A Redox-Switchable α-Cyclodextrin-Based [2]Rotaxane

A Halogen Bonding [2]Rotaxane Shuttle for Chloride-Selective Optical Sensing

The first example of a [2]rotaxane shuttle capable of selective optical sensing of chloride anions over other halides is reported. The rotaxane was synthesised via a chloride ion template-directed cyclisation of an isophthalamide macrocycle around a multi-station axle containing peripheral naphthalene diimide (NDI) stations and a halogen bonding (XB) bis(iodotriazole) based station. Proton NMR studies indicate the macrocycle resides preferentially at the NDI stations in the free rotaxane, where it is stabilised by aromatic donor-acceptor charge transfer interactions between the axle NDI and macrocycle hydroquinone moieties. Addition of chloride ions in an aqueous-acetone solvent mixture induces macrocycle translocation to the XB anion binding station to facilitate the formation of convergent XB⋅⋅⋅Cl- and hydrogen bonding HB⋅⋅⋅Cl- interactions, which is accompanied by a reduction of the charge-transfer absorption band. Importantly, little to no optical response was induced by addition of bromide or iodide to the rotaxane, indicative of the size discriminative steric inaccessibility of the interlocked cavity to the larger halides, demonstrating the potential of using the mechanical bond effect as a potent strategy and tool in chloride-selective chemo-sensing applications in aqueous containing solvent environments.

Unimolecular Chiral Stepping Inversion Machine

Intelligent molecular machines that are driven by light, electricity, and temperature have attracted considerable interest in the fields of chemistry, materials, and biology. Herein, a unimolecular chiral stepping inversion molecular machine (SIMM) was constructed by a coupling reaction between dibromo pillar[5]arene and a tetrathiafulvalene (TTF) derivative (PT3 and PT5). Compared with the longer aliphatic linker PT5, PT3 with a shorter aliphatic linker shows chiral stepping inversion, achieving chiral inversion under a two-electron redox potential. Benefiting from the successive reversible two-electron redox potential of TTF, the self-exclusion and self-inclusion conformational transformations of SIMM can proceed in two steps under redox, leading to the chirality step inversion in the pillar[5]arene core. Electrochemical experiments and circular dichroism (CD) spectra show that the redox processes can cause SIMM CD signaling to reversibly switch. More importantly, as the oxidant Fe(ClO₄)₃ was increased from 0.1 to 1 equiv, the CD spectral signal of SIMM disappeared at 1 equiv, and further addition of Fe(ClO₄)₃ resulted in the CD signal reversed from positive to negative at 309 nm, indicating that the chirality was reversed after chemical oxidation and reached a negative maximum with the addition of 2 equiv Fe(ClO₄)₃; thus, redox-triggered chiral stepping inversion was achieved. Furthermore, the chiral inversion can be restored to its original state after the addition of 2 equiv of reducing agent, sodium ascorbate. This work demonstrates unimolecular chiral stepping inversion, providing a new perspective on stimulus-responsive chirality in molecular machines.

Development of fluorophoric [2]pseudorotaxanes and [2]rotaxane: selective sensing of Zn(II)

Fluorophoric [2]pseudorotaxanes {NiPR1(ClO4)2-NiPR3(ClO4)2} are synthesized by utilizing newly designed fluorophoric bidentate ligands (L1-L3) and a heteroditopic naphthalene containing macrocycle (NaphMC) with high yields via Ni(II) templation and π-π stacking interactions. Subsequently, a fluorophoric [2]rotaxane (NAPRTX) is established through a Cu(I) catalysed click reaction between an azide terminated pseudorotaxane, {NiPR4(ClO4)2}, which contains the newly designed fluorophoric ligand L4, and alkyne terminated bulky stopper units. All these fluorophoric [2]pseudorotaxanes and the [2]rotaxane were characterized using numerous techniques such as mass spectrometry, NMR, UV/Vis, PL, and elemental analysis, wherever applicable. Furthermore, to investigate the effect of the fluorophoric moieties, the coordinating ability of chelating units, and size and shape of the three dimensional cavity generated by the mechanical bond in the interlocked [2]rotaxane (NAPRTX), we have performed a sensing study of various metal ions. Thus, the interlocked [2]rotaxane is found to have potential as a selective fluorescent sensor for Zn(II) metal ions over other transition, alkali and alkaline earth metal ions, where the 2,2'-bipyridyl arylvinylene moiety of the axle acts as a fluorescence signalling unit.

