Organic & Biomolecular Chemistry Blog

For [2]rotaxanes to have viable applications in molecular electronics, full control over the shuttling kinetics of the ring molecule is necessary.  J. Fraser Stoddart from Northwestern University and colleagues have shown that introducing reducible, positively-charged moieties into the rod structure effectively creates ring shuttling ‘speed bumps’.

The team synthesised degenerate [2]rotaxanes  incorporating positively bispyridinium derivatives and two 1,5-dioxynaphthalene (DNP) units on the rod portions of their dumbbell components, encircled by a single cyclobis(paraquat-p-phenylene) tetracationic (CBPQT4+) ring.  By partially reducing the conjugated bipyridinium ring, the electrostatic barrier to shuttling is removed, and the ‘speed bump’ now acts as a further recognition site.  The [2]rotaxane also becomes bistable.

The shuttling of the ring is redox controlled and fully reversible; the group hope that this type of redox-active bistable molecule may pave the way to developing candidates for the next generation of molecular electronic devices.

This interesting HOT article is currently free to access until the end of March:

Degenerate [2]rotaxanes with electrostatic barriers
Hao Li, Yan-Li Zhao, Albert C. Fahrenbach, Soo-Young Kim, Walter F. Paxton and J. Fraser Stoddart
Org. Biomol. Chem., 2011, Advance Article
DOI: 10.1039/C0OB00937G

Illustration of signal control through self-assembly of aromatic chromophores in a molecular beacon (MB). Generation of the fluorescence signal is controlled by conformational rearrangement of the multichromophoric assembly of alkynylpyrene (Y) and PDI (E) building blocks

Hairpin-shaped oligonucleotide probes known as molecular beacons, are comprised of a loop of target recognition sequence and a stem which contains the fluorophore and quencher.  Binding of a target oligonucleotide results in fluorescence, so a key property of a molecular beacon is the ability to efficiently quench the signal in the first place to allow sensitive target detection.

Robert Häner and co-workers from the University of Bern have carried out an detailed study on the properties of the molecular beacon stem which affect signal control.  They have previously reported that DNA strands modified with with pyrene and perylendiimide (PDI) show excellent quenching properties and here extend the work to show that self-assembly of the fluorophores is responsible.

They demonstrate that eximer fluorescence is efficiently quenched by formation of π-stacked pyrene/PDI  aggregates with the pattern EYEY, and that longer base pair stem also yield higher quenching efficiencies. The group hopes the concept of directed assembly of non-nucleosidic chromophores will be useful for other types of fluorescent  switching systems.

Read the full details of this careful study online – the article is free to access until the end of March

Signal control by self-assembly of fluorophores in a molecular beacon—a model study
Sarah M. Biner, Dominic Kummer, Vladimir L. Malinovskii and Robert Häner
Org. Biomol. Chem., 2011, Advance Article
DOI: 10.1039/C0OB01132K, Paper

Computational tools for predicting the viability of reactions are invaluable for making synthetic chemists’ lives easier, and this latest study makes another valuable addition to the metaphorical toolbox.

It is assumed that microwave irradiation assists organic reactions, such as Diels-Alder reactions, by rapid heating of the reactants.  However, to date there are no computational studies which explain the role of microwaves on the course of these reactions.

Now, Maria Pilar Prieto and co-workers from the University of Castilla-La Mancha have used DFT to rationalise the activation of intramolecular Diels-Alder cycloaddition reactions under microwave conditions.  They  found that the activation energy of the reaction and the polarity of the stationary points on the reaction surface are good indicators of whether or not a reaction can be improved by microwave irradiation.

Read the full details of their findings online – the article is free to access for four weeks:

“In silico” mechanistic studies as predictive tools in microwave-assisted organic synthesis
A. M. Rodriguez, P. Prieto, A. de la Hoz and A. Díaz-Ortiz
Org. Biomol. Chem., 2011, Advance Article
DOI: 10.1039/C0OB01037E

This HOT paper by Graham Hutchings and co-workers describes a cautionary tale of solubility, as the group discovered a systematic error in HPLC measurements of the enantiomeric excess of N-arene-sulfonyl-2-phenylaziridines.

They showed that the heterogeneous or homogeneous copper-catalysed synthesis of N-arene-sulfonyl-2-phenlaziridines mainly yields the R enantiomer.  However previous reports significantly over-estimate the percentage enantiomeric excess when hexane was used as the HPLC injection solvent, due to the formation of an insoluble racemic phase.

The group has improved their analytical procedure to afford the correct value, but advise that previous reports on the
enantioselectivity of copper-catalysed aziridination reactions ‘should be regarded with caution if the analytical
procedure involved HPLC’.

Both reviewers thought this well-presented study is of importance to the field.  Download it today – it’s now free to access until 8th February.

On the enantioselectivity of aziridination of styrene catalysed by copper triflate and copper-exchanged zeolite Y: consequences of the phase behaviour of enantiomeric mixtures of N-arene-sulfonyl-2-phenylaziridines

Laura Jeffs, Damien Arquier, Benson Kariuki, Donald Bethell, Philip C. Bulman Page and Graham J. Hutchings

Org. Biomol. Chem., 2011, Advance Article
DOI: 10.1039/C0OB00724B, Paper