Spectroscopic and density functional theory studies of the blue-copper site in M121SeM and C112SeC azurin: Cu-Se versus Cu-S bonding.
ABSTRACT: S K-edge X-ray absorption, UV-vis absorption, magnetic circular dichroism (MCD), and resonance Raman spectroscopies are used to investigate the electronic structure differences among WT, M121SeM, and C112SeC Pseudomonas aeruginosa (P.a) azurin. A comparison of S K-edge XAS of WT and M121SeM azurin and a CuII-thioether model complex shows that the 38% S character in the ground state wave function of the blue-copper (BC) sites solely reflects the Cu-SCys bond. Resonance Raman (rR) data on WT and C112SeC azurin give direct evidence for the kinematic coupling between the Cu-SCys stretch and the cysteine deformation modes in WT azurin, which leads to multiple features in the rR spectrum of the BC site. The UV-vis absorption and MCD data on WT, M121SeM, and C112SeC give very similar C0/D0 ratios, indicating that the C-term MCD intensity mechanism involves Cu-centered spin-orbit coupling (SOC). The spectroscopic data combined with density functional theory (DFT) calculations indicate that SCys and SeCys have similar covalent interactions with Cu at their respective bond lengths of 2.1 and 2.3 A. This reflects the similar electronegativites of S and Se in the thiolate/selenolate ligand fragment and explains the strong spectroscopic similarities between WT and C112SeC azurin.
Project description:The Cu-SCys interaction is known to play a dominant role in defining the type 1 (T1) blue copper center with respect to both its electronic structure and electron transfer function. Despite this importance, its role has yet to be probed by mutagenesis studies without dramatic change of its T1 copper character. We herein report replacement of the conserved Cys112 in azurin with the nonproteinogenic amino acid homocysteine. Based on electronic absorption, electron paramagnetic resonance, and extended x-ray absorption fine structural spectroscopic studies, this variant displays typical type 1 copper site features. Surprisingly, instead of increasing the strength of the Cu-sulfur interaction by the introduction of the extra methylene group, the Cys112Hcy azurin showed a decrease in the covalent interaction between SHcy and Cu(II) when compared with the WT SCys-Cu(II) interaction. This is likely due to geometric adjustment of the center that resulted in the copper ion moving out of the trigonal plane defined by two histidines and one Hcy and closer to Met121. These structural changes resulted in an increase of reduction potential by 35 mV, consistent with lower Cu-S covalency. These results suggest that the Cu-SCys interaction is close to being optimal in native blue copper protein. It also demonstrates the power of using nonproteinogenic amino acids in addressing important issues in bioinorganic chemistry.
Project description:Within Cu-containing electron transfer active sites, the role of the axial ligand in type 1 sites is well defined, yet its role in the binuclear mixed-valent CuA sites is less clear. Recently, the mutation of the axial Met to Leu in a CuA site engineered into azurin (CuA Az) was found to have a limited effect on E(0) relative to this mutation in blue copper (BC). Detailed low-temperature absorption and magnetic circular dichroism, resonance Raman, and electron paramagnetic resonance studies on CuA Az (WT) and its M123X (X = Q, L, H) axial ligand variants indicated stronger axial ligation in M123L/H. Spectroscopically validated density functional theory calculations show that the smaller ?E(0) is attributed to H2O coordination to the Cu center in the M123L mutant in CuA but not in the equivalent BC variant. The comparable stabilization energy of the oxidized over the reduced state in CuA and BC (CuA ? 180 mV; BC ? 250 mV) indicates that the S(Met) influences E(0) similarly in both. Electron delocalization over two Cu centers in CuA was found to minimize the Jahn-Teller distortion induced by the axial Met ligand and lower the inner-sphere reorganization energy. The Cu-S(Met) bond in oxidized CuA is weak (5.2 kcal/mol) but energetically similar to that of BC, which demonstrates that the protein matrix also serves an entatic role in keeping the Met bound to the active site to tune down E(0) while maintaining a low reorganization energy required for rapid electron transfer under physiological conditions.
