Activation of N2O reduction by the fully reduced micro4-sulfide bridged tetranuclear Cu Z cluster in nitrous oxide reductase

The tetranuclear CuZ cluster catalyzes the two-electron reduction of N2O to N2 and H2O in the enzyme nitrous oxide reductase. This study shows that the fully reduced 4CuI form of the cluster correlates with the catalytic activity of the enzyme. This is the first demonstration that the S = 1/2 form of CuZ can be further reduced. Complementary DFT calculations support the experimental findings and demonstrate that N2O binding in a bent mu-1,3-bridging mode to the 4CuI form is most efficient due to strong back-bonding from two reduced copper atoms. This back-donation activates N2O for electrophilic attack by a proton.     

Electronic structure description of the mu(4)-sulfide bridged tetranuclear Cu(Z) center in N(2)O reductase

Spectroscopy coupled with density functional calculations has been used to define the spin state, oxidation states, spin distribution, and ground state wave function of the mu4-sulfide bridged tetranuclear CuZ cluster of nitrous oxide reductase. Initial insight into the electronic contribution to N2O reduction is developed, which involves a sigma superexchange pathway through the bridging sulfide.     

Formation of a cytochrome c-nitrous oxide reductase complex is obligatory for N2O reduction by Paracoccus pantotrophus

Nitrous oxide reductase (N2OR) catalyses the final step of bacterial denitrification, the two-electron reduction of nitrous oxide (N2O) to dinitrogen (N2). N2OR contains two metal centers; a binuclear copper center, CuA, that serves to receive electrons from soluble donors, and a tetranuclear copper-sulfide center, CuZ, at the active site. Stopped flow experiments at low ionic strengths reveal rapid electron transfer (kobs=150 s-1) between reduced horse heart (HH) cytochrome c and the CuA center in fully oxidized N2OR. When fully reduced N2OR was mixed with oxidized cytochrome c, a similar rate of electron transfer was recorded for the reverse reaction, followed by a much slower internal electron transfer from CuZ to CuA(kobs=0.1-0.4 s-1). The internal electron transfer process is likely to represent the rate-determining step in the catalytic cycle. Remarkably, in the absence of cytochrome c, fully reduced N2OR is inert towards its substrate, even though sufficient electrons are stored to initiate a single turnover. However, in the presence of reduced cytochrome c and N2O, a single turnover occurs after a lag-phase. We propose that a conformational change in N2OR is induced by its specific interaction with cytochrome c that in turn either permits electron transfer between CuA and CuZ or controls the rate of N2O decomposition at the active site.     

Insights into the mechanism of N2O reduction by reductively activated N2O reductase from kinetics and spectroscopic studies of pH effects

Nitrous oxide reductase (N2OR) from Achromobacter cycloclastes (Ac) can be reductively activated with reduced methyl viologen over a broad range of pH. Activated Ac N2OR displays a complex activity profile as a function of the pH at which catalytic turnover is measured. Spectroscopic and steady-state kinetics data suggest that [H+] has multiple effects on both the activation and the catalytic reactions. These experimental results are in good agreement with previous theoretical studies, which suggested that the transition state is stabilized by H-bonding interactions between the active site and an N2O-derived intermediate bound to the catalytic CuZ cluster.     

Spectroscopic, computational, and kinetic studies of the mu4-sulfide-bridged tetranuclear CuZ cluster in N2O reductase: pH effect on the edge ligand and its contribution to reactivity

A combination of spectroscopy and density functional theory (DFT) calculations has been used to evaluate the pH effect at the CuZ site in Pseudomonas nautica (Pn) nitrous oxide reductase (N2OR) and Achromobacter cycloclastes (Ac) N2OR and its relevance to catalysis. Absorption, magnetic circular dichroism, and electron paramagnetic resonance with sulfur K-edge X-ray absorption spectra of the enzymes at high and low pH show minor changes. However, resonance Raman (rR) spectroscopy of PnN2OR at high pH shows that the 415 cm-1 Cu-S vibration (observed at low pH) shifts to higher frequency, loses intensity, and obtains a 9 cm-1 18O shift, implying significant Cu-O character, demonstrating the presence of a OH- ligand at the CuICuIV edge. From DFT calculations, protonation of either the OH- to H2O or the mu4-S2- to mu4-SH- would produce large spectral changes which are not observed. Alternatively, DFT calculations including a lysine residue at an H-bonding distance from the CuICuIV edge ligand show that the position of the OH- ligand depends on the protonation state of the lysine. This would change the coupling of the Cu-(OH) stretch with the Cu-S stretch, as observed in the rR spectrum. Thus, the observed pH effect (pKa approximately 9.2) likely reflects protonation equilibrium of the lysine residue, which would both raise E degrees and provide a proton for lowering the barrier for the N-O cleavage and for reduction of the [Cu4S(im)7OH]2+ to the fully reduced 4CuI active form for turnover.     

