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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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Leigh’s small molecule peptide synthesizer, 146.666
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fig57: Leigh’s small molecule peptide synthesizer, 146.666

Mentions: Recently, Leigh et al. reported the first small moleculeartificialmolecular machine (146) capable of sequence-specificpeptide synthesis.666 The machine is basedon a rotaxane architecture, which is used to ensure processivity ina manner reminiscent of both the ribosome-mRNA structure and the DNAclamp of DNA polymerases.68−71 Sequence information contained in the track is directlyconverted into the sequence of the peptide synthesized, and thus thetrack plays some aspects of the role of mRNA in the ribosomal system.Reactive phenolic ester groups take the place of tRNA-bound aminoacids and are sequentially “picked up” by the catalyticarm of the macrocycle. The catalytic arm bears a cysteine group andoperates by native chemical ligation (NCL) chemistry where the thiolateof the cysteine unit reacts first with the ester group before transferringthe activated amino acid to the end of the growing chain.1461 The steric bulk of the loaded amino acid preventsthe macrocycle passing over the barrier unit before this reactionhas taken place but allows free passage of the macrocycle after beingcleaved. This prevents the peptide sequence from being scrambled andallows sequential reaction. Rigid spacing units between each loadedamino acid minimize the likelihood of the catalytic arm encounteringan out of sequence amino acid. The catalytic unit consists of a cysteine-glycine-glycinemotif with the second two amino acids present to prevent an unfavorable1,8-S,N-acyl shift transition stateduring the second ligation (Figure 57).


Artificial Molecular Machines.

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

Leigh’s small molecule peptide synthesizer, 146.666
© Copyright Policy
Related In: Results  -  Collection

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

fig57: Leigh’s small molecule peptide synthesizer, 146.666
Mentions: Recently, Leigh et al. reported the first small moleculeartificialmolecular machine (146) capable of sequence-specificpeptide synthesis.666 The machine is basedon a rotaxane architecture, which is used to ensure processivity ina manner reminiscent of both the ribosome-mRNA structure and the DNAclamp of DNA polymerases.68−71 Sequence information contained in the track is directlyconverted into the sequence of the peptide synthesized, and thus thetrack plays some aspects of the role of mRNA in the ribosomal system.Reactive phenolic ester groups take the place of tRNA-bound aminoacids and are sequentially “picked up” by the catalyticarm of the macrocycle. The catalytic arm bears a cysteine group andoperates by native chemical ligation (NCL) chemistry where the thiolateof the cysteine unit reacts first with the ester group before transferringthe activated amino acid to the end of the growing chain.1461 The steric bulk of the loaded amino acid preventsthe macrocycle passing over the barrier unit before this reactionhas taken place but allows free passage of the macrocycle after beingcleaved. This prevents the peptide sequence from being scrambled andallows sequential reaction. Rigid spacing units between each loadedamino acid minimize the likelihood of the catalytic arm encounteringan out of sequence amino acid. The catalytic unit consists of a cysteine-glycine-glycinemotif with the second two amino acids present to prevent an unfavorable1,8-S,N-acyl shift transition stateduring the second ligation (Figure 57).

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.