Model studies of the Cu(B) site of cytochrome c oxidase utilizing a Zn(II) complex containing an imidazole-phenol cross-linked ligand

Cytochrome c oxidase, the enzyme complex responsible for the four-electron reduction of O2 to H2O, contains an unusual histidine-tyrosine cross-link in its bimetallic heme a3-CuB active site. We have synthesised an unhindered, tripodal chelating ligand, BPAIP, containing the unusual ortho-imidazole-phenol linkage, which mimics the coordination environment of the CuB center. The ligand was used to investigate the physicochemical (pKa, oxidation potential) and coordination properties of the imidazole-phenol linkage when bound to a dication. Zn(II) coordination lowers the pKa of the phenol by 0.6 log units, and increases the potential of the phenolate/phenoxyl radical couple by approximately 50 mV. These results are consistent with inductive withdrawal of electron density from the phenolic ring. Spectroscopic data and theoretical calculations (DFT) were used to establish that the cationic complex [Zn(BPAIP)Br]+ has an axially distorted trigonal bipyramidal structure, with three coordinating nitrogen ligands (two pyridine and one imidazole) occupying the equatorial plane and the bromide and the tertiary amine nitrogen of the tripod in the axial positions. Interestingly, the Zn-Namine bonding interaction is weak or absent in [Zn(BPAIP)Br]+ and the complex gains stability in basic solutions, as indicated by 1H NMR spectroscopy. These observations are supported by theoretical calculations (DFT), which suggest that the electron-donating capacity of the equatorial imidazole ligand can be varied by modulation of the protonation and/or redox state of the cross-linked phenol. Deprotonation of the phenol makes the equatorial imidazole a stronger sigma-donor, resulting in an increased Zn-Nimd interaction and thereby leading to distortion of the axial ligand axis toward a more tetrahedral geometry.     

Electronic structures of heme a of cytochrome c oxidase in the redox states—Charge density migration to the propionate groups of heme a

The electronic structures of heme a of cytochrome c oxidase in the redox states were studied, using hybrid density functional theory with a polarizable continuum model and a point charge model. We found that the most stable electronic configurations of the d electrons of the Fe ion are determined by the orbital interactions of the d orbitals of the Fe ion with the π orbitals of the porphyrin ring and the His residues. The redox reaction of the Fe ion influences the charge density on the formyl group through the π conjugation of the porphyrin ring. In addition, we found the charge transfer from the Fe ion to the propionate group of heme a in the redox change despite the lack of the π‐conjugation. We elucidated that the charge propagation originates from the heme a structure itself and that the origin of the charge delocalization to the heme propionate is the orbital interactions between the d orbital of the Fe ion and the p orbitals of the carboxylate part of the heme propionate via the π conjugation of the porphyrin ring and the σ* orbital of the C? C bond of the propionate group. The electrostatic effect by surrounding proteins enhances the charge transfer from the Fe ion to the propionate group. These results indicate that heme propionate groups serve electron mediators in electron transfer as well as electrostatic anchors, and that proteins surrounding the active site reinforce the congenital abilities of the cofactors. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Spectroscopic evidence for a heme-superoxide/Cu(I) intermediate in a functional model of cytochrome c oxidase

A superstructured tetraphenylporphyrin with a covalently attached proximal imidazole axial base and three distal imidazole pickets has been developed as a model for the active site of terminal oxidases such as cytochrome c oxidase. The oxygen adduct of the Fe-only heme (at low temperature) has a diamagnetic NMR and is EPR silent, which taken together with a resonance Raman oxygen isotope sensitive band (nuFe-O) at 575/554 cm-1 (16O2/18O2) indicates formation of a six-coordinate heme-superoxide complex. Unexpectedly, the Fe/Cu complex, where the copper is in a trisimidazole environment approximately 5 A above the heme plane, displays similar characteristics: a diamagnetic NMR, EPR silence, and nuFe-O at 570/544 cm-1. This indicates the dioxygen adduct of this Fe/Cu system is also a superoxide. This contrasts with previously characterized partially reduced dioxygen intermediates of binuclear heme/copper complexes that form Fe/Cu mu-peroxo complexes.     

