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See detailTHERMODYNAMICS OF CHEMICAL ENGINES: A CHEMICAL REACTION NETWORK APPROACH
Penocchio, Emanuele UL

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 ▲]

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See detailInformation thermodynamics for deterministic chemical reaction networks
Penocchio, Emanuele UL; Avanzini, Francesco UL; Esposito, Massimiliano UL

in Journal of Chemical Physics (2022), 157(3), 034110

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See detailSample size dependence of tagged molecule dynamics in steady-state networks with bimolecular reactions: Cycle times of a light-driven pump
Asnicar, Daniele; Penocchio, Emanuele UL; Frezzato, Diego

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 ▲]

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See detailKinetic and energetic insights into the dissipative non-equilibrium operation of an autonomous light-powered supramolecular pump
Corra, Stefano; Baki, Marina Tranfi; Groppi, Jessica et al

in Nature Nanotechnology (2022)

Natural and artificial autonomous molecular machines operate by constantly dissipating energy coming from an external source to maintain a non-equilibrium state. Quantitative thermodynamic ... [more ▼]

Natural and artificial autonomous molecular machines operate by constantly dissipating energy coming from an external source to maintain a non-equilibrium state. Quantitative thermodynamic characterization of these dissipative states is highly challenging as they exist only as long as energy is provided. Here we report on the detailed physicochemical characterization of the dissipative operation of a supramolecular pump. The pump transduces light energy into chemical energy by bringing self-assembly reactions to non-equilibrium steady states. The composition of the system under light irradiation was followed in real time by 1H NMR for four different irradiation intensities. The experimental composition and photon flow were then fed into a theoretical model describing the non-equilibrium dissipation and the energy storage at the steady state. We quantitatively probed the relationship between the light energy input and the deviation of the dissipative state from thermodynamic equilibrium in this artificial system. Our results provide a testing ground for newly developed theoretical models for photoactivated artificial molecular machines operating away from thermodynamic equilibrium. [less ▲]

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See detailInsights from an information thermodynamics analysis of a synthetic molecular motor
Amano, Shuntaro; Esposito, Massimiliano UL; Kreidt, Elisabeth et al

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 ▲]

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See detailNonequilibrium thermodynamics of light-induced reactions
Penocchio, Emanuele UL; Rao, Riccardo; Esposito, Massimiliano UL

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 ▲]

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See detailNonequilibrium thermodynamics of non-ideal chemical reaction networks
Avanzini, Francesco UL; Penocchio, Emanuele UL; Falasco, Gianmaria UL et al

in Journal of Chemical Physics (2021), 154

All current formulations of nonequilibrium thermodynamics of open chemical reaction networks rely on the assumption of non-interacting species. We develop a general theory that accounts for interactions ... [more ▼]

All current formulations of nonequilibrium thermodynamics of open chemical reaction networks rely on the assumption of non-interacting species. We develop a general theory that accounts for interactions between chemical species within a mean-field approach using activity coefficients. Thermodynamic consistency requires that rate equations do not obey standard mass-action kinetics but account for the interactions with concentration dependent kinetic constants. Many features of the ideal formulations are recovered. Crucially, the thermodynamic potential and the forces driving non-ideal chemical systems out of equilibrium are identified. Our theory is general and holds for any mean-field expression of the interactions leading to lower bounded free energies. [less ▲]

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See detailThermodynamic efficiency in dissipative chemistry
Penocchio, Emanuele UL; Rao, Riccardo; Esposito, Massimiliano UL

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

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See detailNegative differential response in chemical reactions
Falasco, Gianmaria UL; Cossetto, Tommaso UL; Penocchio, Emanuele UL et al

in New Journal of Physics (2019), 21

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See detailIndividual-molecule perspective analysis of chemical reaction networks: the case of a light-driven supramolecular pump
Sabatino, Andrea; Penocchio, Emanuele UL; Ragazzon, Giulio et al

in Angewandte Chemie International Edition (2019)

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