Induction of motion in a synthetic molecular machine: effect of tuning the driving force

Molecular Ratchets and Kinetic Asymmetry: Giving Chemistry Direction

Over the last two decades ratchet mechanisms have transformed the understanding and design of stochastic molecular systems-biological, chemical and physical-in a move away from the mechanical macroscopic analogies that dominated thinking regarding molecular dynamics in the 1990s and early 2000s (e.g. pistons, springs, etc), to the more scale-relevant concepts that underpin out-of-equilibrium research in the molecular sciences today. Ratcheting has established molecular nanotechnology as a research frontier for energy transduction and metabolism, and has enabled the reverse engineering of biomolecular machinery, delivering insights into how molecules 'walk' and track-based synthesisers operate, how the acceleration of chemical reactions enables energy to be transduced by catalysts (both motor proteins and synthetic catalysts), and how dynamic systems can be driven away from equilibrium through catalysis. The recognition of molecular ratchet mechanisms in biology, and their invention in synthetic systems, is proving significant in areas as diverse as supramolecular chemistry, systems chemistry, dynamic covalent chemistry, DNA nanotechnology, polymer and materials science, molecular biology, heterogeneous catalysis, endergonic synthesis, the origin of life, and many other branches of chemical science. Put simply, ratchet mechanisms give chemistry direction. Kinetic asymmetry, the key feature of ratcheting, is the dynamic counterpart of structural asymmetry (i.e. chirality). Given the ubiquity of ratchet mechanisms in endergonic chemical processes in biology, and their significance for behaviour and function from systems to synthesis, it is surely just as fundamentally important. This Review charts the recognition, invention and development of molecular ratchets, focussing particularly on the role for which they were originally envisaged in chemistry, as design elements for molecular machinery. Different kinetically asymmetric systems are compared, and the consequences of their dynamic behaviour discussed. These archetypal examples demonstrate how chemical systems can be driven inexorably away from equilibrium, rather than relax towards it.

A light-operated pillar[6]arene-based molecular shuttle

A molecular shuttle comprising a pillar[6]arene macrocyclic ring and an axle with two equal-energy-level stations connected by an azobenzene unit was synthesised. The E isomer of the azobenzene functioned as "open gate", allowing the pillar[6]arene ring to rapidly shuttle back-and-forth between the two stations. Ultraviolet irradiation induced photo-isomerisation of the azobenzene from E to Z form. The Z isomer of the azobenzene functioned as a "closed gate", inhibiting shuttling of the pillar[6]arene ring.

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.

Light triggers molecular shuttling in rotaxanes: control over proximity and charge recombination

The lifetime of a charge separated state is enhanced by the effects of solvent polarity and the coordination controlled shuttling of a dumbbell in a porphyrin/fullerene rotaxane.

We present the synthesis of novel rotaxanes based on mechanically interlocked porphyrins and fullerene and their advanced investigations by means of photophysical measurements. To this end, a fullerene-capped dumbbell-type axle containing a central triazole was threaded through strapped (metallo)porphyrins—either a free-base or a zinc porphyrin. Femtosecond-resolved transient absorption measurements revealed charge-separation between the porphyrin and fullerene upon light excitation. Solvent polarity and solvent coordination effects induced molecular motion of the rotaxanes upon charge separation and enabled, for the first time, subtle control over the charge recombination by enabling and controlling the directionality of shuttling.

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.

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

A series of [2]rotaxane molecular shuttles was prepared containing a dibenzo[24]crown-8 (DB24C8) wheel and a rigid H-shaped axle with varying track lengths between recognition sites; from 7.4 to 20.3 Å as defined by 1-4 phenyl rings or a naphthyl group. The rate of shuttling was measured by variable temperature 1H NMR spectroscopy for neutral compounds and EXSY experiments for dicationic species. The rates were found to be independent of the length of the axle, except when the distance between the two recognition sites might be short enough (n = 1) to allow the crown ether to simultaneously interact with both recognition sites providing a short-cut mechanism which could lower the energy barrier. This notion is supported by DFT calculations and solid-state characterization of model compounds that mimic possible transition states.

Structural Control of Kinetics for Macrocycle Threading by Fluorescent Squaraine Dye in Water

While the general concept of steric speed bumps has been demonstrated in rotaxane shuttles and macrocycle threading systems, the sensitivity of speed bump effects has not been evaluated as a function of structural geometry. Values of K_a and k_on for macrocycle threading in water are reported for a series of homologous squaraine dyes with different substituents (speed bumps) on the flanking chains and two macrocycles with different cavity sizes. Sensitivity to a steric speed bump effect was found to depend on (a) structural location, being lowest when the speed bump was near the end of a flanking chain, and (b) macrocycle cavity size, which was enhanced when the cavity was constricted. This new insight is broadly applicable to many types of molecular threading systems.

