Combining inorganic, biophysical and structural chemistry, Professor Keith Hodgson investigates how structure at molecular and macromolecular levels relates to function. Studies in the Hodgson lab have pioneered the use of synchrotron x-radiation to probe the electronic and structural environment of biomolecules. Recent efforts focus on the applications of x-ray diffraction, scattering and absorption spectroscopy to examine metalloproteins that are important in Earth’s biosphere, such as those that convert nitrogen to ammonia or methane to methanol.

Keith O. Hodgson was born in Virginia in 1947. He studied chemistry at the University of Virginia (B.S. 1969) and University of California, Berkeley (Ph.D. 1972), with a postdoctoral year at the ETH in Zurich. He joined the Stanford Chemistry Department faculty in 1973, starting up a program of fundamental research into the use of x-rays to study chemical and biological structure that made use of the unique capabilities of the Stanford Synchrotron Radiation Lightsource (SSRL). His lab carried out pioneering x-ray absorption and x-ray crystallographic studies of proteins, laying the foundation for a new field now in broad use worldwide. In the early eighties, he began development of one of the world's first synchrotron-based structural molecular biology research and user programs, centered at SSRL. He served as SSRL Director from 1998 to 2005, and SLAC National Accelerator Laboratory (SLAC) Deputy Director (2005-2007) and Associate Laboratory Director for Photon Science (2007-2011).

Today the Hodgson research group investigates how molecular structure at different organizational levels relates to biological and chemical function, using a variety of x-ray absorption, diffraction and scattering techniques. Typical of these molecular structural studies are investigations of metal ions as active sites of biomolecules. His research group develops and utilizes techniques such as x-ray absorption and emission spectroscopy (XAS and XES) to study the electronic and metrical details of a given metal ion in the biomolecule under a variety of natural conditions.

A major area of focus over many years, the active site of the enzyme nitrogenase is responsible for conversion of atmospheric di-nitrogen to ammonia. Using XAS studies at the S, Fe and Mo edge, the Hodgson group has worked to understand the electronic structure as a function of redox in this cluster. They have developed new methods to study long distances in the cluster within and outside the protein. Studies are ongoing to learn how this cluster functions during catalysis and interacts with substrates and inhibitors. Other components of the protein are also under active study.

Additional projects include the study of iron in dioxygen activation and oxidation within the binuclear iron-containing enzyme methane monooxygenase and in cytochrome oxidase. Lab members are also investigating the role of copper in electron transport and in dioxygen activation. Other studies include the electronic structure of iron-sulfur clusters in models and enzymes.

The research group is also focusing on using the next generation of x-ray light sources, the free electron laser. Such a light source, called the LCLS, is also located at SLAC. They are also developing new approaches using x-ray free electron laser radiation to image noncrystalline biomolecules and study chemical reactivity on ultrafast time scales.

Academic Appointments

Administrative Appointments

  • Chair, Department of Chemistry, Stanford University (2014 - 2017)

Honors & Awards

  • Member, National Academy of Sciences (2011)
  • E.O. Lawrence Award, U.S. Department of Energy (2002)
  • World Bank Lecturer, World Bank (1984)
  • Robert A. Welch Foundation Lecturer, Robert A. Welch Foundation (1981)
  • Sidhu Award for Contributions to X-ray Diffraction, Pittsburgh Diffraction Society (1978)
  • Alfred P. Sloan Fellow, Alfred P. Sloan Foundation (1976-78)
  • NATO Postdoctoral Fellowship, Eidgenössische Technische Hochschule, Zürich, Switzerland (1972-73)

Professional Education

  • NATO Postdoctoral Fellow, Eidgenössische Technische Hochschule, Zürich, Switzerland, Chemistry (1973)
  • PhD, University of California at Berkeley, Chemistry (1972)
  • BS, University of Virginia, Chemistry (1969)

2017-18 Courses

Stanford Advisees

Graduate and Fellowship Programs

All Publications

  • Resonant Inelastic X-ray Scattering on Ferrous and Ferric Bis-imidazole Porphyrin and Cytochrome c: Nature and Role of the Axial Methionine-Fe Bond. Journal of the American Chemical Society Kroll, T., Hadt, R. G., Wilson, S. A., Lundberg, M., Yan, J. J., Weng, T., Sokaras, D., Alonso-Mori, R., Casa, D., Upton, M. H., Hedman, B., Hodgson, K. O., Solomon, E. I. 2014; 136 (52): 18087-18099


    Axial Cu-S(Met) bonds in electron transfer (ET) active sites are generally found to lower their reduction potentials. An axial S(Met) bond is also present in cytochrome c (cyt c) and is generally thought to increase the reduction potential. The highly covalent nature of the porphyrin environment in heme proteins precludes using many spectroscopic approaches to directly study the Fe site to experimentally quantify this bond. Alternatively, L-edge X-ray absorption spectroscopy (XAS) enables one to directly focus on the 3d-orbitals in a highly covalent environment and has previously been successfully applied to porphyrin model complexes. However, this technique cannot be extended to metalloproteins in solution. Here, we use metal K-edge XAS to obtain L-edge like data through 1s2p resonance inelastic X-ray scattering (RIXS). It has been applied here to a bis-imidazole porphyrin model complex and cyt c. The RIXS data on the model complex are directly correlated to L-edge XAS data to develop the complementary nature of these two spectroscopic methods. Comparison between the bis-imidazole model complex and cyt c in ferrous and ferric oxidation states show quantitative differences that reflect differences in axial ligand covalency. The data reveal an increased covalency for the S(Met) relative to N(His) axial ligand and a higher degree of covalency for the ferric states relative to the ferrous states. These results are reproduced by DFT calculations, which are used to evaluate the thermodynamics of the Fe-S(Met) bond and its dependence on redox state. These results provide insight into a number of previous chemical and physical results on cyt c.

    View details for DOI 10.1021/ja5100367

    View details for PubMedID 25475739

  • Goniometer-based femtosecond crystallography with X-ray free electron lasers PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Cohen, A. E., Soltis, S. M., Gonzalez, A., Aguila, L., Alonso-Mori, R., Barnes, C. O., Baxter, E. L., Brehmer, W., Brewster, A. S., Brunger, A. T., Calero, G., Chang, J. F., Chollet, M., Ehrensberger, P., Eriksson, T. L., Feng, Y., Hattne, J., Hedman, B., Hollenbeck, M., Holton, J. M., Keable, S., Kobilka, B. K., Kovaleva, E. G., Kruse, A. C., Lemke, H. T., Lin, G., Lyubimov, A. Y., Manglik, A., Mathews, I. I., McPhillips, S. E., Nelson, S., Peters, J. W., Sauter, N. K., Smith, C. A., Song, J., Stevenson, H. P., Tsai, Y., Uervirojnangkoorn, M., Vinetsky, V., Wakatsuki, S., Weis, W. I., Zadvornyy, O. A., Zeldin, O. B., Zhu, D., Hodgson, K. O. 2014; 111 (48): 17122-17127


    The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. For smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.

    View details for DOI 10.1073/pnas.1418733111

    View details for Web of Science ID 000345920800042

    View details for PubMedID 25362050

    View details for PubMedCentralID PMC4260607

  • Sulfur K-Edge X-ray Absorption Spectroscopy and Density Functional Theory Calculations on Monooxo Mo-IV and Bisoxo Mo-VI Bis-dithiolenes: Insights into the Mechanism of Oxo Transfer in Sulfite Oxidase and Its Relation to the Mechanism of DMSO Reductase JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Ha, Y., Tenderholt, A. L., Holm, R. H., Hedman, B., Hodgson, K. O., Solomon, E. I. 2014; 136 (25): 9094-9105

    View details for DOI 10.1021/ja503316p

    View details for Web of Science ID 000338184200041

  • Spectroscopic and computational insight into the activation of O2 by the mononuclear Cu center in polysaccharide monooxygenases. Proceedings of the National Academy of Sciences of the United States of America Kjaergaard, C. H., Qayyum, M. F., Wong, S. D., Xu, F., Hemsworth, G. R., Walton, D. J., Young, N. A., Davies, G. J., Walton, P. H., Johansen, K. S., Hodgson, K. O., Hedman, B., Solomon, E. I. 2014; 111 (24): 8797-8802


    Strategies for O2 activation by copper enzymes were recently expanded to include mononuclear Cu sites, with the discovery of the copper-dependent polysaccharide monooxygenases, also classified as auxiliary-activity enzymes 9-11 (AA9-11). These enzymes are finding considerable use in industrial biofuel production. Crystal structures of polysaccharide monooxygenases have emerged, but experimental studies are yet to determine the solution structure of the Cu site and how this relates to reactivity. From X-ray absorption near edge structure and extended X-ray absorption fine structure spectroscopies, we observed a change from four-coordinate Cu(II) to three-coordinate Cu(I) of the active site in solution, where three protein-derived nitrogen ligands coordinate the Cu in both redox states, and a labile hydroxide ligand is lost upon reduction. The spectroscopic data allowed for density functional theory calculations of an enzyme active site model, where the optimized Cu(I) and (II) structures were consistent with the experimental data. The O2 reactivity of the Cu(I) site was probed by EPR and stopped-flow absorption spectroscopies, and a rapid one-electron reduction of O2 and regeneration of the resting Cu(II) enzyme were observed. This reactivity was evaluated computationally, and by calibration to Cu-superoxide model complexes, formation of an end-on Cu-AA9-superoxide species was found to be thermodynamically favored. We discuss how this thermodynamically difficult one-electron reduction of O2 is enabled by the unique protein structure where two nitrogen ligands from His1 dictate formation of a T-shaped Cu(I) site, which provides an open coordination position for strong O2 binding with very little reorganization energy.

    View details for DOI 10.1073/pnas.1408115111

    View details for PubMedID 24889637

  • Structure and reactivity of a mononuclear non-haem iron(III)-peroxo complex NATURE Cho, J., Jeon, S., Wilson, S. A., Liu, L. V., Kang, E. A., Braymer, J. J., Lim, M. H., Hedman, B., Hodgson, K. O., Valentine, J. S., Solomon, E. I., Nam, W. 2011; 478 (7370): 502-505


    Oxygen-containing mononuclear iron species--iron(III)-peroxo, iron(III)-hydroperoxo and iron(IV)-oxo--are key intermediates in the catalytic activation of dioxygen by iron-containing metalloenzymes. It has been difficult to generate synthetic analogues of these three active iron-oxygen species in identical host complexes, which is necessary to elucidate changes to the structure of the iron centre during catalysis and the factors that control their chemical reactivities with substrates. Here we report the high-resolution crystal structure of a mononuclear non-haem side-on iron(III)-peroxo complex, [Fe(III)(TMC)(OO)](+). We also report a series of chemical reactions in which this iron(III)-peroxo complex is cleanly converted to the iron(III)-hydroperoxo complex, [Fe(III)(TMC)(OOH)](2+), via a short-lived intermediate on protonation. This iron(III)-hydroperoxo complex then cleanly converts to the ferryl complex, [Fe(IV)(TMC)(O)](2+), via homolytic O-O bond cleavage of the iron(III)-hydroperoxo species. All three of these iron species--the three most biologically relevant iron-oxygen intermediates--have been spectroscopically characterized; we note that they have been obtained using a simple macrocyclic ligand. We have performed relative reactivity studies on these three iron species which reveal that the iron(III)-hydroperoxo complex is the most reactive of the three in the deformylation of aldehydes and that it has a similar reactivity to the iron(IV)-oxo complex in C-H bond activation of alkylaromatics. These reactivity results demonstrate that iron(III)-hydroperoxo species are viable oxidants in both nucleophilic and electrophilic reactions by iron-containing enzymes.

    View details for DOI 10.1038/nature10535

    View details for Web of Science ID 000296194200040

    View details for PubMedID 22031443

  • Solvent tuning of electrochemical potentials in the active sites of HiPIP versus ferredoxin SCIENCE Dey, A., Jenney, F. E., Adams, M. W., Babini, E., Takahashi, Y., Fukuyama, K., Hodgson, K. O., Hedman, B., Solomon, E. I. 2007; 318 (5855): 1464-1468


    A persistent puzzle in the field of biological electron transfer is the conserved iron-sulfur cluster motif in both high potential iron-sulfur protein (HiPIP) and ferredoxin (Fd) active sites. Despite this structural similarity, HiPIPs react oxidatively at physiological potentials, whereas Fds are reduced. Sulfur K-edge x-ray absorption spectroscopy uncovers the substantial influence of hydration on this variation in reactivity. Fe-S covalency is much lower in natively hydrated Fd active sites than in HiPIPs but increases upon water removal; similarly, HiPIP covalency decreases when unfolding exposes an otherwise hydrophobically shielded active site to water. Studies on model compounds and accompanying density functional theory calculations support a correlation of Fe-S covalency with ease of oxidation and therefore suggest that hydration accounts for most of the difference between Fd and HiPIP reduction potentials.

    View details for DOI 10.1126/science.1147753

    View details for Web of Science ID 000251246100050

    View details for PubMedID 18048692

  • Sulfur K-edge X-ray absorption spectroscopy as a probe of ligand-metal bond covalency: Metal vs ligand oxidation in copper and nickel dithiolene complexes JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Sarangi, R., George, S. D., Rudd, D. J., Szilagyi, R. K., Ribas, X., Rovira, C., Almeida, M., Hodgson, K. O., Hedman, B., Solomon, E. I. 2007; 129 (8): 2316-2326


    A combination of Cu L-edge and S K-edge X-ray absorption data and density functional theory (DFT) calculations has been correlated with 33S electron paramagnetic resonance superhyperfine results to obtain the dipole integral (Is) for the S 1s-->3p transition for the dithiolene ligand maleonitriledithiolate (MNT) in (TBA)2[Cu(MNT)2] (TBA= tetra-n-butylammonium). The results have been combined with the Is of sulfide derived from XPS studies to experimentally obtain a relation between the S 1s-->4p transition energy (which reflects the charge on the S atom, QSmol) and the dipole integral over a large range of QSmol. The results show that, for high charges on S, Is can vary from the previously reported Is values, calculated using data over a limited range of QSmol. A combination of S K-edge and Cu K- and L-edge X-ray absorption data and DFT calculations has been used to investigate the one-electron oxidation of [Cu(MNT)2]2- and [Ni(MNT)2]2-. The conversion of [Cu(MNT)2]2- to [Cu(MNT)2]- results in a large change in the charge on the Cu atom in the molecule (QCumol) and is consistent with a metal-based oxidation. This is accompanied by extensive charge donation from the ligands to compensate the high charge on the Cu in [Cu(MNT)2]- based on the increased S K-edge and decreased Cu L-edge intensity, respectively. In contrast, the oxidation of [Ni(MNT)2]2- to [Ni(MNT)2]- results in a small change in QNimol, indicating a ligand-based oxidation consistent with oxidation of a molecular orbital, psiSOMO (singly occupied molecular orbital), with predominant ligand character.

    View details for DOI 10.1021/ja0665949

    View details for Web of Science ID 000244330800033

    View details for PubMedID 17269767

  • Femtosecond diffractive imaging with a soft-X-ray free-electron laser NATURE PHYSICS Chapman, H. N., Barty, A., Bogan, M. J., Boutet, S., Frank, M., Hau-Riege, S. P., Marchesini, S., Woods, B. W., Bajt, S., Benner, H., London, R. A., Ploenjes, E., Kuhlmann, M., Treusch, R., Duesterer, S., Tschentscher, T., Schneider, J. R., Spiller, E., Moeller, T., Bostedt, C., Hoener, M., Shapiro, D. A., Hodgson, K. O., van der Spoel, D., Burmeister, F., Bergh, M., Caleman, C., Huldt, G., Seibert, M. M., Maia, F. R., Lee, R. W., Szoeke, A., Timneanu, N., Hajdu, J. 2006; 2 (12): 839-843

    View details for DOI 10.1038/nphys461

    View details for Web of Science ID 000242478000021

  • Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lesley, S. A., Kuhn, P., Godzik, A., Deacon, A. M., Mathews, I., Kreusch, A., Spraggon, G., Klock, H. E., McMullan, D., Shin, T., VINCENT, J., Robb, A., Brinen, L. S., Miller, M. D., McPhillips, T. M., Miller, M. A., Scheibe, D., Canaves, J. M., Guda, C., Jaroszewski, L., Selby, T. L., Elsliger, M. A., Wooley, J., Taylor, S. S., Hodgson, K. O., Wilson, I. A., Schultz, P. G., Stevens, R. C. 2002; 99 (18): 11664-11669


    Structural genomics is emerging as a principal approach to define protein structure-function relationships. To apply this approach on a genomic scale, novel methods and technologies must be developed to determine large numbers of structures. We describe the design and implementation of a high-throughput structural genomics pipeline and its application to the proteome of the thermophilic bacterium Thermotoga maritima. By using this pipeline, we successfully cloned and attempted expression of 1,376 of the predicted 1,877 genes (73%) and have identified crystallization conditions for 432 proteins, comprising 23% of the T. maritima proteome. Representative structures from TM0423 glycerol dehydrogenase and TM0449 thymidylate synthase-complementing protein are presented as examples of final outputs from the pipeline.

    View details for DOI 10.1073/pnas.142413399

    View details for Web of Science ID 000177843100026

    View details for PubMedID 12193646

  • Spectroscopic and Theoretical Study of Cu-I Binding to His111 in the Human Prion Protein Fragment 106-115 INORGANIC CHEMISTRY Arcos-Lopez, T., Qayyum, M., Rivillas-Acevedo, L., Miotto, M. C., Grande-Aztatzi, R., Fernandez, C. O., Hedman, B., Hodgson, K. O., Vela, A., Solomon, E. I., Quintanar, L. 2016; 55 (6): 2909-2922
  • Spectroscopic and Theoretical Study of Cu(I) Binding to His111 in the Human Prion Protein Fragment 106-115. Inorganic chemistry Arcos-López, T., Qayyum, M., Rivillas-Acevedo, L., Miotto, M. C., Grande-Aztatzi, R., Fernández, C. O., Hedman, B., Hodgson, K. O., Vela, A., Solomon, E. I., Quintanar, L. 2016; 55 (6): 2909-2922


    The ability of the cellular prion protein (PrP(C)) to bind copper in vivo points to a physiological role for PrP(C) in copper transport. Six copper binding sites have been identified in the nonstructured N-terminal region of human PrP(C). Among these sites, the His111 site is unique in that it contains a MKHM motif that would confer interesting Cu(I) and Cu(II) binding properties. We have evaluated Cu(I) coordination to the PrP(106-115) fragment of the human PrP protein, using NMR and X-ray absorption spectroscopies and electronic structure calculations. We find that Met109 and Met112 play an important role in anchoring this metal ion. Cu(I) coordination to His111 is pH-dependent: at pH >8, 2N1O1S species are formed with one Met ligand; in the range of pH 5-8, both methionine (Met) residues bind to Cu(I), forming a 1N1O2S species, where N is from His111 and O is from a backbone carbonyl or a water molecule; at pH <5, only the two Met residues remain coordinated. Thus, even upon drastic changes in the chemical environment, such as those occurring during endocytosis of PrP(C) (decreased pH and a reducing potential), the two Met residues in the MKHM motif enable PrP(C) to maintain the bound Cu(I) ions, consistent with a copper transport function for this protein. We also find that the physiologically relevant Cu(I)-1N1O2S species activates dioxygen via an inner-sphere mechanism, likely involving the formation of a copper(II) superoxide complex. In this process, the Met residues are partially oxidized to sulfoxide; this ability to scavenge superoxide may play a role in the proposed antioxidant properties of PrP(C). This study provides further insight into the Cu(I) coordination properties of His111 in human PrP(C) and the molecular mechanism of oxygen activation by this site.

    View details for DOI 10.1021/acs.inorgchem.5b02794

    View details for PubMedID 26930130

  • A high-resolution XAS study of aqueous Cu(II) in liquid and frozen solutions: Pyramidal, polymorphic, and non-centrosymmetric. journal of chemical physics Frank, P., Benfatto, M., Qayyam, M., Hedman, B., Hodgson, K. O. 2015; 142 (8): 084310-?


    High-resolution EXAFS (k = 18 Å(-1)) and MXAN XAS analyses show that axially elongated square pyramidal [Cu(H2O)5](2+) dominates the structure of Cu(II) in aqueous solution, rather than 6-coordinate JT-octahedral [Cu(H2O)6](2+). Freezing produced a shoulder at 8989.6 eV on the rising XAS edge and an altered EXAFS spectrum, while 1s → 3d transitions remained invariant in energy position and intensity. Core square pyramidal [Cu(H2O)5](2+) also dominates frozen solution. Solvation shells were found at ∼3.6 Å (EXAFS) or ∼3.8 Å (MXAN) in both liquid and frozen phases. However, MXAN analysis revealed that about half the time in liquid solution, [Cu(H2O)5](2+) associates with an axially non-bonding 2.9 Å water molecule. This distant water apparently organizes the solvation shell. When the 2.9 Å water molecule is absent, the second shell is undetectable to MXAN. The two structural arrangements may represent energetic minima of fluxional dissolved aqueous [Cu(H2O)5](2+). The 2.9 Å trans-axial water resolves an apparent conflict of the [Cu(H2O)5](2+) core model with a dissociational exchange mechanism. In frozen solution, [Cu(H2O)5](2+) is associated with either a 3.0 Å axial non-bonded water molecule or an axial ClO4 (-) at 3.2 Å. Both structures are again of approximately equal presence. When the axial ClO4 (-) is present, Cu(II) is ∼0.5 Å above the mean O4 plane. This study establishes [Cu(H2O)5](2+) as the dominant core structure for Cu(II) in water solution, and is the first to both empirically resolve multiple extended solution structures for fluxional [Cu(H2O)5](2+) and to provide direct evidence for second shell dynamics.

    View details for DOI 10.1063/1.4908266

    View details for PubMedID 25725734

  • A Zinc Linchpin Motif in the MUTYH Glycosylase Interdomain Connector Is Required for Efficient Repair of DNA Damage JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Engstrom, L. M., Brinkmeyer, M. K., Ha, Y., Raetz, A. G., Hedman, B., Hodgson, K. O., Solomon, E. I., David, S. S. 2014; 136 (22): 7829-7832

    View details for DOI 10.1021/ja502942d

    View details for Web of Science ID 000337014400012

  • Hydroxo-Bridged Dicopper(II,III) and -(III,III) Complexes: Models for Putative Intermediates in Oxidation Catalysis JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Halvagar, M. R., Solntsev, P. V., Lim, H., Hedman, B., Hodgson, K. O., Solomon, E. I., Cramer, C. J., Tolman, W. B. 2014; 136 (20): 7269-7272


    A macrocyclic ligand (L(4-)) comprising two pyridine(dicarboxamide) donors was used to target reactive copper species relevant to proposed intermediates in catalytic hydrocarbon oxidations by particulate methane monooxygenase and heterogeneous zeolite systems. Treatment of LH4 with base and Cu(OAc)2·H2O yielded (Me4N)2[L2Cu4(μ4-O)] (1) or (Me4N)[LCu2(μ-OH)] (2), depending on conditions. Complex 2 was found to undergo two reversible 1-electron oxidations via cyclic voltammetry and low-temperature chemical reactions. On the basis of spectroscopy and theory, the oxidation products were identified as novel hydroxo-bridged mixed-valent Cu(II)Cu(III) and symmetric Cu(III)2 species, respectively, that provide the first precedence for such moieties as oxidation catalysis intermediates.

    View details for DOI 10.1021/ja503629r

    View details for Web of Science ID 000336416600021

    View details for PubMedID 24821432

  • Biosynthesis of Nitrogenase Metalloclusters CHEMICAL REVIEWS Ribbe, M. W., Hu, Y., Hodgson, K. O., Hedman, B. 2014; 114 (8): 4063-4080

    View details for DOI 10.1021/cr400463x

    View details for Web of Science ID 000335086300003

    View details for PubMedID 24328215

  • XAS spectroscopy, sulfur, and the brew within blood cells from Ascidia ceratodes. Journal of inorganic biochemistry Frank, P., Hedman, B., Hodgson, K. O. 2014; 131: 99-108


    We report the first use of K-edge X-ray absorption spectroscopy (XAS) as a direct spectroscopic probe of pH and cytosolic emf within living cells. A new accuracy metric of model-based fits to K-edge spectra is further developed. Sulfur functional groups in three collections of living blood cells and one sample of cleared blood plasma from the tunicate Ascidia ceratodes were speciated using K-edge XAS. Cysteine and cystine, the preferred thiol-disulfide model, averaged about 12% of total sulfur. Sulfate monoesters and cyclic diesters unexpectedly constituted 36% of blood cell sulfur. Soluble sulfate averaged about 25% across the three blood cell samples, while the ratio of SO4(2-) to HSO4(-) implied average signet ring vacuolar pH values of 0.85, 1.4, or 3.1. Intracellular (VSO4)(+) was unobserved, while [V(RSO3)n]((3-n)+) was detected in the two lowest pH blood cell samples. About 5% of sulfur was distributed as mono- or dibenzothiophene or ethylene-epi-sulfide, or as a thiadiazole reminiscent of the polycarpathiamines. Blood plasma was dominated by sulfate (83%), but with 15% of an alkylsulfate ester and about 2% of low-valent sulfur. Gravimetric analysis of soluble sulfate yielded average concentrations of blood cell sulfur. Average [cysteine] and [cystine] (ranging ~10-30mM and ~20-90mM, respectively) implied blood-cell cytosolic emf values of approximately -0.20V. High cellular [cysteine] is consistent with the proposed model for enzymatic reduction of vanadate by endogenous thiol, wherein the trajectory of metal site-symmetry is controlled and directed through to a thermodynamically favored 7-coordinate V(III) product.

    View details for DOI 10.1016/j.jinorgbio.2013.11.004

    View details for PubMedID 24333825

  • L-Edge X-ray Absorption Spectroscopy and DFT Calculations on Cu2O2 Species: Direct Electrophilic Aromatic Attack by Side-on Peroxo Bridged Dicopper(II) Complexes JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Qayyum, M. F., Sarangi, R., Fujisawa, K., Stack, T. D., Karlin, K. D., Hodgson, K. O., Hedman, B., Solomon, E. I. 2013; 135 (46): 17417-17431


    The hydroxylation of aromatic substrates catalyzed by coupled binuclear copper enzymes has been observed with side-on-peroxo-dicopper(II) (P) and bis-μ-oxo-dicopper(III) (O) model complexes. The substrate-bound-O intermediate in [Cu(II)2(DBED)2(O)2](2+) (DBED = N,N'-di-tert-butyl-ethylenediamine) was shown to perform aromatic hydroxylation. For the [Cu(II)2(NO2-XYL)(O2)](2+) complex, only a P species was spectroscopically observed. However, it was not clear whether this O-O bond cleaves to proceed through an O-type structure along the reaction coordinate for hydroxylation of the aromatic xylyl linker. Accurate evaluation of these reaction coordinates requires reasonable quantitative descriptions of the electronic structures of the P and O species. We have performed Cu L-edge XAS on two well-characterized P and O species to experimentally quantify the Cu 3d character in their ground state wave functions. The lower per-hole Cu character (40 ± 6%) corresponding to higher covalency in the O species compared to the P species (52 ± 4%) reflects a stronger bonding interaction of the bis-μ-oxo core with the Cu(III) centers. DFT calculations show that 10-20% Hartree-Fock (HF) mixing for P and ~38% for O species are required to reproduce the Cu-O bonding; for the P species this HF mixing is also required for an antiferromagnetically coupled description of the two Cu(II) centers. B3LYP (with 20% HF) was, therefore, used to calculate the hydroxylation reaction coordinate of P in [Cu(II)2(NO2-XYL)(O2)](2+). These experimentally calibrated calculations indicate that the electrophilic attack on the aromatic ring does not involve formation of a Cu(III)2(O(2-))2 species. Rather, there is direct electron donation from the aromatic ring into the peroxo σ* orbital of the Cu(II)2(O2(2-)) species, leading to concerted C-O bond formation with O-O bond cleavage. Thus, species P is capable of direct hydroxylation of aromatic substrates without the intermediacy of an O-type species.

    View details for DOI 10.1021/ja4078717

    View details for Web of Science ID 000327413300032

    View details for PubMedID 24102191

  • Metal-Ligand Covalency of Iron Complexes from High-Resolution Resonant Inelastic X-ray Scattering. Journal of the American Chemical Society Lundberg, M., Kroll, T., DeBeer, S., Bergmann, U., Wilson, S. A., Glatzel, P., Nordlund, D., Hedman, B., Hodgson, K. O., Solomon, E. I. 2013; 135 (45): 17121-17134


    Data from Kα resonant inelastic X-ray scattering (RIXS) have been used to extract electronic structure information, i.e., the covalency of metal-ligand bonds, for four iron complexes using an experimentally based theoretical model. Kα RIXS involves resonant 1s→3d excitation and detection of the 2p→1s (Kα) emission. This two-photon process reaches similar final states as single-photon L-edge (2p→3d) X-ray absorption spectroscopy (XAS), but involves only hard X-rays and can therefore be used to get high-resolution L-edge-like spectra for metal proteins, solution catalysts and their intermediates. To analyze the information content of Kα RIXS spectra, data have been collected for four characteristic σ-donor and π-back-donation complexes: ferrous tacn [Fe(II)(tacn)2]Br2, ferrocyanide [Fe(II)(CN)6]K4, ferric tacn [Fe(III)(tacn)2]Br3 and ferricyanide [Fe(III)(CN)6]K3. From these spectra metal-ligand covalencies can be extracted using a charge-transfer multiplet model, without previous information from the L-edge XAS experiment. A direct comparison of L-edge XAS and Kα RIXS spectra show that the latter reaches additional final states, e.g., when exciting into the eg (σ*) orbitals, and the splitting between final states of different symmetry provides an extra dimension that makes Kα RIXS a more sensitive probe of σ-bonding. Another key difference between L-edge XAS and Kα RIXS is the π-back-bonding features in ferro- and ferricyanide that are significantly more intense in L-edge XAS compared to Kα RIXS. This shows that two methods are complementary in assigning electronic structure. The Kα RIXS approach can thus be used as a stand-alone method, in combination with L-edge XAS for strongly covalent systems that are difficult to probe by UV/vis spectroscopy, or as an extension to conventional absorption spectroscopy for a wide range of transition metal enzymes and catalysts.

    View details for DOI 10.1021/ja408072q

    View details for PubMedID 24131028

  • Stepwise Protonation and Electron-Transfer Reduction of a Primary Copper-Dioxygen Adduct JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Peterson, R. L., Ginsbach, J. W., Cowley, R. E., Qayyum, M. F., Himes, R. A., Siegler, M. A., Moore, C. D., Hedman, B., Hodgson, K. O., Fukuzumi, S., Solomon, E. I., Karlin, K. D. 2013; 135 (44): 16454-16467

    View details for DOI 10.1021/ja4065377

    View details for Web of Science ID 000326774300044

  • X-ray absorption spectroscopic investigation of the electronic structure differences in solution and crystalline oxyhemoglobin PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Wilson, S. A., Green, E., Mathews, I. I., Benfatto, M., Hodgson, K. O., Hedman, B., Sarangi, R. 2013; 110 (41): 16333-16338


    Hemoglobin (Hb) is the heme-containing O2 transport protein essential for life in all vertebrates. The resting high-spin (S = 2) ferrous form, deoxy-Hb, combines with triplet O2, forming diamagnetic (S = 0) oxy-Hb. Understanding this electronic structure is the key first step in understanding transition metal-O2 interaction. However, despite intense spectroscopic and theoretical studies, the electronic structure description of oxy-Hb remains elusive, with at least three different descriptions proposed by Pauling, Weiss, and McClure-Goddard, based on theory, spectroscopy, and crystallography. Here, a combination of X-ray absorption spectroscopy and extended X-ray absorption fine structure, supported by density functional theory calculations, help resolve this debate. X-ray absorption spectroscopy data on solution and crystalline oxy-Hb indicate both geometric and electronic structure differences suggesting that two of the previous descriptions are correct for the Fe-O2 center in oxy-Hb. These results support the multiconfigurational nature of the ground state developed by theoretical results. Additionally, it is shown here that small differences in hydrogen bonding and solvation effects can tune the ground state, tipping it into one of the two probable configurations. These data underscore the importance of solution spectroscopy and show that the electronic structure in the crystalline form may not always reflect the true ground-state description in solution.

    View details for DOI 10.1073/pnas.1315734110

    View details for Web of Science ID 000325395600026

    View details for PubMedID 24062465

  • Preparation of Non-heme {FeNO}(7) Models of Cysteine Dioxygenase: Sulfur versus Nitrogen Ligation and Photorelease of Nitric Oxide JOURNAL OF THE AMERICAN CHEMICAL SOCIETY McQuilken, A. C., Ha, Y., Sutherlin, K. D., Siegler, M. A., Hodgson, K. O., Hedman, B., Solomon, E. I., Jameson, G. N., Goldberg, D. P. 2013; 135 (38): 14024-14027


    We present the synthesis and spectroscopic characterization of [Fe(NO)(N3PyS)]BF4 (3), the first structural and electronic model of NO-bound cysteine dioxygenase. The nearly isostructural all-N-donor analogue [Fe(NO)(N4Py)](BF4)2 (4) was also prepared, and comparisons of 3 and 4 provide insight regarding the influence of S vs N ligation in {FeNO}(7) species. One key difference occurs upon photoirradiation, which causes the fully reversible release of NO from 3, but not from 4.

    View details for DOI 10.1021/ja4064487

    View details for Web of Science ID 000330162900007

    View details for PubMedID 24040838

  • Modified Reactivity toward O-2 in First Shell Variants of Fet3p: Geometric and Electronic Structure Requirements for a Functioning Trinuclear Copper Cluster BIOCHEMISTRY Kjaergaard, C. H., Qayyum, M. F., Augustine, A. J., Ziegler, L., Kosman, D. J., Hodgson, K. O., Hedman, B., Solomon, E. I. 2013; 52 (21): 3702-3711

    View details for DOI 10.1021/bi4002826

    View details for Web of Science ID 000319795500012

  • AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery. Acta crystallographica. Section D, Biological crystallography Tsai, Y., McPhillips, S. E., González, A., McPhillips, T. M., Zinn, D., Cohen, A. E., Feese, M. D., Bushnell, D., Tiefenbrunn, T., Stout, C. D., Ludaescher, B., Hedman, B., Hodgson, K. O., Soltis, S. M. 2013; 69: 796-803


    AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data, performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully demonstrated. This workflow was run once on the same 96 samples that the group had examined manually and the workflow cycled successfully through all of the samples, collected data from the same samples that were selected manually and located the same peaks of unmodeled density in the resulting difference Fourier maps.

    View details for DOI 10.1107/S0907444913001984

    View details for PubMedID 23633588

  • Iron L-Edge X-ray Absorption Spectroscopy of Oxy-Picket Fence Porphyrin: Experimental Insight into Fe-O-2 Bonding JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Wilson, S. A., Kroll, T., Decreau, R. A., Hocking, R. K., Lundberg, M., Hedman, B., Hodgson, K. O., Solomon, E. I. 2013; 135 (3): 1124-1136


    The electronic structure of the Fe-O(2) center in oxy-hemoglobin and oxy-myoglobin is a long-standing issue in the field of bioinorganic chemistry. Spectroscopic studies have been complicated by the highly delocalized nature of the porphyrin, and calculations require interpretation of multideterminant wave functions for a highly covalent metal site. Here, iron L-edge X-ray absorption spectroscopy, interpreted using a valence bond configuration interaction multiplet model, is applied to directly probe the electronic structure of the iron in the biomimetic Fe-O(2) heme complex [Fe(pfp)(1-MeIm)O(2)] (pfp ("picket fence porphyrin") = meso-tetra(α,α,α,α-o-pivalamidophenyl)porphyrin or TpivPP). This method allows separate estimates of σ-donor, π-donor, and π-acceptor interactions through ligand-to-metal charge transfer and metal-to-ligand charge transfer mixing pathways. The L-edge spectrum of [Fe(pfp)(1-MeIm)O(2)] is further compared to those of [Fe(II)(pfp)(1-MeIm)(2)], [Fe(II)(pfp)], and [Fe(III)(tpp)(ImH)(2)]Cl (tpp = meso-tetraphenylporphyrin) which have Fe(II)S = 0, Fe(II)S = 1, and Fe(III)S = 1/2 ground states, respectively. These serve as references for the three possible contributions to the ground state of oxy-pfp. The Fe-O(2) pfp site is experimentally determined to have both significant σ-donation and a strong π-interaction of the O(2) with the iron, with the latter having implications with respect to the spin polarization of the ground state.

    View details for DOI 10.1021/ja3103583

    View details for Web of Science ID 000314141200029

    View details for PubMedID 23259487

  • The x-ray absorption spectroscopy model of solvation about sulfur in aqueous L-cysteine JOURNAL OF CHEMICAL PHYSICS Sarangi, R., Frank, P., Benfatto, M., Morante, S., Minicozzi, V., Hedman, B., Hodgson, K. O. 2012; 137 (20)


    The environment of sulfur in dissolved aqueous L-cysteine has been examined using K-edge x-ray absorption spectroscopy (XAS), extended continuum multiple scattering (ECMS) theory, and density functional theory (DFT). For the first time, bound-state and continuum transitions representing the entire XAS spectrum of L-cysteine sulfur are accurately reproduced by theory. Sulfur K-edge absorption features at 2473.3 eV and 2474.2 eV represent transitions to LUMOs that are mixtures of S-C and S-H σ∗ orbitals significantly delocalized over the entire L-cysteine molecule. Continuum features at 2479, 2489, and 2530 eV were successfully reproduced using extended continuum theory. The full L-cysteine sulfur K-edge XAS spectrum could not be reproduced without addition of a water-sulfur hydrogen bond. Density functional theory analysis shows that although the Cys(H)S⋯H-OH hydrogen bond is weak (∼2 kcal) the atomic charge on sulfur is significantly affected by this water. MXAN analysis of hydrogen-bonding structures for L-cysteine and water yielded a best fit model featuring a tandem of two water molecules, 2.9 Å and 5.8 Å from sulfur. The model included a S(cys)⋯H-O(w1)H hydrogen-bond of 2.19 Å and of 2.16 Å for H(2)O(w1)⋯H-O(w2)H. One hydrogen-bonding water-sulfur interaction alone was insufficient to fully describe the continuum XAS spectrum. However, density functional theoretical results are convincing that the water-sulfur interaction is weak and should be only transient in water solution. The durable water-sulfur hydrogen bond in aqueous L-cysteine reported here therefore represents a break with theoretical studies indicating its absence. Reconciling the apparent disparity between theory and result remains the continuing challenge.

