Influence of axle length on the rate and mechanism of shuttling in rigid H-shaped [2]rotaxanes

Correlated translational motions in pseudo-rotaxane complexes controlled by a single chemical stimulus

Coordinated motions are essential in the operation of molecular machines. This feature can be achieved by landscaping the energy surface along the movement coordinates. Herein, we present an approach of using a single stimulus to modify the free energy curve describing the threading and shuttling of a ring along a linear molecule. This approach has been realized by locating two identical ring-binding sites near the axle termini.

Enhanced anion recognition by ammonium [2]catenane functionalisation of a halogen bonding acyclic receptor

Ammonium-dibenzo[24]crown-8 [2]catenane functionalisation of a 3,5-bis-iodotriazole-pyridine motif produces a potent halogen bonding (XB) receptor capable of binding anions in aqueous-acetone solvent mixtures of up to 20% water. Exploiting the kinetically inert nature of the mechanically bonded cationic ammonium [2]catenane substituents, the XB receptor is demonstrated to exhibit superior anion recognition behaviour in comparison to labile sodium cation complexed bis-benzo[15]crown-5 XB and HB triazole-pyridine heteroditopic receptor analogues.

A translationally active ligand based on a [2]rotaxane molecular shuttle with a 2,2'-bipyridyl core

A rigid H-shaped, [2]rotaxane molecular shuttle comprised of an axle containing two benzimidazole recognition sites and a central 2,2'-bipyridyl (bipy) group interlocked with a 24-crown-8 (24C8) wheel was synthesized using a threading followed by stoppering protocol. The central bipy chelating unit was shown to act as a speed bump that raised the barrier to shuttling for the [2]rotaxane. Coordination of a PtCl₂ moiety to the bipy unit in a square planar geometry created an insurmountable steric barrier to shuttling. Addition of one equivalent of NaB(3,5-(CF₃)₂C₆H₃)₄ removed one of the chloride ligands allowing for translation of the crown ether along the axle into the coordination sphere of the Pt(ii) centre but full shuttling of the crown ether could not be activated. In contrast, addition of Zn(ii) ions in a coordinating solvent (DMF) allowed shuttling to occur using a ligand exchange mechanism. DFT calculations showed this likely occurs via coordination of the 24C8 macrocycle to the Zn(ii) centre bound to the bipy chelate. This interplay of the rotaxane axle and wheel components is an example of a translationally active ligand that utilises the large amplitude displacement of a macrocycle along an axle in a molecular shuttle to access ligand coordination modes not possible with conventional ligand designs.

Into the dynamics of rotaxanes at atomistic resolution

Mechanically-interlocked molecules (MIMs) are at the basis of artificial molecular machines and are attracting increasing interest for various applications, from catalysis to drug delivery and nanoelectronics. MIMs are composed of mechanically-interconnected molecular sub-parts that can move with respect to each other, imparting these systems innately dynamical behaviors and interesting stimuli-responsive properties. The rational design of MIMs with desired functionalities requires studying their dynamics at sub-molecular resolution and on relevant timescales, which is challenging experimentally and computationally. Here, we combine molecular dynamics and metadynamics simulations to reconstruct the thermodynamics and kinetics of different types of MIMs at atomistic resolution under different conditions. As representative case studies, we use rotaxanes and molecular shuttles substantially differing in structure, architecture, and dynamical behavior. Our computational approach provides results in agreement with the available experimental evidence and a direct demonstration of the critical effect of the solvent on the dynamics of the MIMs. At the same time, our simulations unveil key factors controlling the dynamics of these systems, providing submolecular-level insights into the mechanisms and kinetics of shuttling. Reconstruction of the free-energy profiles from the simulations reveals details of the conformations of macrocycles on the binding site that are difficult to access via routine experiments and precious for understanding the MIMs' behavior, while their decomposition in enthalpic and entropic contributions unveils the mechanisms and key transitions ruling the intermolecular movements between metastable states within them. The computational framework presented herein is flexible and can be used, in principle, to study a variety of mechanically-interlocked systems.

