Electronic Structures of Metal Sites in Proteins and Models: Contributions to Function in Blue Copper Proteins

A stable thiolato-CuI-thiolato triple linkage that bridges two cobalt(iii) centres

Treatment of Λ-fac-[Co(d-pen-N,S)₃]^3- (d-H₂pen = d-penicillamine) with Cu⁺ in water gave a stable CoCu complex, ΛΛ-[Co₂Cu₃(d-pen)₆]^3- ([1]^3-), having three thiolato-copper(i)-thiolato moieties that bridge two cobalt(iii) centres. Complex [1]^3- was isolated as a coordination polymer of Na₃[1], which was converted to a complex salt of [Cr(H₂O)₆][1] by treatment with Cr(NO₃)₃.

Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy

The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe-S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free-electron laser, determining that the Fe-S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints. The 4 kcal/mol is comparable with calculations of stabilization effects in other systems, demonstrating how biological systems use an entatic state for modest yet accessible energetics to modulate chemical function.

Structural dynamics upon photoexcitation-induced charge transfer in a dicopper(i)–disulfide complex

A study of structural evolution upon photoinduced charge transfer in a dicopper complex with biologically relevant sulfur coordination.

A mixed phenoxo and end-on azide bridged dinuclear copper(ii) Schiff base complex: synthesis, structure, magnetic characterization and DFT study

The magnetic properties of a dinuclear copper(ii) Schiff base complex with dissimilar bridges have been investigated through some theoretical calculations (DFT) using suitable modeled structures.

Ab initio electronic structure calculations of entire blue copper azurins

We present a theoretical study of the blue-copper azurin extracted from Pseudomonas aeruginosa and several of its single amino acid mutants.

Intramolecular metal–ligand electron transfer triggered by co-ligand substitution

Labile co-ligands are attached to a dinuclear copper(i) complex with a redox-active bridging guanidine ligand. Their substitution triggers electron-transfer from the copper atoms to the guanidine.

Study of the Cys-His bridge electron transfer pathway in a copper-containing nitrite reductase by site-directed mutagenesis, spectroscopic, and computational methods

The Cys-His bridge as electron transfer conduit in the enzymatic catalysis of nitrite to nitric oxide by nitrite reductase from Sinorhizobium meliloti 2011 (SmNir) was evaluated by site-directed mutagenesis, steady state kinetic studies, UV-vis and EPR spectroscopic measurements as well as computational calculations. The kinetic, structural and spectroscopic properties of the His171Asp (H171D) and Cys172Asp (C172D) SmNir variants were compared with the wild type enzyme. Molecular properties of H171D and C172D indicate that these point mutations have not visible effects on the quaternary structure of SmNir. Both variants are catalytically incompetent using the physiological electron donor pseudoazurin, though C172D presents catalytic activity with the artificial electron donor methyl viologen (k_cat=3.9(4) s^-1) lower than that of wt SmNir (k_cat=240(50) s^-1). QM/MM calculations indicate that the lack of activity of H171D may be ascribed to the N^δ1H…OC hydrogen bond that partially shortcuts the T1-T2 bridging Cys-His covalent pathway. The role of the N^δ1H…OC hydrogen bond in the pH-dependent catalytic activity of wt SmNir is also analyzed by monitoring the T1 and T2 oxidation states at the end of the catalytic reaction of wt SmNir at pH6 and 10 by UV-vis and EPR spectroscopies. These data provide insight into how changes in Cys-His bridge interrupts the electron transfer between T1 and T2 and how the pH-dependent catalytic activity of the enzyme are related to pH-dependent structural modifications of the T1-T2 bridging chemical pathway.

Synthesis, structure, and excited state kinetics of heteroleptic Cu(i) complexes with a new sterically demanding phenanthroline ligand

In this report we describe the synthesis of a new phenanthroline ligand, 2,9-di(2,4,6-tri-isopropyl-phenyl)-1,10-phenanthroline (bL2) and its use as the blocking ligand in the preparation of two new heteroleptic Cu(i)diimine complexes. Analysis of the CuHETPHEN single crystal structures shows a distinct distortion from an ideal tetrahedral geometry around the Cu(i) center, forced by the secondary phenanthroline ligand rotating to accommodate the isopropyl groups of bL2. The increased steric bulk of bL2 as compared to the more commonly used 2,9-dimesityl-1,10-phenanthroline blocking ligand prohibits intramolecular ligand-ligand interaction, which is unique among CuHETPHEN complexes. The ground state optical and redox properties of CuHETPHEN complexes are responsive to the substitution on the blocking ligand even though the differences in structure are far removed from the Cu(i) center. Transient optical spectroscopy was used to understand the excited state kinetics in both coordinating and non-coordinating solvents following visible excitation. Substitution of the blocking phenanthroline ligand has a significant impact on the ³MLCT decay and can be used to increase the excited state lifetime by 50%. Electronic structure calculations established relationships between ground and excited state properties, and general entatic state concepts are discussed for copper photosensitizers. This work contributes to the growing library of CuHETPHEN complexes and broadens the fundamental understanding of their ground and excited state properties.

