31 results on '"Zhao, Jiyong"'
Search Results
2. Mechanism of selective benzene hydroxylation catalyzed by iron-containing zeolites.
- Author
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Snyder BER, Bols ML, Rhoda HM, Vanelderen P, Böttger LH, Braun A, Yan JJ, Hadt RG, Babicz JT Jr, Hu MY, Zhao J, Alp EE, Hedman B, Hodgson KO, Schoonheydt RA, Sels BF, and Solomon EI
- Subjects
- Catalysis, Catalytic Domain, Hydroxylation, Kinetics, Models, Molecular, Molecular Structure, Oxidation-Reduction, Oxygen chemistry, Phenol chemistry, Benzene chemistry, Iron chemistry, Zeolites chemistry
- Abstract
A direct, catalytic conversion of benzene to phenol would have wide-reaching economic impacts. Fe zeolites exhibit a remarkable combination of high activity and selectivity in this conversion, leading to their past implementation at the pilot plant level. There were, however, issues related to catalyst deactivation for this process. Mechanistic insight could resolve these issues, and also provide a blueprint for achieving high performance in selective oxidation catalysis. Recently, we demonstrated that the active site of selective hydrocarbon oxidation in Fe zeolites, named α-O, is an unusually reactive Fe(IV)=O species. Here, we apply advanced spectroscopic techniques to determine that the reaction of this Fe(IV)=O intermediate with benzene in fact regenerates the reduced Fe(II) active site, enabling catalytic turnover. At the same time, a small fraction of Fe(III)-phenolate poisoned active sites form, defining a mechanism for catalyst deactivation. Density-functional theory calculations provide further insight into the experimentally defined mechanism. The extreme reactivity of α-O significantly tunes down (eliminates) the rate-limiting barrier for aromatic hydroxylation, leading to a diffusion-limited reaction coordinate. This favors hydroxylation of the rapidly diffusing benzene substrate over the slowly diffusing (but more reactive) oxygenated product, thereby enhancing selectivity. This defines a mechanism to simultaneously attain high activity (conversion) and selectivity, enabling the efficient oxidative upgrading of inert hydrocarbon substrates., Competing Interests: The authors declare no conflict of interest.
- Published
- 2018
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3. Structural characterization of a non-heme iron active site in zeolites that hydroxylates methane.
- Author
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Snyder BER, Böttger LH, Bols ML, Yan JJ, Rhoda HM, Jacobs AB, Hu MY, Zhao J, Alp EE, Hedman B, Hodgson KO, Schoonheydt RA, Sels BF, and Solomon EI
- Subjects
- Catalysis, Catalytic Domain, Hydroxylation physiology, Iron metabolism, Methane chemistry, Methane metabolism, Methanol chemistry, Models, Molecular, Molecular Structure, Oxygen chemistry, Spectrophotometry methods, Iron chemistry, Zeolites chemistry, Zeolites metabolism
- Abstract
Iron-containing zeolites exhibit unprecedented reactivity in the low-temperature hydroxylation of methane to form methanol. Reactivity occurs at a mononuclear ferrous active site, α-Fe(II), that is activated by N
2 O to form the reactive intermediate α-O. This has been defined as an Fe(IV)=O species. Using nuclear resonance vibrational spectroscopy coupled to X-ray absorption spectroscopy, we probe the bonding interaction between the iron center, its zeolite lattice-derived ligands, and the reactive oxygen. α-O is found to contain an unusually strong Fe(IV)=O bond resulting from a constrained coordination geometry enforced by the zeolite lattice. Density functional theory calculations clarify how the experimentally determined geometric structure of the active site leads to an electronic structure that is highly activated to perform H-atom abstraction., Competing Interests: The authors declare no conflict of interest.- Published
- 2018
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4. NRVS Studies of the Peroxide Shunt Intermediate in a Rieske Dioxygenase and Its Relation to the Native Fe II O 2 Reaction.
- Author
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Sutherlin KD, Rivard BS, Böttger LH, Liu LV, Rogers MS, Srnec M, Park K, Yoda Y, Kitao S, Kobayashi Y, Saito M, Seto M, Hu M, Zhao J, Lipscomb JD, and Solomon EI
- Subjects
- Comamonas chemistry, Comamonas metabolism, Dioxygenases chemistry, Iron chemistry, Models, Molecular, Peroxides chemistry, Spectrum Analysis, Thermodynamics, Comamonas enzymology, Dioxygenases metabolism, Iron metabolism, Peroxides metabolism
- Abstract
The Rieske dioxygenases are a major subclass of mononuclear nonheme iron enzymes that play an important role in bioremediation. Recently, a high-spin Fe
III -(hydro)peroxy intermediate (BZDOp) has been trapped in the peroxide shunt reaction of benzoate 1,2-dioxygenase. Defining the structure of this intermediate is essential to understanding the reactivity of these enzymes. Nuclear resonance vibrational spectroscopy (NRVS) is a recently developed synchrotron technique that is ideal for obtaining vibrational, and thus structural, information on Fe sites, as it gives complete information on all vibrational normal modes containing Fe displacement. In this study, we present NRVS data on BZDOp and assign its structure using these data coupled to experimentally calibrated density functional theory calculations. From this NRVS structure, we define the mechanism for the peroxide shunt reaction. The relevance of the peroxide shunt to the native FeII /O2 reaction is evaluated. For the native FeII /O2 reaction, an FeIII -superoxo intermediate is found to react directly with substrate. This process, while uphill thermodynamically, is found to be driven by the highly favorable thermodynamics of proton-coupled electron transfer with an electron provided by the Rieske [2Fe-2S] center at a later step in the reaction. These results offer important insight into the relative reactivities of FeIII -superoxo and FeIII -hydroperoxo species in nonheme Fe biochemistry.- Published
- 2018
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5. Nitrosylation of Nitric-Oxide-Sensing Regulatory Proteins Containing [4Fe-4S] Clusters Gives Rise to Multiple Iron-Nitrosyl Complexes.
- Author
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Serrano PN, Wang H, Crack JC, Prior C, Hutchings MI, Thomson AJ, Kamali S, Yoda Y, Zhao J, Hu MY, Alp EE, Oganesyan VS, Le Brun NE, and Cramer SP
- Subjects
- Iron chemistry, Iron-Sulfur Proteins chemistry, Molecular Conformation, Nitric Oxide chemistry, Nitrogen Oxides chemistry, Quantum Theory, Iron metabolism, Iron-Sulfur Proteins metabolism, Nitric Oxide metabolism, Nitrogen Oxides metabolism, Nitroso Compounds metabolism
- Abstract
The reaction of protein-bound iron-sulfur (Fe-S) clusters with nitric oxide (NO) plays key roles in NO-mediated toxicity and signaling. Elucidation of the mechanism of the reaction of NO with DNA regulatory proteins that contain Fe-S clusters has been hampered by a lack of information about the nature of the iron-nitrosyl products formed. Herein, we report nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations that identify NO reaction products in WhiD and NsrR, regulatory proteins that use a [4Fe-4S] cluster to sense NO. This work reveals that nitrosylation yields multiple products structurally related to Roussin's Red Ester (RRE, [Fe
2 (NO)4 (Cys)2 ]) and Roussin's Black Salt (RBS, [Fe4 (NO)7 S3 ]. In the latter case, the absence of32 S/34 S shifts in the Fe-S region of the NRVS spectra suggest that a new species, Roussin's Black Ester (RBE), may be formed, in which one or more of the sulfide ligands is replaced by Cys thiolates., (© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)- Published
- 2016
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6. 3D Motions of Iron in Six-Coordinate {FeNO}(7) Hemes by Nuclear Resonance Vibration Spectroscopy.
