Adiabatic operation of a molecular machine

Abstract

Operation of a molecular machine is often thought of as a ''far from equilibrium'' process in which energy released by some high free energy fuel molecule or by light is used to drive a nonequilibrium ''power stroke'' to do work on the environment. Here we discuss how a molecular machine can be operated arbitrarily close to chemical equilibrium and still perform significant work at an appreciable rate: micrometer per second velocities against piconewton loads. As a specific example, we focus on a motor based on a three-ring catenane similar to that discussed by Leigh T here has been great recent progress in constructing molecular machines from complexes held together by mechanical rather than chemical bonds (1-3). Structures with fascinating topologies have been created (4) and combined to assemble intricate devices, including molecular ''elevators'' (5) and nanoscale switchable valves (6). Perhaps the greatest interest in these mechanically linked molecules lies in the fact that they can be engineered to have large-scale motions controllable through external changes in the environment. This feature facilitates the design of molecular motors (7,8) and rotors (9), devices that can be caused to undergo directional motion by an external source of chemical (10), optical (11), or electrical (12) energy. Control is achieved by incorporating two or more recognition stations (sites where the components of the complex interact strongly) to define several intracomplex binding sites (13,14) and, hence, several configurational states of the molecule. The relative thermodynamic stability of the different sites (and hence states) is controlled by, e.g., protonation/deprotonation, reduction/ oxidation, or absorption of light. By changing the pH, redox potential, or light intensity, the molecule can be switched from one state to another externally.Recently catenanes-structures with two or more interlocked rings-have been designed that allow external control not only of the relative stabilities of the binding sites but also of the relative labilities of the pathways linking the sites (10). By carrying out a sequence of external cyclical changes to the labilities and stabilities of the sites, the rings could be squeezed to undergo directional rotation by a mechanism similar to peristalsis (15), except that the transitions occur by thermal noise so the system operates as a Brownian motor (16).Here I will describe how a molecular machine can be operated arbitrarily close to chemical equilibrium at every instant and still do significant work at an appreciable rate. Consider the threering catenane shown in Fig. 1. The larger gray ring has three distinct recognition stations, labeled 1, 2, and 3, for the two identical yellow rings. The yellow rings cannot pass one another, nor can they occupy the same station, because they make thermally activated transitions from one station to another. Thus, there are a total of three states, labeled A, B, and C. The interaction between a yellow ring with a station is characterized by an interacti...

Efficiency of Autonomous Soft Nanomachines at Maximum Power

“…At present, the latter mostly still need a modulation of external parameters for driving them through a cycle as investigated theoretically in Refs. [19][20][21]. "Soft" is short for working in an aqueous environment which will require some flexibility in the molecule(s) allowing for conformational changes to operate as a machine.…”

Stochastic thermodynamics of hidden pumps

“…To do so we consider systems with hidden states driven by an external cyclic time-dependent force generating currents between the apparent states. The driving is based on adiabatic pumping previously introduced in the literature [29][30][31][32][33][34] but gives rise in our case to a Markovian dynamics at the coarse-grained level. We show that our reversible pumps can be used to generate currents against a bias with zero entropy production.…”

Bimodal dynamics of mechanically constrained hydrogen bonds revealed by vibrational photon echoes

“…4,[15][16][17][18][19] Although the dynamics of catenane-and rotaxane-based systems have been extensively studied on the second and millisecond time scales, 16,20 the fundamental motions within their components, and the thermal fluctuations in the surrounding medium take place in the picosecond or subpicosecond time domain. In order to understand how such elementary motions of individual functional groups determine the global behavior of relatively massive (>500 D) mechanically linked fragments, it is necessary to have a "quantum tool" that provides detailed insight into both structure and dynamics on such time scales.…”