Scientists synthesize diiron subcluster to artificially mature [FeFe]-hydrogenases

A New Chemical Shortcut Could Make One of Nature’s Most Powerful Hydrogen Enzymes Easier to Build

Hydrogen-producing enzymes known as [FeFe]-hydrogenases have long fascinated chemists, biologists and clean-energy researchers because they can rapidly catalyze the reversible conversion between protons, electrons and molecular hydrogen. Their performance is remarkable: under suitable conditions, these enzymes can generate or consume H₂ with an efficiency that has made them attractive as potential biocatalysts and as blueprints for artificial catalysts. Yet their most important component, an iron-based catalytic center known as the H-cluster, is notoriously difficult to assemble. A new protocol from researchers at the University of Rochester and Indiana University presents a practical chemical route to manufacturing a critical diiron fragment of that cluster, potentially simplifying the production of active hydrogenases in the laboratory.

The work, published in Nature Protocols by Xin Yu, Fuxing Wei and Thomas B. Rauchfuss, focuses on synthesizing the anionic complex [Fe₂(μ-SCH₂)₂NH₂(CO)₄]²⁻, commonly referred to as [1]²⁻. This molecular fragment reproduces the diiron portion of the H-cluster, the catalytic center responsible for hydrogen turnover in [FeFe]-hydrogenases. In living cells, the H-cluster is assembled through a sophisticated sequence of enzyme-mediated reactions involving multiple accessory proteins. Recreating that biosynthetic process outside the cell can be laborious and technically demanding. Chemical synthesis of the diiron subcluster offers an alternative: instead of asking the biological machinery to build the entire catalytic center, researchers can prepare the essential cofactor separately and insert it into an otherwise incomplete enzyme.

The H-cluster is chemically distinctive because it combines two iron atoms with carbon monoxide and cyanide ligands, while also incorporating an azadithiolate bridge. The bridge contains two sulfur atoms connected through a nitrogen-bearing framework, producing the unusual Fe₂[(μ-SCH₂)₂NH] architecture. Each sulfur atom binds to one of the iron centers, helping hold the diiron unit in the geometry required for catalysis. The cyanide and carbon monoxide ligands tune the electronic properties of the metals, allowing the cluster to accept and release electrons and protons during hydrogen conversion. Although carbon monoxide and cyanide are toxic as free compounds, they are tightly bound within the engineered coordination complex, where they serve a precise structural and electronic function.

The protocol describes two complementary synthetic strategies. The first, called the condensation route, begins with the reaction of the diiron dithiol complex Fe₂(μ-SH)₂(CO)₆ and a nitrogen-containing formaldehyde equivalent, N₄(CH₂)₆. This process constructs the azadithiolate bridge across the two iron atoms. The resulting iron complex is then subjected to cyanation, replacing selected carbon monoxide ligands with cyanide and producing the targeted [1]²⁻ subcluster. The route resembles a chemical reconstruction of the H-cluster’s central framework, but its most demanding operation is the preparation of Fe₂(μ-S₂)(CO)₆, an important sulfur-containing precursor used along the way. Handling air-sensitive iron carbonyl compounds and controlling the sulfur chemistry are central challenges in this approach.

The second strategy, known as the Fmoc route, uses a protecting group familiar to synthetic chemists who work with peptides and other nitrogen-containing molecules. In this method, the azadithiolate nitrogen is temporarily protected with fluorenylmethoxycarbonyl, or Fmoc, while the diiron framework is assembled. The key intermediate is Fe₂(μ-SCH₂)₂NFmoc₆. Once the desired iron-sulfur structure has been formed, the Fmoc group can be removed to reveal the nitrogen atom and generate the unprotected azadithiolate-containing subcluster. By separating the construction of the metal framework from the handling of the reactive nitrogen center, the route gives chemists additional control over the synthesis and provides a particularly convenient platform for introducing selected isotopes.

