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

Crystal Structure and Electron Configuration of {MNO}8 Heme Complexes

Although research on nitrosyl (NO) heme complexes and their one-electron reduced form, nitroxyl (or nitroxyl anion, NO-) derivatives, has been going on for decades, there are still disagreements about the electrical configuration of nitroxyl complexes, and the majority of the work on this topic is based on theoretical calculations. Following the initial nitroxyl iron porphyrin crystal structure, we present two further polymorphic forms of [CoCp2][Fe(TFPPBr8)(NO)]. Using the same completely halogenated porphyrin ligand, we also present two polymorphic forms of nitrosyl cobalt(II) complexes, which are another sort of {MNO}8 structure. In addition to the EXANES and EPR studies of these {FeNO}7 and {CoNO}8 complexes, the {FeNO}8 [CoCp2][Fe(TFPPBr8)(NO)] complex is also investigated by temperature-dependent Mössbauer experiments for the first time with the {FeNO}7 precursor as a control sample. The analysis of the Mössbauer and crystal structural parameters between these two types of {MNO}8 (M = Fe or Co) species and previously reported analogous ones allow us to conclude that the electronic configuration of [Fe(TFPPBr8)(NO)]- is best described as an intermediate between low-spin Fe(II)-NO- and Fe(I)-NO•.

Acid-catalyzed Transformation of Nitrite to Nitric Oxide on Copper(II)-Cobalt(II) Centers in a Bimetallic Complex

Nitrite (NO2 -) serves as a pool of nitric oxide (NO) in biological systems under hypoxic conditions, and it is transformed to NO by nitrite reductase (NiR) enzyme in the presence of acid (H+ ions). However, NO synthases (NOSs) generate NO via L-arginine oxidation in normoxic conditions. Previously, acid-induced NO2 - reduction chemistry was modeled on mono-metallic 3d-metals, generating metal-nitrosyls or NO(g) with H2O or H2O2 products. Herein, to understand the relative potency of a bimetallic system, we report the acid-induced reductive conversion of η2-bound NO2 - to NO on CuII-CoII centers of a hetero-bimetallic CuII-nitrito-CoII complex, [(LN8H)CuII-NO2 --CoII]3+ (CuII-NO2 --CoII, 2) bearing an octadentate N8-cryptand ligand (LN8H). The CuII-NO2 --CoII generates [CuII(LN8H)CoII]4+ (1) upon reaction with one equiv. acid (HClO4, H+ ions source) with NO(g) via a presumed transient nitrousacid (ONOH) intermediate species. Likewise, this NO2 - reduction was found to form H2O, which is believed to be from the decomposition of H2O2, an intermediate species. In addition, complex 2, in the presence of more than one equiv. H+ ions also showed the formation of NO(g) with H2O. Mechanistic investigations, using 15N-labeled-15NO2 -, 18O-labeled-18O14N16O- and 2H-labeled-DClO4 (D+ source), revealed that the N-atom and O-atom in the 14/15NO and 14N18O gases are derived from NO2 - ligand and H-atom in H2O derived from H+-source, respectively.

Pendant Proton-Relays Systematically Tune the Rate and Selectivity of Electrocatalytic Ammonia Generation in a Fe-Porphyrin Based Metal-Organic Framework

Electrocatalytic nitrite reduction (eNO2RR) is a promising alternative route to produce ammonia (NH3). Until now, several molecular catalysts have shown capability to homogeneously reduce nitrite to NH3, while taking advantage of added secondary-sphere functionalities to direct catalytic performance. Yet, realizing such control over heterogeneous electrocatalytic surfaces remains a challenge. Herein, we demonstrate that heterogenization of a Fe-porphyrin molecular catalyst within a 2D Metal-Organic Framework (MOF), allows efficient eNO2RR to NH3. On top of that, installation of pendant proton relaying moieties proximal to the catalytic site, resulted in significant improvement in catalytic activity and selectivity. Notably, systematic manipulation of NH3 faradaic efficiency (up to 90 %) and partial current (5-fold increase) was achieved by varying the proton relay-to-catalyst molar ratio. Electrochemical and spectroscopic analysis show that the proton relays simultaneously aid in generating and stabilizing of reactive Fe-bound NO intermediate. Thus, this concept offers new molecular tools to tune heterogeneous electrocatalytic systems.

Reaction Discovery Using Spectroscopic Insights from an Enzymatic C-H Amination Intermediate

Engineered hemoproteins can selectively incorporate nitrogen from nitrene precursors like hydroxylamine, O-substituted hydroxylamines, and organic azides into organic molecules. Although iron-nitrenoids are often invoked as the reactive intermediates in these reactions, their innate reactivity and transient nature have made their characterization challenging. Here we characterize an iron-nitrosyl intermediate generated from NH2OH within a protoglobin active site that can undergo nitrogen-group transfer catalysis, using UV-vis, electron paramagnetic resonance (EPR) spectroscopy, and high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) techniques. The mechanistic insights gained led to the discovery of aminating reagents─nitrite (NO2-), nitric oxide (NO), and nitroxyl (HNO)─that are new to both nature and synthetic chemistry. Based on the findings, we propose a catalytic cycle for C-H amination inspired by the nitrite reductase pathway. This study highlights the potential of engineered hemoproteins to access natural nitrogen sources for sustainable chemical synthesis and offers a new perspective on the use of biological nitrogen cycle intermediates in biocatalysis.

Recent mechanistic developments for cytochrome c nitrite reductase, the key enzyme in the dissimilatory nitrate reduction to ammonium pathway

Cytochrome c nitrite reductase, NrfA, is a soluble, periplasmic pentaheme cytochrome responsible for the reduction of nitrite to ammonium in the Dissimilatory Nitrate Reduction to Ammonium (DNRA) pathway, a vital reaction in the global nitrogen cycle. NrfA catalyzes this six-electron and eight-proton reduction of nitrite at a single active site with the help of its quinol oxidase partners. In this review, we summarize the latest progress in elucidating the reaction mechanism of ammonia production, including new findings about the active site architecture of NrfA, as well as recent results that elucidate electron transfer and storage in the pentaheme scaffold of this enzyme.

Ferroheme/Ferriheme Directly Involved in the Synthesis and Decomposition of Hydrazine as an Electron Carrier during Anammox

Anammox bacteria performed the reaction of NH4+ and NO with hydrazine synthase to produce N2H4, followed by the decomposition of N2H4 with hydrazine dehydrogenase to generate N2. Ferroheme/ferriheme, which serves as the active center of both hydrazine synthase and hydrazine dehydrogenase, is thought to play a crucial role in the synthesis and decomposition of N2H4 during Anammox due to its high redox activity. However, this has yet to be proven and the exact mechanisms by which ferroheme/ferriheme is involved in the Anammox process remain unclear. In this study, abiotic and biological assays confirmed that ferroheme participated in NH4+ and NO reactions to generate N2H4 and ferriheme, and the produced N2H4 reacted with ferriheme to generate N2 and ferroheme. In other words, the ferroheme/ferriheme cycle drove the continuous reaction between NH4+ and NO. Raman, ultraviolet-visible spectroscopy, and X-ray absorption fine structure spectroscopy confirmed that ferroheme/ferriheme is involved in the synthesis and decomposition of N2H4 via the core FeII/FeIII cycle. The mechanism of ferroheme/ferriheme participation in the synthesis and decomposition of N2H4 was proposed by density functional theory calculations. These findings revealed for the first time the heme electron transfer mechanisms, which are of great significance for deepening the understanding of Anammox.

