texture, only 40% of blindfolded test subjects can identify food when blended, dairy products should be served at 14°C on account of molecules getting airborne. Organically grown vegetables do not taste different from regular ones. You can use olive oil for frying but not walnut oil because its degree of unsaturation makes it sensitive to oxidation. The secret for making a good broth is to start from cold water (soluble proteins aggregate in large particles that sink), with the lid off (cooling effect prevents boiling) at the optimum temperature of 85°C, among the chemicals present in a good broth are creatine and GMP. Fudge is a 6-phase material with crystalline sugar, aqueous sugar solution, air, liquid fat, crystalline fat and cocoa solids. A gel (boiled egg, gelatine) is a liquid trapped in a polymer network. Spherification (an El Bulli invention ) uses sodium alginate and calcium chloride to turn any beverage into caviar-like beads. Marinating tenderizes meat, a chemical process often done with acids such as vinegar or lemon juice. But why not think out of the box: alkaline marination (unknown in the west but part of Indian cuisine) can take place by injecting sodium bicarbonate solution in the meat which does the job as well.

The reviewers distinguish MG from food science that they argue deals more with industrial food production. But is the review really about MG? At least a big part of it. MG should be about creating high-quality food and the question why highest-quality foods are perceived as such and the of course science behind it. The classic example of the slow-cooked roast is the perfect example. That you can adulterate meat and fish with nitrates or carbon monoxide makes great reading but is the domain of food science not MG. As acknowledged by the review authors, two important instigators of MG Ferran Adrià and Heston Blumenthal have already abandoned the MG concept. In an open letter in 2008 they emphasize innovation in cooking. Science gets zero mentions.

FLP chemistry update

21 March 2010 - Part V

In our continuing coverage of frustrated Lewis pairs or FLP's (see part I , part II , part III and part IV) a brief update. Miller et al. have successfully dehydrocoupled amine-boranes using a phosphine - borane system (DOI). Formation of a polyaminoborane proceeds through the R2N=BH2 monomer. Although technically it is a three-component reaction the phosphine has to be added first.



Schultz et al. did the reverse , taking a TMS protected amine R2NTMS which in the presence of B(C6F5)3 reverts to the amine R2NH and the silyl hydride TMS-H (DOI) More FLP mediated cleavage has been found by Dureen et al. of the Stephan lab with the disulfide PhSSPh (DOI) in reaction with tBu2P(C6F4)B(C6F5)2

In earlier work in 2009 Dureen and Stephan activated terminal alkynes with B(C6F5)3 and phosphines DOI ) and recently Geier et al. tried out phosphorus dimers , cyclic tetramers and pentamers to form novel zwitterions ( DOI) . Jiang et al. also cleaved the C-H bond of a terminal alkene (DOI) but this time with amines instead of phosphines. In the reaction of acetylene, B(C6F5)3 and TMP, the first intermediate is attacked by a second borane unit and one of the C6F5 units shifts a bond (something similar occurs in FLP carbon dioxide reduction).


We are already used to FLP mediated hydrogenations: Schwendemann et al. hydrogenated complex organometallic dienamines (DOI). A new frustrated pair was presented by Stepowska et al. who split hydrogen with a Ru(II) - carbanionic zwitterion DOI)

On the computational / mechanistic front Grimme et al. (DOI) responded to a reaction mechanism proposed by Imre Pápai in 2008 that has a linear P--H--H--B unit in the transition state. Not true says Grimme, the bottleneck in the reaction is the entrance of the dihydrogen molecule (not at all dissociated in the TS) into the FLP interior and once the H2 molecule is within the FLP, the dissociation is practically barrierless.

Sue you in court

14 March 2010 - Patent wars

Chemical company Eastman announced on its website they won a court case (link). against competitor Wellman over patents related to high clarity and high purity PET resins that can be used for the production of PET bottles. The embattled Wellman patents are numbered 7094863 and 7129317 ,date from May and November 2004 (filed) to 2006 (granted) and are now now made obsolete. They deal with a variety of PET that crystallises at a lower temperature and regular PET. In the final stage of PET bottle production a so-called preform (a small test tube shaped container) is reheated to a temperature just above the glass-transition and blow molded to its final dimensions. Slower crystallizing PET means lower processing temperatures without loosing clarity (= crystallisation). The patents also specify how this was done: replacing expensive antimony or germanium catalysts by catalysts based on titanium such as tetrabutyltitanate, titanium being a poor nucleator in crystallisation .Titanium can cause yellowing of the resin but the patents also specify the addition of cobalt which in addition to being a catalyst itself has a native blue color cancelling out the titanium-yellow.

A similar Eastman patent number 7300967 (filed November 12, 2004 granted November 27, 2007) also deals with titanium for improved reheat & clarity but for an entirely different reason: the preforms are reheated with infrared lamps and metallic titanium particles (not titanium catalysts) increases heat absorption in the infrared without affecting color.

Eastman in turn is suing Indorama (Link Link) and DAK LCC (Link Link) for unauthorized use of its IntegRex PET (introduced 2007). Just one of the patents covering this technology is number 5597891 (filed in 1995) and one key aspect is the elimination of so-called solid-stating (Link). In this process PET of intermediate melt viscosity is post-polymerized in the solid state (high vacuum, high temperature, batch or continuous, for many hours and therefore expensive!) to a high viscosity quality that can be used in bottle manufacture. Incidentally the process also removes any acetaldehyde in the resin that can negatively affect the flavor of any liquid in PET bottles produced from it. The trick as described in the patent is to remove volatiles during the extrusion phase. The Indorama and DAK cases are interesting because Eastman sold some of its (outdated?) PET business to each party in 2007.

