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Impossible questions

22 September 2010 - Chemical philosophy

Here is an interesting notion voiced by Fredric M. Menger in Nature Chemistry (DOI): there are questions in chemistry that are impossible to answer. This type of question does not belong to one on the list of unsolved problems in chemistry for example the origin of chirality but ranks among impossible questions found in other branches of science such as the Heisenberg uncertainty principle or Gödel's incompleteness theorems.

Menger sets out to prove his point with an example involving a poly(allylamine). This polymer (DP 1000) can be used as a catalyst in the hydrolysis of certain phosphodiesters. Catalytic activity shows a large variation depending on how the polymer chain is functionalized with carboxylic acids groups with respect to degree and type. Only the average catalytic activity can be measured but it may well be that only 1% or even 0.01% of the polymer chains generate the bulk of it. Addressing all 1016 individual chains in a given sample is of course not an option.
But is this truly a case of fundamental uncertainty in chemistry? In biochemistry the protein folding problem is all about the prediction of the three-dimensional structures of proteins and enzymes and strategies to tackle this problem. DNA enzymes can be synthesized by sequencing to precise specifications. It is just that compared to biomolecules the particular polyallylamine adds additional complexity.
A more viable impossible question that is briefly touched upon in the Menger article is the uncertainty encountered in molecular dynamics: one can never be certain a given structure is located on the global minimum of the energy surface. In chemistry we can be certain that there is always a possibility that a sinkhole lurks somewhere in the vicinity.

Nobel Prize in Chemistry 2010 predictions

18 September 2010 - The crystal ball

It is Nobel time again (October 6) and for the Nobel Prize in Chemistry 2010 prediction we can just rerun the contestants from 2008 and 2009, check their health and scrap the ones who have already won (although there is no law preventing someone winning twice).

That leaves us with Charles Lieber (Nanotechnology), George M. Whitesides (Nanotech, supramolecular chemistry), James Fraser Stoddart (supramolecular chemistry), Krzysztof Matyjaszewski (Atom Transfer Radical Polymerization) , Michaël Grätzel (dye-sensitized solar cell) and Benjamin List (organocatalysis). For Jacqueline Barton Bernd Giese & Gary Schuster also see DNA electron transfer in 30 seconds.

If the h-index is any measure the number one on the 2010 list as published on the Royal Society website is again Whitesides followed by the theoretical chemist Martin Karplus (involved for example in molecular dynamics of biomolecules) and physical chemist Ad Bax involved in protein NMR. Also on the list organic physical chemist Paul von Ragué Schleyer (computational chemistry) and a familiar sight on this blog , see for example the New Ruling On Stability blog and the protobranching blog.

Summing up in terms of clusters the potential winners are Barton/Giese/schuster (DNA electron transfer), Lieber/Whitesides/Stoddard (nanotech advance) and Karplus/Bax (biomolecular structure elucidation). More 2010 predictions in the bloggosphere: by chembark and by Everyday Scientist.

Update 23-09: Thomson predictions are in

Also see: the 2011 predictions

Also see: Meanwhile_in_the_Whitesides_lab

Name that molecule

16 September 2010 - Marketing

klik hier voor de afbeelding op ware grootteThe Sigma-Aldrich company on its website is showing an add for their new Chem Files product. But is the molecule depicted deliberately not supposed to exist? Black usually is carbon, blue is nitrogen and red is oxygen. The central oxygen atom with 4 neighbors is problematic. A substructure search confirmed the company does not sell it.

Also see Previous marketing blog

Building blocks

12 September 2010 - Orgchem

Building blocks Denisenko 2010  In organic chemistry a lot of research effort is spent in creating small easy to make molecules for the sole purpose of creating larger molecules. Chemical libraries are filled this way that can eventually lead to new drugs.
As a representative of the kind of research it involves Denisenko et al. in Organic Letters (DOI) published the synthesis of a fairly small C7H11NO compound thus far overlooked. The reactants are commercially available cyclobutanone 1 and not so commercially available N,N-bis(methoxymethyl)benzylamine 2 in a double Mannich reaction with reagent trimethylsilylchloride. In the second step TFA converts the ketal group in 3 to the ketone 4.