Nitrate reduction to ammonium: a phylogenetic, physiological, and genetic aspects in Prokaryotes and eukaryotes

The microbe-mediated conversion of nitrate (NO3-) to ammonium (NH4+) in the nitrogen cycle has strong implications for soil health and crop productivity. The role of prokaryotes, eukaryotes and their phylogeny, physiology, and genetic regulations are essential for understanding the ecological significance of this empirical process. Several prokaryotes (bacteria and archaea), and a few eukaryotes (fungi and algae) are reported as NO3- reducers under certain conditions. This process involves enzymatic reactions which has been catalysed by nitrate reductases, nitrite reductases, and NH4+-assimilating enzymes. Earlier reports emphasised that single-cell prokaryotic or eukaryotic organisms are responsible for this process, which portrayed a prominent gap. Therefore, this study revisits the similarities and uniqueness of mechanism behind NO3- -reduction to NH4+ in both prokaryotes and eukaryotes. Moreover, phylogenetic, physiological, and genetic regulation also shed light on the evolutionary connections between two systems which could help us to better explain the NO3--reduction mechanisms over time. Reports also revealed that certain transcription factors like NtrC/NtrB and Nit2 have shown a major role in coordinating the expression of NO3- assimilation genes in response to NO3- availability. Overall, this review provides a comprehensive information about the complex fermentative and respiratory dissimilatory nitrate reduction to ammonium (DNRA) processes. Uncovering the complexity of this process across various organisms may further give insight into sustainable nitrogen management practices and might contribute to addressing global environmental challenges.

Appended Lewis Acids Enable Dioxygen Reactivity and Catalytic Oxidations with Ni(II)

We disclose a suite of Ni(II) complexes featuring secondary sphere Lewis acids of varied Lewis acidity and tether lengths. Several of these complexes feature atypical behavior of Ni(II): reactivity with O2 that occurs only in the presence of a tethered Lewis acid. In situ UV-vis spectroscopy revealed that, although adducts are stable at -40 °C, complexes containing 9-borabicyclo[3.3.1]nonane (9-BBN) Lewis acids underwent irreversible oxidative deborylation when warmed to room temperature. We computationally and experimentally identified that oxidative instability of appended 9-BBN moieties can be mitigated using weaker Lewis acids such as pinacolborane (BPin). These insights enabled the realization of catalytic reactions: hydrogen atom abstraction from phenols and room temperature oxygen atom transfer to PPh3.

Electrochemical Nitrate Reduction: Ammonia Synthesis and the Beyond

Natural nitrogen cycle has been severely disrupted by anthropogenic activities. The overuse of N-containing fertilizers induces the increase of nitrate level in surface and ground waters, and substantial emission of nitrogen oxides causes heavy air pollution. Nitrogen gas, as the main component of air, has been used for mass ammonia production for over a century, providing enough nutrition for agriculture to support world population increase. In the last decade, researchers have made great efforts to develop ammonia processes under ambient conditions to combat the intensive energy consumption and high carbon emission associated with the Haber-Bosch process. Among different techniques, electrochemical nitrate reduction reaction (NO3RR) can achieve nitrate removal and ammonia generation simultaneously using renewable electricity as the power, and there is an exponential growth of studies in this research direction. Here, a timely and comprehensive review on the important progresses of electrochemical NO3RR, covering the rational design of electrocatalysts, emerging CN coupling reactions, and advanced energy conversion and storage systems is provided. Moreover, future perspectives are proposed to accelerate the industrialized NH3 production and green synthesis of chemicals, leading to a sustainable nitrogen cycle via prosperous N-based electrochemistry.

Ru(II) based dual nitric oxide donors: electrochemical and photochemical reactivities and vasorelaxant effect with no cytotoxicity

The synthesized complexes, cis-[Ru(NO)(NO2)(phen)2](PF6)2 (NONO2P) and cis-[Ru(NO)(NO2)(bpy)2](PF6)2 (NONO2B), were characterized by using elemental analysis, voltammetry and electronic and vibrational spectroscopy. Under electrochemical and photochemical stimulation in an aqueous medium, there are indications of the formation of complexes, which suggests that the nitro and nitrosyl groups are converted into nitric oxide. Both compounds do not show cytotoxic activity against human umbilical vein endothelial cells (HUVECs). The cis-[Ru(NO)(NO2)(phen)2](PF6)2 complex presented vasorelaxation activity in superior mesenteric arteries from Wistar rats: the biphasic concentration-response curve indicates two sites of action. In the presence of NO scavengers, we observed an impaired relaxing effect induced by NONO2P, suggesting that the vasorelaxant effect is due to NO production from this compound.

Uncovering Nitrosyl Reactivity at N-Heterocyclic Carbene Center

N-heterocyclic carbenes (NHCs) have garnered much attention due to their unique properties, such as strong σ-donating and π-accepting abilities, as well as their transition-metal-like reactivity toward small molecules. In 2015, we discovered that NHCs can react with nitric oxide (NO) gas to form radical adducts that resemble transition metal nitrosyl complexes. To elucidate the analogy between NHC and transition metal NO adducts, here we have undertaken a systematic investigation of the electron- and proton-transfer chemistry of [NHC-NO]⋅ (N-heterocyclic carbene nitric oxide radical) compounds. We have accessed a suite of compounds, comprised of [NHC-NO]+ , [NHC-NO]- , [NHC-NOH]0 , and [NHC-NHOH]+ species. In particular, [NHC-NO]- was isolated as potassium and lithium ion adducts. Most interestingly, a monomeric potassium [NHC-NO]- compound was isolated with the assistance of 18-crown-6, which is the first instance of a monomeric alkali N-oxyl compound to the best of our knowledge. Our results demonstrate that [NHC-NO]⋅ exhibits redox behavior broadly similar to metal nitrosyl complexes, which opens up more possibilities for utilizing NHCs to build on the known reactivity of metal complexes.

Understanding the Synergy between Fe and Mo Sites in the Nitrate Reduction Reaction on a Bio-Inspired Bimetallic MXene Electrocatalyst

Mo- and Fe-containing enzymes catalyze the reduction of nitrate and nitrite ions in nature. Inspired by this activity, we study here the nitrate reduction reaction (NO3 RR) catalyzed by an Fe-substituted two-dimensional molybdenum carbide of the MXene family, viz., Mo2 CTx  : Fe (Tx are oxo, hydroxy and fluoro surface termination groups). Mo2 CTx  : Fe contains isolated Fe sites in Mo positions of the host MXene (Mo2 CTx ) and features a Faradaic efficiency (FE) and an NH3 yield rate of 41 % and 3.2 μmol h-1  mg-1 , respectively, for the reduction of NO3 - to NH4 + in acidic media and 70 % and 12.9 μmol h-1  mg-1 in neutral media. Regardless of the media, Mo2 CTx  : Fe outperforms monometallic Mo2 CTx owing to a more facile reductive defunctionalization of Tx groups, as evidenced by in situ X-ray absorption spectroscopy (Mo K-edge). After surface reduction, a Tx vacancy site binds a nitrate ion that subsequently fills the vacancy site with O* via oxygen transfer. Density function theory calculations provide further evidence that Fe sites promote the formation of surface O vacancies, which are identified as active sites and that function in NO3 RR in close analogy to the prevailing mechanism of the natural Mo-based nitrate reductase enzymes.

