Download or read book Theoretical Studies of Mononuclear Non heme Iron Active Sites written by Arianna Bassan and published by . This book was released on 2004 with total page 86 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Spectroscopic and Theoretical Studies of Mononuclear Non heme Iron Enzymes written by Adrienne Renee Diebold and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Mononuclear non-heme iron enzymes are an important class with a wide range of medical, pharmaceutical and environmental applications. Within this class, the oxygen activating enzymes use Fe(II) to activate O2 for reaction with the substrate. The focus of this thesis is on understanding two major themes of the oxygen activating enzymes - the role of the (2His/1 carboxylate) facial triad and the initial O2 reaction steps of alpha-keto acid-dependent dioxygenases - using a combination of spectroscopic techniques and DFT calculations. For ferrous systems, abs/CD/MCD/VTVH MCD studies define the geometric and electronic structure of the ferrous site. In combination with DFT calculations, a structure/function picture of the ferrous sites is developed. To extend these studies to the initial steps of O2 binding, studies with NO as an O2 analogue ({FeNO}7/{FeO2}8) utilize EPR/abs/CD/MCD/VTVH MCD spectroscopy with DFT calculations to elucidate important effects of the substrate on the {FeNO}7 bond. These effects are used in the computational extension to the experimentally inaccessible O2 bound complexes giving insight into the initial steps of O2 binding and activation. Taken together, these studies shed light on the rational for facial triad ligation at the Fe(II) site in the oxygen activating enzymes and how the Fe(II) ligand set tunes the specific reactivity of these enzymes.

Download or read book Mononuclear Non heme Iron Dependent Enzymes Part B written by and published by Elsevier. This book was released on 2024-09-17 with total page 382 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mononuclear Non-heme Iron Dependent Enzymes, Volume 703 PART B focuses on methods for studying, characterizing, and leveraging the chemistry of mononuclear non-heme iron dependent enzymes. Chapters in this new release include Photoreduction for Rieske oxygenase chemistry, Insights into the Mechanisms of Rieske Oxygenases from Studying the Unproductive Activation of Dioxygen, Non-heme iron and 2-oxoglutarate enzymes catalyze cyclopropane and azacyclopropane formations, Obtaining precise metrics of substrate positioning in Fe(II)/2OG dependent enzymes using Hyperfine Sublevel Correlation Spectroscopy, Xe-pressurization studies for revealing substrate-entrance tunnels, and much more. Additional chapters cover A tale of two dehydrogenases involved in NADH recycling, Rieske oxygenases and/or their partner reductase proteins, Expression, assay and inhibition of 9-cis-epoxycarotenoid dioxygenase (NCED) from Solanum lycopersicum and Zea mays, Biocatalysis and non-heme iron enzymes, In vitro analysis of the three-component Rieske oxygenase cumene dioxygenase from Pseudomonas fluorescens IP01, Structure and function of carbazole 1,9a-dioxygenase, Characterization of a Mononuclear Nonheme Iron-dependent Mono-oxygenase OzmD in Oxazinomycin Biosynthesis, and much more. Provides detailed articles regarding how to study the structures and mechanisms of mononuclear non-heme iron dependent enzymes Guides readers on how to use partner proteins in non-heme iron enzyme catalysis Includes strategies to employ mononuclear non-heme iron enzymes in biocatalytic applications

Download or read book Iron containing Enzymes written by Sam P. De Visser and published by Royal Society of Chemistry. This book was released on 2011 with total page 463 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mononuclear iron containing enzymes are important intermediates in bioprocesses and have potential in the industrial biosynthesis of specific products. This book features topical review chapters by leaders in this field and its various sub-disciplines.

Download or read book X ray Absorption Spectroscopic Studies of Mononuclear Non heme Iron Enzymes written by and published by . This book was released on 1996 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fe-K-edge X-ray absorption spectroscopy (XAS) has been used to investigate the electronic and geometric structure of the iron active site in non-heme iron enzymes. A new theoretical extended X-ray absorption fine structure (EXAFS) analysis approach, called GNXAS, has been tested on data for iron model complexes to evaluate the utility and reliability of this new technique, especially with respect to the effects of multiple-scattering. In addition, a detailed analysis of the 1s-->3d pre-edge feature has been developed as a tool for investigating the oxidation state, spin state, and geometry of iron sites. Edge and EXAFS analyses have then been applied to the study of non-heme iron enzyme active sites.