Spectroscopic properties and electronic structure of pentammineruthenium(II) dinitrogen oxide and corresponding nitrosyl complexes: binding mode of N(2)O and reactivity

The spectroscopic properties and the electronic structure of the only nitrous oxide complex existing in isolated form, [Ru(NH(3))(5)(N(2)O)]X(2) (1, X = Br(-), BF(4)(-)), are investigated in detail in comparison to the nitric oxide precursor, [Ru(NH(3))(5)(NO)]X(3) (2). IR and Raman spectra of 1 and of the corresponding (15)NNO labeled complex are presented and assigned with the help of normal coordinate analysis (NCA) and density functional (DFT) calculations. This allows for the identification of the Ru-N(2)O stretch at approximately 300 cm(-)(1) and for the unambiguous definition of the binding mode of the N(2)O ligand as N-terminal. Obtained force constants are 17.3, 9.6, and 1.4 mdyn/A for N-N, N-O, and Ru-N(2)O, respectively. The Ru(II)-N(2)O bond is dominated by pi back-donation, which, however, is weak compared to the NO complex. This bond is further weakened by Coulomb repulsion between the fully occupied t(2g) shell of Ru(II) and the HOMO of N(2)O. Hence, nitrous oxide is an extremely weak ligand to Ru(II). Calculated free energies and formation constants for [Ru(NH(3))(5)(L)](2+) (L = NNO, N(2), OH(2)) are in good agreement with experiment. The observed intense absorption at 238 nm of 1 is assigned to the t(2g) --> pi(*) charge transfer transition. These data are compared in detail to the spectroscopic and electronic structural properties of NO complex 2. Finally, the transition metal centered reaction of nitrous oxide to N(2) and H(2)O is investigated. Nitrous oxide is activated by back-donation. Initial protonation leads to a weakening of the N-O bond and triggers electron transfer from the metal to the NN-OH ligand through the pi system. The implications of this mechanism for biological nitrous oxide reduction are discussed.     

Is the isotopic composition of nitrous oxide an indicator for its origin from nitrification or denitrification? A theoretical approach from referred data and microbiological and enzyme kinetic aspects

Literature data on the isotopic composition of nitrous oxide indicate a general predominance of the alpha-15N-isotopomer and a parallel 18O-enrichment in N2O from nitrification and denitrification, respectively. As the kinetic isotope effects on any individual reactions of the two processes lead to depletions of the heavy isotopes of nitrogen and oxygen in the products, the observed enrichments could mainly be caused by enzymatic reduction of NO, provided it occurs via a symmetric intermediate like hyponitrite; infrared data are in favour of large differences between the binding constants of the isotopomers and isotopologues of this compound. As a matter of fact one of the mechanisms discussed for the nitric oxide reductase from certain microorganisms implies the parallel binding of two NO molecules and the formation of a symmetrical intermediate, while that of the enzyme from other microorganisms reduces NO in a sequential mechanism. In addition, isotope effects on the reduction of N2O to N2 must contribute to the observed isotope characteristics of N2O, especially in context with denitrification. Therefore, the known enzymatic reaction pathways suggest that the alpha-15N-isotopomer preference and the 18O-signature of the produced N2O is not essentially characteristic for its origin from nitrification or denitrification, respectively, but rather from the involved population of microorganisms and the type of their nitric oxide reductases. This has to be confirmed experimentally.     

A molecular pinwheel multicopper(I) cluster, [(L(S-))6Cu(I)13(S2-)2]3+ with mu4-sulfido, mu3-thiolato and nitrogen ligands

A copper(I) complex with new N2S thiol ligand transforms to a multicopper(I) cluster, [(L(S-))6Cu(I)13(S2-)2]3+ (1); its X-ray structure exhibiting mu4-sulfido and mu3-thiolato coordination is presented and compared to other cuprous thiolato/sulfido clusters including that observed in the copper enzyme nitrous oxide reductase.     

