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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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(a) Tweezer A: in the closed form the arms are boundto the linker unit (blue) by Hg2+ ions through T–Hg2+–T bonds. To open the molecular tweezer, Hg2+ is sequestered by the addition of cysteine. (b) Tweezer B: in acid the arms form an i-motif, thus releasingthe linker unit, whereas at pH = 7.2, the i-motifis destroyed resulting in the stabilization of the closed structure.(c) Tweezer C: the linker unit can be released by a complementarystrand, the antilinker that opens the tweezers. Reprinted with permissionfrom ref (1914). Copyright2010 American National Academy of Sciences.
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fig71: (a) Tweezer A: in the closed form the arms are boundto the linker unit (blue) by Hg2+ ions through T–Hg2+–T bonds. To open the molecular tweezer, Hg2+ is sequestered by the addition of cysteine. (b) Tweezer B: in acid the arms form an i-motif, thus releasingthe linker unit, whereas at pH = 7.2, the i-motifis destroyed resulting in the stabilization of the closed structure.(c) Tweezer C: the linker unit can be released by a complementarystrand, the antilinker that opens the tweezers. Reprinted with permissionfrom ref (1914). Copyright2010 American National Academy of Sciences.

Mentions: DNA tweezers represent a simple class of DNA machines.1884,1912 They are two-armed constructs bridged by a DNA linker that can undergotransitions between open and closed states in response to externaltriggers such as the addition of single-stranded DNA or metal ions,or a change in pH. Willner et al. reported a biomolecular logic gatebased on three different DNA tweezers A, B, and C. These were activated by different inputs: protons,Hg2+ ions, and nucleic acid strands (Figure 71). The output delivered bythis machine depends both on the inputs provided and its initial internalstate. Depending on the input, there are eight possible configurationsof the three tweezers (open or closed for each). The output couldbe studied by measuring the Förster resonance energy transfer(FRET) between different pairs of fluorophore and quenching moleculesattached to the arms of each of the three tweezers. The linker unitis common to all three tweezers, meaning that tweezers A and B can also be opened by the complementary antilinker.Thus, for any pair of tweezers, there are two different inputs thatcause a change in the state of the device. In total, the device canadopt 16 different states and can furthermore be used as a memorystorage system because each state and output is dependent not onlyon the most recent input but also on past states and inputs.1913,1914


Artificial Molecular Machines.

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

(a) Tweezer A: in the closed form the arms are boundto the linker unit (blue) by Hg2+ ions through T–Hg2+–T bonds. To open the molecular tweezer, Hg2+ is sequestered by the addition of cysteine. (b) Tweezer B: in acid the arms form an i-motif, thus releasingthe linker unit, whereas at pH = 7.2, the i-motifis destroyed resulting in the stabilization of the closed structure.(c) Tweezer C: the linker unit can be released by a complementarystrand, the antilinker that opens the tweezers. Reprinted with permissionfrom ref (1914). Copyright2010 American National Academy of Sciences.
© Copyright Policy
Related In: Results  -  Collection

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

fig71: (a) Tweezer A: in the closed form the arms are boundto the linker unit (blue) by Hg2+ ions through T–Hg2+–T bonds. To open the molecular tweezer, Hg2+ is sequestered by the addition of cysteine. (b) Tweezer B: in acid the arms form an i-motif, thus releasingthe linker unit, whereas at pH = 7.2, the i-motifis destroyed resulting in the stabilization of the closed structure.(c) Tweezer C: the linker unit can be released by a complementarystrand, the antilinker that opens the tweezers. Reprinted with permissionfrom ref (1914). Copyright2010 American National Academy of Sciences.
Mentions: DNA tweezers represent a simple class of DNA machines.1884,1912 They are two-armed constructs bridged by a DNA linker that can undergotransitions between open and closed states in response to externaltriggers such as the addition of single-stranded DNA or metal ions,or a change in pH. Willner et al. reported a biomolecular logic gatebased on three different DNA tweezers A, B, and C. These were activated by different inputs: protons,Hg2+ ions, and nucleic acid strands (Figure 71). The output delivered bythis machine depends both on the inputs provided and its initial internalstate. Depending on the input, there are eight possible configurationsof the three tweezers (open or closed for each). The output couldbe studied by measuring the Förster resonance energy transfer(FRET) between different pairs of fluorophore and quenching moleculesattached to the arms of each of the three tweezers. The linker unitis common to all three tweezers, meaning that tweezers A and B can also be opened by the complementary antilinker.Thus, for any pair of tweezers, there are two different inputs thatcause a change in the state of the device. In total, the device canadopt 16 different states and can furthermore be used as a memorystorage system because each state and output is dependent not onlyon the most recent input but also on past states and inputs.1913,1914

View Article: PubMed Central - PubMed

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

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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.