Stiff, and sticky in the right places: the dramatic influence of preorganizing guest binding sites on the hydrogen bond-directed assembly of rotaxanes

A pyridine-N-oxide catenane for cation recognition

The rapid preparation of a pyridine-N-oxide containing [2]catenane is described. The [2]catenane was characterized by NMR spectroscopy, mass spectrometry and X-ray single crystal structure determination. 1H NMR titration experiments reveal the [2]catenane may be reversibly protonated, as well as an ability to bind lithium cations more strongly than sodium cations.

Modulating the shuttling motion of [2]rotaxanes built of p-xylylenediamine units through permethylation at the benzylic positions of the ring

In this study, we show the effect of the gem-dimethyl substitution at the four benzylic carbons of the ring on the internal dynamics of two-station [2]rotaxanes. Such structural modification of the polyamide macrocycles promotes a drastic change of the internal dynamics as shown by variable-temperature (VT) 1H NMR experiments. We determined that the shuttling rates of the octamethylated macrocycle along a series of symmetrical threads were significantly faster compared to the non-substituted ring. This effect was particularly pronounced in the fumaramide-based system, in which the rate was 27 times faster than that of the model system.

Exploring the Chemistry of the Mechanical Bond: Synthesis of a [2]Rotaxane through Multicomponent Reactions

The synthesis of a [2]rotaxane through three- or five-component coupling reactions has been adapted to an organic chemistry experiment for upper-division students. The experimental procedure addresses the search for the most favorable reaction conditions for the synthesis of the interlocked compound, which is obtained in a yield of up to 71%. Moreover, the interlocked nature of the rotaxane is proven by NMR spectroscopy. The content of the sessions has been designed on the basis of a proactive methodology whereby upper-division undergraduate students have a dynamic role. The laboratory experience not only introduces students to the chemistry of the mechanical bond but also reinforces their previous knowledge of basic organic laboratory procedures and their skills with structural elucidation techniques such as NMR and FT-IR spectroscopies. The experiment has been designed in such a customizable way that both experimental procedures and laboratory material can be adapted to a wide range of undergraduate course curricula.

Dual-Way-Switchable Ester Rotaxanes Constructed Using the Recognition of Malonate Diesters

Malonate diesters can thread into the cavity of a di(ethylene glycol)-containing macrocycle under the templating effect of a Na⁺ ion; the corresponding rotaxanes can be synthesized with good efficiency by applying several stoppering reactions. A molecular switch, in which the interlocked macrocycle was moved between two rarely used stations (i.e., malonate and TAA) through the addition of acid/base and the presence/absence of Na⁺ ions, was constructed using this new recognition system.

Progress and prospects toward supramolecular bioactive ion transporters

The majority of cellular physiological processes depend on natural ion channels, which are pore-forming membrane-embedded proteins that let ions flow across the cell membranes selectively. This selective movement of ions across the membranes balances the osmolality within and outside the cell. However, mutations in the genes that encode essential membrane transport proteins or structural reorganisation of these proteins can cause life-threatening diseases like cystic fibrosis. Artificial ion transport systems have opened up a way to replace dysfunctional natural ion channels to cure such diseases through channel replacement therapy. Moreover, recent research has also demonstrated the ability of these systems to kill cancer cells, reigniting interest in the field among scientists. Our contributions to the recent progress in the design and development of artificial chloride ion transporters and their effect on biological systems have been discussed in this review. This review would provide current vistas and future directions toward the development of novel ion transporters with improved biocompatibility and desired anti-cancer properties. Additionally, it strongly emphasises stimuli-responsive ion transport systems, which are crucial for obtaining target-specificity and may speed up the application of these systems in clinical therapeutics.

Hydrogen bond templated synthesis of catenanes and rotaxanes from a single isophthalic acid derivative

Hydrogen bond templated [2]catenanes and [2]rotaxanes have been synthesized using azide precursors derived from a single isophthalic acid derivative precursor. The interlocked molecules were prepared using either stoichiometric or near stoichiometric amounts of macrocycle and CuAAC "click" precursors, with yields of up to 70% for the mechanical bond formation step. Successful preparation of the interlocked structures was confirmed by NMR spectroscopy and mass spectrometry, with detail of co-conformational behaviour being elucidated by a range of ¹H NMR spectroscopic experiments.

