Keith O. Hodgson's research while affiliated with Stanford University and other places

Publications (512)

Article
The direct conversion of methane to methanol would have a wide reaching environmental and industrial impact. Copper-containing zeolites can perform this reaction at low temperatures and pressures at a previously defined O2-activated [Cu2O]2+ site. However, after autoreduction of the copper-containing zeolite mordenite and removal of the [Cu2O]2+ ac...
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Nitrogenase employs a sophisticated electron transfer system and a Mo‐Fe‐S‐C cofactor, designated the M‐cluster [(cit)MoFe7 S9C]), to reduce atmospheric N2 to bioaccessible NH3. Previously, we have shown that the cofactor‐free form of nitrogenase can be repurposed as a protein scaffold for the incorporation of a synthetic Fe‐S cluster [Fe6 S9(SEt)2...
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Nitrogenase is a versatile metalloenzyme that reduces N2, CO and CO2 at its cofactor site. Designated the M-cluster, this complex cofactor has a composition of [(R-homocitrate)MoFe7S9C], and it is assembled through the generation of a unique [Fe8S9C] core prior to the insertion of Mo and homocitrate. NifB is a radical S-adenosyl-L-methionine (SAM)...
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The Fe protein of nitrogenase plays multiple roles in substrate reduction and cluster maturation via its redox active [Fe4S4] cluster. Here we report the synthesis and characterization of a water‐soluble [Fe4Se4] cluster that is used to substitute the [Fe4S4] cluster of the Azotobacter vinelandii Fe protein (AvNifH). Biochemical, EPR and XAS/EXAFS...
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Reduced dithiolene ligands are bound to high valent Mo centers in the active site of the oxotransferase family of enzymes. Related model complexes have been studied with great insight by Prof. Holm and his colleagues. This study focuses on the other limit of dithiolene chemistry: an investigation of the 2-electron oxidized dithiolene bound to low-v...
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The Fe protein of nitrogenase plays multiple roles in substrate reduction and cluster maturation via its redox active [Fe4S4] cluster. Here we report the synthesis and characterization of a water‐soluble [Fe4Se4] cluster that is used to substitute the [Fe4S4] cluster of the Azotobacter vinelandii Fe protein (AvNifH). Biochemical, EPR and XAS/EXAFS...
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Molybdenum nitrogenase catalyses the reduction of N2 to NH3 at its cofactor, an [(R-homocitrate)MoFe7S9C] cluster synthesized via the formation of a [Fe8S9C] L-cluster prior to the insertion of molybdenum and homocitrate. We have previously identified a [Fe8S8C] L*-cluster, which is homologous to the core structure of the L-cluster but lacks the ‘n...
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1s2p resonant inelastic X-ray scattering (1s2p RIXS) has proven successful in the determination of the differential orbital covalency (DOC, the amount of metal vs ligand character in each d molecular orbital) of highly covalent centrosymmetric iron environments including heme models and enzymes. However, many reactive intermediates have noncentrosy...
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The central role of cupric superoxide intermediates proposed in hormone and neurotransmitter biosynthesis by noncoupled binuclear copper monooxygenases like dopamine-β-monooxygenase has drawn significant attention to the unusual methionine ligation of the CuM ("CuB") active site characteristic of this class of enzymes. The copper-sulfur interaction...
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The dynamics of photodissociation and recombination in heme proteins represent an archetypical photochemical reaction widely used to understand the interplay between chemical dynamics and reaction environment. We report a study of the photodissociation mechanism for the Fe(II)-S bond between the heme iron and methionine sulfur of ferrous cytochrome...
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Cu(I) active sites in metalloproteins are involved in O2 activation, but their O2 reactivity is difficult to study due to the Cu(I) d10 closed shell which precludes the use of conventional spectroscopic methods. Kβ X-ray emission spectroscopy (XES) is a promising technique for investigating Cu(I) sites as it detects photons emitted by electronic tr...
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Significance Many iron-dependent enzymes utilize molecular oxygen to functionalize inert C–H bonds in biology. Nonheme ferrous enzymes perform these reactions by reducing dioxygen, often in the presence of a sacrificial electron donor, to form a reactive intermediate that converts substrate to product. In α-ketoglutarate (αKG)–dependent enzymes, th...
