Rotary and linear molecular motors driven by pulses of a chemical fuel

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Science  20 Oct 2017:
Vol. 358, Issue 6361, pp. 340-343
DOI: 10.1126/science.aao1377

Acid fuels the motion of a threaded ring

A central goal in the construction of molecular-scale machines is the efficient achievement of one-way motion. Erbas-Cakmak et al. developed a class of machines that transmit pH changes into the two-stage guided motion of molecular rings threaded on a linear or cyclic axle. The design relies on temporary blocking groups and landing sites along the axle that toggle between active and passive states in response to acid or base. Trichloroacetic acid initiates the first stage of motion until it is decomposed by base in the solution, spurring the second phase.

Science, this issue p. 340


Many biomolecular motors catalyze the hydrolysis of chemical fuels, such as adenosine triphosphate, and use the energy released to direct motion through information ratchet mechanisms. Here we describe chemically-driven artificial rotary and linear molecular motors that operate through a fundamentally different type of mechanism. The directional rotation of [2]- and [3]catenane rotary molecular motors and the transport of substrates away from equilibrium by a linear molecular pump are induced by acid-base oscillations. The changes simultaneously switch the binding site affinities and the labilities of barriers on the track, creating an energy ratchet. The linear and rotary molecular motors are driven by aliquots of a chemical fuel, trichloroacetic acid. A single fuel pulse generates 360° unidirectional rotation of up to 87% of crown ethers in a [2]catenane rotary motor.

The conversion of chemical energy into molecular-level directional motion enables biological systems to perform a myriad of functions. Directional movement has been demonstrated in artificial molecular machines (14), using photoexcitation (511) and/or the sequential addition of chemical reagents (1222), and an autonomous chemically-driven molecular rotary motor that operates through a bio-inspired (23) information ratchet mechanism has been described (24, 25). Here we report on an alternative class of ratchet mechanism, based on acid-base oscillations, that powers both rotary and linear molecular motors. The system uses the change in relative binding affinity of macrocycles for different binding sites on circular or linear tracks and a gating system based on dynamic covalent chemistry (26), which are both affected by switching between acidic and basic conditions. The combination of these processes causes directional rotation of the components in [2]- and [3]catenane rotary motors and the generation of out-of-equilibrium concentrations of a substrate using a linear molecular pump. The acid-base oscillations can be induced by aliquots of trichloroacetic acid (Cl3CCO2H), a chemical fuel that undergoes base-promoted decarboxylation (27), generating chloroform (CHCl3) and carbon dioxide (CO2) as the only waste products of motor operation.

In an energy ratchet mechanism, a Brownian particle is inexorably transported with net directionality, without information regarding the substrate (e.g., its position or velocity) influencing the process (1, 28, 29). One of several ways that this can be accomplished is by repeatedly switching which of two maxima is the highest and which of two minima the lowest on a fluctuating potential energy surface (Fig. 1A). We sought to simultaneously switch the energy barrier heights (which determine the kinetics of movement in each direction) and binding site affinities (which provide a driving force for transport) back and forth to produce a motor-mechanism requiring only a single chemical input. The reversible protonation of an amine group can be used to switch the position of crown ethers in rotaxane-based molecular shuttles (30), whereas potential blocking groups based on bulky hydrazones and disulfides have orthogonal labilities in acids and bases (16, 20). We first demonstrated that these two processes can operate simultaneously with model rotaxanes [supplementary materials (SM) section 4.1 and fig. S1] and then applied them to directional rotation of the components of a [2]catenane rotary motor, 1 (Fig. 1).

Fig. 1 Stepwise operation of [2]catenane rotary motor 1/1∙H+.

