Iron Heme Enzyme-Catalyzed Cyclopropanations with Diazirines as Carbene Precursors: Computational Explorations of Diazirine Activation and Cyclopropanation Mechanism

Abstract

The mechanism of cyclopropanations with diazirines as air-stable and user-friendly alternatives to commonly employed diazo compounds within iron heme enzyme-catalyzed carbene transfer reactions has been studied by means of density functional theory (DFT) calculations of model systems, quantum mechanics/molecular mechanics (QM/MM) calculations, and molecular dynamics (MD) simulations of the iron carbene and the cyclopropanation transition state in the enzyme active site. The reaction is initiated by a direct diazirine-diazo isomerization occurring in the active site of the enzyme. In contrast, an isomerization mechanism proceeding via the formation of a free carbene intermediate in lieu of a direct, one-step isomerization process was observed for model systems. Subsequent reaction with benzyl acrylate takes place through stepwise C−C bond formation via a diradical intermediate, delivering the cyclopropane product. The origin of the observed diastereo-and enantioselectivity in the enzyme was investigated through MD simulations, which indicate a preferred formation of the cis-cyclopropane by steric control.

Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field

“…The results showed that for the WT-RCs and EF1, EF2, and EF4 clusters for the LVRQ variant, the substrate was positioned at distances greater than the reactive range from the CC atom, classifying these states as unreactive (see Table S2). Consistent with other carbene transfer studies, all reactive clusters for the LVRQ, LVRQL, GLVRSQL, and GLAVRSQLL variants, with closed shell singlet spin state, demonstrated a concerted reaction mechanism, lacking stable intermediates and characterized by the asynchronous formation and breaking of bonds. − Initially, the CC and substrate C1 atom bond formation and elongation of the Fe–CC bond is favored, followed by complete breaking of the Fe–CC bond, culminating in the bond formation between CC and C2. For the LVRQ variant with EF3, the Gibbs free energy barrier was identified as 28.8 kcal/mol, coupled with a product stabilization energy of −36.2 kcal/mol.…”