- Author
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Peng Q, Pavlik JW, Silvernail NJ, Alp EE, Hu MY, Zhao J, Sage JT, and Scheidt WR
- Subjects
- Ligands, Magnetic Resonance Spectroscopy, Models, Molecular, Heme chemistry, Imidazoles chemistry, Iron chemistry, Metalloporphyrins chemistry
- Abstract
The vibrational spectrum of a six-coordinate nitrosyl iron porphyrinate, monoclinic [Fe(TpFPP)(1-MeIm)(NO)] (TpFPP=tetra-para-fluorophenylporphyrin; 1-MeIm=1-methylimidazole), has been studied by oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS). The crystal was oriented to give spectra perpendicular to the porphyrin plane and two in-plane spectra perpendicular or parallel to the projection of the FeNO plane. These enable assignment of the FeNO bending and stretching modes. The measurements reveal that the two in-plane spectra have substantial differences that result from the strongly bonded axial NO ligand. The direction of the in-plane iron motion is found to be largely parallel and perpendicular to the projection of the bent FeNO on the porphyrin plane. The out-of-plane Fe-N-O stretching and bending modes are strongly mixed with each other, as well as with porphyrin ligand modes. The stretch is mixed with v50 as was also observed for dioxygen complexes. The frequency of the assigned stretching mode of eight Fe-X-O (X=N, C, and O) complexes is correlated with the Fe-XO bond lengths. The nature of highest frequency band at ≈560 cm(-1) has also been examined in two additional new derivatives. Previously assigned as the Fe-NO stretch (by resonance Raman), it is better described as the bend, as the motion of the central nitrogen atom of the FeNO group is very large. There is significant mixing of this mode. The results emphasize the importance of mode mixing; the extent of mixing must be related to the peripheral phenyl substituents., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2016
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7. Comprehensive Fe-ligand vibration identification in {FeNO}6 hemes.
- Author
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Li J, Peng Q, Oliver AG, Alp EE, Hu MY, Zhao J, Sage JT, and Scheidt WR
- Subjects
- Ligands, Models, Molecular, Molecular Conformation, Quantum Theory, Heme chemistry, Iron chemistry, Vibration
- Abstract
Oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS) has been used to obtain all iron vibrations in two {FeNO}(6) porphyrinate complexes, five-coordinate [Fe(OEP)(NO)]ClO4 and six-coordinate [Fe(OEP)(2-MeHIm)(NO)]ClO4. A new crystal structure was required for measurements of [Fe(OEP)(2-MeHIm)(NO)]ClO4, and the new structure is reported herein. Single crystals of both complexes were oriented to be either parallel or perpendicular to the porphyrin plane and/or axial imidazole ligand plane. Thus, the FeNO bending and stretching modes can now be unambiguously assigned; the pattern of shifts in frequency as a function of coordination number can also be determined. The pattern is quite distinct from those found for CO or {FeNO}(7) heme species. This is the result of unchanging Fe-N(NO) bonding interactions in the {FeNO}(6) species, in distinct contrast to the other diatomic ligand species. DFT calculations were also used to obtain detailed predictions of vibrational modes. Predictions were consistent with the intensity and character found in the experimental spectra. The NRVS data allow the assignment and observation of the challenging to obtain Fe-Im stretch in six-coordinate heme derivatives. NRVS data for this and related six-coordinate hemes with the diatomic ligands CO, NO, and O2 reveal a strong correlation between the Fe-Im stretch and Fe-N(Im) bond distance that is detailed for the first time.
- Published
- 2014
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8. Characterization of the bridged hyponitrite complex {[Fe(OEP)](2)(μ-N(2)O(2))}: reactivity of hyponitrite complexes and biological relevance.
- Author
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Berto TC, Xu N, Lee SR, McNeil AJ, Alp EE, Zhao J, Richter-Addo GB, and Lehnert N
- Subjects
- Magnetics, Models, Molecular, Nitric Oxide chemistry, Nitrous Oxide chemistry, Bridged-Ring Compounds chemistry, Coordination Complexes chemistry, Iron chemistry, Nitrites chemistry
- Abstract
The detoxification of nitric oxide (NO) by bacterial NO reductase (NorBC) represents a paradigm of how NO can be detoxified anaerobically in cells. In order to elucidate the mechanism of this enzyme, model complexes provide a convenient means to assess potential reaction intermediates. In particular, there have been many proposed mechanisms that invoke the formation of a hyponitrite bridge between the heme b3 and nonheme iron (FeB) centers within the NorBC active site. However, the reactivity of bridged iron hyponitrite complexes has not been investigated much in the literature. The model complex {[Fe(OEP)]2(μ-N2O2)} offers a unique opportunity to study the electronic structure and reactivity of such a hyponitrite-bridged complex. Here we report the detailed characterization of {[Fe(OEP)]2(μ-N2O2)} using a combination of IR, nuclear resonance vibrational spectroscopy, electron paramagnetic resonance, and magnetic circular dichroism spectroscopy along with SQUID magnetometry. These results show that the ground-state electronic structure of this complex is best described as having two intermediate-spin (S = (3)/2) iron centers that are weakly antiferromagnetically coupled across the N2O2(2-) bridge. The analogous complex {[Fe(PPDME)]2(μ-N2O2)} shows overall similar properties. Finally, we report the unexpected reaction of {[Fe(OEP)]2(μ-N2O2)} in the presence and absence of 1-methylimidizole to yield [Fe(OEP)(NO)]. Density functional theory calculations are used to rationalize why {[Fe(OEP)]2(μ-N2O2)} cannot be formed directly by dimerization of [Fe(OEP)(NO)] and why only the reverse reaction is observed experimentally. These results thus provide insight into the general reactivity of hyponitrite-bridged iron complexes with general relevance for the N-N bond-forming step in NorBC.
- Published
- 2014
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9. Anisotropic iron motion in nitrosyl iron porphyrinates: natural and synthetic hemes.
