Ryan G. Hadt

Copper Active Sites in Biology

Based on its generally accessible I/II redox couple and bioavailability, copper plays a wide variety of roles in nature that mostly involve electron transfer (ET), O2 binding, activation and reduction, NO2− and N2O reduction and substrate activation. Copper sites that perform ET are the mononuclear blue Cu site that has a highly covalent CuII-S(Cys) bond and the binuclear CuA site that has a Cu2S(Cys)2 core with a Cu-Cu bond that keeps the site delocalized (Cu(1.5)2) in its oxidized state. In contrast to inorganic Cu complexes, these metalloprotein sites transfer electrons rapidly often over long distances, as has been previously reviewed.1–4 Blue Cu and CuA sites will only be considered here in their relation to intramolecular ET in multi-center enzymes. The focus of this review is on the Cu enzymes (Figure 1). Many are involved in O2 activation and reduction, which has mostly been thought to involve at least two electrons to overcome spin forbiddenness and the low potential of the one electron reduction to superoxide (Figure 2).5,6 Since the Cu(III) redox state has not been observed in biology, this requires either more than one Cu center or one copper and an additional redox active organic cofactor. The latter is formed in a biogenesis reaction of a residue (Tyr) that is also Cu catalyzed in the first turnover of the protein. Recently, however, there have been a number of enzymes suggested to utilize one Cu to activate O2 by 1e− reduction to form a Cu(II)-O2•− intermediate (an innersphere redox process) and it is important to understand the active site requirements to drive this reaction. The oxidases that catalyze the 4e−reduction of O2 to H2O are unique in that they effectively perform this reaction in one step indicating that the free energy barrier for the second two-electron reduction of the peroxide product of the first two-electron step is very low. In nature this requires either a trinuclear Cu cluster (in the multicopper oxidases) or a Cu/Tyr/Heme Fe cluster (in the cytochrome oxidases). The former accomplishes this with almost no overpotential maximizing its ability to oxidize substrates and its utility in biofuel cells, while the latter class of enzymes uses the excess energy to pump protons for ATP synthesis. In bacterial denitrification, a mononuclear Cu center catalyzes the 1e- reduction of nitrite to NO while a unique µ4S2−Cu4 cluster catalyzes the reduction of N2O to N2 and H2O, a 2e− process yet requiring 4Cu’s. Finally there are now several classes of enzymes that utilize an oxidized Cu(II) center to activate a covalently bound substrate to react with O2. Figure 1 Copper active sites in biology. Figure 2 Latimer Diagram for Oxygen Reduction at pH = 7.0 Adapted from References 5 and 6. This review presents in depth discussions of all these classes of Cu enzymes and the correlations within and among these classes. For each class we review our present understanding of the enzymology, kinetics, geometric structures, electronic structures and the reaction mechanisms these have elucidated. While the emphasis here is on the enzymology, model studies have significantly contributed to our understanding of O2 activation by a number of Cu enzymes and are included in appropriate subsections of this review. In general we will consider how the covalency of a Cu(II)–substrate bond can activate the substrate for its spin forbidden reaction with O2, how in binuclear Cu enzymes the exchange coupling between Cu’s overcomes the spin forbiddenness of O2 binding and controls electron transfer to O2 to direct catalysis either to perform two e− electrophilic aromatic substitution or 1e− H-atom abstraction, the type of oxygen intermediate that is required for H-atom abstraction from the strong C-H bond of methane (104 kcal/mol) and how the trinuclear Cu cluster and the Cu/Tyr/Heme Fe cluster achieve their very low barriers for the reductive cleavage of the O-O bond. Much of the insight available into these mechanisms in Cu biochemistry has come from the application of a wide range of spectroscopies and the correlation of spectroscopic results to electronic structure calculations. Thus we start with a tutorial on the different spectroscopic methods utilized to study mononuclear and multinuclear Cu enzymes and their correlations to different levels of electronic structure calculations.