Project description:A variety of techniques including absorption, magnetic circular dichroism (MCD), variable-temperature, variable-field MCD (VTVH-MCD), and resonance Raman (rR) spectroscopies are combined with density functional theory (DFT) calculations to elucidate the electronic structure of the end-on (?(1)) bound superoxo-Cu(II) complex [TMG(3)trenCuO(2)](+) (where TMG(3)tren is 1,1,1-tris[2-[N(2)-(1,1,3,3-tetramethylguanidino)]ethyl]amine). The spectral features of [TMG(3)trenCuO(2)](+) are assigned, including the first definitive assignment of a superoxo intraligand transition in a metal-superoxo complex, and a detailed description of end-on superoxo-Cu(II) bonding is developed. The lack of overlap between the two magnetic orbitals of [TMG(3)trenCuO(2)](+) eliminates antiferromagnetic coupling between the copper(II) and the superoxide, while the significant superoxo ?*(?) character of the copper dz(2) orbital leads to its ferromagnetically coupled, triplet, ground state.
Project description:The Cu nanoparticles (Cu NPs) were grown in soda-lime glass matrix through Cu+???Na+ ion exchange methods under thermal annealing in an open environment and studied variation in their size on tunable plasmonic behaviour, optical absorption spectra and photoluminescence (PL). A blue shift from 570 to 560?nm was observed in localized surface plasmon resonance (SPR) of Cu NPs from 550 to 650?°C. A mutual relation between size and surface plasmon resonance with full width half maxima (FWHM) has been derived for plasmonic properties at variable temperatures. Structural investigations of embedded Cu NPs have been confirmed by using HRTEM and EDX. Grazing incidence X-ray diffraction (GIXRD) had identified a crystalline nature of Cu NPs under annealed conditions. XPS, Raman and secondary ion mass spectroscopies (SIMS) have identified an embedding behaviour of Cu NPs in glass matrix. Plasmonic and thermodynamic properties of embedded Cu NPs have explained their in situ thermal growth mechanism for efficient distribution where enthalpy (?H), entropy (?S) and Gibbs free energy (?G) have interpreted their temperature driven Cu NPs growth. An interdependence of ?H, ?S and ?G has been developed vis-a-vis activation energy on an extent of 12.54?J/mol.
Project description:The reactive oxidizing species in the selective oxidation of methane to methanol in oxygen activated Cu-ZSM-5 was recently defined to be a bent mono(?-oxo)dicopper(II) species, [Cu(2)O](2+). In this communication we report the formation of an O(2)-precursor of this reactive site with an associated absorption band at 29,000 cm(-1). Laser excitation into this absorption feature yields a resonance Raman (rR) spectrum characterized by (18)O(2) isotope sensitive and insensitive vibrations, ?O-O and ?Cu-Cu, at 736 (?(18)O(2) = 41 cm(-1)) and 269 cm(-1), respectively. These define the precursor to be a ?-(?(2):?(2)) peroxo dicopper(II) species, [Cu(2)(O(2))](2+). rR experiments in combination with UV-vis absorption data show that this [Cu(2)(O(2))](2+) species transforms directly into the [Cu(2)O](2+) reactive site. Spectator Cu(+) sites in the zeolite ion-exchange sites provide the two electrons required to break the peroxo bond in the precursor. O(2)-TPD experiments with (18)O(2) show the incorporation of the second (18)O atom into the zeolite lattice in the transformation of [Cu(2)(O(2))](2+) into [Cu(2)O](2+). This study defines the mechanism of oxo-active site formation in Cu-ZSM-5.
Project description:In the copper-catalyzed oxidation of alcohols to aldehydes, a Cu(II)-alkoxide (Cu(II)-OR) intermediate is believed to modulate the ?C-H bond strength of the deprotonated substrate to facilitate the oxidation. As a structural model for these intermediates, we characterized the electronic structure of the stable compound Tp(tBu)Cu(II)(OCH2CF3) (Tp(tBu) = hydro-tris(3-tert-butyl-pyrazolyl)borate) and investigated the influence of the trifluoroethoxide ligand on the electronic structure of the complex. The compound exhibits an electron paramagnetic resonance (EPR) spectrum with an unusually large gzz value of 2.44 and a small copper hyperfine coupling Azz of 40 × 10(-4) cm(-1) (120 MHz). Single-crystal electron nuclear double resonance (ENDOR) spectra show that the unpaired spin population is highly localized on the copper ion (?68%), with no more than 15% on the ethoxide oxygen. Electronic absorption and magnetic circular dichroism (MCD) spectra show weak ligand-field transitions between 5000 and 12,000 cm(-1) and an intense ethoxide-to-copper charge transfer (LMCT) transition at 24,000 cm(-1), resulting in the red color of this complex. Resonance Raman (rR) spectroscopy reveals a Cu-O stretch mode at 592 cm(-1). Quantum chemical calculations support the interpretation and assignment of the experimental data. Compared to known Cu(II)-thiolate and Cu(II)-alkylperoxo complexes from the literature, we found an increased ? interaction in the Cu(II)-OR bond that results in the spectroscopic features. These insights lay the basis for further elucidating the mechanism of copper-catalyzed alcohol oxidations.