Rotaxane nanomachines in future molecular electronics

As the electronics industry is integrating more and more new molecules to utilize them in logic circuits and memories to achieve ultra-high efficiency and device density, many organic structures emerged as promising candidates either in conjunction with or as an alternative to conventional semiconducting materials such as but not limited to silicon. Owing to rotaxane's mechanically interlocked molecular structure consisting of a dumbbell-shaped molecule threaded through a macrocycle, they could be excellent nanomachines in molecular switches and memory applications. As a nanomachine, the macrocycle of rotaxane can move reversibly between two stations along its axis under external stimuli, resulting in two stable molecular configurations known as "ON" and "OFF" states of the controllable switch with distinct resistance. There are excellent reports on rotaxane's structure, properties, and function relationship and its application to molecular electronics (Ogino, et al., 1984; Wu, et al., 1991; Bissell, et al., 1994; Collier, et al., 1999; Pease, et al., 2001; Chen, et al., 2003; Green, et al., 2007; Jia, et al., 2016). This comprehensive review summarizes [2]rotaxane and its application to molecular electronics. This review sorts the major research work into a multi-level pyramid structure and presents the challenges of [2]rotaxane's application to molecular electronics at three levels in developing molecular circuits and systems. First, we investigate [2]rotaxane's electrical characteristics with different driving methods and discuss the design considerations and roles based on voltage-driven [2]rotaxane switches that promise the best performance and compatibility with existing solid-state circuits. Second, we examine the solutions for integrating [2]rotaxane molecules into circuits and the limitations learned from these devices keep [2]rotaxane active as a molecular switch. Finally, applying a sandwiched crossbar structure and architecture to [2]rotaxane circuits reduces the fabrication difficulty and extends the possibility of reprogrammable [2]rotaxane arrays, especially at a system level, which eventually promotes the further realization of [2]rotaxane circuits.

Encapsulation within a coordination cage modulates the reactivity of redox-active dyes

Confining molecules within well-defined nanosized spaces can profoundly alter their physicochemical characteristics. For example, the controlled aggregation of chromophores into discrete oligomers has been shown to tune their optical properties whereas encapsulation of reactive species within molecular hosts can increase their stability. The resazurin/resorufin pair has been widely used for detecting redox processes in biological settings; yet, how tight confinement affects the properties of these two dyes remains to be explored. Here, we show that a flexible Pd^II₆L₄ coordination cage can efficiently encapsulate both resorufin and resazurin in the form of dimers, dramatically modulating their optical properties. Furthermore, binding within the cage significantly decreases the reduction rate of resazurin to resorufin, and the rate of the subsequent reduction of resorufin to dihydroresorufin. During our studies, we also found that upon dilution, the Pd^II₆L₄ cage disassembles to afford Pd^II₂L₂ species, which lacks the ability to form inclusion complexes - a process that can be reversed upon the addition of the strongly binding resorufin/resazurin guests. We expect that the herein disclosed ability of a water-soluble cage to reversibly modulate the optical and chemical properties of a molecular redox probe will expand the versatility of synthetic fluorescent probes in biologically relevant environments.

Precise Rate Control of Pseudorotaxane Dethreading by pH-Responsive Selectively Functionalized Cyclodextrins

A family of cyclodextrins functionalized with zero, one, two, or six amines was shown to control the rate of their threading and dethreading on a molecular axle depending on the pH and their substitution pattern. The originality of this system lies in the rate control of the switch by operating the stimulus directly on the macrocycle.

A bistable [2]catenane switched by hetero-radical pairing interactions

A bistable [2]catenane composed of a tetracationic cyclophane, namely cyclobis(paraquat-p-phenylene) (CBPQT⁴⁺) that is mechanically interlocked by a neutral macrocylic component containing both a 1,5-dioxynaphthalene (DNP) and a naphthalene-1,4,5,8-bis(dicarboximide) (NDI) unit, was obtained by using template-directed synthesis via click chemistry. In the fully oxidized state, the CBPQT⁴⁺ component encircles the DNP unit, driven by donor-acceptor interactions. Upon reduction of both the CBPQT⁴⁺ ring and the NDI unit, the CBPQT²⁽˙⁺⁾ ring undergoes shuttling and resides on the NDI˙^- station, driven by coulombic-enhanced spin-pairing interactions between different aromatic radicals.