Suggested role of NosZ in preventing N2O inhibition of dissimilatory nitrite reduction to ammonium

IMPORTANCE

Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is a microbial energy-conserving process that reduces NO3 - and/or NO2 - to NH4 +. Interestingly, DNRA-catalyzing microorganisms possessing nrfA genes are occasionally found harboring nosZ genes encoding nitrous oxide reductases, i.e., the only group of enzymes capable of removing the potent greenhouse gas N2O. Here, through a series of physiological experiments examining DNRA metabolism in one of such microorganisms, Bacillus sp. DNRA2, we have discovered that N2O may delay the transition to DNRA upon an oxic-to-anoxic transition, unless timely removed by the nitrous oxide reductases. These observations suggest a novel explanation as to why some nrfA-possessing microorganisms have retained nosZ genes: to remove N2O that may otherwise interfere with the transition from O2 respiration to DNRA.

Interactions of arylhydroxylamines and alkylaldoximes with a rhodium porphyrin

Heme enzymes are involved in the binding and metabolism of hydroxylamine (RNHOH) and aldoxime (RCH=NOH) compounds (R = H, alkyl, aryl). We report the synthesis and X-ray crystal structure of a metalloporphyrin in complex with an arylhydroxylamine, namely that of (TPP)Rh(PhNHOH)(C6H4Cl) (TPP = tetraphenylpophryinato dianion). The crystal structure reveals, in addition to N-binding of PhNHOH to Rh, the presence of an intramolecular H-bond between the hydroxylamine -OH proton and a porphyrin N-atom. Results from density functional theory (DFT) calculations support the presence of this intramolecular H-bond in this global minimum structure, and a natural bond order (NBO) analysis reveals that this H-bond comprises a donor π N=C (porphyrin) to acceptor σ* O-H (hydroxylamine) interaction of 2.32 kcal/mol. While DFT calculations predict the presence of similar intramolecular H-bond interactions in the related aldoxime complexes (TPP)Rh(RCH=NOH)(C6H4Cl) in their global minima structures, the X-ray crystal structure obtained for the (TPP)Rh(CH3(CH2)2CH=NOH)(C6H4Cl) complex is consistent with the local (non-global) minima conformation that does not have this intramolecular H-bond interaction.

Sequential Deoxygenation of CO2 and NO2- via Redox-Control of a Pyridinediimine Ligand with a Hemilabile Phosphine

The deoxygenation of environmental pollutants CO2 and NO2- to form value-added products is reported. CO2 reduction with subsequent CO release and NO2- conversion to NO are achieved via the starting complex Fe(PPhPDI)Cl2 (1). 1 contains the redox-active pyridinediimine (PDI) ligand with a hemilabile phosphine located in the secondary coordination sphere. 1 was reduced with SmI2 under a CO2 atmosphere to form the direduced monocarbonyl Fe(PPhPDI)(CO) (2). Subsequent CO release was achieved via oxidation of 2 using the NOx- source, NO2-. The resulting [Fe(PPhPDI)(NO)]+ (3) mononitrosyl iron complex (MNIC) is formed as the exclusive reduction product due to the hemilabile phosphine. 3 was investigated computationally to be characterized as {FeNO}7, an unusual intermediate-spin Fe(III) coupled to triplet NO- and a singly reduced PDI ligand.

Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios

Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH4+:NO2-, where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH4+:NO2- ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH4+:NO2- ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89-202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169-200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0-89, compared to 85.49 ± 0.01% from day 89-169, and 83.04 ± 0.01% from day 169-200). When the ratio was slightly increased to 1:1.17-1:1.2 (day 202-253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16 S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH4+:NO2- ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.

Role of distal arginine residue in the mechanism of heme nitrite reductases

Heme nitrite reductases reduce NO₂^- by 1e^-/2H⁺ to NO or by 6e^-/8H⁺ to NH₄⁺ which are key steps in the global nitrogen cycle. Second-sphere residues, such as arginine (with a guanidine head group), are proposed to play a key role in the reaction by assisting substrate binding and hydrogen bonding and by providing protons to the active site for the reaction. The reactivity of an iron porphyrin with a NO₂^- covalently attached to a guanidinium arm in its 2nd sphere was investigated to understand the role of arginine residues in the 2nd sphere of heme nitrite reductases. The presence of the guanidinium residue allows the synthetic ferrous porphyrin to reduce NO₂^- and produce a ferrous nitrosyl species ({FeNO}⁷), where the required protons are provided by the guanidinium group in the 2nd sphere. However, in the presence of additional proton sources in solution, the reaction of ferrous porphyrin with NO₂^- results in the formation of ferric porphyrin and the release of NO. Spectroscopic and kinetic data indicated that re-protonation of the guanidine group in the 2nd sphere by an external proton source causes NO to dissociate from a ferric nitrosyl species ({FeNO}⁶) at rates similar to those observed for enzymatic sites. This re-protonation of the guanidine group mimics the proton recharge mechanism in the active site of NiR. DFT calculations indicated that the lability of the Fe-NO bond in the {FeNO}⁶ species is derived from the greater binding affinity of anions (e.g. NO₂^-) to the ferric center relative to neutral NO due to hydrogen bonding and electrostatic interaction of these bound anions with the protonated guanidium group in the 2nd sphere. The reduced {FeNO}⁷ species, once formed, is not affected significantly by the re-protonation of the guanidine residue. These results provide direct insight into the role of the 2nd sphere arginine residue present in the active sites of heme-based NiRs in determining the fate of NO₂^- reduction. Specifically, the findings using the synthetic model suggest that rapid re-protonation of these arginine residues may trigger the dissociation of NO from the {FeNO}⁶, which may also be the case in the protein active site.

Precipitation, submarine groundwater discharge of nitrogen, and red tides along the southwest Florida Gulf coast

Blooms of the dinoflagellate Karenia brevis occur almost every year along the southwest Florida Gulf coast. Long-duration blooms with especially high concentrations of K. brevis, known as red tides, destroy marine life through production of neurotoxins. Current hypotheses are that red tides originate in oligotrophic waters far offshore using nitrogen (N) from upwelling bottom water or, alternatively, from blooms of Trichodesmium, followed by advection to nearshore waters. But the amount of N available from terrestrial sources does not appear to be adequate to maintain a nearshore red tide. To explain this discrepancy, we hypothesize that contemporary red tides are associated with release of N from offshore submarine groundwater discharge (SGD) that has accumulated in benthic sediment biomass by dissimilatory nitrate reduction to ammonium (DNRA). The release occurs when sediment labile organic carbon (LOC), used as the electron donor in DNRA, is exhausted. Detritus from the resulting destruction of marine life restores the sediment LOC to continue the cycle of red tides. The severity of individual red tides increases with increased bloom-year precipitation in the geographic region where the SGD originates, while the severity of ordinary blooms is relatively unaffected.