(A) Reagents and conditions: (i) [2]Catenane motor 1∙H+ (2.4 μmol, 2.6 mM), thiol 2 (12 μmol), Et3N (36 μmol), disulfide 3 (12 μmol), CD2Cl2, room temperature (r.t.), 94% of macrocycles on triazolium site. (ii) Hydrazide 4 (2.4 μmol), CF3CO2H (60 μmol), CD2Cl2, r.t., >99% of macrocycles on dibenzylammonium site. Blue, protonated dibenzylammonium group; red, crown ether; purple, disulfide group; orange, triazolium group; olive, hydrazone blocking group; green, deprotonated dibenzylammonium group. Capital letters indicate proton environments of the crown ether; lowercase letters denote selected proton environments of the track. Me, methyl; tBu, tert-butyl; Et, ethyl. Potential energy diagrams: Under acidic conditions, the left-hand minimum is the lowest and the left-hand maximum is the highest; under basic conditions, the right-hand minimum is lowest and the right-hand maximum is highest. This energy ratchet mechanism inexorably transports a Brownian particle (here the crown ether) in a clockwise direction around the track. (B) Partial 1H NMR spectra (600 MHz, CD2Cl2, 298 K) of [2]catenane 1∙H+ and 1. ppm, parts per million.

[2]Catenane H+ was synthesized in 24 steps (SM section 4.4), with a key step involving macrocyclization of an intermediate pseudo[2]rotaxane (SM section 4.4.2 and fig. S20). To isolate and characterize the motor in different positional states, we first operated it through sequential additions of base and acid (Fig. 1 and SM section 4.4.4). The crown ether resides on the protonated dibenzylammonium site (shown in blue) in H+. Upon addition of excess triethylamine (Et3N), the dibenzylammonium group is deprotonated (green in 1) making the triazolium group (orange) the thermodynamically preferred binding site in 1 (Fig. 1A, step i) (31). Under these basic conditions, the hydrazone blocking group (olive) is kinetically inert and blocks movement of the macrocycle in that direction, whereas the disulfide group (purple) exchanges with disulfides (3) in the bulk through thiolate catalysis (enabled by 2), allowing passage of the macrocycle to the triazolium group via the right-hand pathway (i.e., a clockwise 180° turn). The 1H nuclear magnetic resonance (NMR) chemical shifts of several protons (e.g., Hc of the dibenzylamine/ammonium group and Ho of the methylene adjacent to a triazolium nitrogen atom) are diagnostic of the position of the crown ether on the track in both 1 and H+ (Fig. 1B).

Trifluoroacetic acid (CF3CO2H) was then added until the solution became acidic (Fig. 1A, step ii). Under these conditions, the dibenzylamine site is reprotonated and once again becomes the thermodynamically preferred binding site for the crown ether. The disulfide barrier is locked under acidic conditions, whereas the hydrazone undergoes exchange (with 4) via a transient aldehyde, and so the macrocycle returns to the dibenzylammonium site via the left-hand pathway (i.e., another clockwise 180° turn). The model rotaxane studies confirm that the crown ether cannot pass a disulfide barrier under acidic conditions or a hydrazone barrier under basic conditions (SM sections 4.1, 4.2.7, and 4.3.7). The ring movements in 1 are highly correlated: 93% of crown ethers starting on the dibenzylammonium site complete one 360° directional rotation after one acid-base cycle (based on 1H NMR integration of Fig. 1, steps i and ii), with the mechanism ensuring that no motors rotate more than once from each fuel pulse.

During the macrocyclization reaction to form [2]catenane 1, a [3]catenane (5) with two crown ethers interlocked onto a large ring featuring two ammonium and two triazolium binding sites was also isolated (SM section 4.5 and fig. S23). [3]Catenane (5) also functions as a chemically-driven rotary motor, with one full rotation requiring two cycles of acid-base addition to ratchet both crown ethers around the larger ring in one direction (Fig. 2 and SM section 4.5.2). From the efficiencies of Fig. 2, steps i to iv, ~65% of crown ethers starting on a dibenzylammonium site in 2H+ undergo 360° directional rotation after two cycles, in a “follow-the-leader” manner.

Fig. 2 Stepwise operation of [3]catenane rotary motor 5/5∙2H+.

