Novel palladium ArX-Y exchanges

29 September 2009 - catalysis

The two reactions depicted below have a lot in common: the substrate is an aryl halide or closely related triflate, the nucleophile is caesium fluoride or caesium hydroxide, the catalyst is based on palladium and the ligand is an organophosphine. Both reactions take place via a oxidative addition / metathesis / reductive elimination reaction mechanism.

The work done in the first set (Watson et al. DOI) by the Buchwald laboratory was inspired by earlier results obtained with reductive elimination of discrete R-Pd-F compounds. Key to the success for the formation of the organofluorine compound is the monomeric nature of the R-Pd-F/tBuBrettPhos intermediate.

Palladium catalysed hydroxylations have already been described in 2006 (Anderson et al. (again Buchwald lab) DOI) and 2007 (Chen et al. DOI) but the 2009 work done by Sergeev et al. ( DOI) takes the reaction to room temperature. As in the above reaction the R-Pd-X/ligand entity is a monomer and not (as is usual in organopalladium chemistry) a dimer.


DNA electron transfer in 30 seconds

27 September 2009 - basics

DNA is a macromolecule that stores genetic information inside a cell. This molecule resembles a spiral staircase with rungs composed of hydrogen bond paired nucleotides. These nucleotides are aromatic and as all rungs are stacked parallel to each other pi stacking occurs as in a "pi way".

A charge transfer complex can form between a donor molecular unit and an acceptor unit along the polymer chain. Electron transfer (ET) between donor and acceptor takes place when an electron is injected into the chain (reductive ET, formation of radical anions) or when an electron is removed (oxidative hole transport, formation of radical cations). The phenomenon is not limited to DNA, proteins also show ET

One way to inject an electron is by photoexcitation of a suitable chromophore. Electron transfer takes place by any of three reaction mechanisms: akin a molecular wire (a delocalized electron moves along the DNA bridge), via a superexchange mechanism (single jump, no localization on the bridge) or via a hopping mechanism (localized electrons move along the bridge in a series of steps).

The rate of electron transfer can be fitted with a modified Marcus equation (k = Ae(-beta.R)) that contains an important constant simply called the beta constant describing the exact nature of distance (R) dependence.

ET in DNA is studied by attaching synthetic light sensitive acceptor and donor chromophores / photo oxidants to it. One way to do this is by sticking a metal to an intercalating ligand (a metallointercalator). Chromophores can also be a part of a hairpin loop and often the chemistry involved is made possible by phosphoramidites. Time-resolved spectroscopy enables the measurement of the time lapsed between exciting the donor molecule and onset of acceptor light emission. Reductive ET processes can also be studied by radiolysis.

The main characteristics of ET are: distances are covered of between 10 and 200 angstrom, the process is extremely fast. ET is also found to depend on many variables such as nucleotide distribution, local DNA conformations and interference from simultaneous proton migration.

ET can also lead to cleavage of the DNA strand, serving not as just the bridge but also as a reactant and guanine is especially vulnerable having the lowest ionization potential of the 4 DNA bases. The guanine radical cation can be studied with ESR. Chemical hole traps stabilize radical cations for example in cyclopropane modified guanine units. Electron transfer thus triggers DNA damage which is biologically relevant. UV radiation and oxidative stress are known to induce cancer. Interestingly electron transfer is also found to trigger certain DNA repair mechanisms.

Nanotech applications: sensitive electrochemical readout for DNA chips. Because of its conductive properties DNA is a building material in molecular electronics.

For the only open-access review on this topic see Wagenknecht, 2006 here.

Nobel prize in biochemistry 2009 predictions

24 September 2009 - News

It is that time of the year again: guessing who will be awarded the Nobel prize in Chemistry (edition 2009). Traditionally, Thompson-Reuters publishes a shortlist based on an extended citation index (that goes all the way back to the year 1900) that can be found here. Embarrassingly, this blog was totally ignorant of 4 of the 5 candidates in the 2009 Thompson list but it suffers from degenerative orgchem tunnel vision. But perhaps equally embarrassing is Wikipedia's ignorance with regard to bio pages and/or scientific topics. It is not the first time essential information is added to en.wikipedia.org post-haste only minutes after the Big Announcement (see last year posts here, and here).

Contender Michaël Grätzel does indeed have a bio page and the dye-sensitized solar cell article gives some indication of what field he is involved in. No problem there then. Top citation: A low-cost, high-efficiency solar cell based on dye-sensitized colloidal TiO2 films (DOI), year 1991, 4816 citations. Bonus points: environmentally relevant. No bio page for Benjamin List thus far but some of his relevant work in organocatalysis is captured in the Hajos-Parrish-Eder-Sauer-Wiechert reaction article, including his top-citation Proline-catalyzed direct asymmetric aldol reactions (DOI), year: 2000 citations: 739. Bonus points: involves green chemistry and age (born 1968!).


Jacqueline Barton too has a bio page but unfortunately zero scientific topic articles link to it suggesting that within the Wikipedia universe her work is irrelevant. Top citation: Long-range photo induced electron transfer through a DNA helix (DOI), year: 1993, citations: 605. Bonus points: female (last woman in the list Dorothy Hodgkin , 1964!). No bio page for Bernd Giese and no page on Sequence dependent long range hole transport in DNA (DOI) (top citation in 1998, 456 and counting) either. Gary Schuster does have a bio page but again not a relevant article associated with him: title most cited article Intramolecular photoinduced electron transfer to anthraquinones linked to duplex DNA: The effect of gaps and traps on long-range radical cation migration (DOI), 1997, 232 citations.

If this year's Nobel theme is something like DNA /charge transfer/ radical reactions / damage, then of course Barton, Giese and Schuster all apply.