Control of the assembly of a cyclic hetero[4]pseudorotaxane from a self-complementary [2]rotaxane

The self-association of a ditopic [2]rotaxane with two macrocycles mainly leads to a [4]pseudorotaxane which can be reversibly disassembled by adding competitive binders, varying the solvent polarity and changing a binding site affinity.

Mechanically interlocked polymers based on rotaxanes

The nature of mechanically interlocked molecules (MIMs) has continued to encourage researchers to design and construct a variety of high-performance materials. Introducing mechanically interlocked structures into polymers has led to novel polymeric materials, called mechanically interlocked polymers (MIPs). Rotaxane-based MIPs are an important class, where the mechanically interlocked characteristic retains a high degree of structural freedom and mobility of their components, such as the rotation and sliding motions of rotaxane units. Therefore, these MIP materials are known to possess a unique set of properties, including mechanical robustness, adaptability and responsiveness, which endow them with potential applications in many emerging fields, such as protective materials, intelligent actuators, and mechanisorption. In this review, we outline the synthetic strategies, structure-property relationships, and application explorations of various polyrotaxanes, including linear polyrotaxanes, polyrotaxane networks, and rotaxane dendrimers.

Photoresponsive Metal-Organic Frameworks as Adjustable Scaffolds in Reticular Chemistry

The easy and remote switching of light makes this stimulus an ideal candidate for a large number of applications, among which the preparation of photoresponsive materials stands out. The interest of several scientists in this area in order to achieve improved functionalities has increase parallel to the growth of the structural complexity of these materials. Thus, metal-organic frameworks (MOFs) turned out to be ideal scaffolds for light-responsive ligands. This review is focused on the integration of photoresponsive organic ligands inside MOF crystalline arrays to prepare enhanced functional materials. Besides the summary of the preparation, properties and applications of these materials, an overview of the future outlook of this research area is provided.

Mechanically interlocked derivatives of carbon nanotubes: synthesis and potential applications

An introduction to mechanically interlocked derivatives of single-walled carbon nanotubes: their main structural features, their potential advantages compared to covalent and supramolecular derivatives, how to synthesize them, and their most promising fields for application.

Molecular Self-Assembly as a Tool to Construct Transmembrane Supramolecular Ion Channels

Self-assembly has become a powerful tool for building various supramolecular architectures with applications in material science, environmental science, and chemical biology. One such area is the development of artificial transmembrane ion channels that mimic naturally occurring channel-forming proteins to unveil various structural and functional aspects of these complex biological systems, hoping to replace the defective protein channels with these synthetically accessible moieties. This account describes our recent approaches to construct supramolecular ion channels using synthetic molecules and their applications in medicinal chemistry.

Mechanically Interlocked Profragrances for the Controlled Release of Scents

The synthesis of a series of interlocked profragrances and the study of the controlled release of the corresponding scents are reported. The structures of the profragrances are based on a [2]pseudorotaxane scaffold with a fumaramate thread derived from perfumery alcohols and a tetrabenzylamido ring. The delivery of the scents was accomplished by sequential thermal dethreading and further enzymatic hydrolysis. Alternatively, the dethreading can be achieved by increasing the polarity of the solvent or photochemical isomerization. The temperature of dethreading can be modulated by the steric demand of the ends of the thread, which allows the selection of different precursor structures depending on the desired rates of delivery. The inputs and outputs for the controlled release of the interlocked profragrances correspond to those of YES or AND logic gates.

Challenges and Opportunities in the Post-Synthetic Modification of Interlocked Molecules

Several strategies have been successfully utilised to obtain a wide range of interlocked molecules. However, some interlocked compounds are still not obtained directly and/or efficiently from non-interlocked components because the requisites for self-assembly cannot always be enforced. To circumvent such a synthetic problem, a strategy that consists of synthesizing an isolable and storable interlocked building block in a step that precedes its modification is an appealing chemical route to more sophisticated interlocked molecules. Synthetic opportunities and challenges are closely linked to the fact that the mechanical bond might greatly affect the reactivity of a functionality of the encircled axle, but that the interlocked architecture needs to be preserved during the synthesis. Hence, the mechanical bond plays a fundamental role in the strategy employed. This Review focuses on the challenging post-synthetic modifications of interlocked molecules, sometimes through cleavage of the axle's main chain, but always with conservation of the mechanical bond.