Download or read book Magnetic Circular Dichroism Spectroscopic Studies of Mononuclear Non heme Iron Sites written by Elizabeth Gottlieb Pavel and published by . This book was released on 1997 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Spectroscopic and Theoretical Studies of Complexes which Model the Active Sites of Non heme Iron Proteins written by Carl A. Brown and published by . This book was released on 1994 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Mononuclear Non heme Iron Dependent Enzymes written by and published by Elsevier. This book was released on 2024-09-01 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mononuclear Non-heme Iron Dependent Enzymes, Volume 703 focuses on methods for studying, characterizing, and leveraging the chemistry of mononuclear non-heme iron dependent enzymes. Chapters in this new release include Photoreduction for Rieske oxygenase chemistry, Insights into the Mechanisms of Rieske Oxygenases from Studying the Unproductive Activation of Dioxygen, Non-heme iron and 2-oxoglutarate enzymes catalyze cyclopropane and azacyclopropane formations, Obtaining precise metrics of substrate positioning in Fe(II)/2OG dependent enzymes using Hyperfine Sublevel Correlation Spectroscopy, Xe-pressurization studies for revealing substrate-entrance tunnels, and much more. Additional chapters cover A tale of two dehydrogenases involved in NADH recycling, Rieske oxygenases and/or their partner reductase proteins, Expression, assay and inhibition of 9-cis-epoxycarotenoid dioxygenase (NCED) from Solanum lycopersicum and Zea mays, Biocatalysis and non-heme iron enzymes, In vitro analysis of the three-component Rieske oxygenase cumene dioxygenase from Pseudomonas fluorescens IP01, Structure and function of carbazole 1,9a-dioxygenase, Characterization of a Mononuclear Nonheme Iron-dependent Mono-oxygenase OzmD in Oxazinomycin Biosynthesis, and much more. Provides detailed articles regarding how to study the structures and mechanisms of mononuclear non-heme iron dependent enzymes Guides readers on how to use partner proteins in non-heme iron enzyme catalysis Includes strategies to employ mononuclear non-heme iron enzymes in biocatalytic applications

Download or read book Oxygen Activation in Mononuclear Non heme Iron Enzymes written by Serra Goudarzi and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Mononuclear non-heme iron (NHFe) enzymes catalyze a variety of reactions that are of pharmaceutical, industrial and environmental importance. A large number of these enzymes use a ferrous site to activate O2 for reaction with organic substrates, often requiring additional electrons from an outside source. These O2-activating NHFe enzymes can be divided into subclasses based on the cofactors used to supply these additional electrons. NHFe(II) enzymes generally possess a 2-His/1-(Asp/Glu) facial triad ligand set for binding of Fe(II), and they have been shown to utilize a general mechanistic strategy (GMS) for reaction with O2. The resting active sites of these enzymes (only Fe(II) bound) are six coordinate (6C) with the three protein derived ligands of the facial triad and three waters. When both cofactor and substrate are bound, the Fe(II) site loses a water ligand to become five coordinate (5C), opening a position for O2 to bind for reaction. NHFe(II) enzymes have d-d ligand field transitions in the near-IR region that are difficult to study because of their low absorption intensity and overlapping water and protein derived vibrations. A ferrous methodology using circular dichroism (CD), magnetic CD (MCD) and variable-temperature, variable-field (VTVH) MCD allows for determination of the active site geometric and electronic structures of these enzymes for development of functional insights. To extend these studies to the initial O2 binding step, NO is used as an unreactive analog of O2. The resulting {FeNO}7 (S = 3/2) complexes can be studied with absorbance, CD, MCD, VTVH MCD and electron paramagnetic resonance (EPR) to define the substrate interaction with the Fe(III) center that results from NO binding. These effects are used to gain insight into the experimentally inaccessible {FeO2}8 complexes with density functional theory calculations that are used to study the initial O2 activation steps. A major study of this thesis involves oxygen activation in deacetoxycephalosporin C synthase (DAOCS), a NHFe(II) enzyme that uses an alpha-ketoglutarate (aKG) cofactor to supply two electrons for its ring expansion of various penicillin substrates. A crystallographic study of DAOCS that did not observe simultaneous aKG and penicillin G (penG) binding to the same Fe(II) center led researchers to suggest a new sequential reaction for this enzyme, where reaction with aKG cofactor and O2 precedes substrate binding. Spectroscopic studies of the DAOCS Fe(II) site and its interaction with aKG and penG showed simultaneous binding of both is possible in solution. They further showed that the complex with aKG only was a mixture of 5C and 6C sites. A mixture of sites has not been observed in other enzymes of this class, which have been shown to remain as a single 6C site when aKG binds. This open coordination site