- Author
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Pavlik JW, Peng Q, Silvernail NJ, Alp EE, Hu MY, Zhao J, Sage JT, and Scheidt WR
- Subjects
- Heme chemical synthesis, Models, Molecular, Oxidation-Reduction, Vibration, Heme chemistry, Iron chemistry, Metalloporphyrins chemistry, Nitrogen Oxides chemistry
- Abstract
The vibrational spectra of two five-coordinate nitrosyl iron porphyrinates, [Fe(OEP)(NO)] (OEP = dianion of 2,3,7,8,12,13,17,18-octaethylporphyrin) and [Fe(DPIX)(NO)] (DPIX = deuteroporphyrin IX), have been studied by oriented single-crystal nuclear resonance vibrational spectroscopy. Single crystals (both are in the triclinic crystal system) were oriented to give vibrational spectra perpendicular to the porphyrin plane. Additionally, two orthogonal in-plane measurements that were also either perpendicular or parallel to the projection of the FeNO plane onto the porphyrin plane yield the complete set of vibrations with iron motion. In addition to cleanly enabling the assignment of the FeNO bending and stretching modes, the measurements reveal that the two in-plane spectra from the parallel and perpendicular in-plane directions for both compounds have substantial differences. The assignment of these in-plane vibrations were aided by density functional theory predictions. The differences in the two in-plane directions result from the strongly bonded axial NO ligand. The direction of the in-plane iron motion is thus found to be largely parallel and perpendicular to the projection of the FeNO plane on the porphyrin plane. These axial ligand effects on the in-plane iron motion are related to the strength of the axial ligand-to-iron bond.
- Published
- 2014
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10. Elucidation of the Fe(IV)=O intermediate in the catalytic cycle of the halogenase SyrB2.
- Author
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Wong SD, Srnec M, Matthews ML, Liu LV, Kwak Y, Park K, Bell CB 3rd, Alp EE, Zhao J, Yoda Y, Kitao S, Seto M, Krebs C, Bollinger JM Jr, and Solomon EI
- Subjects
- Biocatalysis, Halogenation, Hydroxylation, Oxidoreductases metabolism, Pseudomonas syringae enzymology, Iron chemistry, Oxidoreductases chemistry
- Abstract
Mononuclear non-haem iron (NHFe) enzymes catalyse a broad range of oxidative reactions, including halogenation, hydroxylation, ring closure, desaturation and aromatic ring cleavage reactions. They are involved in a number of biological processes, including phenylalanine metabolism, the production of neurotransmitters, the hypoxic response and the biosynthesis of secondary metabolites. The reactive intermediate in the catalytic cycles of these enzymes is a high-spin S = 2 Fe(IV)=O species, which has been trapped for a number of NHFe enzymes, including the halogenase SyrB2 (syringomycin biosynthesis enzyme 2). Computational studies aimed at understanding the reactivity of this Fe(IV)=O intermediate are limited in applicability owing to the paucity of experimental knowledge about its geometric and electronic structure. Synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) is a sensitive and effective method that defines the dependence of the vibrational modes involving Fe on the nature of the Fe(IV)=O active site. Here we present NRVS structural characterization of the reactive Fe(IV)=O intermediate of a NHFe enzyme, namely the halogenase SyrB2 from the bacterium Pseudomonas syringae pv. syringae. This intermediate reacts via an initial hydrogen-atom abstraction step, performing subsequent halogenation of the native substrate or hydroxylation of non-native substrates. A correlation of the experimental NRVS data to electronic structure calculations indicates that the substrate directs the orientation of the Fe(IV)=O intermediate, presenting specific frontier molecular orbitals that can activate either selective halogenation or hydroxylation.
- Published
- 2013
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11. Effects of imidazole deprotonation on vibrational spectra of high-spin iron(II) porphyrinates.
- Author
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Hu C, Peng Q, Silvernail NJ, Barabanschikov A, Zhao J, Alp EE, Sturhahn W, Sage JT, and Scheidt WR
- Subjects
- Models, Molecular, Molecular Conformation, Imidazoles chemistry, Iron chemistry, Metalloporphyrins chemistry, Protons, Spectrum Analysis, Vibration
- Abstract
The effects of the deprotonation of coordinated imidazole on the vibrational dynamics of five-coordinate high-spin iron(II) porphyrinates have been investigated using nuclear resonance vibrational spectroscopy. Two complexes have been studied in detail with both powder and oriented single-crystal measurements. Changes in the vibrational spectra are clearly related to structural differences in the molecular structures that occur when imidazole is deprotonated. Most modes involving the simultaneous motion of iron and imidazolate are unresolved, but the one mode that is resolved is found at higher frequency in the imidazolates. These out-of-plane results are in accord with earlier resonance Raman studies of heme proteins. We also show the imidazole vs imidazolate differences in the in-plane vibrations that are not accessible to resonance Raman studies. The in-plane vibrations are at lower frequency in the imidazolate derivatives; the doming mode shifts are inconclusive. The stiffness, an experimentally determined force constant that averages the vibrational details to quantify the nearest-neighbor interactions, confirms that deprotonation inverts the relative strengths of axial and equatorial coordination.
- Published
- 2013
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12. Heme-protein vibrational couplings in cytochrome c provide a dynamic link that connects the heme-iron and the protein surface.
- Author
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Galinato MG, Kleingardner JG, Bowman SE, Alp EE, Zhao J, Bren KL, and Lehnert N
- Subjects
- Catalytic Domain genetics, Magnetic Resonance Spectroscopy, Molecular Dynamics Simulation, Molecular Structure, Bacteria genetics, Cytochromes c metabolism, Heme metabolism, Iron metabolism, Models, Molecular, Vibration
- Abstract
The active site of cytochrome c (Cyt c) consists of a heme covalently linked to a pentapeptide segment (Cys-X-X-Cys-His), which provides a link between the heme and the protein surface, where the redox partners of Cyt c bind. To elucidate the vibrational properties of heme c, nuclear resonance vibrational spectroscopy (NRVS) measurements were performed on (57)Fe-labeled ferric Hydrogenobacter thermophilus cytochrome c(552), including (13)C(8)-heme-, (13)C(5)(15)N-Met-, and (13)C(15)N-polypeptide (pp)-labeled samples, revealing heme-based vibrational modes in the 200- to 450-cm(-1) spectral region. Simulations of the NRVS spectra of H. thermophilus cytochrome c(552) allowed for a complete assignment of the Fe vibrational spectrum of the protein-bound heme, as well as the quantitative determination of the amount of mixing between local heme vibrations and pp modes from the Cys-X-X-Cys-His motif. These results provide the basis to propose that heme-pp vibrational dynamic couplings play a role in electron transfer (ET) by coupling vibrations of the heme directly to vibrations of the pp at the protein-protein interface. This could allow for the direct transduction of the thermal (vibrational) energy from the protein surface to the heme that is released on protein/protein complex formation, or it could modulate the heme vibrations in the protein/protein complex to minimize reorganization energy. Both mechanisms lower energy barriers for ET. Notably, the conformation of the distal Met side chain is fine-tuned in the protein to localize heme-pp mixed vibrations within the 250- to 400-cm(-1) spectral region. These findings point to a particular orientation of the distal Met that maximizes ET.
- Published
- 2012
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13. New perspectives on iron-ligand vibrations of oxyheme complexes.