Synthesis,structure, redox property and ligand replacement reaction of ruthenium(II) complexes containing a terpyridyl ligand with a redox active moiety

Ruthenium(II) complexes bearing a redox-active tridentate ligand 4′-(2,5-dimethoxyphenyl)-2,2′:6′,2′′-terpyridine (tpyOMe), analogous to terpyridine, and 2,2′-bipyridine (bpy) were synthesized by the sequential replacement of Cl by CH₃CN and CO on the complex. The new ruthenium complexes were characterized by various methods including IR and NMR. The molecular structures of [Ru(tpyOMe)(bpy)(CH₃CN)]²⁺ and two kinds of [Ru(tpyOMe)(bpy)(CO)]²⁺ were determined by X-ray crystallography. The incorporation of monodentate ligands (Cl, CH₃CN and CO) regulated the energy levels of the MLCT transitions and the metal-centered redox potentials of the complexes. The kinetic data observed in this study indicates that the ligand replacement reaction of [Ru(tpyOMe)(bpy)Cl]⁺ to [Ru(tpyOMe)(bpy)(CH₃CN)]²⁺ proceeds by a solvent-assisted dissociation process.     

DFT/electrostatic calculations of pK(a) values in cytochrome c oxidase

Using classical electrostatic calculations, earlier we examined the dependence of the protonation state of bovine cytochrome c oxidase (CcO) on its redox state. Based on these calculations, we have proposed a model of CcO proton pumping that involves His291, one of the Cu(B) histidine ligands, which was found to respond to redox changes of the enzyme Fe(a)(3)-Cu(B) catalytic center. In this work, we employ combined density functional and continuum electrostatic calculations to evaluate the pK(a)() values of His291 and Glu242, two key residues of the model. The pK(a) values are calculated for different redox states of the enzyme, and the influence of different factors on the pK(a)'s is analyzed in detail. The calculated pK(a)() values of Glu242 are between 9.4 and 12.0, depending on the redox state of the protein, which is in excellent agreement with recent experimental measurements. Assuming the reduced state of heme a(3), His291 of the oxidized Cu(B) center possesses a pK(a)() between 2.1 and 4.0, while His291 of the reduced Cu(B) center has a pK(a) above 17. The obtained results support the proposal that the His291 ligand of the Cu(B) center in CcO is a proton pump element.     

Valence-induced assembly of Cu(I)-Cu(II) ions into different discrete coordination architectures by a disk-shaped polypyridyl ligand

The valences of metal ions were found to play key roles in controlling the formation and structures of discrete coordination architectures in a copper and disk-shaped hexa-monodentate ligand system. When Cu(I) and Cu(II) ions react with a polydentate ligand HPDQ, a hexanuclear "double-decker" like discrete "LM(3)M(3)L" coordination architecture (CuI)(6)(HPDQ)(2)(CHCl(3))(8) (complex 1), and a "LM(3)L + LM(3)" composite structure complex (Cu(NO(3))(2))(6)(HPDQ)(3) (complex 2) are formed, respectively.     

Synthesis and structural characterization of cross-linked histidine-phenol Cu(ii) complexes as cytochrome c oxidase active site models

Tridentate cross-linked histidine-phenol Cu(ii) ether and ester complexes, chemical analogs of the active site of several heme-copper oxidases, have been synthesized and crystallized.     

Syntheses,structures, and properties of imidazolate-bridged Cu(II)-Cu(II) and Cu(II)-Zn(II) dinuclear complexes of a single macrocyclic ligand with two hydroxyethyl pendants

The imidazolate-bridged homodinuclear Cu(II)-Cu(II) complex, [(CuimCu)L]ClO(4).0.5H(2)O (1), and heterodinuclear Cu(II)-Zn(II) complex, [(CuimZnL(-)(2H))(CuimZnL(-)(H))](ClO(4))(3) (2), of a single macrocyclic ligand with two hydroxyethyl pendants, L (L = 3,6,9,16,19,22-hexaaza-6,19-bis(2-hydroxyethyl)tricyclo[22,2,2,2(11,14)]triaconta-1,11,13,24,27,29-hexaene), have been synthesized as possible models for copper-zinc superoxide dismutase (Cu(2),Zn(2)-SOD). Their crystal structures analyzed by X-ray diffraction methods have shown that the structures of the two complexes are markedly different. Complex 1 crystallizes in the orthorhombic system, containing an imidazolate-bridged dicopper(II) [Cu-im-Cu](3+) core, in which the two copper(II) ions are pentacoordinated by virtue of an N4O environment with a Cu.Cu distance of 5.999(2) A, adopting the geometry of distorted trigonal bipyramid and tetragonal pyramid, respectively. Complex 2 crystallizes in the triclinic system, containing two similar Cu-im-Zn cores in the asymmetric unit, in which both the Cu(II) and Zn(II) ions are pentacoordinated in a distorted trigonal bipyramid geometry, with the Cu.Zn distance of 5.950(1)/5.939(1) A, respectively. Interestingly, the macrocyclic ligand with two arms possesses a chairlike (anti) conformation in complex 1, but a boatlike (syn) conformation in complex 2. Magnetic measurements and ESR spectroscopy of complex 1 have revealed the presence of an antiferromagnetic exchange interaction between the two Cu(II) ions. The ESR spectrum of the Cu(II)-Zn(II) heterodinuclear complex 2 displayed a typical signal for mononuclear trigonal bipyramidal Cu(II) complexes. From pH-dependent ESR and electronic spectroscopic studies, the imidazolate bridges in the two complexes have been found to be stable over broad pH ranges. The cyclic voltammograms of the two complexes have been investigated. Both of the two complexes can catalyze the dismutation of superoxide and show rather high activity.     