allows for reaction with O2 in the absence of substrate, and this reaction was studied. Kinetic analysis of this reaction excludes the sequential reaction as a mechanistic possibility, because substrate binding cannot outpace the rapid decay of the intermediate that initiates the ring expansion. Comparison to the concerted reaction of the GMS, where both aKG and penG are bound before reaction with O2, shows that substrate binding activates the Fe site for a more kinetically efficient reaction with O2. This confirms the requirement for the general mechanistic strategy. The second major study of this thesis is on ETHE1, a member of a growing subclass of NHFe(II) enzymes that transforms sulfur containing substrates without a cofactor. ETHE1 dioxygenates glutathione persulfide (GSSH) to glutathione (GSH) and sulfite in a reaction that is similar to that of cysteine dioxygenase (CDO), but with monodentate (vs. bidentate in CDO) substrate coordination and a 2-His/1-Asp (vs. 3-His in CDO) ligand field. From MCD, GSS- binds directly to the iron active site causing coordination unsaturation to prime the site for O2 activation. {FeNO}7 complexes without and with GSSH were generated and spectroscopically characterized, and the new spectral features from persulfide binding to the Fe(III) were identified. Time-dependent density functional theory calculations were used to simulate the experimental absorbance spectra to determine the persulfide orientation in the active site (not known from crystallography). Comparison of these spectral features to those from monodentate cysteine binding in another enzyme of this subclass, isopenicillin N synthase (IPNS), shows that persulfide is a poorer donor than thiolate, but still results in an equivalent frontier molecular orbital (FMO) for reactivity. In IPNS, this reaction is an oxidative ring closure without incorporation of O2 atoms into the product. The persulfide dioxygenation reaction coordinate of ETHE1 was calculated, and while the initial steps are similar to the sulfur dioxygenation reaction coordinate of CDO, an additional hydrolysis step is required in ETHE1 to break the persulfide S-S bond. Unlike ETHE1 and CDO, which both oxygenate sulfur, IPNS oxidizes sulfur through an initial H-atom abstraction. Thus, the factors that control oxygenase vs. oxidase activity were evaluated. In general, sulfur oxygenation is thermodynamically favored and has a lower barrier for reactivity. However, in IPNS, second sphere residues in the active site pocket constrain the substrate raising the barrier for sulfur oxygenation relative to oxidation via H-atom abstraction.

Download or read book Spectroscopic Studies of the Non heme Iron Active Sites of Lipoxygenases and S written by Mark A. Pavlosky and published by . This book was released on 1994 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Computational Inorganic and Bioinorganic Chemistry written by Edward I. Solomon and published by John Wiley & Sons. This book was released on 2013-02-19 with total page 980 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the past several decades there have been major advances in our ability to computationally evaluate the electronic structure of inorganic molecules, particularly transition metal systems. This advancement is due to the Moore’s Law increase in computing power as well as the impact of density functional theory (DFT) and its implementation in commercial and freeware programs for quantum chemical calculations. Improved pure and hybrid density functionals are allowing DFT calculations with accuracy comparable to high-level Hartree-Fock treatments, and the results of these calculations can now be evaluated by experiment. When calculations are correlated to, and supported by, experimental data they can provide fundamental insight into electronic structure and its contributions to physical properties and chemical reactivity. This interplay continues to expand and contributes to both improved value of experimental results and improved accuracy of computational predictions. The purpose of this EIC Book is to provide state-of-the-art presentations of quantum mechanical and related methods and their applications, written by many of the leaders in the field. Part 1 of this volume focuses on methods, their background and implementation, and their use in describing bonding properties, energies, transition states and spectroscopic features. Part 2 focuses on applications in bioinorganic chemistry and Part 3 discusses inorganic chemistry, where electronic structure calculations have already had a major impact. This addition to the EIC Book series is of significant value to both experimentalists and theoreticians, and we anticipate that it will stimulate both further development of the methodology and its applications in the many interdisciplinary fields that comprise modern inorganic and bioinorganic chemistry. This volume is also available as part of Encyclopedia of Inorganic Chemistry, 5 Volume Set. This set combines all volumes published as EIC Books from 2007 to 2010, representing areas of key developments in the field of inorganic chemistry published in the Encyclopedia of Inorganic Chemistry. Find out more.

