Bifurcating reactions: distribution of products from energy distribution in a shared reactive mode

Bharadwaz, Priyam; Maldonado-Domínguez, Mauricio; Srnec, Martin

doi:10.1039/d1sc02826j

Cited by 13 publications

(18 citation statements)

References 68 publications

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“…Notably, different physical factors that mediate the PTSB selectivity have been proposed, including transition structure geometries, 10,36,44 transition state momentum distribution, 2,8,9 the shape of potential energy surface, 24 and kinetic energy distribution. 45 In the NgnD-catalyzed ambimodal [6+4]/[4+2] reaction, we examined the influence of the TS geometries on the selectivity. A regression model has been developed to describe the quantitative relationship between TS forming bond lengths and product ratio.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…The ratio of [6+4]- to [4+2]-adduct is 3.1 in the gas phase, 5.9 in water, and 0.9 in enzyme. Notably, different physical factors that mediate the PTSB selectivity have been proposed, including transition structure geometries, ,, transition state momentum distribution, ,, the shape of potential energy surface, and kinetic energy distribution . In the NgnD-catalyzed ambimodal [6+4]/[4+2] reaction, we examined the influence of the TS geometries on the selectivity.…”

Section: Resultsmentioning

confidence: 99%

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Influence of Water and Enzyme on the Post-Transition State Bifurcation of NgnD-Catalyzed Ambimodal [6+4]/[4+2] Cycloaddition

et al. 2021

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The enzyme NgnD catalyzes an ambimodal cycloaddition that bifurcates to [6+4]- and [4+2]-adducts. Both products have been isolated in experiments, but it remains unknown how enzyme and water influence the bifurcation selectivity at the femtosecond time scale. Here, we study the impact of water and enzyme on the post-transition state bifurcation of NgnD-catalyzed [6+4]/[4+2] cycloaddition by integrating quantum mechanics/molecular mechanics quasiclassical dynamics simulations and biochemical assays. The ratio of [6+4]/[4+2] products significantly differs in the gas phase, water, and enzyme. Biochemical assays were employed to validate computational predictions. The study informs how water and enzyme affect the bifurcation selectivity through perturbation of the reaction dynamics in the femtosecond time scale, revealing the fundamental roles of condensed media in dynamically controlling the chemical selectivity for biosynthetic reactions.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Influence of Water and Enzyme on the Post-Transition State Bifurcation of NgnD-Catalyzed Ambimodal [6+4]/[4+2] Cycloaddition

et al. 2021

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“…How to cite this article: M. T. Tremblay, Z. J. Yang, J Phys Org Chem 2022, 35 (11), e4322. https://doi.org/10.1002/poc.4322…”

Section: Supporting Informationmentioning

confidence: 99%

“…Enabled by QCT simulations, previous studies have explored the relationship between various physical factors and the resulting ratio of products or the timing of bond formation. These factors include transition structure geometries, [ 3d,9 ] transition state momentum distribution, [ 1c,3c,10 ] kinetic energy distribution, [ 11 ] and condensed‐media environment (e.g., solvent or enzyme). [ 6b,12 ] In particular, Carpenter has made ground‐breaking contributions to elucidate how transition state momenta mediate bifurcation outcomes, which is known as the “dynamic matching” effect.…”

Section: Introductionmentioning

confidence: 99%

The effect of zero‐point energy in simulating organic reactions with post‐transition state bifurcation

Tremblay

Yang

2022

J of Physical Organic Chem

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Ambimodal reactions involve a single transition state leading to multiple products. To assess the ratio of the bifurcation products, quasiclassical trajectories (QCTs) are initiated from transition state geometries that are randomly sampled using the zero‐point energy (ZPE) plus thermal energy of a molecule's vibrational modes. However, in the QCTs, the influence of ZPE percentage in the resulting bifurcation ratio and time gap between formation of bonds is not well understood. To benchmark the effect of varying the percentage of the molecules' inherent ZPE used in the simulation, three organic reactions with distinct mechanisms that all display post‐transition state bifurcation were selected. The three reactions studied include an intramolecular [6 + 4]/[4 + 2] cycloaddition, an asynchronous nitrene insertion, and an SN2/addition to a carbonyl on an α‐bromoketone. These reactions encompass various modes of bond formation and cleavage, offering a broad view of the influence of ZPE scaling in evaluating the product ratio resulted from post‐transition state bifurcation. Exploring means of tuning selectivity in simulation enables development of more accurate organic reaction modeling for synthetic prediction. This work will establish a basis for future QCT studies of organic reactions.

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“…Enabled by QCT simulations, previous studies have explored the relationship between various physical factors and the resulting ratio of products or the timing of bond formation. These factors include transition structure geometries, 9,21,22 transition state momentum distribution, 3,8,23 kinetic energy distribution, 24 and condensed-media environment (e.g., solvent or enzyme) 13,[25][26][27] . In particular, Carpenter has made ground-breaking contribution to elucidate how transition state momentum mediate bifurcation outcome, which is known as "dynamic matching" effect.…”

Section: Toc Graphics Introductionmentioning

confidence: 99%

The Effect of Zero-Point Energy in Simulating Organic Reactions with Post-Transition State Bifurcation

Tremblay

Yang

2021

Preprint

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Ambimodal reactions involve a single transition state leading to multiple products. To assess the ratio of the bifurcation products, quasiclassical trajectories (QCTs) are initiated from transition state geometries that are randomly sampled using the zero-point energy (ZPE) plus thermal energy of a molecule’s vibrational modes. However, in the QCTs, the influence of ZPE percentage in the resulting bifurcation ratio and time gap between formation of bonds is not well understood. To benchmark the effect of varying the percentage of the molecules’ inherent ZPE used in the simulation, three organic reactions with distinct mechanisms that all display post-transition state bifurcation were selected. The three reactions studied include an intramolecular [6+4]/[4+2] cycloaddition, an asynchronous nitrene insertion, and an SN2/addition to a carbonyl on an α-bromoketone. These reactions encompass various modes of bond formation and cleavage, offering a broad view of the influence of ZPE scaling in evaluating the product ratio resulted from post-transition state bifurcation. This work will establish a basis for future QCT studies of organic reactions.

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Bifurcating reactions: distribution of products from energy distribution in a shared reactive mode

Abstract: Bifurcating reactions yield two different products emerging from one single transition state and are therefore archetypal examples of reactions that cannot be described within the framework of the traditional Eyring’s...

Cited by 13 publications

References 68 publications

Influence of Water and Enzyme on the Post-Transition State Bifurcation of NgnD-Catalyzed Ambimodal [6+4]/[4+2] Cycloaddition

Influence of Water and Enzyme on the Post-Transition State Bifurcation of NgnD-Catalyzed Ambimodal [6+4]/[4+2] Cycloaddition

The effect of zero‐point energy in simulating organic reactions with post‐transition state bifurcation

The Effect of Zero-Point Energy in Simulating Organic Reactions with Post-Transition State Bifurcation

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