THERMODYNAMICS OF CHEMICAL ENGINES: A CHEMICAL REACTION NETWORK APPROACH

Doctoral thesis (2022)

Chemical processes in closed systems inevitably relax to equilibrium. Energy can be employed to counteract such tendency and drive reactions against their spontaneous direction. This nonequilibrium ... [more ▼]

Chemical processes in closed systems inevitably relax to equilibrium. Energy can be employed to counteract such tendency and drive reactions against their spontaneous direction. This nonequilibrium driving is implemented in open systems, which living organisms provide the most spectacular examples of. In recent years, experiments in supramolecular chemistry, photochemistry and electrochemistry demonstrated that, by opening synthetic systems to matter and/or energy exchanges with the environment, artificial systems with life-like behaviours can be realized and used to convert energy inputs of different nature into work at both the nanoscopic and the macroscopic level. However, one tool that is still lacking is a firm grasp of the thermodynamics of these chemical engines. In this thesis, we provide it by leveraging the most recent developments of the thermodynamic description of deterministic chemical reaction networks. As main theoretical results, we extend the current theory to encompass nonideal and light-driven systems, thus providing the fundamental tools to treat electrochemical and photochemical systems in addition to the chemically driven ones. We also expand the scope of information thermodynamics to bipartite chemical reaction networks characterized by macroscopic non-normalized concentration distributions evolving in time with nonlinear dynamics. This framework potentially applies to almost every synthetic chemical engine realized until now, and to many models of biological systems too. Here, we undertake the thermodynamic analysis of some of the epitomes in the field of artificial chemical engines: a model of chemically driven self-assembly, an experimental chemically driven molecular motor, and an experimental photochemical bimolecular pump. The thesis provides a thermodynamic level of understanding of chemical engines that is general, complements previous analyses based on kinetics and stochastic thermodynamics, and has practical implications for designing and improving synthetic systems, regardless of the particular type of powering or chemical structure. [less ▲]

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

in Journal of Chemical Physics (2022), 156(18), 184116

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 ... [more ▼]

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. [less ▲]

Insights from an information thermodynamics analysis of a synthetic molecular motor

in Nature Chemistry (2022), 14(5), 530-537

Information is physical, a realization that has transformed the physics of measurement and communication. However, the flow between information, energy and mechanics in chemical systems remains largely ... [more ▼]

Information is physical, a realization that has transformed the physics of measurement and communication. However, the flow between information, energy and mechanics in chemical systems remains largely unexplored. Here we analyse a minimalist autonomous chemically driven molecular motor in terms of information thermodynamics, a framework that quantitatively relates information to other thermodynamic parameters. The treatment reveals how directional motion is generated by free energy transfer from chemical to mechanical (conformational and/or co-conformational) processes by `energy flow' and `information flow'. It provides a thermodynamic level of understanding of molecular motors that is general, complements previous analyses based on kinetics and has practical implications for machine design. In line with kinetic analysis, we find that power strokes do not affect the directionality of chemically driven machines. However, we find that power strokes can modulate motor velocity, the efficiency of free energy transfer and the number of fuel molecules consumed per cycle. This may help explain the role of such (co-)conformational changes in biomachines and illustrates the interplay between energy and information in chemical systems. [less ▲]

Nonequilibrium thermodynamics of light-induced reactions

in Journal of Chemical Physics (2021), 155

Current formulations of nonequilibrium thermodynamics of open chemical reaction networks only consider chemostats as free-energy sources sustaining nonequilibrium behaviors. Here, we extend the theory to ... [more ▼]

Current formulations of nonequilibrium thermodynamics of open chemical reaction networks only consider chemostats as free-energy sources sustaining nonequilibrium behaviors. Here, we extend the theory to include incoherent light as a source of free energy. We do so by relying on a local equilibrium assumption to derive the chemical potential of photons relative to the system they interact with. This allows us to identify the thermodynamic potential and the thermodynamic forces driving light-reacting chemical systems out-of-equilibrium. We use this framework to treat two paradigmatic photochemical mechanisms describing light-induced unimolecular reactions—namely, the adiabatic and diabatic mechanisms—and highlight the different thermodynamics they lead to. Furthermore, using a thermodynamic coarse-graining procedure, we express our findings in terms of commonly measured experimental quantities, such as quantum yields. [less ▲]

Thermodynamic efficiency in dissipative chemistry

in Nature Communications (2019), 10(1), 1-5

Individual-molecule perspective analysis of chemical reaction networks: the case of a light-driven supramolecular pump

in Angewandte Chemie International Edition (2019)