top part of flask image

Rauchfuss Group

Understanding How Nature Works with Hydrogen: Modeling the Hydrogenases and Related Enzymes

A project supported by the U. S. National Institutes of Health
(RO1 GM61153)

Principal Investigator: Thomas B. Rauchfuss

Stephen Cramer, University of California, Davis
Frédéric Gloaguen, Université Bretagne Occidentale
Wolfgang Lubitz, Max Planck Institute, Mulheim
Luca De Gioia, Universitá di Milano Bicocca
Sharon Hammes-Schiffer, University of Illinois, Urbana-Champaign
Mark Nilges, University of Illinois, Urbana-Champaign
Seiji Ogo, Kyushu University - I2CNER
Matthias Stein, Max Planck Institute for Dynamics, Magdeburg
Giuseppe Zampella, Universitá di Milano Bicocca

Michaela Carlson, B.S. Grinnel University
Geoffrey Chambers, B.S. University of Idaho
Mioy Huynh, B.S. University of North Carolina (advisor: Sharon Hammes-Schiffer)
Yulong Li, Sichuan University of Sicence & Engineering
Edmund Tse, B. S. University of Virginia (advisor: Andrew Gewirth)
Peihua Zhou, North University of China

X-ray Crystallography:
Danielle Gray, University of Illinois, UC
Jeffery Bertke, University of Illinois, UC


Hydrogenases are utilized by microorganisms to "process" H2, i.e. make it or oxidize it.   These processes, which are important in the cellular energy management, broadly affect many redox transformations of environmental significance (e.g. sulfate reduction). Some pathogenic organisms rely on hydrogen-linked metabolic pathways, including the eubacterium Helicobacter pylori, which is responsible for gastric ulcers and cancers that affect many millions of people.

The goal of our research is to understand how these enzymes work.  We pursue this question mainly by studying biomimetic models, i.e. metal complexes that look (somewhat) and behave (somewhat) like the active sites.  We mainly use the techniques of organometallic chemistry.  Students with interests in organometallics are well suited to contribute to this area, especially those students who like to read beyond organometallics, e.g. enzymology, "green energy", organic synthesis, and electrochemistry.

A mechanistic understanding of the hydrogenases is likely to provide the foundations for new technologies for conversions of the ultimate clean fuel, H2. Another attraction is that the catalysts are not based on platinum group metals.


[FeFe]-Hydrogenases are evolutionarily more modern and in fact easier to model. Rapid progress on these sites is being made by us as well as by groups across the globe. The site consists of a diiron dithiolate with cyanide and CO as ligands as well as an appended 4Fe-4S cluster. A vacant or at least labile site is apparent on one Fe center. Substrate turn-over is localized on this site. Substrate activation is complemented by an amine-containing cofactor, which hovers over the catalytic site.

Structure of model for the [FeFe]-hydrogenase containing a terminal iron hydride and protonated amine cofactor

Structure of model for the [FeFe]-hydrogenase containing a terminal iron hydride and protonated amine cofactor