Cu3(mu-S)2]3+ clusters supported by N-donor ligands: progress toward a synthetic model of the catalytic site of nitrous oxide reductase

By treating Cu(I) complexes of neutral, bidentate N-donor ligands with S8, clusters with novel delocalized mixed-valence [Cu3(mu-S)2]3+ cores have been isolated. X-ray crystal structures and UV-vis and resonance Raman spectral features of these clusters reveal similarities to the tetracopper-sulfide "CuZ" site in nitrous oxide reductase. A delocalized S = 1 ground state for the mixed-valent CuIIICu2II cores is supported by the observation of high symmetry in the X-ray structures and 10-line hyperfine features arising from coupling to three equivalent Cu ions in EPR spectra obtained at room temperature (shown) and 10 K. The delocalization we observe contrasts with the localization reported previously for a [Cu3(mu-O)2]3+ analogue (Root, D. E.; Henson, M. J.; Machonkin, T.; Mukherjee, P.; Stack, T. D. P.; Solomon, E. I. J. Am. Chem. Soc. 1998, 120, 4982), which we rationalized through DFT calculations.     

Characterisation of [Cu4S], the catalytic site in nitrous oxide reductase, by EPR spectroscopy

The enzyme nitrous oxide reductase (N(2)OR) has a unique tetranuclear copper centre [Cu(4)S], called Cu(Z), at the catalytic site for the two-electron reduction of N(2)O to N(2). The X- and Q-band EPR spectra have been recorded from two forms of the catalytic site of the enzyme N(2)OR from Paracoccus pantotrophus, namely, a form prepared anaerobically, Cu(Z), that undergoes a one-electron redox cycle and Cu(Z)*, prepared aerobically, which cannot be redox cycled. The spectra of both species are axial with that of Cu(Z) showing a rich hyperfine splitting in the g||-region at X-band. DFT calculations were performed to gain insight into the electronic configuration and ground-state properties of Cu(Z) and to calculate EPR parameters. The results for the oxidation state [Cu(+1)(3)Cu(+2)(1)S](3+) are in good agreement with values obtained from the fitting of experimental spectra, confirming the absolute oxidation state of Cu(Z). The unpaired spin density in this configuration is delocalised over four copper ions, thus, Cu(I) 20.1%, Cu(II) 9.5%, Cu(III) 4.8% and Cu(IV) 9.2%, the mu(4)-sulfide ion and oxygen ligand. The three copper ions carrying the highest spin density plus the sulfide ion lie approximately in the same plane while the fourth copper ion is perpendicular to this plane and carries only 4.8% spin density. It is suggested that the atoms in this plane represent the catalytic core of Cu(Z), allowing electron redistribution within the plane during interaction with the substrate, N(2)O.     

Formation of nitric oxide and nitrous oxide in electron-irradiated H(2)18O/N2 ice mixtures--evidence for the existence of free oxygen atoms in interstellar and solar system analog ices

We investigated the irradiation of low temperature H(2)(18)O/N(2) ice mixtures with energetic electrons in an ultrahigh vacuum chamber. The newly formed species, such as nitric oxide (N(18)O), nitrous oxide (NN(18)O), hydrogen peroxide (H(2)(18)O(2)) and hydrazine (N(2)H(4)), were identified in the experiments with infrared absorption spectroscopy and mass spectrometry. The results suggest that the unimolecular decomposition of water molecules within water ices at 10 K can lead to the formation of transient, suprathermal oxygen atoms. These oxygen atoms may play an important role in the formation of oxygen-containing biomolecules such as amino acids and sugar, as well as the decomposition of the biomolecules in the ices.     

Conversion of ammonia to dinitrogen in wastewater by Nitrosomonas europaea

Because Nitrosomonas europaea contains ammonia-oxidizing enzyme, nitrite reductase, and nitrous oxide reductase, the conversion of ammonia to dinitrogen was tried with different reaction conditions. In aerobic reaction conditions, ammonium was converted to nitrite (NO ₂ ⁻ ), while under oxygen-limiting or oxygen-free conditions, NO ₂ ⁻ -N formed from ammonia oxidation by N. europaea was reduced to N₂O and dinitrogen with 22% conversion. During denitrification, optimal pH for the production of N₂O and dinitrogen was found to be 7.0–8.0. Dinitrogen was not produced in acidic pH<7.0. A low partial oxygen pressure as well as oxygen-free conditions are favorable for high production of dinitrogen.     