NMR Relaxation Dispersion Reveals Macrocycle Breathing Dynamics in a Cyclodextrin-based Rotaxane

A distinctive feature of mechanically interlocked molecules (MIMs) is the relative motion between the mechanically bonded components, and often it is the functional basis for artificial molecular machines and new functional materials. Optimization of machine or materials performance requires knowledge of the underlying atomic-level mechanisms that control the motion. The field of biomolecular NMR spectroscopy has developed a diverse set of pulse schemes that can characterize molecular dynamics over a broad time scale, but these techniques have not yet been used to characterize the motion within MIMs. This study reports the first observation of NMR relaxation dispersion related to MIM motion. The rotary (pirouette) motion of α-cyclodextrin (αCD) wheels was characterized in a complementary pair of rotaxanes with pirouetting switched ON or OFF. ¹³C and ¹H NMR relaxation dispersion measurements reveal previously unknown exchange dynamics for the αCD wheels in the pirouette-ON rotaxane with a rate constant of 2200 s^-1 at 298 K and an activation barrier of ΔF^‡ = 43 ± 3 kJ/mol. The exchange dynamics disappear in the pirouette-OFF rotaxane, demonstrating their switchable nature. The ¹³C and ¹H sites exhibiting relaxation dispersion suggest that the exchange involves "macrocycle breathing", in which the αCD wheel fluctuates between a contracted or expanded state, the latter enabling diffusive rotary motion about the axle. The substantial insight from these NMR relaxation dispersion methods suggests similar dynamic NMR methods can illuminate the fast time scale (microsecond to millisecond) mechanisms of intercomponent motion in a wide range of MIMs.

Semi-Rigid Molecular-Clip-Based Molecular Crystal Gearshift

A new version of molecular clip, with a semi-rigid symmetrical crab-type architecture and flexible cavity size, has been successfully designed and synthesized via a one-pot Friedel-Crafts alkylation reaction. The X-ray single-crystal diffraction data provide a simple and intuitive explanation, not only for its well-preorganized and regulated conformation but also for its selective and tunable guest-binding capability. For the first time, the newly designed molecular clip was demonstrated to be not only a controllable variable-speed nonporous adsorption material in solution iodine capture, but also capable of on-off switching in volatile iodine capture. The presented new concept of molecular crystal gearshift directly from the molecular clip crystals represents an important advance in the development of synthetic receptor chemistry, which will exert a significant influence on small-molecule crystallography.

Tetrathiafulvalene - a redox-switchable building block to control motion in mechanically interlocked molecules

With the rise of artificial molecular machines, control of motion on the nanoscale has become a major contemporary research challenge. Tetrathiafulvalenes (TTFs) are one of the most versatile and widely used molecular redox switches to generate and control molecular motion. TTF can easily be implemented as functional unit into molecular and supramolecular structures and can be reversibly oxidized to a stable radical cation or dication. For over 20 years, TTFs have been key building blocks for the construction of redox-switchable mechanically interlocked molecules (MIMs) and their electrochemical operation has been thoroughly investigated. In this review, we provide an introduction into the field of TTF-based MIMs and their applications. A brief historical overview and a selection of important examples from the past until now are given. Furthermore, we will highlight our latest research on TTF-based rotaxanes.

Chemistry and engineering of cyclodextrins for molecular imaging

Cyclodextrins (CDs) are naturally occurring cyclic oligosaccharides bearing a basket-shaped topology with an "inner-outer" amphiphilic character. The abundance of hydroxyl groups enables CDs to be functionalized with multiple targeting ligands and imaging elements. The imaging time, and the payload of different imaging elements, can be tuned by taking advantage of the commercial availability of CDs with different sizes of the cavity. This review aims to offer an outlook of the chemistry and engineering of CDs for the development of molecular probes. Complexation thermodynamics of CDs, and the corresponding implications for probe design, are also presented with examples demonstrating the structural and physiochemical roles played by CDs in the full ambit of molecular imaging. We hope that this review not only offers a synopsis of the current development of CD-based molecular probes, but can also facilitate translation of the incremental advancements from the laboratory to real biomedical applications by illuminating opportunities and challenges for future research.