Program highlights:
  • In 1999, our group crystallized models of the type [Fe2(SR)2(CO)4(CN)2]2-.
    "First Generation Analogues of the Binuclear Site in the Fe-Only Hydrogenases: Fe2(SR)2(CO)4(CN)2-", Schmidt, M.; Contakes, S. M.; Rauchfuss, T. B., J. Am. Chem. Soc. 1999, 121, 9736-7.
  • In 2001, we discovered that diiron dithiolates catalyze the reduction of protons to H2.
    "Biomimetic Proton Reduction Catalyzed by an Iron Carbonyl Thiolate", Gloaguen, F.; Lawrence, J. D.; Rauchfuss, T. B., J. Am. Chem. Soc. 2001, 123, 9476-7.
  • In 2001, we described the synthesis of diiron complexes containing the implied cofactor, the azadithiolate (SCH2NHCH2S), which was previously unknown.
    "Diiron Azadithiolates: Synthesis, Structure, and Stereoelectronics", Lawrence, J. D.; Li, H.; Rauchfuss, T. B.; Bénard, M.; Rohmer M.-M., Angew. Chem. Int. Ed. 2001, 40, 1768-71.
  • In 2005, we prepared a diiron dithiolato complex containing a terminal hydride ligand.
    "Characterization of the First Terminal Diferrous Hydride: Converging on the Mechanism of the Fe-only Hydrogenases" van der Vlugt, J. I.; Rauchfuss, T. B.; Whaley, C. M.; Wilson, S. R.  J. Am. Chem. Soc., 2005, 127, 16012-3.
  • In 2007, we showed that electronically unsymmetrical diiron(I) dithiolates adopt an Hox-like structure.
    "Nitrosyl Derivatives of Diiron(I) Dithiolates Mimic the Structure and Lewis Acidity of the FeFe-Hydrogenase Active Site" Olsen, M. T.; Bruschi, M.; De Gioia, L.; Rauchfuss, T. B.; Wilson, S. R.  J. Am. Chem. Soc., 2008, 130, 16012-3.
  • In 2008, we reported that the adt cofactor participates in acid-base behavior of diiron hydrides, an essential aspect of hydrogenase action.
    "Aza- and Oxadithiolates Are Probable Proton Relays in Functional Models for the [FeFe]-Hydrogenases" Barton, B. E.; Olsen, M. T.; T. B. Rauchfuss  J. Am Chem, Soc. 2008, 130, 16834-16835.
  • In 2007-8, concurrent with studies by Marcetta Darensbourg at Texas A&M, we prepared mixed valence complexes that reproduce the rotated geometry and EPR properties of the Hox state of the enzyme.
    Justice, A. K.; De Gioia, L.; Nilges, M. J.; Rauchfuss, T. B.; Wilson, S. R. and Zampella, G., "Redox and Structural Properties of Mixed-Valence Models for the Active Site of the [FeFe]-Hydrogenase: Progress and Challenges", Inorg. Chem., 2008, 47, 7405-7414.
  • In 2009-2011, we showed that mixed valence diiron complexes, models for Hox, activate H2 when complemented by a fast oxidant.  The first direct evidence for PCET in hydrogenases.
    Camara, J. M. and Rauchfuss, T. B., "Mild Redox Complementation Enables H2 Activation by [FeFe]-Hydrogenase Models", J. Am. Chem. Soc., 2011, 133, 8098–8101.
  • In 2012, we crystallized the ammonium-terminal hydride, key intermediate in hydrogen activation and production. Addition of one electron gives H2. The crystal was grown by Maria Carroll and the crystallography was analyzed by her father Patrick Carroll (U Penn). The diiron complex with the amine cofactor is an extremely fast catalyst for H2 production. The analogous propanedithiolate is a poor catalyst.
    M. E. Carroll, B. E. Barton, T. B. Rauchfuss and P. J. Carroll, "Synthetic Models for the Active Site of the [FeFe]-Hydrogenase: Catalytic Proton Reduction and the Structure of the Doubly Protonated Intermediate", J. Am. Chem. Soc. 2012, 134, 18843-18852.
  • In 2013 we crystalized a rotated reduced diiron dithiolate, Fe2(2,2-Et2pdt)(CO)4(dppv). Preparation by Dr. Wenguang Wang. Crystallography by Curtis Moore and Arnold Rheingold (UCSD).
diiron dithiolate
diiron dithiolate
  • 2015:
    Ryan Gilbert-Wilson develops a route to Fe(0) from 57Fe and collaborates with the Lubitz group to label the diiron subsite of Hyd-A1 in Chlamydomonas reinhardtii using the Grenoble Insertion method.

    chemical structures in equation of  of hydrogenase reaction

    "Spectroscopic investigations of [FeFe] hydrogenase maturated with [57Fe2(adt)(CN)2(CO)4]2-" Ryan Gilbert-Wilson, Judith F. Siebel, Agnieszka Adamska-Venkatesh, Cindy C. Pham, Edward Reijerse, Hongxin Wang, Stephen P. Cramer, Wolfgang Lubitz, Thomas B. Rauchfuss.