- Author
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Li J, Peng Q, Barabanschikov A, Pavlik JW, Alp EE, Sturhahn W, Zhao J, Schulz CE, Sage JT, and Scheidt WR
- Subjects
- Hemeproteins metabolism, Ligands, Magnetic Resonance Spectroscopy, Models, Molecular, Oxygen metabolism, Spectrum Analysis, Raman, Vibration, Hemeproteins chemistry, Imidazoles chemistry, Iron chemistry, Oxygen chemistry, Porphyrins chemistry
- Abstract
We report our studies of the vibrational dynamics of iron for three imidazole-ligated oxyheme derivatives that mimic the active sites of histidine-ligated heme proteins complexed with dioxygen. The experimental vibrational data are obtained from nuclear resonance vibrational spectroscopy (NRVS) measurements conducted on both powder samples and oriented single crystals, and which includes several in-plane (ip) and out-of-plane (oop) measurements. Vibrational spectral assignments have been made through a combination of the oriented sample spectra and predictions based on density functional theory (DFT) calculations. The two Fe-O(2) modes that have been previously observed by resonance Raman spectroscopy in heme proteins are clearly shown to be very strongly mixed and are not simply either a bending or stretching mode. In addition, a third Fe-O(2) mode, not previously reported, has been identified. The long-sought Fe-Im stretch, not observed in resonance Raman spectra, has been identified and compared with the frequencies observed for the analogous CO and NO species. The studies also suggest that the in-plane iron motion is anisotropic and is controlled by the orientation of the Fe-O(2) group and not sensitive to the in-plane Fe-N(p) bonds and/or imidazole orientations., (Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2011
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14. Dynamics of the [4Fe-4S] cluster in Pyrococcus furiosus D14C ferredoxin via nuclear resonance vibrational and resonance Raman spectroscopies, force field simulations, and density functional theory calculations.
- Author
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Mitra D, Pelmenschikov V, Guo Y, Case DA, Wang H, Dong W, Tan ML, Ichiye T, Jenney FE, Adams MW, Yoda Y, Zhao J, and Cramer SP
- Subjects
- Bacterial Proteins metabolism, Ferredoxins metabolism, Iron metabolism, Magnetic Resonance Spectroscopy, Models, Molecular, Oxidation-Reduction, Spectrum Analysis, Raman, Sulfur metabolism, Bacterial Proteins chemistry, Ferredoxins chemistry, Iron chemistry, Pyrococcus furiosus metabolism, Sulfur chemistry
- Abstract
We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study oxidized and reduced forms of the [4Fe-4S] cluster in the D14C variant ferredoxin from Pyrococcus furiosus (Pf D14C Fd). To assist the normal-mode assignments, we conducted NRVS with D14C ferredoxin samples with (36)S substituted into the [4Fe-4S] cluster bridging sulfide positions, and a model compound without ligand side chains, (Ph(4)P)(2)[Fe(4)S(4)Cl(4)]. Several distinct regions of NRVS intensity are identified, ranging from "protein" and torsional modes below 100 cm(-1), through bending and breathing modes near 150 cm(-1), to strong bands from Fe-S stretching modes between 250 and ∼400 cm(-1). The oxidized ferredoxin samples were also investigated by resonance Raman (RR) spectroscopy. We found good agreement between NRVS and RR frequencies, but because of different selection rules, the intensities vary dramatically between the two types of spectra. The (57)Fe partial vibrational densities of states for the oxidized samples were interpreted by normal-mode analysis with optimization of Urey-Bradley force fields for local models of the [4Fe-4S] clusters. Full protein model calculations were also conducted using a supplemented CHARMM force field, and these calculations revealed low-frequency modes that may be relevant to electron transfer with Pf Fd partners. Density functional theory (DFT) calculations complemented these empirical analyses, and DFT was used to estimate the reorganization energy associated with the [Fe(4)S(4)](2+/+) redox cycle. Overall, the NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.
- Published
- 2011
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15. Nuclear resonance vibrational spectroscopy on the Fe(IV)=O S=2 non-heme site in TMG3tren: experimentally calibrated insights into reactivity.
- Author
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Wong SD, Bell CB 3rd, Liu LV, Kwak Y, England J, Alp EE, Zhao J, Que L Jr, and Solomon EI
- Subjects
- Molecular Structure, Oxygen chemistry, Vibration, Iron chemistry, Nonheme Iron Proteins chemistry, Spectrum Analysis methods
- Published
- 2011
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16. Definition of the intermediates and mechanism of the anticancer drug bleomycin using nuclear resonance vibrational spectroscopy and related methods.
- Author
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Liu LV, Bell CB 3rd, Wong SD, Wilson SA, Kwak Y, Chow MS, Zhao J, Hodgson KO, Hedman B, and Solomon EI
- Subjects
- Antibiotics, Antineoplastic chemistry, Antibiotics, Antineoplastic metabolism, Bleomycin metabolism, Deoxyribose chemistry, Deoxyribose metabolism, Ferric Compounds metabolism, Hydrogen chemistry, Iron metabolism, Models, Molecular, Molecular Structure, Oxygen chemistry, Thermodynamics, Vibration, X-Ray Absorption Spectroscopy, Bleomycin chemistry, Ferric Compounds chemistry, Iron chemistry, Magnetic Resonance Spectroscopy methods
- Abstract
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.
- Published
- 2010
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17. Oriented single-crystal nuclear resonance vibrational spectroscopy of [Fe(TPP)(MI)(NO)]: quantitative assessment of the trans effect of NO.
- Author
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Lehnert N, Sage JT, Silvernail N, Scheidt WR, Alp EE, Sturhahn W, and Zhao J
- Subjects
- Models, Molecular, Molecular Conformation, Quantum Theory, Stereoisomerism, Iron chemistry, Nitric Oxide chemistry, Organometallic Compounds chemistry, Spectrum Analysis, Vibration
- Abstract
This paper presents oriented single-crystal Nuclear Resonance Vibrational Spectroscopy (NRVS) data for the six-coordinate (6C) ferrous heme-nitrosyl model complex [(57)Fe(TPP)(MI)(NO)] (1; TPP(2-) = tetraphenylporphyrin dianion; MI = 1-methylimidazole). The availability of these data enables for the first time the detailed simulation of the complete NRVS data, including the porphyrin-based vibrations, of a 6C ferrous heme-nitrosyl, using our quantum chemistry centered normal coordinate analysis (QCC-NCA). Importantly, the Fe-NO stretch is split by interaction with a porphyrin-based vibration into two features, observed at 437 and 472 cm(-1). The 437 cm(-1) feature is strongly out-of-plane (oop) polarized and shows a (15)N(18)O isotope shift of 8 cm(-1) and is therefore assigned to nu(Fe-NO). The admixture of Fe-N-O bending character is small. Main contributions to the Fe-N-O bend are observed in the 520-580 cm(-1) region, distributed over a number of in-plane (ip) polarized porphyrin-based vibrations. The main component, assigned to delta(ip)(Fe-N-O), is identified with the feature at 563 cm(-1). The Fe-N-O bend also shows strong mixing with the Fe-NO stretching internal coordinate, as evidenced by the oop NRVS intensity in the 520-580 cm(-1) region. Very accurate normal mode descriptions of nu(Fe-NO) and delta(ip)(Fe-N-O) have been obtained in this study. These results contradict previous interpretations of the vibrational spectra of 6C ferrous heme-nitrosyls where the higher energy feature at approximately 550 cm(-1) had usually been associated with nu(Fe-NO). Furthermore, these results provide key insight into NO binding to ferrous heme active sites in globins and other heme proteins, in particular with respect to (a) the effect of hydrogen bonding to the coordinated NO and (b) changes in heme dynamics upon NO coordination. [Fe(TPP)(MI)(NO)] constitutes an excellent model system for ferrous NO adducts of myoglobin (Mb) mutants where the distal histidine (His64) has been removed. Comparison to the reported vibrational data for wild-type (wt) Mb-NO then shows that the effect of H bonding to the coordinated NO is weak and mostly leads to a polarization of the pi/pi* orbitals of bound NO. In addition, the observation that delta(ip)(Fe-N-O) does not correlate well with nu(N-O) can be traced back to the very mixed nature of this mode. The Fe-N(imidazole) stretching frequency is observed at 149 cm(-1) in [Fe(TPP)(MI)(NO)], and spectral changes upon NO binding to five-coordinate ferrous heme active sites are discussed. The obtained high-quality force constants for the Fe-NO and N-O bonds of 2.57 and 11.55 mdyn/A can further be compared to those of corresponding 5C species, which allows for a quantitative analysis of the sigma trans interaction between the proximal imidazole (His) ligand and NO. This is key for the activation of the NO sensor soluble guanylate cyclase. Finally, DFT methods are calibrated against the experimentally determined vibrational properties of the Fe-N-O subunit in 1. DFT is in fact incapable of reproducing the vibrational energies and normal mode descriptions of the Fe-N-O unit well, and thus, DFT-based predictions of changes in vibrational properties upon heme modification or other perturbations of these 6C complexes have to be treated with caution.