Real-Time Fluctuations in Single-Molecule Rotaxane Experiments Reveal an Intermediate Weak Binding State during Shuttling

We report on the use of atomic force microscopy (AFM) to identify and characterize an intermediate state in macrocycle shuttling in a hydrogen bonded amide-based molecular shuttle. The [2]rotaxane consists of a benzylic amide macrocycle mechanically locked onto a thread that bears both fumaramide and succinic amide-ester sites, each of which can bind to the macrocycle through up to four intercomponent hydrogen bonds. Using AFM-based single-molecule force spectroscopy, we mechanically triggered the translocation of the ring between the two principal binding sites ("stations") on the axle. Equilibrium fluctuations reveal another interacting site involving the two oxygen atoms in the middle of the thread. We characterized the ring occupancy distribution over time, which confirms the intermediate in both shuttling directions. The study provides evidence of weak hydrogen bonds that are difficult to detect using other methods and shows how the composition of the thread can significantly influence the shuttling dynamics by slowing down the ring motion between the principal binding sites. More generally, the study illustrates the utility that single-molecule experiments, such as force spectroscopy, can offer for elucidating the structure and dynamics of synthetic molecular machines.

Mechanically Interlocked Nitrogenated Nanographenes

Herein, we report the synthesis of mechanically interlocked nitrogenated nanographenes. These systems have been obtained by clipping different tetralactam macrocycles around a 1.9 nm dumbbell-shaped nitrogenated nanographene. Thermal, optoelectronic, and electrochemical characterization of the different mechanically interlocked nanographenes evidence enhanced thermal and photochemical stability, and also absorption and emission properties that vary with the structure of the macrocycle.

Cyclization of interlocked fumaramides into β-lactams: experimental and computational mechanistic assessment of the key intercomponent proton transfer and the stereocontrolling active pocket

A detailed mechanistic study of the diastereoselective CsOH-promoted cyclization of interlocked fumaramides to give β-lactams is described. The mechanistic analysis comprises the experimental evaluation of the structure-reactivity relationship for a wide range of fumaramides [2]rotaxanes (Hammet-plots), KIE studies with deuterium-labelled interlocked fumaramides and computational analysis of two alternative mechanistic pathways for the cyclization process. The obtained results confirm that: (a) the rate-determining step is the deprotonation of the N-benzyl group of the thread by the amidate group of the macrocycle generated by the external base, (b) the polyamide macrocycle plays an important role not only as activating element but also as the stereodifferenciating factor responsible for the observed diastereoselection and (c) the higher flexibility of the adamantyl core speeds up the cyclization process in diadamantyl-derived rotaxanes.

A mechanistic study of the diastereoselective cyclization of interlocked fumaramides to give β-lactams unveils the key factors for successfully taming the process.

Redox-Responsive H-Bonding: Amplifying the Effect of Electron Transfer Using Proton-Coupled Electron Transfer

A new strategy to create highly redox-responsive H-bond dimers based on proton-coupled electron transfer is proposed that capitalizes on the importance of secondary H-bonds in determining overall binding strength in H-bond dimers. Electron transfer induced proton transfer across a H-bond can be used to significantly strengthen the overall binding by both creating strong ionic H-bonds and changing the secondary H-bonds from unfavorable to favorable. The viability and potency of this approach are demonstrated with an electroactive DAD (A = H-acceptor, D = H-donor) array, H(MQ⁺)H, paired with an electroinactive ADA array, O(NH)O. NMR titration of H(MQ⁺)H with O(NH)O in 0.1 M NBu₄PF₆/CD₂Cl₂ gives a K_assoc of 500 M^-1, typical of DAD-ADA dimers. However, upon two-electron reduction in 0.1 M NBu₄PF₆/CH₂Cl₂, cyclic voltammetry studies indicate a 1.8 × 10⁵ increase in binding strength, corresponding to a very large K_assoc of 9 × 10⁷ M^-1. The latter value is typical of DDD-AAA H-bond dimers, consistent with proton transfer across the central H-bond upon reduction.

Copper-Linked Rotaxanes for the Building of Photoresponsive Metal Organic Frameworks with Controlled Cargo Delivery

We have prepared a photoresponsive metal-organic framework by using an amide-based [2]rotaxane as linker and copper(II) ions as metal nodes. The interlocked linker was obtained by the hydrogen bond-directed approach employing a fumaramide thread as template of the macrocyclic component, this latter incorporating two carboxyl groups. Single crystal X-ray diffraction analysis of the metal-organic framework, prepared under solvothermal conditions, showed the formation of stacked 2D rhombohedral grids forming channels decorated with the interlocked alkenyl threads. A series of metal-organic frameworks differing in the E/Z olefin ratio were prepared either by the previous isomerization of the linker or by postirradiation of the reticulated materials. By dynamic solid state ²H NMR measurements, using deuterium-labeled materials, we proved that the geometry of the olefinic axis of the interlocked struts determined the obtention of materials with different independent local dynamics as a result of the strength of the intercomponent noncovalent interactions. Moreover, the usefulness of these novel copper-rotaxane materials as molecular dosing containers has also been assayed by the diffusion and photorelease of p-benzoquinone, evaluated in different solvents and temperatures.

