Mechanism of nitrite reduction at T2Cu centers: electronic structure calculations of catalysis by copper nitrite reductase and by synthetic model compounds

The mechanism of nitrite reduction at the Cu(II) center of both copper nitrite reductase and a number of corresponding synthetic models has been investigated by using both QM/MM and cluster calculations employing density functional theory methods. The mechanism in both cases is found to be very similar. Initially nitrite is bound in a bidentate fashion to the Cu(II) center via the two oxygen atoms. Upon reduction of the copper center, the two possible coordination modes of the protonated nitrite, by either nitrogen or a single oxygen atom, are close in energy, with nitrogen coordination probably preferred. Further protonation of this species leads to N-O bond cleavage, and an electron transfer from the Cu(I) center to the N-O+ ligand, resulting in loss of NO and regeneration of the resting state of the enzyme having a bound water molecule.     

EPR-ENDOR of the Cu(I)NO complex of nitrite reductase

With limited reductant and nitrite under anaerobic conditions, copper-containing nitrite reductase (NiR) of Rhodobacter sphaeroides yielded endogenous NO and the Cu(I)NO derivative of NiR. (14)N- and (15)N-nitrite substrates gave rise to characteristic (14)NO and (15)NO EPR hyperfine features indicating NO involvement, and enrichment of NiR with (63)Cu isotope caused an EPR line shape change showing copper involvement. A markedly similar Cu(I)NONiR complex was made by anaerobically adding a little endogenous NO gas to reduced protein and immediately freezing. The Cu(I)NONiR signal accounted for 60-90% of the integrated EPR intensity formerly associated with the Type 2 catalytic copper. Analysis of NO and Cu hyperfine couplings and comparison to couplings of inorganic Cu(I)NO model systems indicated approximately 50% spin on the N of NO and approximately 17% spin on Cu. ENDOR revealed weak nitrogen hyperfine coupling to one or more likely histidine ligands of copper. Although previous crystallography of the conservative I289V mutant had shown no structural change beyond the 289 position, this mutation, which eliminates the Cdelta1 methyl of I289, caused the Cu(I)NONiR EPR spectrum to change and proton ENDOR features to be significantly altered. The proton hyperfine coupling that was significantly altered was consistent with a dipolar interaction between the Cdelta1 protons of I289 and electron spin on the NO, where the NO would be located 3.0-3.7 A from these protons. Such a distance positions the NO of Cu(I)NO as an axial ligand to Type 2 Cu(I).     

Synthesis and crystal structure of an unusual mixed crystal containing an oxorhenium(V) and imidorhenium(V) complex

An unusual mixed crystal of a square-pyramidal oxorhenium(V), [ReOCl(Hdua)], and an octahedral imidorhenium(V) complex, [Re(dua)Cl₂(PPh₃)], was prepared from the reaction of trans-[ReOCl₃(PPh₃)₂]_and (6Z)-6-(2-aminobenzylideneamino)- 5-amino-1,3-dimethylpyrimidine-2,4(1H,3H)-dione (H₃dua) in ethanol. Characterization was performed by single crystal X-ray structure determination and IR spectroscopy. The chelate Hdua is coordinated as a tridentate diamido-imine, and dua is chelated as an imido-imino-amide.     

Mapping of the binding site on pseudoazurin in the transient 152 kDa complex with nitrite reductase

Nitrite reductase (NiR) catalyzes the reduction of nitrite to nitrite oxide as a part of the denitrification process. In Alcaligenes faecalis S-6, the copper protein pseudoazurin acts as electron donor to NiR. The binding surface of pseudoazurin involved in the formation of the 152 kDa complex with NiR has been determined by NMR using cross saturation from NiR to perdeuterated pseudoazurin. Due to the transient nature of the complex, saturation effects can be observed on the resonances of the unbound protein. The binding site comprises the hydrophobic area surrounding the exposed copper ligand His81, suggesting that this residue is important for efficient electron transfer.     

