Spectroscopic Probes of the Electronic Structure of Iron Thiolate Complexes and Their Relevance to Iron-sulfur Proteins PDF Download
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Author: Matthew Stewart Gebhard
Publisher:
ISBN:
Category :
Languages : en
Pages : 550
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Author: Matthew Stewart Gebhard
Publisher:
ISBN:
Category :
Languages : en
Pages : 550
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Author: Michael James Knapp
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Category :
Languages : en
Pages : 514
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Author: Ziliang Mao
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Category :
Languages : en
Pages :
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Iron-sulfur (FeS) clusters are ubiquitous in nature and play a wide range of important roles such as electron transfer, FeS cluster biogenesis, regulation of DNA repair, small molecule sensing, and the catalysis of chemical reactions, etc. They are also involved in many essential biological processes including photosynthesis and cellular respiration. Their electronic and vibrational dynamics are important to the understanding of their rich chemistry, but difficult to characterize because of their structural complexity and the fact that a large number of states exist in close proximity. Photo-induced chemical reactions involving FeS clusters have also attracted much attention recently. However, despite many studies on the light-induced dynamics of charge insertion in FeS complexes, the directly excited photodynamics is poorly known. This knowledge is important because it helps to unravel their photochemical properties as well as to learn how to better use them in light-induced charge transfer reactions. In this dissertation, the directly photo-excited dynamics in a series of FeS clusters, including the 1Fe-4S cluster in Pyrococcus furiosus rubredoxin (PfRd), the 2Fe-2S clusters in Rhodobacter capsulatus ferredoxin VI (Rc6) and Pseudomonas putida (Pdx), the 4Fe-4S cluster in nitrogenase iron protein, as well as the 8Fe-7S P-cluster and the 7Fe-9S-1Mo FeMo cofactor in nitrogenase MoFe protein, are characterized using ultrafast laser pump probe spectroscopy. Specifically, Chapter 1 of the thesis gives an overview of FeS clusters and the significance of studying their directly-excited photo-dynamics. Chapter 2 of the thesis introduces the ultrafast laser pump-probe spectroscopic techniques that are used for the study of these FeS complexes. Chapter 3 gives a brief overview of the global analysis methodology adopted for the analysis of the ultrafast transient absorption (TA) spectroscopic data. Chapter 4 reports a study on the ultrafast electronic relaxation dynamics in the 2Fe-2S cluster of Rc6 characterized using ultrafast TA spectroscopy. Multiple ligand-to-metal charge-transfer populations were found to be induced by laser excitation that evolve to low-lying states. Two long-lived states were identified. The longer one was attributed to a potential long-range electron-transfer pathway. Chapter 5 presents the impulsive coherent vibrational spectroscopic (ICVS) study on Rc6’s vibrational relaxation dynamics. Two ICVS bands were identified, with the 484 cm-1 band attributed to excited electronic state vibration. Its time-dependent shift in frequency is also consistent with the excited state evolution characterized in Chapter 4. Chapter 6 extends the study of charge-transfer dynamics in Rc6 to a series of FeS proteins that contain 1-Fe, 2-Fe, 4-Fe, 7-Fe and 8-Fe clusters: the 1Fe-4S cluster from PfRd, the 2Fe-2S cluster from Pdx, the 4Fe-4S cluster from nitrogenase iron protein, and the 8Fe-7S P-cluster and the 7Fe-9S-1Mo FeMo cofactor from nitrogenase MoFe protein. We aim to characterize and ultimately direct critical charge-transfer dynamics in these systems, as well as to study the cluster dependence of their electronic relaxation dynamics. A competition between the cluster dependence of reorganization energies and density of states was proposed to mediate the electronic relaxation lifetimes. Chapter 7 presents the early-stage development of a novel single-shot time-resolved infrared spectroscopic system that, once functional, can be used in the study of nitrogenase reaction intermediates that are too transient for conventional vibrational spectroscopic techniques to capture. Future directions for the improvement of this system are also discussed.In summary, the transient absorption spectroscopic studies on these important FeS clusters have contributed more insights to the directly photo-induced dynamics in these clusters. Understanding these dynamics holds potential to enable the utilization of these clusters in photo-activated chemical reactions such as solar fuel production.
