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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., (© 2024 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

To date, only a small number of chemistries and chemical fueling strategies have been successfully used to operate artificial molecular motors. Here, we report the 360° directionally biased rotation of phenyl groups about a C-C bond, driven by a stepwise Appel reaction sequence. The motor molecule consists of a biaryl-embedded phosphine oxide and phenol, in which full rotation around the biaryl bond is blocked by the P-O oxygen atom on the rotor being too bulky to pass the oxygen atom on the stator. Treatment with SOCl 2 forms a cyclic oxyphosphonium salt (removing the oxygen atom of the phosphine oxide), temporarily linking the rotor with the stator. Conformational exchange via ring flipping then allows the rotor and stator to twist back and forth past the previous limit of rotation. Subsequently, the ring opening of the tethered intermediate with a chiral alcohol occurs preferentially through a nucleophilic attack on one face. Thus, the original phosphine oxide is reformed with net directional rotation about the biaryl bond over the course of the two-step reaction sequence. Each repetition of SOCl 2 -chiral alcohol additions generates another directionally biased rotation. Using the same reaction sequence on a derivative of the motor molecule that forms atropisomers rather than fully rotating 360° results in enantioenrichment, suggesting that, on average, the motor molecule rotates in the "wrong" direction once every three fueling cycles. The interconversion of phosphine oxides and cyclic oxyphosphonium groups to form temporary tethers that enable a rotational barrier to be overcome directionally adds to the strategies available for generating chemically fueled kinetic asymmetry in molecular systems.

Synthetic chemistry has traditionally relied on reactions between reactants of high chemical potential and transformations that proceed energetically downhill to either a global or local minimum (thermodynamic or kinetic control). Catalysts can be used to manipulate kinetic control, lowering activation energies to influence reaction outcomes. However, such chemistry is still constrained by the shape of one-dimensional reaction coordinates. Coupling synthesis to an orthogonal energy input can allow ratcheting of chemical reaction outcomes, reminiscent of the ways that molecular machines ratchet random thermal motion to bias conformational dynamics. This fundamentally distinct approach to synthesis allows multi-dimensional potential energy surfaces to be navigated, enabling reaction outcomes that cannot be achieved under conventional kinetic or thermodynamic control. In this Review, we discuss how ratcheted synthesis is ubiquitous throughout biology and consider how chemists might harness ratchet mechanisms to accelerate catalysis, drive chemical reactions uphill and programme complex reaction sequences., (© 2023. Springer Nature Limited.)

In spite of widespread interest in the unique size-dependent properties and consequent applications of gold nanoparticles (AuNPs), synthetic protocols that reliably allow for independent tuning of surface chemistry and core size, the two critical determinants of AuNP properties, remain limited. Often, core size is inherently affected by the ligand structure in an unpredictable fashion. Functionalized ligands are commonly introduced using postsynthesis exchange procedures, which can be inefficient and operationally delicate. Here, we report a one-step protocol for preparing monolayer-stabilized AuNPs that is compatible with a wide range of ligand functional groups and also allows for the systematic control of core size. In a single-phase reaction using the mild reducing agent tert -butylamine borane, AuNPs that are compatible with solvents spanning a wide range of polarities from toluene to water can be produced without damaging reactive chemical functionalities within the small-molecule surface-stabilizing ligands. We demonstrate that the rate of reduction, which is easily controlled by adjusting the period over which the reducing agent is added, is a simple parameter that can be used irrespective of the ligand structure to adjust the core size of AuNPs without broadening the size distribution. Core sizes in the range of 2-10 nm can thus be generated. The upper size limit appears to be determined by the nature of each specific ligand/solvent pairing. This protocol produces high quality, functionally sophisticated nanoparticles in a single step. By combining the ability to vary size-related nanoparticle properties with the option to incorporate reactive functional groups at the nanoparticle-solvent interface, it is possible to generate chemically reactive colloidal building blocks from which more complex nanoparticle-based devices and materials may subsequently be constructed., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

Autonomous chemically fueled molecular machines that function through information ratchet mechanisms underpin the nonequilibrium processes that sustain life. These biomolecular motors have evolved to be well-suited to the tasks they perform. Synthetic systems that function through similar mechanisms have recently been developed, and their minimalist structures enable the influence of structural changes on machine performance to be assessed. Here, we probe the effect of changes in the fuel and barrier-forming species on the nonequilibrium operation of a carbodiimide-fueled rotaxane-based information ratchet. We examine the machine's ability to catalyze the fuel-to-waste reaction and harness energy from it to drive directional displacement of the macrocycle. These characteristics are intrinsically linked to the speed, force, power, and efficiency of the ratchet output. We find that, just as for biomolecular motors and macroscopic machinery, optimization of one feature (such as speed) can compromise other features (such as the force that can be generated by the ratchet). Balancing speed, power, efficiency, and directionality will likely prove important when developing artificial molecular motors for particular applications.