    View details for DOI 10.1063/1.4767350

    View details for Web of Science ID 000312252100067

    View details for PubMedID 23206038

  • X-ray-induced photo-chemistry and X-ray absorption spectroscopy of biological samples JOURNAL OF SYNCHROTRON RADIATION George, G. N., Pickering, I. J., Pushie, M. J., Nienaber, K., Hackett, M. J., Ascone, I., Hedman, B., Hodgson, K. O., Aitken, J. B., Levina, A., Glover, C., Lay, P. A. 2012; 19: 875-886


    As synchrotron light sources and optics deliver greater photon flux on samples, X-ray-induced photo-chemistry is increasingly encountered in X-ray absorption spectroscopy (XAS) experiments. The resulting problems are particularly pronounced for biological XAS experiments. This is because biological samples are very often quite dilute and therefore require signal averaging to achieve adequate signal-to-noise ratios, with correspondingly greater exposures to the X-ray beam. This paper reviews the origins of photo-reduction and photo-oxidation, the impact that they can have on active site structure, and the methods that can be used to provide relief from X-ray-induced photo-chemical artifacts.

    View details for DOI 10.1107/S090904951203943X

    View details for Web of Science ID 000310151000005

    View details for PubMedID 23093745

  • Spectroscopic and DFT Studies of Second-Sphere Variants of the Type 1 Copper Site in Azurin: Covalent and Nonlocal Electrostatic Contributions to Reduction Potentials JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Hadt, R. G., Sun, N., Marshall, N. M., Hodgson, K. O., Hedman, B., Lu, Y., Solomon, E. I. 2012; 134 (40): 16701-16716


    The reduction potentials (E(0)) of type 1 (T1) or blue copper (BC) sites in proteins and enzymes with identical first coordination spheres around the redox active copper ion can vary by ~400 mV. Here, we use a combination of low-temperature electronic absorption and magnetic circular dichroism, electron paramagnetic resonance, resonance Raman, and S K-edge X-ray absorption spectroscopies to investigate a series of second-sphere variants--F114P, N47S, and F114N in Pseudomonas aeruginosa azurin--which modulate hydrogen bonding to and protein-derived dipoles nearby the Cu-S(Cys) bond. Density functional theory calculations correlated to the experimental data allow for the fractionation of the contributions to tuning E(0) into covalent and nonlocal electrostatic components. These are found to be significant, comparable in magnitude, and additive for active H-bonds, while passive H-bonds are mostly nonlocal electrostatic in nature. For dipoles, these terms can be additive to or oppose one another. This study provides a methodology for uncoupling covalency from nonlocal electrostatics, which, when coupled to X-ray crystallographic data, distinguishes specific local interactions from more long-range protein/active interactions, while affording further insight into the second-sphere mechanisms available to the protein to tune the E(0) of electron-transfer sites in biology.

    View details for DOI 10.1021/ja306438n

    View details for Web of Science ID 000309566400044

    View details for PubMedID 22985400

  • (Fe-IV=O(TBC)(CH3CN)](2+): Comparative Reactivity of Iron(IV)-Oxo Species with Constrained Equatorial Cyclam Ligation JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Wilson, S. A., Chen, J., Hong, S., Lee, Y., Clemancey, M., Garcia-Serres, R., Nomura, T., Ogura, T., Latour, J., Hedman, B., Hodgson, K. O., Nam, W., Solomon, E. I. 2012; 134 (28): 11791-11806


    [Fe(IV)═O(TBC)(CH(3)CN)](2+) (TBC = 1,4,8,11-tetrabenzyl-1,4,8,11-tetraazacyclotetradecane) is characterized, and its reactivity differences relative to [Fe(IV)═O(TMC)(CH(3)CN)](2+) (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane) are evaluated in hydrogen atom (H-atom) abstraction and oxo-transfer reactions. Structural differences are defined using X-ray absorption spectroscopy and correlated to reactivities using density functional theory. The S = 1 ground states are highly similar and result in large activation barriers (~25 kcal/mol) due to steric interactions between the cyclam chelate and the substrate (e.g., ethylbenzene) associated with the equatorial π-attack required by this spin state. Conversely, H-atom abstraction reactivity on an S = 2 surface allows for a σ-attack with an axial substrate approach. This results in decreased steric interactions with the cyclam and a lower barrier (~9 kcal/mol). For [Fe(IV)═O(TBC)(CH(3)CN)](2+), the S = 2 excited state in the reactant is lower in energy and therefore more accessible at the transition state due to a weaker ligand field associated with the steric interactions of the benzyl substituents with the trans-axial ligand. This study is further extended to the oxo-transfer reaction, which is a two-electron process requiring both σ- and π-electron transfer and thus a nonlinear transition state. In oxo-transfer, the S = 2 has a lower barrier due to sequential vs concerted (S = 1) two electron transfer which gives a high-spin ferric intermediate at the transition state. The [Fe(IV)═O(TBC)(CH(3)CN)](2+) complex is more distorted at the transition state, with the iron farther out of the equatorial plane due to the steric interaction of the benzyl groups with the trans-axial ligand. This allows for better orbital overlap with the substrate, a lower barrier, and an increased rate of oxo-transfer.

    View details for DOI 10.1021/ja03046298

    View details for Web of Science ID 000306457900072

    View details for PubMedID 22708532

  • Revisiting the Polyoxometalate-Based Late-Transition-Metal-Oxo Complexes: The "Oxo Wall" Stands INORGANIC CHEMISTRY O'Halloran, K. P., Zhao, C., Ando, N. S., Schultz, A. J., Koetzle, T. F., Piccoli, P. M., Hedman, B., Hodgson, K. O., Bobyr, E., Kirk, M. L., Knottenbelt, S., Depperman, E. C., Stein, B., Anderson, T. M., Cao, R., Geletii, Y. V., Hardcastle, K. I., Musaev, D. G., Neiwert, W. A., Fang, X., Morokuma, K., Wu, S., Koegerler, P., Hill, C. L. 2012; 51 (13): 7025-7031


    Terminal oxo complexes of the late transition metals Pt, Pd, and Au have been reported by us in Science and Journal of the American Chemical Society. Despite thoroughness in characterizing these complexes (multiple independent structural methods and up to 17 analytical methods in one case), we have continued to study these structures. Initial work on these systems was motivated by structural data from X-ray crystallography and neutron diffraction and (17)O and (31)P NMR signatures which all indicated differences from all previously published compounds. With significant new data, we now revisit these studies. New X-ray crystal structures of previously reported complexes K(14)[P(2)W(19)O(69)(OH(2))] and "K(10)Na(3)[Pd(IV)(O)(OH)WO(OH(2))(PW(9)O(34))(2)]" and a closer examination of these structures are provided. Also presented are the (17)O NMR spectrum of an (17)O-enriched sample of [PW(11)O(39)](7-) and a careful combined (31)P NMR-titration study of the previously reported "K(7)H(2)[Au(O)(OH(2))P(2)W(20)O(70)(OH(2))(2)]." These and considerable other data collectively indicate that previously assigned terminal Pt-oxo and Au-oxo complexes are in fact cocrystals of the all-tungsten structural analogues with noble metal cations, while the Pd-oxo complex is a disordered Pd(II)-substituted polyoxometalate. The neutron diffraction data have been re-analyzed, and new refinements are fully consistent with the all-tungsten formulations of the Pt-oxo and Au-oxo polyoxometalate species.

    View details for DOI 10.1021/ic2008914

    View details for Web of Science ID 000305853600009

    View details for PubMedID 22694272

  • Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight NATURE Loh, N. D., Hampton, C. Y., Martin, A. V., Starodub, D., Sierra, R. G., Barty, A., Aquila, A., Schulz, J., Lomb, L., Steinbrener, J., Shoeman, R. L., Kassemeyer, S., Bostedt, C., Bozek, J., Epp, S. W., Erk, B., Hartmann, R., Rolles, D., Rudenko, A., Rudek, B., Foucar, L., Kimmel, N., Weidenspointner, G., Hauser, G., Holl, P., Pedersoli, E., Liang, M., Hunter, M. M., GUMPRECHT, L., Coppola, N., Wunderer, C., Graafsma, H., Maia, F. R., Ekeberg, T., Hantke, M., Fleckenstein, H., Hirsemann, H., Nass, K., White, T. A., Tobias, H. J., Farquar, G. R., Benner, W. H., Hau-Riege, S. P., Reich, C., Hartmann, A., Soltau, H., Marchesini, S., Bajt, S., Barthelmess, M., Bucksbaum, P., Hodgson, K. O., Strueder, L., Ullrich, J., Frank, M., Schlichting, I., Chapman, H. N., Bogan, M. J. 2012; 486 (7404): 513-517


    The morphology of micrometre-size particulate matter is of critical importance in fields ranging from toxicology to climate science, yet these properties are surprisingly difficult to measure in the particles' native environment. Electron microscopy requires collection of particles on a substrate; visible light scattering provides insufficient resolution; and X-ray synchrotron studies have been limited to ensembles of particles. Here we demonstrate an in situ method for imaging individual sub-micrometre particles to nanometre resolution in their native environment, using intense, coherent X-ray pulses from the Linac Coherent Light Source free-electron laser. We introduced individual aerosol particles into the pulsed X-ray beam, which is sufficiently intense that diffraction from individual particles can be measured for morphological analysis. At the same time, ion fragments ejected from the beam were analysed using mass spectrometry, to determine the composition of single aerosol particles. Our results show the extent of internal dilation symmetry of individual soot particles subject to non-equilibrium aggregation, and the surprisingly large variability in their fractal dimensions. More broadly, our methods can be extended to resolve both static and dynamic morphology of general ensembles of disordered particles. Such general morphology has implications in topics such as solvent accessibilities in proteins, vibrational energy transfer by the hydrodynamic interaction of amino acids, and large-scale production of nanoscale structures by flame synthesis.

    View details for DOI 10.1038/nature11222

    View details for Web of Science ID 000305760600039

    View details for PubMedID 22739316

  • Geometric and Electronic Structure of [{Cu(MeAN)}(2)(mu-eta(2):eta(2)(O-2(2-)))](2+) with an Unusually Long O-O Bond: O-O Bond Weakening vs Activation for Reductive Cleavage JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Park, G. Y., Qayyum, M. F., Woertink, J., Hodgson, K. O., Hedman, B., Sarjeant, A. A., Solomon, E. I., Karlin, K. D. 2012; 134 (20): 8513-8524

    View details for DOI 10.1021/ja300674m

    View details for Web of Science ID 000304285700048

  • Spectroscopic and Crystallographic Characterization of "Alternative Resting" and "Resting Oxidized" Enzyme Forms of Bilirubin Oxidase: Implications for Activity and Electrochemical Behavior of Multicopper Oxidases JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Kjaergaard, C. H., Durand, F., Tasca, F., Qayyum, M. F., Kauffmann, B., Gounel, S., Suraniti, E., Hodgson, K. O., Hedman, B., Mano, N., Solomon, E. I. 2012; 134 (12): 5548-5551


    While there is broad agreement on the catalytic mechanism of multicopper oxidases (MCOs), the geometric and electronic structures of the resting trinuclear Cu cluster have been variable, and their relevance to catalysis has been debated. Here, we present a spectroscopic characterization, complemented by crystallographic data, of two resting forms occurring in the same enzyme and define their interconversion. The resting oxidized form shows similar features to the resting form in Rhus vernicifera and Trametes versicolor laccase, characterized by "normal" type 2 Cu electron paramagnetic resonance (EPR) features, 330 nm absorption shoulder, and a short type 3 (T3) Cu-Cu distance, while the alternative resting form shows unusually small A(||) and high g(||) EPR features, lack of 330 nm absorption intensity, and a long T3 Cu-Cu distance. These different forms are evaluated with respect to activation for catalysis, and it is shown that the alternative resting form can only be activated by low-potential reduction, in contrast to the resting oxidized form which is activated via type 1 Cu at high potential. This difference in activity is correlated to differences in redox states of the two forms and highlights the requirement for efficient sequential reduction of resting MCOs for their involvement in catalysis.

    View details for DOI 10.1021/ja211872j

    View details for Web of Science ID 000302489500031

    View details for PubMedID 22413777

  • Substrate and Metal Control of Barrier Heights for Oxo Transfer to Mo and W Bis-dithiolene Sites INORGANIC CHEMISTRY Tenderholt, A. L., Hodgson, K. O., Hedman, B., Holm, R. H., Solomon, E. I. 2012; 51 (6): 3436-3442


    Reaction coordinates for oxo transfer from the substrates Me(3)NO, Me(2)SO, and Me(3)PO to the biologically relevant Mo(IV) bis-dithiolene complex [Mo(OMe)(mdt)(2)](-) where mdt = 1,2-dimethyl-ethene-1,2-dithiolate(2-), and from Me(2)SO to the analogous W(IV) complex, have been calculated using density functional theory. In each case, the reaction first proceeds through a transition state (TS1) to an intermediate with substrate weakly bound, followed by a second transition state (TS2) around which breaking of the substrate X-O bond begins. By analyzing the energetic contributions to each barrier, it is shown that the nature of the substrate and metal determines which transition state controls the rate-determining step of the reaction.

    View details for DOI 10.1021/ic2020397

    View details for Web of Science ID 000301624500013

    View details for PubMedID 22372518

  • The X-ray Absorption Spectroscopic Model of the Copper(II) Imidazole Complex Ion in Liquid Aqueous Solution: A Strongly Solvated Square Pyramid INORGANIC CHEMISTRY Frank, P., Benfatto, M., Hedman, B., Hodgson, K. O. 2012; 51 (4): 2086-2096


    Cu K-edge extended X-ray absorption fine structure (EXAFS) and Minuit X-ray absorption near-edge structure (MXAN) analyses were combined to evaluate the structure of the copper(II) imidazole complex ion in liquid aqueous solution. Both methods converged to the same square-pyramidal inner coordination sphere [Cu(Im)(4)L(ax)](2+) (L(ax) indeterminate) with four equatorial nitrogen atoms at EXAFS, 2.02 ± 0.01 Å, and MXAN, 1.99 ± 0.03 Å. A short-axial N/O scatterer (L(ax)) was found at 2.12 ± 0.02 Å (EXAFS) or 2.14 ± 0.06 Å (MXAN). A second but very weak axial Cu-N/O interaction was found at 2.9 ± 0.1 Å (EXAFS) or 3.0 ± 0.1 Å (MXAN). In the MXAN fits, only a square-pyramidal structural model successfully reproduced the doubled maximum of the rising K-edge X-ray absorption spectrum, specifically excluding an octahedral model. Both EXAFS and MXAN also found eight outlying oxygen scatterers at 4.2 ± 0.3 Å that contributed significant intensity over the entire spectral energy range. Two prominent rising K-edge shoulders at 8987.1 and 8990.5 eV were found to reflect multiple scattering from the 3.0 Å axial scatterer and the imidazole rings, respectively. In the MXAN fits, the imidazole rings took in-plane rotationally staggered positions about copper. The combined (EXAFS and MXAN) model for the unconstrained cupric imidazole complex ion in liquid aqueous solution is an axially elongated square-pyramidal core, with a weak nonbonded interaction at the second axial coordination position and a solvation shell of eight nearest-neighbor water molecules. This core square-pyramidal motif has persisted through [Cu(H(2)O)(5)](2+), [Cu(NH(3))(4)(NH(3),H(2)O)](2+), (1, 2) and now [Cu(Im)(4)L(ax))](2+) and appears to be the geometry preferred by unconstrained aqueous-phase copper(II) complex ions.

    View details for DOI 10.1021/ic2017819

    View details for Web of Science ID 000300466300017

    View details for PubMedID 22316238

  • High-Resolution Analysis of Zn2+ Coordination in the Alkaline Phosphatase Superfamily by EXAFS and X-ray Crystallography JOURNAL OF MOLECULAR BIOLOGY Bobyr, E., Lassila, J. K., Wiersma-Koch, H. I., Fenn, T. D., Lee, J. J., Nikolic-Hughes, I., Hodgson, K. O., Rees, D. C., Hedman, B., Herschlag, D. 2012; 415 (1): 102-117


    Comparisons among evolutionarily related enzymes offer opportunities to reveal how structural differences produce different catalytic activities. Two structurally related enzymes, Escherichia coli alkaline phosphatase (AP) and Xanthomonas axonopodis nucleotide pyrophosphatase/phosphodiesterase (NPP), have nearly identical binuclear Zn(2+) catalytic centers but show tremendous differential specificity for hydrolysis of phosphate monoesters or phosphate diesters. To determine if there are differences in Zn(2+) coordination in the two enzymes that might contribute to catalytic specificity, we analyzed both x-ray absorption spectroscopic and x-ray crystallographic data. We report a 1.29-Å crystal structure of AP with bound phosphate, allowing evaluation of interactions at the AP metal site with high resolution. To make systematic comparisons between AP and NPP, we measured zinc extended x-ray absorption fine structure for AP and NPP in the free-enzyme forms, with AMP and inorganic phosphate ground-state analogs and with vanadate transition-state analogs. These studies yielded average zinc-ligand distances in AP and NPP free-enzyme forms and ground-state analog forms that were identical within error, suggesting little difference in metal ion coordination among these forms. Upon binding of vanadate to both enzymes, small increases in average metal-ligand distances were observed, consistent with an increased coordination number. Slightly longer increases were observed in NPP relative to AP, which could arise from subtle rearrangements of the active site or differences in the geometry of the bound vanadyl species. Overall, the results suggest that the binuclear Zn(2+) catalytic site remains very similar between AP and NPP during the course of a reaction cycle.

    View details for DOI 10.1016/j.jmb.2011.10.040

    View details for Web of Science ID 000299866000010

    View details for PubMedID 22056344

    View details for PubMedCentralID PMC3249517

  • Spectroscopic Elucidation of a New Heme/Copper Dioxygen Structure Type: Implications for O center dot center dot center dot O Bond Rupture in Cytochrome c Oxidase ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Kieber-Emmons, M. T., Qayyum, M. F., Li, Y., Halime, Z., Hodgson, K. O., Hedman, B., Karlin, K. D., Solomon, E. I. 2012; 51 (1): 168-172

    View details for DOI 10.1002/anie.201104080

    View details for Web of Science ID 000298598500025

    View details for PubMedID 22095556

    View details for PubMedCentralID PMC3517061

  • Profiling structured beams using injected aerosols Conference on X-Ray Free-Electron Lasers - Beam Diagnostics, Beamline Instrumentation, and Applications Loh, N. D., Starodub, D., Lomb, L., Hampton, C. Y., Martin, A. V., Sierra, R. G., Barty, A., Aquila, A., Schulz, J., Steinbrener, J., Shoeman, R. L., Kassemeyer, S., Bostedt, C., Bozek, J., Epp, S. W., Erk, B., Hartmann, R., Rolles, D., Rudenko, A., Rudek, B., Foucar, L., Kimmel, N., Weidenspointner, G., Hauser, G., Holl, P., Pedersoli, E., Liang, M., Hunter, M. S., Gumprecht, L., Coppola, N., Wunderer, C., Graafsma, H., Maia, F. R., Ekeberg, T., Hantke, M., Fleckenstein, H., Hirsemann, H., Nass, K., White, T. A., Tobias, H. J., Farquar, G. R., Benner, W. H., Hau-Riege, S., Reich, C., Hartmann, A., Soltau, H., Marchesini, S., Bajt, S., Barthelmess, M., Strueder, L., Ullrich, J., Bucksbaum, P., Hodgson, K. O., Frank, M., Schlichting, I., Chapman, H. N., Bogan, M. J. SPIE-INT SOC OPTICAL ENGINEERING. 2012

    View details for DOI 10.1117/12.930075

    View details for Web of Science ID 000311837900002

  • S K-edge XAS and DFT Calculations on SAM Dependent Pyruvate Formate-Lyase Activating Enzyme: Nature of Interaction between the Fe4S4 Cluster and SAM and its Role in Reactivity JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Dey, A., Peng, Y., Broderick, W. E., Hedman, B., Hodgson, K. O., Broderick, J. B., Solomon, E. I. 2011; 133 (46): 18656-18662


    S K-edge X-ray absorption spectroscopy on the resting oxidized and the S-adenosyl-l-methionine (SAM) bound forms of pyruvate formate-lyase activating enzyme are reported. The data show an increase in pre-edge intensity, which is due to additional contributions from sulfide and thiolate of the Fe(4)S(4) cluster into the C-S σ* orbital. This experimentally demonstrates that there is a backbonding interaction between the Fe(4)S(4) cluster and C-S σ* orbitals of SAM in this inner sphere complex. DFT calculations that reproduce the data indicate that this backbonding is enhanced in the reduced form and that this configurational interaction between the donor and acceptor orbitals facilitates the electron transfer from the cluster to the SAM, which otherwise has a large outer sphere electron transfer barrier. The energy of the reductive cleavage of the C-S bond is sensitive to the dielectric of the protein in the immediate vicinity of the site as a high dielectric stabilizes the more charge separated reactant increasing the reaction barrier. This may provide a mechanism for generation of the 5'-deoxyadenosyl radical upon substrate binding.

    View details for DOI 10.1021/ja203780t

    View details for Web of Science ID 000297398900036

    View details for PubMedID 21992686

  • Structural Models of the [Fe4S4] Clusters of Homologous Nitrogenase Fe Proteins INORGANIC CHEMISTRY Blank, M. A., Lee, C. C., Hu, Y., Hodgson, K. O., Hedman, B., Ribbe, M. W. 2011; 50 (15): 7123-7128


    The iron (Fe) proteins of molybdenum (Mo)-, vanadium (V)-, and iron (Fe)-only nitrogenases are encoded by nifH, vnfH, and anfH, respectively. While the nifH-encoded Fe protein has been extensively studied over recent years, information regarding the properties of the vnfH- and anfH-encoded Fe proteins has remained scarce. Here, we present a combined biochemical, electron paramagnetic resonance (EPR) and X-ray absorption spectroscopy (XAS) analysis of the [Fe(4)S(4)] clusters of NifH, VnfH, and AnfH of Azotobacter vinelandii . Our data show that all three Fe proteins contain [Fe(4)S(4)] clusters of very similar spectroscopic and geometric structural properties, although NifH differs more from VnfH and AnfH with regard to the electronic structure. These observations have an interesting impact on the theory of the plausible sequence of evolution of nitrogenase Fe proteins. More importantly, the results presented herein provide a platform for future investigations of the differential activities of the three Fe proteins in nitrogenase biosynthesis and catalysis.

    View details for DOI 10.1021/ic200636k

    View details for Web of Science ID 000293036000036

    View details for PubMedID 21718019

    View details for PubMedCentralID PMC3143205

  • A Codeposition Route to CuI-Pyridine Coordination Complexes for Organic Light-Emitting Diodes JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Liu, Z., Qayyum, M. F., Wu, C., Whited, M. T., Djurovich, P. I., Hodgson, K. O., Hedman, B., Solomon, E. I., Thompson, M. E. 2011; 133 (11): 3700-3703


    We demonstrate a new approach for utilizing CuI coordination complexes as emissive layers in organic light-emitting diodes that involves in situ codeposition of CuI and 3,5-bis(carbazol-9-yl)pyridine (mCPy). With a simple three-layer device structure, pure green electroluminescence at 530 nm from a Cu(I) complex was observed. A maximum luminance and external quantum efficiency (EQE) of 9700 cd/m(2) and 4.4%, respectively, were achieved. The luminescent species was identified as [CuI(mCPy)(2)](2) on the basis of photophysical studies of model complexes and X-ray absorption spectroscopy.

    View details for DOI 10.1021/ja1065653

    View details for Web of Science ID 000288889900005

    View details for PubMedID 21366248

  • S K-Edge X-Ray Absorption Spectroscopy and Density Functional Theory Studies of High and Low Spin {FeNO}(7) Thiolate Complexes: Exchange Stabilization of Electron Delocalization in {FeNO}(7) and {FeO2}(8) INORGANIC CHEMISTRY Sun, N., Liu, L. V., Dey, A., Villar-Acevedo, G., Kovacs, J. A., Darensbourg, M. Y., Hodgson, K. O., Hedman, B., Solomon, E. I. 2011; 50 (2): 427-436

    View details for DOI 10.1021/ic1006378

    View details for Web of Science ID 000285956600011

  • Spectroscopic Characterization of the Isolated Iron-Molybdenum Cofactor (FeMoco) Precursor from the Protein NifEN ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Fay, A. W., Blank, M. A., Lee, C. C., Hu, Y., Hodgson, K. O., Hedman, B., Ribbe, M. W. 2011; 50 (34): 7787-7790

    View details for DOI 10.1002/anie.201102724

    View details for Web of Science ID 000294175700008

    View details for PubMedID 21726031

  • Definition of the intermediates and mechanism of the anticancer drug bleomycin using nuclear resonance vibrational spectroscopy and related methods PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Liu, L. V., Bell, C. B., Wong, S. D., Wilson, S. A., Kwak, Y., Chow, M. S., Zhao, J., Hodgson, K. O., Hedman, B., Solomon, E. I. 2010; 107 (52): 22419-22424


    Bleomycin (BLM) is a glycopeptide anticancer drug capable of effecting single- and double-strand DNA cleavage. The last detectable intermediate prior to DNA cleavage is a low spin Fe(III) peroxy level species, termed activated bleomycin (ABLM). DNA strand scission is initiated through the abstraction of the C-4' hydrogen atom of the deoxyribose sugar unit. Nuclear resonance vibrational spectroscopy (NRVS) aided by extended X-ray absorption fine structure spectroscopy and density functional theory (DFT) calculations are applied to define the natures of Fe(III)BLM and ABLM as (BLM)Fe(III)─OH and (BLM)Fe(III)(η(1)─OOH) species, respectively. The NRVS spectra of Fe(III)BLM and ABLM are strikingly different because in ABLM the δFe─O─O bending mode mixes with, and energetically splits, the doubly degenerate, intense O─Fe─N(ax) transaxial bends. DFT calculations of the reaction of ABLM with DNA, based on the species defined by the NRVS data, show that the direct H-atom abstraction by ABLM is thermodynamically favored over other proposed reaction pathways.

    View details for DOI 10.1073/pnas.1016323107

    View details for Web of Science ID 000285684200017

    View details for PubMedID 21149675

  • Bis(mu-oxo) Dicopper(III) Species of the Simplest Peralkylated Diamine: Enhanced Reactivity toward Exogenous Substrates INORGANIC CHEMISTRY Kang, P., Bobyr, E., Dustman, J., Hodgson, K. O., Hedman, B., Solomon, E. I., Stack, T. D. 2010; 49 (23): 11030-11038


    N,N,N',N'-tetramethylethylenediamine (TMED), the simplest and most extensively used peralkylated diamine ligand, is conspicuously absent from those known to form a bis(μ-oxo)dicopper(III) (O) species, [(TMED)(2)Cu(III)(2)(μ(2)-O)(2)](2+), upon oxygenation of its Cu(I) complex. Presented here is the characterization of this O species and its reactivity toward exogenous substrates. Its formation is complicated both by the instability of the [(TMED)Cu(I)](1+) precursor and by competitive formation of a presumed mixed-valent trinuclear [(TMED)(3)Cu(III)Cu(II)(2)(μ(3)-O)(2)](3+) (T) species. Under most reaction conditions, the T species dominates, yet, the O species can be formed preferentially (>80%) upon oxygenation of acetone solutions, if the copper concentration is low (<2 mM) and [(TMED)Cu(I)](1+) is prepared immediately before use. The experimental data of this simplest O species provide a benchmark by which to evaluate density functional theory (DFT) computational methods for geometry optimization and spectroscopic predictions. The enhanced thermal stability of [(TMED)(2)Cu(III)(2)(μ(2)-O)(2)](2+) and its limited steric demands compared to other O species allows more efficient oxidation of exogenous substrates, including benzyl alcohol to benzaldehyde (80% yield), highlighting the importance of ligand structure to not only enhance the oxidant stability but also maintain accessibility to the nascent metal/O(2) oxidant.

    View details for DOI 10.1021/ic101515g

    View details for Web of Science ID 000284518800037

    View details for PubMedID 21028910

  • Characterization of Isolated Nitrogenase FeVco JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Fay, A. W., Blank, M. A., Lee, C. C., Hu, Y., Hodgson, K. O., Hedman, B., Ribbe, M. W. 2010; 132 (36): 12612-12618


    The cofactors of the Mo- and V-nitrogenases (i.e., FeMoco and FeVco) are homologous metal centers with distinct catalytic properties. So far, there has been only one report on the isolation of FeVco from Azotobacter chroococcum. However, this isolated FeVco species did not carry the full substrate-reducing capacity, as it is unable to restore the N(2)-reducing ability of the cofactor-deficient MoFe protein. Here, we report the isolation and characterization of a fully active species of FeVco from A. vinelandii. Our metal and activity analyses show that FeVco has been extracted intact, carrying with it the characteristic capacity to reduce C(2)H(2) to C(2)H(6) and, perhaps even more importantly, the ability to reduce N(2) to NH(3). Moreover, our EPR and XAS/EXAFS investigations indicate that FeVco is similar to, yet distinct from FeMoco in electronic properties and structural topology, which could account for the differences in the reactivity of the two cofactors. The outcome of this study not only permits the proposal of the first EXAFS-based structural model of the isolated FeVco but also lays a foundation for future catalytic and structural investigations of this unique metallocluster.

    View details for DOI 10.1021/ja1019657

    View details for Web of Science ID 000282074200023

    View details for PubMedID 20718463

  • Solvation Effects on S K-Edge XAS Spectra of Fe-S Proteins: Normal and Inverse Effects on WT and Mutant Rubredoxin JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Sun, N., Dey, A., Xiao, Z., Wedd, A. G., Hodgson, K. O., Hedman, B., Solomon, E. I. 2010; 132 (36): 12639-12647


    S K-edge X-ray absorption spectroscopy (XAS) was performed on wild type Cp rubredoxin and its Cys --> Ser mutants in both solution and lyophilized forms. For wild type rubredoxin and for the mutants where an interior cysteine residue (C6 or C39) is substituted by serine, a normal solvent effect is observed, that is, the S covalency increases upon lyophilization. For the mutants where a solvent accessible surface cysteine residue is substituted by serine, the S covalency decreases upon lyophilization which is an inverse solvent effect. Density functional theory (DFT) calculations reproduce these experimental results and show that the normal solvent effect reflects the covalency decrease due to solvent H-bonding to the surface thiolates and that the inverse solvent effect results from the covalency compensation from the interior thiolates. With respect to the Cys --> Ser substitution, the S covalency decreases. Calculations indicate that the stronger bonding interaction of the alkoxide with the Fe relative to that of thiolate increases the energy of the Fe d orbitals and reduces their bonding interaction with the remaining cysteines. The solvent effects support a surface solvent tuning contribution to electron transfer, and the Cys --> Ser result provides an explanation for the change in properties of related iron-sulfur sites with this mutation.

    View details for DOI 10.1021/ja102807x

    View details for Web of Science ID 000282074200026

    View details for PubMedID 20726554

  • 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 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Tenderholt, A. L., Wang, J., Szilagyi, R. K., Holm, R. H., Hodgson, K. O., Hedman, B., Solomon, E. I. 2010; 132 (24): 8359-8371


    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.

    View details for DOI 10.1021/ja910369c

    View details for Web of Science ID 000278905700034

    View details for PubMedID 20499905

  • Systematic Perturbation of the Trinuclear Copper Cluster in the Multicopper Oxidases: The Role of Active Site Asymmetry in Its Reduction of O-2 to H2O JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Augustine, A. J., Kjaergaard, C., Qayyum, M., Ziegler, L., Kosman, D. J., Hodgson, K. O., Hedman, B., Solomon, E. I. 2010; 132 (17): 6057-6067


    The multicopper oxidase Fet3p catalyzes the four-electron reduction of dioxygen to water, coupled to the one-electron oxidation of four equivalents of substrate. To carry out this process, the enzyme utilizes four Cu atoms: a type 1, a type 2, and a coupled binuclear, type 3 site. Substrates are oxidized at the T1 Cu, which rapidly transfers electrons, 13 A away, to a trinuclear copper cluster composed of the T2 and T3 sites, where dioxygen is reduced to water in two sequential 2e(-) steps. This study focuses on two variants of Fet3p, H126Q and H483Q, that perturb the two T3 Cu's, T3alpha and T3beta, respectively. The variants have been isolated in both holo and type 1 depleted (T1D) forms, T1DT3alphaQ and T1DT3betaQ, and their trinuclear copper clusters have been characterized in their oxidized and reduced states. While the variants are only mildly perturbed relative to T1D in the resting oxidized state, in contrast to T1D they are both found to have lost a ligand in their reduced states. Importantly, T1DT3alphaQ reacts with O(2), but T1DT3betaQ does not. Thus loss of a ligand at T3beta, but not at T3alpha, turns off O(2) reactivity, indicating that T3beta and T2 are required for the 2e(-) reduction of O(2) to form the peroxide intermediate (PI), whereas T3alpha remains reduced. This is supported by the spectroscopic features of PI in T1DT3alphaQ, which are identical to T1D PI. This selective redox activity of one edge of the trinuclear cluster demonstrates its asymmetry in O(2) reactivity. The structural origin of this asymmetry between the T3alpha and T3beta is discussed, as is its contribution to reactivity.

    View details for DOI 10.1021/ja909143d

    View details for Web of Science ID 000277158500040

    View details for PubMedID 20377263

  • Heme-Copper-Dioxygen Complexes: Toward Understanding Ligand-Environmental Effects on the Coordination Geometry, Electronic Structure, and Reactivity INORGANIC CHEMISTRY Halime, Z., Kieber-Emmons, M. T., Qayyum, M. F., Mondal, B., Gandhi, T., Puiu, S. C., Chufan, E. E., Sarjeant, A. A., Hodgson, K. O., Hedman, B., Solomon, E. I., Karlin, K. D. 2010; 49 (8): 3629-3645


    The nature of the ligand is an important aspect of controlling the structure and reactivity in coordination chemistry. In connection with our study of heme-copper-oxygen reactivity relevant to cytochrome c oxidase dioxygen-reduction chemistry, we compare the molecular and electronic structures of two high-spin heme-peroxo-copper [Fe(III)O(2)(2-)Cu(II)](+) complexes containing N(4) tetradentate (1) or N(3) tridentate (2) copper ligands. Combining previously reported and new resonance Raman and EXAFS data coupled to density functional theory calculations, we report a geometric structure and more complete electronic description of the high-spin heme-peroxo-copper complexes 1 and 2, which establish mu-(O(2)(2-)) side-on to the Fe(III) and end-on to Cu(II) (mu-eta(2):eta(1)) binding for the complex 1 but side-on/side-on (mu-eta(2):eta(2)) mu-peroxo coordination for the complex 2. We also compare and summarize the differences and similarities of these two complexes in their reactivity toward CO, PPh(3), acid, and phenols. The comparison of a new X-ray structure of mu-oxo complex 2a with the previously reported 1a X-ray structure, two thermal decomposition products respectively of 2 and 1, reveals a considerable difference in the Fe-O-Cu angle between the two mu-oxo complexes ( angleFe-O-Cu = 178.2 degrees in 1a and angleFe-O-Cu = 149.5 degrees in 2a). The reaction of 2 with 1 equiv of an exogenous nitrogen-donor axial base leads to the formation of a distinctive low-temperature-stable, low-spin heme-dioxygen-copper complex (2b), but under the same conditions, the addition of an axial base to 1 leads to the dissociation of the heme-peroxo-copper assembly and the release of O(2). 2b reacts with phenols performing H-atom (e(-) + H(+)) abstraction resulting in O-O bond cleavage and the formation of high-valent ferryl [Fe(IV)=O] complex (2c). The nature of 2c was confirmed by a comparison of its spectroscopic features and reactivity with those of an independently prepared ferryl complex. The phenoxyl radical generated by the H-atom abstraction was either (1) directly detected by electron paramagnetic resonance spectroscopy using phenols that produce stable radicals or (2) indirectly detected by the coupling product of two phenoxyl radicals.

    View details for DOI 10.1021/ic9020993

    View details for Web of Science ID 000276556900010

    View details for PubMedID 20380465

  • Crystal Structure of the First Eubacterial Mre11 Nuclease Reveals Novel Features that May Discriminate Substrates During DNA Repair JOURNAL OF MOLECULAR BIOLOGY Das, D., Moiani, D., Axelrod, H. L., Miller, M. D., McMullan, D., Jin, K. K., Abdubek, P., Astakhova, T., Burra, P., Carlton, D., Chiu, H., Clayton, T., Deller, M. C., Duan, L., Ernst, D., Feuerhelm, J., Grant, J. C., Grzechnik, A., Grzechnik, S. K., Han, G. W., Jaroszewski, L., Klock, H. E., Knuth, M. W., Kozbial, P., Krishna, S. S., Kumar, A., Marciano, D., Morse, A. T., Nigoghossian, E., Okach, L., Paulsen, J., Reyes, R., Rife, C. L., Sefcovic, N., Tien, H. J., Trame, C. B., van den Bedem, H., Weekes, D., Xu, Q., Hodgson, K. O., Wooley, J., Elsliger, M., Deacon, A. M., Godzik, A., Lesley, S. A., Tainer, J. A., Wilson, I. A. 2010; 397 (3): 647-663


    Mre11 nuclease plays a central role in the repair of cytotoxic and mutagenic DNA double-strand breaks. As X-ray structural information has been available only for the Pyrococcus furiosus enzyme (PfMre11), the conserved and variable features of this nuclease across the domains of life have not been experimentally defined. Our crystal structure and biochemical studies demonstrate that TM1635 from Thermotoga maritima, originally annotated as a putative nuclease, is an Mre11 endo/exonuclease (TmMre11) and the first such structure from eubacteria. TmMre11 and PfMre11 display similar overall structures, despite sequence identity in the twilight zone of only approximately 20%. However, they differ substantially in their DNA-specificity domains and in their dimeric organization. Residues in the nuclease domain are highly conserved, but those in the DNA-specificity domain are not. The structural differences likely affect how Mre11 from different organisms recognize and interact with single-stranded DNA, double-stranded DNA and DNA hairpin structures during DNA repair. The TmMre11 nuclease active site has no bound metal ions, but is conserved in sequence and structure with the exception of a histidine that is important in PfMre11 nuclease activity. Nevertheless, biochemical characterization confirms that TmMre11 possesses both endonuclease and exonuclease activities on single-stranded and double-stranded DNA substrates, respectively.

