Analogy between Enzyme and Nanoparticle Catalysis: A Single-Molecule Perspective

Ye, Rong; Mao, Xianwen; Sun, Xiangcheng; Chen, Peng

doi:10.1021/acscatal.8b04926

Cited by 39 publications

(39 citation statements)

References 62 publications

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“…However, a couple of recent studies have found this behavior in many other enzyme systems, including paraoxonase 1, 41 , 42 lactate dehydrogenase, 43 and even nanoparticle-catalyzed reactions. 44 Therefore, multiple reaction pathways may exist broadly in nature and should be very carefully investigated when studying an enzyme catalysis process.…”

Section: Discussionmentioning

confidence: 99%

Multiple Reaction Pathways in the Morphinone Reductase-Catalyzed Hydride Transfer Reaction

Chen

Schwartz

2020

ACS Omega

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Morphinone reductase (MR) is an important model system for studying the contribution of protein motions to H-transfer reactions. In this research, we used quantum mechanical/molecular mechanics (QM/MM) simulation together with transition path sampling (TPS) simulation to study two important topics of current research on MR: the existence of multiple catalytic reaction pathways and the involvement of fast protein motions in the catalytic process. We have discovered two reaction pathways for the wild type and three reaction pathways for the N189A mutant. With the committor distribution analysis method, we found reaction coordinates for all five reaction pathways. Only one wild-type reaction pathway has a rate-promoting vibration from His186, while all of the other four pathways do not involve any protein motions in their catalytic process through the transition state. The rate-promoting vibration in the wild-type MR, which comes from a direction perpendicular to the donor–acceptor axis, functions to decrease the donor–acceptor distance by causing a subtle “out-of-plane” motion of a donor atom. By comparing reaction pathways between the two enzymes, we concluded that the major effect of the N189A point mutation is to increase the active site volume by altering the active site backbone and eliminating the Asn189 side chain. This effect causes a different NADH geometry at the reactant state, which very well explains the different reaction mechanisms between the two enzymes, as well as the disappearance of the His186 rate-promoting vibrations in the N189A mutant. The unfavorable geometry of the NADH pyridine ring induced by the N189A point mutation is the potential cause of multiple reaction pathways in N189A mutants.

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Section: Discussionmentioning

confidence: 99%

Multiple Reaction Pathways in the Morphinone Reductase-Catalyzed Hydride Transfer Reaction

Chen

Schwartz

2020

ACS Omega

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“…Then, B and F can be expressed via E by employing (19) and (18), respectively, while A is given by (17). The reaction rate is expressed via E as For the first-order reaction (11), Eq. (21) and expression (22) can be rewritten as and Substituting (24) into (25) results in Expression (26) allows one to identify analytically a few reaction regimes.…”

Section: With the Dirichlet Boundary Conditionsmentioning

confidence: 99%

“…One of the new directions in this area is aimed at reactions occurring on single NPs (see, e.g., Refs. [8][9][10][11][12]). For reactions in the liquid phase, one of the related generic schemes (Fig.…”

Section: Introductionmentioning

confidence: 99%

Kinetics of Reaction on a Single Catalytic Particle in a Fluidic Nanochannel

Zhdanov

2019

Catal Lett

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One of the frontiers in heterogeneous catalysis is focused on reactions occurring on single catalytic nanoparticles. In this context, a reaction taking place on a single nanoparticle in a fluidic nanochannel is herein described by using the equation similar to that employed for a plug-flow reactor with dispersion. In the literature, one can find various boundary conditions for this equation. In the practically interesting case of a relatively long channel, the Dirichlet boundary conditions are shown to be valid. The corresponding analytical and numerical results illustrate the specifics of the profiles of the reactant concentration along the channel and the dependence of the reaction rate on the parameters. For comparison, the Danckwerts boundary conditions were used as well.

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“…In these first studies, it was shown that even text book reactions can show furcations of reaction pathways, still leading to an identical product . Hidden intermediates or static disorder is revealed for single nanoparticles and enzymes . Reactivity mapping of heterogeneous catalysts has been accomplished with spatial resolution .…”

Section: Introductionmentioning

confidence: 99%

Kinetics of Palladium(0)‐Allyl Interactions in the Tsuji‐Trost Reaction, derived from Single‐Molecule Fluorescence Microscopy

et al. 2020

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Single-molecule (SM) chemistry is devoted to unravel reaction steps which are hidden in cuvette experiments. Controversies about the substrate activation during the Tsuji-Trost deallylation motivated us to study, on the single-molecule level, the kinetics of the catalyst precursor Pd(PPh 3 ) 4 with our recently designed two-color fluorescent probes. Photochemical, metal-free bypass reactions were found and taken into account by the combina-tion of spectrally separated single-molecule TIRF-microscopy and state-of-the art analysis procedures. Unselective π-complex formation (K D � 10 3 M À 1 ) precedes the insertion of the active catalyst into the CÀ OR bond (RO À = leaving group), indicated by the lacking immediate change of fluorescence color. The formed intermediate then decomposes on a time scale of � 2 -3 s to the deallylated product.

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Analogy between Enzyme and Nanoparticle Catalysis: A Single-Molecule Perspective

Cited by 39 publications

References 62 publications

Multiple Reaction Pathways in the Morphinone Reductase-Catalyzed Hydride Transfer Reaction

Multiple Reaction Pathways in the Morphinone Reductase-Catalyzed Hydride Transfer Reaction

Kinetics of Reaction on a Single Catalytic Particle in a Fluidic Nanochannel

Kinetics of Palladium(0)‐Allyl Interactions in the Tsuji‐Trost Reaction, derived from Single‐Molecule Fluorescence Microscopy

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