Analysis of resonance Raman data on the blue copper site in pseudoazurin: excited state π and σ charge transfer distortions and their relation to ground state reorganization energy

The short Cu^(2+)-S(Met) bond in pseudoazurin (PAz) results in the presence of two relatively intense S_p(π) and S_p(σ) charge transfer (CT) transitions. This has enabled resonance Raman (rR) data to be obtained for each excited state. The rR data show very different intensity distribution patterns for the vibrations in the 300-500 cm^(-1) region. Time-dependent density functional theory (TDDFT) calculations have been used to determine that the change in intensity distribution between the S_p(π) and S_p(σ) excited states reflects the differential enhancement of S(Cys) backbone modes with Cu-S(Cys)-C_β out-of-plane (oop) and in-plane (ip) bend character in their respective potential energy distributions (PEDs). The rR excited state distortions have been related to ground state reorganization energies (λ s) and predict that, in addition to M-L stretches, the Cu-S(Cys)-C_β oop bend needs to be considered. DFT calculations predict a large distortion in the Cu-S(Cys)-C_β oop bending coordinate upon reduction of a blue copper (BC) site; however, this distortion is not present in the X-ray crystal structures of reduced BC sites. The lack of Cu-S(Cys)-C_β oop distortion upon reduction corresponds to a previously unconsidered constraint on the thiolate ligand orientation in the reduced state of BC proteins and can be considered as a contribution to the entatic/rack nature of BC sites

Activating Metal Sites for Biological Electron Transfer

This review focuses on the unique spectroscopic features of the blue copper active sites. These reflect a novel electronic structure that activates the site for rapid long-range electron transfer in its biological function. The role of the protein in determining the geometric and electronic structure of this site is defined, as is its contribution to function. This has been referred to as the entatic/rack-induced state. These concepts are then extended to cytochrome , which is also determined to be in an entatic state

Long-range electronic communication in free-base meso-poly(ferrocenyl)-containing porphyrins

H_2FcPh_3P [FcPh_3P = 5-ferrocenyl-10,15,20-triphenyl porphyrin(2-)], cis-H_2Fc_2Ph_2P [cis-Fc_2Ph_2P = 5,10-bisferrocenyl-15,20-diphenyl porphyrin(2-)], trans-H_2Fc_2Ph_2P [trans-Fc_2Ph_2P = 5,15-bisferrocenyl-10,20-diphenyl porphyrin(2-)], and H_2Fc_3PhP [Fc_3PhP = 5,10,15-trisferrocenyl-20-phenyl porphyrin(2-)] along with H_2TPP [TPP = 5,10,15,20-tetraphenylporphyrin] and H_2TFcP [TFcP = 5,10,15,20-tetraferrocenyl porphyrin(2-)] were isolated from the direct cross-condensation reaction between pyrrole, benzaldehyde, and ferrocene carboxaldehyde or from the reaction between ferrocenyl-2,2'-dipyrromethane and benzaldehyde, suggesting a scrambling reaction mechanism for the last approach. All compounds were characterized by UV-vis, MCD, and NMR spectroscopy; APCI MS and MS/MS methods; as well as high-resolution ESI MS spectrometry. The conformational flexibility of ferrocene substituents in all compounds was confirmed using variable-temperature NMR and computational methods. DFT calculations were employed to understand the degree of nonplanarity of the porphyrin core as well as the electronic structure of ferrocene-containing porphyrins. In all cases, a set of occupied, predominantly ferrocene-based molecular orbitals was found between the highest occupied and the lowest unoccupied, predominantly porphyrin-based molecular pi orbitals. The redox properties of all ferrocene-containing porphyrins were investigated in a CH_2Cl_2/TFAB [TFAB = tetrabutylammonium tetrakis(perfluorophenyl)borate] system using cyclic voltammetry, differential pulse voltammetry, and square wave voltammetry methods. In all cases, oxidations of individual ferrocene substituent(s) along with porphyrin core oxidation(s) and reductions have been observed. Mixed-valence [cis-H_2Fc_2Ph_2P]^+, [trans-H_2Fc_2Ph_2P]^+, [H_2Fc_3PhP]^+, and [H_2Fc_3PhP]^(2+) complexes were formed in situ under spectroelectrochemical and chemical oxidation conditions and were characterized using UV-vis and MCD approaches. Analysis of intervalence charge-transfer bands observed in the NIR region for all mixed-valence complexes suggests electron localization and thus class II behavior in the Robin-Day classification

Mechanism of selective benzene hydroxylation catalyzed by iron-containing zeolites

A direct, catalytic conversion of benzene to phenol would have wide-reaching economic impacts. Fe zeolites exhibit a remarkable combination of high activity and selectivity in this conversion, leading to their past implementation at the pilot plant level. There were, however, issues related to catalyst deactivation for this process. Mechanistic insight could resolve these issues, and also provide a blueprint for achieving high performance in selective oxidation catalysis. Recently, we demonstrated that the active site of selective hydrocarbon oxidation in Fe zeolites, named α-O, is an unusually reactive Fe(IV)=O species. Here, we apply advanced spectroscopic techniques to determine that the reaction of this Fe(IV)=O intermediate with benzene in fact regenerates the reduced Fe(II) active site, enabling catalytic turnover. At the same time, a small fraction of Fe(III)-phenolate poisoned active sites form, defining a mechanism for catalyst deactivation. Density-functional theory calculations provide further insight into the experimentally defined mechanism. The extreme reactivity of α-O significantly tunes down (eliminates) the rate-limiting barrier for aromatic hydroxylation, leading to a diffusion-limited reaction coordinate. This favors hydroxylation of the rapidly diffusing benzene substrate over the slowly diffusing (but more reactive) oxygenated product, thereby enhancing selectivity. This defines a mechanism to simultaneously attain high activity (conversion) and selectivity, enabling the efficient oxidative upgrading of inert hydrocarbon substrates