Dynamic network of intermolecular interactions in metal-organic frameworks functionalized by molecular machines

Molecular machines enable external control of structural and dynamic phenomena at the atomic level. To efficiently transfer their tunable properties into designated functionalities, a detailed understanding of the impact of molecular embedding is needed. In particular, a comprehensive insight is fundamental to design hierarchical multifunctional systems that are inspired by biological cells. Here, we applied an on-the-fly trained force field to perform atomistic simulations of a systematically modified rotaxane functionalized metal-organic framework. Our atomistic studies reveal a symmetric and asymmetric interplay of the mechanically bonded rings (MBRs) within the framework depending on the local environment. As a result, their translational motion is modulated ranging from fast oscillatory behavior to cooperative and potentially directed shuttling. The derived picture of competitive interactions, which influence the operation mechanism of the MBRs embedded in these soft porous materials, promotes the development of responsive functional materials, which is a key step toward intelligent matter.

Monosulfonated dibenzo-24-crown-8 and its properties

In this paper, we describe a method for preparing a monosulfonated dibenzo-24-crown-8 ether, SDB24C8, by direct sulfonation of the parent crown (DB24C8). Since neutral DB24C8 readily interacts with cationic guests, permanently charged SDB24C8 is an advantageous candidate for future supramolecular applications. SDB24C8 can be isolated as a sulfonic acid to be used as it is or converted to a salt of choice. The crystallographic analysis provides the first known host-guest assembly with a DB24C8-based scaffold complexing hydronium and potassium cations. Supramolecular investigations of the interactions of this anionic macrocycle with alkali cations were also performed. According to the expectations, the introduction of the sulfonic group into the DB24C8 scaffold increases the affinities of the receptor. An unusual selectivity of SDB24C8 towards a sodium cation was also observed and further investigated with DFT calculations.

Rigidity and Flexibility in Rotaxanes and Their Relatives; On Being Stubborn and Easy-Going

Rotaxanes are an emerging class of molecules composed of two building blocks: macrocycles and threads. Rotaxanes, and their pseudorotaxane and polyrotaxane relatives, serve as prototypes for molecular-level switches and machines and as components in materials like elastic polymers and 3D printing inks. The rigidity and flexibility of these molecules is a characteristic feature of their design. However, the mechanical properties of the assembled rotaxane and its components are rarely examined directly, and the translation of these properties from molecules to bulk materials is understudied. In this Review, we consider the mechanical properties of rotaxanes by making use of concepts borrowed from physical organic chemistry. Rigid molecules have fewer accessible conformations with higher energy barriers while flexible molecules have more accessible conformations and lower energy barriers. The macrocycles and threads become rigidified when threaded together as rotaxanes in which the formation of intermolecular interactions and increased steric contacts collectively reduce the conformational space and raise barriers. Conversely, rotational and translational isomerism in rotaxanes adds novel modes of flexibility. We find that rigidification in rotaxanes is almost universal, but novel degrees of flexibility can be introduced. Both have roles to play in the function of rotaxanes.

On-the-Fly Training of Atomistic Potentials for Flexible and Mechanically Interlocked Molecules

Mechanically interlocked molecules have gained significant attention because of their unique ability to perform well-defined motions originating from their entanglement, which is important for the design of artificial molecular machines. Atomistic simulations based on force fields (FFs) provide detailed insights into such architectures at the molecular level enabling one to predict the resulting functionalities. However, the development of reliable FFs is still challenging and time-consuming, in particular for highly dynamic and interlocked structures such as rotaxanes, which exhibit a large number of different conformers. In the present work, we present an on-the-fly training (OTFT) algorithm. By a guided and nonguided phase space sampling, relevant reference data are automatically and continuously generated and included for the on-the-fly parametrization of the FF based on a population swapping genetic algorithm (psGA). The OTFT approach provides a fast and automated FF parametrization scheme and tackles problems caused by missing phase space information or the need for big data. We demonstrate the high accuracy of the developed FF for flexible molecules with respect to equilibrium and out-of-equilibrium properties. Finally, by applying the ab initio parametrized FF, molecular dynamic simulations were performed up to experimentally relevant time scales (ca. 1 μs) enabling capture in detail of the structural evaluation and mapping out of the free-energy topology. The on-the-fly training approach thus provides a strong foundation toward automated FF developments and large-scale investigations of phenomena in and out of thermal equilibrium.

