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Yoshitaka Yoda - One of the best experts on this subject based on the ideXlab platform.
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Nuclear Resonance vibrational spectroscopic definition of the facial triad feiv o intermediate in taurine dioxygenase evaluation of structural contributions to hydrogen atom abstraction
Journal of the American Chemical Society, 2020Co-Authors: Yoshitaka Yoda, Yasuhiro Kobayashi, Kiyoung Park, Kyle D Sutherlin, Martin Srnec, Shyam R Iyer, Laura M K Dassama, Shaun D Wong, Masayuki KurokuzuAbstract:The α-ketoglutarate (αKG)-dependent oxygenases catalyze a diverse range of chemical reactions using a common high-spin FeIV═O intermediate that, in most reactions, abstract a hydrogen atom from the substrate. Previously, the FeIV═O intermediate in the αKG-dependent halogenase SyrB2 was characterized by Nuclear Resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations, which demonstrated that it has a trigonal-pyramidal geometry with the scissile C-H bond of the substrate calculated to be perpendicular to the Fe-O bond. Here, we have used NRVS and DFT calculations to show that the FeIV═O complex in taurine dioxygenase (TauD), the αKG-dependent hydroxylase in which this intermediate was first characterized, also has a trigonal bipyramidal geometry but with an aspartate residue replacing the equatorial halide of the SyrB2 intermediate. Computational analysis of hydrogen atom abstraction by square pyramidal, trigonal bipyramidal, and six-coordinate FeIV═O complexes in two different substrate orientations (one more along [σ channel] and another more perpendicular [π channel] to the Fe-O bond) reveals similar activation barriers. Thus, both substrate approaches to all three geometries are competent in hydrogen atom abstraction. The equivalence in reactivity between the two substrate orientations arises from compensation of the promotion energy (electronic excitation within the d manifold) required to access the π channel by the significantly larger oxyl character present in the pπ orbital oriented toward the substrate, which leads to an earlier transition state along the C-H coordinate.
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caught in the hinact crystal structure and spectroscopy reveal a sulfur bound to the active site of an o2 stable state of fefe hydrogenase
Angewandte Chemie, 2020Co-Authors: Yoshitaka Yoda, Stephen P Cramer, Patricia Rodriguezmacia, Lisa M Galle, Ragnar Bjornsson, Christian Lorent, Ingo Zebger, Serena Debeer, Ingrid SpanAbstract:[FeFe] hydrogenases are the most active H2 converting catalysts in nature, but their extreme oxygen sensitivity limits their use in technological applications. The [FeFe] hydrogenases from sulfate reducing bacteria can be purified in an O2 -stable state called Hinact . To date, the structure and mechanism of formation of Hinact remain unknown. Our 1.65 A crystal structure of this state reveals a sulfur ligand bound to the open coordination site. Furthermore, in-depth spectroscopic characterization by X-ray absorption spectroscopy (XAS), Nuclear Resonance vibrational spectroscopy (NRVS), Resonance Raman (RR) spectroscopy and infrared (IR) spectroscopy, together with hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, provide detailed chemical insight into the Hinact state and its mechanism of formation. This may facilitate the design of O2 -stable hydrogenases and molecular catalysts.
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a Nuclear Resonance vibrational spectroscopic study of oxy myoglobins reconstituted with chemically modified heme cofactors insights into the fe o2 bonding and internal dynamics of the protein
Biochemistry, 2018Co-Authors: Takehiro Ohta, Yoshitaka Yoda, Makoto Seto, Yasuhiro Kobayashi, Tomokazu Shibata, Takashi Ogura, Saburo Neya, Akihiro Suzuki, Yasuhiko YamamotoAbstract:The molecular mechanism of O2 binding to hemoglobin (Hb) and myoglobin (Mb) is a long-standing issue in the field of bioinorganic and biophysical chemistry. The nature of Fe–O2 bond in oxy Hb and Mb had been extensively investigated by Resonance Raman spectroscopy, which assigned the Fe–O2 stretching bands at ∼570 cm–1. However, Resonance Raman assignment of the vibrational mode had been elusive due to the spectroscopic selection rule and to the limited information available about the ground-state molecular structure. Thus, Nuclear Resonance vibrational spectroscopy was applied to oxy Mbs reconstituted with 57Fe-labeled native heme cofactor and two chemically modified ones. This advanced spectroscopy in conjunction with DFT analyses gave new insights into the nature of the Fe–O2 bond of oxy heme by revealing the effect of heme peripheral substitutions on the vibrational dynamics of heme Fe atom, where the main Fe–O2 stretching band of the native protein was characterized at ∼420 cm–1.
