Spectroscopic and computational studies of peroxo intermediates in mononuclear non-heme iron enzymes and their model complexes
Abstract/Contents
- Abstract
- 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.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2013 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Liu, Lei |
|---|---|
| Associated with | Stanford University, Department of Chemistry |
| Primary advisor | Solomon, Edward I |
| Thesis advisor | Solomon, Edward I |
| Thesis advisor | Hodgson, Keith |
| Thesis advisor | Pande, Vijay |
| Advisor | Hodgson, Keith |
| Advisor | Pande, Vijay |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Lei Liu. |
|---|---|
| Note | Submitted to the Department of Chemistry. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2013. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2013 by Lei Liu
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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