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Artificial Molecular Machines.

Erbas-Cakmak S, Leigh DA, McTernan CT, Nussbaumer AL - Chem. Rev. (2015)

View Article: PubMed Central - PubMed

Affiliation: School of Chemistry, University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom.

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Hydrogen-bonding solvents have been shownto disrupt macrocycle–thread interactions in single stationrotaxanes, and here addition of 5% [D4]methanol increased the rate of shuttling 100-fold, consistentwith lowering the energy barrier to migration by disrupting station–macrocycleinteractions and thus raising ground-state energies... The effect of water on the rate of shuttlinghas been investigated and was found to be greatly superior to thatof other protic solvents... Therate of escape from the station energy well can then be modeled byan Arrhenius equation with a contribution from a distance-dependentdiffusion factor to the overall rate of shuttling... A quantum mechanicaltreatment of this system has found that, as the lengthening of thespacer has no effect on the activation for breaking the hydrogen bonds,the effect on the rate of shuttling is due to the widening of theoverall potential energy well... Molecular motion in mechanically interlocked and thus kineticallystable rotaxanes can be controlled using multiple binding sites withaffinities for the macrocycle that vary under different conditions.The conditions can be modified by electrochemical redox processes,light, pH, and environmental changes... Whenthe stilbene unit adopted the E form, the macrocyclecould move randomly along the full length of the thread by Brownianmotion, while when the Z form is adopted, the macrocyclewas trapped in one or the other of the two compartments... As the stretching of the PEOtether continued, and the force exerted by the PEO linker exceededthe hydrogen-bonding forces between the macrocycle and the fumaramidestation, the ring moved away from the fumaramide station... Tensionin the tether decreased as a result of the shuttling... Extracting useful work at the molecular scalerequires the restriction of the thermal movement of submolecular componentsor the exploitation of thermal motion with additional ratcheting.Shuttling, switching, and rotation processes in solution can be modulatedexternally, and the directionality of each motion can be controlledin single molecules... Third, to drive the walker away fromequilibrium, that is, to generate directional motion, a ratchetingprocess (either an energy or an information ratchet) must take place.In addition to the requirements of a Brownian motor, certain additionalcharacteristics are necessary for a motor to be defined as a walker... For the design of processive small molecule synthetic molecularwalkers, mechanically interlocked architectures are good candidates,because the walker (macrocycle) is mechanically bonded to the track(thread)... To perform tasks that cannot be accomplishedby conventional chemical means, it will be necessary to design systemswith multiple integrated parts, each component performing a dedicatedrole within the machine ensemble... This will not be straightforwardbecause unlike a watch where the second hand, say, does not interferewith the components in the escapement mechanism, the components ofa chemical machine are not easily isolated from each other (or theenvironment) and interference from one reactive part of a machinewith another will be a significant issue as complexity increases beyondthe current rather trivial systems. (iii) The machines we arefamiliar with in the macroscopic worldare generally stable, operating unchanged through many cycles, andby and large they do not make “mistakes”... Or it may bethat evolution just did not discover these solutions to such problemsand that mankind, with the whole of the periodic table and known syntheticchemistry to work with, can... Perhaps the most productive approachwill ultimately be found by following neither of these lines of investigationtoo closely, for example, by using chemical principles for “molecularrobotics” in which ratcheted motions of molecular components(i.e., biologically inspired mechanisms) are used to perform tasksthat have their origins in innovations introduced to advance developmentsin macroscopic technology (e.g., factory assembly lines).

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DNA machine reportedby Liu and co-workers, which could be usedto regulate an enzyme cascade reaction. Reprinted with permissionfrom ref (1915). Copyright2013 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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fig72: DNA machine reportedby Liu and co-workers, which could be usedto regulate an enzyme cascade reaction. Reprinted with permissionfrom ref (1915). Copyright2013 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mentions: DNA machines have been used to regulate enzyme cascade reactions.1890,1891 Liu and co-workers reported a machine containing DNA double crossover(DX) motifs, which formed two rigid arms, joined by an immobile four-wayjunction (Figure 72).1915 A DNA motor that could switch betweenstem-loop and double-helix structures, driven by a strand displacementreaction, was incorporated at the center of the machine to cycle betweenopen and closed states. This design amplifies the small motion generatedby the DNA motor into a much greater change in separation betweenthe ends of the two arms where glucose oxidase (GOx) and horseradishperoxidase (HRP) were attached. In this biochemical cascade system,GOx first catalyzed the oxidation of glucose to generate gluconicacid and hydrogen peroxide. Hydrogen peroxide is catalytically reducedby HRP into H2O. At the same time, HRP turns ABTS2– into ABTS–, which allowed the kinetics of theperoxidase to be monitored. HRP has a much higher turnover rate thenGOx, so the distance hydrogen peroxide must diffuse has a crucialinfluence on the rate of reaction. Therefore, when the two enzymesare attached to the two arms, the diffusion distance of hydrogen peroxidecan be changed from 6 to 18 nm by operation of the DNA motor, regulatingthe rate of enzymatic reaction. Sequential addition of fuel and antifuelstrands showed that this regulation was reversible.


