Shuttling Dynamics in an Acid–Base‐Switchable [2]Rotaxane

Garaudée, Sandrine; Silvi, Serena; Venturi, Margherita; Flood, Amar H.

doi:10.1002/cphc.200500295

Cited by 99 publications

(59 citation statements)

References 61 publications

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“…In 1H 3+ the molecular ring encircles almost exclusively the amH + site; in the presence of a suitable base the rotaxane is deprotonated and M translates over the bpy 2+ unit, where it is engaged in charge-transfer interactions (27,29). The acid-base-controlled shuttling reaction is schematized in Fig.…”

Section: +mentioning

confidence: 99%

Remote electrochemical modulation of pK _a in a rotaxane by co-conformational allostery

Ragazzon

Schäfer

Franchi

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Allosteric control, one of Nature's most effective ways to regulate functions in biomolecular machinery, involves the transfer of information between distant sites. The mechanistic details of such a transfer are still an object of intensive investigation and debate, and the idea that intramolecular communication could be enabled by dynamic processes is gaining attention as a complement to traditional explanations. Mechanically interlocked molecules, owing to the particular kind of connection between their components and the resulting dynamic behavior, are attractive systems to investigate allosteric mechanisms and exploit them to develop functionalities with artificial species. We show that the pK a of an ammonium site located on the axle component of a [2]rotaxane can be reversibly modulated by changing the affinity of a remote recognition site for the interlocked crown ether ring through electrochemical stimulation. The use of a reversible ternary redox switch enables us to set the pK a to three different values, encompassing more than seven units. Our results demonstrate that in the axle the two sites do not communicate, and that in the rotaxane the transfer of information between them is made possible by the shuttling of the ring, that is, by a dynamic intramolecular process. The investigated coupling of electron-and proton-transfer reactions is reminiscent of the operation of the protein complex I of the respiratory chain.acid-base processes | electrochemistry | free energy change | molecular machine | molecular switch A llostery-the process by which a chemical transformation at one site causes a change at a distant site within the same molecule or molecular assembly-is a key phenomenon for the regulation of biological activity (1, 2). A most important example is the long-range coupling of redox-active and acid-basesensitive sites, a crucial element of electron transport chains, as exemplified by the respiratory complex I (3). Although allosteric effects are usually described in terms of conformational changes induced by binding at one site directly affecting the affinity of the other site (4), the idea that the transmission of information at the basis of allostery could take place through dynamic mechanisms is receiving increasing attention (5-7). Indeed, despite its importance for life, allosteric regulation remains an elusive biochemical phenomenon.Mechanically interlocked molecules (MIMs) (8) such as rotaxanes and catenanes, because of the lack of strong chemical bonds between their molecular parts, are characterized by a rich dynamic behavior that involves changes of the relative position of the components (co-conformation). Indeed, in appropriately designed MIMs co-conformational rearrangements can be precisely controlled by modulating the noncovalent intercomponent interactions through external stimulation (9, 10). For these reasons, MIMs can be regarded as appealing systems for investigating allosteric communication mechanisms and implementing them within synthetic species to achieve functions (11)....

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Section: +mentioning

confidence: 99%

Remote electrochemical modulation of pK _a in a rotaxane by co-conformational allostery

Ragazzon

Schäfer

Franchi

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…unlink bipy = 0.0072 and unlink nh = 0.4. The aim of the first two simulations depicted in Figure 4 is to check whether the experimentation in silico corresponds to the experimentation in in vitro [8]. The techniques used for the in vitro experimentation did not permit to observe and quantify the deprotonation/reprotonation rates (this is not surprising as these are very fast acid-base reactions).…”

Section: Simulation Resultsmentioning

confidence: 99%

“…In fact, this is a bimolecular reaction with rate is influenced by the concentration of the reactants. For instance, at the concentration considered in [8] We have repeated the two simulations: deprotonation with subsequent "forward" shuttling and reprotonation with subsequent "backward" shuttling considering the two different concentrations. We had to reduce the number of rotaxanes and acid/base molecules to 100 because the simulation required too much time with 1000 molecules.…”

Section: Simulation Resultsmentioning

confidence: 99%

“…Specifically, the macrocycle's shuttling process between the ammonium/amine and bipyridinium stations in this rotaxane, driven by the successive addition of base and acid, have been investigated in solution [8]. The rate constants for the "forward" (Ra→Rb) and "backward" (RbH→RaH) shuttling motions (horizontal processes in Figure 2) of the molecular ring which occur, respectively, upon deprotonation and reprotonation of the ammonium/amine recognition site on the axle (vertical processes in Figure 2), were found to be 0.72s −1 and 40s −1 at 293K, respectively.…”

Section: ∞ −→}mentioning

confidence: 99%

“…We then apply the nanoκ calculus to describe and analyze the "Rotaxane RaH" [15,1], an instance of rotaxane for which the dynamic behaviour has been experimentally characterized in detail [8]. We have considered two groups of simulations.…”

Section: Introductionmentioning

confidence: 99%

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