Individual‐Molecule Perspective Analysis of Chemical Reaction Networks: The Case of a Light‐Driven Supramolecular Pump

Sabatino, Andrea; Penocchio, Emanuele; Ragazzon, Giulio; Frezzato, Diego

doi:10.1002/ange.201908026

Cited by 8 publications

(10 citation statements)

References 38 publications

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“…The profiles for the macroscopic case are comparable to those presented in Ref. 26. Table II collects, for all instances, the average cycle time and the standard deviation of the distribution as obtained from the data.…”

Section: Resultssupporting

confidence: 61%

“…The definitions of cycles given above are the same proposed in Ref. 26, so to establish a continuation with the previous work.…”

Section: B Direct and Inverse Cycles Of Tagged Rings And Axlesmentioning

confidence: 80%

“…The statistical analysis of the cycle times was done in the macroscopic limit. 26 Here, we extend the analysis by also exploring the small-volume context. We note that size effects in the functioning of synthetic molecular motors have not been explored in previous computational studies, 27,28 as the latter focused on the much more common case of unimolecular motors.…”

Section: Introductionmentioning

confidence: 93%

“…Table I reports the values of the rate constants, the same 32 employed in Ref. 26. Some reactions are pure thermal processes (rate constants with the subscript "Δ"), while others are photo-activated processes (subscript "hν"); irradiation wavelength and photon flux intensity are the same as for the experimental conditions of Ref.…”

Section: Rate Constantmentioning

confidence: 99%

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Sample size dependence of tagged molecule dynamics in steady-state networks with bimolecular reactions: Cycle times of a light-driven pump

Asnicar

Penocchio

Frezzato

2022

The Journal of Chemical Physics

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Here, steady-state reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agent-based viewpoint is useful for selectively characterizing the behavior of functional molecules, especially in the presence of bimolecular processes. We present the tools for simulating the jump dynamics both in the macroscopic limit and in the small-volume sample where the numbers of reactive molecules are of the order of few units with an inherently stochastic kinetics. The focus is on how an ideal spatial “compartmentalization” may affect the dynamical features of the tagged molecule. Our general approach is applied to a synthetic light-driven supramolecular pump composed of ring-like and axle-like molecules that dynamically assemble and disassemble, originating an average ring-through-axle directed motion under constant irradiation. In such an example, the dynamical feature of interest is the completion time of direct/inverse cycles of tagged rings and axles. We find a surprisingly strong robustness of the average cycle times with respect to the system’s size. This is explained in the presence of rate-determining unimolecular processes, which may, therefore, play a crucial role in stabilizing the behavior of small chemical systems against strong fluctuations in the number of molecules.

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Section: Resultssupporting

confidence: 61%

“…The definitions of cycles given above are the same proposed in Ref. 26, so to establish a continuation with the previous work.…”

Section: B Direct and Inverse Cycles Of Tagged Rings And Axlesmentioning

confidence: 80%

Section: Introductionmentioning

confidence: 93%

Section: Rate Constantmentioning

confidence: 99%

See 2 more Smart Citations

Sample size dependence of tagged molecule dynamics in steady-state networks with bimolecular reactions: Cycle times of a light-driven pump

Asnicar

Penocchio

Frezzato

2022

The Journal of Chemical Physics

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“…)akin to those in nature [26] and for which the order by which chemical events take place is important. [27]…”

Section: Discussionmentioning

confidence: 99%

From Selection to Instruction and Back: Competing Conformational Selection and Induced Fit Pathways in Abiotic Hosts

et al. 2021

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Tw olimiting cases of molecular recognition, induced fit (IF) and conformational selection (CS), play ac entral role in allosteric regulation of natural systems.T he IF paradigm states that as ubstrate "instructs" the host to change its shape after complexation, while CS asserts that ag uest "selects" the optimal fit from an ensemble of preexisting host conformations.W ithn os tudies that quantitatively address the interplay of two limiting pathways in abiotic systems,weherein and for the first time describe the way by which twisted capsule M-1, encompassing two conformers M-1(+ +)and M-1(À), trap CX 4 (X = Cl, Br) to give CX 4 &M-1(+ +)and CX 4 &M-1(À), with all four states being in thermal equilibrium. With the assistance of 2D EXSY,w ef ound that CBr 4 would, at its lower concentrations,b ind M-1 via a M-1(+ +)!M-1(À)!CBr 4 &M-1(À) pathway corresponding to conformational selection. For M-1 complexing CCl 4 though, data from 2D EXSY measurements and 1D NMR line-shape analysis suggested that lower CCl 4 concentrations would favor CS while the IF pathway prevailed at higher proportions of the guest. Since CS and IF are not mutually exclusive,w er eason that our work sets the stage for characterizing the dynamics of aw ide range of already existing hosts to broaden our fundamental understanding of their action. The objective is to master the way in which encapsulation takes place for designing novel and allosteric sequestering agents,catalysts and chemosensors akin to those found in nature.

show abstract

From Selection to Instruction and Back: Competing Conformational Selection and Induced Fit Pathways in Abiotic Hosts

et al. 2021

View full text Add to dashboard Cite

Two limiting cases of molecular recognition, induced fit (IF) and conformational selection (CS), play a central role in allosteric regulation of natural systems. The IF paradigm states that a substrate “instructs” the host to change its shape after complexation, while CS asserts that a guest “selects” the optimal fit from an ensemble of preexisting host conformations. With no studies that quantitatively address the interplay of two limiting pathways in abiotic systems, we herein and for the first time describe the way by which twisted capsule M‐1, encompassing two conformers M‐1(+) and M‐1(−), trap CX4 (X=Cl, Br) to give CX4⊂M‐1(+) and CX4⊂M‐1(−), with all four states being in thermal equilibrium. With the assistance of 2D EXSY, we found that CBr4 would, at its lower concentrations, bind M‐1 via a M‐1(+)→M‐1(−)→CBr4⊂M‐1(−) pathway corresponding to conformational selection. For M‐1 complexing CCl4 though, data from 2D EXSY measurements and 1D NMR line‐shape analysis suggested that lower CCl4 concentrations would favor CS while the IF pathway prevailed at higher proportions of the guest. Since CS and IF are not mutually exclusive, we reason that our work sets the stage for characterizing the dynamics of a wide range of already existing hosts to broaden our fundamental understanding of their action. The objective is to master the way in which encapsulation takes place for designing novel and allosteric sequestering agents, catalysts and chemosensors akin to those found in nature.

show abstract

Individual‐Molecule Perspective Analysis of Chemical Reaction Networks: The Case of a Light‐Driven Supramolecular Pump

Cited by 8 publications

References 38 publications

Sample size dependence of tagged molecule dynamics in steady-state networks with bimolecular reactions: Cycle times of a light-driven pump

Sample size dependence of tagged molecule dynamics in steady-state networks with bimolecular reactions: Cycle times of a light-driven pump

From Selection to Instruction and Back: Competing Conformational Selection and Induced Fit Pathways in Abiotic Hosts

From Selection to Instruction and Back: Competing Conformational Selection and Induced Fit Pathways in Abiotic Hosts

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