Knotting and threading of molecules: chemistry and chirality of molecular knots and their assemblies

How and why do molecules tangle or thread? Investigations of molecular knots (knotanes) may shed some light on the mechanisms of (supra)molecular templation and the folding of molecules that result in intertwining. The topological chirality of these fascinating molecules leads to new types of isomerism and paves the way to nanosized molecular motors. Their preparation and derivatization makes high demands on modern synthetic methods and analytical separation since molecular knots are formed in a more or less planned design based on metal coordination or hydrogen‐bonding patterns. This Review describes the development of templation techniques for the synthesis of knotanes and their chiral resolution as well as their selective functionalization and use as building blocks in the synthesis of higher knotane assemblies. Such assemblies can possess linear, branched, or even macrocyclic structures which, on the one hand, introduce unprecedented isomeric compositions that arise from multiple topological stereogenic units and, on the other, define new types of artificial macromolecules beyond polymers and dendritic species.     

Amide-based molecular knots as platforms for fluorescent switches

A series of amide-based molecular knots equipped selectively with fluorescent dansyl and/or pyrenesulfonyl moieties were synthesized from the readily available tris(allyloxy)knotane. UV/Vis absorption spectra, emission spectra, and the emission lifetimes of the fluorescent knotanes were investigated in chloroform at 298 K. The absorption spectra of the knotanes correspond to those of mixtures of their UV-active constituents. The fluorescence quantum yields and lifetimes of the dansyl and pyrenesulfonyl moieties are partly quenched by the knotane platform. In the KN(Da)(2)(Py) species, the fluorescent excited state of the dansyl units (lambda(max)=510 nm) lies at lower energy than the fluorescent excited state of the pyrenesulfonyl unit (lambda(max)=385 nm), the emission of which is accordingly quenched with sensitization of the dansyl fluorescence. In the KN(Ao)(2)(Da), KN(Ao)(Da)(2), and KN(Da)(3) species, the addition of acids causes the protonation of their dansyl units with a consequent decrease in the intensity of the dansyl band at 510 nm and appearance of the emission band of the protonated dansyl unit (lambda(max)=340 nm). Each dansyl unit of KN(Ao)(Da)(2) and KN(Da)(3) undergoes the independent protonation. In these incompletely protonated knotanes the fluorescence of the protonated dansyl units is partly quenched by nonprotonated ones. These processes can be quantitatively reversed upon addition of a base. In KN(Da)(2)(Py), an increase of the fluorescence of its pyrenesulfonyl group is observed when the dansyl groups are protonated. The results obtained show that the readily available and easily functionalizable amide-knotanes can be used as an interesting scaffold to obtain fluorescent switches.     

Helicates of chiragen-type ligands and their aptitude for chiral self-recognition

Two (-)-5,6-pinene-bipyridine moieties connected by a para-xylylene bridge (so-called chiragen-type ligands), (-)-L1, undergo self-assembly upon reaction with equimolar amounts of CuI to form enantiopure circular hexanuclear P-helicates. If both enantiomers of L1 are used, mixtures of P and M hexanuclear helicates are exclusively obtained through a complete chiral recognition; that is, no mixing of the (+) and (-) ligands, respectively, occurs upon complexation. This was proven by a) NMR spectroscopy where identical spectra to those for complexes with the enantiomerically pure ligands were obtained and b) circular dichroism (CD) spectroscopy. The reaction is completely changed by the use of the corresponding meso-L1. Instead of well-defined species, oligomeric mixtures are observed, a result demonstrating the crucial role played by ligand chirality in self-assembly processes. Structural variations on the chiral ligand L1, such as a meta-xylylene bridge instead of a para-xylylene one (in L4) or four pinene groups instead of two (in L5 and L6), favor nondiscrete coordination assembly.     

Quantitative conformational study of redox-active [2]rotaxanes, part 2: Switching in flexible and rigid bistable [2]rotaxanes

Translational movement of the macrocycle in two structurally similar bistable [2]rotaxanes, which is induced by a four-step electrochemical process in solution, has been investigated by using a methodology developed in the preceding article (Chem. Eur. J. 2008, 14, 1107-1116). Both [2]rotaxanes contain a crown ether that can be accommodated by either of two interconnected viologen recognition sites. These sites are substantially different in terms of their affinity towards the crown ether and they possess considerably different electrochemical reduction potentials. The two [2]rotaxanes differ in the length and the rigidity of a bridge that links these sites. A combination of molecular mechanics modelling and NOE spectroscopy data provides information about the conformations of both [2]rotaxanes in the parent oxidation state when the crown ether exclusively populates the strong recognition site. To determine the population of the recognition sites at subsequent stages of reduction, a paramagnetic NMR technique and cyclic voltammetry were used. The key finding is that the flexibility of the connecting bridge element between the recognition sites interferes with shuttling of the crown ether in [2]rotaxanes. It can be demonstrated that the more flexible trimethylene bridge is folded, thus limiting the propensity of the crown ether to shuttle. Consequently, the crown ether populates the original site even in the second reduced state of the flexible [2]rotaxane. On the contrary, in the [2]rotaxane in which two viologen sites are connected by a larger and more rigid p-terphenylene bridge, the predominant location of the crown ether at the weak recognition site is achieved after just one single electron reduction.     

