Mechanically Interlocked Molecules (MIMs)—Molecular Shuttles, Switches, and Machines (Nobel Lecture)

Stoddart, J. Fraser

doi:10.1002/anie.201703216

Cited by 844 publications

(760 citation statements)

References 99 publications

(184 reference statements)

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“…Although the push toward application of synthetic molecular machines (69)(70)(71) remains in its infancy (72), there have already been important insights provided to the fundamental aspects of the principles by which molecules use energy input from the environment to carry out mechanical and chemical tasks (73), including self-assembly of complex structures from simpler starting materials. A very important step has recently been taken by the research group of David Leigh.…”

Section: Prospective and Conclusionmentioning

confidence: 99%

Stochastically pumped adaptation and directional motion of molecular machines

Astumian

2018

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

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Recent developments in synthetic molecular motors and pumps have sprung from a remarkable confluence of experiment and theory. Synthetic accomplishments have facilitated the ability to design and create molecules, many of them featuring mechanically bonded components, to carry out specific functions in their environment-walking along a polymeric track, unidirectional circling of one ring about another, synthesizing stereoisomers according to an external protocol, or pumping rings onto a long rod-like molecule to form and maintain high-energy, complex, nonequilibrium structures from simpler antecedents. Progress in the theory of nanoscale stochastic thermodynamics, specifically the generalization and extension of the principle of microscopic reversibility to the single-molecule regime, has enhanced the understanding of the design requirements for achieving strong unidirectional motion and high efficiency of these synthetic molecular machines for harnessing energy from external fluctuations to carry out mechanical and/or chemical functions in their environment. A key insight is that the interaction between the fluctuations and the transition state energies plays a central role in determining the steady-state concentrations. Kinetic asymmetry, a requirement for stochastic adaptation, occurs when there is an imbalance in the effect of the fluctuations on the forward and reverse rate constants. Because of strong viscosity, the motions of the machine can be viewed as mechanical equilibrium processes where mechanical resonances are simply impossible but where the probability distributions for the state occupancies and trajectories are very different from those that would be expected at thermodynamic equilibrium. molecular machine | stochastic pumping | kinetic asymmetry The molecular machines necessary for life must carry out their function in the fluctuating environment of a biological cell. Nowhere is the dynamic aspect of biology at the molecular level more evident than in the bilayer membrane surrounding most cells and organelles, a small portion of which is shown schematically in Fig. 1. Three transmembrane proteins are included in the depiction: (i) an ion channel that provides a conduit for conduction of ions across the membrane; (ii) a molecule that facilitates the transport of some substance, S, across the membrane; and (iii), an NaATPase that uses energy from ATP hydrolysis to maintain ion gradients across the membrane. The transporter acts as a catalyst to reduce the barrier for transport of S. In and of itself, the transporter cannot drive the substance S from low to high chemical potential. The transporter, however, is near a possible source of energy, the ion channel. The ion channel provides a path for conduction of ions from high to low electrochemical potential, thus dissipating energy. Every time the ion channel opens or closes, the local electric field across the membrane changes, and because the flow of ions down the electrochemical gradient when the channel is open dissipates energy, the resulting ...

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Section: Prospective and Conclusionmentioning

confidence: 99%

Stochastically pumped adaptation and directional motion of molecular machines

Astumian

2018

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

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“…[23][24][25][26][27][28][29][30][31] Forthe present study,wechose the two-component slideron-deck systems DS1-DS3 = D·(S1-S3)( Scheme 1) for the following reasons:1)InDS1-DS3,the two-footed sliders S1-S3 should move quickly on the D 3h -symmetric deck D with its three identical zinc porphyrin (ZnPor) binding sites.2 )The speed should be adjustable by changing the binding foot of S1-S3.…”

