Synchrotron-based spectroscopic and computational studies of bioinorganic and organometallic
Office: Room 253
Lab: Room 254 and 258
Chemistry and Biochemistry Building
P.O. Box 173400
Bozeman, MT 59717
- B.Eng.: 1993 University of Veszprém, Hungary
- M.Sc.: 1995 University of Veszprém, Hungary
- Ph.D.: 1998 University of Veszprém, Hungary
- Postdoc.: 1998-2000 Emory University, Atlanta, GA
- Postdoc.: 2000-2003 Stanford University, Stanford, CA
- CHMY 515 STRUCTURE AND BONDING IN INORGANIC CHEMISTRY
Awards and Professional Activities
1999-2001: Recognition for mentoring students by the Council of National Scientific
1995: Pro Scientia Gold Medal from the Hungarian Academy of Sciences and Council of National Scientific Students Associations
2011: Kavli Fellow by the National Academy of Sciences USA
Bioinorganic Structure/Function of Complex Fe-S clusters
We made considerable progress in the understanding of the electronic structure and the composition of the catalytically active, iron-sulfur cluster (H-cluster) of FeFe-hydrogenase. In our 2006 paper in Chemical Communication  we provided experimental evidence from sulfur K-edge X-ray absorption spectroscopy (XAS) that the nature of the unique dithiolate ligand is crucial for tuning the electronic structure of the H-cluster via Fe-S bond covalency and thus modulating its redox potential. From a comparative spectroscopic analysis and supporting density functional calculations employing a non-truncated computational model, we showed that the Hcluster is an electronically inseparable 6Fe cluster and not just a 2Fe cluster as represented in the literature. Independently from us, recent advanced EPR studies also came to the same conclusion. Focusing on the chemical composition of the unique dithiolate ligand, as one of the last unknown yet crucial structural feature of the H-cluster, we reported in our JACS 2008 paper  an unbiased computational analysis of the H-cluster using a close to atomic resolution structure of the FeFe-hydrogenase metalloenzyme from Clostridium pasteurianum in collaboration with the Peters Group at the Department. Contrary to dithiomethylamine which is the currently favored composition in literature, we found that a dithiomethylether composition is more likely. Importantly, we also found that regardless of the composition, the bridge-head group cannot act as a catalytic base. Its protonated state favors an alternative conformation that has not been observed in any structural studies. This conformation effectively shuts down the proton transfer to or from the active site, which is prohibitive if the approximately 9000 molecules of H2 per second per each hydrogenase enzyme turnover rate is considered.
Furthermore, using a computational chemical approach in our FEBS Letter  we proposed
a plausible mechanism for the biosynthesis of the H-cluster. We showed that upon a
single hydrogen abstraction from a free glycine amino acid by an S-adenosylmethionine
(SAM) radical metalloenzyme, which is a known biochemical process, the glycine radical
can spontaneously decompose at a reduced Fe(I) site to CO, CN-, and H2O with the release
of two electrons and four protons. These are the ligands of the iron Fe(I) sites in
a catalytically active subcluster. Using follow up biochemical studies from the Peters
and Broderick groups at the Department, we were able to extend these studies into
the biosynthesis of the dithiolate ligand as well . In a parallel study we have
rigorously evaluate the role of the dithiolate ligand composition in the electron
and spin density distribution of the H-cluster from various angles, and found only
limited indication for the dithiolate bridgehead group being involved in any covalent
interaction within the cluster.
