Chemical Topology: Complex Molecular Knots, Links, and Entanglements

Straightforward synthesis of a double-lasso macrocycle from a nonsymmetrical [c2]daisy chain

The straightforward synthesis of a double-lasso macrocycle from a nonsymmetrical [c2]daisy chain, using the copper(I)-catalyzed Huisgen alkyne-azide 1,3-dipolar cycloaddition, is described. The preparation of the nonsymmetrical alkyne azide [c2]daisy chain precursor was realized in situ via the exchange of the monomers contained in both symmetrical alkyne and azide [c2]daisy chains and was followed by mass spectrometry.

Dynamic magnetic MOFs

In this review we combine the use of coordination chemistry with the concepts of molecular magnetism to design magnetic Metal-Organic Frameworks (MOFs) in which the crystalline network undergoes a dynamic change upon application of an external stimulus. The various approaches so far developed to prepare these kinds of chemically or physically responsive MOFs with tunable magnetic properties are presented.

Spontaneous knotting of self-trapped waves

We describe theory and simulations of a spinning optical soliton whose propagation spontaneously excites knotted and linked optical vortices. The nonlinear phase of the self-trapped light beam breaks the wave front into a sequence of optical vortex loops around the soliton, which, through the soliton's orbital angular momentum and spatial twist, tangle on propagation to form links and knots. We anticipate similar spontaneous knot topology to be a universal feature of waves whose phase front is twisted and nonlinearly modulated, including superfluids and trapped matter waves.

Mechanostereochemistry and the mechanical bond

The chemistry of mechanically interlocked molecules (MIMs), in which two or more covalently linked components are held together by mechanical bonds, has led to the coining of the term mechanostereochemistry to describe a new field of chemistry that embraces many aspects of MIMs, including their syntheses, properties, topologies where relevant and functions where operative. During the rapid development and emergence of the field, the synthesis of MIMs has witnessed the forsaking of the early and grossly inefficient statistical approaches for template-directed protocols, aided and abetted by molecular recognition processes and the tenets of self-assembly. The resounding success of these synthetic protocols, based on templation, has facilitated the design and construction of artificial molecular switches and machines, resulting more and more in the creation of integrated functional systems. This review highlights (i) the range of template-directed synthetic methods being used currently in the preparation of MIMs; (ii) the syntheses of topologically complex knots and links in the form of stable molecular compounds; and (iii) the incorporation of bistable MIMs into many different device settings associated with surfaces, nanoparticles and solid-state materials in response to the needs of particular applications that are perceived to be fair game for mechanostereochemistry.

Modular synthesis of bipyridinium oligomers and corresponding donor-acceptor oligorotaxanes with crown ethers

Donor-acceptor [4]- and [6]rotaxanes have been prepared from bipyridinium (BIPY(2+)) oligomers and 1,5-dinaphtho[38]crown-10 (DN38C10) by a threading-followed-by-stoppering protocol employing click chemistry. An efficient, straightforward route to the BIPY(2+) oligomers has been developed that requires little to no chromatographic purification. Unlike most donor-acceptor oligorotaxanes that have been reported to date, 100% of the recognition sites on the dumbbells are occupied by rings.

NIR emission of cyclic [4]rotaxanes containing π-extended porphyrin chromophores

The photophysical properties of a Cu(I) [4]rotaxane 4(4+) and of the demetalated [4]rotaxane 3 have been determined and compared to those of the component Zn porphyrin 2. All samples emit in the NIR region (700-1200 nm). The luminescence from the interlocked structures is bathochromically shifted with respect to 2 and displays a lower emission quantum yield, much lower for 4(4+) than for 3. The occurrence of intra-molecular electron or energy transfer is excluded and the decrease in luminescence yield is discussed in terms of the energy gap law and of electronic interactions between components of the cyclic interlocked structure. In toluene a dual emission behavior, similar to that of 2, is observed for 3 and ascribed to the presence of two non-equilibrated excited states, π-π* and CT in nature with lifetimes of 0.80 and 0.14 ns, respectively.

Template synthesis of molecular knots

This tutorial review outlines the different template strategies that chemists have employed to synthesise knotted molecular topologies. Metal ion coordination, hydrogen bonding and aromatic donor-acceptor interactions have all been used to direct the formation of well-defined crossing points for molecular strands. Advances in the methods used to covalently capture the interwoven structures are highlighted, including the active metal template strategy in which metal ions both organise crossing points and catalyse the bond forming reactions that close the loop to form the topologically complex product. Although most non-trivial knots prepared to date from small-molecule building blocks have been trefoil knots, the first pentafoil knot was recently synthesised. Possible future directions and strategies in this rapidly evolving area of chemistry are discussed.