Determination of the 15N/14N, 17O/16O, and 18O/16O ratios of nitrous oxide by using continuous-flow isotope-ratio mass spectrometry

We developed a rapid, sensitive, and automated analytical system to determine the delta15N, delta18O, and Delta17O values of nitrous oxide (N2O) simultaneously in nanomolar quantities for a single batch of samples by continuous-flow isotope-ratio mass spectrometry (CF-IRMS) without any cumbersome and time-consuming pretreatments. The analytical system consisted of a vacuum line to extract and purify N2O, a gas chromatograph for further purification of N2O, an optional thermal furnace to decompose N2O to O2, and a CF-IRMS system. We also used pneumatic valves and pneumatic actuators in the system so that we could operate it automatically with timing software on a personal computer. The analytical precision was better than 0.12 per thousand for delta15N with >4 nmol N2O injections, 0.25 per thousand for delta18O with >4 nmol N2O injections, and 0.20 per thousand for Delta17O with >20 nmol N2O injections for a single measurement. We were also easily able to improve the precision (standard errors) to better than 0.05 per thousand for delta15N, 0.10 per thousand for delta18O, and 0.10 per thousand for Delta17O through multiple analyses with more than four repetitions with 190 nmol samples using the automated analytical system. Using the system, the delta15N, delta18O, and Delta17O values of N2O can be quantified not only for atmospheric samples, but also for other gas or liquid samples with low N2O content, such as soil gas or natural water. Here, we showed the first ever Delta17O measurements of soil N2O.     

Multifrequency EPR and redox reactivity investigations of a bis(mu-thiolato)-dicopper(II,II) complex

From a new tripodal ligand [N2SS'H] with mixed N, S(thioether), and S(thiolate) donor set, the corresponding bis(mu-thiolato)dicopper(II) complex has been prepared and characterized. X-ray crystallographic analysis of the complex [Cu2(N2SS')2](ClO4)2.C4H10O (1) demonstrates that the two five-coordinated Cu atoms are bridged by two thiolates leading to a nearly planar Cu2S2 core with a Cu1...Cu1* distance of 3.418(8) A and a large bridging angle Cu1S1Cu1* of 94.92 degrees. X-band (10 GHz), Q-band (34 GHz), and F-Band (115 GHz) EPR spectra of 1 are consistent with a weakly coupled dicopper(II,II) center attributed to an S = 1 state. Simulations for the three frequencies are obtained with a unique set of electronic parameters. The mean values of the spin Hamiltonian parameters for 1 are D = 0.210(3) cm(-1), E = 0.0295(5) cm(-1), |E/D| = 0.140, gx = 2.030(2), gy = 2.032(2), gz = 2.128(2). The electrochemical one-electron reduction of 1 generates the mixed-valent CuIICuI species. EPR and UV-vis spectra are consistent with a type I localized mixed-valent species, while dinuclear CuA centers of native cytochrome c oxidase (CcO)1-3 or nitrous oxide reductase (N2OR)4 have a delocalized CuIICuI mixed-valent state. After reoxidation of the CuIICuI species, the initial complex 1 is regenerated through a reversible interconversion process.     

Mechanism of N2O reduction by the mu4-S tetranuclear CuZ cluster of nitrous oxide reductase

Reaction thermodynamics and potential energy surfaces are calculated using density functional theory to investigate the mechanism of the reductive cleavage of the N-O bond by the mu(4)-sulfide-bridged tetranuclear Cu(Z) site of nitrous oxide reductase. The Cu(Z) cluster provides an exogenous ligand-binding site, and, in its fully reduced 4Cu(I) state, the cluster turns off binding of stronger donor ligands while enabling the formation of the Cu(Z)-N(2)O complex through enhanced Cu(Z) --> N(2)O back-donation. The two copper atoms (Cu(I) and Cu(IV)) at the ligand-binding site of the cluster play a crucial role in the enzymatic function, as these atoms are directly involved in bridged N(2)O binding, bending the ligand to a configuration that resembles the transition state (TS) and contributing the two electrons for N(2)O reduction. The other atoms of the Cu(Z) cluster are required for extensive back-bonding with minimal sigma ligand-to-metal donation for the N(2)O activation. The low reaction barrier (18 kcal mol(-)(1)) of the direct cleavage of the N-O bond in the Cu(Z)-N(2)O complex is due to the stabilization of the TS by a strong Cu(IV)(2+)-O(-) bond. Due to the charge transfer from the Cu(Z) cluster to the N(2)O ligand, noncovalent interactions with the protein environment stabilize the polar TS and reduce the activation energy to an extent dependent on the strength of proton donor. After the N-O bond cleavage, the catalytic cycle consists of a sequence of alternating protonation/one-electron reduction steps which return the Cu(Z) cluster to the fully reduced (4Cu(I)) state for future turnover.     