Ligand-Based Regulation of Dynamics and Reactivity of Hemoproteins

Hemoproteins include several heme-binding proteins with distinct structure and function. The presence of the heme group confers specific reactivity and spectroscopic properties to hemoproteins. In this review, we provide an overview of five families of hemoproteins in terms of dynamics and reactivity. First, we describe how ligands modulate cooperativity and reactivity in globins, such as myoglobin and hemoglobin. Second, we move on to another family of hemoproteins devoted to electron transport, such as cytochromes. Later, we consider heme-based reactivity in hemopexin, the main heme-scavenging protein. Then, we focus on heme-albumin, a chronosteric hemoprotein with peculiar spectroscopic and enzymatic properties. Eventually, we analyze the reactivity and dynamics of the most recently discovered family of hemoproteins, i.e., nitrobindins.

Acid-induced nitrite reduction of nonheme iron(ii)-nitrite: mimicking biological Fe-NiR reactions

Nitrite reductase (NiR) catalyzes nitrite (NO₂ ^-) to nitric oxide (NO) transformation in the presence of an acid (H⁺ ions/pH) and serves as a critical step in NO biosynthesis. In addition to the NiR enzyme, NO synthases (NOSs) participate in NO production. The chemistry involved in the catalytic reduction of NO₂ ^-, in the presence of H⁺, generates NO with a H₂O molecule utilizing two H⁺ + one electron from cytochromes and is believed to be affected by the pH. Here, to understand the effect of H⁺ ions on NO₂ ^- reduction, we report the acid-induced NO₂ ^- reduction chemistry of a nonheme Fe^II-nitrito complex, [(12TMC)Fe^II(NO₂ ^-)]⁺ (Fe^II-NO₂ ^-, 2), with variable amounts of H⁺. Fe^II-NO₂ ^- upon reaction with one-equiv. of acid (H⁺) generates [(12TMC)Fe(NO)]²⁺, {FeNO}⁷ (3) with H₂O₂ rather than H₂O. However, the amount of H₂O₂ decreases with increasing equivalents of H⁺ and entirely disappears when H⁺ reaches ≅ two-equiv. and shows H₂O formation. Furthermore, we have spectroscopically characterized and followed the formation of H₂O₂ (H⁺ = one-equiv.) and H₂O (H⁺ ≅ two-equiv.) and explained why bio-driven NiR reactions end with NO and H₂O. Mechanistic investigations, using ¹⁵N-labeled-¹⁵NO₂ ^- and ²H-labeled-CF₃SO₃D (D⁺ source), revealed that the N atom in the {Fe^14/15NO}⁷ is derived from the NO₂ ^- ligand and the H atom in H₂O or H₂O₂ is derived from the H⁺ source, respectively.

Cooperativity-Driven Reactivity of a Dinuclear Copper Dimethylglyoxime Complex

In this report, we present the dinuclear copper(II) dimethylglyoxime (H₂ dmg) complex [Cu₂ (H₂ dmg)(Hdmg)(dmg)]⁺ (1), which, in contrast to its mononuclear analogue [Cu(Hdmg)₂ ] (2), is subject to a cooperativity-driven hydrolysis. The combined Lewis acidity of both copper centers increases the electrophilicity of the carbon atom in the bridging μ₂ -O-N=C-group of H₂ dmg and thus, facilitates the nucleophilic attack of H₂ O. This hydrolysis yields butane-2,3-dione monoxime (3) and NH₂ OH that, depending on the solvent, is then either oxidized or reduced. In ethanol, NH₂ OH is reduced to NH₄ ⁺ , yielding acetaldehyde as the oxidation product. In contrast, in CH₃ CN, NH₂ OH is oxidized by Cu^II to form N₂ O and [Cu(CH₃ CN)₄ ]⁺ . Herein are presented the combined synthetic, theoretical, spectroscopic and spectrometric methods that indicate and establish the reaction pathway of this solvent-dependent reaction.

An unusual active site architecture in cytochrome c nitrite reductase NrfA-1 from Geobacter metallireducens

Dissimilatory nitrate reduction to ammonia (DNRA) is a central pathway in the biogeochemical nitrogen cycle, allowing for the utilization of nitrate or nitrite as terminal electron acceptors. In contrast to the competing denitrification to N2, a major part of the essential nutrient nitrogen in DNRA is retained within the ecosystem and made available as ammonium to serve as a nitrogen source for other organisms. The second step of DNRA is mediated by the pentahaem cytochrome c nitrite reductase NrfA that catalyzes the six-electron reduction of nitrite to ammonium and is widely distributed among bacteria. A recent crystal structure of an NrfA ortholog from Geobacter lovleyi was the first characterized representative of a novel subclass of NrfA enzymes that lacked the canonical Ca2+ ion close to the active site haem 1. Here, we report the structural and functional characterization of NrfA from the closely related G. metallireducens. We established the recombinant production of catalytically active NrfA with its unique, lysine-coordinated active site haem heterologously in Escherichia coli and determined its three-dimensional structure by X-ray crystallography to 1.9 Å resolution. The structure confirmed GmNrfA as a further calcium-independent NrfA protein, and it also shows an altered active site that contained an unprecedented aspartate residue, D80, close to the substrate-binding site. This residue formed part of a loop that also caused a changed arrangement of the conserved substrate/product channel relative to other NrfA proteins and rendered the protein insensitive to the inhibitor sulphate. To elucidate the relevance of D80, we produced and studied the variants D80A and D80N that showed significantly reduced catalytic activity.

Bilirubin oxidase as a single enzymatic oxygen scavenger for the development of reductase-based biosensors in the open air and its application on a nitrite biosensor

The commercialization of amperometric or voltammetric biosensors that operate at potentials lower than -0.2 V vs SHE has been hindered by the need for anoxic working conditions due to the interference of molecular oxygen, whose electrochemical reduction can potentially mask other redox processes and generate reactive oxygen species (ROS). A deoxygenation step must be thus integrated into the analytical process. To this end, several (bio)chemical oxygen scavenging systems have been proposed, such as the bi-enzyme system, glucose oxidase/catalase. Still, a few issues persist owing to enzyme impurities and the formation of oxygen reactive species. Here in, we propose a new mono-enzymatic oxygen scavenging system composed of a multicopper oxidase as a single biocatalytic oxygen reducer. As a model, we used bilirubin oxidase (BOD), which catalyzes the direct reduction of oxygen to water in the presence of an electron donor substrate, without releasing hydrogen peroxide. Both the direct electron transfer and mediated electrochemical approach using different co-substrates were screened for the ability to promote the enzymatic reduction of oxygen. An optimal combination of BOD with sodium ascorbate proved to be quick (5 min) and effective. It was subsequently employed, as a proof-of-concept, in a voltammetric biosensor based on a multiheme cytochrome c nitrite reductase, which performs the reduction of nitrite to ammonia at potentials below -0.3 V vs SHE. The nitrite biosensor performed well under ambient air, with no need for a second enzyme to account for the build-up of oxygen reactive intermediaries.