Stereochemistry of molecular figures-of-eight

A trans isomer of a figure-of-eight (Fo8) compound was prepared from an electron-withdrawing cyclobis(paraquat-p-phenylene) derivative carrying trans-disposed azide functions between its two phenylene rings. Copper(I)-catalyzed azide-alkyne cycloadditions with a bispropargyl derivative of a polyether chain, interrupted in its midriff by an electron-donating 1,5-dioxynaphthalene unit acting as the template to organize the reactants prior to the onset of two click reactions, afforded the Fo8 compound with C(i) symmetry. Exactly the same chemistry is performed on the cis-bisazide of the tetracationic cyclophane to give a Fo8 compound with C(2) symmetry. Both of these Fo8 compounds exist as major and very minor conformational isomers in solution. The major conformation in the trans series, which has been characterized by X-ray crystallography, adopts a geometry which maximizes its C-H···O interactions, while maintaining its π···π stacking and C-H···π interactions. Ab initio calculations at the M06L level support the conformational assignments to the major and minor isomers in the trans series. Dynamic (1)H NMR spectroscopy, supported by 2D (1)H NMR experiments, indicates that the major and minor isomers in both the cis and trans series equilibrate in solution on the (1)H NMR timescale rapidly above and slowly below room temperature.

Molecular recognition: from solution science to nano/materials technology

In the 25 years since its Nobel Prize in chemistry, supramolecular chemistry based on molecular recognition has been paid much attention in scientific and technological fields. Nanotechnology and the related areas seek breakthrough methods of nanofabrication based on rational organization through assembly of constituent molecules. Advanced biochemistry, medical applications, and environmental and energy technologies also depend on the importance of specific interactions between molecules. In those current fields, molecular recognition is now being re-evaluated. In this review, we re-examine current trends in molecular recognition from the viewpoint of the surrounding media, that is (i) the solution phase for development of basic science and molecular design advances; (ii) at nano/materials interfaces for emerging technologies and applications. The first section of this review includes molecular recognition frontiers, receptor design based on combinatorial approaches, organic capsule receptors, metallo-capsule receptors, helical receptors, dendrimer receptors, and the future design of receptor architectures. The following section summarizes topics related to molecular recognition at interfaces including fundamentals of molecular recognition, sensing and detection, structure formation, molecular machines, molecular recognition involving polymers and related materials, and molecular recognition processes in nanostructured materials.

Stimuli-responsive supramolecular polymeric materials

Supramolecular materials, dynamic materials by nature, are defined as materials whose components are bridged via reversible connections and undergo spontaneous and continuous assembly/disassembly processes under specific conditions. On account of the dynamic and reversible nature of noncovalent interactions, supramolecular polymers have the ability to adapt to their environment and possess a wide range of intriguing properties, such as degradability, shape-memory, and self-healing, making them unique candidates for supramolecular materials. In this critical review, we address recent developments in supramolecular polymeric materials, which can respond to appropriate external stimuli at the fundamental level due to the existence of noncovalent interactions of the building blocks.

Structure-based classification and ontology in chemistry

BACKGROUND

Recent years have seen an explosion in the availability of data in the chemistry domain. With this information explosion, however, retrieving relevant results from the available information, and organising those results, become even harder problems. Computational processing is essential to filter and organise the available resources so as to better facilitate the work of scientists. Ontologies encode expert domain knowledge in a hierarchically organised machine-processable format. One such ontology for the chemical domain is ChEBI. ChEBI provides a classification of chemicals based on their structural features and a role or activity-based classification. An example of a structure-based class is 'pentacyclic compound' (compounds containing five-ring structures), while an example of a role-based class is 'analgesic', since many different chemicals can act as analgesics without sharing structural features. Structure-based classification in chemistry exploits elegant regularities and symmetries in the underlying chemical domain. As yet, there has been neither a systematic analysis of the types of structural classification in use in chemistry nor a comparison to the capabilities of available technologies.

RESULTS

We analyze the different categories of structural classes in chemistry, presenting a list of patterns for features found in class definitions. We compare these patterns of class definition to tools which allow for automation of hierarchy construction within cheminformatics and within logic-based ontology technology, going into detail in the latter case with respect to the expressive capabilities of the Web Ontology Language and recent extensions for modelling structured objects. Finally we discuss the relationships and interactions between cheminformatics approaches and logic-based approaches.

CONCLUSION

Systems that perform intelligent reasoning tasks on chemistry data require a diverse set of underlying computational utilities including algorithmic, statistical and logic-based tools. For the task of automatic structure-based classification of chemical entities, essential to managing the vast swathes of chemical data being brought online, systems which are capable of hybrid reasoning combining several different approaches are crucial. We provide a thorough review of the available tools and methodologies, and identify areas of open research.

Metal-organic frameworks incorporating copper-complexed rotaxanes

MOFs on the move: A copper coordinated [2]pseudorotaxanate which reacts with zinc nitrate to form an extended structure, consisting of three-fold interpenetrated networks, retains most of its solution-state chemistry including its ability to undergo electronic switching of some of the copper(I) ions under redox control.

Combining coordination chemistry and catalysis to tie a knot by an active-metal template strategy

Collar and tie men: the smallest trefoil knot reported to date has been prepared by an active metal template synthesis. Copper(I) ions are able to constrain the well-designed structure so that it can form the loops by complexing to the bipyridine moieties in the core of the thread and the two ends of the entangled lace on opposite faces of the loop, before acting as a catalyst to close the lace.