Understanding the Coordination Modes of [Cu(acac)2(imidazole)n=1,2] Adducts by EPR, ENDOR, HYSCORE, and DFT Analysis

The interaction of imidazole with a [Cu(acac)₂] complex was studied using electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), hyperfine sublevel correlation spectroscopy (HYSCORE), and density functional theory (DFT). At low Im ratios (Cu:Im 1:10), a 5-coordinate [Cu(acac)₂Im_n=1] monoadduct is formed in frozen solution with the spin Hamiltonian parameters g₁ = 2.063, g₂ = 2.063, g₃ = 2.307, A₁ = 26, A₂ = 15, and A₃ = 472 MHz with Im coordinating along the axial direction. At higher Im concentrations (Cu:Im 1:50), a 6-coordinate [Cu(acac)₂Im_n=2] bis-adduct is formed with the spin Hamiltonian parameters g₁ = 2.059, g₂ = 2.059, g₃ = 2.288, A₁ = 30, A₂ = 30, and A₃ = 498 MHz with a poorly resolved ¹⁴N superhyperfine pattern. The isotropic EPR spectra revealed a distribution of species ([Cu(acac)₂], [Cu(acac)₂Im_n=1], and [Cu(acac)₂Im_n=2]) at Cu:Im ratios of 1:0, 1:10, and 1:50. The superhyperfine pattern originates from two strongly coordinating N³ imino nitrogens of the Im ring. Angular selective ¹⁴N ENDOR analysis revealed the ^NA tensor of [34.8, 43.5, 34.0] MHz, with e²qQ/h = 2.2 MHz and η = 0.2 for N³. The hyperfine and quadrupole values for the remote N¹ amine nitrogens (from HYSCORE) were found to be [1.5, 1.4, 2.5] MHz with e²qQ/h = 1.4 MHz and η = 0.9. ¹H ENDOR also revealed three sets of ^HA tensors corresponding to the nearly equivalent H²/H⁴ protons in addition to the H⁵ and H¹ protons of the Im ring. The spin Hamiltonian parameters for the geometry optimized structures of [Cu(acac)₂Im_n=2], including cis-mixed plane, trans-axial, and trans-equatorial, were calculated. The best agreement between theory and experiment indicated the preferred coordination is trans-equatorial [Cu(acac)₂Im_n=2]. A number of other Im derivatives were also investigated. 4(5)-methyl-imidazole forms a [Cu(acac)₂(Im-3)_n=2] trans-equatorial adduct, whereas the bulkier 2-methyl-imidazole (Im-2) and benzimidazole (Im-4) form the [Cu(acac)₂(Im-2,4)_n=1] monoadduct only. Our data therefore show that subtle changes in the substrate structure lead to controllable changes in coordination behavior, which could in turn lead to rational design of complexes for use in catalysis, imaging, and medicine.

Prediction of Reduction Potentials of Copper Proteins with Continuum Electrostatics and Density Functional Theory

Blue copper proteins, such as azurin, show dramatic changes in Cu²⁺/Cu⁺ reduction potential upon mutation over the full physiological range. Hence, they have important functions in electron transfer and oxidation chemistry and have applications in industrial biotechnology. The details of what determines these reduction potential changes upon mutation are still unclear. Moreover, it has been difficult to model and predict the reduction potential of azurin mutants and currently no unique procedure or workflow pattern exists. Furthermore, high‐level computational methods can be accurate but are too time consuming for practical use. In this work, a novel approach for calculating reduction potentials of azurin mutants is shown, based on a combination of continuum electrostatics, density functional theory and empirical hydrophobicity factors. Our method accurately reproduces experimental reduction potential changes of 30 mutants with respect to wildtype within experimental error and highlights the factors contributing to the reduction potential change. Finally, reduction potentials are predicted for a series of 124 new mutants that have not yet been investigated experimentally. Several mutants are identified that are located well over 10 Å from the copper center that change the reduction potential by more than 85 mV. The work shows that secondary coordination sphere mutations mostly lead to long‐range electrostatic changes and hence can be modeled accurately with continuum electrostatics.