Download or read book Spectroscopic and Computational Studies of Peroxo Intermediates in Mononuclear Non heme Iron Enzymes and Their Model Complexes written by Lei Liu and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Mononuclear non-heme iron enzymes catalyze wide varieties of important biological reactions with industrial, medical, and environmental applications. These enzymes can be classified into two classes, O2 activating FeII enzymes and substrate activating FeIII enzymes. This thesis focuses on understanding the geometric and electronic structures of the peroxo level intermediates and their reactivities in two O2 activating FeII enzymes, bleomycin and Rieske dioxygenases related model complexes, by using a combination of spectroscopic and computational methods. Bleomycin 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 S = 1/2 FeIII--OOH species, termed activated bleomycin (ABLM). The 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 (EXAFS) spectroscopy and density functional theory (DFT) calculations are applied to define the natures of FeIIIBLM and ABLM as (BLM)FeIII--OH and (BLM)FeIII([eta]1--OOH) species, respectively. The NRVS spectra of FeIIIBLM and ABLM are strikingly different because in ABLM the Fe--O--O bending mode mixes with, and energetically splits, the doubly degenerate, intense O--Fe--Nax trans-axial 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. Previously, the rate of ABLM decay had been found, based on indirect methods, to be independent of the presence of DNA. In this thesis, we use a circular dichroism (CD) feature unique to ABLM to directly monitor the kinetics of ABLM reaction with a DNA oligonucleotide. Our results show that the ABLM + DNA reaction is appreciably faster, has a different kinetic isotope effect, and has a lower Arrhenius activation energy than does ABLM decay. In the ABLM reaction with DNA, the small normal kH/kD ratio is attributed to a secondary solvent effect through DFT vibrational analysis of reactant and transition state (TS) frequencies, and the lower Ea is attributed to the weaker bond involved in the abstraction reaction (C--H for DNA and N--H for the decay in the absence of DNA). The DNA dependence of the ABLM reaction indicates that DNA is involved in the TS for ABLM decay and thus reacts directly with (BLM)FeIII([eta]1--OOH) instead of its decay product. Oxygen-containing mononuclear iron species, FeIII--peroxo, FeIII--hydroperoxo and FeIV--oxo, are key intermediates in the catalytic activation of dioxygen by iron-containing metalloenzymes. It has been difficult to generate synthetic analogues of these three active iron--oxygen species in identical host complexes, which is necessary to elucidate changes to the structure of the iron center during catalysis and the factors that control their chemical reactivities with substrates. Here we report the high-resolution crystal structure of a mononuclear non-haem side-on FeIII--peroxo complex, [Fe(III)(TMC)(OO)]+. We also report a series of chemical reactions in which this iron(III)--peroxo complex is cleanly converted to the FeIII--hydroperoxo complex, [Fe(III)(TMC)(OOH)]2+, via a short-lived intermediate on protonation. This iron(III)--hydroperoxo complex then cleanly converts to the ferryl complex, [Fe(IV)(TMC)(O)]2+, via homolytic O--O bond cleavage of the iron(III)--hydroperoxo species. All three of these iron species--the three most biologically relevant iron--oxygen intermediates--have been spectroscopically characterized; we note that they have been obtained using a simple macrocyclic ligand. We have performed relative reactivity studies on these three iron species which reveal that the iron(III)--hydroperoxo complex is the most reactive of the three in the deformylation of aldehydes and that it has a similar reactivity to the iron(IV)--oxo complex in C--H bond activation of alkylaromatics. These reactivity results demonstrate that iron(III)--hydroperoxo species are viable oxidants in both nucleophilic and electrophilic reactions by iron-containing enzymes. The geometric and electronic structure and reactivity of an S = 5/2 (HS) mononuclear non-heme (TMC)FeIII-OOH complex was studied by spectroscopy, calculations, and kinetics for comparison to our past study of an S = 1/2 (LS) FeIII-OOH complex to understand their mechanisms of O-O bond homolysis and electrophilic H-atom abstraction. The homolysis reaction of the HS [(TMC)FeIII-OOH]2+ complex is found to involve