chromatographic separation of 57Fe2S2(CO)6 from 57Fe3S2(CO)9

Chromatographic separation of 57Fe2S2(CO)6 from 57Fe3S2(CO)9


[NiFeHydrogenase[NiFe]-Hydrogenases are more pervasive than [FeFe] hydrogenases. Unlike the FeFe] enzymes, the [NiFe] site binds the hydride between the two metal sites, Fe(CO)(CN)2 and Ni(Scys)2 centers linked by a pair of cysteinyl thiolates. The ensemble provides a redox-active receptor for protons.

The main challenge in the biomimetic approach has been the synthesis of models that carry substrate (H2, hydride).

Program highlights:
  • 2003, 2009: Preparation of a HFe(CN)2(CO) center in the form of HFe(CN)2(CO)3]-.
    Whaley, C. M.; Rauchfuss, T. B. and Wilson, S. R., "Coordination Chemistry of [HFe(CN)2(CO)3]- and Its Derivatives: Toward a Model for the Iron Subsite of the [NiFe]-Hydrogenases", Inorg. Chem., 2009, 48, 4462–4469.
  • 2009: The first example of a nickel-iron dithiolato hydride was prepared by our group. We also showed that this species catalyzes the reduction of H+ to H2.
    "Nickel-Iron-Dithiolato-Hydrides Relevant to the [NiFe]-Hydrogenase Active Site", Barton, B. E.; Whaley, C. M.; Rauchfuss, T. B.; Gray, D. L. J. Am. Chem. Soc. 2009, 131, 6942-6943.
    We have since prepared several substituted derivatives of the initial model.
  • 2011: The first example of a mixed valence nickel-iron dithiolate was characterized by our group. This species in an intermediate in the hydrogen evolution reaction.
    "Mixed-Valence Nickel-Iron Dithiolates Models of the Active Site of the [NiFe]-Hydrogenases", Schilter, D.; Nilges, M. J.; Chakrabarti, M.; Lindahl, P. A.; Rauchfuss, T. B.; Stein, M., Inorg. Chem., 2012, 51, 2338-48.
    Cover Inorganic Chemistry, Feb. 20, 2012   c Chemistry
    Click on image for larger image
    Cover, Inorganic Chemistry, Feb. 20, 2012.
  • 2013: The first example of a [NiFe]-H2ase model containing cyanide cofactors was prepared and characterized by Brian Manor. It even oxidizes H2 catalytically.
    Reaction for NiFe model containing cyanide cofactors
    structure of NiFe hydrogenase
  • 2014:
    Mioy Huynh and Dave Schilter collaborate to show that the likely pathway for protonation of Fe(I)-Ni(I) complexes involves a valence isomer Fe(0)-Ni(II) species. The clue was provided by the characterization of Fe(0)-Pt(II) species.

    "Protonation of Nickel–Iron Hydrogenase Models Proceeds after Isomerization at Nickel", Huynh, M. T.; Schilter, D.; Hammes-Schiffer, S.; Rauchfuss, T. B., J. Am. Chem. Soc. 2014, 136, 12385-12395.

    Chemical reaction scheme
  • 2015:
    After establishing Ru(II)-Ni(I) models, Geoffrey Chambers crystallizes an authentic Fe(II)Ni(I) species, the first such species and a first-generation model for the Ni-L state.
    "Organonickel Models of the [NiFe]-Hydrogenase Active Site", Geoffrey M. Chambers, Mioy T. Huynh, Yulong Li, Sharon Hammes-Schiffer, Thomas B. Rauchfuss, Edward Reijerse, Wolfgang Lubitz Inorganic Chemistry, in press (ASAP since 9/15 for a thematic volume on bioinspired catalysis)
    NiFe-hydrongenase active site model

Useful Preps