Individual‐Molecule Perspective Analysis of Chemical Reaction Networks: The Case of a Light‐Driven Supramolecular Pump

Harnessing Maxwell's demon to establish a macroscale concentration gradient

Maxwell's demon describes a thought experiment in which a 'demon' regulates the flow of particles between two adjoining spaces, establishing a potential gradient without appearing to do work. This seeming paradox led to the understanding that sorting entails thermodynamic work, a foundational concept of information theory. In the past centuries, many systems analogous to Maxwell's demon have been introduced in the form of molecular information, molecular pumps and ratchets. Here we report a functional example of a Maxwell's demon that pumps material over centimetres, whereas previous examples operated on a molecular scale. In our system, this demon drives directional transport of o-fluoroazobenzene between the arms of a U-tube apparatus upon light irradiation, transiting through an aqueous membrane containing a coordination cage. The concentration gradient thus obtained is further harnessed to drive naphthalene transport in the opposite direction.

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.

Sample size dependence of tagged molecule dynamics in steady-state networks with bimolecular reactions: Cycle times of a light-driven pump

Here, steady-state reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agent-based viewpoint is useful for selectively characterizing the behavior of functional molecules, especially in the presence of bimolecular processes. We present the tools for simulating the jump dynamics both in the macroscopic limit and in the small-volume sample where the numbers of reactive molecules are of the order of few units with an inherently stochastic kinetics. The focus is on how an ideal spatial "compartmentalization" may affect the dynamical features of the tagged molecule. Our general approach is applied to a synthetic light-driven supramolecular pump composed of ring-like and axle-like molecules that dynamically assemble and disassemble, originating an average ring-through-axle directed motion under constant irradiation. In such an example, the dynamical feature of interest is the completion time of direct/inverse cycles of tagged rings and axles. We find a surprisingly strong robustness of the average cycle times with respect to the system's size. This is explained in the presence of rate-determining unimolecular processes, which may, therefore, play a crucial role in stabilizing the behavior of small chemical systems against strong fluctuations in the number of molecules.

Artificial Supramolecular Pumps Powered by Light

The development of artificial nanoscale motors that can use energy from a source to perform tasks requires systems capable of performing directionally controlled molecular movements and operating away from chemical equilibrium. Here, the design, synthesis and properties of pseudorotaxanes are described, in which a photon input triggers the unidirectional motion of a macrocyclic ring with respect to a non-symmetric molecular axle. The photoinduced energy ratcheting at the basis of the pumping mechanism is validated by measuring the relevant thermodynamic and kinetic parameters. Owing to the photochemical behavior of the azobenzene moiety embedded in the axle, the pump can repeat its operation cycle autonomously under continuous illumination. NMR spectroscopy was used to observe the dissipative non-equilibrium state generated in situ by light irradiation. We also show that fine changes in the axle structure lead to an improvement in the performance of the motor. Such results highlight the modularity and versatility of this minimalist pump design, which provides facile access to dynamic systems that operate under photoinduced non-equilibrium regimes.

From Selection to Instruction and Back: Competing Conformational Selection and Induced Fit Pathways in Abiotic Hosts

Two limiting cases of molecular recognition, induced fit (IF) and conformational selection (CS), play a central role in allosteric regulation of natural systems. The IF paradigm states that a substrate "instructs" the host to change its shape after complexation, while CS asserts that a guest "selects" the optimal fit from an ensemble of preexisting host conformations. With no studies that quantitatively address the interplay of two limiting pathways in abiotic systems, we herein and for the first time describe the way by which twisted capsule M-1, encompassing two conformers M-1(+) and M-1(-), trap CX₄ (X=Cl, Br) to give CX₄ ⊂M-1(+) and CX₄ ⊂M-1(-), with all four states being in thermal equilibrium. With the assistance of 2D EXSY, we found that CBr₄ would, at its lower concentrations, bind M-1 via a M-1(+)→M-1(-)→CBr₄ ⊂M-1(-) pathway corresponding to conformational selection. For M-1 complexing CCl₄ though, data from 2D EXSY measurements and 1D NMR line-shape analysis suggested that lower CCl₄ concentrations would favor CS while the IF pathway prevailed at higher proportions of the guest. Since CS and IF are not mutually exclusive, we reason that our work sets the stage for characterizing the dynamics of a wide range of already existing hosts to broaden our fundamental understanding of their action. The objective is to master the way in which encapsulation takes place for designing novel and allosteric sequestering agents, catalysts and chemosensors akin to those found in nature.