The experimental isolation of H-bond energetics from the typically dominant influence of the solvent remains challenging. Here we use synthetic molecular balances to quantify amine/amide H-bonds in competitive solvents. Over 200 conformational free energy differences were determined using 24 H-bonding balances in 9 solvents spanning a wide polarity range. The correlations between experimental interaction energies and gas-phase computed energies exhibited wild solvent-dependent variation. However, excellent correlations were found between the same computed energies and the experimental data following empirical dissection of solvent effects using Hunter's α/β solvation model. In addition to facilitating the direct comparison of experimental and computational data, changes in the fitted donor and acceptor constants reveal the energetics of secondary local interactions such as competing H-bonds., (© 2022 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

Chemical reaction networks that transform out-of-equilibrium 'fuel' to 'waste' are the engines that power the biomolecular machinery of the cell. Inspired by such systems, autonomous artificial molecular machinery is being developed that functions by catalysing the decomposition of chemical fuels, exploiting kinetic asymmetry to harness energy released from the fuel-to-waste reaction to drive non-equilibrium structures and dynamics. Different aspects of chemical fuels profoundly influence their ability to power molecular machines. Here we consider the structure and properties of the fuels that biology has evolved and compare their features with those of the rudimentary synthetic chemical fuels that have so far been used to drive autonomous non-equilibrium molecular-level dynamics. We identify desirable, but context-specific, traits for chemical fuels together with challenges and opportunities for the design and invention of new chemical fuels to power synthetic molecular machinery and other dissipative nanoscale processes., (© 2022. Springer Nature Limited.)

Biology operates through autonomous chemically fuelled molecular machinery 1 , including rotary motors such as adenosine triphosphate synthase 2 and the bacterial flagellar motor 3 . Chemists have long sought to create analogous molecular structures with chemically powered, directionally rotating, components 4-17 . However, synthetic motor molecules capable of autonomous 360° directional rotation about a single bond have proved elusive, with previous designs lacking either autonomous fuelling 7,10,12 or directionality 6 . Here we show that 1-phenylpyrrole 2,2'-dicarboxylic acid 18,19 (1a) is a catalysis-driven 20,21 motor that can continuously transduce energy from a chemical fuel 9,20-27 to induce repetitive 360° directional rotation of the two aromatic rings around the covalent N-C bond that connects them. On treatment of 1a with a carbodiimide 21,25-27 , intramolecular anhydride formation between the rings and the anhydride's hydrolysis both occur incessantly. Both reactions are kinetically gated 28-30 causing directional bias. Accordingly, catalysis of carbodiimide hydration by the motor molecule continuously drives net directional rotation around the N-C bond. The directionality is determined by the handedness of both an additive that accelerates anhydride hydrolysis and that of the fuel, and is easily reversed additive 31 . More than 97% of fuel molecules are consumed through the chemical engine cycle 24 with a directional bias of up to 71:29 with a chirality-matched fuel and additive. In other words, the motor makes a 'mistake' in direction every three to four turns. The 26-atom motor molecule's simplicity augurs well for its structural optimization and the development of derivatives that can be interfaced with other components for the performance of work and tasks 32-36 ., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)

Biological systems exhibit a range of complex functions at the micro- and nanoscales under non-equilibrium conditions (for example, transportation and motility, temporal control, information processing and so on). Chemists also employ out-of-equilibrium systems, for example in kinetic selection during catalysis, self-replication, dissipative self-assembly and synthetic molecular machinery, and in the form of chemical oscillators. Key to non-equilibrium behaviour are the mechanisms through which systems are able to extract energy from the chemical reactants ('fuel') that drive such processes. In this Perspective we relate different examples of such powering mechanisms using a common conceptual framework. We discuss how reaction cycles can be coupled to other dynamic processes through positive (acceleration) or negative (inhibition) catalysis to provide the thermodynamic impetus for diverse non-equilibrium behaviour, in effect acting as a 'chemical engine'. We explore the way in which the energy released from reaction cycles is harnessed through kinetic selection in a series of what have sometimes been considered somewhat disparate fields (systems chemistry, molecular machinery, dissipative assembly and chemical oscillators), highlight common mechanistic principles and the potential for the synchronization of chemical reaction cycles, and identify future challenges for the invention and application of non-equilibrium systems. Explicit recognition of the use of fuelling reactions to power structural change in catalysts may stimulate the investigation of known catalytic cycles as potential elements for chemical engines, a currently unexplored area of catalysis research., (© 2021. Springer Nature Limited.)