Metagenomic Insights Into Competition Between Denitrification and Dissimilatory Nitrate Reduction to Ammonia Within One-Stage and Two-Stage Partial-Nitritation Anammox Bioreactor Configurations

Anaerobic ammonia oxidizing bacteria (Anammox) are implemented in high-efficiency wastewater treatment systems operated in two general configurations; one-stage systems combine aerobic ammonia oxidizing bacteria (AOB) and Anammox within a single aerated reactor, whereas two-stage configurations separate these processes into discrete tanks. Within both configurations heterotrophic populations that perform denitrification or dissimilatory nitrate reduction to ammonia (DNRA) compete for carbon and nitrate or nitrite and can impact reactor performance because DNRA retains nitrogen in the system. Therefore, it is important to understand how selective pressures imposed by one-stage and two-stage reactor configurations impact the microbial community structure and associated nitrogen transforming functions. We performed 16S rRNA gene and metagenomic sequencing on different biomass fractions (granules, flocs, and suspended biomass) sampled from two facilities treating sludge dewatering centrate: a one-stage treatment facility (Chambers Creek, Tacoma, WA) and a two-stage system (Rotterdam, Netherlands). Similar microbial populations were identified across the different samples, but relative abundances differed between reactor configurations and biomass sources. Analysis of metagenome assembled genomes (MAGs) indicated different lifestyles for abundant heterotrophic populations. Acidobacteria, Bacteroidetes, and Chloroflexi MAGs had varying capacity for DNRA and denitrification. Acidobacteria MAGs possessed high numbers of glycosyl hydrolases and glycosyl transferases indicating a role in biomass degradation. Ignavibacteria and Phycosphaerae MAGs contributed to the greater relative abundance of DNRA associated nrf genes in the two-stage granules and contained genomic features suggesting a preference for an anoxic or microoxic niche. In the one-stage granules a MAG assigned to Burkholderiales accounted for much of the abundant denitrification genes and had genomic features, including the potential for autotrophic denitrification using reduced sulfur, that indicate an ability to adapt its physiology to varying redox conditions. Overall, the competition for carbon substrates between denitrifying and DNRA performing heterotrophs may be impacted by configuration specific selective pressures. In one-stage systems oxygen availability in the bulk liquid and the oxygen gradient within granules would provide a greater niche space for heterotrophic populations capable of utilizing both oxygen and nitrate or nitrite as terminal electron acceptors, compared to two-stage systems where a homogeneous anoxic environment would favor heterotrophic populations primarily adapted to anaerobic metabolism.

Second Sphere Effects on Oxygen Reduction and Peroxide Activation by Mononuclear Iron Porphyrins and Related Systems

Activation and reduction of O₂ and H₂O₂ by synthetic and biosynthetic iron porphyrin models have proved to be a versatile platform for evaluating second-sphere effects deemed important in naturally occurring heme active sites. Advances in synthetic techniques have made it possible to install different functional groups around the porphyrin ligand, recreating artificial analogues of the proximal and distal sites encountered in the heme proteins. Using judicious choices of these substituents, several of the elegant second-sphere effects that are proposed to be important in the reactivity of key heme proteins have been evaluated under controlled environments, adding fundamental insight into the roles played by these weak interactions in nature. This review presents a detailed description of these efforts and how these have not only demystified these second-sphere effects but also how the knowledge obtained resulted in functional mimics of these heme enzymes.

Kinetic Analysis of Nitrite Reduction Reactions by Nitrite Reductase Derived from Spinach in the Presence of One-Electron Reduced Riboflavin

The development of methods for converting nitrogen oxides in water into valuable resources such as ammonia and hydrazine has been given some attention. By utilizing the nitrite-reducing catalytic activity of nitrite reductase (NiR), nitrite in water can be converted into ammonium. However, there are few reports in the research that synthesized ammonium from nitrite using nitrite reductase. Therefore, we aimed to investigate the effect of temperature on the nitrite-reducing catalytic activity of NiR from spinach in the presence of one-electron reduced riboflavin by kinetic analysis to find the optimum temperature conditions. The results of this study showed that the reaction temperature does not need to be higher than 296.15 K in order to improve the efficiency of ammonium production from nitrite using NiR.

Metagenomic insight of corn straw conditioning on substrates metabolism during coal anaerobic fermentation

Increasing methane production from anaerobic digestion of coal is challenging. This study shows that the combined fermentation of coal and corn straw greatly enriched the substrates available to microorganisms. This was mainly manifested in the increased types and abundance of organic matter in the fermentation liquid, which enhanced methane production by 61%. Metagenomic analysis showed that the addition of corn straw enriched the abundance of Methanosarcina in the combined fermentation system and promoted the complementary advantages of the microorganisms. At the same time, the abundance of genes that convert glucose into acetic acid (K00927, K01689, K01905, etc.) in the combined fermentation system increased, which is conducive to acidification process and biomethane production. In addition, there were the two key methanogenic pathways, namely aceticlastic (57.1%-63.5%) and hydrogenotrophic (23.4%-25.1%) methanogenesis, identified in the single coal fermentation system and the combined coal and corn straw fermentation system. Combined fermentation enhanced the hydrogenotrophic and methylotrophic methanogenic pathways by increasing the gene abundance of K00200 (methane production from CO₂ and oxidation of coenzyme M to CO₂), K00440 (participates in the binding to other known physiological receptors with hydrogen as a donor), and K00577 (methyltransferase).

The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity

Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.

Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen

Since the characterization of cytochrome c₅₅₂ as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH₄⁺ produced from NO₂^- is released as NH₃ leading to nitrogen loss, similar to denitrification which generates NO, N₂O, and N₂. NH₄⁺ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO₂^- to NH₄⁺, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.

Azanone (HNO): generation, stabilization and detection

HNO (nitroxyl, azanone), joined the 'biologically relevant reactive nitrogen species' family in the 2000s. Azanone is impossible to store due to its high reactivity and inherent low stability. Consequently, its chemistry and effects are studied using donor compounds, which release this molecule in solution and in the gas phase upon stimulation. Researchers have also tried to stabilize this elusive species and its conjugate base by coordination to metal centers using several ligands, like metalloporphyrins and pincer ligands. Given HNO's high reactivity and short lifetime, several different strategies have been proposed for its detection in chemical and biological systems, such as colorimetric methods, EPR, HPLC, mass spectrometry, fluorescent probes, and electrochemical analysis. These approaches are described and critically compared. Finally, in the last ten years, several advances regarding the possibility of endogenous HNO generation were made; some of them are also revised in the present work.

A Redox-Active Tetrazine-Based Pincer Ligand for the Reduction of N-Oxyanions Using a Redox-Inert Metal

The reaction chemistry of the bis-tetrazinyl pyridine ligand (btzp) towards nitrogen oxyanions coordinated to zinc is studied in order to explore the reduction of the NO_x ^- substrates with a redox-active ligand in the absence of redox activity at the metal. Following syntheses and characterization of (btzp)ZnX₂ for X=Cl, NO₃ and NO₂ , featuring O-Zn linkage of both nitrogen oxyanions, it is shown that a silylating agent selectively delivers silyl substituents to tetrazine nitrogens, without reductive deoxygenation of NO_x ^-1 . A new synthesis of the highly hydrogenated H₄ btzp, containing two dihydrotetrazine reductants is described as is the synthesis and characterization of (H₄ btzp)ZnX₂ for X=Cl and NO₃ , both of which show considerable hydrogen bonding potential of the dihydrotetrazine ring NH groups. The (H₄ btzp)ZnCl₂ complex does not bind zinc in the pincer pocket, but instead H₄ btzp becomes a bridge between neighboring atoms through tetrazine nitrogen atoms, forming a polymeric chain. The reaction of AgNO₂ with (H₄ btzp)ZnCl₂ is shown to proceed with fast nitrite deoxygenation, yielding water and free NO. Half of the H₄ btzp reducing equivalents form Ag⁰ and thus the chloride ligand remains coordinated to the zinc metal center to yield (btzp)ZnCl₂ . To compare with AgNO₂ , experiments of (H₄ btzp)ZnCl₂ with NaNO₂ result in salt metathesis between chloride and nitrite, highlighting the importance of a redox-active cation in the reduction of nitrite to NO.