The structure analysis of triaryl derivatives of the group V elements: V. Spectra,crystal and molecular structure of trimesitylarsine,C27H33As

The complete X-ray structure analysis of trimesitylarsine (TMAS), C₂₇H₃₃As, has been performed. The crystals are triclinic, a 18.718, b 16.418, c 8.204 Å, α 99.99, β 97.85, γ 104.56°, Z = 4, space group P1̄ (two independent molecules in the asymmetric unit); the final value of the R-factor is 0.038. In the electronic spectrum of TMAS the long-wave band has the maximum at 276 nm which differs significantly from that of triphenylarsine (TPAS) at 249 nm. The bathochromic spectral shift and the molecular conformation are caused by the steric effects as a result of bulky methyl groups in the positions 2,4 and 6 in the phenyl rings. Two independent molecules are connected by a pseudo-axis of symmetry.     

An easily accessible Re-based catalyst for the selective conversion of methanol: evidence for an unprecedented active site structure through combined operando techniques

Heterogeneous Re/SiO(2) catalysts prepared using a one pot sol-gel synthesis were found to display high activity in the direct, selective methanol conversion to methylal, which is correlated to an unprecedented rhenium oxide structure.     

Spectroscopic studies of the Met182Thr mutant of nitrite reductase: role of the axial ligand in the geometric and electronic structure of blue and green copper sites

A combination of spectroscopic methods and density functional calculations has been used to describe the electronic structure of the axial mutant (Met182Thr) of Rhodobacter sphaeroides nitrite reductase in which the axial methionine has been changed to a threonine. This mutation results in a dramatic change in the geometric and electronic structure of the copper site. The electronic absorption data imply that the type 1 site in the mutant is like a typical blue copper site in contrast to the wild-type site, which is green. Similar ligand field strength in the mutant and the wild type (from MCD spectra) explains the similar EPR parameters for very different electronic structures. Resonance Raman shows that the Cu-S(Cys) bond is stronger in the mutant relative to the wild type. From a combination of absorption, CD, MCD, and EPR data, the loss of the strong axial thioether (present in the wild-type site) results in an increase of the equatorial thiolate-Cu interaction and the site becomes less tetragonal. Spectroscopically calibrated density functional calculations were used to provide additional insight into the role of the axial ligand. The calculations reproduce well the experimental ground-state bonding and the changes in going from a green to a blue site along this coupled distortion coordinate. Geometry optimizations at the weak and strong axial ligand limits show that the bonding of the axial thioether is the key factor in determining the structure of the ground state. A comparison of plastocyanin (blue), wild-type nitrite reductase (green), and the Met182Thr mutant (blue) sites enables evaluation of the role of the axial ligand in the geometric and electronic structure of type 1 copper sites, which can affect the electron-transfer properties of these sites.     

Effect of the methionine ligand on the reorganization energy of the type-1 copper site of nitrite reductase

Copper-containing nitrite reductase harbors a type-1 and a type-2 Cu site. The former acts as the electron acceptor site of the enzyme, and the latter is the site of catalytic action. The effect of the methionine ligand on the reorganization energy of the type-1 site was explored by studying the electron-transfer kinetics between NiR (wild type (wt) and the variants Met150Gly and Met150Thr) with Fe(II)EDTA and Fe(II)HEDTA. The mutations increased the reorganization energy by 0.3 eV (30 kJ mol-1). A similar increase was found from pulse radiolysis experiments on the wt NIR and three variants (Met150Gly, Met150His, and Met150Thr). Binding of the nearby Met62 to the type-1 Cu site in Met150Gly (under influence of an allosteric effector) lowered the reorganization energy back to approximately the wt value. According to XRD data the structure of the reduced type-1 site in Met150Gly NiR in the presence of an allosteric effector is similar to that in the reduced wt NiR (solved to 1.85 A), compatible with the similarity in reorganization energy.     