We report a rotaxane-based information ratchet in which the macrocycle distribution is pumped away from equilibrium using a carbodiimide fuel. A carboxylate group on the axle, nonequidistant between two macrocycle binding sites, efficiently catalyzes the hydration of a carbodiimide fuel to the corresponding urea waste, with >80% of the fuel molecules reacting through the machine-catalyzed pathway. The energy of the reaction is harnessed by kinetic differentiation of the mechanical states of the machine driving the macrocycle to the binding site distal to the catalyst. Steric hindrance between the macrocycle and the fuel slows the reaction of the carboxylate group (to form a barrier to macrocycle movement) in the proximal co-conformer, whereas hydrogen bonding between the macrocycle and the barrier accelerates hydrolysis of the activated ester proximal isomer. The two directionally biased processes reinforce each other's effect, resulting in a doubly kinetically gated ratchet that achieves 1:18 directionality, an exceptional degree of selectivity for a synthetic chemically fueled molecular motor.

We report the reversible chromism and luminescence of a cyclometalated platinum(ii) complex that forms dimers, with close PtPt interactions that can be modulated by solvent and temperature. The precise reversible control may be exploited in future stimuli-responsive chemosensing or optoelectronic devices.

A (Fe II ) 6 -coordinated triply interlocked ("Star of David") [2]catenane (6 1 2 link) and a (Fe II ) 5 -coordinated pentafoil (5 1 ) knot are found to selectively transport anions across phospholipid bilayers. Allostery, topology, and building block stoichiometry all play important roles in the efficacy of the ionophoric activity. Multiple Fe II cation coordination by the interlocked molecules is crucial: the demetalated catenane exhibits no anion binding in solution nor any transmembrane ion transport properties. However, the topologically trivial, Lehn-type cyclic hexameric Fe II helicates-which have similar anion binding affinities to the metalated Star of David catenane in solution-also display no ion transport properties. The unanticipated difference in behavior between the open- and closed-loop structures may arise from conformational restrictions in the linking groups that likely enhances the rigidity of the channel-forming topologically complex molecules. The (Fe II ) 6 -coordinated Star of David catenane, derived from a hexameric cyclic helicate, is 2 orders of magnitude more potent in terms of ion transport than the (Fe II ) 5 -coordinated pentafoil knot, derived from a cyclic pentamer of the same building block. The reduced efficacy is reminiscent of multisubunit protein ion channels assembled with incorrect monomer stoichiometries.

Interactions between carbonyl groups are prevalent in protein structures. Earlier investigations identified dominant electrostatic dipolar interactions, while others implicated lone pair n→π* orbital delocalisation. Here these observations are reconciled. A combined experimental and computational approach confirmed the dominance of electrostatic interactions in a new series of synthetic molecular balances, while also highlighting the distance-dependent observation of inductive polarisation manifested by n→π* orbital delocalisation. Computational fiSAPT energy decomposition and natural bonding orbital analyses correlated with experimental data to reveal the contexts in which short-range inductive polarisation augment electrostatic dipolar interactions. Thus, we provide a framework for reconciling the context dependency of the dominance of electrostatic interactions and the occurrence of n→π* orbital delocalisation in C=O⋅⋅⋅C=O interactions., (© 2020 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

Synthetic ion channels may have applications in treating channelopathies and as new classes of antibiotics, particularly if ion flow through the channels can be controlled. Here we describe triazole-capped octameric α-aminoisobutyric acid (Aib) foldamers that "switch on" ion channel activity in phospholipid bilayers upon copper(ii) chloride addition; activity is "switched off" upon copper(ii) extraction. X-ray crystallography showed that CuCl 2 complexation gave chloro-bridged foldamer dimers, with hydrogen bonds between dimers producing channels within the crystal structure. These interactions suggest a pathway for foldamer self-assembly into membrane ion channels. The copper(ii)-foldamer complexes showed antibacterial activity against B. megaterium strain DSM319 that was similar to the peptaibol antibiotic alamethicin, but with 90% lower hemolytic activity., (This journal is © The Royal Society of Chemistry 2020.)