A Kinetic Investigation of the Early Steps in Cytochrome c Nitrite Reductase (ccNiR)-Catalyzed Reduction of Nitrite

The decaheme enzyme cytochrome c nitrite reductase (ccNiR) catalyzes reduction of nitrite to ammonium in a six-electron, eight-proton process. With a strong reductant as the electron source, ammonium is the sole product. However, intermediates accumulate when weaker reductants are employed, facilitating study of the ccNiR mechanism. Herein, the early stages of Shewanella oneidensis ccNiR-catalyzed nitrite reduction were investigated by using the weak reductants N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD) and ferrocyanide. In stopped-flow experiments, reduction of nitrite-loaded ccNiR by TMPD generated a transient intermediate, identified as Fe_H1^II(NO₂^-), where Fe_H1 represents the ccNiR active site. Fe_H1^II(NO₂^-) accumulated rapidly and was then more slowly converted to the two-electron-reduced moiety {Fe_H1NO}⁷; ccNiR was not reduced beyond the {Fe_H1NO}⁷ state. The midpoint potentials for sequential reduction of Fe_H1^III(NO₂^-) to Fe_H1^II(NO₂^-) and then to {Fe_H1NO}⁷ were estimated to be 130 and 370 mV versus the standard hydrogen electrode, respectively. Fe_H1^II(NO₂^-) does not accumulate at equilibrium because its reduction to {Fe_H1NO}⁷ is so much easier than the reduction of Fe_H1^III(NO₂^-) to Fe_H1^II(NO₂^-). With weak reductants, free NO• was released from nitrite-loaded ccNiR. The release of NO• from {Fe_H1NO}⁷ is exceedingly slow (k ∼ 0.001 s^-1), but it is somewhat faster (k ∼ 0.050 s^-1) while Fe_H1^III(NO₂^-) is being reduced to {Fe_H1NO}⁷; then, the release of NO• from the undetectable transient {Fe_H1NO}⁶ can compete with reduction of {Fe_H1NO}⁶ to {Fe_H1NO}⁷. CcNiR appears to be optimized to capture nitrite and minimize the release of free NO•. Nitrite capture is achieved by reducing bound nitrite with even weak electron donors, while NO• release is minimized by stabilizing the substitutionally inert {Fe_H1NO}⁷ over the more labile {Fe_H1NO}⁶.

Elucidating Electron Storage and Distribution within the Pentaheme Scaffold of Cytochrome c Nitrite Reductase (NrfA)

Cytochrome c nitrite reductases (CcNIR or NrfA) play important roles in the global nitrogen cycle by conserving the usable nitrogen in the soil. Here, the electron storage and distribution properties within the pentaheme scaffold of Geobacter lovleyi NrfA were investigated via electron paramagnetic resonance (EPR) spectroscopy coupled with chemical titration experiments. Initially, a chemical reduction method was established to sequentially add electrons to the fully oxidized protein, 1 equiv at a time. The step-by-step reduction of the hemes was then followed using ultraviolet-visible absorption and EPR spectroscopy. EPR spectral simulations were used to elucidate the sequence of heme reduction within the pentaheme scaffold of NrfA and identify the signals of all five hemes in the EPR spectra. Electrochemical experiments ascertain the reduction potentials for each heme, observed in a narrow range from +10 mV (heme 5) to -226 mV (heme 3) (vs the standard hydrogen electrode). On the basis of quantitative analysis and simulation of the EPR data, we demonstrate that hemes 4 and 5 are reduced first (before the active site heme 1) and serve the purpose of an electron storage unit within the protein. To probe the role of the central heme 3, an H108M NrfA variant was generated where the reduction potential of heme 3 is shifted positively (from -226 to +48 mV). The H108M mutation significantly impacts the distribution of electrons within the pentaheme scaffold and the reduction potentials of the hemes, reducing the catalytic activity of the enzyme to 1% compared to that of the wild type. We propose that this is due to heme 3's important role as an electron gateway in the wild-type enzyme.

Quantification of Active Site Density and Turnover Frequency: From Single-Atom Metal to Nanoparticle Electrocatalysts

Single-atom catalysts (SACs) featuring atomically dispersed metal cations covalently embedded in a carbon matrix show significant potential to achieve high catalytic performance in various electrocatalytic reactions. Although considerable advances have been achieved in their syntheses and electrochemical applications, further development and fundamental understanding are limited by a lack of strategies that can allow the quantitative analyses of their intrinsic catalytic characteristics, that is, active site density (SD) and turnover frequency (TOF). Here we show an in situ SD quantification method using a cyanide anion as a probe molecule. The decrease in cyanide concentration triggered by irreversible adsorption on metal-based active sites of a model Fe-N-C catalyst is precisely measured by spectrophotometry, and it is correlated to the relative decrease in electrocatalytic activity in the model reaction of oxygen reduction reaction. The linear correlation verifies the surface-sensitive and metal-specific adsorption of cyanide on Fe-N x sites, based on which the values of SD and TOF can be determined. Notably, this analytical strategy shows versatile applicability to a series of transition/noble metal SACs and Pt nanoparticles in a broad pH range (1-13). The SD and TOF quantification can afford an improved understanding of the structure-activity relationship for a broad range of electrocatalysts, in particular, the SACs, for which no general electrochemical method to determine the intrinsic catalytic characteristics is available.

The "Water Problem"(sic), the Illusory Pond and Life's Submarine Emergence-A Review

The assumption that there was a "water problem" at the emergence of life-that the Hadean Ocean was simply too wet and salty for life to have emerged in it-is here subjected to geological and experimental reality checks. The "warm little pond" that would take the place of the submarine alkaline vent theory (AVT), as recently extolled in the journal Nature, flies in the face of decades of geological, microbiological and evolutionary research and reasoning. To the present author, the evidence refuting the warm little pond scheme is overwhelming given the facts that (i) the early Earth was a water world, (ii) its all-enveloping ocean was never less than 4 km deep, (iii) there were no figurative "Icelands" or "Hawaiis", nor even an "Ontong Java" then because (iv) the solidifying magma ocean beneath was still too mushy to support such salient loadings on the oceanic crust. In place of the supposed warm little pond, we offer a well-protected mineral mound precipitated at a submarine alkaline vent as life's womb: in place of lipid membranes, we suggest peptides; we replace poisonous cyanide with ammonium and hydrazine; instead of deleterious radiation we have the appropriate life-giving redox and pH disequilibria; and in place of messy chemistry we offer the potential for life's emergence from the simplest of geochemically available molecules and ions focused at a submarine alkaline vent in the Hadean-specifically within the nano-confined flexible and redox active interlayer walls of the mixed-valent double layer oxyhydroxide mineral, fougerite/green rust comprising much of that mound.

