Deriving New Model Hamiltonians for [2Fe-2S] Iron-Sulfur Clusters
Abstract
Iron–sulfur clusters are common bioinorganic cofactors found in many enzymes. Their open-shell electronic structures, characterized by strongly interacting d-electrons and a dense manifold of near-degenerate electronic states, often require computationally expensive multiconfigurational ab initio methods for their accurate treatment. Therefore, model Hamiltonians using a limited number of physically meaningful parameters are often used to describe their electronic structure properties. The Heisenberg-Dirac-Van Vleck Hamiltonian and the canonical Heisenberg double exchange model, which have traditionally been used to describe the electronic spectra of iron–sulfur clusters, can describe the lowest-energy state of each spin multiplicity. However, these models are limited to a relatively small set of spin degrees of freedom and cannot describe the full range of low-energy electronic excitations and therefore are not sufficient to reproduce the complete low-energy electronic spectrum. This motivates the development of more general model Hamiltonians for these systems. In this work, we employ the density matrix downfolding (DMD) method to derive an improved model Hamiltonian for the [Fe 2 S 2 (SCH 3 ) 4 ] 2-/3- cluster, which serve as models of the active site of ferredoxins containing the [2Fe–2S] motif. A generalized Hubbard-like Hamiltonian derived using DMD provides a substantially improved description of the low-energy spectrum using a relatively small number of physically meaningful parameters. Our matching pursuit analysis further shows that the exchange coupling parameter is selected only at a late stage of the optimization, while most of the exchange interaction is captured by the hopping and electron-electron interaction terms.
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BibTeX
@misc{gibbs2026deriving,
title = {{Deriving New Model Hamiltonians for [2Fe-2S] Iron-Sulfur Clusters}},
author = {Wyatt A. Gibbs and David Wilian Oliveira de Sousa and Elvira R. Sayfutyarova},
howpublished = {ChemRxiv},
year = {2026},
month = sep,
doi = {10.26434/chemrxiv.15008990/v1},
url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008990/v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Deriving New Model Hamiltonians for [2Fe-2S] Iron-Sulfur Clusters
AU - Wyatt A. Gibbs
AU - David Wilian Oliveira de Sousa
AU - Elvira R. Sayfutyarova
PY - 2026
DA - 2026/09/17
PB - ChemRxiv
DO - 10.26434/chemrxiv.15008990/v1
UR - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008990/v1
AB - Iron–sulfur clusters are common bioinorganic cofactors found in many enzymes. Their open-shell electronic structures, characterized by strongly interacting d-electrons and a dense manifold of near-degenerate electronic states, often require computationally expensive multiconfigurational ab initio methods for their accurate treatment. Therefore, model Hamiltonians using a limited number of physically meaningful parameters are often used to describe their electronic structure properties. The Heisenberg-Dirac-Van Vleck Hamiltonian and the canonical Heisenberg double exchange model, which have traditionally been used to describe the electronic spectra of iron–sulfur clusters, can describe the lowest-energy state of each spin multiplicity. However, these models are limited to a relatively small set of spin degrees of freedom and cannot describe the full range of low-energy electronic excitations and therefore are not sufficient to reproduce the complete low-energy electronic spectrum. This motivates the development of more general model Hamiltonians for these systems. In this work, we employ the density matrix downfolding (DMD) method to derive an improved model Hamiltonian for the [Fe 2 S 2 (SCH 3 ) 4 ] 2-/3- cluster, which serve as models of the active site of ferredoxins containing the [2Fe–2S] motif. A generalized Hubbard-like Hamiltonian derived using DMD provides a substantially improved description of the low-energy spectrum using a relatively small number of physically meaningful parameters. Our matching pursuit analysis further shows that the exchange coupling parameter is selected only at a late stage of the optimization, while most of the exchange interaction is captured by the hopping and electron-electron interaction terms.
ER -