See also: DNA electron transfer in 30 seconds

See also 2010 predictions

Molecular dynamics and youtube

18 September 2009 - Art

We all know youtube from the stupid-people videos, the nasty-accident videos and the pirated-movie-or-music video videos but the youtube servers also store a lot of chemical stuff that might be interesting. Take for instance molecular dynamics clips: the origin can be obscure, the copyrights contested, the movie length ultrashort, loading time excessive, the description vague and as with everything on internet the content should probably not be believed but the entertainment value is undeniable. Here is a sampling. In movie 1 we watch 9 billion atoms of copper and aluminum in the melt demonstrating Kelvin-Helmholtz instability. In movie 2 we watch a nanoparticle melt, silica is hydrolyzed in movie 3, a polymer chain snakes through solution in movie 4, water freezes here , nitromethane detonates here , a rotaxane flops around here, a nanotube oscillates here, a beta hairpin folds here, pottasium wriggles it's way through intercalated graphite here and finally - is it art or science? the dynamic simulation of liquid benzene here.

Woodward-Hoffmann rules rescued

18 September 2009 - for now

When epoxides are exposed to light or heat they can form carbonyl ylides in an electrocyclic ring-opening reaction. Some epoxides are used in photochromic sunglasses where the highly colored ylide absorbs the incoming light. Another interesting feature of this epoxide ring opening is that it obeys the Woodward-Hoffmann rules as evidenced by the behaviour of diphenyloxirane, a well-studied epoxide representative. Thus, the thermal 4 electron ring-opening of the trans-epoxide is expected to give the cis-ylide in a conrotatory fashion and the disrotatory photochemical reaction the trans-ylide. How can you tell? By adding a chemical trap such as dicyanoethylene which captured the ylides in a 1,3-dipolar cycloaddition. When left to it's own devices the ylide can fragmentate to the aldehyde (benzaldehyde) and the carbene eventually forming deoxybenzoin by recombination. Predictably in cyclohexane , photolysis of trans-epoxide 1 gives tetrahydrofuran 3 (but not sterically challenged 4), less predictably in acetonitrile 3,4 and 5 are formed in equal amounts (Lipson et al. 1998 DOI).

Is computational chemistry able to predict/confirm the Woodward-Hoffmann rules? The research group of Irmgard Frank (website) is specialized in molecular dynamics of photoreactions and in a most recent venture the entire reaction path for oxirane ring-opening was computationally (CPMD / BLYP) traced (Friedrichs & Frank DOI). In accordance with experiment the weakest link in unsubstituted oxirane is not the carbon-carbon bond at all but the carbon-oxygen bond resulting in biradical formation. In the made-for-movie simulation of this process here we can see the oxygen atom completely dislodged and in the biradical bond breaking and formation continues.

With diphenyloxirane the ground-state reaction predictably proceeds conrotatory to the cis ylide. The singlet state too behaves predictably which is a surprise because until now all static simulations (computing only one reaction coordinate, each snapshot calculated independently) have failed to differentiate between conrotatory and disrotatory paths. The movie can be seen here . Notable features: the C-C bond is gone in 50 femtoseconds well ahead of all other structural rearrangements and preservation of C2 symmetry throughout the rearrangement is an illusion.


Novel zeolite nanosheets

15 September 2009 - Catalysis

Zeolites are microporous aluminosilicate minerals that can be used as catalysts. A substrate diffuses through the microchannel system with size and shape selection based on channel dimensions and catalysis takes place at specific acidic sites. Ideally, surface to mass ratio is optimized for maximum exposure but the production of very thin slices of zeolite is difficult due to interference of Ostwald ripening , the well-known process in which the larger crystals always grow at the expense of the smaller ones.

Choi et al have (DOI) presented a new way to synthesise nanosheet zeolites using a special bis-ammonium surfactant in a mix with the regular components for so-called ZSM-5 zeolite: tetraethyl orthosilicate and aluminium sulfate. After mixing and a lot of heating the crystals form as 20-40 nm wide sheets composed of alternating layers of zeolite (pentasil) with embedded ammonium salts units and aliphatic tail layers.

The surface area of the new material is found to be higher than that of conventional zeolites ( BET area 520 m2/g ). It's catalytic properties have been tested in methanol to gasoline conversion (see methanol economy): catalyst deactivation is slowed down and attributed to slower coke (degraded hydrocarbon) formation.

Catalytic Wittig

4 September 2009 - Organic chemistry

The Wittig reaction discovered in 1954 by George Wittig couples ketones and aldehydes with phosponium ylides to alkenes. Although this organic reaction is extensively used in organic chemistry it suffers from one major drawback: removal of the phosphonium oxide waste product. O'Brien et al. think they have the solution: a Wittig reaction that is catalytic in the ylide (DOI).

This is how their catalytic Wittig works: phosphonium oxide 1 (cyclic and therefore more reactive) can be easily reduced by diphenylsilane forming diphenylsilanediol and phosphine 2. This phosphine reacts with an alkyl halide such as methyl bromoacete and then with base (sodium carbonate) to the phosphonium ylide 3 which then reacts with benzaldehyde to methyl cinnamate. The phosphine oxide is regenerated and the catalytic cycle restarts.



Thus far only Ph2SiH2 was found selective enough not to mess with the aldehyde or the substrate. Painful removal of the silanol via flash chromatography is still required but no doubt the hunt is on for more convenient reducing agents.

O'Brien, C., Tellez, J., Nixon, Z., Kang, L., Carter, A., Kunkel, S., Przeworski, K., & Chass, G. (2009). Recycling the Waste: The Development of a Catalytic Wittig Reaction Angewandte Chemie International Edition, 48 (37), 6836-6839 DOI: 10.1002/anie.200902525