Author: Tracey Rouault
Publisher: Walter de Gruyter GmbH & Co KG
ISBN: 3110478552
Category : Science
Languages : en
Pages : 547
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This volume on iron-sulfur proteins includes chapters that describe the initial discovery of iron-sulfur proteins in the 1960s to elucidation of the roles of iron sulfur clusters as prosthetic groups of enzymes, such as the citric acid cycle enzyme, aconitase, and numerous other proteins, ranging from nitrogenase to DNA repair proteins. The capacity of iron sulfur clusters to accept and delocalize single electrons is explained by basic chemical principles, which illustrate why iron sulfur proteins are uniquely suitable for electron transport and other activities. Techniques used for detection and stabilization of iron-sulfur clusters, including EPR and Mossbauer spectroscopies, are discussed because they are important for characterizing unrecognized and elusive iron sulfur proteins. Recent insights into how nitrogenase works have arisen from multiple advances, described here, including studies of high-resolution crystal structures.
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Category : Dissertation abstracts
Languages : en
Pages : 848
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Author:
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Category :
Languages : en
Pages : 472
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The research outlined in this dissertation focuses on understanding the role of metal-sulfur interactions as applied to bioinorganic and organometallic systems. This metal-sulfur interaction is analyzed using both gas-phase photoelectron spectroscopy (PES) and density functional theory (DFT). Gas-phase photoelectron spectroscopy is the most direct probe of electronic structure and is used in these studies to probe the molecular orbital energy levels of these model compounds, giving rise to an understanding of the metal and sulfur orbital interactions and characters (i.e. is an orbital primarily metal or sulfur based). Using density functional theory, orbital energies, overlap, and characters can be calculated and complement the PES experiments allowing for a detailed understanding of the electronic structure. The first part of my dissertation explains the design and implementation of a dual source gas-phase ultraviolet/X-ray photoelectron spectrometer (UPS/XPS). This gas-phase UPS/XPS can be used to quantify the bonding/antibonding character of frontier molecular orbitals, with specific applications to metal-sulfur interactions, allowing for a thorough analysis of the metal-sulfur interaction. The second part of the dissertation explores using model complexes, of the type Cpsub2subV(dithiolate) (where Cp is cyclopentadienyl and dithiolate is 1,2-ethenedithiolate or 1,2-benzenedithiolate), along with PES and DFT calculations to investigate the role of the pyranopterindithiolate cofactor and the dsup1supelectron configuration in modulating the redox potential and electron transfer in the active sites of molybdenum enzymes. This study shows that the dsup1supelectronic configuration offers a low energy electron transfer pathway for the reoxidation of the active site molybdenum center. The third part of the dissertation explores the use of model compounds that specifically focus on iron-thiolate interactions in biological systems, and the effect of electronic energy matching and sterics on the oxidation potential of this interaction. This study has shown that the metal-sulfur interaction is sensitive to the orientation of the thiolate ligand, and that during oxidation an"electronic-buffering effect"makes assigning a formal oxidation state to the metal center almost meaningless. All of these studies illustrate how the thiolate ligand can modulate the electron density and oxidation potential of the metal-sulfur interaction and the implication of this interaction to biological electron transfer.