Do we need plastic heroes?

09 March 2010 - Recycling

In addition to the separate collection of paper waste, organic waste, glass and PET bottles, households in The Netherlands this year have started with the separate collection of plastics waste whether they like it or not. In the best traditions of polderen, the Dutch Ministry responsible for the environment VROM, the Dutch municipalities united in the VNG and the Dutch packaging industry united in the non-profit organisation Nedvang joined forces in plastic recycling and tasked Nedvang with the collection process. An orange guy called plastic hero featured in several commercials (youtube vid here) to introduce the concept to the citizens and recycling could commence.

Ignoring for now that the mandatory bags Nedvang hands out by the millions to collect the plastic waste in are made of plastic and non-recycled plastic at that, and ignoring that these bags are transparent (collection is by the curb side, lets find out what the neighbors were having for dinner last night) , the question is if the environment is going to profit at all. Several municipalities resist the scheme and create solutions of their own. One group experiments with and are confident with the extraction of plastics waste from general garbage at the garbage collecting plant. The cities of Amsterdam and Rotterdam prefer incineration. To them plastics are masked hydrocarbons and their state-of-the-art garbage incineration plants are able to return up to 30% of the energy content of the waste as electricity compared to the 20% average.

And what to do with all this plastics waste. The commercials are misleading when they speak of re-use as dashboards in cars or as computer mouse because these are high-end applications involving very specific plastics with narrow specifications. Typically recycled plastic winds up in more mundane products as soap containers, carpets and strapping. And you can only sell that much fleece jackets. And the contracts signed by the waste processors are not exactly ironclad: they commit themselves to material reuse of sorted plastic fractions or other useful applications (Uitvoerings- en monitoringprotocol 2009 nedvang website ). Hey, one of these other useful apps would not be selling the waste as high-energy feedstock to power plants?

Organic superconductor at 17 K

05 March 2010 - Chemical physics

Matsuhashi et al. describe superconductivity up to 17 Kelvin in picene doped with potassium (DOI). Organic superconductors are known for example the intercalated fullerene RbCs2C60 at 33 K and graphite intercalation compound KC6 at 11 K but not every alkali-metal/hydrocarbon mix is a winner. For comparison alkali-metal doped pentacene and Cs3C60 have thus far failed to produce the effect.

A new synthetic method allowed the production of picene - closely related to pentacene - at gram scale and black K3picene was obtained by heating it with potassium at 400 K in a glass tube as a black powder. Not its conductivity was measured but rather the magnetic susceptibility which also shows a first order transition at the transition temperature. At the molecular orbital level superconductivity results from electron donation of the alkali metal HOMO to the picene LUMO forming the charge carriers with maximum effect at 50% capacity. The key property for picene appears to be the presence of a LUMO+1 very close to the energy of the LUMO itself creating an almost double degenerate state very similar to the triply degenerate LUMO found for fullerene.
Organic superconductor MitsuHashi 2010

On the web in 2010

03 March 2010 - Blogroll

On the web in 2010: the Carbon Based Curiosities have been just as perplexed about one particular solution to carbon dioxide sequestration as this blog and did the math. Org Prep Daily brings you a Fisher indole synthesis and staying on the indole theme the Organosynthetic & Organometallic Chemistry website is alkylating tryptamine. Free advice from Curlyarrow on catalytic hydrogenation and more free advice from Round Bottom Flask on HPLC.

Totally Synthetic explains Communesin F, Henry Rzepa questions the validity of the quintuple bond (truly quintuple?) and Steven Bachrach shows how Dewar benzene is stable against the odds. In cheminformatics Depth First explains how to create a PubChem mirror. (how about a Wikipedia mirror tool!) and Metamolecular has a bit on Chempedia (the novel open chemical substance registry) on Twitter. In the Pipeline has a delightful blog on FOOF and why to stay away from it. Nanoscale views asks the question why claims of priory are occasionally found in scientific literature, are the editors paying attention?. This blog feels it is the world turned upside down: A claim should be mandatory!. Too often a scientist reports a chemical procedure using this or that method with this or that substrate using a particular set of conditions and monitored using that type of equipment keeping in the dark if the procedure, method, substrate, condition or monitoring device is new. It facilitates second-rate research and relieves editors from the burden of doing actual editorial work (that regrettably is a win:win). But the journal Physical Review A in question actually forbids the use of words like new or novel because all material accepted for publication (...) is expected to contain new results in physics anyway.

Chirik & Wieghardt on radical ligands

01 March 2010 - Catalysis

In an earlier blog several main-group elements were given transition metal powers and in an extension Chirik and Wieghardt upgrade base metals iron and copper to noble metals in a recent journal Science perspective (DOI).

Noble metals such as platinum are effective catalysts because they can switch reversibly between oxidation state zero and two. Redox activity in metals like iron on the other hand are 1 electron events with less appeal to organic chemistry. That so-called non-innocent ligands can alter the oxidation state of the central metal is well established but the key point made by Chirik & Wieghardt is that ligands (as radicals) can also assist metals in redox activity. As always nature provides inspiration: in the two-electron oxidation of an alcohol to an aldehyde by galactose oxidase , its copper atom gives up just one electron and the other is provided by the tyrosine ligand which in the active state is a free radical. In other scenarios the ligands change the oxidation state of the metal and it is even possible for the ligand to do al the redox action.

Some random examples: hydrazine oxidation (Blackmore et al. 2008 DOI) , manganese(IV)-monoradical complex (Mukherjee et al. 2009 DOI) , dihydrogen oxidation (Ringenberg et al. 2008 DOI)