Modeling the heterogeneous catalytic activity of a single nanoparticle using a first passage time distribution formalism

Das, Anusheela; Chaudhury, Srabanti

doi:10.1016/j.cplett.2015.10.063

Cited by 8 publications

(11 citation statements)

References 25 publications

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“…54 Since the latter uses a method different from the CME approach, it is not possible for us to make a direct comparison between the results obtained from two different theoretical approaches. It is possible, however, to make a direct comparison between the randomness parameter obtained using the method of SRP [Eq.…”

Section: Randomness Parameter -A Quantitative Measure Of Temporal mentioning

confidence: 99%

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

Kumar

Chatterjee

Nandi

et al. 2016

The Journal of Chemical Physics

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Dynamic cooperativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic cooperativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative cooperativity. For fewer enzymes, dynamic cooperativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic cooperativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the singlepathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

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Section: Randomness Parameter -A Quantitative Measure Of Temporal mentioning

confidence: 99%

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

Kumar

Chatterjee

Nandi

et al. 2016

The Journal of Chemical Physics

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“…However, this approach could not explain the experimentally observed size-dependent catalytic activity, and because of its mean-field nature it also failed to account for various stochastic effects . A more advanced theoretical method based on first-passage analysis of chemical dynamics, , which could partially take into account the number of active sites and the related stochastic effects, was proposed later. , But this method was also too simplified in many aspects because it did not consider the details of the underlying chemical reactions or the number of intermediates for the chemical processes at each active site. Recently, we developed a new general theoretical framework for investigating the dynamics of chemical reactions with intermediate states on catalytic particles with multiple active sites .…”

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confidence: 99%

“…11 A more advanced theoretical method based on first-passage analysis of chemical dynamics, 16,17 which could partially take into account the number of active sites and the related stochastic effects, was proposed later. 18,19 But this method was also too simplified in many aspects because it did not consider the details of the underlying chemical reactions or the number of intermediates for the chemical processes at each active site. dynamics of chemical reactions with intermediate states on catalytic particles with multiple active sites.…”

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confidence: 99%

Understanding the Reaction Dynamics on Heterogeneous Catalysts Using a Simple Stochastic Approach

Punia

Chaudhury

Kolomeisky

2021

J. Phys. Chem. Lett.

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Recent experimental advances on investigating nanoparticle catalysts with multiple active sites provided a large amount of quantitative information on catalytic processes. These observations stimulated significant theoretical efforts, but the underlying molecular mechanisms are still not well-understood. We introduce a simple theoretical method to analyze the reaction dynamics on catalysts with multiple active sites based on a discrete-state stochastic description and obtain a comprehensive description of the dynamics of chemical reactions on such catalysts. We explicitly determine how the dynamics of catalyzed chemical reactions depend on the number of active sites, on the number of intermediate chemical transitions, and on the topology of underlying chemical reactions. It is argued that the theory provides quantitative bounds for realistic dynamic properties of catalytic processes that can be directly applied to analyze the experimental observations. In addition, this theoretical approach clarifies several important aspects of the molecular mechanisms of chemical reactions on catalysts.

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“…Later, a more advanced theoretical method to analyze chemical processes on nanocatalysts has been proposed. 16,17 It is based on the first-passage analysis of dynamics, and it partially takes into account the number of active sites and the related stochastic effects. However, this approach considers only oversimplified chemical reactions at each catalytic site.…”

mentioning

confidence: 99%

“…Also, this mean-field approach neglects the important stochastic effects due to chemical reactions taking place randomly at each active site, and this prevents the detailed investigations of underlying molecular mechanisms. Later, a more advanced theoretical method to analyze chemical processes on nanocatalysts has been proposed. , It is based on the first-passage analysis of dynamics, and it partially takes into account the number of active sites and the related stochastic effects. However, this approach considers only oversimplified chemical reactions at each catalytic site.…”

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confidence: 99%

Theoretical Investigations of the Dynamics of Chemical Reactions on Nanocatalysts with Multiple Active Sites

Chaudhury

Singh

Kolomeisky

2020

J. Phys. Chem. Lett.

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Recent synthetic advances led to the development of new catalytic particles with well-defined atomic structures and multiple active sites, which are called nanocatalysts. Experimental studies of processes at nanocatalysts uncovered a variety of surprising effects, but the molecular mechanisms of these phenomena remain not well understood. We propose a theoretical method to investigate the dynamics of chemical reactions on catalytic particles with multiple active sites. It is based on a discrete-state stochastic description that allows us to explicitly evaluate dynamic properties of the system. It is found that for independently occurring chemical reactions, the mean turnover times are inversely proportional to the number of active sites, showing no stochastic effects. However, the molecular details of reactions and the number of active sites influence the higher moments of reaction times. Our theoretical method provides a way to quantify the molecular mechanisms of processes at nanocatalysts.

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Modeling the heterogeneous catalytic activity of a single nanoparticle using a first passage time distribution formalism

Cited by 8 publications

References 25 publications

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

Understanding the Reaction Dynamics on Heterogeneous Catalysts Using a Simple Stochastic Approach

Theoretical Investigations of the Dynamics of Chemical Reactions on Nanocatalysts with Multiple Active Sites

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