Another important contribution by our group is the completion of - as one of the reviewers put it - an exhaustive and exhausting study on the chemical composition, charge-, protonation-, and spin-state of the catalytic active cluster, FeMo-co of Mo-nitrogenase . In an unbiased approach we have put all the experimental data from the literature onto the table and evaluated using a spectroscopically validated level of theory and a reasonable computational model. The relative spin state energies of resting and oxidized FeMo-co already allowed exclusion of certain iron oxidation state distributions and interstitial ligand compositions. Geometry-optimized FeMo-co structures of several models further eliminated additional states and compositions, while reduction potentials indicated a strong preference for the most likely charge state of FeMo-co. Mosssbauer and ENDOR parameter calculations were found to be remarkably dependent on the employed training set, density functional, and basis set. Overall, we found that a more oxidized [MoIV-2FeII-5FeIII-9S2â€“-C4â€“] composition with a hydroxyl-protonated homocitrate ligand satisfies all of the available experimental criteria and is thus favored over the currently preferred composition of [MoIV-4FeII-3FeIII-9S2â€“-N3â€“] from the literature.
- Schwab D.E., Tard C., Brecht E., Peters J.W., Pickett C.J., Szilagyi R.K.::On the electronic structure of the hydrogenase H-clusterChemical Communication, 2006, (35), 3696-3698
- Pandey A.S., Harris T.V., Giles L.J., Peters J.W., Szilagyi R.K.: :Dithiomethylether as a Ligand in the Hydrogenase H-ClusterJournal of the American Chemical Society, 2008, 130(13), 4533-4540
- Peters J.W., Szilagyi R.K., Naumov A., Douglas T. :A radical solution for the biosynthesis of the H-cluster of hydrogenaseFEBS Letters, 2006, 580(2), 363-367
- Grigoropoulos A., Szilagyi R.K::Evaluation of biosynthetic pathways for the unique dithiolate ligand of the FeFe hydrogenase H-cluster
- Journal of Biological Inorganic Chemistry, 2010, 15(8), 1177-1182
- Giles L.J., Grigoropoulos A., Szilagyi R.K.: :Electron and Spin Density Topology of the H-Cluster and Its Biomimetic ComplexesEuropean Journal of Inorganic Chemistry, 2011, 2011(17), 2677-2690
- Harris T.V., Szilagyi R.K.::Comparative Assessment of the Composition and Charge State of Nitrogenase FeMo-CofactorInorganic Chemistry, 2011, 50(11), 4811-4824
Structure, Spectroscopy, Physical, Mechanism, Inorganic, Computational, Biophysical, Bioinorganic
While the topics of our 2008 JBIC  and 2006 JACS  papers indicate bioinorganic
structure/function content, I list these here due to their focus on method development.
In these publications we set an example for developing realistic virtual chemistry
models for complex metalloenzymes, where outer coordination sphere-effects have been
observed by site-directed mutagenesis studies. This work has been carried out in collaboration
with the Dooley Group at the Department. We showed that a systematic and careful mapping
of the network of weak interactions around the catalytic active site is critical not
just to reproduce the experimental structure, but also the spectroscopic signatures
and redox potentials. We were able to calculate the two-step redox process in galactose
oxidase within 200 mV accuracy without any empirical parameterization.
An important work for our future studies was accomplished with a considerable contribution from a summer undergraduate student, who systematically evaluated the performance of a large list of density functionals and basis sets for both the geometric and electronic structures of a central 4Fe-4S cluster. We published this work in an invited contribution to a special Computational Bioinorganic Chemistry issue of the Journal of Computational Chemistry . We have shown that for achieving 0.03 Ã… and 0.1 e- or better accuracy in metric parameters and sulfur covalency in the [Fe4S4(SR)4]2- cluster a previously undefined hybrid functional, B(5HF)P86 must be employed with a triple-Î¶ quality basis set containing both polarization and diffuse functions. This particular 4Fe-4S cluster is generally considered the resting form of clusters in hydrogenase, nitrogenase, ferredoxins, high-potential iron-proteins, SAM radical enzymes, etc. With this work, we also published a fast and user friendly way of generating complex wave functions for broken symmetry calculations of antiferromagnetically coupled states that are essential for correct treatment of iron-sulfur clusters.