Crystal structure and carrier transport properties of a new 3D mixed-valence Cu(I)-Cu(II) coordination polymer including pyrrolidine dithiocarbamate ligand

A novel mixed-valence Cu(i)-Cu(ii) coordination polymer having an infinite three-dimensional (3D) structure, {[Cu(I)(4)Cu(II)(2)Br(4)(Pyr-dtc)(4)]·CHCl(3)}(n) (1) (Pyr-dtc(-) = pyrrolidine dithiocarbamate), has been prepared and structurally characterized via X-ray diffraction. This complex consists of 1D Cu(i)-Br chains and bridging mononuclear copper(ii) units of Cu(II)(Pyr-dtc)(2), which form an infinite 3D network. A magnetic study indicates that this complex includes copper(ii) ions exhibiting a weak antiferromagnetic interaction (θ = -0.086 K) between the unpaired electrons of the copper(ii) ions present in the diamagnetic Cu(i)-Br chains. The carrier transport properties of 1 are investigated using an impedance spectroscopy technique and flash-photolysis time-resolved microwave conductivity measurement (FP-TRMC). The impedance spectroscopy reveals that this complex exhibits intriguing semiconducting properties at a small activation energy (E(a) = 0.29 eV (bulk)). The sum of the mobilities of the negative and positive carriers estimated via FP-TRMC is Σμ～ 0.4 cm(2) V(-1) s(-1).     

Phenolate and phenoxyl radical complexes of Cu(II) and Co(III), bearing a new redox active N,O-phenol-pyrazole ligand

The synthesis and characterisation of the new N,O-phenol-pyrazole pro-ligand, (pz)LH, comprising a pyrazole covalently linked to an o,p-di-tert-butyl-substituted phenol, are herein reported. In CH(2)Cl(2) at room temperature, the cyclic voltammogram (CV) of (pz)LH exhibits a quasi-reversible one-electron oxidation process (at E(1/2) = 0.66 V vs. Fc(+)/Fc) attributed to the formation of the phenoxyl radical cation [(pz)LH]˙(+). (pz)LH reacts with M(II)(BF(4))(2) (M = Cu, Co) in a 2:1 ratio to afford the bis-Cu(pz)L(2) (1) and tris-Co(pz)L(3) (2) complexes respectively. The X-ray structure of 1 reveals a Cu(II) ion in a square-planar trans-Cu(II)-N(2)O(2) coordination environment whereas that of 2 consists of a Co(III) ion with an octahedral mer-N(3)O(3) coordination sphere; formed by the chelation of two (in 1) or three (in 2) N,O-bidentate phenolate ligands respectively. Both structures are preserved in CH(2)Cl(2) solution, as revealed by their NMR (for 2) and EPR (for 1) data. The CVs of 1 and 2 consist of two (at E(1/2): 0.43 and 0.58 V vs. Fc(+)/Fc) and three (E(1/2) = 0.12, 0.54 and 0.89 V vs. Fc(+)/Fc) reversible one-electron oxidation processes, respectively. The one-electron electrochemical oxidation of 1 and 2 produces the oxidised species, 1(+) and 2(+), which are stable for several hours at room temperature under inert atmosphere in CH(2)Cl(2). The UV/vis and EPR data obtained for 1(+) and 2(+) are unambiguously consistent with the latter being formulated as Cu(II)- and Co(III)-phenoxyl radical complexes, as [Cu(II)((pz)L˙)((pz)L)](+) and [Co(III)((pz)L˙)((pz)L)(2)](+) respectively.     