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Two samples of living blood cells and of cleared blood plasma from the Phlebobranch tunicate Ascidia ceratodes from Bodega Bay, California, and one of fresh Henze solution from A. ceratodes of Monterey Bay, California, have been examined using sulfur K-edge x-ray absorption spectroscopy (XAS). Biological sulfur included sulfate esters, sulfate and...
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Auf der Gürtellinie: Ein rein Eisen‐haltiger Nitrogenase‐Cofaktor‐Vorläufer (L*‐Cluster genannt) wurde spektroskopisch charakterisiert. Der Strukturvorschlag liefert die Zusammensetzung [Fe8S8C], womit der „9. Schwefel” in der Gürtelregion nicht vorhanden wäre. Die Abwesenheit dieses Schwefels kann günstig für die Markierung dieser Position für mec...
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Nitrogenase catalyzes the reduction of N2 to NH₄+ at its cofactor site. Designated the M‐cluster, this [MoFe₇S₉C(R‐homocitrate)] cofactor is synthesized via transformation of a [Fe₄S₄] cluster pair into an [Fe₈S₉C] precursor (designated the L‐cluster) prior to insertion of Mo and homocitrate. Here we report the characterization of an eight‐iron cof...
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NikR is a nickel-responsive metalloregulator protein that controls the level of Ni2+ ions in living cells. Previous studies have shown that NikR can bind a series of first row transition metal ions, but only binds to DNA with high affinity as a Ni2+ complex. To understand this metal selectivity, S K-edge XAS of NikR bound to different metal ions wa...
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The question of ligand noninnocence in Cu corroles has long been a topic of discussion. Presented herein is a Cu K-edge X-ray absorption spectroscopy (XAS) study, which provides a direct probe of the metal oxidation state, of three Cu corroles, Cu[TPC], Cu[Br8TPC], and Cu[(CF3)8TPC] (TPC = meso-triphenylcorrole), and the analogous Cu(II) porphyrins...
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In situ inventory of sulfurous products from the sulfur K-edge synchrotron X-radiolysis of l-cysteine in solid-phase and anaerobic (pH 5) and air-saturated (pH 5, 7, and 9) solutions without and with 40% glycerol is reported. Sequential K-edge X-ray Absorption Spectroscopic (XAS) spectra were acquired. l-cysteine degraded systematically in the X-ra...
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The formylglycine-generating enzyme (FGE) is required for the posttranslational activation of type I sulfatases by oxidation of an active-site cysteine to C α -formylglycine. FGE has emerged as an enabling biotechnology tool due to the robust utility of the aldehyde product as a bioconjugation handle in recombinant proteins. Here, we show that Cu(I...
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Significance The electronic structure of the heme oxy-iron center in oxyhemoglobin and oxymyoglobin has been the subject of debate for decades. Various experimental and computational methods have been used to study this system, leading to conflicting conclusions. This study uses X-ray spectroscopy to directly probe the iron center in the highly del...
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Significance Fe zeolites are heterogeneous catalysts that show potential in a number of important industrial applications, including the selective partial oxidation of methane to methanol at room temperature, and the selective conversion of benzene to phenol. There are practical limitations associated with Fe-zeolite catalysts that may be resolved...
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While the synthesis and characterization of {FeNO}7,8,9 complexes have been well documented in heme and nonheme iron models, {FeNO}⁶ complexes have been less clearly understood. Herein, we report the synthesis and structural and spectroscopic characterization of mononuclear nonheme {FeNO}⁶ and iron(III)-nitrito complexes bearing a tetraamido macroc...
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Naphthalene oxidation by metal‐oxygen intermediates is one of difficult reactions in environmental and biological chemistry. Herein, we report that a MnIV‐bis(hydroxo) complex, which was fully characterized by various physicochemical methods such as UV‐vis, ESI‐MS, EPR, X‐ray and XAS, shows the naphthalene oxidation in the presence of acid to affor...
