Computational Description of Alkylated Iron–Sulfur Organometallic Clusters

Abstract

The radical S-adenosyl methionine (SAM) enzyme superfamily has widespread roles in hydrogen atom abstraction reactions of crucial biological importance. In these enzymes, reductive cleavage of SAM bound to a [4Fe-4S]1+ cluster generates the 5′-deoxyadenosyl radical (5′-dAdo•) which ultimately abstracts an H atom from the substrate. However, overwhelming experimental evidence has surprisingly revealed an obligatory organometallic intermediate Ω exhibiting an Fe-C5′-adenosyl bond, whose properties are the target of this theoretical investigation. We report a readily applied, two-configuration version of broken symmetry DFT, denoted 2C-DFT, designed to allow the accurate description of the hyperfine coupling constants and g-tensors of an alkyl group bound to a multimetallic iron–sulfur cluster. This approach has been validated by the excellent agreement of its results both with those of multiconfigurational complete active space self-consistent field computations for a series of model complexes and with the results from electron nuclear double-resonance/electron paramagnetic resonance spectroscopic studies for the crystallographically characterized complex, M–CH3, a [4Fe-4S] cluster with a Fe–CH3 bond. The likewise excellent agreement between spectroscopic results and 2C-DFT computations for Ω confirm its identity as an organometallic complex with a bond between an Fe of the [4Fe-4S] cluster and C5′ of the deoxyadenosyl moiety, as first proposed.

The Active-Site [4Fe-4S] Cluster in the Isoprenoid Biosynthesis Enzyme IspH Adopts Unexpected Redox States during Ligand Binding and Catalysis

“…It is possible that the overlap between Mössbauer parameters for 1+ and 2+ species is much larger than previously expected, but it is more likely, however, that the situation for the Red+P species is unique. Here theoretical studies are called for to examine the exact distribution of electron density, as has been very recently done for bioorganometallic radical SAM enzyme intermediates . DFT/SCRF computations have already been applied on the first steps in the reaction mechanism in Figure , indicating that reduction of the active-site clusters results in the η 2 -bound state .…”

“…Here theoretical studies are called for to examine the exact distribution of electron density, as has been very recently done for bioorganometallic radical SAM enzyme intermediates. 87 DFT/SCRF computations have already been applied on the first steps in the reaction mechanism in Figure 2, indicating that reduction of the active-site clusters results in the η 2 -bound state. 38 The information in the present study can thus guide future computational investigations.…”

ENDOR Spectroscopy Reveals the “Free” 5′-Deoxyadenosyl Radical in a Radical SAM Enzyme Active Site Actually is Chaperoned by Close Interaction with the Methionine-Bound [4Fe–4S]2+ Cluster

“…We treat both the mathematically simplest case, S M = 1/2, which would correspond to a low-spin diferric cluster, and the slightly more complicated case of S M = 2, corresponding to a cluster with two high-spin Fe 2+ ions. By treating the latter case, we show: (i) that the treatment can directly address a radical interacting with a high-spin Fe 2+ ion, in what quite plausibly corresponds to the interaction of 5′-dAdo• with the unique Fe ion of the enzyme cluster; (ii) that the induced cluster hyperfine couplings are enhanced by the higher-spin cluster Fe site; and (iii) that this spin-coupling model correlates with a BS-DFT treatment of a radical interacting with a diiron complex (the most complex system amenable to BS-DFT computation), as presented below.…”

“…The observed radical-cluster interaction, as incorporated in this model, is further illuminated by BS-DFT electronic-structure computations − on a corresponding molecular model, Figure A: a Rieske-like diiron center with two antiferromagnetically coupled, high-spin ( S = 2) Fe­(II) ions and total cluster spin, S = 0, interacting with an adjacent “free” •CH 3 radical ( S = 1/2). This model, which builds on a simplified model for the enzymatic intermediate Ω that was used in developing BS-DFT protocols for treating Ω itself, Figure B, allows for spin transfer as well as exchange-induced spin polarization and thus complements the spin-coupling approach of Figure .…”

“…BS–DFT calculations − were performed in vacuo using ORCA version 5.0.3. , Coordinates from a previously computed model complex were utilized, where geometry was optimized in the high-spin configuration, as described . In the current BS calculations, the 5′dAdo group was truncated to a methyl radical, and the distance of the methyl from the unique iron was set to that derived by ENDOR, as described; coordinates are given in Supporting Information.…”