    View details for DOI 10.1016/j.jmb.2010.01.049

    View details for Web of Science ID 000276177300003

    View details for PubMedID 20122942

    View details for PubMedCentralID PMC2839085

  • Fe L-Edge X-ray Absorption Spectroscopy Determination of Differential Orbital Covalency of Siderophore Model Compounds: Electronic Structure Contributions to High Stability Constants JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Hocking, R. K., George, S. D., Raymond, K. N., Hodgson, K. O., Hedman, B., Solomon, E. I. 2010; 132 (11): 4006-4015


    Most bacteria and fungi produce low-molecular-weight iron chelators called siderophores. Although different siderophore structures have been characterized, the iron-binding moieties often contain catecholate or hydroxamate groups. Siderophores function because of their extraordinarily high stability constants (K(STAB) = 10(30)-10(49)) and selectivity for Fe(III), yet the origin of these high stability constants has been difficult to quantify experimentally. Herein, we utilize Fe L-edge X-ray absorption spectroscopy to determine the differential orbital covalency (i.e., the differences in the mixing of the metal d-orbitals with ligand valence orbitals) of a series of siderophore model compounds. The results enable evaluation of the electronic structure contributions to their high stability constants in terms of sigma- and pi-donor covalent bonding, ionic bonding, and solvent effects. The results indicate substantial differences in the covalent contributions to stability constants of hydroxamate and catecholate complexes and show that increased sigma as well as pi bonding contributes to the high stability constants of catecholate complexes.

    View details for DOI 10.1021/ja9090098

    View details for Web of Science ID 000275868700061

    View details for PubMedID 20187651

  • S K-Edge X-Ray Absorption Spectroscopy and Density Functional Theory Studies of High and Low Spin {FeNO}(7) Thiolate Complexes: Exchange Stabilization of Electron Delocalization in {FeNO}(7) and {FeO(2)}(8). Inorganic chemistry 2010


    S K-edge X-ray absorption spectroscopy (XAS) is a direct experimental probe of metal ion electronic structure as the pre-edge energy reflects its oxidation state, and the energy splitting pattern of the pre-edge transitions reflects its spin state. The combination of sulfur K-edge XAS and density functional theory (DFT) calculations indicates that the electronic structures of {FeNO}(7) (S = 3/2) (S(Me2)N(4)(tren)Fe(NO), complex I) and {FeNO}(7) (S = 1/2) ((bme-daco)Fe(NO), complex II) are Fe(III)(S = 5/2)-NO(-)(S = 1) and Fe(III)(S = 3/2)-NO(-)(S = 1), respectively. When an axial ligand is computationally added to complex II, the electronic structure becomes Fe(II)(S = 0)-NO•(S = 1/2). These studies demonstrate how the ligand field of the Fe center defines its spin state and thus changes the electron exchange, an important factor in determining the electron distribution over {FeNO}(7) and {FeO(2)}(8) sites.

    View details for DOI 10.1021/ic1006378

    View details for PubMedID 21158471

  • Formation of a homocitrate-free iron-molybdenum cluster on NifEN: Implications for the role of homocitrate in nitrogenase assembly DALTON TRANSACTIONS Fay, A. W., Blank, M. A., Yoshizawa, J. M., Lee, C. C., Wiig, J. A., Hu, Y., Hodgson, K. O., Hedman, B., Ribbe, M. W. 2010; 39 (12): 3124-3130


    Molybdenum (Mo)-dependent nitrogenase is a complex metalloprotein that catalyzes the biological reduction of dinitrogen (N(2)) to ammonia (NH(3)) at the molybdenum-iron cofactor (FeMoco) site of its molybdenum-iron (MoFe) protein component. Here we report the formation of a homocitrate-free, iron-molybdenum ("FeMo") cluster on the biosynthetic scaffold of FeMoco, NifEN. Such a NifEN-associated "FeMo" cluster exhibits EPR features similar to those of the NifEN-associated, fully-complemented "FeMoco", which originate from the presence of Mo in both cluster species; however, "FeMo" cluster and "FeMoco" display different temperature-dependent changes in the line shape and the signal intensity of their respective EPR features, which reflect the impact of homocitrate on the redox properties of these clusters. XAS/EXAFS analysis reveals that the Mo centers in both "FeMo" cluster and "FeMoco" are present in a similar coordination environment, although Mo in "FeMo" cluster is more loosely coordinated as compared to that in "FeMoco" with respect to the Mo-O distances in the cluster, likely due to the absence of homocitrate that normally serves as an additional ligand for the Mo in the cluster. Subsequent biochemical investigation of the "FeMo" cluster not only facilitates the determination of the sequence of events in the mobilization of Mo and homocitrate during FeMoco maturation, but also permits the examination of the role of homocitrate in the transfer of FeMoco between NifEN and MoFe protein. Combined outcome of these studies establishes a platform for future structural analysis of the interactions between NifEN and MoFe protein, which will provide useful insights into the mechanism of cluster transfer between the two proteins.

    View details for DOI 10.1039/c000264j

    View details for Web of Science ID 000275378500022

    View details for PubMedID 20221547

  • Stepwise formation of P-cluster in nitrogenase MoFe protein PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lee, C. C., Blank, M. A., Fay, A. W., Yoshizawa, J. M., Hu, Y., Hodgson, K. O., Hedman, B., Ribbe, M. W. 2009; 106 (44): 18474-18478


    The P-cluster of nitrogenase is one of the most complex biological metallocenters known to date. Despite the recent advances in the chemical synthesis of P-cluster topologs, the biosynthetic mechanism of P-cluster has not been well defined. Here, we present a combined biochemical, electron paramagnetic resonance, and X-ray absorption spectroscopy/extended X-ray absorption fine-structure investigation of the maturation process of P-clusters in DeltanifH molybdenum-iron (MoFe) protein. Our data indicate that the previously identified, [Fe(4)S(4)]-like cluster pairs in DeltanifH MoFe protein are indeed the precursors to P-clusters, which can be reductively coupled into the mature [Fe(8)S(7)] structures in the presence of Fe protein, MgATP, and dithionite. Moreover, our observation of a biphasic maturation pattern of P-clusters in DeltanifH MoFe protein provides dynamic proof for the previously hypothesized, stepwise assembly mechanism of the two P-clusters in the alpha(2)beta(2)-tetrameric MoFe protein, i.e., one P-cluster is formed in one alphabeta dimer before the other in the second alphabeta dimer.

    View details for DOI 10.1073/pnas.0909149106

    View details for Web of Science ID 000271429800014

    View details for PubMedID 19828444

  • Crystal Structure of Histidine Phosphotransfer Protein ShpA, an Essential Regulator of Stalk Biogenesis in Caulobacter crescentus JOURNAL OF MOLECULAR BIOLOGY Xu, Q., Carlton, D., Miller, M. D., Elsliger, M., Krishna, S. S., Abdubek, P., Astakhova, T., Burra, P., Chiu, H., Clayton, T., Deller, M. C., Duan, L., Elias, Y., Feuerhelm, J., Grant, J. C., Grzechnik, A., Grzechnik, S. K., Han, G. W., Jaroszewski, L., Jin, K. K., Klock, H. E., Knuth, M. W., Kozbial, P., Kumar, A., Marciano, D., McMullan, D., Morse, A. T., Nigoghossian, E., Okach, L., Oommachen, S., Paulsen, J., Reyes, R., Rife, C. L., Sefcovic, N., Trame, C., Trout, C. V., van den Bedem, H., Weekes, D., Hodgson, K. O., Wooley, J., Deacon, A. M., Godzik, A., Lesley, S. A., Wilson, I. A. 2009; 390 (4): 686-698


    Cell-cycle-regulated stalk biogenesis in Caulobacter crescentus is controlled by a multistep phosphorelay system consisting of the hybrid histidine kinase ShkA, the histidine phosphotransfer (HPt) protein ShpA, and the response regulator TacA. ShpA shuttles phosphoryl groups between ShkA and TacA. When phosphorylated, TacA triggers a downstream transcription cascade for stalk synthesis in an RpoN-dependent manner. The crystal structure of ShpA was determined to 1.52 A resolution. ShpA belongs to a family of monomeric HPt proteins that feature a highly conserved four-helix bundle. The phosphorylatable histidine His56 is located on the surface of the helix bundle and is fully solvent exposed. One end of the four-helix bundle in ShpA is shorter compared with other characterized HPt proteins, whereas the face that potentially interacts with the response regulators is structurally conserved. Similarities of the interaction surface around the phosphorylation site suggest that ShpA is likely to share a common mechanism for molecular recognition and phosphotransfer with yeast phosphotransfer protein YPD1 despite their low overall sequence similarity.

    View details for DOI 10.1016/j.jmb.2009.05.023

    View details for Web of Science ID 000268519200009

    View details for PubMedID 19450606

  • Optimization of FeMoco Maturation on NifEN JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Yoshizawa, J. M., Blank, M. A., Fay, A. W., Lee, C. C., Wiig, J. A., Hu, Y., Hodgson, K. O., Hedman, B., Ribbe, M. W. 2009; 131 (26): 9321-9325


    Mo-nitrogenase catalyzes the reduction of dinitrogen to ammonia at the cofactor (i.e., FeMoco) site of its MoFe protein component. Biosynthesis of FeMoco involves NifEN, a scaffold protein that hosts the maturation of a precursor to a mature FeMoco before it is delivered to the target location in the MoFe protein. Previously, we have shown that the NifEN-bound precursor could be converted in vitro to a fully complemented "FeMoco" in the presence of 2 mM dithionite. However, such a conversion was incomplete, and Mo was only loosely associated with the NifEN-bound "FeMoco". Here we report the optimized maturation of the NifEN-associated precursor in 20 mM dithionite. Activity analyses show that upon the optimal conversion of precursor to "FeMoco", NifEN is capable of activating a FeMoco-deficient form of MoFe protein to the same extent as the isolated FeMoco. Furthermore, EPR and XAS/EXAFS analyses reveal the presence of a tightly organized Mo site in NifEN-bound "FeMoco", which allows the observation of a FeMoco-like S = 3/2 EPR signal and the modeling of a NifEN-bound "FeMoco" that adopts a conformation very similar to that of the MoFe protein-associated FeMoco. The sensitivity of FeMoco maturation to dithionite concentration suggests an essential role of redox chemistry in this process, and the optimal potential of dithionite solution could serve as a guideline for future identification of in vivo electron donors for FeMoco maturation.

    View details for DOI 10.1021/ja9035225

    View details for Web of Science ID 000267633300046

    View details for PubMedID 19514721

  • Spectroscopy and Kinetics of Wild-Type and Mutant Tyrosine Hydroxylase: Mechanistic Insight into O-2 Activation JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Chow, M. S., Eser, B. E., Wilson, S. A., Hodgson, K. O., Hedman, B., Fitzpatrick, P. F., Solomon, E. I. 2009; 131 (22): 7685-7698


    Tyrosine hydroxylase (TH) is a pterin-dependent nonheme iron enzyme that catalyzes the hydroxylation of L-tyr to L-DOPA in the rate-limiting step of catecholamine neurotransmitter biosynthesis. We have previously shown that the Fe(II) site in phenylalanine hydroxylase (PAH) converts from six-coordinate (6C) to five-coordinate (5C) only when both substrate + cofactor are bound. However, steady-state kinetics indicate that TH has a different co-substrate binding sequence (pterin + O(2) + L-tyr) than PAH (L-phe + pterin + O(2)). Using X-ray absorption spectroscopy (XAS), and variable-temperature-variable-field magnetic circular dichroism (VTVH MCD) spectroscopy, we have investigated the geometric and electronic structure of the wild-type (WT) TH and two mutants, S395A and E332A, and their interactions with substrates. All three forms of TH undergo 6C --> 5C conversion with tyr + pterin, consistent with the general mechanistic strategy established for O(2)-activating nonheme iron enzymes. We have also applied single-turnover kinetic experiments with spectroscopic data to evaluate the mechanism of the O(2) and pterin reactions in TH. When the Fe(II) site is 6C, the two-electron reduction of O(2) to peroxide by Fe(II) and pterin is favored over individual one-electron reactions, demonstrating that both a 5C Fe(II) and a redox-active pterin are required for coupled O(2) reaction. When the Fe(II) is 5C, the O(2) reaction is accelerated by at least 2 orders of magnitude. Comparison of the kinetics of WT TH, which produces Fe(IV)=O + 4a-OH-pterin, and E332A TH, which does not, shows that the E332 residue plays an important role in directing the protonation of the bridged Fe(II)-OO-pterin intermediate in WT to productively form Fe(IV)=O, which is responsible for hydroxylating L-tyr to L-DOPA.

    View details for DOI 10.1021/ja810080c

    View details for Web of Science ID 000267177900058

    View details for PubMedID 19489646

  • S K-edge XAS and DFT Calculations on Cytochrome P450: Covalent and Ionic Contributions to the Cysteine-Fe Bond and Their Contribution to Reactivity JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Dey, A., Jiang, Y., de Montellano, P. O., Hodgson, K. O., Hedman, B., Solomon, E. I. 2009; 131 (22): 7869-7878


    Experimental covalencies of the Fe-S bond for the resting low-spin and substrate-bound high-spin active site of cytochrome P450 are reported. DFT calculations on the active site indicate that one H-bonding interaction from the protein backbone is needed to reproduce the experimental values. The H-bonding to the thiolate from the backbone decreases the anisotropic pi covalency of the Fe-S bond lowering the barrier of free rotation of the exchangeable axial ligand, which is important for reactivity. The anionic axial thiolate ligand is calculated to lower the Fe(III/II) reduction potential of the active site by more than 1 V compared to a neutral imidazole ligand. About half of this derives from its covalent bonding and half from its electrostatic interaction with the oxidized Fe. This axial thiolate ligand increases the pK(a) of compound 0 (Fe(III)-hydroperoxo) favoring its protonation which promotes O-O bond heterolysis forming compound I. The reactivity of compound I is calculated to be relatively insensitive to the nature of the axial ligand due to opposing reduction potential and proton affinity contributions to the H-atom abstraction energy.

    View details for DOI 10.1021/ja901868q

    View details for Web of Science ID 000267177900077

    View details for PubMedID 19438234

  • Fe L- and K-edge XAS of Low-Spin Ferric Corrole: Bonding and Reactivity Relative to Low-Spin Ferric Porphyrin INORGANIC CHEMISTRY Hocking, R. K., George, S. D., Gross, Z., Walker, F. A., Hodgson, K. O., Hedman, B., Solomon, E. I. 2009; 48 (4): 1678-1688


    Corrole is a tetrapyrrolic macrocycle that has one carbon atom less than a porphyrin. The ring contraction reduces the symmetry from D(4h) to C(2v), changes the electronic structure of the heterocycle, and leads to a smaller central cavity with three protons rather than the two of a porphyrin. The differences between ferric corroles and porphyrins lead to a number of differences in reactivity including increased axial ligand lability and a tendency to form 5-coordinate complexes. The electronic structure origin of these differences has been difficult to study experimentally as the dominant porphyrin/corrole pi --> pi* transitions obscure the electronic transitions of the metal. Recently, we have developed a methodology that allows for the interpretation of the multiplet structure of Fe L-edges in terms of differential orbital covalency (i.e., the differences in mixing of the metal d orbitals with the ligand valence orbitals) using a valence bond configuration interaction model. Herein, we apply this methodology, combined with a ligand field analysis of the Fe K pre-edge to a low-spin ferric corrole, and compare it to a low-spin ferric porphyrin. The experimental results combined with DFT calculations show that the contracted corrole is both a stronger sigma donor and a very anisotropic pi donor. These differences decrease the bonding interactions with axial ligands and contribute to the increased axial ligand lability and reactivity of ferric corroles relative to ferric porphyrins.

    View details for DOI 10.1021/ic802248t

    View details for Web of Science ID 000263227100051

    View details for PubMedID 19149467

  • A Structural Basis for the Regulatory Inactivation of DnaA JOURNAL OF MOLECULAR BIOLOGY Xu, Q., McMullan, D., Abdubek, P., Astakhova, T., Carlton, D., Chen, C., Chiu, H., Clayton, T., Das, D., Deller, M. C., Duan, L., Elsliger, M., Feuerhelm, J., Hale, J., Han, G. W., Jaroszewski, L., Jin, K. K., Johnson, H. A., Klock, H. E., Knuth, M. W., Kozbial, P., Krishna, S. S., Kumar, A., Marciano, D., Miller, M. D., Morse, A. T., Nigoghossian, E., Nopakun, A., Okach, L., Oommachen, S., Paulsen, J., Puckett, C., Reyes, R., Rife, C. L., Sefcovic, N., Trame, C., van den Bedem, H., Weekes, D., Hodgson, K. O., Wooley, J., Deacon, A. M., Godzik, A., Lesley, S. A., Wilson, I. A. 2009; 385 (2): 368-380


    Regulatory inactivation of DnaA is dependent on Hda (homologous to DnaA), a protein homologous to the AAA+ (ATPases associated with diverse cellular activities) ATPase region of the replication initiator DnaA. When bound to the sliding clamp loaded onto duplex DNA, Hda can stimulate the transformation of active DnaA-ATP into inactive DnaA-ADP. The crystal structure of Hda from Shewanella amazonensis SB2B at 1.75 A resolution reveals that Hda resembles typical AAA+ ATPases. The arrangement of the two subdomains in Hda (residues 1-174 and 175-241) differs dramatically from that of DnaA. A CDP molecule anchors the Hda domains in a conformation that promotes dimer formation. The Hda dimer adopts a novel oligomeric assembly for AAA+ proteins in which the arginine finger, crucial for ATP hydrolysis, is fully exposed and available to hydrolyze DnaA-ATP through a typical AAA+ type of mechanism. The sliding clamp binding motifs at the N-terminus of each Hda monomer are partially buried and combine to form an antiparallel beta-sheet at the dimer interface. The inaccessibility of the clamp binding motifs in the CDP-bound structure of Hda suggests that conformational changes are required for Hda to form a functional complex with the clamp. Thus, the CDP-bound Hda dimer likely represents an inactive form of Hda.

    View details for DOI 10.1016/j.jmb.2008.10.059

    View details for Web of Science ID 000262916900004

    View details for PubMedID 19000695

  • Spectroscopic Definition of the Biferrous and Biferric Sites in de Novo Designed Four-Helix Bundle DFsc Peptides: Implications for O-2 Reactivity of Binuclear Non-Heme Iron Enzymes BIOCHEMISTRY Bell, C. B., Calhoun, J. R., Bobyr, E., Wei, P., Hedman, B., Hodgson, K. O., DeGrado, W. F., Solomon, E. T. 2009; 48 (1): 59-73


    DFsc is a single chain de novo designed four-helix bundle peptide that mimics the core protein fold and primary ligand set of various binuclear non-heme iron enzymes. DFsc and the E11D, Y51L, and Y18F single amino acid variants have been studied using a combination of near-IR circular dichroism (CD), magnetic circular dichroism (MCD), variable temperature variable field MCD (VTVH MCD), and X-ray absorption (XAS) spectroscopies. The biferrous sites are all weakly antiferromagnetically coupled with mu-1,3 carboxylate bridges and one 4-coordinate and one 5-coordinate Fe, very similar to the active site of class I ribonucleotide reductase (R2) providing open coordination positions on both irons for dioxygen to bridge. From perturbations of the MCD and VTVH MCD the iron proximal to Y51 can be assigned as the 4-coordinate center, and XAS results show that Y51 is not bound to this iron in the reduced state. The two open coordination positions on one iron in the biferrous state would become occupied by dioxygen and Y51 along the O(2) reaction coordinate. Subsequent binding of Y51 functions as an internal spectral probe of the O(2) reaction and as a proton source that would promote loss of H(2)O(2). Coordination by a ligand that functions as a proton source could be a structural mechanism used by natural binuclear iron enzymes to drive their reactions past peroxo biferric level intermediates.

    View details for DOI 10.1021/bi8016087

    View details for Web of Science ID 000262265900008

    View details for PubMedID 19090676

  • The XAS Model of Dissolved Cu(II) and Its Significance to Biological Electron Transfer 14th International Conference on X-Ray Absorption Fine Structure (XAFS14) Frank, P., Benfatto, M., Hedman, B., Hodgson, K. O. IOP PUBLISHING LTD. 2009
  • Reactive Intermediates in Oxygenation Reactions with Mononuclear Nonheme Iron Catalysts ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Yoon, J., Wilson, S. A., Jang, Y. K., Seo, M. S., Nehru, K., Hedman, B., Hodgson, K. O., Bill, E., Solomon, E. I., Nam, W. 2009; 48 (7): 1257-1260


    An advanced intermediate: A nonheme iron(IV) oxo complex [Fe(IV)(O)(bqen)(L)](n+) (bqen = N,N'-dimethyl-N,N'-bis(8-quinolyl)ethane-1,2-diamine, L = CH(3)CN or CF(3)SO(3)(-)) activates the C-H bonds of alkanes and alcohols by a hydrogen-atom abstraction mechanism. The catalytic oxidation of these species is proposed to occur through a nonheme iron(V) oxo species, with a high reactivity in oxidation reactions (see picture).

    View details for DOI 10.1002/anie.200802672

    View details for Web of Science ID 000263492400010

    View details for PubMedID 19137521

  • Geometric Structure Determination of N694C Lipoxygenase: A Comparative Near-Edge X-Ray Absorption Spectroscopy and Extended X-Ray Absorption Fine Structure Study INORGANIC CHEMISTRY Sarangi, R., Hocking, R. K., Neidig, M. L., Benfatto, M., Holman, T. R., Solomon, E. I., Hodgson, K. O., Hedman, B. 2008; 47 (24): 11543-11550


    The mononuclear nonheme iron active site of N694C soybean lipoxygenase (sLO1) has been investigated in the resting ferrous form using a combination of Fe-K-pre-edge, near-edge (using the minuit X-ray absorption near-edge full multiple-scattering approach), and extended X-ray absorption fine structure (EXAFS) methods. The results indicate that the active site is six-coordinate (6C) with a large perturbation in the first-shell bond distances in comparison to the more ordered octahedral site in wild-type sLO1. Upon mutation of the asparagine to cysteine, the short Fe-O interaction with asparagine is replaced by a weak Fe-(H(2)O), which leads to a distorted 6C site with an effective 5C ligand field. In addition, it is shown that near-edge multiple scattering analysis can give important three-dimensional structural information, which usually cannot be accessed using EXAFS analysis. It is further shown that, relative to EXAFS, near-edge analysis is more sensitive to partial coordination numbers and can be potentially used as a tool for structure determination in a mixture of chemical species.

    View details for DOI 10.1021/ic800580f

    View details for Web of Science ID 000261510100016

    View details for PubMedID 18656914

  • Electronic control of the "Bailar Twist" in formally d(0)-d(2) molybdenum tris(dithiolene) complexes: A sulfur K-edge X-ray absorption spectroscopy and density functional theory study INORGANIC CHEMISTRY Tenderholt, A. L., Szilagyi, R. K., Holm, R. H., Hodgson, K. O., Hedman, B., Solomon, E. I. 2008; 47 (14): 6382-6392


    Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of a series of Mo tris(dithiolene) complexes, [Mo(mdt)3](z) (where mdt = 1,2-dimethylethene-1,2-dithiolate(2-) and z = 2-, 1-, 0), with near trigonal-prismatic geometries (D3h symmetry). These results show that the formally Mo(IV), Mo(V), and Mo(VI) complexes actually have a (dz(2))(2) configuration, that is, remain effectively Mo(IV) despite oxidation. Comparisons with the XAS data of another set of Mo tris(dithiolene) complexes, [Mo(tbbdt)3](z) (where tbbdt = 3,5-ditert-butylbenzene-1,2-dithiolate(2-) and z = 1-, 0), show that both neutral complexes, [Mo(mdt)3] and [Mo(tbbdt)3], have similar electronic structures while the monoanions do not. Calculations reveal that the "Bailar twist" present in the crystal structure of [Mo(tbbdt)3](1-) (D3 symmetry) but not [Mo(mdt)3](1-) (D3h symmetry) is controlled by electronic factors which arise from bonding differences between the mdt and tbbdt ligands. In the former, configuration interaction between the Mo d(z(2)) and a deeper energy, occupied ligand orbital, which occurs in D3 symmetry, destabilizes the Mo d(z(2)) to above another ligand orbital which is half-occupied in the D3h [Mo(mdt)3](1-) complex. This leads to a metal d(1) configuration with no ligand holes (i.e., d(1)[L3](0h)) for [Mo(tbbdt)3](1-) rather than the metal d(2) configuration with one ligand hole (i.e., d(2)[L3](1h)) for [Mo(mdt)3](1-). Thus, the Bailar twist observed in some metal tris(dithiolene) complexes is the result of configuration interaction between metal and ligand orbitals and can be probed experimentally by S K-edge XAS.

    View details for DOI 10.1021/ic800494h

    View details for Web of Science ID 000257642700037

    View details for PubMedID 18517189

  • Solution [Cu(amm)](2+) is a strongly solvated square pyramid: A full account of the copper K-edge XAS spectrum within single-electron theory INORGANIC CHEMISTRY Frank, P., Benfatto, M., Hedman, B., Hodgson, K. O. 2008; 47 (10): 4126-4139


    The solution structure of Cu(II) in 4 M aqueous ammonia, [Cu(amm)](2+), was assessed using copper K-edge extended X-ray absorption fine structure (EXAFS) and Minuit XANes (MXAN) analyses. Tested structures included trigonal planar, planar and D2d -tetragonal, regular and distorted square pyramids, trigonal bipyramids, and Jahn-Teller distorted octahedra. Each approach converged to the same axially elongated square pyramid, 4 x Cu-Neq=2.00+/-0.02 A and 1 x Cu-Nax=2.16+/-0.02 A (EXAFS) or 2.20+/-0.07 A (MXAN), with strongly localized solvation shells. In the MXAN model, four equatorial ammonias averaged 13 degrees below the Cu(II) xy-plane, which was 0.45+/-0.1 A above the mean N4 plane. When the axial ligand equilibrium partial occupancies of about 0.65 ammonia and 0.35 water were included, EXAFS modeling found Cu-Lax distances of 2.16 and 2.31 A, respectively, reproducing the distances found in the crystal structures of [Cu(NH3)5](2+) and [Cu(NH3)4(H2O)](2+). A transverse axially localized solvent molecule was found at 2.8 A (EXAFS) or 3.1 A (MXAN). Six second-shell solvent molecules were also found at about 3.4+/-0.01 (EXAFS) or 3.8+/-0.2 A (MXAN). The structure of Cu(II) in 4 M pH 10 aqueous NH 3 may be notationally described as {[Cu(NH 3)4.62(H2O)0.38](solv)}(2+).6solv, solv=H2O, NH 3. The prominent shoulder and duplexed maximum of the rising K-edge XAS of [Cu(amm)](2+) primarily reflect the durable and well-organized solvation shells, not found around [Cu(H2O)5](2+), rather than two-electron shakedown transitions. Not accounting for solvent scattering thus may confound XAS-based estimates of metal-ligand covalency. [Cu(amm)](2+) continues the dissymmetry previously found for the solution structure of [Cu(H2O)5](2+), again contradicting the rack-bonding theory of blue copper proteins.

    View details for DOI 10.1021/ic7021243

    View details for Web of Science ID 000255770400029

    View details for PubMedID 18426203

  • Perturbations to the geometric and electronic structure of the CUA site: Factors that influence delocalization and their contributions to electron transfer JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Xie, X., Gorelsky, S. I., Sarangi, R., Garner, D. K., Hwang, H. J., Hodgsont, K. O., Hedman, B., Lu, Y., Solornon, E. I. 2008; 130 (15): 5194-5205


    Using a combination of electronic spectroscopies and DFT calculations, the effect of pH perturbation on the geometric and electronic structure of the CuA site has been defined. Descriptions are developed for high pH (pH = 7) and low pH (pH = 4) forms of CuA azurin and its H120A mutant which address the discrepancies concerning the extent of delocalization indicated by multifrequency EPR and ENDOR data (J. Am. Chem. Soc. 2005, 127, 7274; Biophys. J. 2002, 82, 2758). Our resonance Raman and MCD spectra demonstrate that the low pH and H120A mutant forms are essentially identical and are the perturbed forms of the completely delocalized high pH CuA site. However, in going from high pH to low pH, a seven-line hyperfine coupling pattern associated with complete delocalization of the electron (S = 1/2) over two Cu coppers (I(Cu) = 3/2) changes into a four-line pattern reflecting apparent localization. DFT calculations show that the unpaired electron is delocalized in the low pH form and reveal that its four-line hyperfine pattern results from the large EPR spectral effects of approximately 1% 4s orbital contribution of one Cu to the ground-state spin wave function upon protonative loss of its His ligand. The contribution of the Cu-Cu interaction to electron delocalization in this low symmetry protein site is evaluated, and the possible functional significance of the pH-dependent transition in regulating proton-coupled electron transfer in cytochrome c oxidase is discussed.

    View details for DOI 10.1021/ja7102668

    View details for Web of Science ID 000254933000044

    View details for PubMedID 18348522

  • Iron complexes of dendrimer-appended carboxylates for activating dioxygen and oxidizing hydrocarbons JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Zhao, M., Helms, B., Slonkina, E., Friedle, S., Lee, D., DuBois, J., Hedman, B., Hodgson, K. O., Frechet, J. M., Lippard, S. J. 2008; 130 (13): 4352-4363


    The active sites of metalloenzymes are often deeply buried inside a hydrophobic protein sheath, which protects them from undesirable hydrolysis and polymerization reactions, allowing them to achieve their normal functions. In order to mimic the hydrophobic environment of the active sites in bacterial monooxygenases, diiron(II) compounds of the general formula [Fe2([G-3]COO)4(4-RPy)2] were prepared, where [G-3]COO- is a third-generation dendrimer-appended terphenyl carboxylate ligand and 4-RPy is a pyridine derivative. The dendrimer environment provides excellent protection for the diiron center, reducing its reactivity toward dioxygen by about 300-fold compared with analogous complexes of terphenyl carboxylate ([G-1]COO-) ligands. An FeIIFeIII intermediate was characterized by electronic, electron paramagnetic resonance, Mössbauer, and X-ray absorption spectroscopic analyses following the oxygenation of [Fe2([G-3]COO)4(4-PPy)2], where 4-PPy is 4-pyrrolidinopyridine. The results are consistent with the formation of a superoxo species. This diiron compound, in the presence of dioxygen, can oxidize external substrates.

    View details for DOI 10.1021/ja076817a

    View details for Web of Science ID 000254549000036

    View details for PubMedID 18331028

  • The uptake and fate of vanadyl ion in ascidian blood cells and a detailed hypothesis for the mechanism and location of biological vanadium reduction. A visible and X-ray absorption spectroscopic study JOURNAL OF INORGANIC BIOCHEMISTRY Frank, P., Carlson, E. J., Carlson, R. M., Hedman, B., Hodgson, K. O. 2008; 102 (4): 809-823


    Vanadium K-edge X-ray absorption spectroscopy (XAS) has been used to track the uptake and fate of VO(2+) ion in blood cells from Ascidia ceratodes, following exposure to dithiothreitol (DTT) or to DTT plus VO(2+). The full range of endogenous vanadium was queried by fitting the XAS of blood cells with the XAS spectra of model vanadium complexes. In cells exposed only to DTT, approximately 0.4% of a new V(III) species was found in a site similar to Na[V(edta)(H(2)O)]. With exposure to DTT and VO(2+), average intracellular [VO(aq)](2+) increased from 3% to 5%, and 6% of a new complexed form of vanadyl ion appeared evidencing a ligand array similar to [VO(edta)](2-). At the same time, the relative ratio of blood cell [V(H(2)O)(6)](3+) increased at the expense of [V(H(2)O)(5)(SO(4))](+) in a manner consistent with a significant increase in endogenous acidity. In new UV/Visible experiments, VO(2+) could be reduced to 7-coordinate [V(nta)(H(2)O)(3)] or [V(nta)(ida)](2-) with cysteine methyl ester in pH 6.5 solution. Ascorbate reduced [VO(edta)](2-) to 7-coordinate [V(edta)(H(2)O)](-), while [VO(trdta)](2-) was unreactive. These results corroborate the finding that the reductive EMF of VO(2+) is increased by the availability of a 7-coordinate V(III) product. Finally, a new and complete hypothesis is proposed for an ascidian vanadate reductase. The structure of the enzyme active site, the vanadate-vanadyl-vanadic reduction mechanism, the cellular locale, and elements of the regulatory machinery governing the biological reduction of vanadate and vanadyl ion by ascidians are all predicted. Together these constitute the new field of vanadium redox enzymology.

    View details for DOI 10.1016/j.jinorgbio.2007.12.001

    View details for Web of Science ID 000255131500024

    View details for PubMedID 18234345

    View details for PubMedCentralID PMC2945689

  • Spectroscopic and density functional theory studies of the blue-copper site in M121SeM and C112SeC azurin: Cu-Se versus Cu-S bonding JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Sarangi, R., Gorelsky, S. I., Basumallick, L., Hwang, H. J., Pratt, R. C., Stack, T. D., Lu, Y., Hodgson, K. O., Hedman, B., Solomon, E. I. 2008; 130 (12): 3866-3877


    S K-edge X-ray absorption, UV-vis absorption, magnetic circular dichroism (MCD), and resonance Raman spectroscopies are used to investigate the electronic structure differences among WT, M121SeM, and C112SeC Pseudomonas aeruginosa (P.a) azurin. A comparison of S K-edge XAS of WT and M121SeM azurin and a CuII-thioether model complex shows that the 38% S character in the ground state wave function of the blue-copper (BC) sites solely reflects the Cu-SCys bond. Resonance Raman (rR) data on WT and C112SeC azurin give direct evidence for the kinematic coupling between the Cu-SCys stretch and the cysteine deformation modes in WT azurin, which leads to multiple features in the rR spectrum of the BC site. The UV-vis absorption and MCD data on WT, M121SeM, and C112SeC give very similar C0/D0 ratios, indicating that the C-term MCD intensity mechanism involves Cu-centered spin-orbit coupling (SOC). The spectroscopic data combined with density functional theory (DFT) calculations indicate that SCys and SeCys have similar covalent interactions with Cu at their respective bond lengths of 2.1 and 2.3 A. This reflects the similar electronegativites of S and Se in the thiolate/selenolate ligand fragment and explains the strong spectroscopic similarities between WT and C112SeC azurin.

    View details for DOI 10.1021/ja076495a

    View details for Web of Science ID 000254173600045

    View details for PubMedID 18314977

    View details for PubMedCentralID PMC2713798

  • When identical functional groups are not identical: A DFT study of the effects of molecular environment on sulfur K-edge X-ray absorption spectra INORGANICA CHIMICA ACTA Sarangi, R., Frank, P., Hodgson, K. O., Hedman, B. 2008; 361 (4): 956-964
  • Spectroscopic studies of perturbed T1 Cu sites in the multicopper oxidases Saccharomyces cerevisiae Fet3p and Rhus vernicifera laccase: Allosteric coupling between the T1 and trinuclear Cu sites BIOCHEMISTRY Augustine, A. J., Kragh, M. E., Sarangi, R., Fujii, S., Liboiron, B. D., Stoj, C. S., Kosman, D. J., Hodgson, K. O., Hedman, B., Solomon, E. I. 2008; 47 (7): 2036-2045


    The multicopper oxidases catalyze the 4e- reduction of O2 to H2O coupled to the 1e- oxidation of 4 equiv of substrate. This activity requires four Cu atoms, including T1, T2, and coupled binuclear T3 sites. The T2 and T3 sites form a trinuclear cluster (TNC) where O2 is reduced. The T1 is coupled to the TNC through a T1-Cys-His-T3 electron transfer (ET) pathway. In this study the two T3 Cu coordinating His residues which lie in this pathway in Fet3 have been mutated, H483Q, H483C, H485Q, and H485C, to study how perturbation at the TNC impacts the T1 Cu site. Spectroscopic methods, in particular resonance Raman (rR), show that the change from His to Gln to Cys increases the covalency of the T1 Cu-S Cys bond and decreases its redox potential. This study of T1-TNC interactions is then extended to Rhus vernicifera laccase where a number of well-defined species including the catalytically relevant native intermediate (NI) can be trapped for spectroscopic study. The T1 Cu-S covalency and potential do not change in these species relative to resting oxidized enzyme, but interestingly the differences in the structure of the TNC in these species do lead to changes in the T1 Cu rR spectrum. This helps to confirm that vibrations in the cysteine side chain of the T1 Cu site and the protein backbone couple to the Cu-S vibration. These changes in the side chain and backbone provide a possible mechanism for regulating intramolecular T1 to TNC ET in NI and partially reduced enzyme forms for efficient turnover.