Tracking excited-state charge and spin dynamics in iron coordination complexes

Crucial to many light-driven processes in transition metal complexes is the absorption and dissipation of energy by 3d electrons. But a detailed understanding of such non-equilibrium excited-state dynamics and their interplay with structural changes is challenging: a multitude of excited states and possible transitions result in phenomena too complex to unravel when faced with the indirect sensitivity of optical spectroscopy to spin dynamics and the flux limitations of ultrafast X-ray sources. Such a situation exists for archetypal polypyridyl iron complexes, such as [Fe(2,2′-bipyridine)3]2+, where the excited-state charge and spin dynamics involved in the transition from a low- to a high-spin state (spin crossover) have long been a source of interest and controversy. Here we demonstrate that femtosecond resolution X-ray fluorescence spectroscopy, with its sensitivity to spin state, can elucidate the spin crossover dynamics of [Fe(2,2′-bipyridine)3]2+ on photoinduced metal-to-ligand charge transfer excitation. We are able to track the charge and spin dynamics, and establish the critical role of intermediate spin states in the crossover mechanism. We anticipate that these capabilities will make our method a valuable tool for mapping in unprecedented detail the fundamental electronic excited-state dynamics that underpin many useful light-triggered molecular phenomena involving 3d transition metal complexes.

Spectroscopic definition of the copper active sites in mordenite: selective methane oxidation.

Two distinct [Cu-O-Cu](2+) sites with methane monooxygenase activity are identified in the zeolite Cu-MOR, emphasizing that this Cu-O-Cu active site geometry, having a ∠Cu-O-Cu ∼140°, is particularly formed and stabilized in zeolite topologies. Whereas in ZSM-5 a similar [Cu-O-Cu](2+) active site is located in the intersection of the two 10 membered rings, Cu-MOR provides two distinct local structures, situated in the 8 membered ring windows of the side pockets. Despite their structural similarity, as ascertained by electronic absorption and resonance Raman spectroscopy, the two Cu-O-Cu active sites in Cu-MOR clearly show different kinetic behaviors in selective methane oxidation. This difference in reactivity is too large to be ascribed to subtle differences in the ground states of the Cu-O-Cu sites, indicating the zeolite lattice tunes their reactivity through second-sphere effects. The MOR lattice is therefore functionally analogous to the active site pocket of a metalloenzyme, demonstrating that both the active site and its framework environment contribute to and direct reactivity in transition metal ion-zeolites.

Interpretation of the UV−vis Spectra of the meso(Ferrocenyl)-Containing Porphyrins using a TDDFT Approach: Is Gouterman’s Classic Four-Orbital Model Still in Play?

The vertical excitation energies of H(2)TPP [TPP = 5,10,15,20-tetraphenylporphyrin(2-)], H(2)FcPh(3)P [FcPh(3)P = 5-ferrocenyl-10,15,20-triphenylporphyrin(2-)], cis-H(2)Fc(2)Ph(2)P [cis-Fc(2)Ph(2)P = 5,10-bisferrocenyl-15,20-diphenylporphyrin (2-)], trans-H(2)Fc(2)Ph(2)P [trans-Fc(2)Ph(2)P = 5,15-bisferrocenyl-10,20-diphenylporphyrin(2-)], H(2)Fc(3)PhP [H(2)Fc(3)PhP = 5,10,15-trisferrocenyl-20-phenylporphyrin(2-)], and H(2)TFcP [TFcP = 5,10,15,20-tetraferrocenylporphyrin(2-)] were investigated using a time-dependent density functional theory (DFT) approach and compared to their experimental UV-vis spectra in the 10,000-30,000 cm(-1) region. It was shown that the lowest energy transitions in meso(ferrocenyl)-containing porphyrins have predominantly ferrocene-to-porphyrin charge transfer character, while the porphyrin-centered π-π* transitions predicted by the Goutermans classic four-orbital model still have the largest intensities in the UV-vis region. The number of predominantly ferrocene-to-porphyrin charge transfer transitions increases with the number of ferrocene substituents and becomes dominant in H(2)TFcP.