Cu(H4C3N2S)Cl2](n), an unprecedented diazole-bridged one-dimensional copper halide: synthesis,structure, and magnetic properties

The simultaneous desulfurization of 2-mercapto-5-methyl-1,3,4-thiadiazole with CuCl(2) x 2H(2)O via mutual diffusion in solvents results in the isolation of air-stable dark-green crystals of [Cu(H(4)C(3)N(2)S)Cl(2)](n) (approximately 65% yield). The structure is characterized by a unique one-dimensional copper chain bridged by diazine N-N single bonds rather than halogens, in sharp contrast with the halide bridging mode in conventional copper halide coordination polymers. Each Cu(II) ion shows a square planar coordination geometry featuring a strong Jahn-Teller distortion, as also supported by EPR data. The phase follows a Curie-Weiss paramagnetic behavior over 6-300 K. However, the intrachain antiferromagnetic interaction is evident (-2J = 21.1 cm(-1)). Such magnetic coupling is related to the interplay between the Cu(II)-d(x2-y2) and diazine N-N p-orbitals.     

The crystal structure of the Cu+ ion conductor, (C5H5NH)2Cu5Br7

(C₅H₅NH)₂Cu₅Br₇, in which (C₅H₅NH)⁺ is the pyridinium ion, belongs to space group P2₁2₁2₁ with Z = 4 and a = 13.09 ± 0.03 Å, b = 14.04 ± 0.03 Å, c = 11.78 ± 0.02Å. The 20 Cu⁺ ions are distributed non-uniformly over 52 tetrahedral sites. The bromide tetrahedra share faces in such a manner that undulating channels are formed in the [100] and [010] directions, and right- and left-handed helical channels are formed in the c-direction. The channels are interconnected, thereby forming a three-dimensional solid electrolyte. A detailed examination of the conduction pathways and of Cu⁺ ion site occupancies leads to the predictions that σ₂ (|b) should be somewhat greater than σ₁ (|a) but σ₃ (|c) should be substantially less than σ₁. (σ_i is the specific conductivity in the ith direction.) The ratio of available sites to current carriers and the percentage of unit cell volume attributable to the conduction pathways are both rather low and the average conductivity is rather high relative to AgI-based solid electrolytes.     

Hydrotris(triazolyl)borate complexes as functional models for Cu nitrite reductase: the electronic influence of distal nitrogens

Hydrotris(triazolyl)borate (Ttz) ligands form CuNO(x) (x = 2, 3) complexes for structural and functional models of copper nitrite reductase. These complexes have distinct properties relative to complexes of hydrotris(pyrazolyl)borate (Tp) and neutral tridentate N-donor ligands. The electron paramagnetic resonance spectra of five-coordinate copper complexes show rare nitrogen superhyperfine couplings with the Ttz ligand, indicating strong σ donation. The copper(I) nitrite complex [PPN](+)[(Ttz(tBu,Me))Cu(I)NO(2)](-) has been synthesized and characterized and allows for the stoichiometric reduction of NO(2)(-) to NO with H(+) addition. Anionic Cu(I) nitrite complexes are unusual and are stabilized here for the first time because Ttz is a good π acceptor.     

An unprecedented copper(I,II)-octacyanotungstate(V) 2-D network: crystal structure and magnetism of [CuII(tren)]{CuI[W(V)(CN)8]} . 1.5H2O

A novel two-dimensional cyanide-bridged polymer [CuII(tren)]{CuI[W(V)(CN)8]} . 1.5H2O (tren = tris(2-aminoethyl)amine) formed via the simultaneous in situ metal-ligand redox reaction of [Cu(tren)(OH2)]2+ and self-assembly with [W(V)(CN)8]3- consists of a {CuI[W(V)(CN)8]} square grid built of CuI centres of tetrahedral geometry coordinatively saturated by CN bridges and [W(V)(CN)8]3- capped by [CuII(tren)]2+ moieties; it exhibits ferromagnetic coupling J1 = +5.8(1) cm(-1) within the CuII-W(V) dinuclear subunits and weak antiferromagnetic coupling J2 = -0.03(1) cm(-1) between them through diamagnetic CuI spacers.     

