Structure-function correlations of copper active sites : X-ray absorption spectroscopy and DFT calculations
Abstract/Contents
- Abstract
- Copper-containing enzymes are ubiquitous in nature and catalyze diverse reactions including O2 binding, activation and reduction. It has been shown that each class of copper-containing enzyme has active sites with unique structures that determine their diverse specific functions. Thus, the goals of this dissertation are to define the structure-function correlations of Cu active sites in enzymes and related model complexes with a focus on the application of metal K- and L-edge X-ray absorption spectroscopy (XAS) coupled with density functional theory (DFT) calculations. The Cu K-edge methodology developed throughout the dissertation is used to study the structure of an OLED (organic light-emitting diode) Cu complex in the final chapter of this dissertation. A brief summary of the nine different studies discussed in this dissertation is given below. "Geometric and Electronic Structure of [{Cu(MeAN)}2(μ-η2:η2(O22-))]2+ with an Unusually Long O--O Bond: O--O Bond Weakening vs Activation for Reductive Cleavage" Certain side-on peroxo dicopper(II) species with particularly low υO--O (710-730 cm-1) have been found in equilibrium with their bis-μ-oxo dicopper(III) isomer. An issue is whether such side-on peroxo bridges are further activated for O--O cleavage. In a previous study (Liang, H.-C., et al., J. Am. Chem. Soc. 2002, 124, 4170-4171), we showed that oxygenation of the three-coordinate complex [CuI(MeAN)]+ (MeAN=N-methyl-N, N-bis[3-(dimethylamino)propyl]amine) leads to a low-temperature stable [{CuII(MeAN)}2(μ-η2:η2-O22-)]2+ peroxo species with low υO--O (721 cm-1), as characterized by UV-Vis absorption and resonance Raman (rR) spectroscopies. Here, this complex has been crystallized as its SbF6-- salt and an X-ray structure indicates the presence of an unusually long O--O bond (1.540(5) Å) consistent with the low υO--O. EXAFS and rR spectroscopic and reactivity studies indicate the exclusive formation of [{CuII(MeAN)}2(μ-η2:η2-O22-)]2+ without any bis-μ-oxo-dicopper(III) isomer present. This is the first structure of a side-on peroxo dicopper(II) species with a significantly long and weak O--O bond. DFT calculations show that the weak O--O bond results from strong σ donation from the MeAN ligand to Cu that is compensated by a decrease in the extent of peroxo to Cu charge transfer. Importantly, the weak O--O bond does not reflect an increase in backbonding into the σ* orbital of the peroxide. Thus, although the O--O bond is unusually weak, this structure is not further activated for reductive cleavage to form a reactive bis-μ-oxo-dicopper(III) species. These results highlight the necessity of understanding electronic structure changes associated with spectral changes for correlations to reactivity. "L-edge X-ray Absorption Spectroscopy and DFT Calculations on Cu2O2 Species: Electrophilic Reaction Coordinate of Side-on Peroxo Cu(II)2 Bridged Complexes" The hydroxylation of aromatic substrates catalyzed by coupled binuclear copper enzymes has been observed with side-on-peroxo-dicopper(II) (P) and bis-μ-oxo-dicopper(III) (O) model complexes. The substrate-bound-O intermediate in [Cu(II)2(DBED)2(O)2]2+ (DBED=N, N'-di-tert-butyl-ethylenediamine) was shown to perform aromatic hydroxylation. For the [Cu(II)2(NO2-XYL)(O2)]2+ complex, only a P species was spectroscopically observed. However, it was not clear whether this O-O bond cleaves to proceed through an O-type structure along the reaction coordinate for hydroxylation of the aromatic xylyl linker. Accurate evaluation of these reaction coordinates requires reasonable quantitative descriptions of the electronic structures of the P and O species. We have performed Cu L-edge XAS on two well-characterized P and O species to experimentally quantify the Cu 3d character in their ground state wavefunctions. The lower per-hole Cu character (40 ± 6%) corresponding to higher covalency in species O compared to species P (52 ± 4%) reflects a stronger bonding interaction of the bis-μ-oxo core with the Cu(III) centers. DFT calculations show that 10-20% Hartree-Fock (HF) mixing for P and 38% for O species are required to reproduce the Cu-O bonding; for the P species this HF mixing is also required for an antiferromagnetically coupled description of the two Cu(II) centers. B3LYP (with 20% HF) was, therefore, used to calculate the hydroxylation reaction coordinate of P in [Cu(II)2(NO2-XYL)(O2)]2+. These experimentally calibrated calculations indicate that the electrophilic attack on the aromatic ring does not involve formation of a O species. Rather, there is direct electron donation from the aromatic ring into the peroxo σ* orbital, leading to concerted C-O bond formation with O-O bond cleavage. "Heme-Copper-Dioxygen Complexes: Toward Understanding Ligand-Environmental Effects on the Coordination Geometry, Electronic Structure, and Reactivity" The nature of the ligand is an important aspect of controlling structure and reactivity in coordination chemistry. In connection with our study of heme/copper/oxygen reactivity relevant to cytochrome c oxidase O2-reduction chemistry, we compare the molecular and electronic structure of two high-spin heme-peroxo-copper [FeIII-O22--CuII]+ complexes containing N4-tetradentate (1) or N3-tridentate (2) copper