The lubricating role of water in the shuttling of rotaxanes

We have investigated at the atomic level amide-based rotaxanes set in motion in four different solvents, namely, ethyl ether, acetonitrile, ethanol and water. In three non-aqueous solvents, shuttling of the macrocycle between two binding sites separated by a free-energy barrier is coupled with a conformational change and rotation, driven primarily by hydrogen-bonding interactions. The mechanism that underlies the shuttling is completely altered when the non-aqueous solvent is replaced by water. In aqueous solution, hydrophobic interactions chiefly control shuttling of the rotaxane, leading to a sharp decrease of the free-energy barrier, thereby speeding up the process. The binding sites and the reaction pathway describing shuttling vary significantly in water compared with in the other three solvents. We found that the high polarity, the hydrogen-bond donor and acceptor ability, and the minimal steric hindrance of water conspire to modify the mechanism. These three physicochemical properties are also responsible for the lubrication by water. That water completely changes the mechanism underlying the shuttling of rotaxanes, is addressed for the first time in this study, and provides valuable guidelines for the de novo design of molecular machines.

Design and Synthesis of Dendrimers with Facile Surface Group Functionalization, and an Evaluation of Their Bactericidal Efficacy

We report a versatile divergent methodology to construct dendrimers from a tetrafunctional core, utilizing the robust copper(I) catalyzed alkyne-azide cycloaddition (CuAAC, “click”) reaction for both dendrimer synthesis and post-synthesis functionalization. Dendrimers of generations 1–3 with 8–32 protected or free OH and acetylene surface groups, were synthesized using building blocks that included acetylene- or azide-terminated molecules with carboxylic acid or diol end groups, respectively. The acetylene surface groups were subsequently used to covalently link cationic amino groups. A preliminary evaluation indicated that the generation one dendrimer with terminal NH₃⁺ groups was the most effective bactericide, and it was more potent than several previously studied dendrimers. Our results suggest that size, functional end groups and hydrophilicity are important parameters to consider in designing efficient antimicrobial dendrimers.

Threading of various ‘U’ shaped bidentate axles into a heteroditopic macrocyclic wheel via NiII/CuII templation

The Ni^II/Cu^II templated threading of various terminal group embedded ‘U’ shaped axles into an amido–amine macrocyclic wheel towards the development of a new generation of [2]pseudorotaxanes via [3 + 2] coordination assisted by other non-covalent interactions.

Macrocyclic shape-persistency of cyclo[6]aramide results in enhanced multipoint recognition for the highly efficient template-directed synthesis of rotaxanes

Examples of using two-dimensional shape-persistent macrocycles, i.e. those having noncollapsible and geometrically well-defined skeletons, for constructing mechanically interlocked molecules are scarce, which contrasts the many applications of these macrocycles in molecular recognition and functional self-assembly. Herein, we report the crucial role played by macrocyclic shape-persistency in enhancing multipoint recognition for the highly efficient template-directed synthesis of rotaxanes. Cyclo[6]aramides, with a near-planar conformation, are found to act as powerful hosts that bind bipyridinium salts with high affinities. This unique recognition module, composed of two macrocyclic molecules with one bipyridinium ion thread through the cavity, is observed both in the solid state and in solution, with unusually high binding constants ranging from ∼10¹³ M^-2 to ∼10¹⁵ M^-2 in acetone. The high efficacy of this recognition motif is embodied by the formation of compact [3]rotaxanes in excellent yields based on either a "click-capping" (91%) or "facile one-pot" (85%) approach, underscoring the great advantage of using H-bonded aromatic amide macrocycles for the highly efficient template-directed synthesis of mechanically interlocked structures. Furthermore, three cyclo[6]aramides bearing different peripheral chains 1-3 demonstrate high specificity in the synthesis of a [3]rotaxane from 1 and 2, and a [2]rotaxane from 3via a "facile one-pot" approach, in each case as the only isolated product. Analysis of the crystal structure of the [3]rotaxane reveals a highly compact binding mode that would be difficult to access using other macrocycles with a flexible backbone. Leveraging this unique recognition motif, resulting from the shape-persistency of these oligoamide macrocycles, in the template-directed synthesis of compact rotaxanes may open up new opportunities for the development of higher order interlocked molecules and artificial molecular machines.

A multiple-responsive water-soluble [3]pseudorotaxane constructed by pillar[5]arene-based molecular recognition and disulfide bond connection

A multiple-responsive water-soluble [3]pseudorotaxane was constructed by water-soluble pillar[5]arene-based molecular recognition and disulfide bond connection.

Room temperature phosphorescence of 4-bromo-1,8-naphthalic anhydride derivative-based polyacrylamide copolymer with photo-stimulated responsiveness

Room temperature phosphorescence emission was achieved by host–guest recognition between γ-cyclodextrin and a 4-bromo-1,8-naphthalic anhydride polymer, which can be controlled by the photo-isomerization of the azobenzene unit of the other polymer.