- Published
- 2010
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18. Nuclear resonance vibrational spectroscopy applied to [Fe(OEP)(NO)]: the vibrational assignments of five-coordinate ferrous heme-nitrosyls and implications for electronic structure.
- Author
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Lehnert N, Galinato MG, Paulat F, Richter-Addo GB, Sturhahn W, Xu N, and Zhao J
- Subjects
- Computer Simulation, Crystallography, X-Ray, Magnetic Resonance Spectroscopy, Models, Chemical, Models, Molecular, Vibration, Electrons, Heme chemistry, Iron chemistry, Metalloporphyrins chemistry, Nitrogen Oxides chemistry
- Abstract
This study presents Nuclear Resonance Vibrational Spectroscopy (NRVS) data on the five-coordinate (5C) ferrous heme-nitrosyl complex [Fe(OEP)(NO)] (1, OEP(2-) = octaethylporphyrinato dianion) and the corresponding (15)N(18)O labeled complex. The obtained spectra identify two isotope sensitive features at 522 and 388 cm(-1), which shift to 508 and 381 cm(-1), respectively, upon isotope labeling. These features are assigned to the Fe-NO stretch nu(Fe-NO) and the in-plane Fe-N-O bending mode delta(ip)(Fe-N-O), the latter has been unambiguously assigned for the first time for 1. The obtained NRVS data were simulated using our quantum chemistry centered normal coordinate analysis (QCC-NCA). Since complex 1 can potentially exist in 12 different conformations involving the FeNO and peripheral ethyl orientations, extended density functional theory (DFT) calculations and QCC-NCA simulations were performed to determine how these conformations affect the NRVS properties of [Fe(OEP)NO]. These results show that the properties and force constants of the FeNO unit are hardly affected by the conformational changes involving the ethyl substituents. On the other hand, the NRVS-active porphyrin-based vibrations around 340-360, 300-320, and 250-270 cm(-1) are sensitive to the conformational changes. The spectroscopic changes observed in these regions are due to selective mechanical couplings of one component of E(u)-type (in ideal D(4h) symmetry) porphyrin-based vibrations with the in-plane Fe-N-O bending mode. This leads to the observed variations in Fe(OEP) core mode energies and NRVS intensities without affecting the properties of the FeNO unit. The QCC-NCA simulated NRVS spectra of 1 show excellent agreement with experiment, and indicate that conformer F is likely present in the samples of this complex investigated here. The observed porphyrin-based vibrations in the NRVS spectra of 1 are also assigned based on the QCC-NCA results. The obtained force constants of the Fe-NO and N-O bonds are 2.83-2.94 (based on the DFT functional applied) and about 12.15 mdyn/A, respectively. The electronic structures of 5C ferrous heme-nitrosyls in different model complexes are then analyzed, and variations in their properties based on different porphyrin substituents are explained. Finally, the shortcomings of different DFT functionals in describing the axial FeNO subunit in heme-nitrosyls are elucidated.
- Published
- 2010
- Full Text
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19. Vibrational dynamics of iron in cytochrome C.
- Author
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Leu BM, Ching TH, Zhao J, Sturhahn W, Alp EE, and Sage JT
- Subjects
- Iron Isotopes, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Spectrum Analysis, Raman, Vibration, Cytochromes c chemistry, Iron chemistry
- Abstract
Nuclear resonance vibrational spectroscopy (NRVS) and Raman spectroscopy on (54)Fe- and (57)Fe-enriched cytochrome c (cyt c) identify multiple bands involving vibrations of the heme Fe. Comparison with predictions from Fe isotope shifts reveals that 70% of the NRVS signal in the 300-450 cm(-1) frequency range corresponds to vibrations resolved in Soret-enhanced Raman spectra. This frequency range dominates the "stiffness", an effective force constant determined by the Fe vibrational density of states (VDOS), which measures the strength of nearest-neighbor interactions with Fe. The stiffness of the low-spin Fe environment in both oxidation states of cyt c significantly exceeds that for the high-spin Fe in deoxymyoglobin, where the 200-300 cm(-1) frequency range dominates the VDOS. This situation is reflected in the shorter Fe-ligand bond lengths in the former with respect to the latter. The longer Fe-S(Met80) in oxidized cyt c with respect to reduced cyt c leads to a decrease in the stiffness of the iron environment upon oxidation. Comparison with NRVS measurements allows us to assess assignments for vibrational modes resolved in this region of the heme Raman spectrum. We consider the possibility that the 372 cm(-1) band in reduced cyt c involves the Fe-S(Met80) bond.
- Published
- 2009
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20. Resilience of the iron environment in heme proteins.
- Author
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Leu BM, Zhang Y, Bu L, Straub JE, Zhao J, Sturhahn W, Alp EE, and Sage JT
- Subjects
- Cytochromes c chemistry, Cytochromes c metabolism, Models, Molecular, Myoglobin chemistry, Myoglobin metabolism, Protein Conformation, Temperature, Vibration, Hemeproteins chemistry, Hemeproteins metabolism, Iron chemistry, Iron metabolism
- Abstract
Conformational flexibility is essential to the functional behavior of proteins. We use an effective force constant introduced by Zaccai, the resilience, to quantify this flexibility. Site-selective experimental and computational methods allow us to determine the resilience of heme protein active sites. The vibrational density of states of the heme Fe determined using nuclear resonance vibrational spectroscopy provides a direct experimental measure of the resilience of the Fe environment, which we compare quantitatively with values derived from the temperature dependence of atomic mean-squared displacements in molecular dynamics simulations. Vibrational normal modes in the THz frequency range dominate the resilience. Both experimental and computational methods find a higher resilience for cytochrome c than for myoglobin, which we attribute to the increased number of covalent links to the peptide in the former protein. For myoglobin, the resilience of the iron environment is larger than the average resilience previously determined for hydrogen sites using neutron scattering. Experimental results suggest a slightly reduced resilience for cytochrome c upon oxidation, although the change is smaller than reported in previous Mössbauer investigations on a bacterial cytochrome c, and is not reproduced by the simulations. Oxidation state also has no significant influence on the compressibility calculated for cyt c, although a slightly larger compressibility is predicted for myoglobin.