Successive Translocation of the Rings in a [3]Rotaxane

A [2]rotaxane, a [3]rotaxane and the corresponding thread containing two succinamide (succ) binding stations and a central redox-active pyromellitimide (pmi) station were studied. Infrared spectroelectrochemical experiments revealed the translocation of the macrocycle between the succinamide station and the electrochemically reduced pmi station (radical anion and dianion). Remarkably, in the [3]rotaxane, the rings can be selectively translocated. One-electron reduction leads to the translocation of one of the two macrocycles from the succinamide to the pyromellitimide station, whereas activation of the shuttle through two-electron reduction results in the translocation of both macrocycles: the dianion, due to its higher electron density and hence greater hydrogen-bond accepting affinity, is hydrogen bonded to both macrocycles. Systems with such an on-command contraction are known as molecular muscles. The relative strengths of the binding between the macrocycle and the imide anions could be estimated from the hydrogen-bond-induced shifts in the C=O stretching frequencies of hydrogen-bond accepting amide groups of the macrocycle.

The true nature of rotary movements in rotaxanes

Reveal the intricate nature of movements within rotaxanes by means of multidimensional free-energy landscapes.

Disentangling the different movements observed in rotaxanes is critical to characterize their function as molecular and biological motors. How to achieve unidirectional rotation is an important question for successful construction of a highly efficient molecular motor. The motions within a rotaxane composed of a benzylic amide ring threaded on a fumaramide moiety were investigated employing atomistic molecular dynamics simulations. The free-energy profiles describing the rotational process of the ring about the thread were determined from multi-microsecond simulations. Comparing the theoretical free-energy barriers with their experimental counterpart, the syn–anti isomerization of the amide bond within the ring was ruled out. The free-energy barriers arise in fact from the disruption of hydrogen bonds between the ring and the thread. Transition path analysis reveals that complete description of the reaction coordinate requires another collective variable. The free-energy landscape spanned by the two variables characterizing the coupled rotational and shuttling processes of the ring in the rotaxane was mapped. The calculated free-energy barrier, amounting to 9.3 kcal mol^–1, agrees well with experiment. Further analysis shows that shuttling is coupled with the isomerization of the ring, which is not limited to a simplistic chair-to-chair transition. This work provides a cogent example that contrary to chemical intuition, molecular motion can result from complex, entangled movements requiring for their accurate description careful modeling of the underlying reaction coordinate. The methodology described here can be used to evaluate the different components of the multifaceted motion in rotaxanes, and constitutes a robust tool for the rational design of molecular machines.

Directional Dynamic Covalent Motion of a Carbonyl Walker on a Polyamine Track

Controlled directional displacement of a molecular group has been achieved based on dynamic covalent motions implementing the reactional features of the imine bond. ortho-Carboxybenzaldehyde derivatives are able to form stable adducts with both primary and secondary amines as imines or as amino lactones, respectively, depending on the acidity of the medium. They may thus perform pH-driven intramolecular "walking" along a non-symmetric polyamine chain, in which an imine serves as the terminus under basic conditions on one end of the chain and a lactone formed on a secondary hydroxylamine nitrogen on the other end serves as the terminal site upon addition of acid. The displacement between the termini occurs stochastically through reversible change in valency at the carbon site of the carbonyl group between imine, aminal, iminium and amino lactone form. On the other hand, the directionality results from the stabilisation of the terminal products under given pH conditions. By its ability to undergo interconversion between C=N and O-C-N moieties, the ortho-carboxybenzaldehyde group extends the realm of dynamic covalent chemistry of imines to secondary amines and opens new perspectives in this field.

Potential-controlled rotaxane molecular shuttles based on electron-deficient macrocyclic complexes

This communication reports a novel sandwich-like rotaxane shuttle, which exhibits a unique mode of potential-controlled behaviour. Two dynamic processes occur simultaneously - conformational "unfolding" of the DADA stack accompanies translocation of the ring over the rotaxane's axle.

Substitution effect and effect of axle's flexibility at (pseudo-)rotaxanes

This study investigates the effect of substitution with different functional groups and of molecular flexibility by changing within the axle from a single C-C bond to a double C=C bond. Therefore, we present static quantum chemical calculations at the dispersion-corrected density functional level (DFT-D3) for several Leigh-type rotaxanes. The calculated crystal structure is in close agreement with the experimental X-ray data. Compared to a stiffer axle, a more flexible one results in a stronger binding by 1-3 kcal/mol. Alterations of the binding energy in the range of 5 kcal/mol could be achieved by substitution with different functional groups. The hydrogen bond geometry between the isophtalic unit and the carbonyl oxygen atoms of the axle exhibited distances in the range of 2.1 to 2.4 Å for six contact points, which shows that not solely but to a large amount the circumstances in the investigated rotaxanes are governed by hydrogen bonding. Moreover, the complex with the more flexible axle is usually more unsymmetrical than the one with the stiff axle. The opposite is observed for the experimentally investigated axle with the four phenyl stoppers. Furthermore, we considered an implicit continuum solvation model and found that the complex binding is weakened by approximately 10 kcal/mol, and hydrogen bonds are slightly shortened (by up to 0.2 Å).

Axle length does not affect switching dynamics in degenerate molecular shuttles with rigid spacers

For a series of [2]rotaxane molecular shuttles possessing linear rigid rod-like axles of varying lengths between degenerate recognition sites, the activation barrier for shuttling motion was clearly shown to be constant. Moreover, dynamic NMR studies have revealed that both the entropic and enthalpic contributions to the shuttling motion remain constant regardless of the actual length of the rigid rod-like axles employed herein.