Isotopomeric characterization of N2O produced, consumed, and emitted by automobiles

Fossil fuel combustion is the second largest anthropogenic source of nitrous oxide (N2O) after agriculture. The estimated global N2O flux from combustion sources, as well as from other sources, still has a large uncertainty. Herein, we characterize automobile sources using N2O isotopomer ratios (nitrogen and oxygen isotope ratios and intramolecular site preference of 15N, SP) to assess their contributions to total global sources and to deconvolute complex production/consumption processes during combustion and subsequent catalytic treatments of exhaust. Car exhaust gases were sampled under running and idling state, and N2O isotopomer ratios were measured by mass spectrometry. The N2O directly emitted from an engine of a vehicle running at constant velocity had almost constant isotopomer ratios (delta15Nbulk = -28.7 +/- 1.2 per thousand, delta18O = 28.6 +/- 3.3 per thousand, and SP = 4.2 +/- 0.8 per thousand) irrespective of the velocity. After passing through catalytic converters, the isotopomer ratios showed an increase which varied with the temperature and the aging of the catalysts. The increase suggests that both production and consumption of N2O occur on the catalyst and that their rates can be comparable. It was noticed that in the idling state, the N2O emitted from a brand new car has higher isotopomer ratios than that from used cars, which indicate that technical improvements in catalytic converters can reduce the N2O from mobile combustion sources. On average, the isotopomeric signatures of N2O finally emitted from automobiles are not sensitive to running/idling states or to aging of the catalysts. Characteristic average isotopomer ratios of N2O from automobile sources are estimated at -4.9 +/- 8.2 per thousand, 43.5 +/- 13.9 per thousand, and 12.2 +/- 9.1 per thousand for delta15Nbulk, delta18O, and SP, respectively.     

Nitrous oxide tetramer has two highly symmetric isomers

Infrared spectra of the nitrous oxide tetramer, (N(2)O)(4), are studied in the region of the N(2)O ν(1) fundamental band (～2200 cm(-1)). The spectra are observed using a tunable diode laser to probe a pulsed supersonic jet expansion. Parallel (ΔK = 0) bands are observed for the previously observed isomer of (N(2)O)(4), which is confirmed by isotopic substitution to have an oblate symmetric rotor structure with D(2d) symmetry. A distinct new isomer of (N(2)O)(4) is observed by means of a perpendicular (ΔK = ±1) band. It has a prolate symmetric rotor structure with S(4) symmetry. These isomers represent two distinct, but almost equally favorable, ways of bringing together a pair of nonpolar N(2)O dimers to form a tetramer. It is not clear at present which one represents the true ground state.     

Spectroscopic observation of nitrous oxide pentamers

Two new infrared bands in the ν(1) fundamental region of N(2)O are observed in a supersonic jet expansion and assigned to nitrous oxide pentamers. Each band is measured using both (14)N(2)(16)O and (15)N(2)(16)O. Although they are similar in appearance, the bands have slightly different lower state rotational parameters, and are thus assigned to distinct structural isomers of the pentamer. Cluster calculations using two N(2)O intermolecular potentials give results in good agreement with the observed spectra, and indicate that the two isomers probably have the same basic structure (which is unsymmetrical), but differ in the alignment (N-N-O or O-N-N) of one or two of the constituent monomers. Calculations using a resonant dipole interaction model also support the proposed assignment and structure. These are the first reported high-resolution spectra for N(2)O pentamers.     

N2O Reductase Activity of a [Cu4S] Cluster in the 4CuI Redox State Modulated by Hydrogen Bond Donors and Proton Relays in the Secondary Coordination Sphere

The model complex [Cu₄(μ₄‐S)(dppa)₄]²⁺ ( 1 , dppa=μ₂‐(Ph₂P)₂NH) has N₂O reductase activity in methanol solvent, mediating 2 H⁺/2 e^? reduction of N₂O to N₂+H₂O in the presence of an exogenous electron donor (CoCp₂). A stoichiometric product with two deprotonated dppa ligands was characterized, indicating a key role of second‐sphere N?H residues as proton donors during N₂O reduction. The activity of 1 towards N₂O was suppressed in solvents that are unable to provide hydrogen bonding to the second‐sphere N?H groups. Structural and computational data indicate that second‐sphere hydrogen bonding induces structural distortion of the [Cu₄S] active site, accessing a strained geometry with enhanced reactivity due to localization of electron density along a dicopper edge site. The behavior of 1 mimics aspects of the Cu_Z catalytic site of nitrous oxide reductase: activity in the 4Cu^I:1S redox state, use of a second‐sphere proton donor, and reactivity dependence on both primary and secondary sphere effects.