Chemical engines: driving systems away from equilibrium through catalyst reaction cycles

Abstract

Biological systems exhibit a range of complex functions at the micro-and nanoscale under non-equilibrium conditions (e.g. transportation and motility, temporal control, information processing, etc.). Synthetic chemists also use out-of-equilibrium systems, for example in kinetic selection during catalysis, self-replication, dissipative self-assembly, synthetic molecular machines, and in the form of chemical oscillators. Key to non-equilibrium behavior are the mechanisms through which systems are able to extract energy from the fuel. In this Perspective we consider different examples 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 behavior, in effect acting as a chemical engine. We explore the way that the energy released from reaction cycles is harnessed through kinetic selection in a series of what may have previously been considered somewhat disparate fields (systems chemistry, molecular machinery, supramolecular assembly and chemical oscillators), highlight common mechanistic principles, introduce concepts for the synchronization of chemical reaction cycles, and identify future challenges for the invention and application of non-equilibrium systems. MainBiological systems exhibit a broad range of complex functions, from transportation and motility 1-4 to temporal control 5,6 and information processing 7,8 , under non-equilibrium conditions realized by dissipating the chemical potential of high-energy species (typically the hydrolysis of adenosine triphosphate (ATP) or guanosine triphosphate (GTP) [3][4][5]7 ). Synthetic chemists are creating their own non-equilibrium systems, resulting in kinetic selection in catalysis, self-replicating systems 9,10 , dissipative assembly [11][12][13] , synthetic molecular machines 14-17 , and

Rigidity and Flexibility in Rotaxanes and Their Relatives; On Being Stubborn and Easy-Going

“…Diverse components are frequently incorporated into molecular and nanoscale machines ( Qiu et al, 2020b ; Colasson et al, 2020 ; Amano et al, 2021 ), but studies examining the role of rigidity and flexibility in their design ( Chen et al, 2021 ) and operation ( Kistemaker et al, 2021 ) are relatively rare. Exemplary studies involve molecular shuttles ( Nygaard et al, 2007 ; Gholami et al, 2017 ) and switches ( Andersen et al, 2014 ).…”

“…In these cases, both rigidity and flexibility could be beneficial depending on the design requirements of the application. At the same time, molecular switches and machines are a growing platform to perform work at the nanoscale ( McTernan et al, 2020 ; Amano et al, 2021 ). Switches and machines with more rigid building blocks were shown to have fewer conformations and lower barriers to shuttling than their flexible counterparts, which suggests that more rigid designs could lead to more efficient and controllable machines.…”

Autonomous Non-Equilibrium Self-Assembly and Molecular Movements Powered by Electrical Energy

“…Mechanical steps are part of a cyclic network of chemical reactions that occurs directionally under non-equilibrium conditions, operating as a chemical engine. 50 As for other autonomous systems, the autonomous operation was established through a series of individually provable premises. 18 The present system operates according to an energy ratchet mechanism, which so far could operate autonomously only when driven by light irradiation.…”

Information Thermodynamics for Deterministic Chemical Reaction Networks

“…Engines commonly operate such that some components (e.g., pistons) directly interact with the power source to harvest energy, whereas some other components (e.g., wheels) produce the functionality the engine is designed for. Chemical engines [1], such as molecular motors, are no exception [2][3][4]. Indeed, they can be rationally described [5][6][7][8][9] and designed [1,[10][11][12][13] as chemical reaction networks (CRNs) where energy-harvesting chemical [14][15][16][17][18][19][20], photochemical [21][22][23][24][25][26][27] or electrochemical [27][28][29] processes are coupled with large-amplitude intramolecular motions or selfassembly reactions.…”

“…Chemical engines [1], such as molecular motors, are no exception [2][3][4]. Indeed, they can be rationally described [5][6][7][8][9] and designed [1,[10][11][12][13] as chemical reaction networks (CRNs) where energy-harvesting chemical [14][15][16][17][18][19][20], photochemical [21][22][23][24][25][26][27] or electrochemical [27][28][29] processes are coupled with large-amplitude intramolecular motions or selfassembly reactions. ese CRNs are o en bipartite [30,31], as the energy-harvesting processes act on some molecular properties (e.g., phosphorylation state, photo-isomerization state, oxidation/reduction state) while the processes realizing the engine's functionality act on di erent properties (e.g., position in space, assembly state).…”