According to the researchers, each route requires approximately 20 hours of hands-on work, although the procedures are distributed across several operations rather than performed in one continuous reaction. The protocol is designed to make the synthesis reproducible, with detailed guidance for preparing intermediates, carrying out ligand-exchange reactions, purifying the products and handling sensitive compounds. Such practical details matter because [FeFe]-hydrogenase chemistry is highly vulnerable to oxygen. The reduced iron-sulfur cluster can be damaged by exposure to air, meaning that many steps must be conducted under an inert atmosphere using oxygen-free solvents and carefully controlled transfers. The final subcluster is also typically handled in a reduced, negatively charged form, requiring suitable counterions and purification methods compatible with its sensitivity.

The chemical product is intended for artificial maturation, a technique in which an inactive hydrogenase protein is supplied with a synthetic cofactor or cofactor precursor. Many [FeFe]-hydrogenases can be produced without a fully assembled H-cluster, leaving an apoenzyme that lacks catalytic activity. When the chemically prepared diiron subcluster is introduced under appropriate conditions, it can combine with the protein-bound portion of the active site, restoring the complete H-cluster. This approach allows researchers to study the enzyme without relying entirely on the natural maturation machinery. It also makes it possible to alter the synthetic cofactor before insertion, creating carefully controlled variants that can reveal how individual atoms, ligands and oxidation states influence hydrogen catalysis.

Isotopic labeling is one of the most valuable capabilities enabled by the two synthetic routes. Researchers can replace naturally abundant atoms with isotopes such as carbon-13, nitrogen-15 or iron-57 and then monitor the labeled positions using nuclear magnetic resonance, Mössbauer spectroscopy, infrared spectroscopy or other analytical techniques. These measurements can clarify how electrons move through the H-cluster, how protons reach the active site and how carbon monoxide and cyanide ligands respond during catalysis. The authors emphasize that iron-57 labeling is especially straightforward through the Fmoc route. Because iron can be introduced at a defined stage of the synthesis, the method could support high-resolution studies of the electronic structure and magnetic properties of the diiron center.

The broader significance of the protocol lies in the bridge it creates between biological hydrogen production and synthetic inorganic chemistry. [FeFe]-hydrogenases are among nature’s most efficient hydrogen catalysts, but their dependence on elaborate maturation pathways has limited their use in engineered systems. A reliable supply of the synthetic diiron fragment could help researchers transfer hydrogenase chemistry into redesigned proteins, electrode materials or hybrid catalytic platforms. It may also accelerate the development of biomimetic complexes that imitate the H-cluster while avoiding the fragility of the full enzyme. The protocol does not by itself create a commercial hydrogen technology, and substantial challenges remain, including oxygen sensitivity, cofactor delivery and long-term stability. Nevertheless, by making the defining iron-sulfur unit more accessible, the work gives scientists a sharper chemical tool for understanding—and potentially harnessing—one of biology’s most compelling hydrogen machines.

Subject of Research: Chemical synthesis of the diiron subcluster of [FeFe]-hydrogenases for artificial enzyme maturation and isotopic labeling.

Article Title: Synthesis of diiron subcluster [Fe₂(μ-SCH₂)₂NH₂(CO)₄]²⁻ for artificial maturation of [FeFe]-hydrogenases

Article References: Yu, X., Wei, F. & Rauchfuss, T.B. Synthesis of diiron subcluster [Fe₂(μ-SCH₂)₂NH₂(CO)₄]²⁻ for artificial maturation of [FeFe]-hydrogenases. Nature Protocols (2026). https://doi.org/10.1038/s41596-026-01418-x

Image Credits: AI Generated

DOI: https://doi.org/10.1038/s41596-026-01418-x

Keywords: [FeFe]-hydrogenases, hydrogen production, H-cluster, iron-sulfur chemistry, azadithiolate, artificial maturation, biomimetic catalysis, diiron subcluster, isotope labeling, hydrogen energy