ArticleInorganic chemistry2022
Benchmark Study of Redox Potential Calculations for Iron-Sulfur Clusters in Proteins.
Article in Inorganic chemistry, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Mitochondrial complex I as a master regulator of redox signaling: From structural architecture to directionality of electron transport.Free radical biology & medicine · 2026Review
- Geometry, spin coupling, and dielectric control of redox potentials in [4Fe-4S] Clusters.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2026Article
- Benchmark Study for Calculations of pKa Values of Metal Ligands in Proteins.Journal of chemical theory and computation · 2026Article
- Quantum medicine: A quantum-mechanical framework for redox biology, disease and precision medicine.Clinical and translational medicine · 2026Review
- Predicting Metalloprotein Redox Potentials with Machine Learning: A Focus on Iron-Sulfur Systems.Journal of chemical information and modeling · 2025Article
- Iron-sulfur clusters in SARS-CoV-2 exoribonuclease and methyltransferase complexes: relevance for viral genome proofreading and capping.Nature communications · 2025Article
- The Properties That Allow Tuning the Reduction Potentials over a Volt Range in Biological Iron/Sulfur Clusters.The journal of physical chemistry letters · 2025Article
- Predicting Iron-Sulfur Cluster Redox Potentials: A Simple Model Derived from Protein Structures.ACS omega · 2025Article
- Predicting Reduction Potentials of Blue Copper Proteins Using Quantum Mechanical Calculations.Inorganic chemistry · 2025Article
- Electron transfer in biological systems.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2024Review
- Multireference Protonation Energetics of a Dimeric Model of Nitrogenase Iron-Sulfur Clusters.The journal of physical chemistry. A · 2023Article
- Two local minima for structures of [4Fe-4S] clusters obtained with density functional theory methods.Scientific reports · 2023Article
- Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase.Molecules (Basel, Switzerland) · 2022Article
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5 authors.
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Abstract
Redox potentials have been calculated for 12 different iron-sulfur sites of 6 different types with 1-4 iron ions. Structures were optimized with combined quantum mechanical and molecular mechanical (QM/MM) methods, and the redox potentials were calculated using the QM/MM energies, single-point QM methods in a continuum solvent or by QM/MM thermodynamic cycle perturbations. We show that the best results are obtained with a large QM system (∼300 atoms, but a smaller QM system, ∼150 atoms, can be used for the QM/MM geometry optimization) and a large value of the dielectric constant (80). For absolute redox potentials, the B3LYP density functional method gives better results than TPSS, and the results are improved with a larger basis set. However, for relative redox potentials, the opposite is true. The results are insensitive to the force field (charges of the surroundings) used for the QM/MM calculations or whether the protein and solvent outside the QM system are relaxed or kept fixed at the crystal structure. With the best approach for relative potentials, mean absolute and maximum deviations of 0.17 and 0.44 V, respectively, are obtained after removing a systematic error of -0.55 V. Such an approach can be used to identify the correct oxidation states involved in a certain redox reaction.
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