Translational dynamics of a non-degenerate molecular shuttle imbedded in a zirconium metal-organic framework

A new [2]rotaxane molecular shuttle linker based on the binding of a 24-crown-8 ether macrocycle at a benzimidazole recognition site was synthesised. The shuttling dynamics of the linker were studied in solution and the structure confirmed by X-ray crystallography. A multivariate Zr(iv) MOF, UWDM-11, containing the new MIM linker and primary linker tetramethylterphenyldicarboxylate was synthesised and the translational motion of the molecular shuttle studied in the solid state. The use of a 13C enriched MIM linker allowed the dynamics of both activated and mesitylene-solvated UWDM-11 to be elucidated by VT 13C CPMAS SSNMR. The incorporation of mesitylene into the pores of UWDM-11 resulted in a significant increase in the barrier for thermally driven translation of the macrocycle.

Dual-stimuli pseudorotaxane switches under kinetic control

Dual-stimuli pseudorotaxane switches: Threaded complexes dissociate upon deprotonation or oxidation. A mechanical bond changes the influence of a ‘speed bump’ on the outcome of a switching event.

Exploring the dynamics of Zr-based metal-organic frameworks containing mechanically interlocked molecular shuttles

Zr(iv) metal-organic frameworks (MOFs) UiO-68 and PCN-57, containing triphenylene dicarboxylate (TPDC) and tetramethyl-triphenylene dicarboxylate (TTDC) linkers, respectively, were doped with an H-shaped tetracarboxylate linker that contains a [2]rotaxane molecular shuttle. The new MOFs, UWDM-8 and UWDM-9, contain a [2]rotaxane crossbar spanning the tetrahedral cavities of the fcu topology while the octahedral cavities remain empty. ¹³C solid-state NMR (SSNMR) spectra and solution ¹H NMR spectra verified that the [2]rotaxanes were included as designed. Variable-temperature (VT) cross polarization (CP) magic-angle spinning (MAS) ¹³C SSNMR was used to explore the translational motion of the macrocyclic ring in both MOFs. The SSNMR results clearly show that the structure of the linker (TPDCvs.TTDC) affects the shuttling rate of the macrocyclic ring, although questions remain as to how rotation of the central phenylene unit of the strut might also affect the motion of the macrocycle.

Fluorophoric [2]rotaxanes: post-synthetic functionalization, conformational fluxionality and metal ion chelation

Fluorophoric [2]rotaxanes form an exciplex upon interpenetration and the exciplex signals are used to monitor the chelation properties of the interlocked systems.

Accelerating the Shuttling in Hydrogen-Bonded Rotaxanes: Active Role of the Axle and the End Station

The relation between the chemical structure and the mechanical behavior of molecular machines is of paramount importance for a rational design of superior nanomachines. Here, we report on a mechanistic study of a nanometer scale translational movement in two bistable rotaxanes. Both rotaxanes consist of a tetra-amide macrocycle interlocked onto a polyether axle. The macrocycle can shuttle between an initial succinamide station and a 3,6-dihydroxy- or 3,6-di-tert-butyl-1,8-naphthalimide end stations. Translocation of the macrocycle is controlled by a hydrogen-bonding equilibrium between the stations. The equilibrium can be perturbed photochemically by either intermolecular proton or electron transfer depending on the system. To the best of our knowledge, utilization of proton transfer from a conventional photoacid for the operation of a molecular machine is demonstrated for the first time. The shuttling dynamics are monitored by means of UV–vis and IR transient absorption spectroscopies. The polyether axle accelerates the shuttling by ∼70% compared to a structurally similar rotaxane with an all-alkane thread of the same length. The acceleration is attributed to a decrease in activation energy due to an early transition state where the macrocycle partially hydrogen bonds to the ether group of the axle. The dihydroxyrotaxane exhibits the fastest shuttling speed over a nanometer distance (τ_shuttling ≈ 30 ns) reported to date. The shuttling in this case is proposed to take place via a so-called harpooning mechanism where the transition state involves a folded conformation due to the hydrogen-bonding interactions with the hydroxyl groups of the end station.