- Published
- 2008
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21. Quantitative vibrational dynamics of iron in carbonyl porphyrins.
- Author
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Leu BM, Silvernail NJ, Zgierski MZ, Wyllie GR, Ellison MK, Scheidt WR, Zhao J, Sturhahn W, Alp EE, and Sage JT
- Subjects
- Computational Biology, Magnetic Resonance Spectroscopy, Models, Chemical, Iron chemistry, Porphyrins chemistry
- Abstract
We use nuclear resonance vibrational spectroscopy and computational predictions based on density functional theory (DFT) to explore the vibrational dynamics of (57)Fe in porphyrins that mimic the active sites of histidine-ligated heme proteins complexed with carbon monoxide. Nuclear resonance vibrational spectroscopy yields the complete vibrational spectrum of a Mössbauer isotope, and provides a valuable probe that is not only selective for protein active sites but quantifies the mean-squared amplitude and direction of the motion of the probe nucleus, in addition to vibrational frequencies. Quantitative comparison of the experimental results with DFT calculations provides a detailed, rigorous test of the vibrational predictions, which in turn provide a reliable description of the observed vibrational features. In addition to the well-studied stretching vibration of the Fe-CO bond, vibrations involving the Fe-imidazole bond, and the Fe-N(pyr) bonds to the pyrrole nitrogens of the porphyrin contribute prominently to the observed experimental signal. All of these frequencies show structural sensitivity to the corresponding bond lengths, but previous studies have failed to identify the latter vibrations, presumably because the coupling to the electronic excitation is too small in resonance Raman measurements. We also observe the FeCO bending vibrations, which are not Raman active for these unhindered model compounds. The observed Fe amplitude is strongly inconsistent with three-body oscillator descriptions of the FeCO fragment, but agrees quantitatively with DFT predictions. Over the past decade, quantum chemical calculations have suggested revised estimates of the importance of steric distortion of the bound CO in preventing poisoning of heme proteins by carbon monoxide. Quantitative agreement with the predicted frequency, amplitude, and direction of Fe motion for the FeCO bending vibrations provides direct experimental support for the quantum chemical description of the energetics of the FeCO unit.
- Published
- 2007
- Full Text
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22. Direct probe of iron vibrations elucidates NO activation of heme proteins.
- Author
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Zeng W, Silvernail NJ, Wharton DC, Georgiev GY, Leu BM, Scheidt WR, Zhao J, Sturhahn W, Alp EE, and Sage JT
- Subjects
- Nuclear Magnetic Resonance, Biomolecular, Vibration, Hemeproteins chemistry, Iron chemistry, Nitric Oxide chemistry
- Abstract
We use nuclear resonance vibrational spectroscopy (NRVS) to identify the Fe-NO stretching frequency in the NO adduct of myoglobin (MbNO) and in the related six-coordinate porphyrin Fe(TPP)(1-MeIm)(NO). Frequency shifts observed in MbNO Raman spectra upon isotopic substitution of Fe or the nitrosyl nitrogen confirm and extend the NRVS results. In contrast with previous assignments, the Fe-NO frequency of these six-coordinate complexes lies 70-100 cm-1 lower than in the analogous five-coordinate nitrosyl complexes, indicating a significant weakening of the Fe-NO bond in the presence of a trans imidazole ligand. This result supports proposed mechanisms for NO activation of heme proteins and underscores the value of NRVS as a direct probe of metal reactivity in complex biomolecules.
- Published
- 2005
- Full Text
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23. Nitrosylation of Nitric‐Oxide‐Sensing Regulatory Proteins Containing [4Fe‐4S] Clusters Gives Rise to Multiple Iron–Nitrosyl Complexes
- Author
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Serrano, Pauline N, Wang, Hongxin, Crack, Jason C, Prior, Christopher, Hutchings, Matthew I, Thomson, Andrew J, Kamali, Saeed, Yoda, Yoshitaka, Zhao, Jiyong, Hu, Michael Y, E., Ercan, Oganesyan, Vasily S, Le Brun, Nick E, and Cramer, Stephen P
- Subjects
Inorganic Chemistry ,Chemical Sciences ,Genetics ,Iron ,Iron-Sulfur Proteins ,Molecular Conformation ,Nitric Oxide ,Nitrogen Oxides ,Nitroso Compounds ,Quantum Theory ,gene regulation ,iron-sulfur clusters ,nitric oxide ,nuclear vibrational resonance spectroscopy ,synchrotron radiation ,Organic Chemistry ,Chemical sciences - Abstract
The reaction of protein-bound iron-sulfur (Fe-S) clusters with nitric oxide (NO) plays key roles in NO-mediated toxicity and signaling. Elucidation of the mechanism of the reaction of NO with DNA regulatory proteins that contain Fe-S clusters has been hampered by a lack of information about the nature of the iron-nitrosyl products formed. Herein, we report nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations that identify NO reaction products in WhiD and NsrR, regulatory proteins that use a [4Fe-4S] cluster to sense NO. This work reveals that nitrosylation yields multiple products structurally related to Roussin's Red Ester (RRE, [Fe2 (NO)4 (Cys)2 ]) and Roussin's Black Salt (RBS, [Fe4 (NO)7 S3 ]. In the latter case, the absence of 32 S/34 S shifts in the Fe-S region of the NRVS spectra suggest that a new species, Roussin's Black Ester (RBE), may be formed, in which one or more of the sulfide ligands is replaced by Cys thiolates.
- Published
- 2016
24. Hidden carbon in Earth's inner core revealed by shear softening in dense Fe₇C₃
- Author
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Chen, Bin, Li, Zeyu, Zhang, Dongzhou, Liu, Jiachao, Hu, Michael Y., Zhao, Jiyong, Bi, Wenli, Alp, E. Ercan, Xiao, Yuming, Chow, Paul, and Li, Jie
- Published
- 2014
25. Measurements of the Lamb-Mössbauer factor at simultaneous high-pressure-temperature conditions and estimates of the equilibrium isotopic fractionation of iron.
- Author
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Zhang, Dongzhou, Jackson, Jennifer M., Sturhahn, Wolfgang, Zhao, Jiyong, Ercan Alp, E., and Hu, Michael Y.