As representative examples for providing computational training for visiting undergraduate and graduate students, I wish to highlight a collaborative effort with Prof. Karen McFarlane from Willamette University, and Prof. Jalilehvandâ€™s group at University of Calgary. While both have a strong inorganic spectroscopy tone, my groupâ€™s contribution consisted of electronic structural support that actually tied the various measurements together carried out by the collaboratorâ€™s group. The students spent few weeks to few months in my group to complete a full electronic structure analysis that was essential in assigning all spectral features. These work allowed us to gain understanding into coordination chemistry of Ru-based anticancer drugs  and transition-metal coordination to cysteine residues .
With a collaborative project from the Chemical and Biological Engineering Department on campus, we opened up a new research direction for the group that we are actively pursuing . This entails the molecular level description of the chemical toxicity of depleted uranium. The main driving force for this research from our interest is the remarkable coordination chemistry of high valent uranium with completely empty 5d and 4f valence orbitals. This allows for the existence of seven or even higher coordinate complexes with remarkable variability of coordination environment. However, for the aqueous form of U(VI) we found selective and strong coordination affinity to a biologically common [ONO] coordination environment. In the light of the in vivo studies showing that high valent uranium can show toxicity in or even below the currently allowed EPA limits, we are developing a research program to identify additional biological cofactors that may be susceptible to U(VI) coordination and thus can lead us to identification of previously undocumented acute toxicity mechanism.
- Rokhsana D., Dooley D.M., Szilagyi R.K.: :Structure of the Oxidized Active Site of Galactose Oxidase from Realistic In Silico ModelsJournal of the American Chemical Society, 2006, 128(49), 15550-15551
- Rokhsana D., Dooley D.M., Szilagyi R.K.: :Systematic development of computational models for the catalytic site in galactose oxidase: impact of outer-sphere residues on the geometric and electronic structuresJournal of Biological Inorganic Chemistry, 2008, 13(3), 371-383
- Harris T.V., Szilagyi R.K., McFarlane Holman K.L.::Electronic Structural Investigations of Ru-containing Compounds and Anticancer ProdrugsJournal of Biological Inorganic Chemistry, 2009, 14(6), 891-898
- Leung B.O., Jalilehvand F., Szilagyi R.K.: Electronic Structure of Transition Metal-Cysteine Complexes from X-ray Absorption SpectroscopyJournal of Physical Chemistry B, 2008, 112(15), 4770-4778
- VanEngelen M.R., Szilagyi R.K., Gerlach R., Lee B.D., Apel W.A., Peyton B.M.::Uranium Exerts Acute Toxicity by Binding to Pyrroloquinoline Quinone CofactorEnvironmental Science and Technology, 2011, 45(3), 937-942
Structure, Physical, Inorganic, Computational, Bioinorganic
In addition to my curiosity in bioinorganic chemistry and systematic approach to computational
chemistry, synchrotron science truly has become my passion. Just thinking about the
uncharted areas of the Periodic Table waiting to be explored by various synchrotron-enabled
absorption and emission spectroscopic and scattering techniques gives me chills. Thus,
in the past few years I have focused more and more on accessing various energy ranges
at different synchrotron facilities and beamlines to be able to collect as much experimental
information as technically feasible about the electronic structure of catalytically
important inorganic and organometallic compounds. While at first this may have looked
like a fishing expedition, with four publications we demonstrated a converging effort
to illustrate the power of the multi-edge X-ray absorption spectroscopic (meXAS) technique.
In collaboration with the Peters at Caltech and Mindiola groups at Indiana University,
we published three papers in JACS, where the meXAS technique was critical to unambiguously
demonstrate experimentally the previously undocumented non-innocent nature of the
PPP and PNP pincer-type ligands for dinuclear Cu  and mononuclear Ni . as well
as aminyl ligands for mononuclear Cu  complexes, respectively. Their complexes
gave me the opportunity to have demonstrative examples for the information content
of the meXAS technique in addition to understanding the fundamental electronic structures
of some catalytically important complexes.