(A) Reagents and conditions: (i) [3]Catenane 5∙2H+ (1.2 μmol, 2 mM), Et3N (36 μmol), thiol 2 (24 μmol), disulfide 3 (120 μmol), hydrazide 4 (2.4 μmol), CD2Cl2, 94%. (ii) CF3CO2H (60 μmol), 91%. (iii) Et3N (60 μmol), 86%. (iv) CF3CO2H (120 μmol), 88%. The asterisk differentiates the movement of the (indistinguishable) macrocycles in the mechanism. (B) Partial 1H NMR spectra (600 MHz, CD2Cl2, 298 K) of [3]catenane 5∙2H+ and 5.

In the stepwise operation of 1 and 5, increasing amounts of acid and base have to be added, forming salt by-products as waste (SM sections 4.4.4 and 4.5.2). Recently, the base-catalyzed decarboxylation of 2-cyano-2-phenylpropanoic acid was used to switch between the well-defined protonated coconformation of a [2]catenane and a deprotonated state with minimal favorable interactions between the rings (32). We investigated whether a similar process could be used to drive directional rotations in molecular motors. As decarboxylation of 2-cyano-2-phenylpropanoic acid results in 2-phenylpropanonitrile, a potentially persistent organic waste product, we instead used trichloroacetic acid (Cl3CCO2H), which undergoes efficient Et3N-catalyzed decarboxylation at room temperature to produce chloroform (CHCl3), a common and volatile solvent, and carbon dioxide (CO2) (27) (Fig. 3). In principle, as little as one molar equivalent of fuel is required to power each chemically-fueled cycle (32), but the acid-catalyzed hydrazone barrier exchange is slow at the dilute (millimolar) concentrations employed here, so it proved convenient to use excess Cl3CCO2H for motor operation (33). We also found it helpful to add 2-methyl-2-butene for long motor runs to scavenge trace by-products from CHCl3 decomposition (34).

Fig. 3 Operation of rotary motor 1/1[H+] using pulses of a chemical fuel.

(A) Reagents and conditions: [2]Catenane 1 (1.2 μmol, 2 mM), Et3N (23 μmol), thiol 2 (12 μmol), disulfide 3 (60 μmol), hydrazide 4 (4.2 μmol), 2-methyl-2-butene (0.94 μmol), CD3CN. Each pulse of fuel contained 96 μmol of trichloroacetic acid. (B) 1H NMR signal (600 MHz, CD3CN, 298 K) of proton Ho in [2]catenane 1 over four pulses of chemical fuel. Times shown are for operations at room temperature (left, cumulative time; right, time taken for that pulse). At 60°C, the first pulse cycle is complete within 1 hour (33). Numbers under peaks indicate relative integrals.

An initial 4:1 acid:base ratio (80:19:1 trichloroacetic acid:triethylamine:1) in acetonitrile protonates the dibenzylammonium site in the [2]catenane motor and catalyzes hydrazone barrier exchange, leading to 180° directional rotation of 90% of the crown ethers originally at the triazolium group, forming H+ after 15 hours (Fig. 3). While the acid-promoted rotation is occurring, triethylamine catalyzes decarboxylation of the trichloroacetic acid until, after 17 hours, almost all of the trichloroacetic acid has been converted to CO2 and CHCl3 and the reaction mixture has become sufficiently basic to deprotonate the dibenzylammonium group and promote disulfide exchange, as required for the second 180° directional rotation of the motor (the combined quantity of Et3N and Et3NH+ remains constant; as the fuel decarboxylates, progressively more Et3N exists as the free base). A single pulse of the chemical fuel drives autonomous 360° rotation of up to 87% of the crown ethers in 1. At millimolar concentrations of motor, the first unidirectional rotation is complete within 1 hour at 60°C (33). Additional pulses of fuel cause further rotations with little or no change in fidelity of the motor mechanism, although the time required to complete each rotation increases as dilution of the reaction mixture slows the rate of hydrazone and disulfide exchange (Fig. 3B). Analogous operation of [3]catenane 5 leads to up to 82% of crown ethers directionally advancing 180° in response to each fuel pulse.