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Nuclear Resonance vibrational spectroscopy definition of o2 intermediates in an extradiol dioxygenase correlation to crystallography and reactivity
Journal of the American Chemical Society, 2018Co-Authors: Kyle D Sutherlin, Kiyoung Park, Yuko Wasadatsutsui, Michael M Mbughuni, Melanie S Rogers, Yeonju Kwak, Martin Srnec, Lars H Bottger, Mathieu Frenette, Yoshitaka YodaAbstract:The extradiol dioxygenases are a large subclass of monoNuclear nonheme 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 O2. The extradiol dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) provides an opportunity to study this process, as two O2 intermediates have been trapped and crystallographically defined using the slow substrate 4-nitrocatechol (4NC): a side-on Fe–O2–4NC species and a Fe–O2–4NC 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 FeIII-superoxo-catecholate and FeIII-peroxy-semiquinone, their geometric structures are unknown. Nuclear Resonance vibrational spectroscopy (NRVS) is an important tool for struc...
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nrvs studies of the peroxide shunt intermediate in a rieske dioxygenase and its relation to the native feii o2 reaction
Journal of the American Chemical Society, 2018Co-Authors: Kyle D Sutherlin, Yoshitaka Yoda, Shinji Kitao, Kiyoung Park, Melanie S Rogers, Martin Srnec, Lars H Bottger, Brent S Rivard, Yasuhiro KobayashiAbstract:The Rieske dioxygenases are a major subclass of monoNuclear nonheme iron enzymes that play an important role in bioremediation. Recently, a high-spin FeIII–(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...
Hongxin Wang - One of the best experts on this subject based on the ideXlab platform.
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high frequency fe h vibrations in a bridging hydride complex characterized by nrvs and dft
Angewandte Chemie, 2018Co-Authors: Vladimir Pelmenschikov, Hongxin Wang, Stephen P Cramer, Cory K Macleod, Sean F Mcwilliams, Kazimer L Skubi, Patrick L HollandAbstract:: High-spin iron species with bridging hydrides have been detected in species trapped during nitrogenase catalysis, but there are few general methods of evaluating Fe-H bonds in high-spin multiNuclear iron systems. An 57 Fe Nuclear Resonance vibrational spectroscopy (NRVS) study on an Fe(μ-H)2 Fe model complex reveals Fe-H stretching vibrations for bridging hydrides at frequencies greater than 1200 cm-1 . These isotope-sensitive vibrational bands are not evident in infrared (IR) spectra, showing the power of NRVS for identifying hydrides in this high-spin iron system. Complementary density functional theory (DFT) calculations elucidate the normal modes of the rhomboidal iron hydride core.
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reaction coordinate leading to h2 production in fefe hydrogenase identified by Nuclear Resonance vibrational spectroscopy and density functional theory
Journal of the American Chemical Society, 2017Co-Authors: Vladimir Pelmenschikov, Hongxin Wang, Edward J Reijerse, Cindy C Pham, Kenji Tamasaku, James A Birrell, Nakul Mishra, Constanze Sommer, Casseday P Richers, Yoshitaka YodaAbstract:[FeFe]-hydrogenases are metalloenzymes that reversibly reduce protons to molecular hydrogen at exceptionally high rates. We have characterized the catalytically competent hydride state (Hhyd) in the [FeFe]-hydrogenases from both Chlamydomonas reinhardtii and Desulfovibrio desulfuricans using 57Fe Nuclear Resonance vibrational spectroscopy (NRVS) and density functional theory (DFT). H/D exchange identified two Fe–H bending modes originating from the biNuclear iron cofactor. DFT calculations show that these spectral features result from an iron-bound terminal hydride, and the Fe–H vibrational frequencies being highly dependent on interactions between the amine base of the catalytic cofactor with both hydride and the conserved cysteine terminating the proton transfer chain to the active site. The results indicate that Hhyd is the catalytic state one step prior to H2 formation. The observed vibrational spectrum, therefore, provides mechanistic insight into the reaction coordinate for H2 bond formation by [FeF...