Threading-gated photochromism in [2]pseudorotaxanes

Rigid, Y-shaped imidazole compounds containing the bis(thienyl)ethene moiety were designed and synthesized. The 4,5-bis(benzothienyl)-2-phenylimidazolium cations were then used as axles for [2]pseudorotaxane formation with 24-membered crown ether wheels. It was demonstrated using 1H NMR spectroscopy, UV-Vis absorption and emission spectroscopies that this host-guest interaction results in significant changes in the photochromic properties of the imidazolium axles. This is a rare example of gated photochromism, which exploits the recognition event of an interpenetrated molecular system to tune the photochromic properties in one of the components.

Anion and pH dependent molecular motion by a halogen bonding [2]rotaxane

A bistable [2]rotaxane containing a halogen bonding benzimidazole-iodotriazole station directly conjugated to a naphthalimide station axle component is demonstrated to undergo macrocycle shuttling translocation only upon both protonation and chloride anion recognition. A naked-eye detectable colour response results from the co-conformational change of the host structure.

Restricting shuttling in bis(imidazolium)…pillar[5]arene rotaxanes using metal coordination

Metal coordination to a series of bis (imidazolium)…pillar[5]arene [2]rotaxanes through the formation of metal-carbene bonds facilitates a new strategy to restrict the shuttling motion in [2]rotaxanes. Whereas the pillar[5]arene macrocycle rapidly shuttles along the full length of the bis (imidazolium) rod for the parent [2]rotaxane, Ag(i) coordination to the imidazolium groups through the formation of N-heterocyclic carbenes leads to restricted motion, effectively confining the shuttling motion of the [2]rotaxane. The Ag(i) coordinated [2]rotaxanes can be reacted further, either removing the Ag-carbene species to recreate the parent [2]rotaxane, or reaction with more bulky Pd(ii) species to further restrict the shuttling motion through steric inhibition.

Spacer Length-Independent Shuttling of the Pillar[5]arene Ring in Neutral [2]Rotaxanes

For a series of neutral [2]rotaxanes consisting of a pillar[5]arene ring and axles possessing two stations separated by flexible spacers of different lengths, the free energies of activation for the ring shuttling between the stations were found to be independent of the spacer length. The constitution of the spacer affects the activation energies: replacement of CH₂ groups by repulsive oxygen atoms in the axle increases the barrier. The explanation for the observed length‐independence lies in the presence of a barrier for re‐forming the stable co‐conformation, which makes the ring travel back and forth along the thread in an intermediate state.

Oscillating Emission of [2]Rotaxane Driven by Chemical Fuel

A molecular shuttle consisting of a dibenzo-24-crown-8 macrocycle and an axle with two degenerate peripheral triazolium stations, a central dibenzyl ammonium station, and two anthracenes stoppers was exposed to 2-cyano-2-phenylpropanoic acid as a chemical fuel. Protonation/deprotonation of the amine reversibly switches the rotaxane from a static and little emissive to a dynamic fluorescent shuttling device, the latter exhibiting rapid motion (15 kHz at 25 °C). Four fuel cycles were run.

Light-driven exchange between extended and contracted lasso-like isomers of a bistable [1]rotaxane

A photoactive hydrogen-bonded lasso having an amide-based [1]rotaxane structure has been constructed from acyclic precursors through a self-templating approach. The stability, structural integrity and switching are described.