Influence of iron doping on tetravalent nickel content in catalytic oxygen evolving films

Significance Iron-doped nickel oxide films are the most active nonnoble metal oxygen evolution reaction (OER) catalysts in alkaline electrolyte. Since Corrigan’s original discovery of enhanced activity with Fe doping in nickel oxides, the chemical basis for this synergy remains unclear. Recent studies suggest iron to assume a high valent oxidation state, thus promoting OER. We provide evidence for an alternative role of Fe3+ as a Lewis acid in the host nickel oxide. We observe that Fe3+ promotes the formation of Ni4+, which leads to enhanced catalytic activity. This result is consistent with Fe3+ to be one of the strongest Lewis acidic metals by any measure of Lewis acidity, including hard–soft acid base theory, metal ion pKas, and chemical inertness. Iron doping of nickel oxide films results in enhanced activity for promoting the oxygen evolution reaction (OER). Whereas this enhanced activity has been ascribed to a unique iron site within the nickel oxide matrix, we show here that Fe doping influences the Ni valency. The percent of Fe3+ doping promotes the formation of formal Ni4+, which in turn directly correlates with an enhanced activity of the catalyst in promoting OER. The role of Fe3+ is consistent with its behavior as a superior Lewis acid.

Bilirubin oxidase from Bacillus pumilus: A promising enzyme for the elaboration of efficient cathodes in biofuel cells

A CotA multicopper oxidase (MCO) from Bacillus pumilus, previously identified as a laccase, has been studied and characterized as a new bacterial bilirubin oxidase (BOD). The 59 kDa protein containing four coppers, was successfully over-expressed in Escherichia coli and purified to homogeneity in one step. This 509 amino-acid enzyme, having 67% and 26% sequence identity with CotA from Bacillus subtilis and BOD from Myrothecium verrucaria, respectively, shows higher turnover activity towards bilirubin compared to other bacterial MCOs. The current density for O(2) reduction, when immobilized in a redox hydrogel, is only 12% smaller than the current obtained with Trachyderma tsunodae BOD. Under continuous electrocatalysis, an electrode modified with the new BOD is more stable, and has a higher tolerance towards NaCl, than a T. tsunodae BOD modified electrode. This makes BOD from B. pumilus an attractive new candidate for application in biofuel cells (BFCs) and biosensors.

Spectroscopic and DFT studies of second-sphere variants of the type 1 copper site in azurin: covalent and nonlocal electrostatic contributions to reduction potentials.

The reduction potentials (E(0)) of type 1 (T1) or blue copper (BC) sites in proteins and enzymes with identical first coordination spheres around the redox active copper ion can vary by ~400 mV. Here, we use a combination of low-temperature electronic absorption and magnetic circular dichroism, electron paramagnetic resonance, resonance Raman, and S K-edge X-ray absorption spectroscopies to investigate a series of second-sphere variants--F114P, N47S, and F114N in Pseudomonas aeruginosa azurin--which modulate hydrogen bonding to and protein-derived dipoles nearby the Cu-S(Cys) bond. Density functional theory calculations correlated to the experimental data allow for the fractionation of the contributions to tuning E(0) into covalent and nonlocal electrostatic components. These are found to be significant, comparable in magnitude, and additive for active H-bonds, while passive H-bonds are mostly nonlocal electrostatic in nature. For dipoles, these terms can be additive to or oppose one another. This study provides a methodology for uncoupling covalency from nonlocal electrostatics, which, when coupled to X-ray crystallographic data, distinguishes specific local interactions from more long-range protein/active interactions, while affording further insight into the second-sphere mechanisms available to the protein to tune the E(0) of electron-transfer sites in biology.