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confidence: 99%

Catalytic Three‐Component Machinery: Control of Catalytic Activity by Machine Speed

et al. 2017

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Three supramolecular slider-on-deck systems DS1-DS3 were obtained as two-component aggregates from the sliders S1-S3 and deck D with its three zinc porphyrin (ZnPor) binding sites.T he binding of the two-footed slider to the deck varies with the donor qualities of and the steric hindrance at the pyridine/pyrimidine (pyr) feet, and was effected by two N pyr ! ZnPor interactions.A ccordingly,t he sliders move over the three zinc porphyrins in the deck at different speeds,n amely with 32.2, 220, and 440 kHz at room temperature.The addition of N-methylpyrrolidine as an organocatalyst to DS1-DS3 generates catalytic three-component machineries.B yu sing ac onjugate addition as ap robe reaction, we observed ac orrelation between the operating speed of the slider-ondeck systems and the yields of the catalytic reaction. As the thermodynamic binding of the slider decreases,b oth the frequency of the sliding motion and the yield of the catalytic reaction increase.The connection between protein conformational dynamics and enzymatic activity has been intensely debated [1,2] because the precise spatial arrangement and high dynamics have to work together synergistically for high turnover rates in enzymes.[3] It is thus an appealing challenge to systematically use dynamic effects in artificial catalysts to speed up ap articular process. [4,5] Herein, we describe how ad ynamic slider-on-deck system can be coupled to an organocatalyst and how the sliding speed (machine speed) in this threecomponent aggregate impacts catalysis.T he results show clearly the prevalence of kinetic over thermodynamic factors in the liberation of catalyst into solution and highlight the usefulness of dynamic multicomponent machinery.Although most biological machine archetypes are multiprotein complexes,very few examples of artificial devices [6][7][8][9][10][11][12][13][14][15][16][17][18] that arise from the self-sorting of diverse components [19][20][21] have been reported, quite in contrast to the large gamut of known covalently or topologically constructed machines. [23][24][25][26][27][28][29][30][31] Forthe present study,wechose the two-component slideron-deck systems DS1-DS3 = D·(S1-S3)( Scheme 1) for the following reasons:1)InDS1-DS3,the two-footed sliders S1-S3 should move quickly on the D 3h -symmetric deck D with its three identical zinc porphyrin (ZnPor) binding sites.2 )The speed should be adjustable by changing the binding foot of S1-S3.3 )The addition of one equiv of an organocatalyst to DS1-DS3 is expected to generate the catalytic three-component machinery cat·D·(S1-S3). 4) Thes lidersf oot (various pyridine/pyrimidine derivatives:p yr) and the organocatalyst should have comparable affinity towards the binding sites of the deck, so that liberation of the catalyst into solution may be triggered by the motion of the slider. 5) Thea mount of catalyst in solution shall be quantifiable through ac atalytic process.T hereby,s ignificantly different sliding speeds in DS1-DS3 should lead to divergent yields in the catalytic reaction.B...

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“…[1][2][3] Fundamental developments have discovered fascinating phenomena and enabled a wealth of applications in the gas phase, [4][5][6][7][8] in solution, 4,[9][10][11] in crystals, 4,12 on surfaces, [4][5][6][13][14][15] and in biosystems. 16 Here we use a molecular model rotor to demonstrate the way from molecular quantum dynamics to explicitly time dependent statistical thermodynamics.…”

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confidence: 99%

From coherent quasi-irreversible quantum dynamics towards the second law of thermodynamics: The model boron rotor B13+

2018

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The planar boron cluster B13+ provides a model to investigate the microscopic origin of the second law of thermodynamics in a small system. It is a molecular rotor with an inner wheel that rotates in an outer bearing. The cyclic reaction path of B13+ passes along thirty equivalent global minimum structures (GMi, i = 1, 2, ..., 30). The GMs are embedded in a cyclic thirty-well potential. They are separated by thirty equivalent transition states with potential barrier Vb. If the boron rotor B13+ is prepared initially in one of the thirty GMs, with energy below Vb, then it tunnels sequentially to its nearest, next-nearest etc. neighbors (520 fs per step) such that all the other GMs get populated. As a consequence, the entropy of occupying the GMs takes about 6 ps to increases from zero to a value close to the maximum value for equi-distribution. Perfect recurrences are practically not observable.

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Mechanically Interlocked Molecules (MIMs)—Molecular Shuttles, Switches, and Machines (Nobel Lecture)

Cited by 844 publications

References 99 publications

Stochastically pumped adaptation and directional motion of molecular machines

Stochastically pumped adaptation and directional motion of molecular machines

Catalytic Three‐Component Machinery: Control of Catalytic Activity by Machine Speed

From coherent quasi-irreversible quantum dynamics towards the second law of thermodynamics: The model boron rotor B13+

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