The exact same procedure but with other cyclic ketones was already pioneered by McLeod in 2006 (DOI). The accompanying patent covers a large batch of cyclic ketones but for some reason not the C4 ones , an omission Denisenko has now successfully exploited.

Chemists embrace nuclear energy

10 September 2010 - Well, at least two of them

Uranium nitride (UN)x is an alternative nuclear fuel that outsmarts competing uranium trioxide because of higher melting point and better thermal conductivity. And where ever two elements combine (uranium and nitrogen), chemists are just around the corner. Thompson at al. of the Los Alamos National Laboratory (where else) looked at ways to generate a terminal uranium nitride (RUN, transient or not) and its fate (DOI). Compound 1 is a compound of uranium with two pentamethylcyclopentadienyl ligands and a diisopropylamide ligand. It can be oxidized by the gold azide Ph3PAu(N3) to uranium(IV) compound 2 which at photolysis forms amide 4 and according to Thompson through C-H activation of one of the Cp* methyl groups via transient uranium nitride 3. According to DFT computing the favored reaction mechanism is proton abstraction by the nucleophilic nitride unit and formation of a temporary C-U bond followed by a 1,2 methylene group migration over the U-N bond. The similarity of this reaction with that of Fe=O with C-H bonds in Cytochrome P450 is noted.

As an aside the Thompson article in Nature Chemistry happily endorses nuclear energy as a Weapon Against Global Warming. In an accompanying editorial commentary Paula L. diaconescu is equally enthusiastic, that makes two!

UraniumAzidePhotolysis Thompson 2010

Happy birthday fullerene

04 September 2010 - Circumstellar chemistry

fullerenesinSpace.jpgThis blog would have missed the 25th birthday of the discovery of fullerene if it was not for Google who on their website replaced the second letter O by (surprise) a rotating buckyball. Fortunately for this occasion it was not difficult to find new fullerene research to report on. This week for example Cami et al. explain in the journal Science how to spot fullerenes in outer space (DOI). They pointed the Spitzer Space Telescope at one of 3000 known planetary nebula which have nothing to do with planets but everything to do with clusters of dust ejected by stars at the end of their life cycle. In one particular young system (Tc 1 if you have to know) they detected both C60 and C70 buckyballs in the produced IRS spectra.

The region is characterised by the absence of typical hydrogen-containing molecules such as ethylene or HCN, the fullerene band-widths reveal an excitation temperature of 180 K, the fullerene molecules are expected to be neutral as typical ion peaks are absent in the spectra and the molecule is alo expected to reside on carbonaceous grain particles. The C60 molecules are hotter than the C70 molecules and therefore expected to be located on the grain closer to the central star.

The abundance of C60 in this region of space is explained by the hydrogen-poor environment. In an estimate fullerenes lock down 1.5% of all carbon. In terrestrial laboratories absence of hydrogen is also key in fullerene recipes and maximum yield also never exceeds 1.5%. As to the why the hydrogen is missing, another simple explanation: the star in question ejected its hydrogen envelope several thousands of years ago exposing the helium core that in a second thermal pulse now ejects carbon rich material as the main helium fusion product.

Fructose to dimethylfuran

03 September 2010 - Biofuels

dimethylfuran production Thananatthanachon 2010  In a new proposal by Thananatthanachon and Rauchfuss (University of Illinois) the biofuel dimethylfuran (DMF) can from now on be made from fructose in a single reactor with formic acid and palladium on carbon (DOI). Fructose can be obtained from glucose by isomerization and ultimately from cellulose while DMF is an attractive biofuel because of its high boiling point (around 100°C), its high energy density and its high research octane number (little below ethanol).

The purpose of formic acid in the new procedure is threefold: proton source for fructose dehydration (acid catalyst) to the hydroxymethylfurfural (HMF) intermediate, a hydrogen source for the hydrogenation step (to the bis(hydroxymethyl)furan intermediate) and as a deoxygenation agent.