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Modelling the Hydrolysis of Iron-Sulfur Clusters

preprint
submitted on 04.10.2019 and posted on 09.10.2019 by Murilo H. Teixeira, Felipe Curtolo, Sofia R. G. Camilo, Martin J. Field, Peng Zheng, Hongbin Li, Guilherme M. Arantes
Iron-sulfur (FeS) clusters are essential metal cofactors involved in a wide variety of biological functions. Their catalytic efficiency, biosynthesis and regulation depend on FeS stability in aqueous solution. Here, molecular modelling is used to investigate the hydrolysis of an oxidized (ferric) mononuclear FeS cluster by bare dissociation and water substitution mechanisms in neutral and acidic solution. First, approximate electronic structure descriptions of FeS reactions by density functional theory are validated against high-level wave-function CCSD(T) calculations. Solvation contributions are evaluated by an all-atom model with hybrid quantum chemical/molecular mechanical (QM/MM) potentials and enhanced sampling molecular dynamics simulations. The free energy profile obtained for FeS cluster hydrolysis indicates the hybrid functional M06 together with an implicit solvent correction capture the most important aspects of FeS cluster reactivity in aqueous solution. Then, 20 reaction channels leading to two consecutive Fe--S bond ruptures were explored with this calibrated model. For all protonation states, nucleophilic substitution with concerted bond breaking and forming to iron is the preferred mechanism, both kinetic and thermodynamically. In neutral solution, proton transfer from water to the sulfur leaving group is also concerted. Dissociative reactions show higher barriers and will not be relevant for FeS reactivity when exposed to solvent. These hydrolysis mechanisms may help to explain the stability and catalytic mechanisms of FeS clusters of multiple sizes and proteins

Funding

FAPESP 2016/24096-5

FAPESP 2018/08311-9

History

Email Address of Submitting Author

garantes@iq.usp.br

Institution

Universidade de Sao Paulo

Country

Brazil

ORCID For Submitting Author

0000-0001-5356-7703

Declaration of Conflict of Interest

There are no conflicts of interest.

Version Notes

version 1.0

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in Journal of Chemical Information and Modeling

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