An Allosterically Regulated Molecular Shuttle

Marlin, Dana S.; Cabrera, Diego Gonzàlez; Leigh, David A.; Slawin, Alexandra M. Z.

doi:10.1002/anie.200502624

Cited by 83 publications

(45 citation statements)

References 47 publications

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“…Photoinduced isomerization of azobenene has found broad applications in molecular switches [1][2][3][4] , molecular shuttles and rotors [5][6][7][8] , in photoregulation of biological molecules 9,10 , and in optical data storage 11 , etc. Azobenzene and derivatives can also serve as a light-to-mechanical energy converter in specifically designed molecular settings 12 , or within a movable molecular track-walker [13][14][15][16][17] .…”

Section: Introductionmentioning

confidence: 99%

Nonadiabatic simulation study of photoisomerization of azobenzene: Detailed mechanism and load-resisting capacity

Shao

Lei²,

Wen³

et al. 2008

The Journal of Chemical Physics

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Non-adiabatic dynamical simulations were carried out to study cis-to-trans isomerization of azobenzene under laser irradiation and/or external mechanical loads. We used a semiclassical electron-radiation-ion dynamics method that is able to describe the co-evolution of the structural dynamics and the underlying electronic dynamics in a real-time manner. It is found that azobenzene photoisomerization occurs predominantly by an out-of-plane rotation mechanism even under a non trivial resisting force of several tens pN. We have repeated the simulations systematically for a broad range of parameters for laser pulses, but could not find any photoisomerization event by a previously suggested in-plane inversion mechanism. The simulations found that the photoisomerization process can be held back by an external resisting force of 90-200 picoNewtons depending on the frequency and intensity of the lasers. This study also found that a pure mechanical isomerization is possible from the cis to trans state if the azobenzene molecule is stretched by an external force of ~ 1250 -1650 pN. Remarkably, the mechanical isomerization first proceeds through a mechanically activated inversion, and then is diverted to an ultrafast, downhill rotation that accomplishes the isomerization. Implications of these findings to azobenzene-based nanomechanical devices are discussed.

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Section: Introductionmentioning

confidence: 99%

Nonadiabatic simulation study of photoisomerization of azobenzene: Detailed mechanism and load-resisting capacity

Shao

Lei²,

Wen³

et al. 2008

The Journal of Chemical Physics

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“…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). Nevertheless, studies of allosteric effects in rotaxanes and catenanes are rare (12) and have been limited so far to a pioneering work by Sauvage and coworkers (13) and, more recently, to the realization of stimuli-responsive switches (14,15) for controlling catalytic functions (16)(17)(18)(19)(20).…”

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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“…Notably, template assembled interlocked architectures feature prominently as prototypes of molecular machines 30,31 and drug delivery vehicles, 32 whilst the role of molecular design in obtaining protein-surface binding ligands relies upon the principles of supramolecular chemistry and will form the basis for sensing 33 and treatment of disease in future. Increasingly, supramolecular chemistry finds itself at multidisciplinary interfaces as a key component of programs in nanotechnology and chemical biology.…”

Section: Discussionmentioning

confidence: 99%

Supramolecular chemistry

Wilson

2007

Annu. Rep. Prog. Chem., Sect. B: Org. Chem.

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The following review describes significant advances in the field of supramolecular chemistry for the year 2006. As for previous articles in this series, it is not a comprehensive treatment of the literature. The review is split into three sections covering (i) molecular recognition, (ii) structure and assembly and (iii) functional systems. View Online entire system, self-sorting must necessarily occur. Interestingly the authors also observed an extremely slow dissociation rate (8.5 Â 10 À10 s À1 ) for disassembly of 3.6, which, married with its relatively low affinity, would make it an ideal motif for applications such as affinity chromatography.Anion recognition also remains a key goal in supramolecular chemistry. Gale and co-workers have reported on the different anion binding modes observed for the binding interactions of macrocyclic amidourea 7. 7 They found that carboxylates bound with high-affinity in 0.5% water in DMSO as observed by 1 H NMR titration, but that phosphates and chloride bound less well. The behaviour was attributed to the different binding geometry that each anion class could adopt. For carboxylates, downfield changes in chemical shift were observed for the urea protons and the dicarboxamidopyridine, whereas only the latter underwent changes for phosphate. For chloride, downfield shifts were observed for the urea protons but upfield shifts for the dicarboxamidopyridine, suggesting solvent reorganization presumably due to a lack of shape complementarity for this anion.Anthony Davis and co-workers devised a synthesis of the triamino derivative of methyl allocholate which could be functionalized with isocyanates to form a receptor 8 for various anions (AcO À , EtSO 3 À , Cl À , Br À , NO 3 À , I À , ClO 4 À ). 8 The derivative 8 was found to bind these anions with affinities almost double that observed for the more established tris-urea derivative of cholic acid 9. This was rationalized by the fact that in the original cholapod 9, free rotation about the amine at position 3 results in formation of intramolecular hydrogen-bonds, whereas unfavourable diaxial interactions prevent this in the new derivative 9.

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An Allosterically Regulated Molecular Shuttle

Cited by 83 publications

References 47 publications

Nonadiabatic simulation study of photoisomerization of azobenzene: Detailed mechanism and load-resisting capacity

Nonadiabatic simulation study of photoisomerization of azobenzene: Detailed mechanism and load-resisting capacity

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

Supramolecular chemistry

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An Allosterically Regulated Molecular Shuttle

Cited by 83 publications

References 47 publications

Nonadiabatic simulation study of photoisomerization of azobenzene: Detailed mechanism and load-resisting capacity

Nonadiabatic simulation study of photoisomerization of azobenzene: Detailed mechanism and load-resisting capacity

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

Supramolecular chemistry

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