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hydride bridge in nife hydrogenase observed by Nuclear Resonance vibrational spectroscopy
Nature Communications, 2015Co-Authors: Hideaki Ogata, Frank Neese, Hongxin Wang, Tobias Kramer, David Schilter, Vladimir Pelmenschikov, Maurice Van Gastel, Thomas B RauchfussAbstract:The metabolism of many anaerobes relies on [NiFe]-hydrogenases, whose characterization when bound to substrates has proven non-trivial. Presented here is direct evidence for a hydride bridge in the active site of the (57)Fe-labelled fully reduced Ni-R form of Desulfovibrio vulgaris Miyazaki F [NiFe]-hydrogenase. A unique 'wagging' mode involving H(-) motion perpendicular to the Ni(μ-H)(57)Fe plane was studied using (57)Fe-specific Nuclear Resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(μ-D)(57)Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe-CO/CN bands. Spectra have been interpreted by comparison with Ni(μ-H/D)(57)Fe enzyme mimics [(dppe)Ni(μ-pdt)(μ-H/D)(57)Fe(CO)3](+) and DFT calculations, which collectively indicate a low-spin Ni(II)(μ-H)Fe(II) core for Ni-R, with H(-) binding Ni more tightly than Fe. The present methodology is also relevant to characterizing Fe-H moieties in other important natural and synthetic catalysts.
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spectroscopic investigations of fefe hydrogenase maturated with 57fe2 adt cn 2 co 4 2
Journal of the American Chemical Society, 2015Co-Authors: Ryan Gilbertwilson, Wolfgang Lubitz, Hongxin Wang, Stephen P Cramer, Edward J Reijerse, Cindy C Pham, Agnieszka Adamskavenkatesh, Judith F Siebel, Thomas B RauchfussAbstract:The preparation and spectroscopic characterization of a CO-inhibited [FeFe] hydrogenase with a selectively (57)Fe-labeled biNuclear subsite is described. The precursor [(57)Fe2(adt)(CN)2(CO)4](2-) was synthesized from the (57)Fe metal, S8, CO, (NEt4)CN, NH4Cl, and CH2O. (Et4N)2[(57)Fe2(adt)(CN)2(CO)4] was then used for the maturation of the [FeFe] hydrogenase HydA1 from Chlamydomonas reinhardtii, to yield the enzyme selectively labeled at the [2Fe]H subcluster. Complementary (57)Fe enrichment of the [4Fe-4S]H cluster was realized by reconstitution with (57)FeCl3 and Na2S. The Hox-CO state of [2(57)Fe]H and [4(57)Fe-4S]H HydA1 was characterized by Mossbauer, HYSCORE, ENDOR, and Nuclear Resonance vibrational spectroscopy.
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synthesis and vibrational spectroscopy of 57fe labeled models of nife hydrogenase first direct observation of a nickel iron interaction
Chemical Communications, 2014Co-Authors: David Schilter, Hongxin Wang, Thomas B Rauchfuss, Vladimir Pelmenschikov, Yoshitaka Yoda, Leland B Gee, Florian Meier, Martin Kaupp, Stephen P CramerAbstract:A new route to iron carbonyls has enabled synthesis of (57)Fe-labeled [NiFe] hydrogenase mimic (OC)3(57)Fe(pdt)Ni(dppe). Its study by Nuclear Resonance vibrational spectroscopy revealed Ni-(57)Fe vibrations, as confirmed by calculations. The modes are absent for [(OC)3(57)Fe(pdt)Ni(dppe)](+), which lacks Ni-(57)Fe bonding, underscoring the utility of the analyses in identifying metal-metal interactions.
Stephen P Cramer - One of the best experts on this subject based on the ideXlab platform.
