Articles in 2015

The piston-like, translational motion of a molecular shuttle — a process that is fundamental to many mechanically interlocked molecular switches and machines — has now been demonstrated to occur inside the highly organized and dense structure (containing approximately 10²¹ shuttles per cm³) of a metal–organic framework material.

During the early stages of life on Earth sophisticated RNA catalysts must have formed from simple precursors. Here it is shown that freeze–thaw cycles can drive the assembly of complex RNA polymerase ribozymes from networks of short RNA oligonucleotides through an unanticipated RNA chaperone effect.

Metallacycles made up of six copper ions and six cyclotriguaiacylene-based ligands form a unique topological entanglement in the solid state. Individual metallacycles are interwoven into an infinite 2D chainmail network where each one forms multiple Borromean-ring-like associations with its neighbours. Crystals of the complex grow in an unusual tubular morphology.

Molecular SiO₂ and other simple silicon oxides have remained elusive despite the importance of silicon dioxide materials in advanced electronic devices. Clusters Si₂O₃ and Si₂O₄ have now been experimentally realized by direct oxidation of a carbene-stabilized disilicon using N₂O and O₂, respectively.

Lipid bilayers containing porphyin-phospholipid that is chelated with cobalt have been shown to capture his-tagged proteins and peptides. This method offers a simple route for functionalizing pre-formed lipid bilayers without disrupting their integrity. Using this approach homing peptides were attached to cargo-loaded liposomes to enable tumour targeting, and an HIV-derived protein fragment elicited antibodies following binding to immunogenic liposomes.

Structural elucidation of a peptide natural product has revealed an unprecedented post-translational modification involving formation of a carbon–carbon bond between the side-chains of lysine and tryptophan. This motif defines a new family of cyclic peptides. Biochemical studies reveal that this C-C bond is generated by a radical SAM enzyme, and delineate its catalytic mechanism.

In the ground state, aromatic rings contain [4n + 2] π electrons whereas antiaromatic systems have [4n] π-electrons. Baird's rule states that this situation is reversed in the lowest triplet excited state. It has now been shown using a combination of spectroscopy and quantum chemical calculations that two closely related bis-rhodium hexaphyrins exhibit properties consistent with Baird's rule.

The highest-energy stereoisomer of 1,2,3,4,5,6-hexafluorocyclohexane, with all the fluorines ‘up’, has been prepared in a 12-step protocol. The molecule adopts a chair conformation with three triaxial C–F bonds on one face generating a polarized ring. In the solid state the molecules pack in an orientation consistent with electrostatic ordering.

It is difficult to develop a selective ligand for point mutations in proteins that are not found in easily addressable locations. Now, an all-chemical, epitope-targeting strategy has been reported, and was used to discover an inhibitory peptide with selectivity for the E17K point mutation in the PH Domain of the Akt1 oncoprotein.

Photoswitching of phytochromes is based on the isomerization of the tetrapyrrole chromophore, and eventually leads to the (de)activation of an enzymatic output module. Now it has been shown that both the structural changes associated with photoswitching and the thermal decay of the light-activated state are coupled to proton translocations in the chromophore pocket.

Genotoxic small molecules from the bacterial colibactin pathway — a gut-associated non-ribosomal peptide synthetase–polyketide synthase hybrid gene cluster linked to colorectal cancer — have remained elusive due to their instability. Now, one of these, the colibactin warhead, an unprecedented substituted spirobicyclic structure, has been characterized and shown to crosslink duplex DNA in vitro.

A method for engineering site-specific modifications of histone proteins within cellular chromatin has been developed using protein trans-splicing. This approach enabled a native histone modification, H2BK120 ubiquitination, to be incorporated in isolated nuclei, which was shown to trigger a downstream epigenetic effect.

Scaling relations between the adsorption energies of reaction intermediates facilitate the computational design of catalysts. However, these relations are restricted to low-index surfaces and how they differ from surface to surface cannot be predicted. Structural sensitivity has now been incorporated into scaling relations by elucidating how they are affected by the coordination number of an adsorption site.

A series of molecular fractals, specifically Sierpiński triangles, can be assembled on a Ag(111) surface from small, bent oligophenyls with a bromo group at each end. The self-assembly is driven by the formation of synergistic halogen and hydrogen bonds between the molecular building blocks, and defect-free structures with more than 100 individual components are observed.

Interlocked molecules represent some of the most challenging synthetic targets in terms of non-natural products. It has now been demonstrated how a cyclic [3]catenane composed of three mutually interpenetrating rings can be prepared in two stages using a selective imine exchange reaction on a self-assembled triangular precursor.

Long-lived molecular collision complexes — or ‘resonances’ — are difficult to identify experimentally. Now crossed-beam experiments and quantum calculations are reported for rotationally inelastic CO−He collisions at energies corresponding to temperatures as low as 4 K. Quantum dynamical resonances that are predicted by theory were detected and fully characterized.

A method to predict the stability, structure and properties of as-yet-unreported materials has been devised. For 18-valence electron ABX materials, 15 such ‘missing’ compounds identified to be thermodynamically stable were successfully synthesized, and showed crystal structures and properties in good agreement with the predicted ones.

The extraction of (bio)molecules from fluid mixtures is vital for applications ranging from biomedical diagnostics to environmental analysis. Now a robust chemomechanical sorting system for the extraction of thrombin is described in which pH-dependent binding of the analyte to a specific aptamer is combined with volume changes of the pH-responsive hydrogel in a biphasic microfluidic regime, resulting in a catch-and-release system.

Two metallacages containing Pt(II) phosphine centres bridged by organic donors are shown to display dynamic emission behaviour across a range of concentrations. At low concentrations, the individual cages emit. At high concentrations, or on introduction of additional solvents, aggregation occurs that manifests in colour-tunable fluorescence and white-light emission in THF.

Designing synthetic molecular receptors that can differentiate between specific monosaccharide guests is very challenging. Now, a helically folded oligoamide that selectively encapsulates fructose has been designed using an iterative approach that exploits the modular structure of folded synthetic oligomer sequences, in conjunction with molecular modelling and structural characterization.