Robert K. Szilagyi

Dithiomethylether as a ligand in the hydrogenase h-cluster.

An X-ray crystallographic refinement of the H-cluster of [FeFe]-hydrogenase from Clostridium pasteurianum has been carried out to close-to atomic resolution and is the highest resolution [FeFe]-hydrogenase presented to date. The 1.39 A, anisotropically refined [FeFe]-hydrogenase structure provides a basis for examining the outstanding issue of the composition of the unique nonprotein dithiolate ligand of the H-cluster. In addition to influencing the electronic structure of the H-cluster, the composition of the ligand has mechanistic implications due to the potential of the bridge-head gamma-group participating in proton transfer during catalysis. In this work, sequential density functional theory optimizations of the dithiolate ligand embedded in a 3.5-3.9 A protein environment provide an unbiased approach to examining the most likely composition of the ligand. Structural, conformational, and energetic considerations indicate a preference for dithiomethylether as an H-cluster ligand and strongly disfavor the dithiomethylammonium as a catalytic base for hydrogen production.

A Mononuclear Fe(III) Single Molecule Magnet with a 3/2↔5/2 Spin Crossover

The air stable complex [(PNP)FeCl(2)] (1) (PNP = N[2-P(CHMe(2))(2)-4-methylphenyl](2)(-)), prepared from one-electron oxidation of [(PNP)FeCl] with ClCPh(3), displays an unexpected S = 3/2 to S = 5/2 transition above 80 K as inferred by the dc SQUID magnetic susceptibility measurement. The ac SQUID magnetization data, at zero field and between frequencies 10 and 1042 Hz, clearly reveal complex 1 to have frequency dependence on the out-of-phase signal and thus being a single molecular magnet with a thermally activated barrier of U(eff) = 32-36 cm(-1) (47-52 K). Variable-temperature Mössbauer data also corroborate a significant temperature dependence in δ and ΔE(Q) values for 1, which is in agreement with the system undergoing a change in spin state. Likewise, variable-temperature X-band EPR spectra of 1 reveals the S = 3/2 to be likely the ground state with the S = 5/2 being close in energy. Multiedge XAS absorption spectra suggest the electronic structure of 1 to be highly covalent with an effective iron oxidation state that is more reduced than the typical ferric complexes due to the significant interaction of the phosphine groups in PNP and Cl ligands with iron. A variable-temperature single crystal X-ray diffraction study of 1 collected between 30 and 300 K also reveals elongation of the Fe-P bond lengths and increment in the Cl-Fe-Cl angle as the S = 5/2 state is populated. Theoretical studies show overall similar orbital pictures except for the d(z(2)) orbital, which has the most sensitivity to change in the geometry and bonding, where the quartet ((4)B) and the sextet ((6)A) states are close in energy.

Structural, Spectroscopic, and Theoretical Elucidation of a Redox-Active Pincer-Type Ancillary Applied in Catalysis

Pincer-type ligands are believed to be very robust scaffolds that can support multifarious functionalities as well as highly reactive metal motifs applied in organometallic chemistry, especially in the realm of catalysis. In this paper, we describe the redox and, therefore, noninnocent behavior of a PNP (PNP- = N[2-P(CHMe2)2-4-methylphenyl]2) pincer ancillary bound to nickel. A combination of structural, spectroscopic, and theoretical techniques suggests that this type of framework can house an electron hole when coordinated to Ni(II).