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caught in the hinact crystal structure and spectroscopy reveal a sulfur bound to the active site of an o2 stable state of fefe hydrogenase
Angewandte Chemie, 2020Co-Authors: Yoshitaka Yoda, Stephen P Cramer, Patricia Rodriguezmacia, Lisa M Galle, Ragnar Bjornsson, Christian Lorent, Ingo Zebger, Serena Debeer, Ingrid SpanAbstract:[FeFe] hydrogenases are the most active H2 converting catalysts in nature, but their extreme oxygen sensitivity limits their use in technological applications. The [FeFe] hydrogenases from sulfate reducing bacteria can be purified in an O2 -stable state called Hinact . To date, the structure and mechanism of formation of Hinact remain unknown. Our 1.65 A crystal structure of this state reveals a sulfur ligand bound to the open coordination site. Furthermore, in-depth spectroscopic characterization by X-ray absorption spectroscopy (XAS), Nuclear Resonance vibrational spectroscopy (NRVS), Resonance Raman (RR) spectroscopy and infrared (IR) spectroscopy, together with hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, provide detailed chemical insight into the Hinact state and its mechanism of formation. This may facilitate the design of O2 -stable hydrogenases and molecular catalysts.
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high frequency fe h vibrations in a bridging hydride complex characterized by nrvs and dft
Angewandte Chemie, 2018Co-Authors: Vladimir Pelmenschikov, Hongxin Wang, Stephen P Cramer, Cory K Macleod, Sean F Mcwilliams, Kazimer L Skubi, Patrick L HollandAbstract:: High-spin iron species with bridging hydrides have been detected in species trapped during nitrogenase catalysis, but there are few general methods of evaluating Fe-H bonds in high-spin multiNuclear iron systems. An 57 Fe Nuclear Resonance vibrational spectroscopy (NRVS) study on an Fe(μ-H)2 Fe model complex reveals Fe-H stretching vibrations for bridging hydrides at frequencies greater than 1200 cm-1 . These isotope-sensitive vibrational bands are not evident in infrared (IR) spectra, showing the power of NRVS for identifying hydrides in this high-spin iron system. Complementary density functional theory (DFT) calculations elucidate the normal modes of the rhomboidal iron hydride core.
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Nuclear Resonance Vibrational Spectroscopy and Electron Paramagnetic Resonance Spectroscopy of 57Fe-Enriched [FeFe] Hydrogenase Indicate Stepwise Assembly of the H‑Cluster
2016Co-Authors: Stephen P CramerAbstract:ABSTRACT: The [FeFe] hydrogenase from Clostridium pasteurianum (CpI) harbors four Fe−S clusters that facilitate the transfer of an electron to the H-cluster, a ligand-coordinated six-iron prosthetic group that catalyzes the redox interconversion of protons and H2. Here, we have used 57Fe Nuclear Resonance vibrational spectroscopy (NRVS) to study the iron centers in CpI, and we compare our data to that for a [4Fe-4S] ferredoxin as well as a model complex resembling the [2Fe]H catalytic domain of the H-cluster. To enrich the hydrogenase with 57Fe nuclei, we used cell-free methods to post-translationally mature the enzyme. Specifically, inactive CpI apoprotein with 56Fe-labeled Fe−S clusters was activated in vitro using 57Fe-enriched maturation proteins. This approach enabled us to selectively label the [2Fe]H subcluster with 57Fe, which NRVS confirms b
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spectroscopic investigations of fefe hydrogenase maturated with 57fe2 adt cn 2 co 4 2
Journal of the American Chemical Society, 2015Co-Authors: Ryan Gilbertwilson, Wolfgang Lubitz, Hongxin Wang, Stephen P Cramer, Edward J Reijerse, Cindy C Pham, Agnieszka Adamskavenkatesh, Judith F Siebel, Thomas B RauchfussAbstract:The preparation and spectroscopic characterization of a CO-inhibited [FeFe] hydrogenase with a selectively (57)Fe-labeled biNuclear subsite is described. The precursor [(57)Fe2(adt)(CN)2(CO)4](2-) was synthesized from the (57)Fe metal, S8, CO, (NEt4)CN, NH4Cl, and CH2O. (Et4N)2[(57)Fe2(adt)(CN)2(CO)4] was then used for the maturation of the [FeFe] hydrogenase HydA1 from Chlamydomonas reinhardtii, to yield the enzyme selectively labeled at the [2Fe]H subcluster. Complementary (57)Fe enrichment of the [4Fe-4S]H cluster was realized by reconstitution with (57)FeCl3 and Na2S. The Hox-CO state of [2(57)Fe]H and [4(57)Fe-4S]H HydA1 was characterized by Mossbauer, HYSCORE, ENDOR, and Nuclear Resonance vibrational spectroscopy.