Project description: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.
Project description:Cu(A) is a binuclear electron transfer (ET) center found in cytochrome c oxidases (CcOs), nitrous oxide reductases (N?ORs), and nitric oxide reductase (NOR). In these proteins, the Cu(A) centers facilitate efficient ET (kET > 10?s?¹) under low thermodynamic driving forces (10-90 mV). While the structure and functional properties of Cu(A) are well understood, a detailed mechanism of the incorporation of copper into the protein and the identity of the intermediates formed during the Cu(A) maturation process are still lacking. Previous studies of the Cu(A) assembly mechanism in vitro using a biosynthetic model Cu(A) center in azurin (Cu(A)Az) identified a novel intermediate X (Ix) during reconstitution of the binuclear site. However, because of the instability of Ix and the coexistence of other Cu centers, such as Cu(A)' and type 1 copper centers, the identity of this intermediate could not be established. Here, we report the mechanism of Cu(A) assembly using variants of Glu114XCuAAz (X = Gly, Ala, Leu, or Gln), the backbone carbonyl of which acts as a ligand to the Cu(A) site, with a major focus on characterization of the novel intermediate Ix. We show that Cu(A) assembly in these variants proceeds through several types of Cu centers, such as mononuclear red type 2 Cu, the novel intermediate Ix, and blue type 1 Cu. Our results show that the backbone flexibility of the Glu114 residue is an important factor in determining the rates of T2Cu ? Ix formation, suggesting that Cu(A) formation is facilitated by swinging of the ligand loop, which internalizes the T2Cu capture complex to the protein interior. The kinetic data further suggest that the nature of the Glu114 side chain influences the time scales on which these intermediates are formed, the wavelengths of the absorption peaks, and how cleanly one intermediate is converted to another. Through careful understanding of these mechanisms and optimization of the conditions, we have obtained Ix in ?80-85% population in these variants, which allowed us to employ ultraviolet-visible, electron paramagnetic resonance, and extended X-ray absorption fine structure spectroscopic techniques to identify the Ix as a mononuclear Cu(Cys)(2)(His) complex. Because some of the intermediates have been proposed to be involved in the assembly of native Cu(A), these results shed light on the structural features of the important intermediates and mechanism of Cu(A) formation.
Project description:We report a single-step route to co-deposit Cu nanoparticles with a graphitic carbon nitride (gCN) support using nanosecond Ce:Nd:YAG pulsed laser ablation from a Cu metal target coated using acetonitrile (CH3CN). The resulting Cu/gCN hybrids showed strong optical absorption in the visible to near-IR range and exhibited surface-enhanced Raman or resonance Raman scattering (SERS or SERRS) enhancement for crystal violet (CV), methylene blue (MB), and rhodamine 6G (R6G) used as probe analyte molecules adsorbed on the surface. We have characterized the Cu nanoparticles and the nature of the gCN support materials using a range of spectroscopic, structural, and compositional analysis techniques.
Project description:A series of metal-varied [ML(SC6F5)] model complexes (where L = hydrotris(3,5-diisopropyl-1-pyrazolyl)borate and M = Mn, Fe, Co, Ni, Cu, and Zn) related to blue copper proteins has been studied by a combination of absorption, MCD, resonance Raman, and S K-edge X-ray absorption spectroscopies. Density functional calculations have been used to characterize these complexes and calculate their spectra. The observed variations in geometry, spectra, and bond energies are interpreted in terms of changes in the nature of metal-ligand bonding interactions. The metal 3d-ligand orbital interaction, which contributes to covalent bonding in these complexes, becomes stronger going from Mn(II) to Co(II) (the sigma contribution) and to Cu(II) (the pi contribution). This change in the covalency results from the increased effective nuclear charge of the metal atom in going from Mn(II) to Zn(II) and the change in the 3d orbital populations (d5-->d10). Ionic bonding also plays an important role in determining the overall strength of the ML(+)-SC6F5(-) interaction. However, there is a compensating effect: as the covalent contribution to the metal-ligand bonding increases, the ionic contribution decreases. These results provide insight into the Irving-Williams series, where it is found that the bonding of the ligand being replaced by the thiolate makes a major contribution to the observed order of the stability constants over the series of metal ions.