Reactions of nitric oxide with a low-spin Fe(III) center ligated to a tetradentate dicarboxamide N4 ligand: parallels between heme and non-heme systems

Reaction of excess NO with the non-heme Fe(III) complex [(bpb)Fe(py)2]ClO4 in MeCN under strictly anaerobic conditions affords the {Fe-NO}6(nitro)(nitrosyl) complex [(bpb)Fe(NO)(NO2)] (1) via metal-promoted NO disproportionation, while in a MeOH/MeCN mixture, the same reaction leads to reductive nitrosylation and generation of the {Fe-NO}7 species [(bpb)Fe(NO)] (2). Exposure of a solution of 1 in DMF to dioxygen leads to formation of the ring-nitrosylated product [(bpb-NO2)Fe(NO3)(DMF)] (3). The present system therefore exhibits all the NO reactivities reported so far with the iron-porphyrins.     

Loops, chains, sheets, and networks from variable coordination of Cu(hfac)2 with a flexibly hinged aminoxyl radical ligand

One pair of reactants, Cu(hfac)(2) = M and the hinge-flexible radical ligand 5-(3-N-tert-butyl-N-aminoxylphenyl)pyrimidine (3PPN = L), yields a diverse set of five coordination complexes: a cyclic loop M(2)L(2) dimer; a 1:1 cocrystal between an M(2)L(2) loop and an ML(2) fragment; a 1D chain of M(2)L(2) loops linked by M; two 2D M(3)L(2) networks of (M-L)(n) chains cross-linked by M with different repeat length pitches; a 3D M(3)L(2) network of M(2)L(2) loops cross-linking (M-L)(n)-type chains with connectivity different from those in the 2D networks. Most of the higher dimensional complexes exhibit reversible, temperature-dependent spin-state conversion of high-temperature paramagnetic states to lower magnetic moment states having antiferromagnetic exchange within Cu-ON bonds upon cooling, with accompanying bond contraction. The 3D complex also exhibited antiferromagnetic exchange between Cu(II) ions linked in chains through pyrimidine rings.     

Effect of mono-CDNP substitution of lysine residues on the redox reaction of cytochrome c electrostatically adsorbed on a mercaptoheptanoic acid modified Au(111) surface

The effect of charge-inverting modification of single surface lysine residue on the electron transfer (ET) reaction of horse heart cytochrome c (cyt c) is examined for 12 different types of mono-4-chloro-2,5-dinitrobenzoic acid substituted cyt c (mCDNPc) adsorbed on a Au(111) electrode modified with a self-assembled monolayer (SAM) of 7-mercapto-heptanoic acid (MHA). A negative shift in the redox potential by 10-35 mV as compared to that of native cyt c and a monolayer coverage in the range of 13-17 pmol cm(-2) are observed for electroactive mCDNPc's. The magnitude of the decrease in the ET rate constant (k(et)) of mCDNPc's compared with that of native cyt c depends on the position of the CDNP substitution. For mCDNPc's in which the modified lysine residue is outside of the interaction domain of cyt c with the SAM, the ratio of the k(et) of mCDNPc to that of native cyt c is correlated to the change in the dipole moment vector of cyt c due to the CDNP modification. This correlation suggests that the dipole moment of cyt c determines its orientation of adsorption on the SAM of MHA and significantly affects the rate of the ET. The CDNP modification of lysine residues at the interaction domain significantly decreases the rate, demonstrating the importance of the local charge environment in determining the rate of ET.     

First insights into the electronic properties of a Cu(II) center embedded in the PN3 cap of a calix[6]arene-based ligand

The first metal complex based on the calix[6]PN3 cryptand is described. The solid-state and solution studies show a 5-coordinate Cu(II) center due to its coordination to the PN3 cap and to an exchangeable guest molecule. Spectroscopic and electrochemical studies evidence surprising properties of the metal ion, which are tentatively assigned to the unusual P-Cu(II) bond enforced by the cryptand.     

Zn(II), Ni(II), Cu(II), and Fe(III) complexes of potentially bimetalating tris(pyridine- and imidazole-appended) picket-fence naphthylporphyrins with benzyl ether spacers: implications for cytochrome c oxidase active-site modeling

Two new unsymmetrical picket-fence naphthylporphyrin ligands, 1 and 2, and several of their metalated porphyrinato complexes have been synthesized as precursor model compounds for the binuclear (Fe/Cu) cytochrome c oxidase (CcO) active site. 1 and 2 have a naphthylporphyrin superstructure that has been specifically incorporated to confer long-term configurational stability to the atropisomeric products. The two picket-fence porphyrin ligands also bear covalently linked, axially offset tris(heterocycle) coordination sites for a copper ion, much like that found in the native enzyme. Monometallic porphyrin complexes [M = Zn(II), Ni(II), Cu(II), and Fe(III)] of the pyridine-appended ligand 1 have been prepared and spectroscopically and magnetically characterized. An unusual monomeric iron(III) hydroxo porphyrin complex was isolated upon workup of the compound formed under ferrous sulfate/acetic acid reflux conditions. There is general difficulty in forming binuclear complexes of 1, which is attributed to the conformational flexibility of the benzyl ether type picket spacers. The potential of ligands such as 1 and 2 for future CcO active-site modeling studies is considered.     