Transcriptional and Post-transcriptional Control of the Nitrate Respiration in Bacteria

In oxygen (O2) limiting environments, numerous aerobic bacteria have the ability to shift from aerobic to anaerobic respiration to release energy. This process requires alternative electron acceptor to replace O2 such as nitrate (NO3 -), which has the next best reduction potential after O2. Depending on the organism, nitrate respiration involves different enzymes to convert NO3 - to ammonium (NH4 +) or dinitrogen (N2). The expression of these enzymes is tightly controlled by transcription factors (TFs). More recently, bacterial small regulatory RNAs (sRNAs), which are important regulators of the rapid adaptation of microorganisms to extremely diverse environments, have also been shown to control the expression of genes encoding enzymes or TFs related to nitrate respiration. In turn, these TFs control the synthesis of multiple sRNAs. These results suggest that sRNAs play a central role in the control of these metabolic pathways. Here we review the complex interplay between the transcriptional and the post-transcriptional regulators to efficiently control the respiration on nitrate.

Selective electrochemical reduction of nitric oxide to hydroxylamine by atomically dispersed iron catalyst

Electrocatalytic conversion of nitrogen oxides to value-added chemicals is a promising strategy for mitigating the human-caused unbalance of the global nitrogen-cycle, but controlling product selectivity remains a great challenge. Here we show iron-nitrogen-doped carbon as an efficient and durable electrocatalyst for selective nitric oxide reduction into hydroxylamine. Using in operando spectroscopic techniques, the catalytic site is identified as isolated ferrous moieties, at which the rate for hydroxylamine production increases in a super-Nernstian way upon pH decrease. Computational multiscale modelling attributes the origin of unconventional pH dependence to the redox active (non-innocent) property of NO. This makes the rate-limiting NO adsorbate state more sensitive to surface charge which varies with the pH-dependent overpotential. Guided by these fundamental insights, we achieve a Faradaic efficiency of 71% and an unprecedented production rate of 215 μmol cm-2 h-1 at a short-circuit mode in a flow-type fuel cell without significant catalytic deactivation over 50 h operation.

Influence of the heme distal pocket on nitrite binding orientation and reactivity in Sperm Whale myoglobin

Nitrite binding to recombinant wild-type Sperm Whale myoglobin (SWMb) was studied using a combination of spectroscopic methods including room-temperature magnetic circular dichroism. These revealed that the reactive species is free nitrous acid and the product of the reaction contains a nitrite ion bound to the ferric heme iron in the nitrito- (O-bound) orientation. This exists in a thermal equilibrium with a low-spin ground state and a high-spin excited state and is spectroscopically distinct from the purely low-spin nitro- (N-bound) species observed in the H64V SWMb variant. Substitution of the proximal heme ligand, histidine-93, with lysine yields a novel form of myoglobin (H93K) with enhanced reactivity towards nitrite. The nitrito-mode of binding to the ferric heme iron is retained in the H93K variant again as a thermal equilibrium of spin-states. This proximal substitution influences the heme distal pocket causing the pK_a of the alkaline transition to be lowered relative to wild-type SWMb. This change in the environment of the distal pocket coupled with nitrito-binding is the most likely explanation for the 8-fold increase in the rate of nitrite reduction by H93K relative to WT SWMb.

Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2nd sphere interactions in catalysis

Reduction of oxides and oxoanions of carbon and nitrogen are of great contemporary importance as they are crucial for a sustainable environment.

Updating NO•/HNO interconversion under physiological conditions: A biological implication overview

Azanone (HNO/NO^-), also called nitroxyl, is a highly reactive compound whose biological role is still a matter of debate. A key issue that remains to be clarified regarding HNO and its biological activity is that of its endogenous formation. Given the overlap of the molecular targets and reactivity of nitric oxide (NO•) and HNO, its chemical biology was perceived to be similar to that of NO• as a biological signaling agent. However, despite their closely related reactivity, NO• and HNO's biochemical pathways are quite different. Moreover, the reduction of nitric oxide to azanone is possible but necessarily coupled to other reactions, which drive the reaction forward, overcoming the unfavorable thermodynamic barrier. The mechanism of this NO•/HNO interplay and its downstream effects in different contexts were studied recently, showing that more than fifteen moderate reducing agents react with NO• producing HNO. Particularly, it is known that the reaction between nitric oxide and hydrogen sulfide (H₂S) produces HNO. However, this rate constant was not reported yet. In this work, firstly the NO•/H₂S effective rate constant was measured as a function of the pH. Then, the implications of these chemical (non-enzymatic), biologically compatible, routes to endogenous HNO formation was discussed. There is no doubt that HNO could be (is?) a new endogenously produced messenger that mediates specific physiological responses, many of which were attributed yet to direct NO• effects.

Octaheme nitrite reductase: The mechanism of intramolecular electron transfer and kinetics of nitrite bioelectroreduction

Detailed impedance and voltammetric studies of hexameric octaheme nitrite reductase immobilized on carbon-based nanomaterials, specifically nanotubes and nanoparticles, were performed. Well-pronounced bioelectrocatalytic reduction of nitrite on enzyme-modified electrodes was obtained. Analysis of the impedance data indicated the absence of long-lived intermediates involved in the nitrite reduction. Cyclic voltammograms of biomodified electrodes had a bi-sigmoidal shape, which pointed to the presence of two enzyme orientations on carbon supports. The maximum (limiting) catalytic currents were determined and, by applying the correction by the mixed kinetics equation, the Tafel dependences were plotted for each catalytic wave/each enzyme orientation. Finally, two schemes for the rate-limiting processes during bioelectrocatalysis were proposed, viz. for low- and high-potential orientations.

DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems

This paper reviews dissimilatory nitrate reduction to ammonium (DNRA) in soils - a newly appreciated pathway of nitrogen (N) cycling in the terrestrial ecosystems. The reduction of NO₃^- occurs in two steps; in the first step, NO₃^- is reduced to NO₂^-; and in the second, unlike denitrification, NO₂^- is reduced to NH₄⁺ without intermediates. There are two sets of NO₃^-/NO₂^- reductase enzymes, i.e., Nap/Nrf and Nar/Nir; the former occurs on the periplasmic-membrane and energy conservation is respiratory via electron-transport-chain, whereas the latter is cytoplasmic and energy conservation is both respiratory and fermentative (Nir, substrate-phosphorylation). Since, Nir catalyzes both assimilatory- and dissimilatory-nitrate reduction, the nrfA gene, which transcribes the NrfA protein, is treated as a molecular-marker of DNRA; and a high nrfA/nosZ (N₂O-reductase) ratio favours DNRA. Recently, several crystal structures of NrfA have been presumed to producee N₂O as a byproduct of DNRA via the NO (nitric-oxide) pathway. Meta-analyses of about 200 publications have revealed that DNRA is regulated by oxidation state of soils and sediments, carbon (C)/N and NO₂^-/NO₃^- ratio, and concentrations of ferrous iron (Fe²⁺) and sulfide (S^2-). Under low-redox conditions, a high C/NO₃^- ratio selects for DNRA while a low ratio selects for denitrification. When the proportion of both C and NO₃^- are equal, the NO₂^-/NO₃^- ratio modulates partitioning of NO₃^-, and a high NO₂^-/NO₃^- ratio favours DNRA. A high S^2-/NO₃^- ratio also promotes DNRA in coastal-ecosystems and saline sediments. Soil pH, temperature, and fine soil particles are other factors known to influence DNRA. Since, DNRA reduces NO₃^- to NH₄⁺, it is essential for protecting NO₃^- from leaching and gaseous (N₂O) losses and enriches soils with readily available NH₄⁺-N to primary producers and heterotrophic microorganisms. Therefore, DNRA may be treated as a tool to reduce ground-water NO₃^- pollution, enhance soil health and improve environmental quality.