Artificial Molecular Machines.

Erbas-Cakmak S, Leigh DA, McTernan CT, Nussbaumer AL - Chem. Rev. (2015)

DNA machine reportedby Liu and co-workers, which could be usedto regulate an enzyme cascade reaction. Reprinted with permissionfrom ref (1915). Copyright2013 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585175&req=5

fig72: DNA machine reportedby Liu and co-workers, which could be usedto regulate an enzyme cascade reaction. Reprinted with permissionfrom ref (1915). Copyright2013 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Mentions: DNA machines have been used to regulate enzyme cascade reactions.1890,1891 Liu and co-workers reported a machine containing DNA double crossover(DX) motifs, which formed two rigid arms, joined by an immobile four-wayjunction (Figure 72).1915 A DNA motor that could switch betweenstem-loop and double-helix structures, driven by a strand displacementreaction, was incorporated at the center of the machine to cycle betweenopen and closed states. This design amplifies the small motion generatedby the DNA motor into a much greater change in separation betweenthe ends of the two arms where glucose oxidase (GOx) and horseradishperoxidase (HRP) were attached. In this biochemical cascade system,GOx first catalyzed the oxidation of glucose to generate gluconicacid and hydrogen peroxide. Hydrogen peroxide is catalytically reducedby HRP into H2O. At the same time, HRP turns ABTS2– into ABTS–, which allowed the kinetics of theperoxidase to be monitored. HRP has a much higher turnover rate thenGOx, so the distance hydrogen peroxide must diffuse has a crucialinfluence on the rate of reaction. Therefore, when the two enzymesare attached to the two arms, the diffusion distance of hydrogen peroxidecan be changed from 6 to 18 nm by operation of the DNA motor, regulatingthe rate of enzymatic reaction. Sequential addition of fuel and antifuelstrands showed that this regulation was reversible.

View Article: PubMed Central - PubMed

Affiliation: School of Chemistry, University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom.

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Hydrogen-bonding solvents have been shownto disrupt macrocycle–thread interactions in single stationrotaxanes, and here addition of 5% [D4]methanol increased the rate of shuttling 100-fold, consistentwith lowering the energy barrier to migration by disrupting station–macrocycleinteractions and thus raising ground-state energies... The effect of water on the rate of shuttlinghas been investigated and was found to be greatly superior to thatof other protic solvents... Therate of escape from the station energy well can then be modeled byan Arrhenius equation with a contribution from a distance-dependentdiffusion factor to the overall rate of shuttling... A quantum mechanicaltreatment of this system has found that, as the lengthening of thespacer has no effect on the activation for breaking the hydrogen bonds,the effect on the rate of shuttling is due to the widening of theoverall potential energy well... Molecular motion in mechanically interlocked and thus kineticallystable rotaxanes can be controlled using multiple binding sites withaffinities for the macrocycle that vary under different conditions.The conditions can be modified by electrochemical redox processes,light, pH, and environmental changes... Whenthe stilbene unit adopted the E form, the macrocyclecould move randomly along the full length of the thread by Brownianmotion, while when the Z form is adopted, the macrocyclewas trapped in one or the other of the two compartments... As the stretching of the PEOtether continued, and the force exerted by the PEO linker exceededthe hydrogen-bonding forces between the macrocycle and the fumaramidestation, the ring moved away from the fumaramide station... Tensionin the tether decreased as a result of the shuttling... Extracting useful work at the molecular scalerequires the restriction of the thermal movement of submolecular componentsor the exploitation of thermal motion with additional ratcheting.Shuttling, switching, and rotation processes in solution can be modulatedexternally, and the directionality of each motion can be controlledin single molecules... Third, to drive the walker away fromequilibrium, that is, to generate directional motion, a ratchetingprocess (either an energy or an information ratchet) must take place.In addition to the requirements of a Brownian motor, certain additionalcharacteristics are necessary for a motor to be defined as a walker... For the design of processive small molecule synthetic molecularwalkers, mechanically interlocked architectures are good candidates,because the walker (macrocycle) is mechanically bonded to the track(thread)... To perform tasks that cannot be accomplishedby conventional chemical means, it will be necessary to design systemswith multiple integrated parts, each component performing a dedicatedrole within the machine ensemble... This will not be straightforwardbecause unlike a watch where the second hand, say, does not interferewith the components in the escapement mechanism, the components ofa chemical machine are not easily isolated from each other (or theenvironment) and interference from one reactive part of a machinewith another will be a significant issue as complexity increases beyondthe current rather trivial systems. (iii) The machines we arefamiliar with in the macroscopic worldare generally stable, operating unchanged through many cycles, andby and large they do not make “mistakes”... Or it may bethat evolution just did not discover these solutions to such problemsand that mankind, with the whole of the periodic table and known syntheticchemistry to work with, can... Perhaps the most productive approachwill ultimately be found by following neither of these lines of investigationtoo closely, for example, by using chemical principles for “molecularrobotics” in which ratcheted motions of molecular components(i.e., biologically inspired mechanisms) are used to perform tasksthat have their origins in innovations introduced to advance developmentsin macroscopic technology (e.g., factory assembly lines).

No MeSH data available.