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The two-datapoint plot

29 August 2010 - Statistics

Wieland rearrangement DiLAbio.jpgIt should be a thing of the past , the two-data point plot, at present occasionally observed in classroom projects or with lazy coworkers but surely not in serious research?. Yet DiLabio at el. accomplished such a feat in Angewandte Chemie (DOI). The article in question is about the Wieland radical Ph3CO. that rearranges to the Ph2C.OPh radical (see: 1,2-rearrangement for details). The two data points in the plot on the left are two experimental first-order reaction rate measurements at two different temperatures allowing the calculation of the activation energy (5.6 kcal/mol) for the rearrangement via the Arrhenius equation. The reader is spared the straight line connecting the two points but the obvious course of action would be to analyse the reaction rates at more temperatures increasing the accuracy of the end result. If there were any practical limitations to the temperature window the authors do not share it with the reader. The second set of data points - this time with an accompanying line - is based on DFT computational chemistry which is odd as well. The actual value computed is the activation energy itself (6,2 kcal/mole , energy radical vs energy spiro transition state) so instead of just 5 data points you can have as many as you like and that with a certified correlation coefficient of 1. No need for the datapoints then?


28 August 2010 - Total synthesis

Cylindrophane A Nicolaou 2010  Cylindrocyclophane F's only claim to fame would be being one of the first cyclophanes ever discovered in nature (in an algae) if it wasn't for its tumor-cell cytotoxic properties. The most recent total synthesis effort by the group of K. C. Nicolaou is all about the Ramberg-Bäcklund reaction (DOI). Chunk 1 was dimerised to the di(thioether) by coupling the thioacetate group with the mesylate group with sodium methoxide in methanol followed by oxidation to the bissulfone 2 using hydrogen peroxide and ammonium heptamolybdate. The Ramberg-Bäcklund reaction takes place next with KOH/ Al2O3 the dialkene 3, EE isomerization requiring further treatment with palladium chloride. asymmetric dihydroxylation (AD-mix) gave the tetrol and Barton-McCombie deoxygenation produced the diol 4. In the final steps methylation (mesityl chloride aluminum chloride ) and demethylation (BBr3) produced cylindrocyclophane F.

Chemical graphiti

21 August 2010 - Nanotechnology

chemical graphiti.jpgChemists occasionally fool around as graffiti artists, see an earlier episode here. Xinran Wang and Hongjie Dai (Stanford university) have been making some graffiti of their own using graphene or rather graphene nanoribbons (DOI). With regular electron beam lithography these ribbons are just too wide (20-50 nm) and outside the range for good electronic properties (sufficient band gap). Wang & Dai exposed the ribbons to a low-pressure mixture of oxygen , ammonia and argon at temperatures of up to 800°C and observed an etching process with carbon being eaten away from the edges with a typical speed of 1 nanometer per minute. In the mechanistic picture oxygen dissociates and reacts with surface carbon atoms preferably the more reactive edge carbon ones. In step two carbon monoxide or carbon dioxide dissociates removing one carbon. The addition of ammonia is designed to slow down the edging process to manageable speeds. It does so by reducing away surface bound oxygen interrupting the process.

Chemistry on the web

15 August 2010 - The blogs published an amusing letter written in 1996 by Erick M. Carreira (Caltech) to one of his postdocs complaining about the post doc's lack of commitment i.e. his refusal to work evenings and weekends in the lab in addition to his regular daytime work hours . Of course this is typically an American problem , in The Netherlands it is strictly forbidden to work evenings and weekends in a lab due to safety regulations! Also see Chembark on the right use of the words postdoc and Carreira in a sentence.

In The Pipeline discusses the apparent lack of challenges in organic chemistry: research is too incremental and too many worthless papers get written. The comments mention lack of funding for fundamental research, over-emphasis on total synthesis (serves no purpose) and organic chemists being service providers to other disciplines such as materials science. The comments are also not very kind to R.B. Woodward: meager publication record in the first 10 years of his career (not acceptable by todays standards) and wasting his time on strychnine total synthesis when he could have discovered DNA.

Henry Rzepa blogs about the recent discovery of cyclobutadiene encapsulated in a calixarene stable enough for X-ray crystallography . Rzepa wonders why this molecule does not simply recombine with carbon dioxide also trapped in the cavity. Staying in the realm of research blogging All Things Metathesis present an update on enantioselective metathesis catalysts and Totally Synthetic one on the Cortistatins.

Drug Discovery Opinion alerts us to a new tool for converting chemical names to structures and they are happy about it and Orgprep Daily alerts us to the molecular editor symyx they are not happy about because this software apparently hijacks file formats.

Silver particles, molecules, ions?

01 August 2010 - Deodorant marketing

nivea zilver moleculen3.jpgSome time last year cosmetics company Nivea introduced a deodorant based on silver technology. The antimicrobial properties of silver are well-known see for example medical uses of silver so the idea has merit. But what kind of silver is Nivea actually using?

In the Nivea ads (see pic top) the deodorant bottle is invariably accompanied by what looks like shiny silver-colored polymers or clusters (?) One possibility is that is silver is in the form of colloidal silver as in silver nanoparticles. Yet the ads of a year ago speak of silver molecules (...) not particles. Of course in Europe anything to do with nanotechnology is suspect just like genetic engineering so the Nivea marketing people could have opted for the innocent sounding molecule over the ominous sounding nanoparticle. The Nivea website even assures the consumer that its silver technology should not be confused with nanotechnology.

In any event, in a brand new advertising campaign launched June 2010 the molecules have been replaced by ions! (see pic bottom) From now on not silver molecules but silver ions battle it out with the bacteria. The bottle states silver citrate as the silver ingredient (a salt) so it appears that in this respect the marketing people have come to their senses. The funny looking silvery molecule issue remains to be solved.