Hydroxylamine Complexes of Cytochrome c': Influence of Heme Iron Redox State on Kinetic and Spectroscopic Properties

Hydroxylamine (NH₂OH or HA) is a redox-active nitrogen oxide that occurs as a toxic intermediate in the oxidation of ammonium by nitrifying and methanotrophic bacteria. Within ammonium containing environments, HA is generated by ammonia monooxygenase (nitrifiers) or methane monooxygenase (methanotrophs). Subsequent oxidation of HA is catalyzed by heme proteins, including cytochromes P460 and multiheme hydroxylamine oxidoreductases, the former contributing to emissions of N₂O, an ozone-depleting greenhouse gas. A heme-HA complex is also a proposed intermediate in the reduction of nitrite to ammonia by cytochrome c nitrite reductase. Despite the importance of heme-HA complexes within the biogeochemical nitrogen cycle, fundamental aspects of their coordination chemistry remain unknown, including the effect of the Fe redox state on heme-HA affinity, kinetics, and spectroscopy. Using stopped-flow UV-vis and resonance Raman spectroscopy, we investigated HA complexes of the L16G distal pocket variant of Alcaligenes xylosoxidans cytochrome c'-α (L16G AxCP-α), a pentacoordinate c-type cytochrome that we show binds HA in its Fe(III) (K_d ∼ 2.5 mM) and Fe(II) (K_d = 0.0345 mM) states. The ∼70-fold higher HA affinity of the Fe(II) state is due mostly to its lower k_off value (0.0994 s^-1 vs 11 s^-1), whereas k_on values for Fe(II) (2880 M^-1 s^-1) and Fe(III) (4300 M^-1 s^-1) redox states are relatively similar. A comparison of the HA and imidazole affinities of L16G AxCP-α was also used to predict the influence of Fe redox state on HA binding to other proteins. Although HA complexes of L16G AxCP-α decompose via redox reactions, the lifetime of the Fe(II)HA complex was prolonged in the presence of excess reductant. Spectroscopic parameters determined for the Fe(II)HA complex include the N-O stretching vibration of the NH₂OH ligand, ν(N-O) = 906 cm^-1. Overall, the kinetic trends and spectroscopic benchmarks from this study provide a foundation for future investigations of heme-HA reaction mechanisms.

Cytochrome c nitrite reductase from the bacterium Geobacter lovleyi represents a new NrfA subclass

Cytochrome c nitrite reductase (NrfA) catalyzes the reduction of nitrite to ammonium in the dissimilatory nitrate reduction to ammonium (DNRA) pathway, a process that competes with denitrification, conserves nitrogen, and minimizes nutrient loss in soils. The environmental bacterium Geobacter lovleyi has recently been recognized as a key driver of DNRA in nature, but its enzymatic pathway is still uncharacterized. To address this limitation, here we overexpressed, purified, and characterized G. lovleyi NrfA. We observed that the enzyme crystallizes as a dimer but remains monomeric in solution. Importantly, its crystal structure at 2.55-Å resolution revealed the presence of an arginine residue in the region otherwise occupied by calcium in canonical NrfA enzymes. The presence of EDTA did not affect the activity of G. lovleyi NrfA, and site-directed mutagenesis of this arginine reduced enzymatic activity to <3% of the WT levels. Phylogenetic analysis revealed four separate emergences of Arg-containing NrfA enzymes. Thus, the Ca²⁺-independent, Arg-containing NrfA from G. lovleyi represents a new subclass of cytochrome c nitrite reductase. Most genera from the exclusive clades of Arg-containing NrfA proteins are also represented in clades containing Ca²⁺-dependent enzymes, suggesting convergent evolution.

The role of porphyrin peripheral substituents in determining the reactivities of ferrous nitrosyl species

Ferrous nitrosyl {FeNO}⁷ species is an intermediate common to the catalytic cycles of Cd₁NiR and CcNiR, two heme-based nitrite reductases (NiR), and its reactivity varies dramatically in these enzymes.

Ferrous nitrosyl {FeNO}⁷ species is an intermediate common to the catalytic cycles of Cd₁NiR and CcNiR, two heme-based nitrite reductases (NiR), and its reactivity varies dramatically in these enzymes. The former reduces NO₂^– to NO in the denitrification pathway while the latter reduces NO₂^– to NH₄⁺ in a dissimilatory nitrite reduction. With very similar electron transfer partners and heme based active sites, the origin of this difference in reactivity has remained unexplained. Differences in the structure of the heme d₁ (Cd₁NiR), which bears electron-withdrawing groups and has saturated pyrroles, relative to heme c (CcNiR) are often invoked to explain these reactivities. A series of iron porphyrinoids, designed to model the electron-withdrawing peripheral substitution as well as the saturation present in heme d₁ in Cd₁NiR, and their NO adducts were synthesized and their properties were investigated. The data clearly show that the presence of electron-withdrawing groups (EWGs) and saturated pyrroles together in a synthetic porphyrinoid (FeDEsC) weakens the Fe–NO bond in {FeNO}⁷ adducts along with decreasing the bond dissociation free energies (BDFE_NH) of the {FeHNO}⁸ species. The EWG raises the E° of the {FeNO}^7/8 process, making the electron transfer (ET) facile, but decreases the pK_a of {FeNO}⁸ species, making protonation (PT) difficult, while saturation has the opposite effect. The weakening of the Fe–NO bonding biases the {FeNO}⁷ species of FeDEsC for NO dissociation, as in Cd₁NiR, which is otherwise set-up for a proton-coupled electron transfer (PCET) to form an {FeHNO}⁸ species eventually leading to its further reduction to NH₄⁺.

Reduction of Substrates by Nitrogenases

Nitrogenase is the enzyme that catalyzes biological N₂ reduction to NH₃. This enzyme achieves an impressive rate enhancement over the uncatalyzed reaction. Given the high demand for N₂ fixation to support food and chemical production and the heavy reliance of the industrial Haber-Bosch nitrogen fixation reaction on fossil fuels, there is a strong need to elucidate how nitrogenase achieves this difficult reaction under benign conditions as a means of informing the design of next generation synthetic catalysts. This Review summarizes recent progress in addressing how nitrogenase catalyzes the reduction of an array of substrates. New insights into the mechanism of N₂ and proton reduction are first considered. This is followed by a summary of recent gains in understanding the reduction of a number of other nitrogenous compounds not considered to be physiological substrates. Progress in understanding the reduction of a wide range of C-based substrates, including CO and CO₂, is also discussed, and remaining challenges in understanding nitrogenase substrate reduction are considered.