Importantly with these two papers, we have not yet exhausted the possibility of future publications as we are gearing up for extending the earlier measurements to other metals and ligand derivatives. In a more methodological paper published in a special issue of Inorganica Chimica Acta , we laid the foundation of a new spectroscopic technique developed for experimentally mapping the catalytically important intermediates in palladium catalyzed organic and organometallic transformations. Using simple chloropalladium complexes we showed that transition dipole integrals for palladium L-shell core electron excitations can be empirically derived using already established dipole integrals for chloride K-shell excitation. Furthermore, we pointed out that caution is needed when comparing quantitative meXAS obtained on different beamlines at different synchrotron facilities. This has not been addressed previously in the literature. By developing the data normalization and quantitative analysis protocols for the palladium L-edge, we are in the position to continue this method development work for phosphorous, carbon, nitrogen, and oxygen-containing ligands.
An inspiring Department seminar triggered the idea of a sulfur K-edge XAS study on S-nitroso compounds that resulted in a BBRC publication . Already from a â€˜quick/dirtyâ€™ electronic structure analysis carried out immediately after the seminar we saw that there are at least three unique molecular orbitals in S-nitroso thiolates that could be used for detecting biochemically important S-nitrosated proteins. Importantly our experimental measurements further supported this assumption and we were even able to predict a possible spectrum for an S-nitrosated hemoglobin sample. These measurements provided solid preliminary results for a section of an institutional NIH COBRE grant. While our proposal for using XAS as a detection tool is still valid, unfortunately the orders of magnitude detection limit of XAS (milimolar) and the biologically relevant S-nitroso compound concentrations (micromolar) prohibits the use of this particular experimental technique. Recent development in high brightness synchrotron storage rings and beamlines soon will open up the possibility for these measurements.
An new direction for our research group grew out of research funded by the local node (ABRC center)of the NASA Astrobiology Institute. We teamed up the Minton group from the Department in creating and then characterizing modified Fe-S mineral surfaces. A recent publication  revealed the presence of a unique reduced Fe surface dubbed as Fe(I)2S that was formed from Fe(II)S2 pyrite upon exposure to beam of hydrogen atoms. This reduced Fe-S surface shows electronic structural similarity to the catalytically active cluster of hydrogenase and likely the nitrogenase (see Bioinorganic Structure/Function project).
- Harkins S.B., Mankad N.P., Miller A.J.M., Szilagyi R.K., Peters J.C. :Probing the Electronic Structures of [Cu2(mu-XR2)]n+Cores as a Function of the Bridging X Atom (X=N/P) and Charge (n=0/1/2)Journal of the American Chemical Society, 2008, 130(11), 3478-3485
- Adhikari D., Mossin S., Basuli F., Huffman J.C., Szilagyi R.K., Meyer K., Mindiola D.J.:Structural, Spectroscopic, and Theoretical Elucidation of a Redox-Active Pincer-Type Ancillary Applied in CatalysisJournal of the American Chemical Society, 2008, 130(11), 3676-3682
- Mankad N.P., Antholine W.E., Szilagyi R.K., Peters J.C.:Three-Coordinate Copper(I) Amido and Aminyl Radical ComplexesJournal of the American Chemical Society, 2009, 131(11), 3878-3881
- Boysen R.B., Szilagyi R.K.: :Development of Palladium L-Edge X-Ray Absorption Spectroscopy and its Application for Chloropalladium ComplexesInorganica Chimica Acta, 2008, 361(4), 1047-1058
- Szilagyi R.K., Schwab D.E.:Sulfur K-edge X-ray absorption spectroscopy as an experimental probe for S-nitroso proteinsBiochemical Biophysical Research Communication33060-64 (2005)
- Che Li, Gardenghi D.J., Szilagyi R.K., Minton T.K. :Production of a Biomimetic Fe(I)-S Phase on Pyrite by Atomic Hydrogen Beam Surface Reactive ScatteringLangmuir, 2011, 27(11), 6814-6821
Structure, Spectroscopy, Physical, Inorganic, Biophysical, Analytical