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synthesis and vibrational spectroscopy of 57fe labeled models of nife hydrogenase first direct observation of a nickel iron interaction
Chemical Communications, 2014Co-Authors: David Schilter, Hongxin Wang, Thomas B Rauchfuss, Vladimir Pelmenschikov, Yoshitaka Yoda, Leland B Gee, Florian Meier, Martin Kaupp, Stephen P CramerAbstract:A new route to iron carbonyls has enabled synthesis of (57)Fe-labeled [NiFe] hydrogenase mimic (OC)3(57)Fe(pdt)Ni(dppe). Its study by Nuclear Resonance vibrational spectroscopy revealed Ni-(57)Fe vibrations, as confirmed by calculations. The modes are absent for [(OC)3(57)Fe(pdt)Ni(dppe)](+), which lacks Ni-(57)Fe bonding, underscoring the utility of the analyses in identifying metal-metal interactions.
Yuming Xiao - One of the best experts on this subject based on the ideXlab platform.
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dynamics of rhodobacter capsulatus 2fe 2s ferredoxin vi and aquifex aeolicus ferredoxin 5 via Nuclear Resonance vibrational spectroscopy nrvs and Resonance raman spectroscopy
Biochemistry, 2008Co-Authors: Yuming Xiao, Toshiko Ichiye, Hongxin Wang, W Sturhahn, Jiyong Zhao, Yoshitaka Yoda, Matthew Smith, Jacques Meyer, Stephen P CramerAbstract:We have used 57Fe Nuclear Resonance vibrational spectroscopy (NRVS) to study the Fe2S2(Cys)4 sites in oxidized and reduced [2Fe-2S] ferredoxins from Rhodobacter capsulatus (Rc FdVI) and Aquifex aeolicus (Aa Fd5). In the oxidized forms, nearly identical NRVS patterns are observed, with strong bands from Fe−S stretching modes peaking around 335 cm−1, and additional features observed as high as the B2u mode at ∼421 cm−1. Both forms of Rc FdVI have also been investigated by Resonance Raman (RR) spectroscopy. There is good correspondence between NRVS and Raman frequencies, but because of different selection rules, intensities vary dramatically between the two kinds of spectra. For example, the B3u mode at ∼288 cm−1, attributed to an asymmetric combination of the two FeS4 breathing modes, is often the strongest Resonance Raman feature. In contrast, it is nearly invisible in the NRVS, as there is almost no Fe motion in such FeS4 breathing. NRVS and RR analysis of isotope shifts with 36S-substituted into bridging...
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characterization of the fe site in iron sulfur cluster free hydrogenase hmd and of a model compound via Nuclear Resonance vibrational spectroscopy nrvs
Inorganic Chemistry, 2008Co-Authors: Yuming Xiao, Hongxin Wang, Thomas B Rauchfuss, Vladimir Pelmenschikov, Sonja Vogt, Rudolf K Thauer, Seigo Shima, Phillip I Volkers, David A CaseAbstract:We have used 57 Fe Nuclear Resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO)2-ligated Fe model compound, Fe(S2C2H4)(CO)2(PMe3)2 ,a s well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey–Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results. For Hmd, previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm -1 , interpreted as evidence for cis-Fe(CO)2 ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm -1 , consistent with the proposed cis-Fe(CO)2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at ∼311 cm -1 and another reproducible feature at ∼380 cm -1 . The 57 Fe partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey–Bradley force field for a five-coordinate cis-(CO)2-ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A “truncated” model without a water ligand can also be used to match the NRVS data. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a three-dimensional structure for the active site.