Author: American Chemical Society. Committee on Professional Training
Publisher:
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Category : Chemical engineering
Languages : en
Pages : 1646
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Author: Xiangjin Xie
Publisher:
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Category :
Languages : en
Pages :
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Metal sites that are known to be involved in biological electron transfer (ET) include Type 1 Copper (T1 Cu), CuA, cytochromes, and the 1-, 2-, 3-, and 4-iron sulfur centers (rubredoxin, ferredoxins, and high potential iron-sulfur proteins (HiPIPs)). These ET sites generally exhibit unusual spectroscopic features reflecting novel geometric and electronic structures that contribute to function. My focuses are on T1 Cu, CuA, cytochrome c proteins utilizing a wide-range of spectroscopies combined with density functional calculations to understand active site electronic structures, the origin of their geometric structures, and possible contributions to function. Five major achievements are: 1) defined the temperature dependent absorption feature of T1 Cu site in nitrite reductase (NIR) and provided insight into the entatic/rack nature of the blue Cu site in plastocyanin; 2) addressed the interesting absorption features of the T1 Cu site in P. pantotrophus pseudoazurin and demonstrated the spectral probes of the weak axial ligation in metalloprotein; 3) resolved a two-state issue in the mixed-valence binuclear CuA centers in cytochrome c oxidases (CcO) and nitrous oxide reductases (N2O) by a combination of density functional calculations and spectroscopy analyses, and evaluated proteins role in CuA sites and their contributions to ET function; 4) determined that the Cu-Cu interaction in CuA keeps the site delocalized even upon loss of a Histidine (NHis) ligand due to protonation, and defined the contribution of [sigma] delocalization to efficient ET; 5) investigated the nature of the Fe-SMet bond in ferricytochrome c. (1) Thermodynamic Equilibrium between Blue and Green Copper Sites and the Role of the Protein in Controlling Function Spectroscopies and density functional theory calculations indicate that there are large temperature-dependent absorption spectral changes present in green nitrite reductases (NiRs) due to a thermodynamic equilibrium between a green and a blue type 1 (T1) copper site. The axial methionine (Met) ligand is unconstrained in the oxidized NiRs, which results in an enthalpically favored ([delta]H [approximately equal to] 4.6 kcal/mol) Met-bound green copper site at low temperatures, and an entropically favored (T[delta]S [approximately equal to] 4.5 kcal/mol, at room temperature) Met-elongated blue copper site at elevated temperatures. In contrast to the NiRs, the classic blue copper sites in plastocyanin and azurin show no temperature-dependent behavior, indicating that a single species is present at all temperatures. For these blue copper proteins, the polypeptide matrix opposes the gain in entropy that would be associated with the loss of the weak axial Met ligand at physiological temperatures by constraining its coordination to copper. The potential energy surfaces of Met binding indicate that it stabilizes the oxidized state more than the reduced state. This provides a mechanism to tune down the reduction potential of blue copper sites by> 200 mV. (2) Variable Temperature Spectroscopic Study on Pseudoazurin: Effects of Protein Constraints on the Blue Cu Site. The T1 copper site of Paracoccus pantotrophus pseudoazurin exhibits significant absorption intensity in both the 450 and 600 nm regions. These are [sigma] and [pi] SCys to Cu2+ charge transfer (CT) transitions. The temperature dependent absorption, EPR, and resonance Raman (rR) vibrations enhanced by these bands indicate that a single species is present at all temperatures. This contrasts the temperature dependent behavior of the T1 center in nitrite reductase, which has a thioether ligand that is unconstrained by the protein. The lack of temperature dependence in the T1 site in pseudoazurin indicates the presence of a protein constraint similar to the blue Cu site in plastocyanin where the thioether ligand is constrained at 2.8 Å. However, plastocyanin exhibits only [pi] CT. This spectral difference between pseudoazurin and plastocyanin reflects a coupled distortion of the site where the axial thioether in pseudoazurin is also constrained, but at a shorter Cu--SMet bond length. This leads to an increase in the Cu2+--SCys bond length, and the site undergoes a partial tetragonal distortion in pseudoazurin. Thus, its ground state wavefunction has both [sigma] and [pi] character in the Cu2+--SCys bond. (3) The Two State Issue in the Mixed-Valence Binuclear CuA Center in Cytochrome c Oxidase and N2O Reductase For the CuA site in the protein, the ground and lowest energy