Inter- and Intramolecular Electron Transfer in Copper Complexes: Electronic Entatic State with Redox-Active Guanidine Ligands

Fast and efficient electron transfer in blue copper proteins is realized by a structural harmonization between the Cu^I and Cu^II complex pair ("entatic state" model). Herein, we present now a Cu^I /Cu^II complex pair with redox-active guanidine ligands showing almost perfect match between both redox states. By modifying the ligand electron donor strength, the redox chemistry of the copper complex can be controlled to be either metal-centered or to cross the borderline to ligand-centered. This work is the first systematic study of complexes with redox-active ligands within the concept of the entatic state.

Tunable Biogenic Manganese Oxides

Influence of the conditions for aerobic oxidation of Mn2+(aq) catalysed by the MnxEFG protein complex on the morphology, structure and reactivity of the resulting biogenic manganese oxides (MnO_x ) is explored. Physical characterisation of MnO_x includes scanning and transmission electron microscopy, and X-ray photoelectron and K-edge Mn, Fe X-ray absorption spectroscopy. This characterisation reveals that the MnO_x materials share the structural features of birnessite, yet differ in the degree of structural disorder. Importantly, these biogenic products exhibit strikingly different morphologies that can be easily controlled. Changing the substrate-to-protein ratio produces MnO_x either as nm-thin sheets, or rods with diameters below 20 nm, or a combination of the two. Mineralisation in solutions that contain Fe2+(aq) makes solids with significant disorder in the structure, while the presence of Ca2+(aq) facilitates formation of more ordered materials. The (photo)oxidation and (photo)electrocatalytic capacity of the MnO_x minerals is examined and correlated with their structural properties.

Copper-Based Metal-Organic Framework Nanoparticles with Peroxidase-Like Activity for Sensitive Colorimetric Detection of Staphylococcus aureus

Cu-MOF nanoparticles with an average diameter of 550 nm were synthesized from 2-aminoterephthalic acid and Cu(NO₃)₂ by a mixed solvothermal method. The Cu-MOF nanoparticles can show peroxidase-like activity that can catalyze 3,3',5,5'-tetramethylbenzidine to produce a yellow chromogenic reaction in the presence of H₂O₂. The presence of abundant amine groups on the surfaces of Cu-MOF nanoparticles enables facile modification of Staphylococcus aureus (S. aureus) aptamer on Cu-MOF nanoparticles. By combining Cu-MOF-catalyzed chromogenic reaction with aptamer recognition and magnetic separation, a simple, sensitive, and selective colorimetric method for the detection of S. aureus was developed.

Multielectron Chemistry within a Model Nickel Metalloprotein: Mechanistic Implications for Acetyl-CoA Synthase

The acetyl coenzyme A synthase (ACS) enzyme plays a central role in the metabolism of anaerobic bacteria and archaea, catalyzing the reversible synthesis of acetyl-CoA from CO and a methyl group through a series of nickel-based organometallic intermediates. Owing to the extreme complexity of the native enzyme systems, the mechanism by which this catalysis occurs remains poorly understood. In this work, we have developed a protein-based model for the Ni_P center of acetyl coenzyme A synthase using a nickel-substituted azurin protein (NiAz). NiAz is the first model nickel protein system capable of accessing three (Ni^I/Ni^II/Ni^III) distinct oxidation states within a physiological potential range in aqueous solution, a critical feature for achieving organometallic ACS activity, and binds CO and -CH₃ groups with biologically relevant affinity. Characterization of the Ni^I-CO species through spectroscopic and computational techniques reveals fundamentally similar features between the model NiAz system and the native ACS enzyme, highlighting the potential for related reactivity in this model protein. This work provides insight into the enzymatic process, with implications toward engineering biological catalysts for organometallic processes.