    View details for DOI 10.1021/bi7020052

    View details for Web of Science ID 000253102000021

    View details for PubMedID 18197705

  • Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 angstrom resolution PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Mathews, I. I., McMullan, D., Miller, M. D., Canaves, J. M., Elsliger, M., Floyd, R., Grzechnik, S. K., Jaroszewski, L., Klock, H. E., Koesema, E., Kovarik, J. S., Kreusch, A., Kuhn, P., McPhillips, T. M., Morse, A. T., Quijano, K., Rife, C. L., Schwarzenbacher, R., Spraggon, G., Stevens, R. C., van den Bedem, H., Weekes, D., Wolf, G., Hodgson, K. O., Wooley, J., Deacon, A. M., Godzik, A., Lesley, S. A., Wilson, I. A. 2008; 70 (2): 603-608

    View details for DOI 10.1002/prot.21842

    View details for Web of Science ID 000252208900033

    View details for PubMedID 18004772

  • X-ray absorption spectroscopic and theoretical studies on (L)(2)[Cu-2(S-2)n](2+) complexes: Disulfide versus disulfide(center dot 1-) bonding JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Sarangi, R., York, J. T., Helton, M. E., Fujisawa, K., Karlin, K. D., Tolman, W. B., Hodgson, K. O., Hedman, B., Solomon, E. I. 2008; 130 (2): 676-686


    Cu K-, Cu L-, and S K-edge X-ray absorption spectroscopic (XAS) data have been combined with density functional theory (DFT) calculations on [{(TMPA)Cu}2S2](ClO4)2 (1), [{Cu[HB(3,5-Pr(i)2pz)3]}2(S2)] (2), and [{(TMEDA)Cu}2(S2)2](OTf)2 (3) to obtain a quantitative description of their ground state wavefunctions. The Cu L-edge intensities give 63 and 37% Cu d-character in the ground state of 1 and 2, respectively, whereas the S K-pre-edge intensities reflect 20 and 48% S character in their ground states, respectively. These data indicate a more than 2-fold increase in the total disulfide bonding character in 2 relative to 1. The increase in the number of Cu-S bonds in 2 (mu-eta(2):eta(2) S2(2-) bridge) compared to 1 ((mu-eta(1):eta(1) S2(2-) bridge) dominantly determines the large increase in covalency and Cu-disulfide bond strength in 2. Cu K- and L- and S K-pre-edge energy positions directly demonstrate the Cu(II)/(S2(-))2 nature of 3. The two disulfide(*1-)'s in 3 undergo strong bonding interactions that destabilize the resultant filled antibonding pi* orbitals of the (S2(-))2 fragment relative to the Cu 3d levels. This leads to an inverted bonding scheme in 3 with dominantly ligand-based holes in its ground state, consistent with its description as a dicopper(II)-bis-disulfide(*1-) complex.

    View details for DOI 10.1021/ja0762745

    View details for Web of Science ID 000252292500063

    View details for PubMedID 18076173

  • LATE TRANSITION METAL-OXO COMPOUNDS AND OPEN-FRAMEWORK MATERIALS THAT CATALYZE AEROBIC OXIDATIONS ADVANCES IN INORGANIC CHEMISTRY, VOL 60 Cao, R., Han, J. W., Anderson, T. M., Hillesheim, D. A., Hardcastle, K. I., Slonkina, E., Hedman, B. B., Hodgson, K. O., Kirk, M. L., Musaev, D. G., Morokuma, K., Geletii, Y. V., Hill, C. L. 2008; 60: 245-272
  • SK-Edge XAS and DFT calculations on square-planar NiII-thiolate complexes: Effects of active and passive H-bonding INORGANIC CHEMISTRY Dey, A., Green, K. N., Jenkins, R. M., Jeffrey, S. P., Darensbourg, M., Hodgson, K. O., Hedman, B., Solomon, E. I. 2007; 46 (23): 9655-9660


    S K-edge XAS for a low-spin NiII-thiolate complex shows a 0.2 eV shift to higher pre-edge energy but no change in Ni-S bond covalency upon H-bonding. This is different from the H-bonding effect we observed in high-spin FeIII-thiolate complexes where there is a significant decrease in Fe-S bond covalency but no change in energy due to H-bonding (Dey, A.; Okamura, T.-A.; Ueyama, N.; Hedman, B.; Hodgson, K. O.; Solomon, E. I. J. Am. Chem. Soc. 2005, 127, 12046-12053). These differences were analyzed using DFT calculations, and the results indicate that two different types of H-bonding interactions are possible in metal-thiolate systems. In the high-spin FeIII-thiolate case, the H-bonding involves a thiolate donor orbital which is also involved in bonding with the metal (active), while in the low-spin NiII-thiolate, the orbital involved in H-bonding is nonbonding with respect to the M-S bonding (passive). The contributions of active and passive H-bonds to the reduction potential and Lewis acid properties of a metal center are evaluated.

    View details for DOI 10.1021/ic7006292

    View details for Web of Science ID 000250732000024

    View details for PubMedID 17949080

  • Sulfur K-edge XAS of W-V=O vs. Mo-V=O bis(dithiolene) complexes: Contributions of relativistic effects to electronic structure and reactivity of tungsten enzymes JOURNAL OF INORGANIC BIOCHEMISTRY Tenderholt, A. L., Szilagyi, R. K., Holm, R. H., Hodgson, K., Hedman, B., Solomon, E. 2007; 101 (11-12): 1594-1600


    Molybdenum- or tungsten-containing enzymes catalyze oxygen atom transfer reactions involved in carbon, sulfur, or nitrogen metabolism. It has been observed that reduction potentials and oxygen atom transfer rates are different for W relative to Mo enzymes and the isostructural Mo/W complexes. Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations on [Mo(V)O(bdt)(2)](-) and [W(V)O(bdt)(2)](-), where bdt=benzene-1,2-dithiolate(2-), have been used to determine that the energies of the half-filled redox-active orbital, and thus the reduction potentials and MO bond strengths, are different for these complexes due to relativistic effects in the W sites.

    View details for DOI 10.1016/j.jinorgbio.2007.07.011

    View details for Web of Science ID 000251523100008

    View details for PubMedID 17720249

  • Crystal structure of NMA 1982 from Neisseria meningiddis at 1.5 angstrom resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Krishna, S. S., Tautz, L., Xu, Q., McMullan, D., Miller, M. D., Abdubek, P., Ambing, E., Astakhova, T., Axelrod, H. L., Carlton, D., Chiu, H., Clayton, T., DiDonato, M., Duan, L., Elsliger, M., Grzechnik, S. K., Hale, J., Hampton, E., Han, G. W., Haugen, J., Jaroszewski, L., Jin, K. K., Klock, H. E., Knuth, M. W., Koesema, E., Morse, A. T., Mustelin, T., Nigoghossian, E., Oommachen, S., Reyes, R., Rife, C. L., van den Bedem, H., Weekes, D., White, A., Hodgson, K. O., Wooley, J., Deacon, A. M., Godzik, A., Lesley, S. A., Wilson, I. A. 2007; 69 (2): 415-421

    View details for DOI 10.1002/prot.21314

    View details for Web of Science ID 000249714400018

    View details for PubMedID 17636569

  • Sulfur K-edge X-ray absorption Spectroscopy and density functional theory calculations on superoxide reductase: Role of the axial thiolate in reactivity JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Dey, A., Jenney, F. E., Adams, M. W., Johnson, M. K., Hodgson, K. O., Hedman, B., Solomon, E. I. 2007; 129 (41): 12418-12431


    Superoxide reductase (SOR) is a non-heme iron enzyme that reduces superoxide to peroxide at a diffusion-controlled rate. Sulfur K-edge X-ray absorption spectroscopy (XAS) is used to investigate the ground-state electronic structure of the resting high-spin and CN- bound low-spin FeIII forms of the 1Fe SOR from Pyrococcus furiosus. A computational model with constrained imidazole rings (necessary for reproducing spin states), H-bonding interaction to the thiolate (necessary for reproducing Fe-S bond covalency of the high-spin and low-spin forms), and H-bonding to the exchangeable axial ligand (necessary to reproduce the ground state of the low-spin form) was developed and then used to investigate the enzymatic reaction mechanism. Reaction of the resting ferrous site with superoxide and protonation leading to a high-spin FeIII-OOH species and its subsequent protonation resulting in H2O2 release is calculated to be the most energetically favorable reaction pathway. Our results suggest that the thiolate acts as a covalent anionic ligand. Replacing the thiolate with a neutral noncovalent ligand makes protonation very endothermic and greatly raises the reduction potential. The covalent nature of the thiolate weakens the FeIII bond to the proximal oxygen of this hydroperoxo species, which raises its pKa by an additional 5 log units relative to the pKa of a primarily anionic ligand, facilitating its protonation. A comparison with cytochrome P450 indicates that the stronger equatorial ligand field from the porphyrin results in a low-spin FeIII-OOH species that would not be capable of efficient H2O2 release due to a spin-crossing barrier associated with formation of a high-spin 5C FeIII product. Additionally, the presence of the dianionic porphyrin pi ring in cytochrome P450 allows O-O heterolysis, forming an FeIV-oxo porphyrin radical species, which is calculated to be extremely unfavorable for the non-heme SOR ligand environment. Finally, the 5C FeIII site that results from the product release at the end of the O2- reduction cycle is calculated to be capable of reacting with a second O2-, resulting in superoxide dismutase (SOD) activity. However, in contrast to FeSOD, the 5C FeIII site of SOR, which is more positively charged, is calculated to have a high affinity for binding a sixth anionic ligand, which would inhibit its SOD activity.

    View details for DOI 10.1021/ja064167p

    View details for Web of Science ID 000250105500039

    View details for PubMedID 17887751

    View details for PubMedCentralID PMC2533108

  • Terminal gold-oxo complexes JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Cao, R., Anderson, T. M., Piccoli, P. M., Schultz, A. J., Koetzle, T. F., Geletii, Y. V., Slonkina, E., Hedman, B., Hodgson, K. O., Hardcastle, K. I., Fang, X., Kirk, M. L., Knottenbelt, S., Koegerler, P., Musaev, D. G., Morokuma, K., Takahashi, M., Hill, C. L. 2007; 129 (36): 11118-11133


    In contradiction to current bonding paradigms, two terminal Au-oxo molecular complexes have been synthesized by reaction of AuCl3 with metal oxide-cluster ligands that model redox-active metal oxide surfaces. Use of K10[alpha2-P2W17O61].20H2O and K2WO4 (forming the [A-PW9O34]9- ligand in situ) produces K15H2[Au(O)(OH2)P2W18O68].25H2O (1); use of K10[P2W20O70(OH2)2].22H2O (3) produces K7H2[Au(O)(OH2)P2W20O70(OH2)2].27H2O (2). Complex 1 crystallizes in orthorhombic Fddd, with a=28.594(4) A, b=31.866(4) A, c=38.241(5) A, V=34844(7) A3, Z=16 (final R=0.0540), and complex 2 crystallizes in hexagonal P6(3)/mmc, with a=16.1730(9) A, b=16.1730(9) A, c=19.7659(15) A, V=4477.4(5) A3, Z=2 (final R=0.0634). The polyanion unit in 1 is disorder-free. Very short (approximately 1.76 A) Au-oxo distances are established by both X-ray and 30 K neutron diffraction studies, and the latter confirms oxo and trans aqua (H2O) ligands on Au. Seven findings clarify that Au and not W is present in the Au-oxo position in 1 and 2. Five lines of evidence are consistent with the presence of d8 Au(III) centers that are stabilized by the flanking polytungstate ligands in both 1 and 2: redox titrations, electrochemical measurements, 17 K optical spectra, Au L2 edge X-ray absorption spectroscopy, and Au-oxo bond distances. Variable-temperature magnetic susceptibility data for crystalline 1 and 2 establish that both solids are diamagnetic, and 31P and 17O NMR spectroscopy confirm that both remain diamagnetic in solution. Both complexes have been further characterized by FT-IR, thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and other techniques.

    View details for DOI 10.1021/ja072456n

    View details for Web of Science ID 000249372400047

    View details for PubMedID 17711276

  • Photoreduction of the active site of the metalloprotein putidaredoxin by synchrotron radiation ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY Corbett, M. C., Latimer, M. J., Poulos, T. L., Sevrioukova, I. F., Hodgson, K. O., Hedman, B. 2007; 63: 951-960


    X-ray damage to protein crystals is often assessed on the basis of the degradation of diffraction intensity, yet this measure is not sensitive to the rapid changes that occur at photosensitive groups such as the active sites of metalloproteins. Here, X-ray absorption spectroscopy is used to study the X-ray dose-dependent photoreduction of crystals of the [Fe(2)S(2)]-containing metalloprotein putidaredoxin. A dramatic decrease in the rate of photoreduction is observed in crystals cryocooled with liquid helium at 40 K compared with those cooled with liquid nitrogen at 110 K. Whereas structural changes consistent with cluster reduction occur in the active site of the crystal measured at 110 K, no such changes occur in the crystal measured at 40 K, even after an eightfold increase in dose. When the structural results from extended X-ray absorption fine-structure measurements are compared with those obtained by crystallography on this and similar proteins, it is apparent that X-ray-induced photoreduction has had an impact on the crystallographic data and subsequent structure solutions. These results strongly indicate the importance of using liquid-helium-based cooling for metalloprotein crystallography in order to avoid the subtle yet important changes that can take place at the metalloprotein active sites when liquid-nitrogen-based cooling is used. The study also illustrates the need for direct measurement of the redox states of the metals, through X-ray absorption spectroscopy, simultaneously with the crystallographic measurements.

    View details for DOI 10.1107/S0907444907035160

    View details for Web of Science ID 000249167300003

    View details for PubMedID 17704563

  • The two oxidized forms of the trinuclear Cu cluster in the multicopper oxidases and mechanism for the decay of the native intermediate PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Yoon, J., Liboiron, B. D., Sarangi, R., Hodgson, K. O., Hedman, B., Solomona, E. I. 2007; 104 (34): 13609-13614


    Multicopper oxidases (MCOs) catalyze the 4e(-) reduction of O(2) to H(2)O. The reaction of the fully reduced enzyme with O(2) generates the native intermediate (NI), which undergoes a slow decay to the resting enzyme in the absence of substrate. NI is a fully oxidized form, but its spectral features are very different from those of the resting form (also fully oxidized), because the type 2 and the coupled-binuclear type 3 Cu centers in the O(2)-reducing trinuclear Cu cluster site are isolated in the resting enzyme, whereas these are all bridged by a micro(3)-oxo ligand in NI. Notably, the one azide-bound NI (NI(Az)) exhibits spectral features very similar to those of NI, in which the micro(3)-oxo ligand in NI has been replaced by a micro(3)-bridged azide. Comparison of the spectral features of NI and NI(Az), combined with density functional theory (DFT) calculations, allows refinement of the NI structure. The decay of NI to the resting enzyme proceeds via successive proton-assisted steps, whereas the rate-limiting step involves structural rearrangement of the micro(3)-oxo-bridge from inside to outside the cluster. This phenomenon is consistent with the slow rate of NI decay that uncouples the resting enzyme from the catalytic cycle, leaving NI as the catalytically relevant fully oxidized form of the MCO active site. The all-bridged structure of NI would facilitate electron transfer to all three Cu centers of the trinuclear cluster for rapid proton-coupled reduction of NI to the fully reduced form for catalytic turnover.

    View details for Web of Science ID 000249064700017

    View details for PubMedID 17702865

  • Copper(I) complex O-2-reactivity with a N3S thioether ligand: A copper-dioxygen adduct including sulfur ligation, ligand oxygenation, and comparisons with all nitrogen ligand analogues INORGANIC CHEMISTRY Lee, D., Hatcher, L. Q., Vance, M. A., Sarangi, R., Milligan, A. E., Sarjeant, A. A., Incarvito, C. D., Rheingold, A. L., Hodgson, K. O., Hedman, B., Solomon, E. I., Karlin, K. D. 2007; 46 (15): 6056-6068


    In order to contribute to an understanding of the effects of thioether sulfur ligation in copper-O(2) reactivity, the tetradentate ligands L(N3S) (2-ethylthio-N,N-bis(pyridin-2-yl)methylethanamine) and L(N3S')(2-ethylthio-N,N-bis(pyridin-2-yl)ethylethanamine) have been synthesized. Corresponding copper(I) complexes, [CuI(L(N3S))]ClO(4) (1-ClO(4)), [CuI(L(N3S))]B(C(6)F(5))(4) (1-B(C(6)F(5))(4)), and [CuI(L(N3S'))]ClO(4) (2), were generated, and their redox properties, CO binding, and O(2)-reactivity were compared to the situation with analogous compounds having all nitrogen donor ligands, [CuI(TMPA)(MeCN)](+) and [Cu(I)(PMAP)](+) (TMPA = tris(2-pyridylmethyl)amine; PMAP = bis[2-(2-pyridyl)ethyl]-(2-pyridyl)methylamine). X-ray structures of 1-B(C(6)F(5))(4), a dimer, and copper(II) complex [Cu(II)(L(N3S))(MeOH)](ClO(4))(2) (3) were obtained; the latter possesses axial thioether coordination. At low temperature in CH(2)Cl(2), acetone, or 2-methyltetrahydrofuran (MeTHF), 1 reacts with O(2) and generates an adduct formulated as an end-on peroxodicopper(II) complex [{Cu(II)(L(N3S))}(2)(mu-1,2-O(2)(2-))](2+) (4)){lambda(max) = 530 (epsilon approximately 9200 M(-1) cm(-1)) and 605 nm (epsilon approximately 11,800 M(-1) cm(-1))}; the number and relative intensity of LMCT UV-vis bands vary from those for [{Cu(II)(TMPA)}(2)(O(2)(2-))](2+) {lambda(max) = 524 nm (epsilon = 11,300 M(-1) cm(-1)) and 615 nm (epsilon = 5800 M(-1) cm(-1))} and are ascribed to electronic structure variation due to coordination geometry changes with the L(N3S) ligand. Resonance Raman spectroscopy confirms the end-on peroxo-formulation {nu(O-O) = 817 cm(-1) (16-18O(2) Delta = 46 cm(-1)) and nu(Cu-O) = 545 cm(-1) (16-18O(2) Delta = 26 cm(-1)); these values are lower in energy than those for [{Cu(II)(TMPA)}(2)(O(2)(2-))](2+) {nu(Cu-O) = 561 cm(-1) and nu(O-O) = 827 cm(-1)} and can be attributed to less electron density donation from the peroxide pi* orbitals to the Cu(II) ion. Complex 4 is the first copper-dioxygen adduct with thioether ligation; direct evidence comes from EXAFS spectroscopy {Cu K-edge; Cu-S = 2.4 Angstrom}. Following a [Cu(I)(L(N3S))](+)/O(2) reaction and warming, the L(N3S) thioether ligand is oxidized to the sulfoxide in a reaction modeling copper monooxygenase activity. By contrast, 2 is unreactive toward dioxygen probably due to its significantly increased Cu(II)/Cu(I) redox potential, an effect of ligand chelate ring size (in comparison to 1). Discussion of the relevance of the chemistry to copper enzyme O(2)-activation, and situations of biological stress involving methionine oxidation, is provided.

    View details for DOI 10.1021/ic700541k

    View details for Web of Science ID 000248011300034

    View details for PubMedID 17580938

  • Conformational differences between Azotobacter vinelandii nitrogenase MoFe proteins as studied by small-angle X-ray scattering BIOCHEMISTRY Corbett, M. C., Hu, Y., Fay, A. W., Tsuruta, H., Ribbe, M. W., Hodgson, K. O., Hedman, B. 2007; 46 (27): 8066-8074


    The nitrogenase MoFe protein is a heterotetramer containing two unique high-nuclearity metalloclusters, FeMoco and the P-cluster. FeMoco is assembled outside the MoFe protein, whereas the P-cluster is assembled directly on the MoFe protein polypeptides. MoFe proteins isolated from different genetic backgrounds have been analyzed using biochemical and spectroscopic techniques in attempting to elucidate the pathway of P-cluster biosynthesis. The DeltanifH MoFe protein is less stable than other MoFe proteins and has been shown by extended X-ray absorption fine structure studies to contain a variant P-cluster that most likely exists as two separate [Fe4S4]-like clusters instead of the subunit-bridging [Fe8S7] cluster found in the wild-type and DeltanifB forms of the MoFe protein [Corbett, M. C., et al. (2004) J. Biol. Chem. 279, 28276-28282]. Here, a combination of small-angle X-ray scattering and Fe chelation studies is used to show that there is a correlation between the state of the P-cluster and the conformation of the MoFe protein. The DeltanifH MoFe protein is found to be larger than the wild-type or DeltanifB MoFe proteins, an increase in size that can be modeled well by an opening of the subunit interface consistent with P-cluster fragmentation and solvent exposure. Importantly, this opening would allow for the insertion of P-cluster precursors into a region of the MoFe protein that is buried in the wild-type conformation. Thus, DeltanifH MoFe protein could represent an early intermediate in MoFe protein biosynthesis where the P-cluster precursors have been inserted, but P-cluster condensation and tetramer stabilization have yet to occur.

    View details for DOI 10.1021/bi7005064

    View details for Web of Science ID 000247677700014

    View details for PubMedID 17567155

  • Sulfur K-edge XAS and DFT studies on Ni-II complexes with oxidized thiolate ligands: Implications for the roles of oxidized thiolates in the active sites of Fe and Co nitrile hydratase INORGANIC CHEMISTRY Dey, A., Jeffrey, S. P., Darensbourg, M., Hodgson, K. O., Hedman, B., Solomon, E. I. 2007; 46 (12): 4989-4996


    S K-edge X-ray absorption spectroscopy data on a series of NiII complexes with thiolate (RS-) and oxidized thiolate (RSO2-) ligands are used to quantify Ni-S bond covalency and its change upon ligand oxidation. Analyses of these results using geometry-optimized density functional theory (DFT) calculations suggest that the Ni-S sigma bonds do not weaken on ligand oxidation. Molecular orbital analysis indicates that these oxidized thiolate ligands use filled high-lying S-O pi* orbitals for strong sigma donation. However, the RSO2- ligands are poor pi donors, as the orbital required for pi interaction is used in the S-O sigma-bond formation. The oxidation of the thiolate reduces the repulsion between electrons in the filled Ni t2 orbital and the thiolate out-of-plane pi-donor orbital leading to shorter Ni-S bond length relative to that of the thiolate donor. The insights obtained from these results are relevant to the active sites of Fe- and Co-type nitrile hydratases (Nhase) that also have oxidized thiolate ligands. DFT calculations on models of the active site indicate that whereas the oxidation of these thiolates has a major effect in the axial ligand-binding affinity of the Fe-type Nhase (where there is both sigma and pi donation from the S ligands), it has only a limited effect on the sixth-ligand-binding affinity of the Co-type Nhases (where there is only sigma donation). These oxidized residues may also play a role in substrate binding and proton shuttling at the active site.

    View details for DOI 10.1021/ic070244l

    View details for Web of Science ID 000246907800034

    View details for PubMedID 17500514

  • Fe L-edge x-ray absorption spectroscopy of low-spin heme relative to non-heme Fe complexes: Delocalization of Fe d-electrons into the porphyrin ligand JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Hocking, R. K., Wasinger, E. C., Yan, Y., deGroot, F. M., Walker, F. A., Hodgson, K. O., Hedman, B., Solomon, E. I. 2007; 129 (1): 113-125


    Hemes (iron porphyrins) are involved in a range of functions in biology, including electron transfer, small-molecule binding and transport, and O2 activation. The delocalization of the Fe d-electrons into the porphyrin ring and its effect on the redox chemistry and reactivity of these systems has been difficult to study by optical spectroscopies due to the dominant porphyrin pi-->pi(*) transitions, which obscure the metal center. Recently, we have developed a methodology that allows for the interpretation of the multiplet structure of Fe L-edges in terms of differential orbital covalency (i.e., differences in mixing of the d-orbitals with ligand orbitals) using a valence bond configuration interaction (VBCI) model. Applied to low-spin heme systems, this methodology allows experimental determination of the delocalization of the Fe d-electrons into the porphyrin (P) ring in terms of both P-->Fe sigma and pi-donation and Fe-->P pi back-bonding. We find that pi-donation to Fe(III) is much larger than pi back-bonding from Fe(II), indicating that a hole superexchange pathway dominates electron transfer. The implications of the results are also discussed in terms of the differences between heme and non-heme oxygen activation chemistry.

    View details for DOI 10.1021/ja065627h

    View details for Web of Science ID 000243195100032

    View details for PubMedID 17199290

  • PySpline: A modern, cross-platform program for the processing of raw averaged XAS edge and EXAFS data 13th International Conference on X-Ray Absorption Fine Structure (XAFS13) Tenderholt, A., Hedman, B., Hodgson, K. O. AMER INST PHYSICS. 2007: 105–107
  • Toward the Biological Reduction Mechanism of Vanadyl Ion in the Blood Cells of Vanadium-Sequestering Tunicates 5th International Symposium on Chemistry and Biological Chemistry of Vanadium Frank, P., Carlson, E. J., Carlson, R. M., Hedman, B., Hodgson, K. O. AMER CHEMICAL SOC. 2007: 281–295
  • Dioxygen reactivity of a copper(I) complex with a N3S thioether chelate; Peroxo-dicopper(II) formation including sulfur-ligation INORGANIC CHEMISTRY Hatcher, L. Q., Lee, D., Vance, M. A., Milligan, A. E., Sarangi, R., Hodgson, K. O., Hedman, B., Solomon, E. I., Karlin, K. D. 2006; 45 (25): 10055-10057


    Employing a tetradentate N3S(thioether) ligand, LN3S, dioxygen reactivity of a copper(I) complex, [(LN3S)CuI]+ (1) was examined. In CH2Cl2, acetone (at -80 degrees C), or 2-methyltetrahydrofuran (at -128 degrees C), 1 reacts with O2 producing the end-on bound peroxodicopper(II) complex [{(LN3S)CuII}2(mu-1,2-O2(2-))]2+ (2), the first reported copper-dioxygen adduct with sulfur (thioether) ligation. Its absorption spectrum contains an additional low-energy feature (but not a Cu-S CT band) compared to the previously well-characterized N4 ligand complex, [{(TMPA)CuII}2(mu-1,2-O2(2-))]2+ (3) (TMPA = tris(2-pyridylmethyl)amine). Resonance Raman spectroscopy confirms the peroxo formulation {nu(O-O) = 817 cm-1 (16-18O2 Delta = 46 cm-1) and nu(Cu-O) = 545 cm-1 (16-18O2 Delta = 26 cm-1), in close analogy to that known for 3 {nu(O-O) = 827 cm-1 and nu(Cu-O) = 561 cm-1}. Direct evidence for thioether ligation comes from EXAFS spectroscopy {Cu K-edge; Cu-S = 2.4 A}.

    View details for DOI 10.1021/ic061813c

    View details for Web of Science ID 000242479700022

    View details for PubMedID 17140210

  • A systematic resolution of sulfur in reticulated vitreous carbon using X-ray absorption spectroscopy INORGANIC CHEMISTRY Frank, P., George, S. D., Anxolabehere-Mallart, E., Hedman, B., Hodgson, K. O. 2006; 45 (24): 9864-9876


    Sulfur K-edge X-ray absorption spectroscopy (XAS) was used to characterize the approximately 0.1% sulfur found both in native reticulated vitreous carbon (RVC) foam and in RVC oxidatively modified using 0.2 M KMnO4 in 2 M H2SO4. Sulfur valences and functional groups were assessed using K-edge XAS spectral curve-fitting and employing explicit sulfur compounds as models. For native RVC, these were episulfide (approximately 3%), thianthrene (approximately 9%), disulfide (approximately 10%), sulfenate ester (approximately 12%), benzothiophene (approximately 24%), N,N'-thiobisphthalimide (approximately 30%), alkyl sulfonate (approximately 1.2%), alkyl sulfate monoester (approximately 6%), and sulfate dianion (approximately 6%). Permanganate oxidation of RVC diminished sulfenic sulfur to approximately 9%, thianthrenic sulfur to approximately 7%, and sulfate dianion to approximately 1% but increased sulfate monoester to approximately 12%, and newly produced sulfone (approximately 2%) and sulfate diester (approximately 5%). A simple thermodynamic model was derived that allows proportionate functional group comparisons despite differing (approximately +/-15%) total sulfur contents between RVC batches. The limits of accuracy in the XAS curve-fitting analysis are discussed in terms of microenvironments and extended structures in RVC carbon that cannot be exactly modeled by small molecules. Sulfate esters cover approximately 0.15% of the RVC surface, increasing to approximately 0.51% following permanganate/sulfuric acid treatment. The detection of episulfide directly corroborates a proposed mechanism for the migration of elemental sulfur through carbon.

    View details for DOI 10.1021/ic0610637

    View details for Web of Science ID 000242124300039

    View details for PubMedID 17112284

  • FeMo cofactor maturation on NifEN PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Hu, Y., Corbett, M. C., Fay, A. W., Webber, J. A., Hodgson, K. O., Hedman, B., Ribbe, M. W. 2006; 103 (46): 17119-17124


    FeMo cofactor (FeMoco) biosynthesis is one of the most complicated processes in metalloprotein biochemistry. Here we show that Mo and homocitrate are incorporated into the Fe/S core of the FeMoco precursor while it is bound to NifEN and that the resulting fully complemented, FeMoco-like cluster is transformed into a mature FeMoco upon transfer from NifEN to MoFe protein through direct protein-protein interaction. Our findings not only clarify the process of FeMoco maturation, but also provide useful insights into the other facets of nitrogenase chemistry.

    View details for DOI 10.1073/pnas.0602647103

    View details for Web of Science ID 000242249400012

    View details for PubMedID 17050696

  • Nitrogenase Fe protein: A molybdate/homocitrate insertase PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Hu, Y., Corbettt, M. C., Fay, A. W., Webber, J. A., Hodgson, K. O., Hedman, B., Ribbe, M. W. 2006; 103 (46): 17125-17130


    The Fe protein is indispensable for nitrogenase catalysis and biosynthesis. However, its function in iron-molybdenum cofactor (FeMoco) biosynthesis has not been clearly defined. Here we show that the Fe protein can act as a Mo/homocitrate insertase that mobilizes Mo/homocitrate for the maturation of FeMoco precursor on NifEN. Further, we establish that Mo/homocitrate mobilization by the Fe protein likely involves hydrolysis of MgATP and protein-protein interaction between the Fe protein and NifEN. Our findings not only clarify the role of the Fe protein in FeMoco assembly and assign another function to this multitask enzyme but also provide useful insights into a mechanism of metal trafficking required for the assembly of complex metalloproteins such as nitrogenase.

    View details for DOI 10.1073/pnas.0602651103

    View details for Web of Science ID 000242249400013

    View details for PubMedID 17062756

  • How does single oxygen atom addition affect the properties of an Fe-nitrile hydratase analogue? The compensatory role of the unmodified thiolate JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Lugo-Mas, P., Dey, A., Xu, L., Davin, S. D., Benedict, J., Kaminsky, W., Hodgson, K. O., Hedman, B., Solomon, E. I., Kovacs, J. A. 2006; 128 (34): 11211-11221


    Nitrile hydratase (NHase) is one of a growing number of enzymes shown to contain post-translationally modified cysteine sulfenic acids (Cys-SOH). Cysteine sulfenic acids have been shown to play diverse roles in cellular processes, including transcriptional regulation, signal transduction, and the regulation of oxygen metabolism and oxidative stress responses. The function of the cysteine sulfenic acid coordinated to the iron active site of NHase is unknown. Herein we report the first example of a sulfenate-ligated iron complex, [Fe(III)(ADIT)(ADIT-O)](+) (5), and compare its electronic and magnetic properties with those of structurally related complexes in which the sulfur oxidation state and protonation state have been systematically altered. Oxygen atom addition was found to decrease the unmodified thiolate Fe-S bond length and blue-shift the ligand-to-metal charge-transfer band (without loss of intensity). S K-edge X-ray absorption spectroscopy and density functional theory calculations show that, although the modified RS-O(-) fragment is incapable of forming a pi bond with the Fe(III) center, the unmodified thiolate compensates for this loss of pi bonding by increasing its covalent bond strength. The redox potential shifts only slightly (75 mV), and the magnetic properties are not affected (the S = (1)/(2) spin state is maintained). The coordinated sulfenate S-O bond is activated and fairly polarized (S(+)-O(-)). Addition of strong acids at low temperatures results in the reversible protonation of sulfenate-ligated 5. An X-ray structure demonstrates that Zn(2+) binds to the sulfenate oxygen to afford [Fe(III)(ADIT)(ADIT-O-ZnCl(3))] (6). The coordination of ZnCl(3)(-) to the RS-O(-) unit causes the covalent overlap with the unmodified thiolate to increase further. A possible catalytic role for the unmodified NHase thiolate, involving its ability to "tune" the electronics in response to protonation of the sulfenate (RS-O(-)) oxygen and/or substrate binding, is discussed.

    View details for DOI 10.1021/ja062706k

    View details for Web of Science ID 000239932500051

    View details for PubMedID 16925440

  • Fe L-edge XAS studies of K-4[Fe(CN)(6)] and K-3[Fe(CN)(6)]: A direct probe of back-bonding JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Hocking, R. K., Wasinger, E. C., de Groot, F. M., Hodgson, K. O., Hedman, B., Solomon, E. I. 2006; 128 (32): 10442-10451


    Distinct spectral features at the Fe L-edge of the two compounds K3[Fe(CN)6] and K4[Fe(CN)6] have been identified and characterized as arising from contributions of the ligand pi orbitals due to metal-to-ligand back-bonding. In addition, the L-edge energy shifts and total intensities allow changes in the ligand field and effective nuclear charge to be determined. It is found that the ligand field term dominates the edge energy shift. The results of the experimental analysis were compared to BP86 DFT calculations. The overall agreement between the calculations and experiment is good; however, a larger difference in the amount of pi back-donation between Fe(II) and Fe(III) is found experimentally. The analysis of L-edge spectral shape, energy shift, and total intensity demonstrates that Fe L-edge X-ray absorption spectroscopy provides a direct probe of metal-to-ligand back-bonding.

    View details for DOI 10.1021/ja061802i

    View details for Web of Science ID 000239618700027

    View details for PubMedID 16895409

  • X-ray absorption spectroscopy and density functional theory studies of [(H(3)buea)Fe-III-X](n-) (X = S2-, O2-, OH-): Comparison of bonding and hydrogen bonding in oxo and sulfido complexes JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Dey, A., Hocking, R. K., Larsen, P., Borovik, A. S., Hodgson, K. O., Hedman, B., Solomon, E. I. 2006; 128 (30): 9825-9833


    Iron L-edge, iron K-edge, and sulfur K-edge X-ray absorption spectroscopy was performed on a series of compounds [Fe(III)H(3)buea(X)](n-) (X = S(2-), O(2-), OH(-)). The experimentally determined electronic structures were used to correlate to density functional theory calculations. Calculations supported by the data were then used to compare the metal-ligand bonding and to evaluate the effects of H-bonding in Fe(III)(-)O vs Fe(III)(-)S complexes. It was found that the Fe(III)(-)O bond, while less covalent, is stronger than the Fe(III)(-)S bond. This dominantly reflects the larger ionic contribution to the Fe(III)(-)O bond. The H-bonding energy (for three H-bonds) was estimated to be -25 kcal/mol for the oxo as compared to -12 kcal/mol for the sulfide ligand. This difference is attributed to the larger charge density on the oxo ligand resulting from the lower covalency of the Fe-O bond. These results were extended to consider an Fe(IV)(-)O complex with the same ligand environment. It was found that hydrogen bonding to Fe(IV)(-)O is less energetically favorable than that to Fe(III)(-)O, which reflects the highly covalent nature of the Fe(IV)(-)O bond.

    View details for DOI 10.1021/ja061618x

    View details for Web of Science ID 000239278600060

    View details for PubMedID 16866539

  • Reversible O-O bond cleavage in copper-dioxygen isomers: Impact of anion basicity JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Ottenwaelder, X., Rudd, D. J., Corbett, M. C., Hodgson, K. O., Hedman, B., Stack, T. D. 2006; 128 (29): 9268-9269


    Low-temperature oxygenation of copper(I) complexes of N,N,N',N'-tetraethylpropane-1,3-diamine yields solutions containing both mu-eta2:eta2-peroxodicopper(II) (P) and bis(mu-oxo)dicopper(III) (O) valence isomers. The P/O equilibrium position depends on the nature of the counteranion; P is favored with more basic anions. Titration and EXAFS experiments as well as DFT calculations suggest that axial donation from a sulfonate anion to the copper centers imparts an electronic/electrostatic bias toward the P isomer.

    View details for DOI 10.1021/ja061132g

    View details for Web of Science ID 000239120700005

    View details for PubMedID 16848427

  • X-ray absorption edge spectroscopy and computational studies on LCuO2 species: Superoxide-Cu-II versus peroxide-Cu-III bonding JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Sarangi, R., Aboelella, N., Fujisawa, K., Tolman, W. B., Hedman, B., Hodgson, K. O., Solomon, E. I. 2006; 128 (25): 8286-8296


    The geometric and electronic structures of two mononuclear CuO2 complexes, [Cu(O2){HB(3-Ad-5-(i)Prpz)3}] (1) and [Cu(O2)(beta-diketiminate)] (2), have been evaluated using Cu K- and L-edge X-ray absorption spectroscopy (XAS) studies in combination with valence bond configuration interaction (VBCI) simulations and spin-unrestricted broken symmetry density functional theory (DFT) calculations. Cu K- and L-edge XAS data indicate the Cu(II) and Cu(III) nature of 1 and 2, respectively. The total integrated intensity under the L-edges shows that the 's in 1 and 2 contain 20% and 28% Cu character, respectively, indicative of very covalent ground states in both complexes, although more so in 1. Two-state VBCI simulations also indicate that the ground state in 2 has more Cu (/3d8) character. DFT calculations show that the in both complexes is dominated by O2(n-) character, although the O2(n-) character is higher in 1. It is shown that the ligand L plays an important role in modulating Cu-O2 bonding in these LCuO2 systems and tunes the ground states of 1 and 2 to have dominant Cu(II)-superoxide-like and Cu(III)-peroxide-like character, respectively. The contributions of ligand field (LF) and the charge on the absorbing atom in the molecule (Q(mol)M) to L- and K-edge energy shifts are evaluated using DFT and time-dependent DFT calculations. It is found that LF makes a dominant contribution to the edge energy shift, while the effect of Q(mol)M is minor. The charge on the Cu in the Cu(III) complex is found to be similar to that in Cu(II) complexes, which indicates a much stronger interaction with the ligand, leading to extensive charge transfer.