Observation of an unprecedented body centered cubic micellar mesophase from rod-coil molecules

We have demonstrated that rod-coil molecules based on a tetra-p-phenylene rod and a poly(propylene oxide) coil self-assemble into an unprecedented body centered cubic micellar structure in the melt, through detailed morphological analysis by X-ray scattering and transmission electron microscopy experiments.     

The importance of the long type 1 copper-binding loop of nitrite reductase for structure and function

The long 15-residue type 1 copper-binding loop of nitrite reductase has been replaced with that from the cupredoxin amicyanin (7 residues). This sizable loop contraction does not have a significant effect on the spectroscopy, and therefore, the structures of both the type 1 and type 2 Cu(II) sites. The crystal structure of this variant with Zn(II) at both the type 1 and type 2 sites has been determined. The coordination geometry of the type 2 site is almost identical to that found in the wild-type protein. However, the structure of the type 1 centre changes significantly upon metal substitution, which is an unusual feature for this class of site. The positions of most of the coordinating residues are altered of which the largest difference was observed for the coordinating His residue in the centre of the mutated loop. This ligand moves away from the active site, which results in a more open metal centre with a coordinating water molecule. Flexibility has been introduced into this region of the protein. The 200 mV increase in the reduction potential of the type 1 copper site indicates that structural changes upon reduction must stabilise the cuprous form. The resulting unfavourable driving force for electron transfer between the two copper sites, and an increased reorganisation energy for the type 1 centre, contribute to the loop variant having very little nitrite reductase activity. The extended type 1 copper-binding loop of this enzyme makes a number of interactions that are important for maintaining quaternary structure.     

Mechanism of the six-electron reduction of nitrite to ammonia by cytochrome c nitrite reductase

Cytochrome c nitrite reductase catalyzes the six-electron reduction of nitrite to ammonia without the release of potential reaction intermediates, such as NO or hydroxylamine. On the basis of the crystallographic observation of reaction intermediates and of density functional calculations, we present a working hypothesis for the reaction mechanism of this multiheme enzyme which carries a novel lysine-coordinated heme group (Fe-Lys). It is proposed that nitrite reduction starts with a heterolytic cleavage of the N-O bond which is facilitated by a pronounced back-bonding interaction of nitrite coordinated through nitrogen to the reduced (Fe(II)) but not the oxidized (Fe(III)) active site iron. This step leads to the formation of an [FeNO](6) species and a water molecule and is further facilitated by a hydrogen bonding network that induces an electronic asymmetry in the nitrite molecule that weakens one N-O bond and strengthens the other. Subsequently, two rapid one-electron reductions lead to an [FeNO](8) form and, by protonation, to an Fe(II)-HNO adduct. Hereafter, hydroxylamine will be formed by a consecutive two-electron two-proton step which is dehydrated in the final two-electron reduction step to give ammonia and an additional water molecule. A single electron reduction of the active site closes the catalytic cycle.     

Alkylamine-ligated H93G myoglobin cavity mutant: a model system for endogenous lysine and terminal amine ligation in heme proteins such as nitrite reductase and cytochrome f

His93Gly sperm whale myoglobin (H93G Mb) has the proximal histidine ligand removed to create a cavity for exogenous ligand binding, providing a remarkably versatile template for the preparation of model heme complexes. The investigation of model heme adducts is an important way to probe the relationship between coordination structure and catalytic function in heme enzymes. In this study, we have successfully generated and spectroscopically characterized the H93G Mb cavity mutant ligated with less common alkylamine ligands (models for Lys or the amine group of N-terminal amino acids) in numerous heme iron states. All complexes have been characterized by electronic absorption and magnetic circular dichroism spectroscopy in comparison with data for parallel imidazole-ligated H93G heme iron moieties. This is the first systematic spectral study of models for alkylamine- or terminal amine-ligated heme centers in proteins. High-spin mono- and low-spin bis-amine-ligated ferrous and ferric H93G Mb adducts have been prepared together with mixed-ligand ferric heme complexes with alkylamine trans to nitrite or imidazole as heme coordination models for cytochrome c nitrite reductase or cytochrome f, respectively. Six-coordinate ferrous H93G Mb derivatives with CO, NO, and O(2) trans to the alkylamine have also been successfully formed, the latter for the first time. Finally, a novel high-valent ferryl species has been generated. The data in this study represent the first thorough investigation of the spectroscopic properties of alkylamine-ligated heme iron systems as models for naturally occurring heme proteins ligated by Lys or terminal amines.     

