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

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

Microcontact click printing for templating ultrathin films of metal-organic frameworks

The controlled growth of metal-organic frameworks (MOFs) over surfaces has been investigated using a variety of surface analytical techniques. The use of microcontact printing to prepare surfaces, patterned with regions capable of nucleating the growth of MOFs, has been explored by employing copper-catalyzed alkyne-azide cycloaddition (CuAAC) to pattern silicon wafers with carboxylic acids, a functional group that has been shown to nucleate the growth of MOFs on surfaces. Upon subjecting the patterned silicon surfaces to solvothermal conditions, MOF thin films were obtained and characterized subsequently by AFM, SEM, and grazing-incidence XRD (GIXRD). Large crystals ( 0.5 mm) have also been nucleated, as indicated by the presence of a bas-relief of the original pattern on one surface of the crystal, suggesting that it is possible to transfer the template surface pattern onto a single crystal of a MOF

Degenerate [2]rotaxanes with electrostatic barriers

A synthetic approach to the preparation of [2]rotaxanes (1–5·6PF6) incorporating bispyridinium derivatives and two 1,5-dioxynaphthalene (DNP) units situated in the rod portions of their dumbbell components that are encircled by a single cyclobis(paraquat-p-phenylene) tetracationic (CBPQT4+) ring has been developed. Since the π-electron-deficient bispyridinium units are introduced into the dumbbell components of the [2]rotaxanes 1–5·6PF6, there are Coulombic charge–charge repulsions between these dicationic units and the CBPQT4+ ring in the [2]rotaxanes. Thus, the CBPQT4+ rings in the degenerate [2]rotaxanes exhibit slow shuttling between two DNP recognition sites on the 1H NMR time-scale on account of the electrostatic barrier posed by the bispyridinium units, as demonstrated by variable-temperature 1H NMR spectroscopy. Electrochemical experiments carried out on the [2]rotaxanes 1·6PF6 and 2·6PF6 indicate that the one-electron reduced bipyridinium radical cation in the dumbbell components of the [2]rotaxanes serves as an additional recognition site for the two-electron reduced CBPQT2(˙+) diradical cationic ring. Under appropriate conditions, the ring components in the degenerate rotaxanes 1·6PF6 and 2·6PF6 can shuttle along the recognition sites – two DNP units and one-electron reduced bipyridinium radical cation – under redox control.Accepted versio