Spectroscopy and Redox Chemistry of Copper in Mordenite

Copper-containing zeolites, such as mordenite (MOR), have recently gained increased attention as a consequence of their catalytic potential. While the preferred copper loadings in these catalytic studies are generally high, the literature lacks appropriate spectroscopic and structural information on such Cu-rich zeolite samples. Higher copper loadings increase the complexity of the copper identity and their location in the zeolite host, but they also provide the opportunity to create novel Cu sites, which are perhaps energetically less favorable, but possibly more reactive and more suitable for catalysis. In order to address the different role of each Cu site in catalysis, we here report a combined electron paramagnetic resonance (EPR), UV/Vis-NIR and temperature-programmed reduction (TPR) study on highly copper-loaded MOR. Highly resolved diffuse reflectance (DR) spectra of the CuMOR samples were obtained due to the increased copper loading, allowing the differentiation of two isolated mononuclear Cu(2+) sites and the unambiguous correlation with extensively reported features in the EPR spectrum. Ligand field theory is applied together with earlier suggested theoretical calculations to determine their coordination chemistry and location within the zeolite matrix, and the theoretical analysis further allowed us to define factors governing their redox behavior. In addition to monomeric species, an EPR-silent, possibly dimeric, copper site is present in accordance with its charge transfer absorption feature at 22200 cm(-1), and quantified with TPR. Its full description and true location in MOR is currently being investigated.

X-ray Spectroscopic Characterization of Co(IV) and Metal–Metal Interactions in Co4O4: Electronic Structure Contributions to the Formation of High-Valent States Relevant to the Oxygen Evolution Reaction

The formation of high-valent states is a key factor in making highly active transition-metal-based catalysts of the oxygen evolution reaction (OER). These high oxidation states will be strongly influenced by the local geometric and electronic structures of the metal ion, which are difficult to study due to spectroscopically active and complex backgrounds, short lifetimes, and limited concentrations. Here, we use a wide range of complementary X-ray spectroscopies coupled to DFT calculations to study Co(III)4O4 cubanes and their first oxidized derivatives, which provide insight into the high-valent Co(IV) centers responsible for the activity of molecular and heterogeneous OER catalysts. The combination of X-ray absorption and 1s3p resonant inelastic X-ray scattering (Kβ RIXS) allows Co(IV) to be isolated and studied against a spectroscopically active Co(III) background. Co K- and L-edge X-ray absorption data allow for a detailed characterization of the 3d-manifold of effectively localized Co(IV) centers and provide a direct handle on the t2g-based redox-active molecular orbital. Kβ RIXS is also shown to provide a powerful probe of Co(IV), and specific spectral features are sensitive to the degree of oxo-mediated metal-metal coupling across Co4O4. Guided by the data, calculations show that electron-hole delocalization can actually oppose Co(IV) formation. Computational extension of Co4O4 to CoM3O4 structures (M = redox-inactive metal) defines electronic structure contributions to Co(IV) formation. Redox activity is shown to be linearly related to covalency, and M(III) oxo inductive effects on Co(IV) oxo bonding can tune the covalency of high-valent sites over a large range and thereby tune E(0) over hundreds of millivolts. Additionally, redox-inactive metal substitution can also switch the ground state and modify metal-metal and antibonding interactions across the cluster.

Exploring the ground and excited state potential energy landscapes of the mixed-valence biferrocenium complex.

Density functional theory (DFT) and time-dependent DFT (TDDFT) have been used to explore the potential energy landscapes in the class II (in Robin and Day classification) mixed-valence biferrocenium mono-cation (BF(+)) in an effort to evaluate factors affecting optical and thermal intramolecular electron transfer rates. Both energy- and spectroscopy-based benchmarks were used to explore the adiabatic potential energy surfaces (PESs) of the mixed-valence BF(+) cation along with the optimization of appropriate ground-, excited-, and transition-state geometries. The calculation of Mossbauer isomer shifts and quadrupole splittings, UV-vis excitation energies, and the electronic coupling matrix element, H(ab), corroborate the PES analyses. The adiabatic electron transfer pathway is also analyzed with respect to several possible vibronic coordinates. The degree of the electronic coupling between iron sites, the value of H(ab), and the nature of the electron transfer pathway correlate with the amount of Hartree-Fock exchange involved in the DFT calculation with hybrid (approximately 20% of Hartree-Fock exchange) methods providing the best agreement between theory and experiment. DFT (B3LYP) predicted values of H(ab) (839, 1085, and 1265 cm(-1)) depend on the computational method and are in good agreement with experimental data.