ligands. Combining previously reported and new resonance Raman and EXAFS data coupled to DFT calculations we report a geometric structure and more complete electronic description of the high-spin heme-peroxo-copper complexes 1 and 2, which establish μ-(O22-) side-on to the FeIII and end-on to CuII (μ-η2:η1) binding for the complex 1 but side-on/side-on (μ-η2:η2) μ-peroxo coordination for the complex 2. We also compare and summarize the differences and similarities of these two complexes in their reactivity toward CO, PPh3, acid and phenols. The comparison of a new X-ray structure of µ-oxo complex 1a with the previously reported 2a X-ray structure, two thermal decomposition products respectively of 1 and 2, reveals a considerable difference in the Fe-O-Cu angle between the two µ-oxo complexes (∠Fe-O-Cu = 178.2° in 1a, ∠Fe-O-Cu = 149.5° in 2a). The reaction of 2 with one equivalent of exogenous N-donor axial base leads to the formation of new low-temperature stable low-spin heme-peroxo-Cu complex (2b), but under the same conditions the addition of an axial base to 1 leads to the dissociation of the heme-peroxo-Cu assembly and the release of O2. 2b react with phenols performing Hydrogen-atom (e- + H+) abstraction resulting in O-O bond cleavage and the formation of high-valence ferryl-oxo [FeIV=O] complex (2c). The nature of 2c was confirmed by comparison of its spectroscopic features and reactivity with those of an authentic ferryl complex. The phenoxyl radical generated by the hydrogen-atom abstraction was directly detected by EPR spectroscopy using phenols that produce stable radicals or by detection of the coupling product of two phenoxyl radicals. "Spectroscopic Elucidation of a New Structure Type in Heme/Cu Dioxygen Chemistry: Implications for O—O Bond Rupture in Cytochrome c Oxidase" This study details the structural characterization of the low-spin (S = 0) heme-peroxo-Cu complex {[(F8)Fe(DCHIm)]-O2-[Cu(AN)]}+ (2) that reacts with phenols performing hydrogen-atom abstraction and results in O-O bond cleavage and the formation of a high-valence ferryl-oxo [FeIV=O] complex. A similar ferryl-oxo species is formed in cytochrome c oxidase (CcO) following the four electron reduction of dioxygen by the binuclear heme Fe-Cu site. Species 2 is thus a reactive analog of CcO. It is generated by addition of a coordinating base to the high-spin (S = 2) parent complex {[(F8)Fe]- O2-[Cu(AN)]}+ (1) in which the O22- bridges the metals in an μ-η2:η2 or "side-on" mode. Cu and Fe K-edge X-ray absorption and resonance Raman (rR) spectroscopies have been coupled to density functional theory (DFT) calculations to determine that the O22- bridging ligand in 2 is bound to the metals in a μ-1,2 or "end-on" configuration. This low-spin (S = 0) end-on peroxo species is compared to the high-spin (S = 2) end-on peroxo species formed in resting CcO to gain insight into possible factors that affect dioxygen reduction by the enzyme. "Systematic Perturbation of the Trinuclear Copper Cluster in the Multicopper Oxidases: The Role of Active Site Asymmetry in its Reduction of O2 to H2O" The multicopper oxidase Fet3p catalyzes the four-electron reduction of dioxygen to water, coupled to the one-electron oxidation of four equivalents of substrate. To carry out this process the enzyme utilizes four Cu atoms: a type 1, a type 2, and a coupled binuclear, type 3 site. Substrates are oxidized at the T1 Cu, which rapidly shuttles electrons, 13 Å away, to a trinuclear copper cluster (TNC) composed of the T2 and T3 sites where dioxygen is reduced to water. This study focuses on two variants of Fet3p, H126Q and H483Q; H126 is ligand to T3 Cuα and H483 is ligand to T3 Cuβ. The variants have been isolated in both holo and type 1 depleted (T1D) form and their TNCs have been characterized in their oxidized and reduced states. Importantly, while the two variants are spectroscopically similar, T1DH126Q (T3α mutation) reacts with O2 to form the peroxide intermediate (PI) while T1DH483Q (T3β mutation) does not. This is shown to be due to the structural asymmetry of the TNC. The reduced T3β Cu is structurally activated to react with O2 and residue D94 provides a negative charge that drives the two-electron reduction of dioxygen to peroxide specifically on the T3β-T2 edge of the TNC. Furthermore, this asymmetry promotes tight binding of peroxide in PI, rapid electron transfer from T1 to the TNC and strong frontier molecular orbital (FMO) interactions to rapidly cleave the O-O bond, and facile elimination of water from the TNC upon reduction of NI. "Modified Reactivity Towards O2 in First Shell Variants ... .
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 | Qayyum, Munzarin Fatema |
|---|---|
| Associated with | Stanford University, Department of Chemistry. |
| Primary advisor | Hodgson, Keith |
| Primary advisor | Solomon, Edward I |
| Thesis advisor | Hodgson, Keith |
| Thesis advisor | Solomon, Edward I |
| Thesis advisor | Hedman, B. (Britt), 1949- |
| Thesis advisor | Zare, Richard N |
| Advisor | Hedman, B. (Britt), 1949- |
| Advisor | Zare, Richard N |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Munzarin Fatema Qayyum. |
|---|---|
| Note | Submitted to the Department of Chemistry. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2013. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2013 by Munzarin Fatema Qayyum
Also listed in
Loading usage metrics...