Molecular Ratchets and Kinetic Asymmetry: Giving Chemistry Direction

Angewandte Chemie International Edition, Journal Year: 2024, Volume and Issue: 63(23)

Published: April 3, 2024

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

Language: Английский

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Using Catalysis to Drive Chemistry Away from Equilibrium: Relating Kinetic Asymmetry, Power Strokes, and the Curtin–Hammett Principle in Brownian Ratchets

Journal of the American Chemical Society, Journal Year: 2022, Volume and Issue: 144(44), P. 20153 - 20164

Published: Oct. 26, 2022

Chemically fueled autonomous molecular machines are catalysis-driven systems governed by Brownian information ratchet mechanisms. One fundamental principle behind their operation is kinetic asymmetry, which quantifies the directionality of motors. However, it difficult for synthetic chemists to apply this concept design because asymmetry usually introduced in abstract mathematical terms involving experimentally inaccessible parameters. Furthermore, two seemingly contradictory mechanisms have been proposed chemically driven machines: and power stroke This Perspective addresses both these issues, providing accessible useful principles machinery. We relate Curtin–Hammett using a rotary motor kinesin walker as illustrative examples. Our approach describes motors mechanism but pinpoints chemical gating strokes tunable elements that can affect asymmetry. explain why consistent with previous ones outline conditions where be elements. Finally, we discuss role information, used different meanings literature. hope will broad range chemists, clarifying parameters usefully controlled synthesis related systems. It may also aid more comprehensive interdisciplinary understanding biomolecular

Language: Английский

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The role of kinetic asymmetry and power strokes in an information ratchet

Chem, Journal Year: 2023, Volume and Issue: 9(10), P. 2902 - 2917

Published: June 19, 2023

Biomolecular machines are driven by information ratchet mechanisms, where kinetic asymmetry in the machine's chemomechanical cycle of fuel-to-waste catalysis induces net directional dynamics. A large-scale energetically downhill conformational change, termed a "power stroke," has often been erroneously implicated as mechanistic driving feature such machines. We investigated roles and power strokes series rotaxane-based ratchets found that alone determines directionality all use same amount fuel to reach normalized steady state. However, can nonetheless influence performance, how fast state is reached. Moreover, nonequilibrium thermodynamic analysis revealed alter form (information [Shannon entropy] versus intercomponent binding energy) free energy stored ratchets. These findings have implications for both understanding biological design principles artificial (supra)molecular

Language: Английский

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Artificial Molecular Ratchets: Tools Enabling Endergonic Processes

Angewandte Chemie International Edition, Journal Year: 2023, Volume and Issue: 62(47)

Published: Aug. 7, 2023

Abstract Non‐equilibrium chemical systems underpin multiple domains of contemporary interest, including supramolecular chemistry, molecular machines, prebiotic and energy transduction. Experimental chemists are now pioneering the realization artificial that can harvest away from equilibrium. In this tutorial Review, we provide an overview ratchets: mechanisms enabling absorption environment. By focusing on mechanism type—rather than application domain or source—we offer a unifying picture seemingly disparate phenomena, which hope will foster progress in fascinating science.

Language: Английский

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Ratcheting synthesis

Nature Reviews Chemistry, Journal Year: 2023, Volume and Issue: 8(1), P. 8 - 29

Published: Dec. 15, 2023

Language: Английский

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Suppressing catalyst poisoning in the carbodiimide-fueled reaction cycle

Chemical Science, Journal Year: 2023, Volume and Issue: 14(44), P. 12653 - 12660

Published: Jan. 1, 2023

In biology, cells regulate the function of molecules using catalytic reaction cycles that convert reagents with high chemical potential (fuel) to waste molecules. Inspired by synthetic analogs such have been devised, and a widely used cycle uses carboxylates as catalysts accelerate hydration carbodiimides. The is versatile easy use, so it applied motors, pumps, self-assembly, phase separation. However, suffers from side reactions, especially formation N-acylurea. cycles, reactions are disastrous they decrease fuel's efficiency and, more importantly, destroy molecular machinery or assembling Therefore, this work tested how suppress N-acylurea screening precursor concentration, its structure, carbodiimide additives, temperature, pH. It turned out combination low pH, 10% pyridine fraction fuel could significantly product keep highly effective successful assembly. We anticipate our will provide guidelines for carbodiimide-fueled choose optimal conditions.

Language: Английский

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Structural Influence of the Chemical Fueling System on a Catalysis-Driven Rotary Molecular Motor

Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 27, 2025

Continuous directionally biased 360° rotation about a covalent single bond was recently realized in the form of chemically fueled 1-phenylpyrrole 2,2′-dicarboxylic acid rotary molecular motor. However, original fueling system and reaction conditions resulted motor directionality only ∼3:1 (i.e., on average backward for every three forward rotations), along with catalytic efficiency operation 97% fuel 14%. Here, we report efficacy series chiral carbodiimide fuels hydrolysis promoters (pyridine pyridine N-oxide derivatives) driving improved directional this motor-molecule. We outline complete network operation, composed directional, futile, slip cycles. Using derivatives where final conformational step is either very slow or completely blocked, phenylpyrrole diacid becomes enantiomerically enriched, allowing kinetic gating individual steps cycle to be measured. The that produces highest gives 13% enantiomeric excess (e.e.) anhydride-forming kinetically gated step, while most effective promoter generates 90% e.e. step. Combining best-performing into results 92% e.e.. Under dilute chemostated regime (to avoid N-acyl urea formation at high concentrations promoters), continuously rotates ∼24:1 24 rotations) >99% 51%.

Language: Английский

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Conformational selection accelerates catalysis by an organocatalytic molecular motor

Chem, Journal Year: 2023, Volume and Issue: 10(3), P. 855 - 866

Published: Nov. 22, 2023

Conformational dynamics are increasingly recognized as an important contributor to enzyme catalysis but often overlooked in synthetic catalyst design. Here, we experimentally demonstrate faster by conformational selection caused stochastic interconversion of two conformations a catenane-based organocatalyst. The dependencies the reaction rates on relative positioning components during different stages catalytic cycle enable dynamic organocatalyst achieve order-of-magnitude rate accelerations over static or predominantly single-conformer analogs. acceleration results emergent property acting directionally rotating motor. In demonstrating that can overcome linear scaling relationships, these findings have implications for theories and artificial link between biased may suggest "motor molecules" could first arisen primitive form due prebiotic evolutionary pressure catalysis.

Language: Английский

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New insights and discoveries in anion receptor chemistry

Chem, Journal Year: 2023, Volume and Issue: 9(11), P. 3045 - 3112

Published: Sept. 12, 2023

Language: Английский

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Chemically Fueled Autonomous Sol→Gel→Sol→Gel→Sol Transitions

Angewandte Chemie International Edition, Journal Year: 2023, Volume and Issue: 62(23)

Published: April 4, 2023

Complex non-equilibrium phase behaviors are a hallmark of natural self-assembling systems. Here we show how intricate transitions can be achieved through chemically fueled reaction cycle to yield autonomous sol→gel→sol→gel→sol transitions. A relay chemical transformations based on thiazinane metathesis leads two consecutive transient gelations in closed system. Within seconds fuel addition deactivated monomers, an imine-based hydrogel forms that consists fibrillar microspheres. This gel quickly loses its mechanical strength and solution, from which second aldehyde-based nucleates remains stable for over one day. Overall, our gives rise re-entrant without any experimental intervention.

Language: Английский

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