Article
Naphthalene oxidation by metal‐oxygen intermediates is one of difficult reactions in environmental and biological chemistry. Herein, we report that a MnIV‐bis(hydroxo) complex, which was fully characterized by various physicochemical methods such as UV‐vis, ESI‐MS, EPR, X‐ray and XAS, shows the naphthalene oxidation in the presence of acid to affor...
Article
Significance Understanding the structure of iron active sites that form in zeolites is critical to understanding the extreme reactivity of Fe-zeolite catalysts, which show promise in important industrial applications. This study defines the geometric structure of an Fe-zeolite active site that cleaves the inert C–H bond of methane at room temperatu...
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Peroxynitrite (–OON=O, PN) is a reactive nitrogen species (RNS) which can effect deleterious nitrative or oxidative (bio)chemistry. It may derive from reaction of superoxide anion (O2•–) with nitric oxide (•NO) and has been suggested to form an as-yet unobserved bound heme-iron-PN intermediate in the catalytic cycle of Nitric Oxide Dioxygenase (NOD...
Article
S K-edge X-ray Absorption Spectroscopy (XAS) was used to study the [Fe4S4] clusters in the DNA repair glycosylases EndoIII and MutY to evaluate the effects of DNA binding and solvation on Fe-S bond covalencies (ie. the amount of S 3p character mixed into the Fe 3d valence orbitals). Increased covalencies in both iron-thiolate and iron-sulfide bonds...
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Sulfur's balancing act in cytochrome c Cytochrome c enzymes have two distinct functions that depend on the position of a methionine residue. When the sulfur in the methionine side chain coordinates with iron in the enzyme's active site, the protein is optimized for electron transfer; otherwise, it is poised for peroxidase activity. Mara et al. used...
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Continual advancements in the development of synchrotron radiation sources have resulted in X-ray based spectroscopic techniques capable of probing the electronic and structural properties of numerous systems. This review gives an overview of the application of metal K-edge and L-edge X-ray absorption spectroscopy (XAS), as well as Kα resonant inel...
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The sulfur K-edge X-ray absorption spectroscopy spectra of open-shell 3d transition-metal sulfates show multiple preedge transitions, including one fully 8.7 eV below the rising K-edge. Density functional theory (DFT) and time-dependent DFT calculations show that these transitions indicate metal-induced ligand radicalization and spin polarization t...
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NO is a classic non-innocent ligand and iron nitrosyls can have different electronic structure descriptions depending on their spin-state and coordination environment. These highly covalent ligands are found in metalloproteins and are also used as models for Fe-O2 systems. This study utilizes iron L-edge X-ray absorption spectroscopy (XAS), interpr...
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Galactose oxidase (GO) is a copper-dependent enzyme that accomplishes 2e(-) substrate oxidation by pairing a single copper with an unusual cysteinylated tyrosine (Cys-Tyr) redox cofactor. Previous studies have demonstrated that the post-translational biogenesis of Cys-Tyr is copper- and O2-dependent, resulting in a self-processing enzyme system. To...
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Significance This work provides direct evidence for the formation of an M-cluster on the assembly scaffold NifEN, establishing NifEN as the second known protein that houses a nitrogenase cofactor. A “half-on, half-off” scheme of cofactor biosynthesis can be proposed based on the outcome of this study, which suggests an asymmetric nature of the asse...
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Three-dimensional models for the aqueous solvation structures of chloride, bromide, and iodide are reported. K-edge extended X-ray absorption fine structure (EXAFS) and Minuit X-ray absorption near edge (MXAN) analyses found well-defined single shell solvation spheres for bromide and iodide. However, dissolved chloride proved structurally distinct,...
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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(...
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Significance V-nitrogenase catalyzes two important reactions for environment- and energy-related areas: reduction of nitrogen to ammonia, and conversion of CO to hydrocarbons. The CO-bound conformation reported herein represents the first well-defined, substrate-bound nitrogenase with turnover capacity. Binding of CO to the resting-state V-nitrogen...
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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 remai...
Article
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 a...
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Significance The extremely short and bright X-ray pulses produced by X-ray free-electron lasers unlock new opportunities in crystallography-based structural biology research. Efficient methods to deliver crystalline material are necessary due to damage or destruction of the crystal by the X-ray pulse. Crystals for the first experiments were 5 µm or...