Synthesis and crystal structure of unprecedented oxo/hydroxo-bridged polynuclear gallium(III) aqua complexes

Two new polynuclear oxo/hydroxo-bridged polynuclear gallium(III) aqua complexes are obtained upon treatment of Ga(3+)(aq) with pyridine: the supramolecular compound of macrocyclic cavitand cucurbit[6]uril with gallium complex containing 32 metal atoms [Ga(32)(mu(4)-O)(12)(mu(3)-O)(8)(mu(2)-O)(7)(mu(2)-OH)(39)(H(2)O)(20)](PyH subsetC(36)H(36)N(24)O(12))(3)(NO(3))(6).53H(2)O (1) and the tridecanuclear complex [Ga(13)(mu(3)-OH)(6)(mu(2)-OH)(18)(H(2)O)(24)](NO(3))(15).12H(2)O (2). It follows that two modes of nucleation exist when Ga(3+)(aq) is hydrolyzed: one around the tetrahedral GaO(4) units (complex 1) and the other around the octahedral GaO(6) units (complex 2). This is the first time that polynuclear oxo/hydroxo-bridged aqua complexes of Ga(III) have been isolated without the use of other ligands to control or block olygomerization.     

A novel enzyme electrode method for the determination of nitrite based on nitrite reductase

The enzyme, nitrite reductase, can be extracted and purified from spinach leaves; the freeze-dried preparation is completely stable for at least 4 months if kept in a freezer. The enzyme catalyzes the reduction of nitrite to ammonia in the presence of reduced methyl viologen as electron donor. An assay of nitrite can be based on the measurement of the ammonia formation, with an air-gap electrode as sensor. Nitrite in the 10⁻⁴ M—5 · lO⁻² M range can be accurately determined with either soluble or immobilized enzyme, but the latter is stable for at least 3 weeks, is less susceptible to interferences during assay, and can be used repeatedly for about a hundred runs. These advantages make the method very simple, valuable and economical for the routine analysis of nitrite ion.     

[Cu(NBOCTB)][Cu(NO3)4].H2O的合成、晶体结构及热分解过程

本文制备了水合四硝基合铜(Ⅱ)酸N, N, N', N'-四[(1'-苄基-2'-苯并咪唑)甲基]-反式-1, 2-环己二胺合铜(Ⅱ), [Cu(NBOCTB)][Cu(NO3)4].H2O。X射线衍射实验表明, 其晶体属三斜晶系, 空间群P1, a=1.4723(3), b=1.5089(4),c=1.7157(6)nm; α=99.35(2), β=110.68(3), γ=103.66(2)°, Z=2,Dc=1.38g/cm^3。用TG-DTG技术对配合物的热分解过程进行了初步研究。     

The binding of nitric oxide at the Cu(i) site of copper nitrite reductase and of inorganic models: DFT calculations of the energetics and EPR parameters of side-on and end-on structures

Density functional theory calculations have been used to probe the end-on and side-on bonding motifs of nitric oxide at the Cu(i) centre in the enzyme copper nitrite reductase and in three inorganic model systems. We find that irrespective of a range of functionals used, the end-on structure is preferred by up to 40 kJ mol(-1), although this preference is smaller for the enzyme than for the inorganic model systems. We have calculated the g-tensor and atomic hyperfine coupling constants for these structures. When compared to available experimental data, for one model compound the calculated EPR parameters definitely favour an end-on structure, although this preference is somewhat less for the enzyme. Our prediction of NO end-on binding in the enzyme is at variance with structural data.