Strategies and tactics for the metal-directed synthesis of rotaxanes, knots, catenanes, and higher order links

More than a quarter of a century after the first metal template synthesis of a [2]catenane in Strasbourg, there now exists a plethora of strategies available for the construction of mechanically bonded and entwined molecular level structures. Catenanes, rotaxanes, knots and Borromean rings have all been successfully accessed by methods in which metal ions play a pivotal role. Originally metal ions were used solely for their coordination chemistry; acting either to gather and position the building blocks such that subsequent reactions generated the interlocked products or by being an integral part of the rings or "stoppers" of the interlocked assembly. Recently the role of the metal has evolved to encompass catalysis: the metal ions not only organize the building blocks in an entwined or threaded arrangement but also actively promote the reaction that covalently captures the interlocked structure. This Review outlines the diverse strategies that currently exist for forming mechanically bonded molecular structures with metal ions and details the tactics that the chemist can utilize for creating cross-over points, maximizing the yield of interlocked over non-interlocked products, and the reactions-of-choice for the covalent capture of threaded and entwined intermediates.     

Covalent Capture: Merging Covalent and Noncovalent Synthesis

Coming together : The act of bringing the right molecules together is enough to induce irreversible or reversible formation of a covalent bond. The covalent capture strategy, in which a supramolecular interaction leads to the formation of a covalent bond (see scheme), can be utilized in very different biological and synthetic systems and can be used for numerous applications.

     

Kinetic versus Thermodynamic Control Over Multiple Conformations of Di-2,7-naphthihexaphyrin(1.1.1.1.1.1)

Di-2,7-naphthihexaphyrin(1.1.1.1.1.1), a non-aromatic carba-analogue of the hexaphyrin(1.1.1.1.1.1), incorporating two built-in 2,7-naphthylene moieties was synthesized as two separate, conformationally locked stereoisomers. Both conformers followed complex protonation pathways involving structurally different species, which can be targeted under kinetic and thermodynamic control. The neutralization of the ultimate dicationic product, accessible from both stereoisomers of the free base, allowed to realize the complex conformational switching cycle involving six structurally different species.     

Theory and experiment in concert: templated synthesis of amide rotaxanes, catenanes, and knots

The synthesis of amide rotaxanes, amide catenanes, and trefoil amide knots is based on template effects mediated by hydrogen bonds. While a large body of experimental data is available, in-depth theoretical studies of these template syntheses are virtually unavailable, although they would provide a more profound insight into the exact details of the hydrogen-bonding patterns involved in the formation of these mechanically interlocked species. In this article we present a density functional study of the conformational properties of tetralactam macrocycles and the threading mechanism that produces the immediate precursor for rotaxane and catenane formation. Predictions of the geometries and relative energies made on the basis of semi-empirical AM1 calculations are compared with these results in order to judge the reliability of the simpler approach. Since these calculations yield good agreement with the structural features, they have been used to extend the calculations in order to understand the mechanism of formation of a trefoil dodecaamide knot that has recently been synthesized. The inherent topological chirality of the knot is reflected in the intermediates generated during its formation; these involve helical loops. These loops parallel the rotaxane and catenane wheels with respect to the arrangement of the functional groups that mediate the template effect and may well serve as wheel analogues through which one of the precursor molecules can be threaded. This threading step finally results in the knotted structure. Good agreement between the results of the calculations presented here and experimental findings is achieved.     

Dynamic Covalent Chemistry within Biphenyl Scaffolds: Reversible Covalent Bonding,Control of Selectivity,and Chirality Sensing with a Single System

Axial chirality is a prevalent and important phenomenon in chemistry. Herein we report a combination of dynamic covalent chemistry and axial chirality for the development of a versatile platform for the binding and chirality sensing of multiple classes of mononucleophiles. An equilibrium between an open aldehyde and its cyclic hemiaminal within biphenyl derivatives enabled the dynamic incorporation of a broad range of alcohols, thiols, primary amines, and secondary amines with high efficiency. Selectivity toward different classes of nucleophiles was also achieved by regulating the distinct reactivity of the system with external stimuli. Through induced helicity as a result of central‐to‐axial chirality transfer, the handedness and ee values of chiral monoalcohol and monoamine analytes were reported by circular dichroism. The strategies introduced herein should find application in many contexts, including assembly, sensing, and labeling.     

Template-Free Self-Assembly of Molecular Trefoil Knots and Double Trefoil Knots Featuring Cp*Rh Building Blocks

Understanding and controlling the topology of self-assembled structures plays a fundamental role in supramolecular chemistry. Herein, the preparation of a series of tetranuclear metallarectangles and hexanuclear trefoil knots featuring Cp*Rh building blocks by template-free self-assembly with four different rigid and flexible ligands is described. Transformations between the trefoil knots and the corresponding macrocycles can be induced by using concentration effects. Remarkably, the hexanuclear trefoil knot 5 was shown to assemble further to provide rare examples of [12+1] heteronuclear double trefoil knots ( 5 a/5 b/5 c/5 d ) through coordination of the amide oxygen atoms to the secondary metal ions Na⁺/K⁺/Ca²⁺/Cd²⁺. The synthetic results are supported by single-crystal XRD.     