The same mechanism was used to drive a molecular pump. Linear motor 6 features the same ratcheting unit as rotary motors 1 and 5 (Fig. 4). The thread has hydrazone groups at either end and dibenzylamine/ammonium sites partitioned by disulfide barriers from an internal compartment containing two triazolium rings. Although triazolium groups act as modest affinity binding sites for crown ethers within interlocked structures, the binding is too weak to promote threading (35), and so despite being local energy minima, crown ethers binding to those sites (or nonprotonated amine sites) are not global low-energy species (Fig. 4B). However, without the triazolium groups present on the axle, we found that the internal compartment was too high in energy for crown ethers to be efficiently displaced from the dibenzylamine region during ratcheting. The ratcheting units are capped with adamantyl groups, small enough to allow threading of the crown ether macrocycle when the adjacent hydrazone group is labile, but large enough to prevent dethreading when the hydrazone is locked in place.

Fig. 4 Operation of molecular pump 6 with a pulsed chemical fuel.

(A) Reagents and conditions: Pump 6 (0.6 μmol, 1 mM), crown ether (0.18 mmol), thiol 2 (12 μmol), disulfide 3 (60 μmol), Et3N (24 μmol), hydrazide 4 (4.2 μmol), trichloroacetic acid (120 μmol), CD2Cl2:CD3CN 9:1. (B) Potential energy diagram for the pumping of the crown ether from bulk solution to form [5]rotaxane 8.

In the operation of pump 6, a single pulse of trichloroacetic acid fuel generated a rotaxane with an average of 1.9 ± 0.1 (based on 1H NMR integration) crown ether macrocycles on the axle (SM section 4.7.3). Mass spectrometry showed that, after one cycle of operation, no thread had more than two macrocycles, consistent with the initial cycle of an energy ratchet mechanism. After a second pulse of fuel, an average of 3.1 ± 0.1 crown ethers had been pumped from solution onto each axle, with mass spectroscopy confirming that no thread had more than four macrocycles. After four rounds of operation, each motor-molecule had pumped an average of 3.7 macrocycles from solution, forming predominantly [5]rotaxane 8. The four crown ethers in 8 are all in higher-energy states as compared with unthreaded crown ethers (Fig. 4B). With an analogous thread bearing the same binding sites but no barriers, pulses of trichloroacetic acid in triethylamine led initially to two crown ethers on the thread, but these dethreaded following trichloroacetic acid decarboxylation, leaving only the original unthreaded components. Other than with 6, we were unable to thread more than two crown ethers onto axles of this type with only two dibenzylammonium sites, and no crown ethers onto axles with unprotonated dibenzylamine sites.

The use of pulses of chemical fuel to directionally transport components and substrates via an energy ratchet mechanism is operationally simple and effective, generates relatively innocuous waste products, and can function in a range of rotary and linear molecular motor and pump designs. The motor movements are correlated by the pulsing of fuel, with up to 87% of molecules of 1 completing one directional 360° rotation in response to each addition of chemical fuel and no motors directionally rotating more than the number of aliquots of fuel added. We anticipate that such a generally applicable motor mechanism may prove useful in powering task performance in molecular nanotechnology.

Supplementary Materials

Materials and Methods

Supplementary Text

Figs. S1 to S41

NMR Spectra

References (3638)

References and Notes

  1. Increasing the temperature and/or concentration reduces the time needed for each motor cycle.
  2. Acknowledgments: This research was funded by the European Research Council (Advanced grant 339019). We thank the Engineering and Physical Sciences Research Council National Mass Spectrometry Service Centre (Swansea, UK) for high-resolution mass spectrometry. D.A.L. is a Royal Society Research Professor. The data that support the findings of this study are available within the paper and its supplementary materials or from the Mendeley data repository with the identifier doi: 10.17632/8w3r64c3k3.1.
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