Activation of HydAΔEFG Requires a Preformed [4Fe-4S] Cluster

The H-cluster is a complex bridged metal assembly at the active site of [FeFe]-hydrogenases that consists of a [4Fe-4S] subcluster bridged to a 2Fe-containing subcluster with unique nonprotein ligands, including carbon monoxide, cyanide, and a dithiolate ligand of unknown composition. Specific biosynthetic gene products (HydE, HydF, and HydG) responsible for the biosynthesis of the H-cluster and the maturation of active [FeFe]-hydrogenase have previously been identified and shown to be required for the heterologous expression of active [FeFe]-hydrogenase [Posewitz, M. C., et al. (2004) J. Biol. Chem. 279, 25711-25720]. The precise roles of the maturation proteins are unknown; the most likely possibility is that they are directed at the synthesis of the entire 6Fe-containing H-cluster, the 2Fe subcluster, or only the unique ligands of the 2Fe subcluster. The spectroscopic and biochemical characterization of HydA(DeltaEFG) (the [FeFe]-hydrogenase structural protein expressed in the absence of the maturation machinery) reported here indicates that a [4Fe-4S] cluster is incorporated into the H-cluster site. The purified protein in a representative preparation contains Fe (3.1 +/- 0.5 Fe atoms per HydA(DeltaEFG)) and S(2-) (1.8 +/- 0.5 S(2-) atoms per HydA(DeltaEFG)) and exhibits UV-visible spectroscopic features characteristic of iron-sulfur clusters, including a bleaching of the visible chromophore upon addition of dithionite. The reduced protein gave rise to an axial S = (1)/(2) EPR signal (g = 2.04 and 1.91) characteristic of a reduced [4Fe-4S](+) cluster. Mossbauer spectroscopic characterization of (57)Fe-enriched HydA(DeltaEFG) provided further evidence of the presence of a redox active [4Fe-4S](2+/+) cluster. Iron K-edge EXAFS data provided yet further support for the presence of a [4Fe-4S] cluster in HydA(DeltaEFG). These spectroscopic studies were combined with in vitro activation studies that demonstrate that HydA(DeltaEFG) can be activated by the specific maturases only when a [4Fe-4S] cluster is present in the protein. In sum, this work supports a model in which the role of the maturation machinery is to synthesize and insert the 2Fe subcluster and/or its ligands and not the entire 6Fe-containing H-cluster bridged assembly.

A radical solution for the biosynthesis of the H-cluster of hydrogenase

Fe‐only or FeFe hydrogenases, as they have more recently been termed, possess a uniquely organometallic enzyme active site, termed the H‐cluster, where the electronic properties of an iron–sulfur cluster are tuned with distinctly non‐biological ligands, carbon monoxide and cyanide. Recently, it was discovered that radical S‐adenosylmethionine enzymes were involved in active hydrogenase expression. In the current work, we present a mechanistic scheme for hydrogenase H‐cluster biosynthesis in which both carbon monoxide and cyanide ligands can be derived from the decomposition of a glycine radical. The ideas presented have broader implications in the context of the prebiotic origin of amino acids.

On the accuracy of density functional theory for iron—sulfur clusters

A simple, yet powerful wave function manipulation method was introduced utilizing a generalized ionic fragment approach that allows for systematic mapping of the wave function space for multispin systems with antiferromagnetic coupling. The use of this method was demonstrated for developing ground state electronic wave function for [2Fe‐2S] and [Mo‐3Fe‐4S] clusters. Using well‐defined ionic wave functions for ferrous and ferric irons, sulfide, and thiolate fragments, the accuracy of various density functionals and basis sets including effective core potentials were evaluated on a [4Fe‐4S] cluster by comparing the calculated geometric and electronic structures with crystallographic data and experimental atomic spin densities from X‐ray absorption spectroscopy, respectively. We found that the most reasonable agreement for both geometry and atomic spin densities is obtained by a hybrid functional with 5% HF exchange and 95% density functional exchange supplemented with Perdews 1986 correlation functional. The basis set seems to saturate only at the triple‐ζ level with polarization and diffuse functions. Reasonably preoptimized structures can be obtained by employing computationally less expensive effective core potentials, such as the Stuttgart–Dresden potential with a triple‐ζ valence basis set. The extension of the described calibration methodology to other biologically important and more complex iron–sulfur clusters, such as hydrogenase H‐cluster and nitrogenase FeMo‐co will follow.

Three-coordinate copper(I) amido and aminyl radical complexes.