Metallophilic interactions are increasingly recognized as playing an important role in molecular assembly, catalysis, and bio-imaging. However, present knowledge of these interactions is largely derived from solid-state structures and gas-phase computational studies rather than quantitative experimental measurements. Here, we have experimentally quantified the role of aurophilic (Au I ⋅⋅⋅Au I ), platinophilic (Pt II ⋅⋅⋅Pt II ), palladophilic (Pd II ⋅⋅⋅Pd II ), and nickelophilic (Ni II ⋅⋅⋅Ni II ) interactions in self-association and ligand-exchange processes. All of these metallophilic interactions were found to be too weak to be well-expressed in several solvents. Computational energy decomposition analyses supported the experimental finding that metallophilic interactions are overall weak, meaning that favorable dispersion and orbital hybridization contributions from M⋅⋅⋅M binding are largely outcompeted by electrostatic or dispersion interactions involving ligand or solvent molecules. This combined experimental and computational study provides a general understanding of metallophilic interactions and indicates that great care must be taken to avoid over-attributing the energetic significance of metallophilic interactions., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Nanopores are emerging as a powerful tool for the investigation of nanoscale processes at the single-molecule level. Here, we demonstrate the methionine-selective synthetic diversification of α-hemolysin (α-HL) protein nanopores and their exploitation as a platform for investigating reaction mechanisms. A wide range of functionalities, including azides, alkynes, nucleotides, and single-stranded DNA, were incorporated into individual pores in a divergent fashion. The ion currents flowing through the modified pores were used to observe the trajectory of a range of azide-alkyne click reactions and revealed several short-lived intermediates in Cu(I)-catalyzed azide-alkyne [3 + 2] cycloadditions (CuAAC) at the single-molecule level. Analysis of ion-current fluctuations enabled the populations of species involved in rapidly exchanging equilibria to be determined, facilitating the resolution of several transient intermediates in the CuAAC reaction mechanism. The versatile pore-modification chemistry offers a useful approach for enabling future physical organic investigations of reaction mechanisms at the single-molecule level.

Guest encapsulation is a fundamental property of coordination cages. However, there is a paucity of methods capable of quantifying the dynamics of guest binding processes. Here, we demonstrate nanopore detection of single-molecule binding within metallosupramolecular cages. Real-time monitoring of the ion current flowing through a transmembrane α-hemolysin nanopore resolved the binding of different guests to both cage enantiomers. This enabled the single-molecule kinetics of guest binding to be quantified, whereas the ordering and durations of events were consistent with a guest-exchange mechanism that does not involve ligand dissociation. In addition to providing a new approach for single-molecule interrogation of dynamic supramolecular processes, this work also establishes that cage complexes which are too large to enter the nanopore can be exploited for detecting small molecules, thus constituting a new class of molecular adapter., (© 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Monitoring current flow through a single nanopore has proved to be a powerful technique for the in situ detection of molecular structure, binding, and reactivity. Transmembrane proteins, such as α-hemolysin, provide particularly attractive platforms for nanopore sensing applications due to their atomically precise structures. However, many nanopore applications require the introduction of functional groups to tune selectivity. To date, such modifications have required genetic modification of the protein prior to functionalization. Here we demonstrate the in situ synthetic modification of a wild-type α-hemolysin nanopore embedded in a membrane. We show that reversible dynamic covalent iminoboronate formation and the resulting changes in the ion current flowing through an individual nanopore can be used to map the reactive behavior of lysine residues within the nanopore channel. Crucially, the modification of lysine residues located outside the nanopore channel was found not to affect the stability or utility of the nanopore. Finally, knowledge of the reactivity patterns enabled the irreversible functionalization of a single, assignable lysine residue within the nanopore channel. The approach constitutes a simple, generic tool for the rapid, in situ synthetic modification of protein nanopores that circumvents the need for prior genetic modification.

Supramolecular chirality may emerge from self-assembly processes to yield architectures that differ only in the topological arrangement of their constituent parts. Since the properties of the resulting enantiomeric assemblies are identical, purification and characterisation can be challenging. Here, we have examined the hypothesis that the intrinsic chirality of a protein nanopore can be exploited to detect supramolecular chirality. Transient blockages in the ion current flowing through a single membrane-spanning α-haemolysin nanopore were shown to discriminate between M 4 L 6 tetrahedral coordination cages of opposing chiralities. The single-molecule nature of the approach facilitated direct access to the rates of association and dissociation with the nanopore, which allowed the concentrations of the enantiomeric supramolecular assemblies to be determined in situ . Thus, we have established that a protein nanopore can be used to discriminate the chiral topologies of supramolecular assemblies, even when they are too large to fully enter the nanopore.

The quantitative assembly and disassembly of a new type of dynamic covalent nanoparticle (NP) building block is reported. In situ spectroscopic characterization reveals constitutionally adaptive NP-bound monolayers of boronate esters. Ditopic linker molecules are used to produce covalently connected AuNP assemblies, displaying open dendritic morphologies, and which, despite being linked by covalent bonds, can be fully disassembled on application of an appropriate chemical stimulus.

We demonstrate a straightforward nonbiomolecular approach for self-assembly of binary NP planet-satellite superstructures, which display remarkable colloidal and structural stability under variations in temperature, pH, ionic strength and solvent. The readily scalable process produces highly homogeneous samples and is tolerant to variations in building block size and shape, giving rapid access to a structurally diverse range of robust binary NP assemblies.