A Push-Button Molecular Switch

The preparation, characterization, and switching mechanism of a unique single-station mechanically switchable hetero[2]catenane are reported. The facile synthesis utilizing a “threading-followed-by-clipping” protocol features Cu^(2+)-catalyzed Eglinton coupling as a mild and efficient route to the tetrathiafulvalene-based catenane in high yield. The resulting mechanically interlocked molecule operates as a perfect molecular switch, most readily described as a “push-button” switch, whereby two discrete and fully occupied translational states are toggled electrochemically at incredibly high rates. This mechanical switching was probed using a wide variety of experimental techniques as well as quantum-mechanical investigations. The fundamental distinctions between this single-station [2]catenane and other more traditional bi- and multistation molecular switches are significant

Rapid and Efficient Removal of Perfluorooctanoic Acid from Water with Fluorine-Rich Calixarene-Based Porous Polymers

On account of its nonbiodegradable nature and persistence in the environment, perfluorooctanoic acid (PFOA) accumulates in water resources and poses serious environmental issues in many parts of the world. Here, we present the development of two fluorine-rich calix[4]arene-based porous polymers, FCX4-P and FCX4-BP, and demonstrate their utility for the efficient removal of PFOA from water. These materials featured Brunauer–Emmett–Teller (BET) surface areas of up to 450 m^{2} g^{-1}, which is slightly lower than their nonfluorinated counterparts (up to 596 m^{2} g^{-1}). FCX4-P removes PFOA at environmentally relevant concentrations with a high rate constant of 3.80 g mg^{-1} h^{-1} and reached an exceptional maximum PFOA uptake capacity of 188.7 mg g^{-1}. In addition, it could be regenerated by simple methanol wash and reused without a significant decrease in performance

Topologically non-trivial metal-organic assemblies inhibit \u3b22-microglobulin amyloidogenesis

Inhibiting amyloid aggregation through high-turnover dynamic interactions could be an efficient strategy that is already used by small heat-shock proteins in different biological contexts. We report the interactions of three topologically non-trivial, zinc-templated metal-organic assemblies, a [2]catenane, a trefoil knot (TK), and Borromean rings, with two \u3b22-microglobulin (\u3b22m) variants responsible for amyloidotic pathologies. Fast exchange and similar patterns of preferred contact surface are observed by NMR, consistent with molecular dynamics simulations. In vitro fibrillation is inhibited by each complex, whereas the zinc-free TK induces protein aggregation and does not inhibit fibrillogenesis. The metal coordination imposes structural rigidity that determines the contact area on the \u3b22m surface depending on the complex dimensions, ensuring in vitro prevention of fibrillogenesis. Administration of TK, the best protein-contacting species, to a disease-model organism, namely a Caenorhabditis elegans mutant expressing the D76N \u3b22m variant, confirms the bioactivity potential of the knot topology and suggests new developments

Redox-triggered buoyancy and size modulation of a dynamic covalent gel

The development of stimuli-responsive materials capable of transducing external stimuli into mechanical and physical changes has always been an intriguing challenge and an inspiration for scientists. Several stimuli-responsive gels have been developed and applied to biomimetic actuators or artificial muscles. Redox active actuators in which the mechanical motion is driven chemically or electrochemically have attracted much interest and their actuation mechanism is based on the change in electrostatic repulsion and the loss or gain of counterions to balance newly formed charges. Actuation can also be promoted by changing the hydration state of the material leading to the release/adsorption of water molecules from the network, inducing a direct shrinking/swelling of the material respectively. A cationic crystalline dynamic covalent gel was obtained via the formation of imine bonds between 2,6-diformyl pyridine and triamino guanidinium chloride. The gel exhibits a reversible contraction/expansion behavior in response to base (oxidation, –H+, –e–) and acid (reduction +H+, +e–) respectively. The oxidation induces a color change and contraction of the gel with a concomitant increase in its strength. As synthesized, the cationic gel is denser than water and sinks when placed in water. Upon oxidation, the radical cationic gel expels water molecules rendering it less dense than water and the gel is propelled to the surface without any loss of its structural integrity. These results demonstrate that a careful choice of amine and aldehyde linkers can give rise to imine-linked materials capable of tolerating and resisting extreme acidic and basic conditions while performing work

