Probing intermediate folding patterns determined the carbon skeleton construction mechanism of cyathane diterpene

Abstract

Cyathane diterpenes exhibit a range of notable pharmacological activities. These compounds share a common skeleton, the cyathin tricyclic core, whose synthesis is intricate, involving carbon cation rearrangement that results in the formation of three carbon rings and multiple stereocenters. Through DFT calculations, we found that the folding pattern of intermediates significantly impacts the reaction. Firstly, the A ring adopts a chair-like conformation, which is more favorable than the boat-like conformation. Secondly, a hydrogen atom attached to the terminal double bond can adopt either an up or down conformation, leading to different mechanisms for B expansion and C ring formation: concerted or stepwise, respectively. The stepwise mechanism, induced by the up conformation, is energetically more favorable than the down conformation. Further analysis of bond order, key distances and natural bond orbital revealed that the transition from the concerted mechanism to the stepwise mechanism is due to van der Waals repulsion between two H atoms attached to the reactive carbons involved in C ring formation. Finally, during QM(GFN2-xTB)/MM MD simulations, it was observed that the A ring transitions from a boat-like conformation to a chair-like conformation, and the H-down conformation switches to the H-up conformation within the cyathane synthase pocket. These transitions are consistent with the preferences observed in gas-phase calculations. This research reveals that distinct conformations give rise to different reaction mechanisms, an intriguing finding that provides deeper insight into the biosynthetic pathways of natural compounds and offers theoretical guidance for their biomimetic synthesis.