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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...
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For over a decade, the Joint Center for Structural Genomics (JCSG.org) has been at the forefront of developing tools and methodologies that enable the application of high-throughput structural biology (HTBSB) approaches to a broad range of challenging biological and biomedical problems. In PSI:Biology (2010-2015) to meet the challenges and embrace...
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Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of two complexes [MoIVO(bdt)2]2– and [MoVIO2(bdt)2]2– (bdt = benzene-1,2-dithiolate(2−)) that relate to the reduced and oxidized forms of sulfite oxidase (SO). These are compared with those of prev...
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Significance Activation of the O-O bond in dioxygen is difficult but fundamental in biology. Nature has evolved several strategies to achieve this, often including copper as an enzyme cofactor. Copper-dependent enzymes usually use more than one metal to activate O 2 by multielectron reduction, but recently it was discovered that cellulose and chiti...
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Mammalian MutY glycosylases have a unique architecture that features an interdomain connector (IDC) that joins the catalytic N-terminal domain and 8-oxoguanine (OG) recognition C-terminal domain. The IDC has been shown to be a hub for interactions with protein partners in-volved in coordinating downstream repair events and signaling apoptosis. Here...
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A macrocyclic ligand (L4–) 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...
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Nitrogenase is a complex metalloenzyme that is best known for its function in biological nitrogen fixation. Three homologous nitrogenases, the molybdenum (Mo), vanadium (V), and iron (Fe)-only nitrogenases, have been identified to date. The P- and M-clusters are the most complex metalloclusters found in nature. Consequently, the biosynthetic pathwa...
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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 tunic...
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The protonation-reduction of a dioxygen adduct with [LCu(I)][B(C6F5)4], cupric superoxo complex [LCu(II)(O2(•-))](+) (1) (L = TMG3tren (1,1,1-tris[2-[N(2)-(1,1,3,3-tetramethylguanidino)]ethyl]amine)) has been investigated. Trifluoroacetic acid (HOAcF) reversibly associates with the superoxo ligand in ([LCu(II)(O2(•-))](+)) in a 1:1 adduct [LCu(II)(...
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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 reach...
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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 [...
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Significance The electronic structure of oxyhemoglobin has been under intense scrutiny since the geometric structure of this bent, end-on bound Fe-O 2 species was first determined over three decades ago, but a consensus description has not yet been reached. Here, solution and crystalline X-ray absorption spectroscopies have been combined with time-...
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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...
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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, sele...
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Multicopper Oxidases (MCOs) carry out the most energy efficient reduction of O<sub> to H<sub>O known, i.e. with the lowest overpotential. This four-electron process requires an electron mediating type 1 (T1) Cu site, and an oxygen reducing trinuclear Cu cluster (TNC), consisting of a binuclear type 3 (T3)- and a mononuclear type 2 (T2) Cu center. T...
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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 multi-determinant wavefunctions for a highly covalent metal site....
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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 re...
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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...
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Profiling structured beams produced by X-ray free-electron lasers (FELs) is crucial to both maximizing signal intensity for weakly scattering targets and interpreting their scattering patterns. Earlier ablative imprint studies describe how to infer the X-ray beam profile from the damage that an attenuated beam inflicts on a substrate. However, the...
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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...
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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 reso...
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[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 ar...
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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...
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Certain side-on peroxo-dicopper(II) species with particularly low ν(O-O) (710-730 cm(-1)) have been found in equilibrium with their bis-μ-oxo-dicopper(III) isomer. An issue is whether such side-on peroxo bridges are further activated for O-O cleavage. In a previous study (Liang, H.-C., et al. J. Am. Chem. Soc.2002, 124, 4170), we showed that oxygen...
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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 o...
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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...
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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...
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All's well that ends well: The geometric and electronic structure of the first end-on heme-peroxo-copper adduct was elucidated using UV/Vis, resonance Raman, and X-ray absorption spectroscopy and is supported by DFT calculations. Coordination of the axial base is correlated to a spin-state change, leading to enhanced biomimetic reactivity, and yiel...
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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 experime...