    View details for DOI 10.1021/ja0615223

    View details for Web of Science ID 000238418000045

    View details for PubMedID 16787093

  • A new structural motif for biological iron: Iron K-edge XAS reveals a [Fe-4-mu-(OR)(5)(OR)(9-10)] cluster in the ascidian Perophora annectens INORGANIC CHEMISTRY Frank, P., DeTomaso, A., Hedman, B., Hodgson, K. O. 2006; 45 (10): 3920-3931


    The Phlebobranch ascidian Perophora annectens surprisingly exhibited a biological Fe/V ratio of approximately 15:1 on multichannel X-ray fluorescence analysis of two independent collections of organisms. Iron K-edge X-ray absorption spectroscopy (XAS) indicated a single form of iron. The XAS K-edge of the first collection of blood cells was shifted approximately +1 eV relative to that of the second, indicating redox activity with average iron oxidation states of 2.67+ and 2.60+. The first-derivative iron XAS K-edge features at 7120.5, 7124, and 7128 eV resembled the XAS of magnetite but not of ferritin or of dissolved Fe(II) or Fe(III). Pseudo-Voigt fits to blood-cell iron K-edge XAS spectra yielded 12.4 integrated units of preedge intensity, indicating a noncentrosymmetric environment. The non-phase-corrected extended X-ray absorption fine structure (EXAFS) Fourier transform spectrum showed a first-shell O/N peak at 1.55 angstroms and an intense Fe-Fe feature at 2.65 angstroms. Fits to the EXAFS required a split first shell with two O at 1.93 angstroms and three O at 2.07 angstroms, consistent with terminal and bridging alkoxide ligands, respectively. More distant shells included three C at 2.87 angstroms, two Fe at 3.08 angstroms, three O at 3.29 angstroms, and one Fe at 3.8 angstroms. Structural models consistent with these findings include a [Fe4(OR)13](2-/3-) broken-edged Fe4O5 cuboid or a [Fe4(OR)14](3-/4-) "Jacob's ladder" with three edge-fused Fe2(OR)2 rhombs. Either of these models represents an entirely new structural motif for biological iron. Vanadium domination of blood-cell metals cannot be a defining trait of Phlebobranch tunicates so long as P. annectens is included among them.

    View details for DOI 10.1021/ic051445x

    View details for Web of Science ID 000237593100018

    View details for PubMedID 16676950

  • Reinvestigation of the method used to map the electronic structure of blue copper proteins by NMR relaxation JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY Hansen, D. F., Gorelsky, S. I., Sarangi, R., Hodgson, K. O., Hedman, B., Christensen, H. E., SOLOMON, E. I., Led, J. J. 2006; 11 (3): 277-285


    A previous method for mapping the electron spin distribution in blue copper proteins by paramagnetic nuclear magnetic resonance (NMR) relaxation (Hansen DF, Led JJ, 2004, J Am Chem Soc 126:1247-1253) suggested that the blue copper site of plastocyanin from Anabaena variabilis (A.v.) is less covalent than those found for other plastocyanins by other experimental methods, such as X-ray absorption spectroscopy. Here, a detailed spectroscopic study revealed that the electronic structure of A.v. plastocyanin is similar to those of other plastocyanins. Therefore, the NMR approach was reinvestigated using a more accurate geometric structure as the basis for the mapping, in contrast to the previous approach, as well as a more complete spin distribution model including Gaussian-type natural atomic orbitals instead of Slater-type hydrogen-like atomic orbitals. The refinement results in a good agreement between the electron spin density derived from paramagnetic NMR and the electronic structure description obtained by the other experimental methods. The refined approach was evaluated against density functional theory (DFT) calculations on a model complex of the metal site of plastocyanin in the crystal phase. In general, the agreement between the experimental paramagnetic relaxation rates and the corresponding rates obtained by the DFT calculations is good. Small deviations are attributed to minor differences between the solution structure and the crystal structure outside the first coordination sphere. Overall, the refined approach provides a complementary experimental method for determining the electronic structure of paramagnetic metalloproteins, provided that an accurate geometric structure is available.

    View details for DOI 10.1007/s00775-005-0070-9

    View details for Web of Science ID 000236586000003

    View details for PubMedID 16432723

  • mu-eta(2):eta(2)-Peroxodicopper(II) complex with a secondary diamine ligand: A functional model of tyrosinase JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Mirica, L. M., Rudd, D. J., Vance, M. A., SOLOMON, E. I., Hodgson, K. O., Hedman, B., Stack, T. D. 2006; 128 (8): 2654-2665


    The activation of dioxygen (O(2)) by Cu(I) complexes is an important process in biological systems and industrial applications. In tyrosinase, a binuclear copper enzyme, a mu-eta(2):eta(2)-peroxodicopper(II) species is accepted generally to be the active oxidant. Reported here is the characterization and reactivity of a mu-eta(2):eta(2)-peroxodicopper(II) complex synthesized by reacting the Cu(I) complex of the secondary diamine ligand N,N'-di-tert-butyl-ethylenediamine (DBED), [(DBED)Cu(MeCN)](X) (1.X, X = CF(3)SO(3)(-), CH(3)SO(3)(-), SbF(6)(-), BF(4)(-)), with O(2) at 193 K to give [[Cu(DBED)](2)(O(2))](X)(2) (2.X(2)). The UV-vis and resonance Raman spectroscopic features of 2 vary with the counteranion employed yet are invariant with change of solvent. These results implicate an intimate interaction of the counteranions with the Cu(2)O(2) core. Such interactions are supported further by extended X-ray absorption fine structure (EXAFS) analyses of solutions that reveal weak copper-counteranion interactions. The accessibility of the Cu(2)O(2) core to exogenous ligands such as these counteranions is manifest further in the reactivity of 2 with externally added substrates. Most notable is the hydroxylation reactivity with phenolates to give catechol and quinone products. Thus the strategy of using simple bidentate ligands at low temperatures provides not only spectroscopic models of tyrosinase but also functional models.

    View details for DOI 10.1021/ja056740v

    View details for Web of Science ID 000235787200041

    View details for PubMedID 16492052

  • Structural insights into a protein-bound iron-molybdenum cofactor precursor PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Corbett, M. C., Hu, Y. L., Fay, A. W., Ribbe, M. W., Hedman, B., Hodgson, K. O. 2006; 103 (5): 1238-1243


    The iron-molybdenum cofactor (FeMoco) of the nitrogenase MoFe protein is a highly complex metallocluster that provides the catalytically essential site for biological nitrogen fixation. FeMoco is assembled outside the MoFe protein in a stepwise process requiring several components, including NifB-co, an iron- and sulfur-containing FeMoco precursor, and NifEN, an intermediary assembly protein on which NifB-co is presumably converted to FeMoco. Through the comparison of Azotobacter vinelandii strains expressing the NifEN protein in the presence or absence of the nifB gene, the structure of a NifEN-bound FeMoco precursor has been analyzed by x-ray absorption spectroscopy. The results provide physical evidence to support a mechanism for FeMoco biosynthesis. The NifEN-bound precursor is found to be a molybdenum-free analog of FeMoco and not one of the more commonly suggested cluster types based on a standard [4Fe-4S] architecture. A facile scheme by which FeMoco and alternative, non-molybdenum-containing nitrogenase cofactors are constructed from this common precursor is presented that has important implications for the biosynthesis and biomimetic chemical synthesis of FeMoco.

    View details for DOI 10.1073/pnas.0507853103

    View details for Web of Science ID 000235094300017

    View details for PubMedID 16423898

  • Sulfur K-Edge XAS and DFT calculations on nitrile hydratase: Geometric and electronic structure of the non-heme iron active site JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Dey, A., CHOW, M., Taniguchi, K., Lugo-Mas, P., Davin, S., Maeda, M., Kovacs, J. A., Odaka, M., Hodgson, K. O., Hedman, B., Solomon, E. I. 2006; 128 (2): 533-541


    The geometric and electronic structure of the active site of the non-heme iron enzyme nitrile hydratase (NHase) is studied using sulfur K-edge XAS and DFT calculations. Using thiolate (RS(-))-, sulfenate (RSO(-))-, and sulfinate (RSO(2)(-))-ligated model complexes to provide benchmark spectral parameters, the results show that the S K-edge XAS is sensitive to the oxidation state of S-containing ligands and that the spectrum of the RSO(-) species changes upon protonation as the S-O bond is elongated (by approximately 0.1 A). These signature features are used to identify the three cysteine residues coordinated to the low-spin Fe(III) in the active site of NHase as CysS(-), CysSOH, and CysSO(2)(-) both in the NO-bound inactive form and in the photolyzed active form. These results are correlated to geometry-optimized DFT calculations. The pre-edge region of the X-ray absorption spectrum is sensitive to the Z(eff) of the Fe and reveals that the Fe in [FeNO](6) NHase species has a Z(eff) very similar to that of its photolyzed Fe(III) counterpart. DFT calculations reveal that this results from the strong pi back-bonding into the pi antibonding orbital of NO, which shifts significant charge from the formally t(2)(6) low-spin metal to the coordinated NO.

    View details for DOI 10.1021/ja0549695

    View details for Web of Science ID 000234814900038

    View details for PubMedID 16402841

  • MXAN analysis of the XANES energy region of a mononuclear copper complex: Applications to bioinorganic systems INORGANIC CHEMISTRY Sarangi, R., Benfatto, M., Hayakawa, K., Bubacco, L., SOLOMON, E. I., Hodgson, K. O., Hedman, B. 2005; 44 (26): 9652-9659


    The near edge XAS spectra of the mononuclear copper complex [Cu(TMPA)(OH(2))](ClO(4))(2) (1) have been simulated using the multiple scattering edge simulation package MXAN (or Minuit XANes). These simulations, which employ the muffin-tin (MT) approximation, have been compared to simulations generated using the finite-difference method (FDM) to evaluate the effect of MT corrections. The sensitivity of the MXAN method was tested using structural models that included several different variations on the bond angles and bond distances for the first-shell atoms of 1. The sensitivity to small structural changes was also evaluated by comparing MXAN simulations of 1 and of structurally modified [Cu(TMPA)(L)](n)(+) complexes [where L = -O-(F(8)TPP)Fe(III), -F, -OPO(2)(O-p-nitrophenyl)Zn(II)(TMPA), and -NCMe] to the experimental data. The accuracy of the bond distances obtained from the MXAN simulations was then examined by comparison to the metrics of the crystal structures. The results show that MXAN can successfully extract geometric information from the edge structure of an XAS spectrum. The systematic application of MXAN to 1 indicates that this approach is sensitive to small structural changes in the molecule that are manifested in the XAS edge spectrum. These results represent the first step toward the application of this methodology to bioinorganic and biological systems.

    View details for DOI 10.1021/ic050703n

    View details for Web of Science ID 000234192300017

    View details for PubMedID 16363833

  • Sulfur K-edge XAS and DFT calculations on [Fe4S4](2+) clusters: Effects of H-bonding and structural distortion on covalency and spin topology INORGANIC CHEMISTRY Dey, A., Roche, C. L., Walters, M. A., Hodgson, K. O., Hedman, B., Solomon, E. I. 2005; 44 (23): 8349-8354


    Sulfur K-edge X-ray absorption spectroscopy of a hydrogen-bonded elongated [Fe4S4]2+ cube is reported. The data show that this synthetic cube is less covalent than a normal compressed cube with no hydrogen bonding. DFT calculations reveal that the observed difference in electronic structure has significant contributions from both the cluster distortion and from hydrogen bonding. The elongated and compressed Fe4S4 structures are found to have different spin topologies (i.e., orientation of the delocalized Fe2S2 subclusters which are antiferromagnetically coupled to each other). It is suggested that the H-bonding interaction with the counterion does not contribute to the cluster elongation. A magneto-structural correlation is developed for the Fe4S4 cube that is used to identify the redox-active Fe2S2 subclusters in active sites of HiPIP and ferredoxin proteins involving these clusters.

    View details for DOI 10.1021/ic050981m

    View details for Web of Science ID 000233180600029

    View details for PubMedID 16270973

  • Nitrogenase reactivity with P-cluster variants PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Hu, Y. L., Corbett, M. C., Fay, A. W., Webber, J. A., Hedman, B., Hodgson, K. O., Ribbe, M. W. 2005; 102 (39): 13825-13830


    Nitrogenase is a multicomponent metalloenzyme that catalyzes the conversion of atmospheric dinitrogen to ammonia. For decades, it has been generally believed that the [8Fe-7S] P-cluster of nitrogenase component 1 is indispensable for nitrogenase activity. In this study, we identified two catalytically active P-cluster variants by activity assays, metal analysis, and EPR spectroscopic studies. Further, we showed that both P-cluster variants resemble [4Fe-4S]-like centers based on x-ray absorption spectroscopic experiments. We believe that our findings challenge the dogma that the standard P-cluster is the only cluster species capable of supporting substrate reduction at the FeMo cofactor and provide important insights into the general mechanism of nitrogenase catalysis and assembly.

    View details for DOI 10.1073/pnas.0506967102

    View details for Web of Science ID 000232231900023

    View details for PubMedID 16166259

  • Geometric and electronic structure of the heme-peroxo-copper complex [(F8TPP)Fe-III-(O-2(2-))-Cu-II(TMPA)](CIO4) JOURNAL OF THE AMERICAN CHEMICAL SOCIETY del Rio, D., Sarangi, R., Chufan, E. E., Karlin, K. D., Hedman, B., Hodgson, K. O., Solomon, E. I. 2005; 127 (34): 11969-11978


    The geometric and electronic structure of the untethered heme-peroxo-copper model complex [(F(8)TPP)Fe(III)-(O(2)(2)(-))-Cu(II)(TMPA)](ClO(4)) (1) has been investigated using Cu and Fe K-edge EXAFS spectroscopy and density functional theory calculations in order to describe its geometric and electronic structure. The Fe and Cu K-edge EXAFS data were fit with a Cu...Fe distance of approximately 3.72 A. Spin-unrestricted DFT calculations for the S(T) = 2 spin state were performed on [(P)Fe(III)-(O(2)(2)(-))-Cu(II)(TMPA)](+) as a model of 1. The peroxo unit is bound end-on to the copper, and side-on to the high-spin iron, for an overall mu-eta(1):eta(2) coordination mode. The calculated Cu...Fe distance is approximately 0.3 A longer than that observed experimentally. Reoptimization of [(P)Fe(III)-(O(2)(2)(-))-Cu(II)(TMPA)](+) with a 3.7 A Cu...Fe constrained distance results in a similar energy and structure that retains the overall mu-eta(1):eta(2)-peroxo coordination mode. The primary bonding interaction between the copper and the peroxide involves electron donation into the half-occupied Cu d(z)2 orbital from the peroxide pi(sigma) orbital. In the case of the Fe(III)-peroxide eta(2) bond, the two major components arise from the donor interactions of the peroxide pi*(sigma) and pi*(v) orbitals with the Fe d(xz) and d(xy) orbitals, which give rise to sigma and delta bonds, respectively. The pi*(sigma) interaction with both the half-occupied d(z)2 orbital on the copper (eta(1)) and the d(xz) orbital on the iron (eta(2)), provides an effective superexchange pathway for strong antiferromagnetic coupling between the metal centers.

    View details for DOI 10.1021/ja043374r

    View details for Web of Science ID 000231605900044

    View details for PubMedID 16117536

  • A palladium-oxo complex. Stabilization of this proposed catalytic intermediate by an encapsulating polytungstate ligand JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Anderson, T. M., Cao, R., Slonkina, E., Hedman, B., Hodgson, K. O., Hardcastle, K. I., Neiwert, W. A., Wu, S. X., Kirk, M. L., Knottenbelt, S., Depperman, E. C., Keita, B., Nadjo, L., Musaev, D. G., Morokuma, K., Hill, C. L. 2005; 127 (34): 11948-11949


    A terminal Pd-oxo unit is reported. The unit is encapsulated in a cavity defined by two [A-alpha-PW9O34]9- units fused together by one [WO(OH2)]4+ center and forms from Pd(II) in buffered media in the presence of O2. Both X-ray diffraction and EXAFS data are consistent with a Pd-oxo bond distance of ca. 1.65 A. 17O NMR studies confirm that the solid-state structure is maintained in solution.

    View details for DOI 10.1021/ja054131h

    View details for Web of Science ID 000231605900035

    View details for PubMedID 16117527

  • Sulfur K-edge XAS and DFT calculations on P450 model complexes: Effects of hydrogen bonding on electronic structure and redox potentials JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Dey, A., Okamura, T., Ueyama, N., Hedman, B., Hodgson, K. O., Solomon, E. I. 2005; 127 (34): 12046-12053


    Hydrogen bonding (H-bonding) is generally thought to play an important role in tuning the electronic structure and reactivity of metal-sulfur sites in proteins. To develop a quantitative understanding of this effect, S K-edge X-ray absorption spectroscopy (XAS) has been employed to directly probe ligand-metal bond covalency, where it has been found that protein active sites are significantly less covalent than their related model complexes. Sulfur K-edge XAS data are reported here on a series of P450 model complexes with increasing H-bonding to the ligated thiolate from its substituent. The XAS spectroscopic results show a dramatic decrease in preedge intensity. DFT calculations reproduce these effects and show that the observed changes are in fact solely due to H-bonding and not from the inductive effect of the substituent on the thiolate. These calculations also indicate that the H-bonding interaction in these systems is mainly dipolar in nature. The -2.5 kcal/mol energy of the H-bonding interaction was small relative to the large change in ligand-metal bond covalency (30%) observed in the data. A bond decomposition analysis of the total energy is developed to correlate the preedge intensity change to the change in Fe-S bonding interaction on H-bonding. This effect is greater for the reduced than the oxidized state, leading to a 260 mV increase in the redox potential. A simple model shows that E degrees should vary approximately linearly with the covalency of the Fe-S bond in the oxidized state, which can be determined directly from S K-edge XAS.

    View details for DOI 10.1021/ja0519031

    View details for Web of Science ID 000231605900053

    View details for PubMedID 16117545

  • Spectroscopic and DFT investigation of [M{HB(3,5-(i)Pr(2)pz)(3)}(SC6F5)] (M = Mn, Fe, Co, Ni, Cu, and Zn) model complexes: Periodic trends in metal-thiolate bonding INORGANIC CHEMISTRY Gorelsky, S. I., Basumallick, L., Vura-Weis, J., Sarangi, R., Hodgson, K. O., Hedman, B., Fujisawa, K., Solomon, E. I. 2005; 44 (14): 4947-4960


    A series of metal-varied [ML(SC6F5)] model complexes (where L = hydrotris(3,5-diisopropyl-1-pyrazolyl)borate and M = Mn, Fe, Co, Ni, Cu, and Zn) related to blue copper proteins has been studied by a combination of absorption, MCD, resonance Raman, and S K-edge X-ray absorption spectroscopies. Density functional calculations have been used to characterize these complexes and calculate their spectra. The observed variations in geometry, spectra, and bond energies are interpreted in terms of changes in the nature of metal-ligand bonding interactions. The metal 3d-ligand orbital interaction, which contributes to covalent bonding in these complexes, becomes stronger going from Mn(II) to Co(II) (the sigma contribution) and to Cu(II) (the pi contribution). This change in the covalency results from the increased effective nuclear charge of the metal atom in going from Mn(II) to Zn(II) and the change in the 3d orbital populations (d5-->d10). Ionic bonding also plays an important role in determining the overall strength of the ML(+)-SC6F5(-) interaction. However, there is a compensating effect: as the covalent contribution to the metal-ligand bonding increases, the ionic contribution decreases. These results provide insight into the Irving-Williams series, where it is found that the bonding of the ligand being replaced by the thiolate makes a major contribution to the observed order of the stability constants over the series of metal ions.

    View details for DOI 10.1021/ic050371m

    View details for Web of Science ID 000230555400014

    View details for PubMedID 15998022

  • X-ray, absorption spectroscopic study of the reduced hydroxylases of methane monooxygenase and toluene/o-xylene monooxygenase: Differences in active site structure and effects of the coupling proteins MMOB and ToMOD INORGANIC CHEMISTRY Rudd, D. J., Sazinsky, M. H., LIPPARD, S. J., Hedman, B., Hodgson, K. O. 2005; 44 (13): 4546-4554


    The diiron active sites of the reduced hydroxylases from methane monooxygenase (MMOH(red)) and toluene/o-xylene monooxygenase (ToMOH(red)) have been investigated by X-ray absorption spectroscopy (XAS). Results of Fe K-edge and extended X-ray absorption fine structure analysis reveal subtle differences between the hydroxylases that may be correlated to access of the active site. XAS data were also recorded for each hydroxylase in the presence of its respective coupling protein. MMOB affects the outer-shell scattering contributions in the diiron site of MMOH(red), whereas ToMOD exerts its main effect on the first-shell ligation of ToMOH(red); it also causes a slight decrease in the Fe-Fe separation. These results provide an initial step toward delineating the differences in structure and reactivity in bacterial multicomponent monooxygenase proteins.

    View details for DOI 10.1021/ic048794w

    View details for Web of Science ID 000229982700019

    View details for PubMedID 15962961

  • Tyrosinase reactivity in a model complex: An alternative hydroxylation mechanism SCIENCE Mirica, L. M., Vance, M., Rudd, D. J., Hedman, B., Hodgson, K. O., Solomon, E. I., Stack, T. D. 2005; 308 (5730): 1890-1892


    The binuclear copper enzyme tyrosinase activates O2 to form a mu-eta2:eta2-peroxodicopper(II) complex, which oxidizes phenols to catechols. Here, a synthetic mu-eta2:eta2-peroxodicopper(II) complex, with an absorption spectrum similar to that of the enzymatic active oxidant, is reported to rapidly hydroxylate phenolates at -80 degrees C. Upon phenolate addition at extreme temperature in solution (-120 degrees C), a reactive intermediate consistent with a bis-mu-oxodicopper(III)-phenolate complex, with the O-O bond fully cleaved, is observed experimentally. The subsequent hydroxylation step has the hallmarks of an electrophilic aromatic substitution mechanism, similar to tyrosinase. Overall, the evidence for sequential O-O bond cleavage and C-O bond formation in this synthetic complex suggests an alternative intimate mechanism to the concerted or late stage O-O bond scission generally accepted for the phenol hydroxylation reaction performed by tyrosinase.

    View details for DOI 10.1126/science.1112081

    View details for Web of Science ID 000230120000034

    View details for PubMedID 15976297

  • Cooperativity and intermediates in the equilibrium reactions of Fe(II,III) with ethanethiolate in N-methylformamide solution JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY Frank, P., Hodgson, K. O. 2005; 10 (4): 373-382


    The reaction of FeCl(2) or FeCl(3) with sodium ethanethiolate (SEt) in N-methylformamide (NMF) has been reevaluated to rectify a previous Fe(II) oxidation artifact. On titrating Fe(II) with EtS(-) concentrations up to 12 mol Eq, new features in the UV/vis spectrum (epsilon(344)=(3.1+/-0.2)x10(3) M(-1) cm(-1); epsilon(486)=(4.5+/-0.1)x10(2) M(-1) cm(-1)) indicated that the first observable step was the formation of a single complex different from the known tetrahedral tetrathiolate, [Fe(SEt)(4)](2-) . As the EtS(-) concentration increased past 12.5 mol Eq the UV/vis spectrum gradually transformed to that of [Fe(SEt)(4)](2-) (lambda(max)=314 nm). A Hill-formalism fit to the titration data of the initially formed complex indicated cooperative ligation by three ethanethiolate ions, with K(coop)=(1.7+/-0.1)x10(3) M(-3) and Hill "n"=2.4+/-0.1 (r=0.997). The 3:1 EtS(-)-Fe(II) complex is proposed to be [Fe(2)(SEt)(6)](2-). Titration of Fe(III) with EtS(-) showed direct cooperative formation of [Fe(SEt)(4)](-) [epsilon(340)=(3.4+/-0.5)x10(3) M(-1) cm(-1)] with a Hill-formalism K(coop)=(4.3+/-0.1)x10(2) M(-4) and a Hill coefficient "n"=3.7+/-0.2 (r=0.996). Further ligation past [Fe(SEt)(4)](-) was observed at EtS(-) concentrations above 35 mol Eq. The Fe(III) Hill constants are at variance with our previous report. However, the UV/vis spectrum of Fe(III) in NMF solution was found to change systematically over time, consistent with a slow progressive deprotonation of [Fe(nmf)](3+). The observed time-to-time differences in the equilibrium chemistry of Fe(III) with ethanethiolate in NMF thus reflect variation in the microscopic solution composition of FeCl(3) in alkaline NMF solvent. These results are related to the chemistry of nitrogenase FeMo cofactor in alkaline NMF solution.

    View details for DOI 10.1007/s00775-005-0645-5

    View details for Web of Science ID 000229733600006

    View details for PubMedID 15864505

  • The solution structure of [Cu(aq)](2+) and its implications for rack-induced bonding in blue copper protein active INORGANIC CHEMISTRY Frank, P., Benfatto, M., Szilagyi, R. K., D'Angelo, P., Della Longa, S., Hodgson, K. O. 2005; 44 (6): 1922-1933


    The structure of [Cu(aq)]2+ has been investigated by using full multiple-scattering theoretical (MXAN) analysis of the copper K-edge X-ray absorption (XAS) spectrum and density functional theory (DFT) to test both ideal Td and square-planar four-coordinate, five-coordinate square-pyramidal, and six-coordinate octahedral [Cu(aq)]2+ models. The best fit was an elongated five-coordinate square pyramid with four Cu-O(eq) bonds (2 x 1.98 +/- 0.03 A and 2 x 1.95 +/- 0.03 A) and a long Cu-O(ax) bond (2.35 +/- 0.05 A). The four equatorial ligands were D2d-distorted from the mean equatorial plane by +/-(17 +/- 4) degrees, so that the overall symmetry of [Cu(H2O)5]2+ is C2v. The four-coordinate MXAN fit was nearly as good, but the water ligands (4 x 1.96 +/- 0.02 A) migrated +/-(13 +/- 4) degrees from the mean equatorial plane, making the [Cu(H2O)4]2+ model again D2d-distorted. Spectroscopically calibrated DFT calculations were carried out on the C2v elongate square-pyramidal and D2d-distorted four-coordinate MXAN copper models, providing comparative electronic structures of the experimentally observed geometries. These calculations showed 0.85e spin on Cu(II) and 0.03e electron spin on each of the four equatorial water oxygens. All covalent bonding was restricted to the equatorial plane. In the square-pyramidal model, the electrostatic Cu-O(ax) bond was worth only 96.8 kJ mol(-1), compared to 304.6 kJ mol(-1) for each Cu-O(eq) bond. Both MXAN and DFT showed the potential well of the axial bond to be broad and flat, allowing large low-energy excursions. The irregular geometry and D2d-distorted equatorial ligand set sustained by unconstrained [Cu(H2O)5]2+ warrants caution in drawing conclusions regarding structural preferences from small molecule crystal structures and raises questions about the site-structural basis of the rack-induced bonding hypothesis of blue copper proteins. Further, previously neglected protein folding thermodynamic consequences of the rack-bonding hypothesis indicate an experimental disconfirmation.

    View details for DOI 10.1021/ic0400639

    View details for Web of Science ID 000227764700029

    View details for PubMedID 15762718

  • Spectroscopic and density functional studies of the red copper site in nitrosocyanin: Role of the protein in determining active site geometric and electronic structure JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Basumallick, L., Sarangi, R., George, S. D., Elmore, B., Hooper, A. B., Hedman, B., Hodgson, K. O., Solomon, E. I. 2005; 127 (10): 3531-3544


    The electronic structure of the red copper site in nitrosocyanin is defined relative to that of the well understood blue copper site of plastocyanin by using low-temperature absorption, circular dichroism, magnetic circular dichroism, resonance Raman, EPR and X-ray absorption spectroscopies, combined with DFT calculations. These studies indicate that the principal electronic structure change in the red copper site is the sigma rather than the pi donor interaction of the cysteine sulfur with the Cu 3d(x2-y2) redox active molecular orbital (RAMO). Further, MCD data show that there is an increase in ligand field strength due to an increase in coordination number, whereas resonance Raman spectra indicate a weaker Cu-S bond. The latter is supported by the S K-edge data, which demonstrate a less covalent thiolate interaction with the RAMO of nitrosocyanin at 20% relative to plastocyanin at 38%. EXAFS results give a longer Cu-S(Cys) bond distance in nitrosocyanin (2.28 A) compared to plastocyanin (2.08 A) and also show a large change in structure with reduction of the red copper site. The red copper site is the only presently known blue copper-related site with an exogenous water coordinated to the copper. Density functional calculations reproduce the experimental properties and are used to determine the specific protein structure contributions to exogenous ligand binding in red copper. The relative orientation of the CuNNS and the CuSC(beta) planes (determined by the protein sequence) is found to be key in generating an exchangeable coordination position at the red copper active site. The exogenous water ligation at the red copper active site greatly increases the reorganization energy (by approximately 1.0 eV) relative to that of the blue copper protein site, making the red site unfavorable for fast outer-sphere electron transfer, while providing an exchangeable coordination position for inner-sphere electron transfer.

    View details for DOI 10.1021/ja044412+

    View details for Web of Science ID 000227627800062

    View details for PubMedID 15755175

  • X-ray absorption spectroscopic investigation of the spin-transition character in a series of single-site perturbed iron(II) complexes INORGANIC CHEMISTRY Rudd, D. J., Goldsmith, C. R., Cole, A. P., Stack, D. P., Hodgson, K. O., Hedman, B. 2005; 44 (5): 1221-1229


    Select ferrous spin-transition complexes with the pentadentate ligand 2,6-bis(bis(2-pyridyl)methoxymethane)pyridine (PY5) were examined using variable-temperature solution solid-state magnetic susceptibility, crystallography, X-ray absorption spectroscopy (XAS), and UV/vis absorption spectroscopy. Altering the single exogeneous ligand, X, of [Fe(PY5)(X)]n)+ is sufficient to change the spin-state of the complexes. When X is the weak-field ligand Cl-, the resultant Fe complex is high-spin from 4 to 300 K, whereas the stronger-field ligand MeCN generates a low-spin complex over this temperature range. With intermediate-strength exogenous ligands (X = N3-, MeOH), the complexes undergo a spin-transition. [Fe(PY5)(N3)]+, as a crystalline solid, transitions gradually from a high-spin to a low-spin complex as the temperature is decreased, as evidenced by X-ray crystallography and solid-state magnetic susceptibility measurements. The spin-transition is also evident from changes in the pre-edge and EXAFS regions of the XAS Fe K-edge spectra on a ground crystalline sample. The spin-transition observed with [Fe(PY5)(MeOH)]2+ appears abrupt by solid-state magnetic susceptibility measurements, but gradual by XAS analysis, differences attributed to sample preparation. This research highlights the strengths of XAS in determining the electronic and geometric structure of such spin-transition complexes and underscores the importance of identical sample preparation in the investigation of these physical properties.

    View details for DOI 10.1021/ic0487651

    View details for Web of Science ID 000227346300021

    View details for PubMedID 15732962

  • Mo K- and L-edge X-ray absorption spectroscopic study of the ADP.AlF4--stabilized nitrogenase complex: comparison with MoFe protein in solution and single crystal. Journal of synchrotron radiation Corbett, M. C., Tezcan, F. A., Einsle, O., Walton, M. Y., Rees, D. C., Latimer, M. J., Hedman, B., Hodgson, K. O. 2005; 12: 28-34


    The utility of using X-ray absorption spectroscopy (XAS) to study metalloproteins and, specifically, the enzyme complex nitrogenase, is highlighted by this study comparing both the structural and Mo-localized electronic features of the iron-molybdenum cofactor (FeMoco) in isolated MoFe protein and in the ADP.AlF4--stabilized complex of the MoFe protein with the Fe protein. No major differences are found at Mo between the two protein forms. The excellent quality of the data at both the Mo K and L edges will provide a baseline for analysis of other intermediates in the nitrogenase cycle. A new capability to delineate various contributions in the resting state of FeMoco is being pursued through polarized single-crystal XAS. The initial results point to the feasibility of using this technique for the analysis of scattering from the as yet unidentified atom at the center of FeMoco.

    View details for PubMedID 15616362

  • Metallogenomics and biological X-ray absorption spectroscopy JOURNAL OF SYNCHROTRON RADIATION Ascone, I., Fourme, R., Hasnain, S., Hodgson, K. 2005; 12: 1-3


    An overview of the second special issue of the journal on biological applications of X-ray absorption spectroscopy (BioXAS) is presented. The emphasis is on the study of metalloproteins in the context of structural genomics programmes (metallogenomics).

    View details for DOI 10.1107/S0909049504033412

    View details for Web of Science ID 000225960900001

    View details for PubMedID 15616356

  • MoK- and L-edge X-ray absorption spectroscopic study of the ADP center dot AIF(4)(-)-stabilized nitrogenase complex: comparison with MoFe protein in solution and single crystal JOURNAL OF SYNCHROTRON RADIATION Corbett, M. C., Tezcan, F. A., Einsle, O., Walton, M. Y., Rees, D. C., Latimer, M. J., Hedman, B., Hodgson, K. O. 2005; 12: 28-34
  • Investigation of the local structure of Fe(II) bleomycin and peplomycins using theoretical analysis of XANES PHYSICA SCRIPTA Smolentsev, G., Soldatov, A. V., Wasinger, E., Solomon, E., Hodgson, K., Hedman, B. 2005; T115: 862-863
  • Ligand K-edge X-ray absorption spectroscopy: covalency of ligand-metal bonds COORDINATION CHEMISTRY REVIEWS Solomon, E. I., Hedman, B., Hodgson, K. O., Dey, A., Szilagyi, R. K. 2005; 249 (1-2): 97-129
  • Ligand K-edge X-ray absorption spectroscopy and DFT calculations on [Fe3S4](0,+) clusters: Delocalization, redox, and effect of the protein environment JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Dey, A., Glaser, T., Moura, J. J., HOLM, R. H., Hedman, B., Hodgson, K. O., Solomon, E. I. 2004; 126 (51): 16868-16878


    Ligand K-edge XAS of an [Fe3S4]0 model complex is reported. The pre-edge can be resolved into contributions from the mu(2)S(sulfide), mu(3)S(sulfide), and S(thiolate) ligands. The average ligand-metal bond covalencies obtained from these pre-edges are further distributed between Fe(3+) and Fe(2.5+) components using DFT calculations. The bridging ligand covalency in the [Fe2S2]+ subsite of the [Fe3S4]0 cluster is found to be significantly lower than its value in a reduced [Fe2S2] cluster (38% vs 61%, respectively). This lowered bridging ligand covalency reduces the superexchange coupling parameter J relative to its value in a reduced [Fe2S2]+ site (-146 cm(-1) vs -360 cm(-1), respectively). This decrease in J, along with estimates of the double exchange parameter B and vibronic coupling parameter lambda2/k(-), leads to an S = 2 delocalized ground state in the [Fe3S4]0 cluster. The S K-edge XAS of the protein ferredoxin II (Fd II) from the D. gigas active site shows a decrease in covalency compared to the model complex, in the same oxidation state, which correlates with the number of H-bonding interactions to specific sulfur ligands present in the active site. The changes in ligand-metal bond covalencies upon redox compared with DFT calculations indicate that the redox reaction involves a two-electron change (one-electron ionization plus a spin change of a second electron) with significant electronic relaxation. The presence of the redox inactive Fe(3+) center is found to decrease the barrier of the redox process in the [Fe3S4] cluster due to its strong antiferromagnetic coupling with the redox active Fe2S2 subsite.

    View details for DOI 10.1021/ja0466208

    View details for Web of Science ID 000225910400045

    View details for PubMedID 15612726

  • Dioxygen activation at a single copper site: Structure, bonding, and mechanism of formation of 1 : 1 Cu-O-2 adducts JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Aboelella, N. W., Kryatov, S. V., Gherman, B. F., Brennessel, W. W., Young, V. G., Sarangi, R., Rybak-Akimova, E. V., Hodgson, K. O., Hedman, B., SOLOMON, E. I., Cramer, C. J., Tolman, W. B. 2004; 126 (51): 16896-16911


    To evaluate the fundamental process of O(2) activation at a single copper site that occurs in biological and catalytic systems, a detailed study of O(2) binding to Cu(I) complexes of beta-diketiminate ligands L (L(1) = backbone Me; L(2) = backbone tBu) by X-ray crystallography, X-ray absorption spectroscopy (XAS), cryogenic stopped-flow kinetics, and theoretical calculations was performed. Using synchrotron radiation, an X-ray diffraction data set for L(2)CuO(2) was acquired, which led to structural parameters in close agreement to theoretical predictions. Significant Cu(III)-peroxo character for the complex was corroborated by XAS. On the basis of stopped-flow kinetics data and theoretical calculations for the oxygenation of L(1)Cu(RCN) (R = alkyl, aryl) in THF and THF/RCN mixtures between 193 and 233 K, a dual pathway mechanism is proposed involving (a) rate-determining solvolysis of RCN by THF followed by rapid oxygenation of L(1)Cu(THF) and (b) direct, bimolecular oxygenation of L(1)Cu(RCN) via an associative process.

    View details for DOI 10.1021/ja045678j

    View details for Web of Science ID 000225910400048

    View details for PubMedID 15612729

  • High covalence in CuSO4 and the radicalization of sulfate: An X-ray absorption and density functional study INORGANIC CHEMISTRY Szilagyi, R. K., Frank, P., George, S. D., Hedman, B., Hodgson, K. O. 2004; 43 (26): 8318-8329


    Sulfur K-edge X-ray absorption spectroscopy (XAS) of anhydrous CuSO(4) reveals a well-resolved preedge transition feature at 2478.8 eV that has no counterpart in the XAS spectra of anhydrous ZnSO(4) or copper sulfate pentahydrate. Similar but weaker preedge features occur in the sulfur K-edge XAS spectra of [Cu(itao)SO(4)] (2478.4 eV) and [Cu[(CH(3))(6)tren]SO(4)] (2477.7 eV). Preedge features in the XAS spectra of transition metal ligands are generally attributed to covalent delocalization of a metal d-orbital hole into a ligand-based orbital. Copper L-edge XAS of CuSO(4) revealed that 56% of the Cu(II) 3d hole is delocalized onto the sulfate ligand. Hybrid density functional calculations on the two most realistic models of the covalent delocalization pathways in CuSO(4) indicate about 50% electron delocalization onto the sulfate oxygen-based 2p orbitals; however, at most 14% of that can be found on sulfate sulfur. Both experimental and computational results indicated that the high covalence of anhydrous CuSO(4) has made sulfate more like the radical monoanion, inducing an extensive mixing and redistribution of sulfur 3p-based unoccupied orbitals to lower energy in comparison to sulfate in ZnSO(4). It is this redistribution, rather than a direct covalent interaction between Cu(II) and sulfur, that is the origin of the observed sulfur XAS preedge feature. From pseudo-Voigt fits to the CuSO(4) sulfur K-edge XAS spectrum, a ground-state 3p character of 6% was quantified for the orbital contributing to the preedge transition, in reasonable agreement with the DFT calculation. Similar XAS fits indicated 2% sulfur 3p character for the preedge transition orbitals in [Cu(itao)SO(4)] and [Cu[(CH(3))(6)tren]SO(4)]. The covalent radicalization of ligands similar to sulfate, with consequent energy redistribution of the virtual orbitals, represents a new mechanism for the induction of ligand preedge XAS features. The high covalence of the Cu sites in CuSO(4) was found to be similar to that of Cu sites in oxidized cupredoxins, including its anistropic nature, and can serve as the simplest inorganic examples of intramolecular electron-transfer processes.