Five-component, one-pot synthesis of an electroactive rotaxane comprising a bisferrocene macrocycle

The templated clipping of a ferrocene-grafted isophthalic acid derivative to encircle a hydrogen-bonding axle through the reaction with 1,4-bis(aminomethyl)benzene is described. The constituent electroactive macrocycle of the resultant [2]rotaxane is a homologue of the versatile benchmark tetraamide variant developed by Leigh and co-workers. The relative templating effect of different hydrogen-bonding motifs in rotaxane and pseudorotaxane generation is compared, with yields varying from 0 to 41%. The electrochemical properties and single crystal X-ray structure of a doubly ferrocene-decorated [2]rotaxane are further reported.

A Potent Halogen-Bonding Donor Motif for Anion Recognition and Anion Template Mechanical Bond Synthesis

The covalent attachment of electron deficient perfluoroaryl substituents to a bis-iodotriazole pyridinium group produces a remarkably potent halogen bonding donor motif for anion recognition in aqueous media. Such a motif also establishes halogen bonding anion templation as a highly efficient method for constructing a mechanically interlocked molecule in unprecedented near quantitative yield. The resulting bis-perfluoroaryl substituted iodotriazole pyridinium axle containing halogen bonding [2]rotaxane host exhibits exceptionally strong halide binding affinities in competitive 50 % water containing aqueous media, by a factor of at least three orders of magnitude greater in comparison to a hydrogen bonding rotaxane host analogue. These observations further champion and advance halogen bonding as a powerful tool for recognizing anions in aqueous media.

Molecular recognition using tetralactam macrocycles with parallel aromatic sidewalls

This review summarizes the supramolecular properties of tetralactam macrocycles that have parallel aromatic sidewalls and four NH residues directed into the macrocyclic cavity. These macrocycles are versatile hosts for a large number of different guest structures in water and organic solvents, and they are well-suited for a range of supramolecular applications. The macrocyclic cavity contains a mixture of polar functional groups and non-polar surfaces which is reminiscent of the amphiphilic binding pockets within many proteins. In water, the aromatic surfaces in the tetralactam cavity drive high affinity due the hydrophobic effect and the NH groups provide secondary interactions that induce binding selectivity. In organic solvents, the supramolecular factors are reversed; the polar NH groups drive high affinity and the aromatic surfaces provide the secondary interactions. In addition to an amphiphilic cavity, macrocyclic tetralactams exhibit conformational flexibility, and the combination of properties enables them to be effective hosts for a wide range of guest molecules including organic biscarbonyl derivatives, near-infrared dyes, acenes, precious metal halide complexes, trimethylammonium ion-pairs, and saccharides.

[2]Rotaxane End-Capping Synthesis by Click Michael-Type Addition to the Vinyl Sulfonyl Group

We report the application of the click Michael-type addition reaction to vinyl sulfone or vinyl sulfonate groups in the synthesis of rotaxanes through the threading-and-capping method. This methodology has proven to be efficient and versatile as it allowed the preparation of rotaxanes using template approaches based on different noncovalent interactions (i.e., donor-acceptor π-π interactions or hydrogen bonding) in yields of generally 60-80 % and up to 91 % aided by the mild conditions required (room temperature or 0 °C and a mild base such as Et₃ N or 4-(N,N-dimethylamino)pyridine (DMAP)). Furthermore, the use of vinyl sulfonate moieties, which are suitable motifs for coupling-and-decoupling (CAD) chemistry, implies another advantage because it allows the controlled chemical disassembly of the rotaxanes into their components through nucleophilic substitution of the sulfonates resulting from the capping step with a thiol under mild conditions (Cs₂ CO₃ and room temperature).

Homo and heteroassembly of amide-based [2]rotaxanes using α,α′-dimethyl-p-xylylenediamines

The selective formation of [2]rotaxanes affords two out of seven possible interlocked isomers thanks to a marked conformational preference.