Changes in an Enzyme Ensemble During Catalysis Observed by High Resolution XFEL Crystallography

Enzymes populate ensembles of structures with intrinsically different catalytic proficiencies that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL) to observe catalysis in a designed mutant (G150T) isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations and formation of the thioimidate catalytic intermediate selects for catalytically competent substates. A prior proposal for active site cysteine charge-coupled conformational changes in ICH is validated by determining structures of the enzyme over a range of pH values. A combination of large molecular dynamics simulations of the enzyme in crystallo and timeresolved electron density maps shows that ionization of the general acid Asp17 during catalysis causes additional conformational changes that propagate across the dimer interface, connecting the two active sites. These ionization-linked changes in the ICH conformational ensemble permit water to enter the active site in a location that is poised for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics

Mechanism of selective benzene hydroxylation catalyzed by iron-containing zeolites

A direct, catalytic conversion of benzene to phenol would have wide-reaching economic impacts. Fe zeolites exhibit a remarkable combination of high activity and selectivity in this conversion, leading to their past implementation at the pilot plant level. There were, however, issues related to catalyst deactivation for this process. Mechanistic insight could resolve these issues, and also provide a blueprint for achieving high performance in selective oxidation catalysis. Recently, we demonstrated that the active site of selective hydrocarbon oxidation in Fe zeolites, named α-O, is an unusually reactive Fe(IV)=O species. Here, we apply advanced spectroscopic techniques to determine that the reaction of this Fe(IV)=O intermediate with benzene in fact regenerates the reduced Fe(II) active site, enabling catalytic turnover. At the same time, a small fraction of Fe(III)-phenolate poisoned active sites form, defining a mechanism for catalyst deactivation. Density-functional theory calculations provide further insight into the experimentally defined mechanism. The extreme reactivity of α-O significantly tunes down (eliminates) the rate-limiting barrier for aromatic hydroxylation, leading to a diffusion-limited reaction coordinate. This favors hydroxylation of the rapidly diffusing benzene substrate over the slowly diffusing (but more reactive) oxygenated product, thereby enhancing selectivity. This defines a mechanism to simultaneously attain high activity (conversion) and selectivity, enabling the efficient oxidative upgrading of inert hydrocarbon substrates

Analysis of resonance Raman data on the blue copper site in pseudoazurin: excited state π and σ charge transfer distortions and their relation to ground state reorganization energy

The short Cu^(2+)-S(Met) bond in pseudoazurin (PAz) results in the presence of two relatively intense S_p(π) and S_p(σ) charge transfer (CT) transitions. This has enabled resonance Raman (rR) data to be obtained for each excited state. The rR data show very different intensity distribution patterns for the vibrations in the 300-500 cm^(-1) region. Time-dependent density functional theory (TDDFT) calculations have been used to determine that the change in intensity distribution between the S_p(π) and S_p(σ) excited states reflects the differential enhancement of S(Cys) backbone modes with Cu-S(Cys)-C_β out-of-plane (oop) and in-plane (ip) bend character in their respective potential energy distributions (PEDs). The rR excited state distortions have been related to ground state reorganization energies (λ s) and predict that, in addition to M-L stretches, the Cu-S(Cys)-C_β oop bend needs to be considered. DFT calculations predict a large distortion in the Cu-S(Cys)-C_β oop bending coordinate upon reduction of a blue copper (BC) site; however, this distortion is not present in the X-ray crystal structures of reduced BC sites. The lack of Cu-S(Cys)-C_β oop distortion upon reduction corresponds to a previously unconsidered constraint on the thiolate ligand orientation in the reduced state of BC proteins and can be considered as a contribution to the entatic/rack nature of BC sites

A variable temperature spectroscopic study on Paracoccus pantotrophus pseudoazurin: protein constraints on the blue Cu site

The blue or Type 1 (T1) copper site of Paracoccuspantotrophus pseudoazurin exhibits significant absorption intensity in both the 450 and 600 nm regions. These are sigma and π S_(Cys) to Cu^(2+) 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 [S. Ghosh, X. Xie, A. Dey, Y. Sun, C. Scholes, E. Solomon, Proc. Natl. Acad. Sci. 106 (2009) 4969-4974] 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 A. However, plastocyanin exhibits only π 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-S_(Met) bond length. This leads to an increase in the Cu^(2+)-S_(Cys) 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 Cu^(2+)-S(Cys) bond

A variable temperature spectroscopic study on Paracoccus pantotrophus pseudoazurin: protein constraints on the blue Cu site

The blue or Type 1 (T1) copper site of Paracoccuspantotrophus pseudoazurin exhibits significant absorption intensity in both the 450 and 600 nm regions. These are sigma and π S_(Cys) to Cu^(2+) 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 [S. Ghosh, X. Xie, A. Dey, Y. Sun, C. Scholes, E. Solomon, Proc. Natl. Acad. Sci. 106 (2009) 4969-4974] 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 A. However, plastocyanin exhibits only π 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-S_(Met) bond length. This leads to an increase in the Cu^(2+)-S_(Cys) 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 Cu^(2+)-S(Cys) bond