axial ligand coordination and a crossing to the LS surface for O-O bond homolysis. Both HS and LS FeIII-OOH complexes are found to perform direct H-atom abstraction reactions but with very different reaction coordinates. For the LS FeIII-OOH, the transition state is late in O-O and early in C-H coordinates. However, for the HS FeIII-OOH, the transition state is early in O-O and further along in the C-H coordinate. In addition, there is a significant amount of electron transfer from substrate to HS FeIII-OOH at transition state, but does not occur in the LS transition state. Thus in contrast to the behavior of LS FeIII-OOH, the H-atom abstraction reactivity of HS FeIII-OOH is found to be highly dependent on both the ionization potential and C-H bond strength of substrate. LS FeIII-OOH is found to be more effective in H-atom abstraction for strong C-H bonds, while the higher reduction potential of HS FeIII-OOH allows it be active in electrophilic reactions without the requirement of O-O cleavage. This is relevant to the Rieske dioxygenases, which are proposed to use a HS FeIII-OOH to catalyze cis-dihydroxylation of a wide range of aromatic compounds. S K-edge XAS is a direct experimental probe of metal ion electronic structure as the pre-edge energy reflects its oxidation state, and the energy splitting pattern of the pre-edge transitions reflects its spin state. The combination of sulfur K-edge XAS and DFT calculations indicates that the electronic structures of {FeNO}7 (S = 3/2) (SMe2N4(tren)Fe(NO), complex I) and {FeNO}7 (S = 1/2) ((bme-daco)Fe(NO), complex II) are FeIII(S=5/2)--NO-- (S = 1) and FeIII(S=3/2)--NO-- (S = 1), respectively. When an axial ligand is computationally added to complex II, the electronic structure becomes FeII(S = 0)--NO[*] (S = 1/2). These studies demonstrate how the ligand field of the Fe center defines its spin state and thus changes the electron exchange, an important factor in determining the electron distribution over {FeNO}7 and {FeO2}8 sites.

Download or read book Models for Mononuclear Nonheme Iron Proteins written by Yu-Min Catherine Chiou and published by . This book was released on 1994 with total page 534 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Spectroscopic and Reactivity Studies of Mononuclear and Binuclear Non heme Iron Complexes written by Bala Sundari T. Kasibhatla and published by . This book was released on 1998 with total page 478 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book X ray Absorption Spectroscopic Studies of Mononuclear Non heme Iron Enzymes written by Tami E. Westre and published by . This book was released on 1996 with total page 674 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Spectroscopic Studies of Mononuclear Non heme Iron Sites in Lipoxygenases Clavaminate Synthase 2 and 1 aminocyclopropane 1 carboxylate Oxidase written by Jing Zhou and published by . This book was released on 2000 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Iron Containing Enzymes written by Samuel P de Visser and published by Royal Society of Chemistry. This book was released on 2011-08-04 with total page 463 pages. Available in PDF, EPUB and Kindle. Book excerpt: There are many mononuclear iron containing enzymes in nature that utilize molecular oxygen and transfer one or both oxygen atoms of O2 to substrates. These enzymes catalyze many processes including the biosynthesis of hormones, the metabolism of drugs, DNA and RNA base repair and, the biosynthesis of antibiotics. Therefore, mononuclear iron containing enzymes are important intermediates in bioprocesses and have great potential in the commercial biosynthesis of specific products since they often catalyze reactions regioselectively or stereospecifically. Understanding their mechanism and function is important and will assist in searches for commercial exploitation. In recent years, advances in experimental as well as theoretical methodologies have made it possible to study the mechanism and function of these enzymes and much information on their properties has been gained. This book highlighting recent developments in the field is, therefore, a timely addition to the literature and will interest a broad readership in the fields of biochemistry, inorganic chemistry and computational chemistry. The Editors, leaders in the field of nonheme and heme iron containing monoxygenases, have filled the book with topical review chapters by leaders in the various sub-disciplines.