A redox-controllable molecular switch based on weak recognition of BPX26C6 at a diphenylurea station

The Na⁺ ion–assisted recognition of urea derivatives by BPX26C6 has allowed the construction of a redox-controllable [2]rotaxane-type molecular switch based on two originally very weakly interacting host/guest systems. Using NOBF₄ to oxidize the triarylamine terminus into a corresponding radical cation attracted the macrocyclic component toward its adjacent carbamate station; subsequent addition of Zn powder moved the macrocyclic component back to its urea station.

Significant emission enhancement of a bola-amphiphile with salicylaldehyde azine moiety induced by the formation of [2]pseudorotaxane with γ-cyclodextrin

The emission of a bola-amphiphile with salicyladazine moiety was significantly enhanced by the formation of [2]pseudorotaxane with γ-cyclodextrin, which can specifically localize in mitochondria of living cells.

Facile method for preparing surface-mounted cucurbit[8]uril-based rotaxanes

Surface-immobilized rotaxanes are of practical interest for myriad applications including molecular rotors and analytical sensing. Herein, we present a facile method for the preparation of cucurbit[8]uril (CB[8])-based rotaxanes on gold (Au) surfaces threaded onto a viologen (MV(2+)) axle. The surface-bound CB[8] rotaxanes were characterized by contact angle measurements and optical microscopy. Direct imaging of the rotaxanes was accomplished by attaching either azobenzene-functionalized silica (Si-azo) colloids or fluorescein-labeled dopamine that were bound to the Au surface through a supramolecular heteroternary (1:1:1) complex with CB[8]. The surface density of CB[8] rotaxanes was examined based on their detection of dopamine. The calculated surface density is 4.8 × 10(13) molecules·cm(-2), which is only slightly lower than the theoretical value of 5.0 × 10(13) molecules·cm(-2). Surface-functionalized rotaxanes can be reversibly switched using external stimuli to bind electron-rich second guests for CB[8], including both small molecules such as dopamine and appropriately-functionalized colloidal particles. Such controlled reversibility gives rise to potential applications including selective sensing or reusable templates for preparing well-defined colloidal arrays. The formation of the surface-bound rotaxane structure is critical for successfully anchoring CB[8] host molecules onto Au substrates, yielding an interlocked architecture and preventing the dissociation of binary host-guest complex MV(2+)⊂CB[8]. The MV(2+)⊂CB[8] rotaxane structure thus effectively maintains the material density on the Au surface and dramatically enhances the stability of the functional surface.

Cooperative Binding of Cyclodextrin Dimers to Isoflavone Analogues Elucidated by Free Energy Calculations

Dimerization of cyclodextrin (CD) molecules is an elementary step in the construction of CD-based nanostructured materials. Cooperative binding of CD cavities to guest molecules facilitates the dimerization process and, consequently, the overall stability and assembly of CD nanostructures. In the present study, all three dimerization modes (head-to-head, head-to-tail, and tail-to-tail) of β-CD molecules and their binding to three isoflavone drug analogues (puerarin, daidzin, and daidzein) were investigated in explicit water surrounding using molecular dynamics simulations. Total and individual contributions from the binding partners and solvent environment to the thermodynamics of these binding reactions are quantified in detail using free energy calculations. Cooperative drug binding to two CD cavities gives an enhanced binding strength for daidzin and daidzein, whereas for puerarin no obvious enhancement is observed. Head-to-head dimerization yields the most stable complexes for inclusion of the tested isoflavones (templates) and may be a promising building block for construction of template-stabilized CD nanostructures. Compared to the case of CD monomers, the desolvation of CD dimers and entropy changes upon complexation prove to be influential factors of cooperative binding. Our results shed light on key points of the design of CD-based supramolecular assemblies. We also show that structure-based calculation of binding thermodynamics can quantify stabilization caused by cooperative effects in building blocks of nanostructured materials.

INHIBIT logic operations based on light-driven β-cyclodextrin pseudo[1]rotaxane with room temperature phosphorescence addresses

INHIBIT logic gates based on light-driven β-cyclodextrin pseudo[1]rotaxane were fabricated conveniently utilizing reversible ICD and RTP as output addresses respectively.

Cyclodextrin-based molecular machines

This chapter overviews molecular machines based on cyclodextrins (CDs). The categories of CD-based molecular machines, external stimuli for CD-based molecular machines, and typical examples of CD-based molecular machines are briefly described.