Radically enhanced molecular recognition

The tendency for viologen radical cations to dimerize has been harnessed to establish a recognition motif based on their ability to form extremely strong inclusion complexes with cyclobis(paraquat-p-phenylene) in its diradical dicationic redox state. This previously unreported complex involving three bipyridinium cation radicals increases the versatility of host–guest chemistry, extending its practice beyond the traditional reliance on neutral and charged guests and hosts. In particular, transporting the concept of radical dimerization into the field of mechanically interlocked molecules introduces a higher level of control within molecular switches and machines. Herein, we report that bistable and tristable [2]rotaxanes can be switched by altering electrochemical potentials. In a tristable [2]rotaxane composed of a cyclobis(paraquat-p-phenylene) ring and a dumbbell with tetrathiafulvalene, dioxynaphthalene and bipyridinium recognition sites, the position of the ring can be switched. On oxidation, it moves from the tetrathiafulvalene to the dioxynaphthalene, and on reduction, to the bipyridinium radical cation, provided the ring is also reduced simultaneously to the diradical dication

AVID: An integrative framework for discovering functional relationships among proteins

BACKGROUND: Determining the functions of uncharacterized proteins is one of the most pressing problems in the post-genomic era. Large scale protein-protein interaction assays, global mRNA expression analyses and systematic protein localization studies provide experimental information that can be used for this purpose. The data from such experiments contain many false positives and false negatives, but can be processed using computational methods to provide reliable information about protein-protein relationships and protein function. An outstanding and important goal is to predict detailed functional annotation for all uncharacterized proteins that is reliable enough to effectively guide experiments. RESULTS: We present AVID, a computational method that uses a multi-stage learning framework to integrate experimental results with sequence information, generating networks reflecting functional similarities among proteins. We illustrate use of the networks by making predictions of detailed Gene Ontology (GO) annotations in three categories: molecular function, biological process, and cellular component. Applied to the yeast Saccharomyces cerevisiae, AVID provides 37,451 pair-wise functional linkages between 4,191 proteins. These relationships are ~65–78% accurate, as assessed by cross-validation testing. Assignments of highly detailed functional descriptors to proteins, based on the networks, are estimated to be ~67% accurate for GO categories describing molecular function and cellular component and ~52% accurate for terms describing biological process. The predictions cover 1,490 proteins with no previous annotation in GO and also assign more detailed functions to many proteins annotated only with less descriptive terms. Predictions made by AVID are largely distinct from those made by other methods. Out of 37,451 predicted pair-wise relationships, the greatest number shared in common with another method is 3,413. CONCLUSION: AVID provides three networks reflecting functional associations among proteins. We use these networks to generate new, highly detailed functional predictions for roughly half of the yeast proteome that are reliable enough to drive targeted experimental investigations. The predictions suggest many specific, testable hypotheses. All of the data are available as downloadable files as well as through an interactive website at . Thus, AVID will be a valuable resource for experimental biologists

Radically Enhanced Molecular Switches

The mechanism governing the redox-stimulated switching behavior of a tristable [2]rotaxane consisting of a cyclobis(paraquat-p-phenylene) (CBPQT^4+) ring encircling a dumbbell, containing tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP) recognition units which are separated from each other along a polyether chain carrying 2,6-diisopropylphenyl stoppers by a 4,4′-bipyridinium (BIPY^2+) unit, is described. The BIPY^2+ unit acts to increase the lifetime of the metastable state coconformation (MSCC) significantly by restricting the shuttling motion of the CBPQTT^4+ ring to such an extent that the MSCC can be isolated in the solid state and is stable for weeks on end. As controls, the redox-induced mechanism of switching of two bistable [2]rotaxanes and one bistable [2]catenane composed of CBPQT^4+ rings encircling dumbbells or macrocyclic polyethers, respectively, that contain a BIPY2+ unit with either a TTF or DNP unit, is investigated. Variable scan-rate cyclic voltammetry and digital simulations of the tristable and bistable [2]rotaxanes and [2]catenane reveal a mechanism which involves a bisradical state coconformation (BRCC) in which only one of the BIPY^•+ units in the CBPQT^2(•+) ring is oxidized to the BIPY2+ dication. This observation of the BRCC was further confirmed by theoretical calculations as well as by X-ray crystallography of the [2]catenane in its bisradical tetracationic redox state. It is evident that the incorporation of a kinetic barrier between the donor recognition units in the tristable [2]rotaxane can prolong the lifetime and stability of the MSCC, an observation which augurs well for the development of nonvolatile molecular flash memory devices

An Organic Spin Crossover Material in Water from a Covalently Linked Radical Dyad

A covalently linked viologen radical cation dyad acts as a reversible thermomagnetic switch in water. Cycling between diamagnetic and paramagnetic forms by heating and cooling is accompanied by changes in optical and magnetic properties with high radical fidelity. Thermomagnetic switches in water may eventually find use as novel biological thermometers and in temperature-responsive organic materials where the changes in properties originate from a change in electronic spin configuration rather than a change in structure