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observation of terahertz vibrations in pyrococcus furiosus rubredoxin via impulsive coherent vibrational spectroscopy and Nuclear Resonance vibrational spectroscopy interpretation by molecular mechanics
Journal of Inorganic Biochemistry, 2007Co-Authors: Anna Rita Bizzarri, Toshiko Ichiye, Cristian Manzoni, Giulio Cerullo, Salvatore Cannistraro, Yuming XiaoAbstract:We have used impulsive coherent vibrational spectroscopy (ICVS) to study the Fe(S-Cys)(4) site in oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). In this experiment, a 15 fs visible laser pulse is used to coherently pump the sample to an excited electronic state, and a second <10 fs pulse is used to probe the change in transmission as a function of the time delay. PfRd was observed to relax to the ground state by a single exponential decay with time constants of approximately 255-275 fs. Superimposed on this relaxation are oscillations caused by coherent excitation of vibrational modes in both excited and ground electronic states. Fourier transformation reveals the frequencies of these modes. The strongest ICV mode with 570 nm excitation is the symmetric Fe-S stretching mode near 310 cm(-1), compared to 313 cm(-1) in the low temperature Resonance Raman. If the rubredoxin is pumped at 520 nm, a set of strong bands occurs between 20 and 110 cm(-1). Finally, there is a mode at approximately 500 cm(-1) which is similar to features near 508 cm(-1) in blue Cu proteins that have been attributed to excited state vibrations. Normal mode analysis using 488 protein atoms and 558 waters gave calculated spectra that are in good agreement with previous Nuclear Resonance vibrational spectra (NRVS) results. The lowest frequency normal modes are identified as collective motions of the entire protein or large segments of polypeptide. Motion in these modes may affect the polar environment of the redox site and thus tune the electron transfer functions in rubredoxins.
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normal mode analysis of pyrococcus furiosus rubredoxin via Nuclear Resonance vibrational spectroscopy nrvs and Resonance raman spectroscopy
Journal of the American Chemical Society, 2005Co-Authors: Yuming Xiao, Francis E. Jenney, Michael W W Adams, Hongxin Wang, Simon J George, Matt C Smith, W Sturhahn, Jiyong Zhao, Yoshitaka Yoda, Edward I SolomonAbstract:We have used 57Fe Nuclear Resonance vibrational spectroscopy (NRVS) to study the Fe(Scys)4 site in reduced and oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). The oxidized form has also bee...
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normal mode analysis of fecl4 and fe2s2cl42 via vibrational mossbauer Resonance raman and ft ir spectroscopies
Inorganic Chemistry, 2005Co-Authors: Matt C Smith, Yuming Xiao, Hongxin Wang, Simon J George, W Sturhahn, Jiyong Zhao, Ercan E Alp, Dimitri Coucouvanis, Markos Koutmos, Stephen P CramerAbstract:[NEt4][FeCl4], [P(C6H5)4][FeCl4], and [NEt4]2[Fe2S2Cl4] have been examined using 57Fe Nuclear Resonance vibrational spectroscopy (NRVS). These complexes serve as simple models for Fe−S clusters in metalloproteins. The 57Fe partial vibrational density of states (PVDOS) spectra were interpreted by computation of the normal modes assuming Urey−Bradley force fields, using additional information from infrared and Raman spectra. Previously published force constants were used as initial values; the new constraints from NRVS frequencies and amplitudes were then used to refine the force field parameters in a nonlinear least-squares analysis. The normal-mode calculations were able to quantitatively reproduce both the frequencies and the amplitudes of the intramolecular-mode 57Fe PVDOS. The optimized force constants for bending, stretching, and nonbonded interactions agree well with previously reported values. In addition, the NRVS technique also allowed clear observation of anion−cation lattice modes below 100 cm-1...
W Sturhahn - One of the best experts on this subject based on the ideXlab platform.
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sound velocity and density of magnesiowustites implications for ultralow velocity zone topography
Geophysical Research Letters, 2017Co-Authors: W Sturhahn, Jennifer M Jackson, J K Wicks, Dongzhou ZhangAbstract:We explore the effect of Mg/Fe substitution on the sound velocities of iron-rich (Mg_(1 – x)Fe_x)O, where x = 0.84, 0.94, and 1.0. Sound velocities were determined using Nuclear Resonance inelastic X-ray scattering as a function of pressure, approaching those of the lowermost mantle. The systematics of cation substitution in the Fe-rich limit has the potential to play an important role in the interpretation of seismic observations of the core-mantle boundary. By determining a relationship between sound velocity, density, and composition of (Mg,Fe)O, this study explores the potential constraints on ultralow-velocity zones at the core-mantle boundary.