excited-states are [sigma]u* and [pi]u, respectively, denoting the types of Cu-Cu interactions. EPR data on CuA proteins show a low g[vertical line][vertical line] value of 2.19 deriving from spin-orbital coupling between [sigma]u* and [pi]u, which requires an energy gap between [sigma]u* and [pi]u of 3000-4500 cm-1. On the other hand, from paramagnetic NMR studies, it has been observed that the first excited-state is thermally accessible and the energy gap between the ground state and the thermally accessible state is 350 cm-1. This study addressed this apparent discrepancy and evaluated the roles of the two electronic states, [sigma]u* and [pi]u, in electron transfer (ET) of CuA. The potential energy surface calculations show that both NMR and EPR results are consistent within the electronic/geometric structure of CuA. The anti-Curie behavior observed in paramagnetic NMR studies of CuA results from the thermal equilibrium between the [sigma]u* and [pi]u states, which are at very close energies in their respective equilibrium geometries. Alternatively, the EPR g-value analysis involves the [sigma]u* ground state in the geometry with a short dCu-Cu where the [pi]u state is a Frank-Condon excited-state with the energy of 3200 cm-1. The protein environment plays a role in maintaining CuA in the [sigma]u* state as a lowest-energy state with the lowest reorganization energy and high-covalent coupling to the Cys and His ligands for efficient intra- and intermolecular ET with a low-driving force. (4) Perturbations to the Geometric and Electronic Structure of the CuA Site: Factors that Influence Delocalization and their Contributions to Electron Transfer Using a combination of electronic spectroscopies and DFT calculations, the effect of pH perturbation on the geometric and electronic structure of the CuA site has been defined. Descriptions are developed for high pH (pH = 7) and low pH (pH = 4) forms of CuA azurin and its H120A mutant which address the discrepancies concerning the extent of delocalization indicated by multifrequency EPR and ENDOR data. Our resonance Raman and MCD spectra demonstrate that the low pH and H120A mutant forms are essentially identical and are the perturbed forms of the completely delocalized high pH CuA site. However, in going from high pH to low pH, a seven-line hyperfine coupling pattern associated with complete delocalization of the electron (S = 1/2) over two Cu coppers (ICu = 3/2) changes into a four-line pattern reflecting apparent localization. DFT calculations show that the unpaired electron is delocalized in the low pH form and reveal that its four-line hyperfine pattern results from the large EPR spectral effects of 1% 4s orbital contribution of one Cu to the ground-state spin wave function upon protonative loss of its His ligand. The contribution of the Cu-Cu interaction to electron delocalization in this low symmetry protein site is evaluated, and the possible functional significance of the pH-dependent transition in regulating proton-coupled electron transfer in cytochrome c oxidase is discussed. (5) The Fe-Smet Bond in Ferricytochrome c DFT calculations calibrated with experiment data were used to define the nature of the Fe-SMet bond in ferricytochrome c. This is inspired by the studies of NiR.
Author: G.J Long
Publisher: Springer Science & Business Media
ISBN: 148992289X
Category : Science
Languages : en
Pages : 652
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In 1988 the Mossbauer effect community completed 30 years of continual contribution to the fields of nuclear physics, solid state science, and a variety of related disciplines. To celebrate this anniversary, Professor Gonser of the Universitat des Saarlandes has contributed a chapter to this volume on the history of the effect. Although Mossbauer spectroscopy has reached its mature years, the chapters in this volume illustrate that it is still a dynamic field of science with applications to topics ranging from permanent magnets to biologi cal mineralization. During the discussion of a possible chapter for this volume, a potential author asked, "Do we really need another Mossbauer book?" The editors responded in the affirmative because they believe that a volume of this type offers several advantages. First, it provides the author with an opportunity to write a personal view of the subject, either with or without extensive pedagogic content. Second, there is no artificially imposed restriction on length. In response to the question, "How long should my chapter be?," we have responded that it should be as long as is necessary to clearly present, explain, and evaluate the topic. In this type of book, it is not necessary to condense the topic into two, four, or eight pages as is now so often a requirement for publication in the research literature.
Author:
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 776
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