Quantifying Possible Routes for SpnF-Catalyzed Formal Diels–Alder Cycloaddition

Abstract

The Diels-Alder reaction is a cornerstone of modern organic synthesis. Despite this, it remains essentially inaccessible to biosynthetic approaches. Only a few natural enzymes catalyze even a formal [4 + 2] cycloaddition, and it remains uncertain if any of them proceed via the Diels-Alder mechanism. In this study, we focus on the [4 + 2] cycloaddition step in the biosynthesis of spinosyn A, a reaction catalyzed by SpnF enzyme, one of the most promising "true Diels-Alderase" candidates. The four currently proposed mechanisms (including the Diels-Alder one) for this reaction in water (as a first-order approximation of the enzymatic reaction) are evaluated by an exhaustive quantum mechanical search for possible transition states (728 were found in total). We find that the line between the recently proposed bis-pericyclic [J. Am. Chem. Soc. 2016, 138 (11), 3631] and Diels-Alder routes is blurred, and favorable transition states of both types may coexist. Application of the Curtin-Hammett principle, however, reveals that the bis-pericyclic mechanism accounts for ∼83% of the reaction flow in water, while the classical Diels-Alder mechanism contributes only ∼17%. The current findings provide a route for modeling this reaction inside the SpnF active site and inferring the catalytic architecture of possible Diels-Alderases.

The Dynamics of Chemical Reactions: Atomistic Visualizations of Organic Reactions, and Homage to van ’t Hoff

“…SpnF is the first stand-alone Diels-Alderase reported by Hung-wen Liu at UT-Austin. [127] Trajectory simulations were performed in the gas phase by our group in collaboration with Singleton, which shows an ambimodalT S that leads to both [4+ +2] and [6+ +4] adducts with ar atio of 1t o 2.5 using the B3LYP-D2 method, and 1to1 .1 using the M06-2X method.H ess et al [128] and Medvedev et al [129] show that both the Diels-Alder TS and the ambimodal TS conformation were potentially involved in the reaction. The EPTSS method was performed to understand how water and enzymem odify the nature of the TS and dynamically alter the product ratio.…”

Response to Comment on “Density functional theory is straying from the path toward the exact functional”

“…M06-L was the first functional to show (5) that a meta-GGA can describe intermediaterange van der Waals interactions. More generally, Minnesota functionals have shown that carefully fitted flexible forms can make accurate predictions for systems and properties similar to those on which they were fitted [e.g., for diverse possible transition states of the SpnF-catalyzed formal Diels-Alder cycloaddition (12)]. However, their neglect of some exact constraints can lead to uncontrolled errors for systems and properties that are very different [e.g., in (2), and for Au bonding, as recently noted by Kepp (13)].…”

Biocatalytic Strategies towards [4+2] Cycloadditions

“…There have been extensive computational investigations into the SpnF‐catalysed reaction utilising multiple approaches (Scheme B) . These simulations are based on the SpnF crystal structure and computational docking and show multiple mechanisms in the gas‐phase leading to the [4+2] product 23 .…”

“…[60,64] There have been extensive computational investigations into the SpnF-catalysed reaction utilisingm ultiple approaches (Scheme 4B). [61][62][63][65][66][67][68] These simulations are based on the SpnF crystal structurea nd computational docking [64] and show multiple mechanisms in the gas-phase leading to the [4+ +2] product 23.A longside the direct route via ac oncerted [4+ +2] transition state, Patel et al [67] proposed an alternative route via [6+ +4] intermediate 24 whichundergoes aCope rearrangement to revealt he [4+ +2] product 23.F urthermore, they propose that the initial transition state is ambimodal and able to lead to either [4+ +2] or [6+ +4] adducts.…”