Study of protonation and Zn(II), Cd(II), Cu(II) and Mn(II) complexation with a glutamic acid N-pyrimidine derivative: Crystal structure of a neutral Cd(II) complex of the bianionic ligand

The compound N-(4-amino-1-methyl-5-nitroso-6-oxo-1,6-dihydropyrimidin-2-yl)-(s)-glutamic acid (H₃L) was synthesised and structurally characterised by analytical methods and ¹H, ¹³C and ¹⁵N NMR spectroscopy. This compound (H₃L) shows the same topology as other model receptors previously used to develop chemical functionalization at the surface of an active carbon when they adsorb on it. Protonation of H₃L and its coordination ability towards Cd²⁺, Zn²⁺, Cu²⁺ and Mn²⁺ ions in water solution was also studied by potentiometric methods, UV–Vis and ¹H, ¹³C NMR spectroscopies. The obtained results allow us to fit the operative conditions for the use of the activated carbon–H₃L adsorbent for the retaining of the above-mentioned metal ions in aqueous solutions. The molecular structure of {[Cd(HL)H₂O] · 3H₂O}_n was solved by single-crystal X-ray diffraction methods.     

Redox dependent conformational changes in the mixed valence form of the cytochrome c oxidase from p. The reorganization of glutamic acid 278 is coupled to the electron transfer from/to heme a and the binuclear center. denitrificans

In this work we present the separation of FTIR difference signals induced by electron transfer to/from the redox centers of the cytochrome c oxidase from P. denitrificans and compare electrochemically induced FTIR difference spectra with those induced by CO photolysis. FTIR difference spectra of rebinding of CO to the half reduced (mixed valence) form of the cytochrome c oxidase after photolysis reflect the conformational changes induced by the rebinding of CO and by electron transfer reactions from heme a3 to heme a and further on to CUA. During this process, heme a3 (and CUB) are oxidized, whereas heme a and CuA are reduced. By subtracting these difference spectra from an electrochemically induced FTIR difference spectrum, where all four cofactors are reduced, the contributions for heme a3 (and CuB) could be separated. Correspondingly, the spectral contributions of heme a and CuA have been separated. The comparison of these spectra with the spectra calculated for the hemes on the basis of their redox dependent changes previously published in Hellwig et al., (Biochemistry 38, (1999) 1685-1694) show a high degree of similarity, except for additional signals coupled to the reorganization of the binuclear center upon CO rebinding. The separated spectra clearly show that the signals attributed to Glu278, an amino acid discussed to be crucial for proton pumping, is coupled to electron transfer to/from heme a and the binuclear heme a3-CuB center.     

Active-site models of bacterial nitric oxide reductase featuring tris-histidyl and glutamic acid mimics: influence of a carboxylate ligand on Fe(B) binding and the heme Fe/Fe(B) redox potential

Active-site models of bacterial nitric oxide reductase (NOR) featuring a heme Fe and a trisimidazole- and glutaric acid-bound non-heme Fe (Fe(B)) have been synthesized. These models closely replicate the proposed active site of native NORs. Examination of these models shows that the glutamic acid mimic is required for both Fe(B) retention in the distal binding site and proper modulation of the redox potentials of both the heme and non-heme Fe's.     

Synthesis and characterization of Co(II), Ni(II), Zn(II) and Cu(II) complexes with a new tetraazamacrocyclic Schiff base ligand containing a piperazine moiety: X-ray crystal structure determination of the Co(II) complex

Two macrocyclic Schiff base ligands, L¹ [1+1] and L² [2+2], have been obtained in a one-pot cyclocondensation of 1,4-bis(2-formylphenyl)piperazine and 1,3-diaminopropane. Unfortunately, because of the low solubility of both ligands, their separation was unsuccessful. In the direct reaction of these mixed ligands (L¹ and L²) and the appropriate metal ions only [CoL¹(NO₃)]ClO₄, [NiL¹](ClO₄)₂, [CuL¹](ClO₄)₂ and [ZnL¹(NO₃)]ClO₄ complexes have been isolated. All the complexes were characterized by elemental analyses, IR, FAB-MS, conductivity measurements and in the case of the [ZnL¹(NO₃)]ClO₄ complex with NMR spectroscopy.