[Cu6 (NGuaS)6 ]2+ and its oxidized and reduced derivatives: Confining electrons on a torus

The hexanuclear thioguanidine mixed-valent copper complex cation [Cu₆ (NGuaS)₆ ]⁺² (NGuaS = o-SC₆ H₄ NC(NMe₂ )₂ ) and its oxidized/reduced states are theoretically analyzed by means of density functional theory (DFT) (TPSSh + D3BJ/def2-TZV (p)). A detailed bonding analysis using overlap populations is performed. We find that a delocalized Cu-based ring orbital serves as an acceptor for donated S p electrons. The formed fully delocalized orbitals give rise to a confined electron cloud within the Cu₆ S₆ cage which becomes larger on reduction. The resulting strong electrostatic repulsion might prevent the fully reduced state. Experimental UV/Vis spectra are explained using time-dependent density functional theory (TD-DFT) and analyzed with a natural transition orbital analysis. The spectra are dominated by MLCTs within the Cu₆ S₆ core over a wide range but LMCTs are also found. The experimental redshift of the reduced low energy absorption band can be explained by the clustering of the frontier orbitals. © 2017 Wiley Periodicals, Inc.

Spectroscopic investigation and in vitro cytotoxic activity toward HepG2 cells of a copper compound complexed with human serum albumin

The human serum albumin (HSA) interaction of a mixed-ligand copper compound (1) with an imidazole and taurine Schiff base derived from salicylaldehyde and taurine was investigated using fluorescence spectroscopy, UV-vis spectroscopy, time-resolved fluorescence spectroscopy, circular dichroism (CD) spectroscopy, Fourier transform infrared (FT-IR) spectroscopy and a molecular docking technique. The results of fluorescence and time-resolved fluorescence spectroscopy indicated that 1 can effectively quench the HSA fluorescence by a static mechanism. Binding constants (K) and the number of binding sites (n ≈ 1) were calculated using modified Stern-Volmer equations. The thermodynamic parameters were calculated. UV-vis, CD and FT-IR spectroscopy measurements confirm the alterations in the HSA secondary structure induced by 1. The site marker competitive experiment confirms that 1 is located in subdomain IB of HSA. The combination of molecular docking results and fluorescence experimental results reveal that hydrophobic interaction and hydrogen bonds are the predominant intermolecular forces stabilizing the 1-HSA complex. The 1-HSA complex increases approximately three times its cytotoxicity in cancer cells but has no effect on normal cells in vitro. Compared with unbound 1, the 1-HSA complex promotes HepG2 cells apoptosis and also has a stronger capacity for cell cycle arrest at the S phase of HepG2 cells.

New molecular packing in a crystal of pseudoazurin from Alcaligenes faecalis: a double-helical arrangement of blue copper

Pseudoazurin from the denitrifying bacterium Alcaligenes faecalis (AfPAz) is a blue copper protein and functions as an electron donor to copper-containing nitrite reductase (CuNIR). Conventionally, AfPAz has been crystallized using highly concentrated ammonium sulfate as a precipitant. Here, a needle-like crystal of AfPAz grown in a solution containing a macromolecular precipitant, polyethylene glycol 8000 (PEG 8000), is reported. The crystal belonged to space group P61, with unit-cell parameters a = b = 68.7, c = 94.2 Å. The structure has been determined and refined at 2.6 Å resolution. The asymmetric unit contained two AfPAz molecules contacting each other on negatively charged surfaces. The molecular packing of the crystal showed a right-handed double-helical arrangement of AfPAz molecules and hence of blue copper sites. This structure provides insight into the excluded-volume effect of PEG and the manner of assembly of AfPAz.

Metal Ion Modeling Using Classical Mechanics

Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.

Effect of circular permutation on the structure and function of type 1 blue copper center in azurin

Type 1 copper (T1Cu) proteins are electron transfer (ET) proteins involved in many important biological processes. While the effects of changing primary and secondary coordination spheres in the T1Cu ET function have been extensively studied, few report has explored the effect of the overall protein structural perturbation on active site configuration or reduction potential of the protein, even though the protein scaffold has been proposed to play a critical role in enforcing the entatic or "rack-induced" state for ET functions. We herein report circular permutation of azurin by linking the N- and C-termini and creating new termini in the loops between 1st and 2nd β strands or between 3rd and 4th β strands. Characterization by electronic absorption, electron paramagnetic spectroscopies, as well as crystallography and cyclic voltammetry revealed that, while the overall structure and the primary coordination sphere of the circular permutated azurins remain the same as those of native azurin, their reduction potentials increased by 18 and 124 mV over that of WTAz. Such increases in reduction potentials can be attributed to subtle differences in the hydrogen-bonding network in secondary coordination sphere around the T1Cu center.