    View details for DOI 10.1021/ic030311l

    View details for Web of Science ID 000225906700024

    View details for PubMedID 15606178

  • Determination by X-ray absorption spectroscopy of the Fe-Fe separation in the oxidized form of the hydroxylase of methane monooxygenase alone and in the presence of MMOD INORGANIC CHEMISTRY Rudd, D. J., Sazinsky, M. H., Merkx, M., LIPPARD, S. J., Hedman, B., Hodgson, K. O. 2004; 43 (15): 4579-4589


    The diiron active site in the hydroxylase of Methylococcus capsulatus (Bath) methane monooxygenase (MMOH) has been studied in the oxidized form by X-ray absorption spectroscopy (XAS). Previous investigations by XAS and X-ray crystallography have identified two different distances (3.0 and 3.4 angstroms) between the two Fe atoms in the dinuclear site. The present study has employed a systematic extended X-ray absorption fine structure (EXAFS) fitting methodology, utilizing known and simulated active site and relevant model structures, to determine unambiguously the Fe-Fe separation in the oxidized form of MMOH. Consistent and unique fits were only possible for an Fe-Fe distance of 3.0 angstroms. This methodology was then applied to study potential changes in the active site local structure in the presence of MMOD, a protein of unknown function in multicomponent MMO. Fe K-edge and EXAFS analyses revealed negligible changes in the diiron site electronic and geometric structure upon addition of MMOD to oxidized MMOH.

    View details for DOI 10.1021/ic049716b

    View details for Web of Science ID 000222846300015

    View details for PubMedID 15257585

  • Ligand K-Edge X-ray absorption spectroscopy of [Fe4S4](1+,2+,3+) clusters: Changes in bonding and electronic relaxation upon redox JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Dey, A., Glaser, T., Couture, M. M., Eltis, L. D., HOLM, R. H., Hedman, B., Hodgson, K. O., Solomon, E. I. 2004; 126 (26): 8320-8328


    Sulfur K-edge X-ray absorption spectroscopy (XAS) is reported for [Fe(4)S(4)](1+,2+,3+) clusters. The results are quantitatively and qualitatively compared with DFT calculations. The change in covalency upon redox in both the [Fe(4)S(4)](1+/2+) (ferredoxin) and the [Fe(4)S(4)](2+/3+) (HiPIP) couple are much larger than that expected from just the change in number of 3d holes. Moreover, the change in the HiPIP couple is higher than that of the ferredoxin couple. These changes in electronic structure are analyzed using DFT calculations in terms of contributions from the nature of the redox active molecular orbital (RAMO) and electronic relaxation. The results indicate that the RAMO of HiPIP has 50% ligand character, and hence, the HiPIP redox couple involves limited electronic relaxation. Alternatively, the RAMO of the ferredoxin couple is metal-based, and the ferredoxin redox couple involves extensive electronic relaxation. The contributions of these RAMO differences to ET processes in the different proteins are discussed.

    View details for Web of Science ID 000222405400058

    View details for PubMedID 15225075

  • Comparison of iron-molybdenum cofactor-deficient nitrogenase MoFe proteins by X-ray absorption spectroscopy - Implications for P-cluster biosynthesis JOURNAL OF BIOLOGICAL CHEMISTRY Corbett, M. C., Hu, Y. L., Naderi, F., Ribbe, M. W., Hedman, B., Hodgson, K. O. 2004; 279 (27): 28276-28282


    Nitrogenase, the enzyme system responsible for biological nitrogen fixation, is believed to utilize two unique metalloclusters in catalysis. There is considerable interest in understanding how these metalloclusters are assembled in vivo. It has been presumed that immature iron-molybdenum cofactor-deficient nitrogenase MoFe proteins contain the P-cluster, although no biosynthetic pathway for the assembly of this complex cluster has been identified as yet. Through the comparison by iron K-edge x-ray absorption edge and extended fine structure analyses of cofactor-deficient MoFe proteins resulting from nifH and nifB deletion strains of Azotobacter vinelandii, a novel [Fe-S] cluster is identified in the DeltanifH MoFe protein. The iron-iron scattering displayed by the DeltanifH MoFe protein is more similar to that of a standard [Fe(4)S(4)]-containing protein than that of the DeltanifB MoFe protein, which is shown to contain a "normal" P-cluster. The iron-sulfur scattering of the DeltanifH MoFe protein, however, indicates differences in its cluster from an [Fe(4)S(4)](Cys)(4) site that may be consistent with the presence of either oxygenic or nitrogenic ligation. Based on these results, models for the [Fe-S] center in the DeltanifH MoFe protein are constructed, the most likely of which consist of two separate [Fe(4)S(4)] sites, each with some non-cysteinyl coordination. This type of model suggests that the P-cluster is formed by the condensation of two [Fe(4)S(4)] fragments, possibly concomitant with Fe protein (NifH)-induced conformational change.

    View details for DOI 10.1074/jbc.M403156200

    View details for Web of Science ID 000222265400058

    View details for PubMedID 15102840

  • Future possibilities of the Linac Coherent Light Source JOURNAL OF SYNCHROTRON RADIATION Cornacchia, M., ARTHUR, J., Bane, K., Bolton, P., Carr, R., Decker, F. J., Emma, P., Galayda, J., Hastings, J., Hodgson, K., Huang, Z., LINDAU, I., Nuhn, H. D., Paterson, J. M., Pellegrini, C., Reiche, S., Schlarb, H., Stohr, J., Stupakov, G., Walz, D., Winick, H. 2004; 11: 227-238


    A study of the potential for the development of the Linac Coherent Light Source (LCLS) beyond the specifications of the baseline design is presented. These future developments include delivery of X-ray pulses in the 1 fs regime, extension of the spectral range, increase of the FEL power, exploitation of the spontaneous emission, and a more flexible time structure. As this potential is exploited, the LCLS can maintain its role as a world-leading instrument for many years beyond its commissioning in 2008 and initial operation as the world's first X-ray free-electron laser.

    View details for DOI 10.1107/S090904950400370X

    View details for Web of Science ID 000220974600001

    View details for PubMedID 15103109

  • S K-edge X-ray absorption spectroscopic investigation of the Ni-containing superoxide dismutase active site: New structural insight into the mechanism JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Szilagyi, R. K., Bryngelson, P. A., Maroney, M. J., Hedman, B., Hodgson, K. O., Solomon, E. I. 2004; 126 (10): 3018-3019


    Superoxide dismutases protect cells from the toxic effects of reactive oxygen species derived from superoxide. Nickel-containing superoxide dismutases (NiSOD), found in Streptomyces species and in cyanobacteria, are distinct from Mn-, Fe-, or Cu/Zn-containing SODs in amino acid sequence and metal ligand environment. Sulfur K-edge X-ray absorption spectroscopic investigations were carried out for a series of mono- and binuclear Ni model compounds with varying sulfur ligation, and for oxidized and reduced NiSOD to elucidate the types of Ni-S interactions found in the two oxidation states. The S K-edge XAS spectra clearly indicate the presence of Ni(III)-bound terminal thiolate in the oxidized enzyme and the absence of such coordination to Ni(II) in the peroxide-reduced enzyme. This striking change in the S ligation for Ni with redox suggests that, upon peroxide reduction, an electron is transferred to the Ni(III) site and the terminal thiolate becomes protonated, providing an efficient mechanism for proton-coupled electron transfer.

    View details for DOI 10.1021/ja039106v

    View details for Web of Science ID 000220192000007

    View details for PubMedID 15012109

  • Taking X-ray diffraction to the limit: Macromolecular structures from femtosecond X-ray pulses and diffraction microscopy of cells with synchrotron radiation ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE Miao, J. W., Chapman, H. N., Kirz, J., Sayre, D., Hodgson, K. O. 2004; 33: 157-176


    Recent work is extending the methodology of X-ray crystallography to the structure determination of noncrystalline specimens. The phase problem is solved using the oversampling method, which takes advantage of "continuous" diffraction patterns from noncrystalline specimens. Here we review the principle of this newly developed technique and discuss the ongoing experiments of imaging nonperiodic objects, such as cells and cellular structures, using coherent and bright X rays produced by third-generation synchrotron sources. In the longer run, the technique may be applicable to image single biomolecules using anticipated X-ray free electron lasers. Here, computer simulations have so far demonstrated two important steps: (a) by using an extremely intense femtosecond X-ray pulse, a diffraction pattern can be recorded from a macromolecule before radiation damage manifests itself; and (b) the phase information can be retrieved in an ab initio fashion from a set of calculated noisy diffraction patterns of single protein molecules.

    View details for Web of Science ID 000222339700010

    View details for PubMedID 15139809

  • L-edge X-ray absorption spectroscopy of non-heme iron sites: Experimental determination of differential orbital covalency JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Wasinger, E. C., de Groot, F. M., Hedman, B., Hodgson, K. O., Solomon, E. I. 2003; 125 (42): 12894-12906


    X-ray absorption spectroscopy has been utilized to obtain the L-edge multiplet spectra for a series of non-heme ferric and ferrous complexes. Using these data, a methodology for determining the total covalency and the differential orbital covalency (DOC), that is, differences in covalency in the different symmetry sets of the d orbitals, has been developed. The integrated L-edge intensity is proportional to the number of one-electron transition pathways to the unoccupied molecular orbitals as well as to the covalency of the iron site, which reduces the total L-edge intensity and redistributes intensity, producing shake-up satellites. Furthermore, differential orbital covalency leads to differences in intensity for the different symmetry sets of orbitals and, thus, further modifies the experimental spectra. The ligand field multiplet model commonly used to simulate L-edge spectra does not adequately reproduce the spectral features, especially the charge transfer satellites. The inclusion of charge transfer states with differences in covalency gives excellent fits to the data and experimental estimates of the different contributions of charge transfer shake-up pathways to the t(2g) and e(g) symmetry orbitals. The resulting experimentally determined DOC is compared to values calculated from density functional theory and used to understand chemical trends in high- and low-spin ferrous and ferric complexes with different covalent environments. The utility of this method toward problems in bioinorganic chemistry is discussed.

    View details for DOI 10.1021/ja034634s

    View details for Web of Science ID 000185990300050

    View details for PubMedID 14558838

  • Spectroscopic and electronic structure studies of 2,3-dihydroxybiphenyl 1,2-dioxygenase: O-2 reactivity of the non-heme ferrous site in extradiol dioxygenases JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Davis, M. I., Wasinger, E. C., Decker, A., Pau, M. Y., Vaillancourt, F. H., Bolin, J. T., Eltis, L. D., Hedman, B., Hodgson, K. O., Solomon, E. I. 2003; 125 (37): 11214-11227


    The extradiol dioxygenase, 2,3-dihydroxybiphenyl 1,2-dioxygenase (DHBD, EC, has been studied using magnetic circular dichroism (MCD), variable-temperature variable-field (VTVH) MCD, X-ray absorption (XAS) pre-edge, and extended X-ray absorption fine structure (EXAFS) spectroscopies, which are analogous to methods used in earlier studies on the extradiol dioxygenase catechol 2,3-dioxygenase [Mabrouk et al. J. Am. Chem Soc. 1991, 113, 4053-4061]. For DHBD, the spectroscopic data can be correlated to the results of crystallography and with the results from density functional calculations to obtain detailed geometric and electronic structure descriptions of the resting and substrate (DHB) bound forms of the enzyme. The geometry of the active site of the resting enzyme, square pyramidal with a strong Fe-glutamate bond in the equatorial plane, localizes the redox active orbital in an orientation appropriate for O(2) binding. However, the O(2) reaction is not favorable, as it would produce a ferric superoxide intermediate with a weak Fe-O bond. Substrate binding leads to a new square pyramidal structure with the strong Fe-glutamate bond in the axial direction as indicated by a decrease in the (5)E(g) and increase in the (5)T(2g) splitting. Electronic structure calculations provide insight into the relative lack of dioxygen reactivity for the resting enzyme and its activation upon substrate binding.

    View details for DOI 10.1021/ja029746i

    View details for Web of Science ID 000185341800039

    View details for PubMedID 16220940

  • Spectroscopic investigation of stellacyanin mutants: Axial ligand interactions at the blue copper site JOURNAL OF THE AMERICAN CHEMICAL SOCIETY George, S. D., Basumallick, L., Szilagyi, R. K., Randall, D. W., Hill, M. G., Nersissian, A. M., Valentine, J. S., Hedman, B., Hodgson, K. O., Solomon, E. I. 2003; 125 (37): 11314-11328


    Detailed electronic and geometric structural descriptions of the blue copper sites in wild-type (WT) stellacyanin and its Q99M and Q99L axial mutants have been obtained using a combination of XAS, resonance Raman, MCD, EPR, and DFT calculations. The results show that the origin of the short Cu-S(Cys) bond in blue copper proteins is the weakened axial interaction, which leads to a shorter (based on EXAFS results) and more covalent (based on S K-edge XAS) Cu-S bond. XAS pre-edge energies show that the effective nuclear charge on the copper increases going from O(Gln) to S(Met) to no axial (Leu) ligand, indicating that the weakened axial ligand is not fully compensated for by the increased donation from the thiolate. This is further supported by EPR results. MCD data show that the decreased axial interaction leads to an increase in the equatorial ligand field, indicating that the site acquires a more trigonally distorted tetrahedral structure. These geometric and electronic structural changes, which result from weakening the bonding interaction of the axial ligand, allow the site to maintain efficient electron transfer (high H(DA) and low reorganization energy), while modulating the redox potential of the site to the biologically relevant range. These spectroscopic studies are complemented by DFT calculations to obtain insight into the factors that allow stellacyanin to maintain a trigonally distorted tetrahedral structure with a relatively strong axial Cu(II)-oxygen bond.

    View details for DOI 10.1021/ja035802j

    View details for Web of Science ID 000185341800053

    View details for PubMedID 16220954

  • Spectroscopic studies of the interaction of ferrous bleomycin with DNA JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Kemsley, J. N., Zaleski, K. L., Chow, M. S., Decker, A., Shishova, E. Y., Wasinger, E. C., Hedman, B., Hodgson, K. O., Solomon, E. I. 2003; 125 (36): 10810-10821


    Bleomycin is an antibiotic used in cancer chemotherapy for its ability to achieve both single- and double-strand cleavage of DNA through abstraction of the deoxyribose C4'-H. Magnetic circular dichroism (MCD) and X-ray absorption (XAS) spectroscopies have been used to study the interaction of the biologically relevant FeIIBLM complex with DNA. Calf thymus DNA was used as the substrate as well as short oligonucleotides, including one with a preferred 5'-G-pyrimidine-3' cleavage site [d(GGAAGCTTCC)2] and one without [d(GGAAATTTCC)2]. DNA binding to FeIIBLM significantly perturbs the FeII active site, resulting in a change in intensity ratio of the d d transitions and a decrease in excited-state orbital splitting (5Eg). Although this effect is somewhat dependent on length and composition of the oligonucleotide, it is not correlated to the presence of a 5'-G-pyrimidine-3' cleavage site. No effect is observed on the charge-transfer transitions, indicating that the H-bonding recognition between the pyrimidine and guanine base does not perturb Fe-pyrimidine backbonding. Azide binding studies indicate that FeIIBLM bound to either oligomer has the same affinity for N3-. Parallel studies of BLM structural derivatives indicate that FeIIiso-PEPLM, in which the carbamoyl group is shifted on the mannose sugar, forms the same DNA-bound species as FeIIBLM. In contrast, FeIIDP-PEPLM, in which the -aminoalanine group is absent, forms a new species upon DNA binding. These data are consistent with a model in which the primary amine from the -aminoalanine is an FeII ligand and the mannose carbamoyl provides either a ligand to the FeII or significant second-sphere effects on the FeII site; intercalation of the bithiazole tail into the double helix likely brings the metal-bound complex close enough to the DNA to create steric interactions that remove the sugar groups from interaction with the FeII. The fact that the FeII active site is perturbed regardless of DNA sequence is consistent with the fact that cleavage is observed for both 5'-GC-3' and nonspecific oligomers and indicates that different reaction coordinates may be active, depending on orientation of the deoxyribose C4'-H.

    View details for DOI 10.1021/ja034579n

    View details for Web of Science ID 000185154300021

    View details for PubMedID 12952460

  • X-ray absorption spectroscopy of a structural analogue of the oxidized active sites in the sulfite oxidase enzyme family and related molybdenum(V) complexes INORGANIC CHEMISTRY Jalilehvand, F., Lim, B. S., HOLM, R. H., Hedman, B., Hodgson, K. O. 2003; 42 (18): 5531-5536


    X-ray absorption spectroscopy (XAS) (edge and extended X-ray absorption fine structure (EXAFS)) has been applied to the characterization of three molybdenum(V,VI) monodithiolene complexes with unidentate coligands, [MoO(SC(6)H(2)-2,4,6-Pr(i)()(3))(2)(bdt)](-) (1), [MoOCl(SC(6)H(2)-2,4,6-Pr(i)(3))(bdt)](-) (2), and [MoO(2)(SC(6)H(2)-2,4,6-Pr(i)(3))(bdt)](-) (3) (bdt = benzene-1,2-dithiolate). These complexes are related to the active site in the xanthine oxidase and sulfite oxidase families and, as in the enzyme sites, bind monodentate thiolate. By comparison to the data of crystalline oxidized chicken sulfite oxidase, it is shown that complex 3, whose thiolate simulates binding by the highly conserved cysteine, is an accurate structural analogue of the oxidized site of this enzyme. Normalized edge spectra, EXAFS data, Fourier transforms, and GNXAS-based fit results are presented. As in earlier studies, this provides characterization of new analogue complexes by XAS to facilitate identification of related sites in proteins.

    View details for DOI 10.1021/ic030039f

    View details for Web of Science ID 000185219500019

    View details for PubMedID 12950200

  • Description of the ground state wave functions of Ni dithiolenes using sulfur K-edge X-ray absorption spectroscopy JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Szilagyi, R. K., Lim, B. S., Glaser, T., Holm, R. H., Hedman, B., Hodgson, K. O., Solomon, E. I. 2003; 125 (30): 9158-9169


    The pterin-dithiolene cofactor is an essential component of the catalytic sites of all molybdoenzymes except nitrogenase. Understanding its bonding to transition metals allows for development of electronic structure/function correlations in catalysis. The electronic structure description for a series of bis(dithiolene) complexes ([NiL(2)](Z)(), L = 1,2-Me(2)C(2)S(2); Z = 2-, 1-, 0) using sulfur XAS provides the basis for extension to the biologically relevant metal-containing dithiolenes. The transition dipole integral has been developed for the dithiolene sulfur through correlation of XAS pre-edge energy positions of sulfide-, thiolate-, and enedithiolate-S. The ground state wave functions of all three NiL(2) complexes have more than 50% S character experimentally demonstrating the noninnocent behavior of the dithiolene ligand. The S K-edge experimental results are correlated with spin-unrestricted, broken-symmetry density functional calculations. These show only limited spin polarization in the neutral complex and delocalized, ligand based ground states for the mono- and dianionic complexes. These XAS and DFT results are correlated with other spectroscopic features and provide insight into reactivity.

    View details for DOI 10.1021/ja029806k

    View details for Web of Science ID 000184364500049

    View details for PubMedID 15369373

  • Direct determination of the absolute electron density of nanostructured and disordered materials at sub-10-nm resolution PHYSICAL REVIEW B Miao, J., Amonette, J. E., Nishino, Y., Ishikawa, T., Hodgson, K. O. 2003; 68 (1)
  • Spectroscopic and kinetic studies of PKU-inducing mutants of phenylalanine hydroxylase: Arg158Gln and Glu280Lys JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Kemsley, J. N., Wasinger, E. C., Datta, S., Mitic, N., Acharya, T., Hedman, B., Caradonna, J. P., Hodgson, K. O., SOLOMON, E. I. 2003; 125 (19): 5677-5686


    Phenylalanine hydroxylase (PAH) is a tetrahydrobiopterin-dependent, nonheme iron enzyme that catalyzes the hydroxylation of L-Phe to L-Tyr in the rate-limiting step of phenylalanine catabolism. This reaction is tightly coupled in the wild-type enzyme to oxidation of the tetrahydropterin cofactor. Dysfunction of PAH activity in humans leads to the disease phenylketonuria (PKU). We have investigated two PKU-inducing mutants, Arg158Gln and Glu280Lys, using kinetic methods, magnetic circular dichrosim (MCD) spectroscopy, and X-ray absorption spectroscopy (XAS). Analysis of the products produced by the mutant enzymes shows that although both oxidize pterin at more than twice the rate of wild-type enzyme, these reactions are only approximately 20% coupled to production of L-Tyr. Previous MCD and XAS studies had demonstrated that the resting Fe(II) site is six-coordinate in the wild-type enzyme and converts to a five-coordinate site when both L-Phe and reduced pterin are present in the active site. Although the Arg158Gln mutant forms the five-coordinate site when both cosubstrates are bound, the Fe(II) site of the Glu280Lys mutant remains six-coordinate. These results provide insight into the PAH reaction and disease mechanism at a molecular level, indicating that the first step of the mechanism is formation of a peroxy-pterin species, which subsequently reacts with the Fe(II) site if the pterin is properly oriented for formation of an Fe-OO-pterin bridge and an open coordination position is available on the Fe(II).

    View details for DOI 10.1021/ja029106f

    View details for Web of Science ID 000182769400039

    View details for PubMedID 12733906

  • Medium-dependence of vanadium K-edge X-ray absorption spectra with application to blood cells from phlebobranch tunicates 3rd International Symposium on Chemistry and Biological Chemistry of Vanadium Frank, P., Carlson, R. M., Carlson, E. J., Hodgson, K. O. ELSEVIER SCIENCE SA. 2003: 31–39
  • The vanadium environment in blood cells of Ascidia ceratodes is divergent at all organismal levels: an XAS and EPR spectroscopic study JOURNAL OF INORGANIC BIOCHEMISTRY Frank, P., Carlson, R. M., Carlson, E. J., Hodgson, K. O. 2003; 94 (1-2): 59-71


    K-edge X-ray absorption and EPR spectroscopies were used to test the variation in blood cell vanadium between and within specimens of the tunicate Ascidia ceratodes from Bodega Bay, California. Intracellular vanadium was speciated by fitting the XAS spectra of whole blood cells with linear combinations of the XAS spectra of models. Blood cell samples representing one specimen each, respectively, revealed 92.5 and 38.7% of endogenous vanadium as [V(H(2)O)(6)](3+), indicating dissimilar distributions. Conversely, vanadium distributions within blood cell samples respectively representing one and six specimens proved very similar. The derived array of V(III) complexes was consistent with multiple intracellular regions that differ both in pH and c(sulfate), both within and between specimens. No systematic effect on vanadium distribution was apparent on mixing blood cells. EPR and XAS results indicated at least three forms of endogenous vanadyl ion, two of which may be dimeric. An inverse linear correlation was found between soluble and complexed forms of vanadyl ion, implying co-regulation. The EPR A value of endogenous vanadyl ion [A(0)=(1.062+/-0.008)x10(-2) cm(-1)] was marginally different from that representing Monterey Bay A. ceratodes [A(0)=(1.092+/-0.006) x10(-2) cm(-1)]. Comparisons indicate that Bodega Bay A. ceratodes maintain V(III) in a more acidic intracellular environment on average than do those from Monterey Bay, showing variation across populations. Blood cell vanadium thus noticeably diverges at all organismal levels among A. ceratodes.

    View details for DOI 10.1016/S0162-0134(02)00636-0

    View details for Web of Science ID 000181499700008

    View details for PubMedID 12620674

  • Spectroscopic studies of the effect of ligand donor strength on the Fe-NO bond in intradiol dioxygenases INORGANIC CHEMISTRY Wasinger, E. C., Davis, M. I., Pau, M. Y., Orville, A. M., Zaleski, J. M., Hedman, B., Lipscomb, J. D., Hodgson, K. O., SOLOMON, E. I. 2003; 42 (2): 365-376


    The geometric and electronic structure of NO bound to reduced protocatechuate 3,4-dioxygenase and its substrate (3,4-dihydroxybenzoate, PCA) complex have been examined by X-ray absorption (XAS), UV-vis absorption (Abs), magnetic circular dichroism (MCD), and variable temperature variable field (VTVH) MCD spectroscopies. The results are compared to those previously published on model complexes described as [FeNO]7 systems in which an S = 5/2 ferric center is antiferromagnetically coupled to an S = 1 NO-. XAS pre-edge analysis indicates that the Fe-NO units in FeIIIPCD[NO-] and FeIIIPCD[PCA,NO-] lack the greatly increased pre-edge intensity representative of most [FeNO]7 model sites. Furthermore, from extended X-ray absorption fine structure (EXAFS) analysis, the FeIIIPCD[NO-] and FeIIIPCD[PCA,NO-] active sites are shown to have an Fe-NO distance of at least 1.91 A, approximately 0.2 A greater than those found in the model complexes. The weakened Fe-NO bond is consistent with the overall lengthening of the bond lengths and the fact that VTVH MCD data show that NO(-)-->FeIII CT transitions are no longer polarized along the z-axis of the zero-field splitting tensor. The weaker Fe-NO bond derives from the strong donor interaction of the endogenous phenolate and substrate catecholate ligands, which is observed from the increased intensity in the CT region relative to that of [FeNO]7 model complexes, and from the shift in XAS edge position to lower energy. As NO is an analogue of O2, the effect of endogenous ligand donor strength on the Fe-NO bond has important implications with respect to O2 activation by non-heme iron enzymes.

    View details for DOI 10.1021/ic025906f

    View details for Web of Science ID 000180594400017

    View details for PubMedID 12693216

  • Imaging whole Escherichia coli bacteria by using single-particle x-ray diffraction PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Miao, J. W., Hodgson, K. O., Ishikawa, T., Larabell, C. A., Legros, M. A., Nishino, Y. 2003; 100 (1): 110-112


    We report the first experimental recording, to our knowledge, of the diffraction pattern from intact Escherichia coli bacteria using coherent x-rays with a wavelength of 2 A. By using the oversampling phasing method, a real space image at a resolution of 30 nm was directly reconstructed from the diffraction pattern. An R factor used for characterizing the quality of the reconstruction was in the range of 5%, which demonstrated the reliability of the reconstruction process. The distribution of proteins inside the bacteria labeled with manganese oxide has been identified and this distribution confirmed by fluorescence microscopy images. Compared with lens-based microscopy, this diffraction-based imaging approach can examine thicker samples, such as whole cultured cells, in three dimensions with resolution limited only by radiation damage. Looking forward, the successful recording and reconstruction of diffraction patterns from biological samples reported here represent an important step toward the potential of imaging single biomolecules at near-atomic resolution by combining single-particle diffraction with x-ray free electron lasers.

    View details for Web of Science ID 000180307100021

    View details for PubMedID 12518059

  • Atomic resolution three-dimensional electron diffraction microscopy PHYSICAL REVIEW LETTERS Miao, J., Ohsuna, T., Terasaki, O., Hodgson, K. O., O'Keefe, M. A. 2002; 89 (15)


    We report the development of a novel form of diffraction-based 3D microscopy to overcome resolution barriers inherent in high-resolution electron microscopy and tomography. By combining coherent electron diffraction with the oversampling phasing method, we show that the 3D structure of a nanocrystal can be determined ab initio at a resolution of 1 A from 29 simulated noisy diffraction patterns. This new form of microscopy can be used to image the 3D structures of nanocrystals and noncrystalline samples, with resolution limited only by the quality of sample diffraction.

    View details for DOI 10.1103/PhysRevLett.89.155502

    View details for Web of Science ID 000178195500027

    View details for PubMedID 12365999

  • Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 angstrom resolution PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Kuhn, P., Lesley, S. A., Mathews, I. I., Canaves, J. M., Brinen, L. S., Dai, X. P., Deacon, A. M., Elsliger, M. A., Eshaghi, S., Floyd, R., Godzik, A., Grittini, C., Klock, H. E., Koesema, E., Kovarik, J. M., Kreusch, A. T., McMullan, D., McPhillips, T. M., Miller, M. A., Miller, M., Morse, A., Moy, K., Ouyang, J., Robb, A., Rodrigues, K., Selby, T. L., Spraggon, G., Stevens, R. C., Taylor, S. S., Van den Bedem, H., Velasquez, J., Vincnet, J., Wang, X. H., West, B., Wolf, G., Wooley, J., Wilson, I. A. 2002; 49 (1): 142-145

    View details for DOI 10.1002/prot.10202

    View details for Web of Science ID 000177797300016

    View details for PubMedID 12211025

  • Spectroscopic comparison of the five-coordinate [Cu(SMeIm)(HB(3,5-iPr(2)pz)(3))] with the four-coordinate [Cu(SCPh3)(HB(3,5-iPr(2)pz)(3))]: effect of coordination number increase on a blue cop per type site INORGANICA CHIMICA ACTA Basumallick, L., George, S. D., Randall, D. W., Hedman, B., Hodgson, K. O., Fujisawa, K., Solomon, E. I. 2002; 337: 357-365
  • A stabilized mu-eta(2):eta(2) peroxodicopper(II) complex with a secondary diamine ligand and its tyrosinase-like reactivity JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Mirica, L. M., Vance, M., Rudd, D. J., Hedman, B., Hodgson, K. O., SOLOMON, E. I., Stack, T. D. 2002; 124 (32): 9332-9333


    The activation of dioxygen (O(2)) by Cu(I) complexes is an ubiquitous process in biology and industrial applications. In tyrosinase, a binuclear copper enzyme, a mu-eta(2):eta(2)-peroxodicopper(II) species is generally accepted to be the active oxidant. Reported here is the characterization and reactivity of a stable mu-eta(2):eta(2)-peroxodicopper(II) complex at -80 degrees C using a secondary diamine ligand, N,N'-di-tert-butyl-ethylenediamine (DBED). The spectroscopic characteristics of this complex (UV-vis, resonance Raman) prove to be strongly dependent on the counteranion employed and not on the solvent, suggesting an intimate interaction of the counteranions with the Cu-O(2) cores. This interaction is also supported by solution EXAFS data. This new complex exhibits hydroxylation reactivity by converting phenolates to catechols, proving to be a functional model of tyrosinase. Additional interest in this Cu/O(2) species results from the use of Cu(I)-DBED as a polymerization catalyst of phenols to polyphenylene oxide (PPO) with O(2) as the terminal oxidant.

    View details for DOI 10.1021/ja026905p

    View details for Web of Science ID 000177358600005

    View details for PubMedID 12167002

  • Cooperative ligation, back-bonding, and possible pyridine-pyridine interactions in tetrapyridine-vanadium(II): A visible and X-ray spectroscopic study INORGANIC CHEMISTRY Frank, P., Ghosh, P., Hodgson, K. O., TAUBE, H. 2002; 41 (12): 3269-3279


    The binding of pyridine by V(II) in aqueous solution shows evidence for the late onset of cooperativity. The K(1) governing formation of [V(py)](2+) (lambda(max) = 404 nm, epsilon(max) = 1.43 +/- 0.3 M(-1) cm(-1)) was determined spectrophotometrically to be 11.0 +/- 0.3 M(-)(1), while K(1) for isonicotinamide was found to be 5.0 +/- 0.1 M(-1). These values are in the low range for 3d M(2+) ions and indicate that V(II).py back-bonding is not significant in the formation of the 1:1 complex. Titration of 10.5 mM V(II) with pyridine in aqueous solution showed an absorption plateau at about 1 M added pyridine, indicating a reaction terminus. Vanadium K-edge EXAFS analysis of 63 mM V(II) in 2 M pyridine solution revealed six first-shell N/O ligands at 2.14 A and 4 +/- 1 pyridine ligands per V(II). UV/vis absorption spectroscopy indicated that the same terminal V(II) species was present in both experiments. Model calculations showed that in the absence of back-bonding only 2.0 +/- 0.2 and 2.4 +/- 0.2 pyridine ligands would be present, respectively. Cooperativity in multistage binding of pyridine by [V(aq)](2+) is thus indicated. XAS K-edge spectroscopy of crystalline [V(O(3)SCF(3))(2)(py)(4)] and of V(II) in 2 M pyridine solution each exhibited the analogous 1s --> (5)E(g) and 1s --> (5)T(2g) transitions, at 5465.5 and 5467.5 eV, and 5465.2 and 5467.4 eV, respectively, consistent with the EXAFS analysis. In contrast, [V(py)(6)](PF(6))(2) and [V(H(2)O)(6)]SO(4) show four 1s --> 3d XAS transitions suggestive of a Jahn-Teller distorted excited state. Comparison of the M(II)[bond]N(py) bond lengths in V(II) and Fe(II) tetrapyridines shows that the V(II)[bond]N(py) distances are about 0.06 A shorter than predicted from ionic radii. For [VX(2)(R-py)(4)] (X = Cl(-), CF(3)SO(3)(-); R = 4-Et, H, 3-EtOOC), the E(1/2) values of the V(II)/V(III) couples correlate linearly with the Hammett sigma values of the R group. These findings indicate that pi back-bonding is important in [V(py)(4)](2+) even though absent in [V(py)](2+). The paramagnetism of [V(O(3)SCF(3))(2)(py)(4)] in CHCl(3), 3.8 +/- 0.2 mu(B), revealed that the onset of back-bonding is not accompanied by a spin change. Analysis of the geometries of V(II) and Fe(II) tetrapyridines indicates that the ubiquitous propeller motif accompanying tetrapyridine ligation may be due to eight dipole interactions arising from the juxtaposed C-H edges and pi clouds of adjoining ligands, worth about -6 kJ each. However, this is not the source of the cooperativity in the binding of multiple pyridines by V(II) because the same interactions are present in the Fe(II)-tetrapyridines, which do not show cooperative ligand binding. Cooperativity in the binding of pyridine by V(II) is then assigned by default to V(II)-pyridine back-bonding, which emerges only after the first pyridine is bound.

    View details for DOI 10.1021/ic011221o

    View details for Web of Science ID 000176219400025

    View details for PubMedID 12055006

  • Structural and spectroscopic studies of valence-delocalized diiron(III) complexes supported by carboxylate-only bridging ligands INORGANIC CHEMISTRY Lee, D., Dubois, J. L., Pierce, B., Hedman, B., Hodgson, K. O., Hendrich, M. P., Lippard, S. J. 2002; 41 (12): 3172-3182


    The synthesis, molecular structures, and spectroscopic properties of a series of valence-delocalized diiron(II,III) complexes are described. One-electron oxidation of diiron(II) tetracarboxylate complexes afforded the compounds [Fe(2)(mu-O(2)CAr(Tol))(4)L(2)]X, where L = 4-(t)BuC(5)H(4)N (1b), C(5)H(5)N (2b), and THF (3b); X = PF(6)(-) (1b and 3b) and OTf(-) (2b). In 1b-3b, four mu-1,3 carboxylate ligands span relatively short Fe...Fe distances of 2.6633(11)-2.713(3) A. Intense (epsilon = 2700-3200 M(-1) cm(-1)) intervalence charge transfer bands were observed at 620-670 nm. EPR spectroscopy confirmed the S = (9)/(2) ground spin state of 1b-3b, the valence-delocalized nature of which was probed by X-ray absorption spectroscopy. The electron delocalization between paramagnetic metal centers is described by double exchange, which, for the first time, is observed in diiron clusters having no single-atom bridging ligand(s).

    View details for DOI 10.1021/ic011050n

    View details for Web of Science ID 000176219400015

    View details for PubMedID 12054996

  • Nature of the intermediate formed in the reduction of O-2 to H2O at the trinuclear copper cluster active site in native laccase JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Lee, S. K., George, S. D., Antholine, W. E., Hedman, B., Hodgson, K. O., Solomon, E. I. 2002; 124 (21): 6180-6193


    The multicopper oxidases contain at least four copper atoms and catalyze the four-electron reduction of O(2) to H(2)O at a trinuclear copper cluster. An intermediate, termed native intermediate, has been trapped by a rapid freeze-quench technique from Rhus vernicifera laccase when the fully reduced form reacts with dioxygen. This intermediate had been described as an oxygen-radical bound to the trinuclear copper cluster with one Cu site reduced. XAS, however, shows that all copper atoms are oxidized in this intermediate. A combination of EXAFS, multifrequency EPR, and VTVH MCD has been used to understand how this fully oxidized trinuclear Cu cluster relates to the fully oxidized resting form of the enzyme. It is determined that in the native intermediate all copper atoms of the cluster are bridged by the product of full O(2) reduction. In contrast, the resting form has one copper atom of the cluster (the T2 Cu) magnetically isolated from the others. The native intermediate decays to the resting oxidized form with a rate that is too slow to be in the catalytic cycle. Thus, the native intermediate appears to be the catalytically relevant fully oxidized form of the enzyme, and its role in catalysis is considered.

