NNNS chemistry blog

CRD in trouble

16 June 2013 - Copy rights

This blog is still very much committed to the CRD (Chemical Reaction Database) project under construction, see for example the previous entry here but the project has run into trouble over legal issues so it seems. A Nature article by Richard van Noorden gives a summary of the ongoing negotiations (organised by the European Commission) between scientific researchers interested in data mining and scientific publishers or rather the lack of it. The scientists have walked out. Unsurprisingly the publishers claim copy rights even when the scientists are subscribed to every journal involved through their institutions.
One of the parties involved, the Association of European Research Libraries, have published a letter to the commissioners here. In it they stress the importance of Big Data and its exploitation and the contribution it could make to scientific discovery. The issue appears specific to Europe, In the US the Fair use doctrine applies.

Graphene, the bottom up way

15 June 2013 - Nano

Graphene can famously be produced from simple graphite and sticky tape stripping of layer after layer but that does not mean new production methods are continuously investigated. Take for example recent work from Lang Jiang et al. in JACS (DOI). They opted for a bottom-up approach starting from hexabromobenzene. The rationale: by heating a thin layer of the compound on a copper surface, all bromine will be expelled and in a series of Ullmann couplings a graphene chickenwire framework will form with potentially infinite size.
In the experimental implementation hexabromobenzene was sublimed in a furnace 120°C, then the radical intermediates were transported in a carrier gas and deposited on a copper foil kept at 250°C. In this way the production of 3 by 3 square centimetre pieces with 1 nm thickness have been reported.
In AFM mode the process could be followed in more detail: bromine is not just expelled, it first forms little bromine islands in a carbon sea. EPR spectra confirm the radical nature of the process although the evidence for a C6 hexaradical as suggested in the illustration is thin.

C2 debate erupts in Angewandte

14 June 2013 - Theo

Some time ago Shaik, Rzepa and Hoffmann (SR&H) conducted a so-called trialogue on the topic of diatomic carbon titled "One Molecule, Two Atoms, Three Views, Four Bonds?" (DOI). In it they expressed their fascination with C2 as a quadruple bonded molecule that goes against the mainstream double bonded model. They also managed to step on some toes with the predictable result that the trialogue has now received complaints.

In a letter to the Angewandte, Gernot Frenking and Markus Hermann (F&H) write they found the trialogue "more confusing than enlightening" and although they do not express a favoured model themselves they certainly do not buy into the quadrupled one (DOI). The SR&H rebuttal is also out (DOI) so let's see what is the disagreement all about.

According to SR&H the C2 molecule not only has 4 bonds, the C-C bond in C2 is also stronger than that of acetylene. Not true say F&H: the force constants can be measured experimentally and that of C2 is smaller. The Badger rule applies. To this SR&H counter that many exceptions exist to this rule and that calculated C2 force constants vary wildly depending on the degree of mixing in of excited states, something F&H again strongly oppose.

Moving on to argument number two, SR&H offered experimental evidence for the existence of the fourth bond: it's bond strength is 16.8 kcal/mole as the difference in bond dissociation energy of removing the first hydrogen atom from acetylene and then the other. What both parties agree to that this is an experimental value but if this article is the source, does it count as such? In the SR&H rebuttal "using the experimental and theoretical data (...) leads to (...) as the experimental bond energy of the 4th bond" which does not sound right. The disagreement starts when F&H argue that BDE's cannot be compared if properties of other bonds vary over the different species. If there is a stabilisation on going from the HCC radical to the CC diradical, it originates from the electronic structure of the carbon atoms themselves. In response SR&H have calculated the carbon energies as function of C-C length and found no differences.

And then there are the insults. SR&H in their trialogue state in so many words that any attempt to measure stability in molecules that cannot be stored in a bottle because of their instability, is "silly". F&H are not amused. How about astrochemists! C2 may be pretty obscure on planet Earth but is abundant in space. The point is made and in the rebuttal SR&H concede.

The Hoffmann remark on QTAIM studies is also revisited: "I have yet to see one that makes a chemical prediction, or suggests an experiment". F&H go out of their way to defend the theory and laud its utility but SR&H appear unimpressed. No apologies here.

And what are we supposed to take from all of this? One conclusion could be that the theorists are incapable on distinguishing experiment from calculation and when it comes to calculations anything can happen.

Novel use for sulfur

02 June 2013 - Acid rain cleanup

Remember acid rain? Chemists found a way to clean up the mess with the invention of hydrodesulfurization but now we are stuck with tons of elemental sulfur we do not know what to do with. The planet needs only that much sulfuric acid. Nice to know Woo Jin Chung and 17 of his best friends propose a way to get rid of this sulfur: as a new polymer material (DOI). The quick summary: elemental sulfur is mixed with 30% 1,3-diisopropenylbenzene (DIP) and heated to 180°C. This forms a copolymer with glass transition temperature 17°C. With slightly more DIP the material is soluble in non-polar solvents. GPC reveals a large degree of branching (PD = 2.7). The process is called inverse vulcanisation because in regular vulcanisation the amount of sulfur used is very small rather than very large. The chemical process is ring-opening polymerisation with S₈ diradicals. As a proof of concept the new material was created as a micropatterned film. Only thing still to find out, according to the researchers: why is the new material red?

Web-based flow chemistry experiment

01 June 2013 - Teaching

Here is a novel idea. Researchers from the Free University Amsterdam are running a website that allows students to remotely conduct an organic synthesis experiment (DOI). The experiment is based on flow chemistry in a microreactor. The reaction itself is an azo coupling of sulfanilic acid with dimethylaniline to form methyl orange.
Through a web interface the students can fiddle with temperatures and flow rates of the reagents through a labview platform and hit the start button. In the remote lab product leaving the reactor is monitored via UV-VIS. The microreactor setup limits the explosion risk and we are assured the application on a whole is idiot proof. Main objective for the students: optimise the reaction yield.

So if you are a middle school chemistry teacher and you are lacking laboratory resources or you simply do not trust your students with chemicals here is the website!