Cu(I) complexes of bis(methyl)(thia/selena) salen ligands: Synthesis, characterization, redox behavior and DNA binding studies

Mononuclear cuprous complexes 1 and 2, [{CH₃E(o-C₆H₄)CH=NCH₂}₂Cu]ClO₄; E=S/Se, have been synthesized by the reaction of bis(methyl)(thia/selena) salen ligands and [Cu(CH₃CN)₄]ClO₄. Both the products were characterized by elemental analysis, ESI-MS, FT-IR, ¹H/¹³C/⁷⁷Se NMR, and cyclic voltammetry. The complexes possess tetrahedral geometry around metal center with the N₂S₂/N₂Se₂ coordination core. Cyclic voltammograms of complexes 1 and 2 displayed reversible anodic waves at E_1/2=+0.08V and +0.10V, respectively, corresponding to the Cu(I)/Cu(II) redox couple. DNA binding studies of both the complexes were performed applying absorbance, fluorescence and molecular docking techniques. Competitive binding experiment of complexes with ct-DNA against ethidium bromide is performed to predict the mode of binding. The results indicate the groove binding mode of complexes 1 and 2 to DNA. The binding constants revealed the strong binding affinity of complexes towards ct-DNA.

Dynamic Flexibility of Hydrogenase Active Site Models Studied with 2D-IR Spectroscopy

Hydrogenase enzymes enable organisms to use H₂ as an energy source, having evolved extremely efficient biological catalysts for the reversible oxidation of molecular hydrogen. Small-molecule mimics of these enzymes provide both simplified models of the catalysis reactions and potential artificial catalysts that might be used to facilitate a hydrogen economy. We have studied two diiron hydrogenase mimics, μ-pdt-[Fe(CO)₃]₂ and μ-edt-[Fe(CO)₃]₂ (pdt = propanedithiolate, edt = ethanedithiolate), in a series of alkane solvents and have observed significant ultrafast spectral dynamics using two-dimensional infrared (2D-IR) spectroscopy. Since solvent fluctuations in nonpolar alkanes do not lead to substantial electrostatic modulations in a solute's vibrational mode frequencies, we attribute the spectral diffusion dynamics to intramolecular flexibility. The intramolecular origin is supported by the absence of any measurable solvent viscosity dependence, indicating that the frequency fluctuations are not coupled to the solvent motional dynamics. Quantum chemical calculations reveal a pronounced coupling between the low-frequency torsional rotation of the carbonyl ligands and the terminal CO stretching vibrations. The flexibility of the CO ligands has been proposed to play a central role in the catalytic reaction mechanism, and our results highlight that the CO ligands are highly flexible on a picosecond time scale.

Spectroscopic Studies of the EutT Adenosyltransferase from Salmonella enterica: Evidence of a Tetrahedrally Coordinated Divalent Transition Metal Cofactor with Cysteine Ligation

The EutT enzyme from Salmonella enterica, a member of the family of ATP:cobalt(I) corrinoid adenosyltransferase (ACAT) enzymes, requires a divalent transition metal ion for catalysis, with Fe(II) yielding the highest activity. EutT contains a unique cysteine-rich HX₁₁CCX₂C(83) motif (where H and the last C occupy the 67th and 83rd positions, respectively, in the amino acid sequence) not found in other ACATs and employs an unprecedented mechanism for the formation of adenosylcobalamin. Recent kinetic and spectroscopic studies of this enzyme revealed that residues in the HX₁₁CCX₂C(83) motif are required for the tight binding of the divalent metal ion and are critical for the formation of a four-coordinate (4c) cob(II)alamin [Co(II)Cbl] intermediate in the catalytic cycle. However, it remained unknown which, if any, of the residues in the HX₁₁CCX₂C(83) motif bind the divalent metal ion. To address this issue, we have characterized Co(II)-substituted wild-type EutT (EutT^WT/Co) by using electronic absorption, electron paramagnetic resonance, and magnetic circular dichroism (MCD) spectroscopies. Our results indicate that the reduced catalytic activity of EutT^WT/Co relative to that of the Fe(II)-containing enzyme arises from the incomplete incorporation of Co(II) ions and, thus, a decrease in the relative population of 4c Co(II)Cbl. Our MCD data for EutT^WT/Co also reveal that the Co(II) ions reside in a distorted tetrahedral coordination environment with direct cysteine sulfur ligation. Additional spectroscopic studies of EutT/Co variants possessing a single alanine substitution of either His67, His75, Cys79, Cys80, or Cys83 indicate that Cys80 coordinates to the Co(II) ion, while the additional residues are important for maintaining the structural integrity and/or high affinity of the metal binding site.

Engineering the metal-binding loop at a type 1 copper center by circular permutation

Circular permutation of the cupredoxin azurin creates a break on the metal binding loop, highlighting the loop's flexibility.