A three-coordinate Cu-NR(2) system (R = p-tolyl) supported by the anionic bis(phosphino)borate ligand [Ph(2)B(CH(2)P(t)Bu(2))(2)](-) has been isolated and structurally characterized in both its anionic Cu(I) and neutral (formally) Cu(II) oxidation states. A large rate constant for the self-exchange electron-transfer reaction (k(S) >or= 10(7) M(-1) s(-1)) makes this system a functional model for the type-1 active sites in blue copper proteins. Multiedge X-ray absorption spectroscopy, multifrequency electron paramagnetic resonance, and density functional theory analyses collectively indicate that the oxidized form is best regarded as a Cu(I)-aminyl radical complex rather than a Cu(II)-amido species, with about 70% localization of the unpaired electron on the NR(2) unit. Hydrogen-atom transfer and C-C coupling reactions are presented as examples of chemical reactivity manifested by this unusual electronic structure.

Probing the Electronic Structures of [Cu2(μ-XR2)]n+ Diamond Cores as a Function of the Bridging X Atom (X = N or P) and Charge (n = 0, 1, 2)

A series of dicopper diamond core complexes that can be isolated in three different oxidation states ([Cu2(mu-XR2)]n+, where n = 0, 1, 2 and X = N or P) is described. Of particular interest is the relative degree of oxidation of the respective copper centers and the bridging XR2 units, upon successive oxidations. These dicopper complexes feature terminal phosphine and either bridging amido or phosphido donors, and as such their metal-ligand bonds are highly covalent. Cu K-edge, Cu L-edge, and P K-edge spectroscopies, in combination with solid-state X-ray structures and DFT calculations, provides a complementary electronic structure picture for the entire set of complexes that tracks the involvement of a majority of ligand-based redox chemistry. The electronic structure picture that emerges for these inorganic dicopper diamond cores shares similarities with the Cu2(mu-SR)2 CuA sites of cytochrome c oxidases and nitrous oxide reductases.

COMPARATIVE ASSESSMENT OF THE COMPOSITION AND CHARGE STATE OF NITROGENASE FeMo-COFACTOR

A significant limitation in our understanding of the molecular mechanism of biological nitrogen fixation is the uncertain composition of the FeMo-cofactor (FeMo-co) of nitrogenase. In this study we present a systematic, density functional theory-based evaluation of spin-coupling schemes, iron oxidation states, ligand protonation states, and interstitial ligand composition using a wide range of experimental criteria. The employed functionals and basis sets were validated with molecular orbital information from X-ray absorption spectroscopic data of relevant iron-sulfur clusters. Independently from the employed level of theory, the electronic structure with the greatest number of antiferromagnetic interactions corresponds to the lowest energy state for a given charge and oxidation state distribution of the iron ions. 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. Mössbauer 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 [Mo(IV)-2Fe(II)-5Fe(III)-9S(2-)-C(4-)] composition with a hydroxyl-protonated homocitrate ligand satisfies all of the available experimental criteria and is thus favored over the currently preferred composition of [Mo(IV)-4Fe(II)-3Fe(III)-9S(2-)-N(3-)] from the literature.

Sulfur K-edge X-ray absorption spectroscopy and density functional calculations on Mo(IV) and Mo(VI)=O bis-dithiolenes: insights into the mechanism of oxo transfer in DMSO reductase and related functional analogues.

Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of two Mo bis-dithiolene complexes, [Mo(OSi)(bdt)(2)](1-) and [MoO(OSi)(bdt)(2)](1-), where OSi = [OSiPh(2)(t)Bu](1-) and bdt = benzene-1,2-dithiolate(2-), that model the Mo(IV) and Mo(VI)=O states of the DMSO reductase family of molybdenum enzymes. These results show that the Mo(IV) complex undergoes metal-based oxidation unlike Mo tris-dithiolene complexes, indicating that the dithiolene ligands are behaving innocently. Experimentally validated calculations have been extended to model the oxo transfer reaction coordinate using dimethylsulfoxide (DMSO) as a substrate. The reaction proceeds through a transition state (TS1) to an intermediate with DMSO weakly bound, followed by a subsequent transition state (TS2) which is the largest barrier of the reaction. The factors that control the energies of these transition states, the nature of the oxo transfer process, and the role of the dithiolene ligand are discussed.