A Doubly Kinetically-Gated Information Ratchet Autonomously Driven by Carbodiimide Hydration

Borsley, Stefan; Leigh, David A.; Roberts, Benjamin M W

doi:10.1021/jacs.1c01172

Cited by 78 publications

(123 citation statements)

References 77 publications

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“…24 Gating of both fueling and waste-forming reactions (SI section VI B3) was recently demonstrated in a [2]rotaxane information ratchet. 24 Inverting chemical gating is predicted to reverse the direction of the motor and could be achieved if the macrocycle activates, rather than hinders, proximal barrier formation (Fig. 4c).…”

Section: Kinetic Modificationsmentioning

confidence: 99%

Insights from an information thermodynamics analysis of a synthetic molecular motor

Amano

Esposito

Kreidt

et al. 2021

Preprint

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Information is a physical quantity, the realisation of which transformed the physics of measurement and communication in the latter half of the 20th Century. However, the relationship and flow between information, energy and mechanics in chemical systems and mechanisms remains largely unexplored. Here we analyze a minimalist experimental example of an autonomous artificial chemically-driven molecular motor -a molecular information ratchet -in terms of information thermodynamics, a framework that quantitatively relates information to other thermodynamic parameters. This treatment reveals how directional motion is generated by free energy transfer from the chemical to the mechanical processes involving the motor. We find that the free energy transfer consists of two distinct contributions that can be considered as "energy flow" and "information flow". We identify the efficiency with which the chemical fuel powers the free energy transfer and show that this is a useful quantity with which to compare and evaluate mechanisms of, and guide designs for, molecular machines. The study provides a thermodynamic level of understanding of molecular motors that is general, complements previous analyses based on kinetics, and has practical implications for designing and improving synthetic molecular machines, regardless of the particular type of machine or chemical structure. In particular, the study confirms that, in line with kinetic analysis, power strokes do not affect the directionality of chemically-driven molecular machines. However, we also find that under some conditions power strokes can modulate the molecular motor current (how fast the components rotate), efficiency with respect to how free energy is dissipated, and the number of fuel molecules consumed per cycle. This may help explain the role of such conformational changes in biomolecular machine mechanisms and illustrates the interplay between energy and information in chemical systems.

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Section: Kinetic Modificationsmentioning

confidence: 99%

Insights from an information thermodynamics analysis of a synthetic molecular motor

Amano

Esposito

Kreidt

et al. 2021

Preprint

Self Cite

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“…Synthetic chemically-fueled molecular pump 1 drives macrocycles from bulk solution into an organised, high energy, threaded assembly, and dissipatively maintains the out-of-equilibrium state for as long as unreacted chemical fuel remains. The pump uses a doubly kinetically-gated catalysis-driven information ratchet mechanism that is wholly artificial and minimalist in design, 38 yet fundamentally analogous to that of biomolecular pumps. It is kinetic asymmetry in the act of threading under catalysis that drives the pumping away from equilibrium.…”

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confidence: 99%

A catalysis-driven artificial molecular pump

Amano

Fielden

Leigh

2021

Nature

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164

134

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All biological pumps are autonomous catalysts; they maintain the out-of-equilibrium conditions of the cell by harnessing the energy released from their catalytic decomposition of a chemical fuel. 1-3 A number of artificial molecular pumps have been reported to date, 4 however they are all either fueled by light 5-10 or require repetitive sequential additions of reagents or varying of an electric potential during each cycle to operate 11-16 . Here we report on an autonomous chemicallyfueled information ratchet 17-20 that in the presence of fuel continuously pumps crown ether macrocycles from bulk solution onto a molecular axle without the need for further intervention. The mechanism uses the position of a crown ether on an axle to both promote barrier attachment behind it upon threading and to suppress subsequent barrier removal until the ring has migrated to a catchment region. Tuning the dynamics of both processes 20, 21 enables the molecular machine 22-25 to continuously pump macrocycles from their lowest energy state in bulk solution to a higher energy state on the axle. The ratchet action is experimentally demonstrated by the progressive pumping of up to three macrocycles onto the axle from bulk solution under conditions where barrier formation and removal occur continuously. The out-of-equilibrium [n]rotaxanes (characterised with n up to 4) are maintained for as long as unreacted fuel is present, after which the rings slowly de-thread. The use of catalysis to drive artificial molecular pumps opens up new opportunities, insights and research directions at the interface of catalysis and molecular machinery. Main The structure and mode of operation of the catalysis-driven molecular pump, 1, is shown in Fig. 1. One end of the axle is permanently blocked by a bulky triarylmethine group (brown); the other end of the axle (the N-terminus) is open for threading when in the form of a benzyl amine group (orange). The axle includes a chain of triazole heterocycles linked by short, propyl (-(CH 2 ) 3 -), spacers. Triazoles only

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“…In its finite lifetime, the activated product can be temporarily part of a dynamic assembly which is thus regulated by the kinetics of the reaction cycle. This strategy has resulted chemically fueled dynamic fibers 33,34 , droplets 35 , colloids 36 , and small molecular machines 37 . Developments in chemically fueled self-assembly have resulted in fast reaction cycles in which activated products have half-lives in the range of tens of seconds.…”

Section: Introductionmentioning

confidence: 99%

Regulating the dynamic folding of a DNA hairpin at the expense of a small, molecular fuel

Stasi

Sureda

Babl

et al. 2021

Preprint

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Molecular machines, such as ATPases or motor proteins, couple the catalysis of a chemical reaction, most commonly hydrolysis of nucleotide triphosphates, to their conformational change. In essence, they continuously convert a chemical fuel to drive their motion. An outstanding goal of nanotechnology remains to synthesize a nanomachine with similar functions, precision, and speed. The field of DNA nan- otechnology has given rise to the engineering precision required for such a device. Simultaneously, the field of systems chemistry developed fast chemical reaction cycles that convert fuel to change the function of molecules. In this work, we thus combined a fast, chemical reaction cycle with the precision of DNA nanotechnology to yield kinetic control over the conformational state of a DNA hairpin. Future work on such systems will result in fast and precise DNA nanodevices.

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A Doubly Kinetically-Gated Information Ratchet Autonomously Driven by Carbodiimide Hydration

Cited by 78 publications

References 77 publications

Insights from an information thermodynamics analysis of a synthetic molecular motor

Insights from an information thermodynamics analysis of a synthetic molecular motor

A catalysis-driven artificial molecular pump

Regulating the dynamic folding of a DNA hairpin at the expense of a small, molecular fuel

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