    View details for DOI 10.1021/ja0114052

    View details for Web of Science ID 000175781600044

    View details for PubMedID 12022853

  • X-ray absorption spectroscopic investigation of the resting ferrous and cosubstrate-bound active sites of phenylalanine hydroxylase BIOCHEMISTRY Wasinger, E. C., Mitic, N., Hedman, B., Caradonna, J., SOLOMON, E. I., Hodgson, K. O. 2002; 41 (20): 6211-6217


    Previous studies of ferrous wild-type phenylalanine hydroxylase, [Fe(2+)]PAH(T)[], have shown the active site to be a six-coordinate distorted octahedral site. After the substrate and cofactor bind to the enzyme ([Fe(2+)]PAH(R)[L-Phe,5-deaza-6-MPH(4)]), the active site converts to a five-coordinate square pyramidal structure in which the identity of the missing ligand had not been previously determined. X-ray absorption spectroscopy (XAS) at the Fe K-edge further supports this coordination number change with the binding of both cosubstrates to the enzyme, and determines this to be due to the loss of a water ligand.

    View details for DOI 10.1021/bi0121510

    View details for Web of Science ID 000175651400001

    View details for PubMedID 12009881

  • Structural characterization of metallopeptides designed as scaffolds for the stabilization of nickel(II)-Fe4S4 bridged assemblies by X-ray absorption spectroscopy JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Musgrave, K. B., Laplaza, C. E., HOLM, R. H., Hedman, B., Hodgson, K. O. 2002; 124 (12): 3083-3092


    In earlier work, de novo designed peptides with a helix-loop-helix motif and 63 residues have been synthesized as potential scaffolds for stabilization of the [Ni(II)-X-Fe(4)S(4)] bridged assembly that is the spectroscopically deduced structure of the A-Cluster in clostridial carbon monoxide dehydrogenase. The 63mers contain a consensus tricysteinyl ferredoxin domain in the loop for binding an Fe(4)S(4) cluster and Cys and His residues proximate to the loop for binding Ni(II), with one Cys residue designed as the bridge X. The metallopeptides HC(4)H(2)-[Fe(4)S(4)]-Ni and HC(5)H-[Fe(4)S(4)]-M, containing three His and one Cys residue for Ni(II) coordination and two His and two Cys residues for binding M = Ni(II) and Co(II), have been examined by Fe-, Ni-, and Co-K edge spectroscopy and EXAFS. All peptides bind an [Fe(4)S(4)](2+) cubane-type cluster. Interpretation of the Ni and Co data is complicated by the presence of a minority population of six-coordinate species with low Z ligands, designated for simplicity as [M(OH(2))(6)](2+). Best fits of the data were obtained with ca. 20% [M(OH(2))(6)](2+) and ca. 80% M(II) with mixed N/S coordination. The collective XAS results for HC(4)H(2)-[Fe(4)S(4)]-Ni and HC(5)H-[Fe(4)S(4)]-M demonstrate the presence of an Fe(4)S(4) cluster and support the existence of the distorted square-planar coordination units [Ni(II)(S.Cys)(N.His)(3)] and [Ni(II)(S.Cys)(2)(N.His)(2)] in the HC(4)H(2) and HC(5)H metallopeptides, respectively. In the HC(5)H metallopeptide, tetrahedral [Co(II)(S.Cys)(2)(N.His)(2)] is present. We conclude that the designed scaffolded binding sites, including Ni-(mu(2)-S.Cys)-Fe bridges, have been achieved. This is the first XAS study of a de novo designed metallopeptide intended to stabilize a bridged biological assembly, and one of a few XAS analyses of metal derivatives of designed peptides. The scaffolding concept should be extendable to other bridged metal assemblies.

    View details for DOI 10.1021/ja011861q

    View details for Web of Science ID 000174520500041

    View details for PubMedID 11902899

  • Electronic structure description of the mu(4)-sulfide bridged tetranuclear Cu-z center in N2O reductase JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Chen, P., George, S. D., Cabrito, I., Antholine, W. E., Moura, J. J., Moura, I., Hedman, B., Hodgson, K. O., SOLOMON, E. I. 2002; 124 (5): 744-745


    Spectroscopy coupled with density functional calculations has been used to define the spin state, oxidation states, spin distribution, and ground state wave function of the mu4-sulfide bridged tetranuclear CuZ cluster of nitrous oxide reductase. Initial insight into the electronic contribution to N2O reduction is developed, which involves a sigma superexchange pathway through the bridging sulfide.

    View details for DOI 10.1021/ja0169623

    View details for Web of Science ID 000173628900010

    View details for PubMedID 11817937

  • X-ray absorption spectroscopic investigation of Fe(II)-peplomycin and peplomycin derivatives: the effect of axial ligation on Fe-pyrimidine back-bonding JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY Wasinger, E. C., Zaleski, K. L., Hedman, B., Hodgson, K. O., SOLOMON, E. I. 2002; 7 (1-2): 157-164


    X-ray absorption spectroscopy (XAS) is used to study ferrous complexes of a bleomycin (BLM) congener, peplomycin (PEP), and two of its derivatives, iso-peplomycin (ISO) and depyruvamide peplomycin (DP), in which potential axial ligands have been perturbed and removed, respectively. Application of extended X-ray absorption fine structure analysis shows an elongation of the short-distance component of the first coordination sphere in DP and ISO relative to PEP. The XAS pre-edge intensity concomitantly decreases with increased axial perturbation. The short-distance component of PEP is correlated to the Fe-pyrimidine bond and is related to the amount of pi-back-bonding. Thus, the XAS analysis of these complexes provides structural information relevant to their differences in O2 reactivity.

    View details for DOI 10.1007/s007750100283

    View details for Web of Science ID 000173024100018

    View details for PubMedID 11862552

  • Aryl C-H activation by Cu-II to form an organometallic Aryl-Cu-III species: A novel twist on copper disproportionation ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Ribas, X., JACKSON, D. A., Donnadieu, B., Mahia, J., Parella, T., Xifra, R., Hedman, B., Hodgson, K. O., Llobet, A., Stack, T. D. 2002; 41 (16): 2991-2994

    View details for Web of Science ID 000177597700023

    View details for PubMedID 12203435

  • Unprecedented forms of vanadium observed within the blood cells of Phallusia nigra using K-edge X-ray absorption spectroscopy JOURNAL OF INORGANIC BIOCHEMISTRY Frank, P., Robinson, W. E., Kustin, K., Hodgson, K. O. 2001; 86 (4): 635-648


    Fits to the vanadium K-edge X-ray absorption spectra (XAS) of five whole blood cell samples from the tunicate Phallusia nigra revealed unprecedented forms of intracellular vanadium. Endogenous vanadium was divided between the V(III) ion (74.2+/-5.1% of total V) and the vanadyl ion [V(IV)=O](2+) (25.2+/-5.4% of total V). The V(III) fraction included both [V(H(2)O)(6)](3+) (36.7+/-5.5%) modeled as VCl(3) in 1 M HCl, and three previously unprecedented chelated V(III) forms (37.5+/-4.6%). Two of these could be represented by the model ligand environments V(acetylacetonate)(3) (17.9+/-3.2%) and K(3)V(catecholate)(3) (13.1+/-4.7%), implying DOPA-like complexation. The third chelated form was represented by the 7-coordinate N(2)O(5) complex Na[V(edta)(H(2)O)] (8.0+/-1.8%). This coordination array, suggestive of a novel mononuclear V(III) protein site, contributed only to fits to samples 1, 2, 3 and 5, which were prepared in the presence of DTT. Endogenous V(IV) (25.2+/-5.4%) was principally modeled as VOCl(2) in 1 M HCl. EPR spectra (averages: A(parallel)=(1.842+/-0.006)x10(-2) cm(-1); A( perpendicular)=(0.718+/-0.007)x10(-2) cm(-1); g(parallel)=1.936+/-0.002; g( perpendicular)=1.990+/-0.001) confirmed the predominance of the aquated vanadyl ion. Blood cell sample five uniquely required the XAS spectrum of VOSO(4) in 0.1 M H(2)SO(4) solution (13.0%) and of [OV(V)(pivalate)(3)] (3.1%) to successfully fit the XAS pre-edge energy region. This endogenous V(V) signal is also unprecedented. These results are compared with those of analogous fits to the blood cells of Ascidia ceratodes and may support assignment of P. nigra to a different genus.

    View details for Web of Science ID 000171655800001

    View details for PubMedID 11583781

  • Determination of ligand binding constants for the iron-molybdenum cofactor of nitrogenase: monomers, multimers, and cooperative behavior JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY Frank, P., Angove, H. C., Burgess, B. K., Hodgson, K. O. 2001; 6 (7): 683-697


    Equilibrium titrations in N-methylformamide (NMF) of G-25 gel filtered (ox)-state FeMo cofactor [FeMoco(ox)] from Azotobacter vinelandii nitrogenase were carried out using sodium ethanethiolate and followed using UV/Vis absorption spectroscopy. For Fe-Moco(ox), a non-linear least squares (NLLSQ) fit to the data indicated a strong equilibrium thiolate-binding step with Keq = 1.3+/-0.2x10(6) M(-1). With 245 molar excess imidazole, cooperative binding of three ethanethiolates was observed. The best NLLSQ fit gave Keq=2.0+/-0.1x10(5) M(-2) and a Hill coefficient n=2.0+/-0.3. A Scatchard plot of these data was concave upward, indicating positive cooperativity. The fit to previously published data involving benzenethiol titration of the one-electron reduced (semi-reduced) cofactor, FeMoco(sr), as followed by EPR required a model that included both a sub-stoichiometric ratio of thiol to FeMoco(sr) and about five cooperative ligand binding sites. These constraints were met by modeling FeMoco(sr) as an aggregate, with fewer thiol binding sites than FeMoco(sr) units. The best fit model was that of FeMoco(sr) as a dodecamer with five cooperative benzenethiol binding sites, yielding a thiol binding constant of 3.32+/-0.09x10(4) M(-4.8) and a Hill coefficient n=4.8+/-0.6. The results of all the other published ligand titrations of FeMoco(sr) were similarly analyzed successfully in terms of equilibrium models that include both cooperative ligand binding and dimer-level aggregation. A possible structural model for FeMoco aggregation in NMF solution is proposed.

    View details for Web of Science ID 000171469600003

    View details for PubMedID 11681702

  • A quantitative description of the ground-state wave function of Cu-A by X-ray absorption spectroscopy: Comparison to plastocyanin and relevance to electron transfer JOURNAL OF THE AMERICAN CHEMICAL SOCIETY George, S. D., Metz, M., Szilagyi, R. K., Wang, H. X., Cramer, S. P., Lu, Y., Tolman, W. B., Hedman, B., Hodgson, K. O., Solomon, E. I. 2001; 123 (24): 5757-5767


    To evaluate the importance of the electronic structure of Cu(A) to its electron-transfer (ET) function, a quantitative description of the ground-state wave function of the mixed-valence (MV) binuclear Cu(A) center engineered into Pseudomonas aeruginosa azurin has been developed, using a combination of S K-edge and Cu L-edge X-ray absorption spectroscopies (XAS). Parallel descriptions have been developed for a binuclear thiolate-bridged MV reference model complex ([(L(i)(PrdacoS)Cu)(2)](+)) and a homovalent (II,II) analogue ([L(i)(Pr2tacnS)Cu)(2)](2+), where L(i)(PrdacoS) and L(i)(Pr2tacnS) are macrocyclic ligands with attached thiolates that bridge the Cu ions. Previous studies have qualitatively defined the ground-state wave function of Cu(A) in terms of ligand field effects on the orbital orientation and the presence of a metal--metal bond. The studies presented here provide further evidence for a direct Cu--Cu interaction and, importantly, experimentally quantify the covalency of the ground-state wave function. The experimental results are further supported by DFT calculations. The nature of the ground-state wave function of Cu(A) is compared to that of the well-defined blue copper site in plastocyanin, and the importance of this wave function to the lower reorganization energy and ET function of Cu(A) is discussed. This wave function incorporates anisotropic covalency into the intra- and intermolecular ET pathways in cytochrome c oxidase. Thus, the high covalency of the Cys--Cu bond allows a path through this ligand to become competitive with a shorter His path in the intramolecular ET from Cu(A) to heme a and is particularly important for activating the intermolecular ET path from heme c to Cu(A).

    View details for DOI 10.1021/ja004109i

    View details for Web of Science ID 000169338400020

    View details for PubMedID 11403610

  • Sulfur K-edge X-ray absorption spectroscopy of 2Fe-2S ferredoxin: Covalency of the oxidized and reduced 2Fe forms and comparison to model complexes JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Anxolabehere-Mallart, E., Glaser, T., Frank, P., Aliverti, A., Zanetti, G., Hedman, B., Hodgson, K. O., SOLOMON, E. I. 2001; 123 (23): 5444-5452


    Ligand K-edge X-ray absorption spectroscopy (XAS) provides a direct experimental probe of ligand-metal bonding. In previous studies, this method has been applied to mononuclear Fe-S and binuclear 2Fe-2S model compounds as well as to rubredoxins and the Rieske protein. These studies are now extended to the oxidized and reduced forms of ferredoxin I from spinach. Because of its high instability, the mixed-valence state was generated electrochemically in the protein matrix, and ligand K-edge absorption spectra were recorded using an XAS spectroelectrochemical cell. The experimental setup is described. The XAS edge data are analyzed to independently determine the covalencies of the iron-sulfide and -thiolate bonds. The results are compared with those obtained previously for the Rieske protein and for 2Fe-2S model compounds. It is found that the sulfide covalency is significantly lower in oxidized FdI compared to that of the oxidized model complex. This decrease is interpreted in terms of H bonding present in the protein, and its contribution to the reduction potential E degrees is estimated. Further, a significant increase in covalency for the Fe(III)-sulfide bond and a decrease of the Fe(II)-sulfide bond are observed in the reduced Fe(III)Fe(II) mixed-valence species compared to those of the Fe(III)Fe(III) homovalent site. This demonstrates that, upon reduction, the sulfide interactions with the ferrous site decrease, allowing greater charge donation to the remaining ferric center. That is the dominant change in electronic structure of the Fe(2)S(2)RS(4) center upon reduction and can contribute to the redox properties of this active site.

    View details for Web of Science ID 000169176300010

    View details for PubMedID 11389625

  • An approach to three-dimensional structures of biomolecules by using single-molecule diffraction images PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Miao, J. W., Hodgson, K. O., Sayre, D. 2001; 98 (12): 6641-6645


    We describe an approach to the high-resolution three-dimensional structural determination of macromolecules that utilizes ultrashort, intense x-ray pulses to record diffraction data in combination with direct phase retrieval by the oversampling technique. It is shown that a simulated molecular diffraction pattern at 2.5-A resolution accumulated from multiple copies of single rubisco biomolecules, each generated by a femtosecond-level x-ray free electron laser pulse, can be successfully phased and transformed into an accurate electron density map comparable to that obtained by more conventional methods. The phase problem is solved by using an iterative algorithm with a random phase set as an initial input. The convergence speed of the algorithm is reasonably fast, typically around a few hundred iterations. This approach and phasing method do not require any ab initio information about the molecule, do not require an extended ordered lattice array, and can tolerate high noise and some missing intensity data at the center of the diffraction pattern. With the prospects of the x-ray free electron lasers, this approach could provide a major new opportunity for the high-resolution three-dimensional structure determination of single biomolecules.

    View details for Web of Science ID 000169151500022

    View details for PubMedID 11390993

  • Protein effects on the electronic structure of the [Fe4S4](2+) cluster in ferredoxin and HiPIP JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Glaser, T., Bertini, I., Moura, J. J., Hedman, B., Hodgson, K. O., SOLOMON, E. I. 2001; 123 (20): 4859-4860

    View details for DOI 10.1021/ja0155940

    View details for Web of Science ID 000168912000033

    View details for PubMedID 11457306

  • The AneuRx stent graft: Four-year results and worldwide experience 2000 JOURNAL OF VASCULAR SURGERY Zarins, C. K., White, R. A., Moll, F. L., Crabtree, T., Bloch, D. A., Hodgson, K. J., Fillinger, M. F., Fogarty, T. J. 2001; 33 (2): S135-S145


    The objective was to review the current results of endovascular abdominal aortic aneurysm repair with the AneuRx stent graft and to determine the effectiveness of the device in achieving the primary objective of preventing aneurysm rupture.The outcome of all patients treated during the past 4 years in the U.S. AneuRx clinical trial was determined, and the worldwide clinical experience was reviewed.A total of 1192 patients were treated with the AneuRx stent graft during all phases of the U.S. Clinical Trial from June 1996 to November 1999, with follow-up extending to June 2000. Ten (0.8%) patients have had aneurysm rupture, with most ruptures (n = 6) occurring in 174 (3.4%) patients treated with an early stiff bifurcation stent graft design used in phase I and in the initial stages of phase II. Since the current, flexible, segmented bifurcation stent graft design was introduced, four (0.4%) ruptures have occurred among 1018 patients treated. Of these, one was during implantation, two were placed too far below the renal arteries, and one patient refused treatment of a type I endoleak. Kaplan-Meier analysis of all 1192 patients treated with the AneuRx stent graft including both stent graft designs revealed the patient survival rate to be 93% at 1 year, 88% at 2 years, and 86% at 3 years, freedom from conversion to open repair to be 98% at 1 year, 97% at 2 years, and 93% at 3 years, and freedom from secondary procedure to be 94% at 1 year, 92% at 2 years, and 88% at 3 years. Freedom from aneurysm rupture with the commercially available segmented bifurcation stent graft was 99.7% at 1 year, 99.5% at 2 years, and 99.5% at 3 years. The presence or absence of endoleak on contrast computed tomography scanning after stent graft placement was not found to be a significant predictor of long-term outcome measures. Worldwide experience with the AneuRx device now approaches 10,000 patients.Endovascular management of abdominal aortic aneurysms with the AneuRx stent graft has markedly reduced the risk of aneurysm rupture while eliminating the need for open aneurysm surgery in 98% of patients at 1 year and 93% of patients at 3 years. The device was effective in preventing aneurysm rupture in 99.5% of patients over a 3-year period. The overall patient survival rate was 93% at 1 year and 86% at 3 years.

    View details for Web of Science ID 000167332500020

    View details for PubMedID 11174825

  • SK-edge X-ray absorption studies of tetranuclear iron-sulfur clusters: mu-sulfide bonding and its contribution to electron delocalization JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Glaser, T., Rose, K., Shadle, S. E., Hedman, B., Hodgson, K. O., SOLOMON, E. I. 2001; 123 (3): 442-454


    X-ray absorption spectroscopy (XAS) at the sulfur ( approximately 2470 eV) and chlorine ( approximately 2822 eV) K-edges has been applied to a series of 4Fe-4S model complexes. These are compared to 2Fe-2S model complexes to obtain insight into the localized ground state in the mixed-valence dimer versus the delocalized ground state in the mixed-valence tetramer. The preedges of hypothetical delocalized mixed-valence dimers [Fe(2)S(2)](+) are estimated using trends from experimental data and density functional calculations, for comparison to the delocalized mixed-valence tetramer [Fe(4)S(4)](2+). The differences between these two mixed-valence sites are due to the change of the sulfide-bridging mode from micro(2) to micro(3). The terminal chloride and thiolate ligands are used as spectator ligands for the electron density of the iron center. From the intensity of the preedge, the covalency of the terminal ligands is found to increase in the tetramer as compared to the dimer. This is associated with a higher effective nuclear charge on the iron in the tetramer (derived from the energies of the preedge). The micro(3)-bridging sulfide in the tetramer has a reduced covalency per bond (39%) as compared to the micro(2)-bridging sulfide in the dimer (51%). A simple perturbation model is used to derive a quadratic dependence of the superexchange coupling constant J on the covalency of the metal ions with the bridging ligands. This relationship is used to estimate the superexchange contribution in the tetramer (J = -156 cm(-)(1)) as compared to the mixed-valence dimer (J = -360 cm(-)(1)). These results, combined with estimates for the double exchange and the vibronic coupling contributions of the dimer sub-site of the tetramer, lead to a delocalized S(t) = (9)/(2) spin ground state for the mixed-valence dimer in the tetramer. Thus, the decrease in the covalency, hence the superexchange pathway associated with changing the bridging mode of the sulfides from micro(2) to micro(3) on going from the dimer to the tetramer, significantly contributes to the delocalization of the excess electron over the dimer sub-site in the tetramer.

    View details for DOI 10.1021/ja002183v

    View details for Web of Science ID 000166698000011

    View details for PubMedID 11456546

  • A short copper-copper distance in a (mu-1,2-peroxo)dicopper(II) complex having a 1,8-naphthyridine unit as an additional bridge ANGEWANDTE CHEMIE-INTERNATIONAL EDITION He, C., Dubois, J. L., Hedman, B., Hodgson, K. O., LIPPARD, S. J. 2001; 40 (8): 1484-?
  • Defining chemical species in complex environments using K-edge X-ray absorption spectroscopy: Vanadium in intact blood cells and Henze solution from the tunicate Ascidia ceratodes INORGANIC CHEMISTRY Frank, P., Hodgson, K. O. 2000; 39 (26): 6018-6027


    A K-edge X-ray absorption spectrum (XAS) fitting approach has been developed to speciate elements of interest in complex materials and used here to model the storage of biological vanadium within whole blood cells from the tunicate Ascidia ceratodes. The response of the K-edge XAS of solution-phase V(III) to increasing c(sulfate) at constant pH 1.8 produced specific and systematic effects in the preedge transition at 5468.8 eV (preedge transitions: 1s-->4A2 at 5464.9 +/- 0.1 eV, 1s-->4T2 at 5466.9 +/- 0.1 eV, and 1s-->4T1 at 5468.8 +/- 0.1 eV for 11 different V(III)/sulfate solutions). In contrast, variations in acidity (as pH) at constant c(sulfate) systematically modified the V(III) preedge XAS at 5466.9 eV. The energy position of the K-edge absorption maximum also serially shifted -0.32 eV/pH unit, from 5483.7 eV (pH 3.0) to 5484.7 eV (pH 0.3). Fits to the V-K XAS of two samples of A. ceratodes whole blood cells representing dozens of animals implied storage of V(III) ions in four predominant solution regimes: approximately 10% high sulfate/pH 0 acid; approximately 40% high sulfate/pH 1.8 acid; approximately 40% moderate sulfate/pH 1.8 acid; approximately 10% moderate sulfate/pH 3 acid. For lysed blood cells, the best fit represented 63% of the V(III) in a pH 1.6 sulfate-free environment and a further 16% in acidic sulfate solution. Nearly 18% of lysed cells vanadium(III) appeared in a tris(catecholate)-like environment. A detailed speciation of biological vanadium complex ions was calculated from these fits by application of the known equilibrium constants governing V(III) and sulfate in acidic aqueous solution. The utility of blood cell V(III) to ascidians is discussed. Fits to K-edge XAS spectra using the XAS spectra of appropriate models are suggested to be generally applicable to elucidating the state of metal ions in a wide variety of complex environments.

    View details for DOI 10.1021/ic000546m

    View details for Web of Science ID 000166019200018

    View details for PubMedID 11151502

  • Ligand K-edge X-ray absorption spectroscopy: A direct probe of ligand-metal covalency ACCOUNTS OF CHEMICAL RESEARCH Glaser, T., Hedman, B., Hodgson, K. O., SOLOMON, E. I. 2000; 33 (12): 859-868


    Ligand K-edge X-ray absorption spectroscopy (XAS) is a new experimental probe of the covalency of a metal-ligand bond. The intensity of the ligand pre-edge feature is proportional to the mixing of ligand orbitals into the metal d orbitals. The methodology to determine covalencies in one-electron (hole) and many-electron systems is described and demonstrated for a series of metal tetrachlorides [MCl(4)](n)(-), metal tetrathiolates [M(SR)(4)](n)(-), and dimeric iron-sulfur (Fe-S) clusters [Fe(2)S(2)(SR)(4)](2-). It is then applied to blue Cu proteins, the Cu(A) site, hydrogen bonding in Fe-S clusters, and the delocalization behavior in [2Fe-2S] vs [4Fe-4S] clusters. The covalencies determined in these studies provide important electronic structure insight into function.

    View details for Web of Science ID 000166180700006

    View details for PubMedID 11123885

  • Spectroscopic and electronic structural studies of blue copper model complexes. 2. Comparison of three- and four-coordinate Cu(II)-thiolate complexes and fungal laccase JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Randall, D. W., George, S. D., Holland, P. L., Hedman, B., Hodgson, K. O., Tolman, W. B., Solomon, E. I. 2000; 122 (47): 11632-11648

    View details for DOI 10.1021/ja001592o

    View details for Web of Science ID 000165696800008

  • X-ray absorption edge and EXAFS studies of the blue copper site in stellacyanin: Effects of axial amide coordination JOURNAL OF PHYSICAL CHEMISTRY B DeBeer, S., Randall, D. W., Nersissian, A. M., Valentine, J. S., Hedman, B., Hodgson, K. O., Solomon, E. I. 2000; 104 (46): 10814-10819

    View details for DOI 10.1021/jp001334d

    View details for Web of Science ID 000165647300012

  • X-ray spectroscopy of enzyme active site analogues and related molecules: Bis(dithiolene)molybdenum(IV) and -tungsten(IV,VI) complexes with variant terminal ligands INORGANIC CHEMISTRY Musgrave, K. B., Lim, B. S., Sung, K. M., HOLM, R. H., Hedman, B., Hodgson, K. O. 2000; 39 (23): 5238-5247


    The X-ray absorption spectra at the molybdenum and selenium K-edges and the tungsten L2,3-edges are acquired for a set of 14 Mo(IV) and W(IV,VI) bis(dithiolene) complexes related to the active sites of molybdo- and tungstoenzymes. The set includes square pyramidal [MoIVL(S2C2Me2)2]- (L = O2-, R3SiO-, RO-, RS-, RSe-) and [WIV(OR)(S2C2Me2)2]-, distorted trigonal prismatic [MoIV(CO)(SeR)(S2C2Me2)2]- and [WIV(CO)L(S2C2Me2)2]- (L = RS-, RSe-), and distorted octahedral [WVIO(OR)(S2C2Me2)2]-. The dithiolene simulates the pterin-dithiolene cofactor ligand, and L represents a protein ligand. Bond lengths are determined by EXAFS analysis using the GNXAS protocol. Normalized edge spectra, non-phase-shift-corrected Fourier transforms, and EXAFS data and fits are presented. Bond lengths determined by EXAFS and X-ray crystallography agree to < or = 0.02 A as do the M-Se distances determined by both metal and selenium EXAFS. The complexes [MoIV(QR)(S2C2Me2)2]- simulate protein ligation by the DMSO reductase family of enzymes, including DMSO reductase itself (Q = O), dissimilatory nitrate reductase (Q = S), and formate dehydrogenase (Q = Se). Edge shifts of these complexes correlate with the ligand electronegativities. Terminal ligand binding is clearly distinguished in the presence of four Mo-S(dithiolene) interactions. Similarly, five-coordinate [ML(S2C2Me2)2]- and six-coordinate [M(CO)L(S2C2Me2)2]- are distinguishable by edge and EXAFS spectra. This study expands a previous XAS investigation of bis(dithiolene)metal(IV,V,VI) complexes (Musgrave, K. B.; Donahue, J. P.; Lorber, C.; Holm, R. H.; Hedman, B.; Hodgson, K. O. J. Am. Chem. Soc. 1999, 121, 10297) by including a larger inventory of molecules with variant physiologically relevant terminal ligation. The previous and present XAS results should prove useful in characterizing and refining metric features and structures of enzyme sites.

    View details for Web of Science ID 000165386300011

    View details for PubMedID 11154582

  • Endoleak as a predictor of outcome after endovascular aneurysm repair: AneuRx multicenter clinical trial 14th Annual Meeting of the Western-Vascular-Society Zarins, C. K., White, R. A., Hodgson, K. J., Schwarten, D., Fogarty, T. J. MOSBY-ELSEVIER. 2000: 90–107


    The purpose of this study was to determine whether evidence of blood flow in the aneurysm sac (endoleak) is a meaningful predictor of clinical outcome after successful endovascular aneurysm repair.We reviewed all patients in Phase II of the AneuRx Multicenter Clinical Trial with successful stent graft implantation and predischarge contrast computed tomographic (CT) imaging. The clinical outcome of patients with evidence of endoleak was compared with the outcome of patients without evidence of endoleak. The CT endoleak status before hospital discharge at 6, 12, and 24 months was determined by each clinical center as well as by an independent core laboratory. Endoleak status at 1 month was assessed with duplex scanning examination or CT at each center without confirmation by the core laboratory.Centers reported endoleaks in 152 (38%) of 398 patients on predischarge CT, whereas the core laboratory reported endoleaks in 50% of these patients (P <.001). The center-reported endoleak rate decreased to 13% at 1 month. Follow-up extended to 2 years (mean, 10 +/- 4 months). One patient had aneurysm rupture and underwent successful open repair at 14 months. This patient had a Type I endoleak at discharge but no endoleak at 1 month or at subsequent follow-up times. There were no differences between patients with and patients without endoleak at discharge in the following outcome measures: patient survival, aneurysm rupture, surgical conversion, the need for an additional procedure for endoleak or graft patency, aneurysm enlargement more than 5 mm, the appearance of a new endoleak, or stent graft migration. Despite a higher endoleak rate identified by the core laboratory, neither the endoleak rate reported by the core laboratory nor the endoleak rate reported by the center at discharge was significantly related to subsequent outcome measures. Patients with endoleak at 1 month were more likely to undergo an additional procedure for endoleak than patients without endoleaks. Patients with Type I endoleaks at discharge and patients with endoleak at 1 month were more likely to experience aneurysm enlargement at 1 year. However, there was no difference in patient survival, aneurysm rupture rate, or primary or secondary success rate between patients with or without endoleak. Actuarial survival of all patients undergoing endovascular aneurysm repair was 96% at 1 year and was independent of endoleak status. Primary outcome success was 92% at 12 months and 88% at 18 months. Secondary outcome success was 96% at 12 months and 94% at 18 months.The presence or absence of endoleak on CT scan before hospital discharge does not appear to predict patient survival or aneurysm rupture rate after endovascular aneurysm repair using the AneuRx stent graft. Although the identification of blood flow in the aneurysm sac after endovascular repair is a meaningful finding and may at times indicate inadequate stent graft fixation, the usefulness of endoleak as a primary indicator of procedural success or failure is unclear. Therefore, all patients who have undergone endovascular aneurysm repair should be carefully followed up regardless of endoleak status.

    View details for Web of Science ID 000088172500019

    View details for PubMedID 10876210

  • Transient dimer in the refolding kinetics of cytochrome c characterized by small-angle X-ray scattering BIOCHEMISTRY Segel, D. J., ELIEZER, D., Uversky, V., Fink, A. L., Hodgson, K. O., Doniach, S. 1999; 38 (46): 15352-15359


    The equilibrium unfolding and the kinetic refolding of cytochrome c (Cyt c) in the presence of imidazole were studied with small-angle X-ray scattering (SAXS). The equilibrium unfolding experiments showed the radius of gyration, R(g), of native Cyt c to swell approximately 1 A with the addition of imidazole. The thermodynamic parameter m also reflects an expansion of the protein as its lower value demonstrates an increase in solvent-accessible surface area over that of native Cyt c in the absence of imidazole. Refolding was studied in the presence of imidazole as it prevents misligated intermediate states from forming during the refolding process, simplifying the kinetics, and making them easier to resolve. Time-resolved decreases in the forward scattering amplitude, I(0), demonstrated the transient formation of an aggregated intermediate. Final protein and denaturant concentrations were varied in the refolding kinetics, and the singular value decomposition (SVD) method was employed to characterize the associated state. This state was determined to be a dimer, with properties consistent with a molten globule.

    View details for Web of Science ID 000083899400034

    View details for PubMedID 10563821

  • Investigation of the anomalous spectroscopic features of the copper sites in chicken ceruloplasmin: Comparison to human ceruloplasmin BIOCHEMISTRY Machonkin, T. E., Musci, G., Zhang, H. H., di Patti, M. C., Calabrese, L., Hedman, B., Hodgson, K. O., Solomon, E. I. 1999; 38 (34): 11093-11102


    Chicken ceruloplasmin has been previously reported to display a number of key differences relative to human ceruloplasmin: a lower copper content and a lack of a type 2 copper signal by electron paramagnetic resonance (EPR) spectroscopy. We have studied the copper sites of chicken ceruloplasmin in order to probe the origin of these differences, focusing on two forms of the enzyme: "resting" (as isolated by a fast, one-step procedure) and "peroxide-oxidized". From X-ray absorption, EPR, and UV/visible absorption spectroscopies, we have shown that all of the copper sites are oxidized in peroxide-oxidized chicken ceruloplasmin and that none of the type 1 copper sites display the EPR features typical for type 1 copper sites that lack an axial methionine. In the resting form, the type 2 copper center is reduced. Upon oxidation, it does not appear in the EPR spectrum at 77 K, but it can be observed by using magnetic susceptibility, EPR at approximately 8 K, and magnetic circular dichroism spectroscopy. It displays unusually fast relaxation, indicative of coupling with the adjacent type 3 copper pair of the trinuclear copper cluster. From reductive titrations, we have found that the reduction potential of the type 2 center is higher than those of the other copper sites, thus explaining why it is reduced in the resting form. These results provide new insight into the nature of the additional type 1 copper sites and the redox distribution among copper sites in the different ceruloplasmins relative to other multicopper oxidases.

    View details for Web of Science ID 000082342600021

    View details for PubMedID 10460165

  • Spectroscopic investigation of reduced protocatechuate 3,4-dioxygenase: Charge-induced alterations in the active site iron coordination environment INORGANIC CHEMISTRY Davis, M. I., Wasinger, E. C., Westre, T. E., Zaleski, J. M., Orville, A. M., Lipscomb, J. D., Hedman, B., Hodgson, K. O., SOLOMON, E. I. 1999; 38 (16): 3676-3683
  • Exogenous substrate reactivity with a [Cu(III)(2)O-2](2+) core: Structural implications JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Mahadevan, V., Dubois, J. L., Hedman, B., Hodgson, K. O., Stack, T. D. 1999; 121 (23): 5583-5584
  • Characterization of transient intermediates in lysozyme folding with time-resolved small-angle X-ray scattering JOURNAL OF MOLECULAR BIOLOGY Segel, D. J., Bachmann, A., Hofrichter, J., Hodgson, K. O., Doniach, S., Kiefhaber, T. 1999; 288 (3): 489-499


    We have used synchrotron radiation, together with stopped-flow and continuous-flow mixing techniques to monitor refolding of lysozyme at pH 5.2. From data measured at times which range from 14 ms to two seconds, we can monitor changes in the size, the shape and the pair distribution function of the polypeptide chain during the folding process. Comparison of the results with the properties of native and GdmCl-unfolded lysozyme shows that a major chain collapse occurs in the dead-time of mixing. During this process about 50 % of the change in radius of gyration between the unfolded protein and the native state occurs and the polypeptide chain adopts a globular shape. Time-resolved fluorescence spectra of this collapsed state suggest that the hydrophobic side-chains are still highly solvent accessible. A subsequently formed intermediate with helical structure in the alpha-domain is nearly identical in size and shape with native lysozyme and has a solvent-inaccessible hydrophobic core. Despite its native-like properties, this intermediate is only slightly more stable (DeltaG0=-4 kJ/mol) than the collapsed state and still much less stable than native lysozyme (DeltaDeltaG0=36 kJ/mol) at 20 degrees C.

    View details for Web of Science ID 000080204600014

    View details for PubMedID 10329156

  • A study of solid [{Cu(MePY2)}(2)O-2](2+) using resonance Raman and X-ray absorption spectroscopies: An intermediate Cu2O2 core structure or a solid solution? JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Pidcock, E., DeBeer, S., Obias, H. V., Hedman, B., Hodgson, K. O., Karlin, K. D., Solomon, E. I. 1999; 121 (9): 1870-1878
  • AneuRx stent graft versus open surgical repair of abdominal aortic aneurysms: Multicenter prospective clinical trial 46th Scientific Meeting of the International-Society-for-Cardiovascular-Surgery Zarins, C. K., White, R. A., Schwarten, D., Kinney, E., Diethrich, E. B., Hodgson, K. J., Fogarty, T. J. MOSBY-ELSEVIER. 1999: 292–306


    The results of a prospective, nonrandomized, multicenter clinical trial that compared endovascular stent graft exclusion of abdominal aortic aneurysms with open surgical repair are presented. During an 18-month period, 250 patients with infrarenal aneurysms underwent treatment at 12 study sites-190 patients underwent endovascular repair using the Medtronic AneuRx stent graft (Sunnyvale, Calif), and 60 underwent open surgical repair. There was no significant difference in operative mortality rates between the groups. The patients who underwent stent grafting had significant reductions in blood loss, time to extubation, and days in the intensive care unit and in the hospital, with an earlier return to function. The major morbidity rate was reduced from 23% in the surgery group to 12% (P <. 05) in the stent graft group. There was no difference in the combined morbidity/mortality rates between the two groups. Primary technical success at the time of discharge for the patients with stent grafts was 77%, largely as a result of a 21% endoleak rate. At 1 month, the endoleak rate had decreased to 9%. There was no difference in the primary or secondary procedure success rates at 30 days between the surgery and stent graft groups. The primary graft patency rate at 6 months was 98% in the surgery group and 97% in the stent graft group. The aneurysm exclusion rate at 1 month and 6 months was 100% in patients who underwent surgery and 91% in patients who underwent stent grafting. Stent graft migration occurred in three patients and resulted in late endoleaks; each endoleak was corrected by means of endovascular placement of a stent graft extender cuff. There have been no aneurysm ruptures and no surgical conversions to open repair in the stent graft group. Stent graft repair compares favorably with open surgical repair, with a reduced morbidity rate, shortened hospital stays, and satisfactory short term outcomes.