- Subjects
ISOTOPIC fractionation ,IRON isotopes ,DEBYE temperatures ,IRON ,MELTING points ,X-ray scattering ,IRON powder ,INELASTIC neutron scattering - Abstract
Isotopic fractionation has been linked to the lattice vibrations of materials through their phonon spectra. The Lamb-Mössbauer factor (fLM) has the potential to provide information about the lattice vibrations in materials. We constrain the temperature evolution of the fLM of γ- and ε-Fe at in situ high-P-T conditions between 1650 K and the melting point. We find that the vibrations of γ- and ε-Fe can be described using a quasiharmonic model with a pressure- and temperature-dependent Debye temperature computed from the measured fLM. From the Debye temperature, we derive the equilibrium isotopic fractionation β-factor of iron. Our results show that the quasiharmonic behavior of metallic iron would lower the value of lnβ
Fe 57/54 by 0.1‰ at 1600–2800 K and 50 GPa when compared to the extrapolation of room temperature nuclear resonant inelastic X‑ray scattering data. Our study suggests that anharmonicity may be more prevalent in Fe metal than in lower mantle minerals at 2800 K and 50 GPa, a relevant condition for the core formation, and the silicate mantle may be isotopically heavy in iron. [ABSTRACT FROM AUTHOR]- Published
- 2022
- Full Text
- View/download PDF
26. NRVS definition of O2 intermediates in an extradiol dioxygenase: correlation to crystallography and reactivity
- Author
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Sutherlin, Kyle D., Wasada-Tsutsui, Yuko, Mbughuni, Michael M., Rogers, Melanie S., Park, Kiyoung, Liu, Lei V., Kwak, Yeonju, Srnec, Martin, Böttger, Lars H., Frenette, Mathieu, Yoda, Yoshitaka, Kobayashi, Yasuhiro, Kurokuzu, Masayuki, Saito, Makina, Seto, Makoto, Hu, Michael, Zhao, Jiyong, Alp, E. Ercan, Lipscomb, John D., and Solomon, Edward I.
- Subjects
Molecular Structure ,Iron ,Spectrum Analysis ,Catechols ,Crystallography, X-Ray ,Vibration ,Article ,Dioxygenases ,Oxygen ,Bacterial Proteins ,Models, Chemical ,Coordination Complexes ,Mutation ,Brevibacterium ,Histidine ,Density Functional Theory - Abstract
The extradiol dioxygenases are a large subclass of mononuclear non-heme Fe enzymes that catalyze the oxidative cleavage of catechols distal to their OH groups. These enzymes are important in bioremediation, and there has been significant interest in understanding how they activate O(2). The extradiol dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) provides an opportunity to study this process, as two O(2) intermediates have been trapped and crystallographically defined using the slow substrate 4-nitrocatechol (4NC): a side-on Fe-O(2)-4NC species and a Fe-O(2)-4NC peroxy bridged species. Also with 4NC, two solution intermediates have been trapped in the H200N variant, where H200 provides a second-sphere hydrogen bond in the wild-type enzyme. While the electronic structure of these solution intermediates has been defined previously as Fe(III)-superoxo-catecholate and Fe(III)-peroxysemiquinone, their geometric structures are unknown. Nuclear resonance vibrational spectroscopy (NRVS) is an important tool for structural definition of non-heme Fe-O(2) intermediates, as all normal modes with Fe displacement have intensity in the NRVS spectrum. In this study, NRVS is used to define the geometric structure of the H200N-4NC solution intermediates in HPCD as an end-on Fe(III)-superoxocatecholate and an end-on Fe(III)-hydroperoxo-semiquinone. Parallel calculations are performed to define the electronic structures and protonation states of the crystallographically defined wild-type HPCD-4NC intermediates, where the side-on intermediate is found to be a Fe(III)-hydroperoxo-semiquinone. The assignment of this crystallographic intermediate is validated by correlation to the NRVS data through computational removal of H200. While the side-on hydroperoxo semiquinone intermediate is computationally found to be nonreactive in peroxide bridge formation, it is isoenergetic with a superoxo catecholate species that is competent in performing this reaction. This study provides insight into the relative reactivities of Fe(III)-superoxo and Fe(III)-hydroperoxo intermediates in non-heme Fe enzymes and into the role H200 plays in facilitating extradiol catalysis.
- Published
- 2018
27. Elucidation of the iron(IV)–oxo intermediate in the non-haem iron halogenase SyrB2
- Author
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Wong, Shaun D., Srnec, Martin, Matthews, Megan L., Liu, Lei V., Kwak, Yeonju, Park, Kiyoung, Bell, Caleb B., Alp, E. Ercan, Zhao, Jiyong, Yoda, Yoshitaka, Kitao, Shinji, Seto, Makoto, Krebs, Carsten, Bollinger, J. Martin, and Solomon, Edward I.
- Subjects
Halogenation ,Iron ,Biocatalysis ,Pseudomonas syringae ,Hydroxylation ,Oxidoreductases ,Article - Abstract
Mononuclear non-haem iron (NHFe) enzymes catalyse a broad range of oxidative reactions, including halogenation, hydroxylation, ring closure, desaturation and aromatic ring cleavage reactions. They are involved in a number of biological processes, including phenylalanine metabolism, the production of neurotransmitters, the hypoxic response and the biosynthesis of secondary metabolites. The reactive intermediate in the catalytic cycles of these enzymes is a high-spin S = 2 Fe(IV)=O species, which has been trapped for a number of NHFe enzymes, including the halogenase SyrB2 (syringomycin biosynthesis enzyme 2). Computational studies aimed at understanding the reactivity of this Fe(IV)=O intermediate are limited in applicability owing to the paucity of experimental knowledge about its geometric and electronic structure. Synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) is a sensitive and effective method that defines the dependence of the vibrational modes involving Fe on the nature of the Fe(IV)=O active site. Here we present NRVS structural characterization of the reactive Fe(IV)=O intermediate of a NHFe enzyme, namely the halogenase SyrB2 from the bacterium Pseudomonas syringae pv. syringae. This intermediate reacts via an initial hydrogen-atom abstraction step, performing subsequent halogenation of the native substrate or hydroxylation of non-native substrates. A correlation of the experimental NRVS data to electronic structure calculations indicates that the substrate directs the orientation of the Fe(IV)=O intermediate, presenting specific frontier molecular orbitals that can activate either selective halogenation or hydroxylation.
- Published
- 2013
28. 3D Motions of Iron in Six-Coordinate {FeNO}7 Hemes by Nuclear Resonance Vibration Spectroscopy.
- Author
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Peng, Qian, Pavlik, Jeffrey W., Silvernail, Nathan J., Alp, E. Ercan, Hu, Michael Y., Zhao, Jiyong, Sage, J. Timothy, and Scheidt, W. Robert
- Subjects
IRON ,HEME ,NUCLEAR resonance reactions ,VIBRATIONAL spectra ,PORPHYRINS - Abstract
The vibrational spectrum of a six-coordinate nitrosyl iron porphyrinate, monoclinic [Fe(T pFPP)(1-MeIm)(NO)] (T pFPP=tetra- para-fluorophenylporphyrin; 1-MeIm=1-methylimidazole), has been studied by oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS). The crystal was oriented to give spectra perpendicular to the porphyrin plane and two in-plane spectra perpendicular or parallel to the projection of the FeNO plane. These enable assignment of the FeNO bending and stretching modes. The measurements reveal that the two in-plane spectra have substantial differences that result from the strongly bonded axial NO ligand. The direction of the in-plane iron motion is found to be largely parallel and perpendicular to the projection of the bent FeNO on the porphyrin plane. The out-of-plane Fe-N-O stretching and bending modes are strongly mixed with each other, as well as with porphyrin ligand modes. The stretch is mixed with v
50 as was also observed for dioxygen complexes. The frequency of the assigned stretching mode of eight Fe-X-O (X=N, C, and O) complexes is correlated with the Fe−XO bond lengths. The nature of highest frequency band at ≈560 cm−1 has also been examined in two additional new derivatives. Previously assigned as the Fe−NO stretch (by resonance Raman), it is better described as the bend, as the motion of the central nitrogen atom of the FeNO group is very large. There is significant mixing of this mode. The results emphasize the importance of mode mixing; the extent of mixing must be related to the peripheral phenyl substituents. [ABSTRACT FROM AUTHOR]- Published
- 2016
- Full Text
- View/download PDF
29. Melting and phase relations of Fe-Ni-Si determined by a multi-technique approach.
- Author
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Dobrosavljevic, Vasilije V., Zhang, Dongzhou, Sturhahn, Wolfgang, Zhao, Jiyong, Toellner, Thomas S., Chariton, Stella, Prakapenka, Vitali B., Pardo, Olivia S., and Jackson, Jennifer M.