Self-assembly of small-molecule fumaramides allows transmembrane chloride channel formation

Intermolecular hydrogen bonding of N¹,N⁴-dicyclohexylfumaramide favors the formation of self-assembled ion channels, which facilitates selective Cl⁻ transport across a lipid bilayer membrane.

Effects on Rotational Dynamics of Azo and Hydrazodicarboxamide-Based Rotaxanes

The synthesis of novel hydrogen-bonded [2]rotaxanes having two pyridine rings in the macrocycle and azo- and hydrazodicarboxamide-based templates decorated with four cyclohexyl groups is described. The different affinity of the binding sites for the benzylic amide macrocycle and the formation of programmed non-covalent interactions between the interlocked components have an important effect on the dynamic behavior of these compounds. Having this in mind, the chemical interconversion between the azo and hydrazo forms of the [2]rotaxane was investigated to provide a chemically-driven interlocked system enable to switch its circumrotation rate as a function of the oxidation level of the binding site. Different structural modifications were carried out to further functionalize the nitrogen of the pyridine rings, including oxidation, alkylation or protonation reactions, affording interlocked azo-derivatives whose rotation dynamics were also analyzed.

Pyridyl-Acyl Hydrazone Rotaxanes and Molecular Shuttles

We report on rotaxanes featuring a pyridyl-acyl hydrazone moiety on the axle as a photo/thermal-switchable macrocycle binding site. The pyridyl-acyl E-hydrazone acts as a hydrogen bonding template that directs the assembly of a benzylic amide macrocycle around the axle to form [2]rotaxanes in up to 85% yield; the corresponding Z-hydrazone thread affords no rotaxane under similar conditions. However, the E-rotaxane can be smoothly converted into the Z-rotaxane in 98% yield under UV irradiation. The X-ray crystal structures of the E- and Z-rotaxanes show different intercomponent hydrogen bonding patterns. In molecular shuttles containing pyridyl-acyl hydrazone and succinic amide ester binding sites, the change of position of the macrocycle on the thread can be achieved through a series of light irradiation and heating cycles with excellent positional integrity (>95%) and switching fidelity (98%) in each state.

Competition between the donor and acceptor hydrogen bonds of the threads in the formation of [2]rotaxanes by clipping reaction

The steric effect of thet-butyl group of 1′5′-thread prevents the formation of [2]rotaxane. On the other hand, the 1′3′-thread acts a template to obtain [2]rotaxanes.

Rapidly accessible “click” rotaxanes utilizing a single amide hydrogen bond templating motif

The rapid synthesis (in yields of up to 47%) and co-conformational study of hydrogen bond templated rotaxanes are presented.

The relationship between the conformational degree of freedom of template-containing threads and slippage in the formation of [2]rotaxane building blocks

Slippage is correlated with the degree of freedom of the molecular thread to be encircled. The straighter the thread, the faster is the slippage.

The synthesis of a pyridine-N-oxide isophthalamide rotaxane utilizing supplementary amide hydrogen bond interactions

A pyridine-N-oxide containing rotaxane has been prepared in 32% yield. The role of macrocycle structure in successful pseudo-rotaxane formation has been rationalised by a combination of NMR spectroscopy, X-ray crystallography and computational modelling.

Rapid Macrocycle Threading by a Fluorescent Dye-Polymer Conjugate in Water with Nanomolar Affinity

A macrocyclic tetralactam host is threaded by a highly fluorescent squaraine dye that is flanked by two polyethylene glycol (PEG) chains with nanomolar dissociation constants in water. Furthermore, the rates of bimolecular association are very fast with k(on) ≈ 10(6)-10(7) M(-1) s(-1). The association is effective under cell culture conditions and produces large changes in dye optical properties including turn-on near-infrared fluorescence that can be imaged using cell microscopy. Association constants in water are ∼1000 times higher than those in organic solvents and strongly enthalpically favored at 27 °C. The threading rate is hardly affected by the length of the PEG chains that flank the squaraine dye. For example, macrocycle threading by a dye conjugate with two appended PEG2000 chains is only three times slower than threading by a conjugate with triethylene glycol chains that are 20 times shorter. The results are a promising advance toward synthetic mimics of streptavidin/biotin.

The rapid synthesis and dynamic behaviour of an isophthalamide [2]catenane

A [2]catenane has been prepared in three steps from commerically available starting materials. In solution, the rings of the catenane are able to rotate relative to one another, in a process that varies depending on solvent and temperature.