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Nuclear Resonance vibrational spectroscopy applied to fe oep no the vibrational assignments of five coordinate ferrous heme nitrosyls and implications for electronic structure
Inorganic Chemistry, 2010Co-Authors: Nicolai Lehnert, W Sturhahn, Florian Paulat, Mary Grace I Galinato, George B Richteraddo, Jiyong ZhaoAbstract:This study presents Nuclear Resonance Vibrational Spectroscopy (NRVS) data on the five-coordinate (5C) ferrous heme−nitrosyl complex [Fe(OEP)(NO)] (1, OEP2− = octaethylporphyrinato dianion) and the corresponding 15N18O 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 ν(Fe−NO) and the in-plane Fe−N−O bending mode δip(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 forc...
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dynamics of rhodobacter capsulatus 2fe 2s ferredoxin vi and aquifex aeolicus ferredoxin 5 via Nuclear Resonance vibrational spectroscopy nrvs and Resonance raman spectroscopy
Biochemistry, 2008Co-Authors: Yuming Xiao, Toshiko Ichiye, Hongxin Wang, W Sturhahn, Jiyong Zhao, Yoshitaka Yoda, Matthew Smith, Jacques Meyer, Stephen P CramerAbstract:We have used 57Fe Nuclear Resonance vibrational spectroscopy (NRVS) to study the Fe2S2(Cys)4 sites in oxidized and reduced [2Fe-2S] ferredoxins from Rhodobacter capsulatus (Rc FdVI) and Aquifex aeolicus (Aa Fd5). In the oxidized forms, nearly identical NRVS patterns are observed, with strong bands from Fe−S stretching modes peaking around 335 cm−1, and additional features observed as high as the B2u mode at ∼421 cm−1. Both forms of Rc FdVI have also been investigated by Resonance Raman (RR) spectroscopy. There is good correspondence between NRVS and Raman frequencies, but because of different selection rules, intensities vary dramatically between the two kinds of spectra. For example, the B3u mode at ∼288 cm−1, attributed to an asymmetric combination of the two FeS4 breathing modes, is often the strongest Resonance Raman feature. In contrast, it is nearly invisible in the NRVS, as there is almost no Fe motion in such FeS4 breathing. NRVS and RR analysis of isotope shifts with 36S-substituted into bridging...
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interplay of structure and vibrational dynamics in six coordinate heme nitrosyls
Journal of the American Chemical Society, 2007Co-Authors: Nathan J Silvernail, W Sturhahn, Jiyong Zhao, Ercan E Alp, Alexander Barabanschikov, Jeffrey W Pavlik, Bruce C Noll, Timothy J Sage, Robert W ScheidtAbstract:The isolation of two polymorphic forms of nitrosyl(1-methylimidazole)(tetra-p-fluorophenylporphinato)iron(II) provides a unique opportunity to explore the interplay of structure and vibrational dynamics in six-coordinate {FeNO}7 nitrosyliron porphyrinates. The two species display differing vibrational spectroscopic properties both in νNO (IR) and the iron vibrational modes obtained through the use of Nuclear Resonance vibrational spectroscopy. Structural characterization of the two complexes has yielded extremely high-quality structures that further confirm that coordination of NO leads to ligand tilting and asymmetry in the equatorial Fe−Np bond distances. The two polymorphic structures (monoclinic and triclinic crystal systems) differ in the relative orientations of the two axial ligands and small but significant differences in coordination group bond distances. Although DFT calculations suggest that the NO/imidazole orientations should be indistinguishable, real experimental (structural and vibrational...
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first principles calculation of Nuclear Resonance vibrational spectra
Hyperfine Interactions, 2007Co-Authors: Taras Petrenko, W Sturhahn, Frank NeeseAbstract:We present a ‘first-principles’ methodology for the calculation of the parameters that are required for the simulation of Nuclear Resonance vibrational spectra (NRVS) of molecular systems. Formulae are given for the intensities of vibrational transitions corresponding to the so-called single- and double-phonon contributions to the NRVS signal. The method is also valid for those vibrations that are not in the high-frequency/low-temperature limit. We have rigorously treated the issue of orientational averaging of the Lamb–Mossbauer factor and the effect of the neglect of its anisotropy on the calculated NRVS pattern. Normal mode composition factors are determined in a compact form as appropriate components of an orthogonal matrix that diagonalizes the Hessian matrix. The method is illustrated by simulating the NRVS spectra and the partial vibrational density of states of [FeO(H2O)5]2+ on the basis of vibrational frequencies and normal mode composition factors obtained from density functional theory (DFT) calculations.