- Subjects
- *
MELTING , *IRON alloys , *MOSSBAUER spectroscopy , *CORE materials , *EARTH'S core , *IRON powder , *IRON - Abstract
• We measure the melting and solid phase relations of Fe 0.8 Ni 0.1 Si 0.1 up to 83 GPa. • Independent melt detection techniques show excellent agreement and reproducibility. • Synchrotron Mössbauer spectroscopy detects the very first onset of melting. • X-ray diffraction constrains in-situ sample pressure evolution during heating. • 10 mol% Si decreases the melting temperature of Fe 0.9 Ni 0.1 by up to 500 K at 150 GPa. Many studies have suggested silicon as a candidate light element for the cores of Earth and Mercury. However, the effect of silicon on the melting temperatures of core materials and thermal profiles of cores is poorly understood, due to disagreements among melt detection techniques, uncertainties in sample pressure evolution during heating, and sparsity of studies investigating the combined effects of nickel and silicon on the phase diagram of iron. In this study we develop a multi-technique approach for measuring the high-pressure melting and solid phase relations of iron alloys and apply it to Fe 0.8 Ni 0.1 Si 0.1 (Fe-11wt%Ni-5.3wt%Si), a composition compatible with recent estimates for the cores of Earth and Mercury. This approach combines results (20-83 GPa) from two atomic-level techniques: synchrotron Mössbauer spectroscopy (SMS) and synchrotron x-ray diffraction (XRD). Melting is independently detected by the loss of the Mössbauer signal, produced exclusively by solid-bound iron nuclei, and the onset of a liquid diffuse x-ray scattering signal. The use of a burst heating and background updating method for quantifying changes in the reference background during heating facilitates the determination of liquid diffuse signal onsets and leads to strong reproducibility and excellent agreement in melting temperatures determined separately by the two techniques. XRD measurements additionally constrain the hcp-fcc phase boundary and in-situ pressure evolution of the samples during heating. We apply our updated thermal pressure model to published SMS melting data on fcc -Fe and fcc -Fe 0.9 Ni 0.1 to precisely evaluate the effect of silicon on melting temperatures. We find that the addition of 10 mol% Si to Fe 0.9 Ni 0.1 reduces melting temperatures by ∼250 K at low pressures (<60 GPa) and flattens the hcp-fcc phase boundary. Extrapolating our results, we constrain the location of the hcp-fcc-liquid quasi-triple point at 147±14 GPa and 3140±90 K, which implies a melting temperature reduction of 500 K compared with Fe 0.9 Ni 0.1. The results demonstrate the advantages of combining complementary experimental techniques in investigations of melting under extreme conditions. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
30. Melting of compressed iron by monitoring atomic dynamics
- Author
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Jackson, Jennifer M., Sturhahn, Wolfgang, Lerche, Michael, Zhao, Jiyong, Toellner, Thomas S., Alp, E. Ercan, Sinogeikin, Stanislav V., Bass, Jay D., Murphy, Caitlin A., and Wicks, June K.
- Subjects
- *
SOLID-liquid interfaces , *SYNCHROTRONS , *SPECTRUM analysis , *MELTING points , *TEMPERATURE effect , *BANDWIDTHS , *PRESSURE , *INDUSTRIAL lasers - Abstract
Abstract: We present a novel method for detecting the solid–liquid phase boundary of compressed iron at high temperatures using synchrotron Mössbauer spectroscopy (SMS). Our approach is unique because the dynamics of the iron atoms are monitored. This process is described by the Lamb–Mössbauer factor, which is related to the mean-square displacement of the iron atoms. Focused synchrotron radiation with 1meV bandwidth passes through a laser-heated 57Fe sample inside a diamond-anvil cell, and the characteristic SMS time signature vanishes when melting occurs. At our highest compression measurement and considering thermal pressure, we find the melting point of iron to be T M =3025±115K at P=82±5GPa. When compared with previously reported melting points for iron using static compression methods with different criteria for melting, our melting trend defines a steeper positive slope as a function of pressure. The obtained melting temperatures represent a significant step toward a reliable melting curve of iron at Earth''s core conditions. For other terrestrial planets possessing cores with liquid portions rich in metallic iron, such as Mercury and Mars, the higher melting temperatures for compressed iron may imply warmer internal temperatures. [Copyright &y& Elsevier]
- Published
- 2013
- Full Text
- View/download PDF
31. Shear wave anisotropy of textured hcp-Fe in the Earth's inner core
- Author
-
Lin, Jung-Fu, Mao, Zhu, Yavaş, Hasan, Zhao, Jiyong, and Dubrovinsky, Leonid
- Subjects
- *
SHEAR waves , *ANISOTROPY , *ELASTICITY , *SEISMOLOGY , *HIGH pressure (Science) , *X-ray scattering , *IRON crystals , *EARTH'S core , *EARTH (Planet) - Abstract
Abstract: Many seismological studies have confirmed that Vp travels 3–4% faster along the rotation axis of the Earth than along the equatorial plane in the inner core, indicating that the inner core is elastically anisotropic. However, seismic and mineral physics observations of the polarized Vs are still emerging. Thus far, the Vs anisotropy of the constitute iron crystals at relevant pressures of the Earth''s core has remained mostly theoretical mainly because of the technical difficulties involved in measuring reliable Vs velocities of iron crystals. Here we have measured azimuthal Vs anisotropy of highly textured hcp-Fe at high pressures using nuclear resonant inelastic X-ray scattering, a technique sensitive to Vs, in a diamond anvil cell. Our results show that the azimuthal Vs is 2–4% faster along the crystallographic c axis than along the a axis at 158GPa and 172GPa. If one describes the Vp anisotropy of the inner core as a result of the textured hcp-Fe crystals, it is conceivable that azimuthal and polarized Vs anisotropies with a magnitude of a few percent also exist in the region. Since Vp and Vs of candidate iron phases behave quite differently in theoretical predictions, our results here indicate that future seismic observations of the Vs and Vp anisotropies of the inner core thus hold the key to deciphering the causes for the seismic and dynamic signatures as well as constitute iron phase(s) of the region. [Copyright &y& Elsevier]
- Published
- 2010
- Full Text
- View/download PDF
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