Regulation of the chiral twist and supramolecular chirality in co-assemblies of amphiphilic L-glutamic acid with bipyridines

A series of amphiphilic L-glutamic acid derivatives with various saturated alkyl chains has been designed and their co-assembly with 4,4'-bipyridine in aqueous media has been investigated. While the individual amphiphiles formed hydrogels with water and self-assembled into fine fiber networks, the addition of 4,4'-bipyridine caused significant changes in the co-assembled nanostructures such that twisted chiral ribbons were formed. In these supramolecular systems, either fine structural changes or adjustment of the stoichiometric ratio of the two components had crucial effects on the formation of the chiral twists. Based on detailed investigations by SEM and XRD analyses, FTIR, CD, and UV/Vis spectroscopies, and molecular simulation, it is considered that a delicate synergistic balance between π-π stacking, hydrophobic, and chiral interactions is responsible for the formation of the chiral twists. An interesting sandwich structure, in which an excess of 4,4'-bipyridine is inserted into the space of primary cages constructed from the amphiphile and 4,4'-bipyridine, is proposed. Remarkably, the handedness of these chiral twists is related not only to the chiral center of the glutamic unit, but also the chain length of the alkyl tails. This work provides a deeper understanding of the formation mechanism of chiral twists, and exemplifies a feasible shortcut to the rational design of chiral structures from basic molecular structures to supramolecular systems.     

Designing structural motifs for clickamers: exploiting the 1,2,3-triazole moiety to generate conformationally restricted molecular architectures

Noncovalent interactions, especially hydrogen-bonding interactions as well as electrostatic forces, confined within one macromolecule are the key to designing foldamers that adopt well-defined conformations in solution. In the context of significant recent activities in the area of triazole-connected foldamers, so-called clickamers, we present a fundamental study that compares various model compounds that bear adjacent N-, O-, or F-heteroatom substituents. The interplay of attractive and repulsive interactions leads to rotational constraints around the single bonds attached to both the 1- and 4-positions of the 1,2,3-triazole moiety and should therefore be able to induce well-defined conformational preferences in higher oligomers and polymers, that is, foldamers. Various compounds were synthesized and characterized with regard to their preferred conformations in all three aggregation states--that is, in the gas phase, in solution as well as in the solid state--by employing DFT calculations, NMR spectroscopic experiments, and X-ray crystallography, respectively. On the basis of the thus-obtained general understanding of the conformational behavior of the individual connection motifs, heterostructures were prepared from different motifs without affecting their distinct folding characteristics. Therefore, this work provides a kind of foldamer construction kit, which should enable the design of various clickamers with specific shape and incorporated functionality.     

Two-component dendritic gel: effect of stereochemistry on the supramolecular chiral assembly

The self-assembly of diaminododecane solubilised by four different stereoisomeric dendritic peptides to form gel-phase materials in toluene was investigated. The second generation dendritic peptides were based on D- and L-lysine building blocks, and each contained three chiral centres. By designing dendritic peptides in which the configurations of the chiral centres were modified, and applying them as gelator units, the assembly of stereoisomers could be investigated. In all cases, the self-assembly of gelator units resulted in macroscopic gelation. However, the degree of structuring was modulated by the stereoisomers employed, an effect which changed the morphology and macroscopic behavior of the self-assembled state. Enantiomeric (L,L,L or D,D,D) gelator units formed fibrous molecular assemblies, whilst the racemic gel (50 % L,L,L : 50 % D,D,D) formed a flat structure with a "woven" appearance. Gelator units based on L,D,D or D,L,L dendritic peptides also formed fibrous assemblies, but small-angle X-ray scattering indicated significant morphological differences were caused by the switch in chirality. Furthermore, the macroscopic stability of the gel was diminished when these peptides were compared with their L,L,L or D,D,D analogues. In this paper it is clearly shown that individual stereocentres, on the molecular level, are directly related to the helicity within the fibre. It is argued that the chirality controls the pattern of hydrogen bonding within the assembly, and hence determines the extent of fibre formation and the macroscopic gel strength.     

The Self‐Sorting Behavior of Circular Helicates and Molecular Knots and Links

We report on multicomponent self‐sorting to form open circular helicates of different sizes from a primary monoamine, Fe^II ions, and dialdehyde ligand strands that differ in length and structure by only two oxygen atoms. The corresponding closed circular helicates that are formed from a diamine—a molecular Solomon link and a pentafoil knot—also self‐sort, but up to two of the Solomon‐link‐forming ligand strands can be accommodated within the pentafoil knot structure and are either incorporated or omitted depending on the stage that the components are mixed.