Kinetic Asymmetry and Directionality of Nonequilibrium Molecular Systems

Abstract

Scientists have long been fascinated by the biomolecular machines in living systems that process energy and information to sustain life. The first synthetic molecular rotor capable of performing repeated 360° rotations due to a combination of photo‐ and thermally activated processes was reported in 1999. The progress in designing different molecular machines in the intervening years has been remarkable, with several outstanding examples appearing in the last few years. Despite the synthetic accomplishments, there remains confusion regarding the fundamental design principles by which the motions of molecules can be controlled, with significant intellectual tension between mechanical and chemical ways of thinking about and describing molecular machines. A thermodynamically consistent analysis of the kinetics of several molecular rotors and pumps shows that while light driven rotors operate by a power‐stroke mechanism, kinetic asymmetry—the relative heights of energy barriers—is the sole determinant of the directionality of catalysis driven machines. Power‐strokes—the relative depths of energy wells—play no role whatsoever in determining the sign of the directionality. These results, elaborated using trajectory thermodynamics and the nonequilibrium pump equality, show that kinetic asymmetry governs the response of many non‐equilibrium chemical phenomena.

Catalytic Resonance Theory: The Catalytic Mechanics of Programmable Ratchets

“…In the weak-binding state, the catalyst has a higher transition state energy than the purple molecule in the gas phase, forming what has been referred to as an 'energy ratchet.' [8,9] The net positive energy input has the role of promoting the reaction forward in a mechanism that has been shown to promote reactions past chemical equilibrium, [2,10,11] raising the surface product energy using input work.…”

“…When decomposed to their fundamental design parameters, each mechanism can be varied within large parameter space such that identifying conditions of effective operation cannot currently be determined a priori, including the direction of the programmable ratchet (forward or reverse bias), the condition at which molecules traverse the ratchet (weak or strong catalyst binding state), and the temperatures and applied frequencies for which the ratchet becomes relevant to a catalytic reaction system. While characterization of stochastic energy ratchets has been extensively examined, [11,12] this work will focus on the characteristics of programmable energy ratchets for catalysis. These fundamental descriptors of elementary catalytic ratchets will then serve to understand the more complicated behaviors of multi-step catalytic θi None Surface coverage of species i θi,eq None The equilibrium surface coverage of species i 𝜃 𝑖,ℎ𝑓…”

Catalytic Resonance Theory: The Catalytic Mechanics of Programmable Ratchets

“…In the weak-binding state, the catalyst has a higher transition state energy than the purple molecule in the gas phase, forming what has been referred to as an 'energy ratchet.' [8,9] The net positive energy input has the role of promoting the reaction forward in a mechanism that has been shown to promote reactions past chemical equilibrium, [2,10,11] raising the surface product energy using input work.…”

“…When decomposed to their fundamental design parameters, each mechanism can be varied within large parameter space such that identifying conditions of effective operation cannot currently be determined a priori, including the direction of the programmable ratchet (forward or reverse bias), the condition at which molecules traverse the ratchet (weak or strong catalyst binding state), and the temperatures and applied frequencies for which the ratchet becomes relevant to a catalytic reaction system. While characterization of stochastic energy ratchets has been extensively examined, [11,12] this work will focus on the characteristics of programmable energy ratchets for catalysis. These fundamental descriptors of elementary catalytic ratchets will then serve to understand the more complicated behaviors of multi-step catalytic θi None Surface coverage of species i θi,eq None The equilibrium surface coverage of species i 𝜃 𝑖,ℎ𝑓…”