    View details for Web of Science ID 000078528900018

    View details for PubMedID 9950987

  • Spectroscopic Investigation of Reduced Protocatechuate 3,4-Dioxygenase: Charge-Induced Alterations in the Active Site Iron Coordination Environment. Inorganic chemistry Davis, M. I., Wasinger, E. C., Westre, T. E., Zaleski, J. M., Orville, A. M., Lipscomb, J. D., Hedman, B., Hodgson, K. O., Solomon, E. I. 1999; 38 (16): 3676–83


    Chemical reduction of the mononuclear ferric active site in the bacterial intradiol cleaving catecholic dioxygenase protocatechuate 3,4-dioxygenase (3,4-PCD, Brevibacterium fuscum) produces a high-spin ferrous center. We have applied circular dichroism (CD), magnetic circular dichroism (MCD), variable-temperature-variable-field (VTVH) MCD, X-ray absorption (XAS) pre-edge, and extended X-ray absorption fine structure (EXAFS) spectroscopies to investigate the geometric and electronic structure of the reduced iron center. Excited-state ligand field CD and MCD data indicate that the site is six-coordinate where the (5)E(g) excited-state splitting is 2033 cm(-)(1). VTVH MCD analysis of the ground state indicates that the site has negative zero-field splitting with a small rhombic splitting of the lowest doublet (delta = 1.6 +/- 0.3 cm(-)(1)). XAS pre-edge analysis also indicates a six-coordinate site while EXAFS analysis provides accurate bond lengths. Since previous spectroscopic analysis and the crystal structure of oxidized 3,4-PCD indicate a five-coordinate ferric active site, the results presented here show that the coordination number increases upon reduction. This is attributed to the coordination of a second solvent ligand. The coordination number increase relative to the oxidized site also appears to be associated with a large decrease in the ligand donor strength in the reduced enzyme due to protonation of the original hydroxide ligand.

    View details for PubMedID 11671125

  • Relationship between the Dipole Strength of Ligand Pre-Edge Transitions and Metal-Ligand Covalency. Inorganic chemistry Neese, F., Hedman, B., Hodgson, K. O., Solomon, E. I. 1999; 38 (21): 4854–60


    The electric dipole contributions to the observed pre-edge intensities in ligand K-edge X-ray absorption (XAS) spectra are analyzed in terms of covalent-bonding contributions between the metal and ligand for a prototype system with one hole in the d shell. One- and two-center contributions to the intensity are identified. By direct evaluation of the integrals involved in the intensity expression, the two-center terms are shown to be at least 1 order of magnitude smaller than the one-center terms and can be ignored to a reasonable approximation. The one-center terms reflect the amount of ligand character in the partially occupied metal-based MOs and are proportional to the intrinsic transition moment of a ligand-centered 1s --> np transition. The final intensity does not contain terms proportional to the square of the metal-ligand distance as might have been expected on the basis of the analogy between ligand K-edge and ligand-to-metal charge transfer (LMCT) transitions that both formally lead to transfer of electron density from the ligand to the metal. This is due to the fact that the transition density is completely localized on the ligand in the case of a ligand K-edge transition but is delocalized over the metal and the ligand in the case of a LMCT transition. The effective nuclear charge dependence of the one-center transition moment integral was studied by Hartree-Fock level calculations and was found to be small. Electronic relaxation effects were considered and found to be small from a Hartree-Fock calculation on a cupric chloride model.

    View details for PubMedID 11671216

  • X-ray Absorption Spectra of the Oxidized and Reduced Forms of C112D Azurin from Pseudomonas aeruginosa. Inorganic chemistry DeBeer, S., Kiser, C. N., Mines, G. A., Richards, J. H., Gray, H. B., Solomon, E. I., Hedman, B., Hodgson, K. O. 1999; 38 (3): 433–38


    The oxidized and reduced forms of a mutant of Pseudomonas aeruginosa azurin, in which the Cys112 has been replaced by an aspartate, have been studied by X-ray absorption spectroscopy. It is well established that the characteristic approximately 600 nm absorption feature of blue copper proteins is due to the S(Cys112) 3ppi --> Cu 3d(x)()()2(-)(y)()()2 charge-transfer transition. While other mutagenesis studies have involved the creation of an artificial blue copper site, the present work involves a mutant in which the native blue copper site has been destroyed, thus serving as a direct probe of the importance of the copper-thiolate bond to the spectroscopy, active site structure, and electron-transfer function of azurin. Of particular interest is the dramatic decrease in electron-transfer rates, both electron self-exchange (k(ese) approximately 10(5) M(-)(1) s(-)(1) wild-type azurin vs k(ese) approximately 20 M(-)(1) s(-)(1) C112D azurin) and intramolecular electron transfer to ruthenium-labeled sites (k(et) approximately 10(6) s(-)(1) wild-type azurin vs k(et)

    View details for PubMedID 11673945

  • A wide-bandpass multilayer monochromator for biological small-angle scattering and fiber diffraction studies JOURNAL OF APPLIED CRYSTALLOGRAPHY Tsuruta, H., Brennan, S., Rek, Z. U., Irving, T. C., Tompkins, W. H., Hodgson, K. O. 1998; 31: 672-682
  • Vanadium K-edge x-ray absorption spectroscopy reveals species differences within the same ascidian genera - A comparison of whole blood from Ascidia nigra and Ascidia ceratodes JOURNAL OF BIOLOGICAL CHEMISTRY Frank, P., Hodgson, K. O., Kustin, K., Robinson, W. E. 1998; 273 (38): 24498-24503


    Vanadium K-edge x-ray absorption spectroscopy (XAS) was used to examine whole blood preparations from the tunicates Ascidia nigra and Ascidia ceratodes. Each XAS spectrum exhibits a rising edge inflection near 5480 eV characteristic of vanadium(III) and an intensity maximum at 5484.0 eV. In A. ceratodes blood cells, intrinsic aquo-VSO4+ complex ion is indicated by an inflection feature at 5476 eV in the first derivative of the vanadium K-edge XAS spectrum, but this feature is notably absent from the first derivative of the vanadium K-edge spectrum of blood cells from A. nigra. A strong pre-edge feature at 5468.6 eV also uniquely distinguishes the vanadium K-edge XAS spectrum of A. nigra blood cells, implying that vanadyl ion represents approximately 25% of the endogenous vanadium. However, the energy position of the rising edge inflection of the vanadium K-edge XAS spectrum of A. nigra (5479.5 eV) is 1 eV lower than that of A. ceratodes (5480.5 eV), the reverse of any expected shift arising from the endogenous vanadyl ion. Thus, in contrast to A. ceratodes, a significant fraction of the blood cell vanadium(III) in A. nigra is apparently in a ligation environment substantially different from that provided by water. These novel species-related differences may have taxonomic significance.

    View details for Web of Science ID 000076007300035

    View details for PubMedID 9733743

  • Protein denaturation: A small-angle X-ray scattering study of the ensemble of unfolded states of cytochrome c BIOCHEMISTRY Segel, D. J., Fink, A. L., Hodgson, K. O., Doniach, S. 1998; 37 (36): 12443-12451


    Solution X-ray scattering was used to study the equilibrium unfolding of cytochrome c as a function of guanidine hydrochloride concentration at neutral pH. The radius of gyration (Rg) shows a cooperative transition with increasing denaturant with a similar Cm to that observed with circular dichroism. However, the lack of an isoscattering point in the X-ray scattering patterns suggests the equilibrium unfolding is not simply a two-state process. Singular value decomposition (SVD) analysis was applied to the scattering patterns to determine the number of distinct scattering species. SVD analysis reveals the existence of three components, suggesting that at least three equilibrium states of the protein exist. A model was employed to determine the thermodynamic parameters and the scattering profiles of the three equilibrium states. These scattering profiles show that one state is native (N). The other two states (U1, U2) are unfolded, with U2 being fully unfolded and U1 having some residual structure. Using the thermodynamic parameters to calculate fractional populations, U1 is maximally populated at intermediate denaturant concentrations while U2 is maximally populated at high denaturant concentrations. It is likely that there is a multiplicity of denatured states with U1 and U2 representing an average of the denatured states populated at intermediate and high denaturant concentrations, respectively.

    View details for Web of Science ID 000075909800009

    View details for PubMedID 9730816

  • EXAFS studies on the P-N and P-OX states of the P-clusters in nitrogenase JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY Musgrave, K. B., Liu, H. I., Ma, L., Burgess, B. K., WATT, G., Hedman, B., Hodgson, K. O. 1998; 3 (4): 344-352
  • An edge with XAS NATURE STRUCTURAL BIOLOGY George, G. N., Hedman, B., Hodgson, K. O. 1998; 5: 645-647

    View details for Web of Science ID 000075169700011

    View details for PubMedID 9699615

  • Spectroscopic and magnetic studies of human ceruloplasmin: Identification of a redox-inactive reduced Type 1 copper site BIOCHEMISTRY Machonkin, T. E., Zhang, H. H., Hedman, B., Hodgson, K. O., Solomon, E. I. 1998; 37 (26): 9570-9578


    Ceruloplasmin is unique among the multicopper oxidases in that in addition to the usual copper stoichiometry of one Type 1 copper site and a Type 2/Type 3 trinuclear copper cluster, it contains two other Type 1 sites. This assignment of copper sites, based on copper quantitation, sequence alignment, and crystallography, is difficult to reconcile with the observed spectroscopy. Furthermore, some chemical or spectroscopic differences in ceruloplasmin have been reported depending on the method of purification. We have studied the resting (as isolated by a fast, one-step procedure) and peroxide-oxidized forms of human ceruloplasmin. Using a combination of X-ray absorption spectroscopy, a chemical assay, magnetic susceptibility, electron paramagnetic resonance spectroscopy, and absorption spectroscopy, we have determined that peroxide-oxidized ceruloplasmin contains one permanently reduced Type 1 site. This site is shown to have a reduction potential of approximately 1.0 V. Thus, one of the additional Type 1 sites in ceruloplasmin cannot be catalytically relevant in the form of the enzyme studied. Furthermore, the resting form of the enzyme contains an additional reducing equivalent, which is distributed among the remaining five copper sites as expected from their relative potentials. This may indicate that the resting form of ceruloplasmin in plasma under aerobic conditions is a four-electron oxidized form, which is consistent with its function in the four-electron reduction of dioxygen to water.

    View details for Web of Science ID 000074585100040

    View details for PubMedID 9649340

  • All-ferrous titanium(III) citrate reduced Fe protein of nitrogenase: An XAS study of electronic and metrical structure JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Musgrave, K. B., Angove, H. C., Burgess, B. K., Hedman, B., Hodgson, K. O. 1998; 120 (21): 5325-5326
  • Kinetics of lysozyme refolding: Structural characterization of a non-specifically collapsed state using time-resolved X-ray scattering JOURNAL OF MOLECULAR BIOLOGY Chen, L. L., Wildegger, G., Kiefhaber, T., Hodgson, K. O., Doniach, S. 1998; 276 (1): 225-237


    We report time-resolved small angle X-ray scattering (SAXS) studies of the structural characteristics of the collapsed state of lysozyme from henegg white (HEL) obtained on initiating refolding by rapidly changing solvent conditions from 8 M to 1.1 M urea at pH 2.9. At this reduced pH the lifetime, of about one second, of the non-specifically collapsed ensemble is considerably prolonged relative to its value at pH 5.2. The SAXS studies are combined with time resolved measurements of tryptophan fluorescence and of the rate of formation of native molecules using interrupted refolding experiments. We observe large burst phase changes in intrinsic tryptophan fluorescence and in the radius of gyration (Rg) which is reduced from 22 A in the fully unfolded state to approximately 19 to 20 A. Subsequent decrease of the Rg to the value for native lysozyme (15 A) follows the time course of formation of native molecules. Single exponential fits to the singular value decomposition (SVD) components of the SAXS data allow reconstruction of the SAXS profile at early time points of refolding. The results of this analysis suggest a globular shape of the collapsed state. A similar fit to the forward scattering amplitude, I(0), suggests that the collapsed state has a solvent accessible surface area which is considerably increased relative to that of the native protein. These results show directly that the non-specifically collapsed state formed during the burst phase in lysozyme refolding indeed represents a molecular compaction and a change in shape from a fully denatured random coil state (albeit restricted by disulfide bonds) to an ensemble of globular conformations which, however, have not yet formed a solvent-protected hydrophobic core.

    View details for Web of Science ID 000072310200016

    View details for PubMedID 9514723

  • Catalytic galactose oxidase models: Biomimetic Cu(II)-phenoxyl-radical reactivity SCIENCE Wang, Y. D., Dubois, J. L., Hedman, B., Hodgson, K. O., Stack, T. D. 1998; 279 (5350): 537-540


    Biomimetic functional models of the mononuclear copper enzyme galactose oxidase are presented that catalytically oxidize benzylic and allylic alcohols to aldehydes with O2 under mild conditions. The mechanistic fidelity between the models and the natural system is pronounced. Modest structural mimicry proves sufficient to transfer an unusual ligand-based radical mechanism, previously unprecedented outside the protein matrix, to a simple chemical system.

    View details for Web of Science ID 000071616000038

    View details for PubMedID 9438841

  • Early work with synchrotron radiation at Stanford JOURNAL OF SYNCHROTRON RADIATION Doniach, S., Hodgson, K., LINDAU, I., Pianetta, P., Winick, H. 1997; 4: 380-395


    The use of synchrotron radiation in the soft and hard X-ray spectral region received major impetus with the start of parasitic operation of the Stanford Synchrotron Radiation Project (SSRP) in 1974. This was the first time that synchrotron radiation from a multi-GeV electron storage ring was made available in a user facility for studying the structure of matter. Here we review the early work at SSRP as well as the activities that preceded it, highlighting the scientific accomplishments (soft X-ray photoemission, EXAFS, protein crystallography), beamline instrumentation developments and source improvements. The early work using bending-magnet radiation led to the funding of several dedicated facilities in the US and elsewhere in the world - the so-called second-generation light sources. Early work with wiggler and undulator insertion devices led to funding of third-generation sources better optimized for insertion device sources, particularly undulators.

    View details for Web of Science ID A1997YH05900007

    View details for PubMedID 16699252

  • Multiple-edge xas studies of iron-copper bridged molecular assemblies relevant to heme-copper oxidases. Zhang, H. H., Filipponi, A., DICICCO, A., Scott, M. J., Hedman, B., Hodgson, K. O. AMER CHEMICAL SOC. 1997: 483-INOR
  • Multiple-edge XAS studies of cyanide-bridged iron-copper molecular assemblies relevant to cyanide-inhibited heme-copper oxidases using four-body multiple-scattering analysis JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Zhang, H. H., Filipponi, A., DICICCO, A., Scott, M. J., HOLM, R. H., Hedman, B., Hodgson, K. O. 1997; 119 (10): 2470-2478
  • A lysozyme folding intermediate revealed by solution X-ray scattering JOURNAL OF MOLECULAR BIOLOGY Chen, L. L., Hodgson, K. O., Doniach, S. 1996; 261 (5): 658-671


    Equilibrium unfolding of hen egg lysozyme as a function of urea concentration at pH 2.9 has been studied by solution X-ray scattering. Differences in the unfolding transition are observed as monitored by the radius of gyration Rg, and by far and near UV CD (circular dichroism) at 222 nm and 298 nm, respectively. This suggests the existence of a third unfolding species, in addition to the native and the unfolded states. A singular value decomposition (SVD) analysis was made of the scattering curves at different urea concentrations. This analysis shows clear evidence of a third basis component in the X-ray scattering curves, thus supporting the results of the Rg and CD measurements. The denaturant binding model was employed to estimate the thermodynamic parameters of denaturation for the intermediate and unfolded states. Use of these parameters to refine the SVD analysis allows us to reconstruct a scattering profile for the pure intermediate state. Simplified partially folded models, based on the crystal structure of hen lysozyme, support a working model for the intermediate, whose structure may be correlated with that of the kinetic intermediate found in the refolding pathway studied by Dobson and coworkers.

    View details for Web of Science ID A1996VF29600007

    View details for PubMedID 8800214

  • Multiple-Edge XAS Studies of Synthetic Iron-Copper Bridged Molecular Assemblies Relevant to Cytochrome c Oxidase. Structure Determination Using Multiple-Scattering Analysis with Statistical Evaluation of Errors. Inorganic chemistry Zhang, H. H., Filipponi, A., Di Cicco, A., Lee, S. C., Scott, M. J., Holm, R. H., Hedman, B., Hodgson, K. O. 1996; 35 (17): 4819–28


    An X-ray absorption spectroscopy study has been carried out at the Fe and Cu K-edges for two bridged molecular assemblies, both of which contain an Fe-X-Cu (X = O(2)(-), OH(-)) bridge unit, some of whose features are relevant to the binuclear site of cytochrome c oxidase. The two complexes [(OEP)Fe-O-Cu(Me(6)tren)](1+) and [(OEP)Fe-(OH)-Cu(Me(5)tren)(OClO(3))](1+) have similar structural fragments around the metal centers except that they differ significantly in the bridge structure (the former contains a linear oxo bridge while the latter has a bent hydroxo bridge). We report a comparative study of these complexes using multiple-scattering (MS) EXAFS analysis and the program package GNXAS. It is found that there is a dramatic increase in the amplitude of the Fe-X-Cu MS pathway as the bridge unit approaches linearity. Full EXAFS MS analysis enables accurate quantitation of bridge metrical details and geometry for both complexes. These studies were done with an expanded version of GNXAS, which allows for simultaneous multiple-edge fitting. Such multiple-edge analysis (using both Fe and Cu edge data) allows common pathways (in this case involving the Fe-X-Cu bridge) to be constrained to be the same, thus improving the observation/variable ratio and enhancing sensitivity for determination of the bridge structure. The accuracy of the structural determination for the bridge units is evaluated by a statistical analysis methodology in which correlations among fitting parameters are identified and contour plots are used to determine random error. The overall error in the EXAFS structural determination is found by establishing the variance with the crystallographically determined values: for the EXAFS-determined parameters at distances below 4 Å, distances and angles deviated on average from crystallographic values by 0.014 Å and 1.5 degrees, respectively. It is also established that structural features in the Fe absorption preedge are diagnostic of oxo vs hydroxo ligation. The relevance of this study to the structural definition of binuclear bridged sites in cytochrome c oxidase and other metalloenzymes is considered.

    View details for PubMedID 11666681

  • THE RADIUS OF GYRATION OF AN APOMYOGLOBIN FOLDING INTERMEDIATE SCIENCE ELIEZER, D., Jennings, P. A., WRIGHT, P. E., Doniach, S., Hodgson, K. O., Tsuruta, H. 1995; 270 (5235): 487-488

    View details for Web of Science ID A1995TA37400046

    View details for PubMedID 7570004



    Solution X-ray scattering experiments have been carried out on recombinant bovine Hsc70 (with 650 amino acid residues), a 60 kDa subfragment (residues 1-554) which has ATPase- and peptide-binding activities, a 44kDa subfragment (residues 1-386) which has only ATPase activity, and a peptide-binding fragment (residues 388-554). Modeling based on steady-state values of radii of gyration (Rg's) and P(r) functions shows that the 44 kDa and peptide-binding domains are oblate fragments while Hsc70 and the 60 kDa fragment are prolate and relatively elongated. Rg values decrease significantly in the presence of MgATP relative to their values in the presence of MgADP (delta Rg approximately 4-5 A) for Hsc70 and the 60 kDa fragment; in contrast, they are essentially equal in the presence of either nucleotide for the 44 kDa ATPase fragment. The kinetics of the change of Rg for Hsc70 and the 60 kDa fragment under single-ATPase cycle conditions show that the transition to the ATP-induced Rg occurs significantly more rapidly than ATP hydrolysis while the reverse transition to the larger Rg value does not occur before product release. Altogether, the solution scattering data support a model in which a conformational change in Hsc70 (presumably to the low-peptide-affinity state) is predicated on ATP binding while the reverse transition is predicated on product release.

    View details for Web of Science ID A1995RX23500002

    View details for PubMedID 7547949



    The low spin ferric and low and high spin ferrous forms of myoglobin, bacterial cytochrome P-450-CAM, and chloroperoxidase have been examined by Fe-K x-ray absorption edge spectroscopy. The positions of the absorption edge and the shapes of preedge and edge regions of imidazole adducts of ferric P-450-CAM and chloroperoxidase are essentially the same when compared with thiolate-ligated ferric myoglobin. As these three protein derivatives all have six-coordinate, low spin, ferric hemes with axial imidazole and thiolate ligands, the superposition of x-ray absorption edge spectral properties demonstrates that the protein environment does not effect the spectra, provided one compares heme iron centers with identical coordination numbers, spin and oxidation states, and ligand sets. In contrast, a 0.96 eV difference is observed in the energy of the absorption edge for imidazole- and thiolate-ligated ferric myoglobin with the latter shifted to lower energy as observed for ferrous myoglobin states. Similarly, in the low spin ferric-imidazole and ferrous-CO states, the energies of the absorption edge for chloroperoxidase and P-450-CAM are shifted in the direction of the ferrous state (to lower energy) when compared with those for analogous myoglobin derivatives. In the deoxyferrous high spin state, comparison of the edge spectra of chloroperoxidase with analogous data for cytochrome P-450-CAM suggests that the electron density at the iron is similar for these two protein states. The shifts observed in the energies of the x-ray absorption edge for the thiolate-ligated states of these proteins relative to derivatives lacking a thiolate ligand provide a direct measure of the electron releasing character of a thiolate axial ligand. These results therefore support the suggested role of the cysteinate proximal ligand of P-450 as a strong internal electron donor to promote O-O bond cleavage in the putative ferric-peroxide intermediate to generate the proposed ferryl-oxo "active oxygen" state of the reaction cycle.

    View details for Web of Science ID A1995QW60100030

    View details for PubMedID 7737989

  • USING GNXAS, A MULTIPLE-SCATTERING EXAFS ANALYSIS, FOR DETERMINATION OF THE FE-N-O ANGLE IN (FENO)(7) COMPLEXES 8th International Conference on X-Ray Absorption Fine Structure (XAFS VIII) Westre, T. E., DICICCO, A., Filipponi, A., Natoli, C. R., Hedman, B., SOLOMON, E. I., Hodgson, K. O. ELSEVIER SCIENCE BV. 1995: 137–39


    Freshly-prepared blue membranes from Halobacterium halobium, previously reported to be disordered, are shown to have a distinct crystal lattice structure, slightly different from the native form. The lattice of the blue form is disrupted irreversibly when dehydrated. The disorder process was observed using time-resolved small-angle X-ray diffraction and analyzed by radial autocorrelation functions. The diffraction peaks of the in-plane lattice first sharpen and increase due to improved membrane orientation, then the trimer lattice becomes disordered and the unit cell dimension decreases by 1.8 A. In contrast, dehydration of purple membranes does not disorder the lattice, and the unit cell dimension shrinks by only 1.0 A. Comparisons of radial autocorrelation functions for the blue membrane during drying show drastic loss of inter-trimer, long-range correlation while the intra-trimer, short-range correlations remain more or less unchanged. This suggests that the deionized protein trimers can maintain their overall structure during the dehydration, even though the lattice dimension decreases appreciably and the two-dimensional crystallinity is disrupted.

    View details for Web of Science ID A1994NK09700003

    View details for PubMedID 8167134



    The biological N2-fixation reaction is catalyzed by the enzyme nitrogenase. The metal cluster active site of this enzyme, the iron-molybdenum cofactor (FeMoco), can be studied either while bound within the MoFe protein component of nitrogenase or after it has been extracted into N-methylformamide. The two species are similar but not identical. For example, the addition of thiophenol or selenophenol to isolated FeMoco causes its rather broad S = 3/2 electron paramagnetic resonance signal to sharpen and more closely approach the signal exhibited by protein-bound FeMoco. The nature of this thiol/selenol binding site has been investigated by using Se-K edge extended x-ray absorption fine structure (EXAFS) to study selenophenol ligated to FeMoco, and the results are reported here. EXAFS data analysis at the ligand Se-K edge was performed with a set of software, GNXAS, that provides for direct calculation of the theoretical EXAFS signals and least-squares fits to the experimental data. Data analysis results show definitively that the selenol (and by inference thiol) binds to Fe at a distance of 2.4 A. In contrast, unacceptable fits are obtained with either Mo or S as the liganded atom (instead of Fe). These results provide quantitative details about an exchangeable thiol/selenol binding site on FeMoco in its isolated, solution state and establish an Fe atom as the site of this reaction. Furthermore, the utility of ligand-based EXAFS as a probe of coordination in polynuclear metal clusters is demonstrated.

    View details for Web of Science ID A1994MX21000021

    View details for PubMedID 8108404



    Small angle x-ray scattering experiments have been carried out on the purified iron proteins of nitrogenase from wild-type Azotobacter vinelandii and from a Nif- mutant strain, A. vinelandii UW91 (which has an A157S mutation). This study was designed to investigate the influence of MgATP and MgADP binding on the protein structure in solution. For the wild-type protein, the binding of MgATP induces a significant conformational change that is observed as a decrease of about 2.0 A in the radius of gyration. In contrast, the binding of MgADP to the wild-type iron protein does not detectably affect the radius of gyration. In the absence of nucleotides, the radius of gyration for the UW91 mutant is indistinguishable from that of the wild-type. However, unlike for the wild-type protein, the radius of gyration of the UW91 iron protein is unaffected by the addition of MgATP. We have previously shown that the UW91 iron protein has a normal [4Fe-4S] cluster and MgATP binding ability but that it is completely blocked for electron transfer and MgATP hydrolysis (Gavini, N., and Burgess, B. K. (1992) J. Biol. Chem. 267, 21179-21186). These x-ray scattering measurements suggest that a conformation different from that of the native state is therefore required for the iron protein to perform electron transfer to the MoFe protein. These results also support the hypothesis that Ala-157 is crucial for the iron protein to establish the electron-transfer-favored conformation induced by MgATP binding.

    View details for Web of Science ID A1994MV63100028

    View details for PubMedID 8106367



    The nitrogenase enzyme complex, consisting of the molybdenum-iron protein and the iron protein, plays a critical role in the biological reduction of dinitrogen to ammonia (nitrogen fixation). The nitrogen-fixing site within the molybdenum-iron protein is an iron-molybdenum-sulfur cofactor (FeMoco) of roughly 1000-2000 Dalton mass. Structural aspects of FeMoco have been determined by spectroscopic and more recently by crystallographic studies. In order to determine the radius of gyration (Rg) of isolated FeMoco, we have performed small-angle x-ray scattering studies of FeMoco in N-methylformamide solution, in the absence of the molybdenum-iron protein. Model compounds of known structure have also been examined in similar solvents, N,N-dimethylformamide and acetonitrile, as controls and for calibration purposes. The Rg values obtained for the models are in good agreement with calculations based upon their respective crystal structures. However, the Rg obtained for FeMoco clearly indicates that the cofactor is not monomeric in solution, but rather aggregated and possibly polydisperse. Further, Rg values were also measured after addition of thiol, dithionite, and thiol and dithionite, to the FeMoco samples. The results indicate, surprisingly, that oxidation state and putative thiol coordination have no detectable effect on the aggregation behavior of FeMoco in solution, as determined by these measurements.

    View details for Web of Science ID A1993MA28800050

    View details for PubMedID 8407930



    Time-resolved small-angle x-ray scattering using the stopped-flow method has been applied successfully to investigate the refolding of myoglobin. This is the only method to date that yields direct information on protein physical dimensions during the folding process. It has the potential to detect and probe important processes, such as protein compaction and association, on a millisecond time scale. Initial experiments were performed with horse myoglobin denatured in high concentrations of urea. The denatured protein was diluted rapidly into a buffer containing no urea or low concentrations of urea. The time-course of the forward-scattered intensity shows a decrease in amplitude which is clearly not engendered by the compaction of the protein, but does correspond well to a dimer dissociation process. Initial and final radii of gyration correspond well to a dimer and a monomer, respectively. Kratky plots of the initial and final states also support the transient dimerization model. The apparent dissociation rate constant was obtainable directly from the data. An association rate constant and an equilibrium constant could be estimated. The dimerizing intermediate is speculated to be a globular non-native state with an exposed hydrophobic surface.

    View details for Web of Science ID A1993LU23300038

    View details for PubMedID 8218914



    The nickel/iron/sulfur center of the carbon monoxide dehydrogenase (carbon monoxide:(acceptor)oxidoreductase; EC enzyme from Rhodospirillum rubrum (Rr-CODH) was studied by x-ray absorption spectroscopy at the Ni K edge. Extended x-ray absorption fine structure data show that the first Ni coordination shell consists of 2 S atoms at 2.23 A and 2-3 N/O atoms at 1.87 A. The edge structure indicates a distorted tetrahedral or five-coordinate Ni environment in both oxidized and reduced Rr-CODH. By comparing second-shell extended x-ray absorption fine structure data of Rr-CODH to that of (Et4N)3[NiFe3S4(SEt)4], a cubane-type cluster, it was clearly established that Ni in the Rr-CODH center is not involved in the core of a NiFe3S4 cubane cluster. One model consistent with the results is a mononuclear Ni2+ site, bridged by S-Cys or sulfide to one or both of the Fe4S4 clusters of the enzyme, with the remaining coordination sites occupied by additional S-Cys or N/O-liganding amino acid residues.

    View details for Web of Science ID A1992HU97700043

    View details for PubMedID 1584775



    19F NMR and x-ray absorption experiments have been performed with both the isolated FeMo cofactor and the MoFe protein of nitrogenase in search of direct evidence for substrate or inhibitor binding. Using 19F NMR as a probe and p-CF3C6H4S- as the receptor ligand, the data show that the nitrogenase inhibitors CN- and CH3NC bind to the isolated FeMo cofactor-RFS- complex in N-methylformamide with a finite formation constant. Their binding increases the electronic relaxation time of the complex and increases the life-time of the FeMo cofactor-p-CF3C6H4S- bond, Parallel molybdenum K edge and extended x-ray absorption fine structure experiments show that CH3NC does not bind to molybdenum. Although CO and N3- both relieve CN- and CH3NC inhibition of electron flow through nitrogenase, unlike the latter, they do not appear to bind to isolated FeMo cofactor. In experiments with the dithionite-reduced MoFe protein, we did not detect any changes in the molybdenum K edge or extended x-ray absorption fine structure spectra upon addition of CO, N2, C2H2, NaCN, CH3NC, or azide demonstrating that either these substrates and inhibitors do not bind to molybdenum or that the FeMo cofactor site of nitrogenase is inaccessible to substrate binding except under turnover conditions.

    View details for Web of Science ID A1989AQ95000040

    View details for PubMedID 2777773



    The iron-molybdenum cofactor from Azotobacter vinelandii can be removed from significant amounts of extraneous iron and other contaminants using anaerobic gel filtration. Electronic absorption spectra of the so-purified FeMoco along with analysis of the so-called 'easily complexed' iron are suggestive that FeMoco occupies at least two different states in N-methylformamide solution. Batch-related differences in spectral characteristics of independently isolated FeMoco samples are demonstrated. Non-cofactor iron, found in unpurified FeMoco, may affect the interpretation of ligand binding and other experiments probing FeMoco structure and reactivity. Oxidized FeMoco is shown to be clearly discernable from the semi-reduced species by means of electronic spectroscopy, and this method now forms a convenient analytical tool for study of the chemistry and electronic structure of FeMoco.

    View details for Web of Science ID A1989AP83300012

    View details for PubMedID 2783119

  • ABINITIO EXAFS AND MULTIPLE-SCATTERING ANALYSIS OF SF6 PHYSICA B-CONDENSED MATTER Tyson, T. A., Benfatto, M., Natoli, C. R., Hedman, B., Hodgson, K. O. 1989; 158 (1-3): 425-427


    X-ray crystallographic studies of troponin C (Herzberg, O., and James, M.N.G. (1985) Nature 313, 653-659; Sundaralingam, M., Bergstrom, R., Strasburg, G., Rao, S.T., and Roychowdhury, P. (1985a) Science 227, 945-948) have revealed a novel protein structure consisting of two globular domains, each containing two Ca2+-binding sites, connected via a nine-turn alpha-helix, three turns of which are fully exposed to solvent. Since the crystals were grown at pH approximately 5, it is of interest to determine whether this structure is applicable to the protein in solution under physiological conditions. We have used small-angle x-ray scattering to examine the solution structure of troponin C at pH 6.8 and the effect of Ca2+ on the structure. The scattering data are consistent with an elongated structure in solution with a radius of gyration of approximately 23.0 A, which is quite comparable to that computed for the crystal structure. The experimental scattering profile and the scattering profile computed from the crystal structure coordinates do, however, exhibit differences at the 40-A level. A weak Ca2+-facilitated dimerization of troponin C was observed. The data rule out large Ca2+-induced structural changes, indicating rather that the molecule with Ca2+ bound is only slightly more compact than the Ca2+-free molecule.

    View details for Web of Science ID A1988M662000018

    View details for PubMedID 3346242



    The study of sulfur within the plasma cells of Ascidia ceratodes [Carlson, R. M. K. (1975) Proc. Natl. Acad. Sci. U.S.A. 72, 2217-2221; Frank, P., Carlson, R. M. K., & Hodgson, K. O. (1986) Inorg. Chem. 25, 470-478; Hedman, B., Frank, P., Penner-Hahn, J. E., Roe, A. L., Hodgson, K. O., Carlson, R. M. K., Brown, G., Cerino, J., Hettel, R., Troxel, T., Winick, H., & Yang, J. (1986) Nucl. Instrum. Methods Phys. Res., Sect. A 246, 797-800] has been extended with X-ray absorption near-edge structure (XANES) spectroscopy. An intense absorption feature at 2482.4 eV and a second feature at 2473.7 eV indicate a large endogenous sulfate concentration, as well as smaller though significant amounts of thiol or thioether sulfur, respectively. A strong shoulder was observed at 2481.7 eV on the low-energy side of the sulfate absorption edge, deriving from a novel type of sulfur having a slightly lower oxidation state than sulfate sulfur. The line width of the primary transition on the sulfur edge of a vanadium (III) sulfate solution was found to be broadened relative to that of sodium sulfate, possibly deriving from the formation of the VSO4+ complex ion [Britton, H. T. S., & Welford, G. (1940) J. Chem. Soc., 761-764; Duffy, J. A., & Macdonald, W. J. D. (1970) J. Chem. Soc., 977-980; Kimura, T., Morinaga, M., & Nakano, J. (1972) Nippon Kagaku Zaishi, 664-667]. Similar broadening appears to characterize the oxidized sulfur types in vanadocytes. A very good linear correlation between oxidation state and peak position (in electronvolts) was found for a series of related sulfur compounds. This correlation was used to determine a 5+ oxidation state for the additional sulfur type at 2481.7 eV. (ABSTRACT TRUNCATED AT 250 WORDS)

    View details for Web of Science ID A1987J557100014

    View details for PubMedID 3663639

  • POLARIZED X-RAY ABSORPTION NEAR-EDGE STRUCTURE OF HIGHLY OXIDIZED CHROMIUM PORPHYRINS INORGANIC CHEMISTRY PENNERHAHN, J. E., Benfatto, M., Hedman, B., Takahashi, T., Doniach, S., Groves, J. T., Hodgson, K. O. 1986; 25 (13): 2255-2259


    We have used anomalous small-angle x-ray scattering as a structural probe for solutions of rabbit parvalbumin labeled with terbium. This technique makes use of the large changes in the terbium scattering factor that occur when the x-ray energy is tuned around an L3 absorption edge of this heavy-atom label. These changes in scattering result in changes in the small-angle scattering curve of the labeled protein as a whole, which can then be analyzed to derive structural information concerning the distribution of labels in the protein. Based on a Gaussian model for the protein electron density, the mean distance from the terbiums to the protein center of mass is determined to be 13.2 A and is consistent with crystallographic results. Our results demonstrate the usefulness of terbium as an anomalous scattering label and provide criteria to help establish anomalous scattering as a reliable structural technique for proteins in solution.

    View details for Web of Science ID A1983QF79700008

    View details for PubMedID 6838970

  • GRAMICIDIN-A CRYSTALS CONTAIN 2 CATION BINDING-SITES PER CHANNEL NATURE Koeppe, R. E., Berg, J. M., Hodgson, K. O., Stryer, L. 1979; 279 (5715): 723-725

    View details for Web of Science ID A1979GZ95900041

    View details for PubMedID 88018


    View details for Web of Science ID A1978FB39600003

    View details for PubMedID 77905



    The primary coordination environment of the "blue" copper ion in oxidized azurin has been elucidated by x-ray absorption spectroscopy. The most striking feature is the unambiguous presence of a very short copper-sulfur distance at 2.10 +/- 0.02 A. Nitrogen ligands, presumed to be from imidazoles, are found at 1.97 A. There is some evidence that the copper coordination sphere may be completed by a second sulfur, the distance of which is determined with much less certainty.

    View details for Web of Science ID A1978FS46500001

    View details for PubMedID 16592557

  • SELENIUM SUBSTITUTION IN [FE4S4(SR)4]2- - SYNTHESIS AND COMPARATIVE PROPERTIES OF [FE4X4(YC6H5)4]2-(X, Y = S, SE) AND STRUCTURE OF [(CH3)4N]2[FE4SE4(SC6H5)4] INORGANIC CHEMISTRY BOBRIK, M. A., Laskowski, E. J., Johnson, R. W., GILLUM, W. O., Berg, J. M., Hodgson, K. O., HOLM, R. H. 1978; 17 (6): 1402-1410

    View details for Web of Science ID A1977DN51700049

    View details for PubMedID 194942


    View details for Web of Science ID A1976CN37400031

    View details for PubMedID 993517


    View details for Web of Science ID A1975BA17400006

    View details for PubMedID 1206706



    Crystals of monellin, a sweet protein from Dioscoreophyllum cumminsii, were grown by vapor diffusion of 20% ethanol into buffered protein solution. The crystals are orthorhombic, belonging to space group P2(1)2(1)2, with a = 54.4 A, b = 113.0 A, c = 40.8 A, and V = 250,300 A(3). The asymmetric unit contains two complete molecules of monellin. The diffraction pattern of this crystal form extends to at least 2.5 A, indicating that x-ray structural analysis is possible to near-atomic resolution.

    View details for Web of Science ID A1975V479600087

    View details for PubMedID 16592216



    Crystals of the nerve growth factor protein were grown by vapor diffusion from ethanol solution. The crystals are hexagonal, belonging to space group P622 (or its enantiomorph) with a equals 56.1 A, c equals 181.4 A, and V equals 494,400 A. The unit cell contains six molecules of dimeric protein and thus has one monomer per asymmetric unit. The diffraction pattern extends to at least 2.7 A, indicating that this crystal form is suitable for structural analysis to near-atomic resolution.

    View details for Web of Science ID A1975W171200001

    View details for PubMedID 1055377