Dimerization of HNO in Aqueous Solution: An Interplay of Solvation Effects, Fast Acid–Base Equilibria, and Intramolecular Hydrogen Bonding?

Unraveling the Mechanism of Ammonia Electrooxidation by Coupled Differential Electrochemical Mass Spectrometry and Surface-Enhanced Infrared Absorption Spectroscopic Studies

Ammonia electrooxidation has received considerable attention in recent times due to its potential application in direct ammonia fuel cells, ammonia sensors, and denitrification of wastewater. In this work, we used differential electrochemical mass spectrometry (DEMS) coupled with attenuated total reflection-surface-enhanced infrared absorption (ATR-SEIRA) spectroscopy to study adsorbed species and solution products during the electrochemical ammonia oxidation reaction (AOR) on Pt in alkaline media, and to correlate the product distribution with the surface ad-species. Hydrazine electrooxidation, hydroxylamine electrooxidation/reduction, and nitrite electroreduction on Pt have also been studied to enhance the understanding of the AOR mechanism. NH3, NH2, NH, NO, and NO2 ad-species were identified on the Pt surface with ATR-SEIRA spectroscopy, while N2, N2O, and NO were detected with DEMS as products of the AOR. N2 is formed through the coupling of two NH ad-species and then subsequent further dehydrogenation, while the dimerization of HNOad leads to the formation of N2O. The NH-NH coupling is the rate-determining step (rds) at high potentials, while the first dehydrogenation step is the rds at low potentials. These new spectroscopic results about the AOR and insights could advance the search and design of more effective AOR catalysts.

Hydroxylamine supplementation accelerated the rates of cell growth, aerobic denitrification and nitrous oxide emission of Pseudomonas taiwanensis EN-F2

Hydroxylamine can disrupt the protein translation process of most reported nitrogen-converting bacteria, and thus hinder the reproduction of bacteria and nitrogen conversion capacity. However, the effect of hydroxylamine on the denitrification ability of strain EN-F2 is unclear. In this study, the cell growth, aerobic denitrification ability, and nitrous oxide (N2O) emission by Pseudomonas taiwanensis were carefully investigated by addition of hydroxylamine at different concentrations. The results demonstrated that the rates of nitrate and nitrite reduction were enhanced by 2.51 and 2.78 mg/L/h after the addition of 8.0 and 12.0 mg/L hydroxylamine, respectively. The N2O production from nitrate and nitrite reaction systems were strongly promoted by 4.39 and 8.62 mg/L, respectively, through the simultaneous acceleration of cell growth and both of nitrite and nitrate reduction. Additionally, the enzymatic activities of nitrate reductase and nitrite reductase climbed from 0.13 and 0.01 to 0.22 and 0.04 U/mg protein when hydroxylamine concentration increased from 0 to 6.0 and 12.0 mg/L. This may be the main mechanism for controlling the observed higher denitrification rate and N2O release. Overall, hydroxylamine supplementation supported the EN-F2 strain cell growth, denitrification and N2O emission rates.

An ab Initio Study of High-Energetic Trioxatriazinane Derivatives: Conformational Analysis, Nitrogen Inversion, Heats of Formation, Dissociation Reaction, and Dimerization

High-energetic materials belong to two main classes: propellants and explosives. The still rather unexplored family of 1,3,5,2,4,6-trioxatriazinanes, N3O3R3, has a representative of each class. We have selected three compounds, R = H, R = CH3 and R = NO2, this last compound being known as TNTOTA, "trinitro-trioxa-triazinane". Of these compounds we have studied the conformational analysis, the nitrogen inversion, the heats of formation, and the dissociation reaction into the three monomers. In addition, the corresponding 1,3,2,4-dioxadiazetidines (N2O2R2) have also been studied.

Efficient catalyst-free N2 fixation by water radical cations under ambient conditions

The growth and sustainable development of humanity is heavily dependent upon molecular nitrogen (N2) fixation. Herein we discover ambient catalyst-free disproportionation of N2 by water plasma which occurs via the distinctive HONH-HNOH+• intermediate to yield economically valuable nitroxyl (HNO) and hydroxylamine (NH2OH) products. Calculations suggest that the reaction is prompted by the coordination of electronically excited N2 with water dimer radical cation, (H2O)2+•, in its two-center-three-electron configuration. The reaction products are collected in a 76-needle array discharge reactor with product yields of 1.14 μg cm-2 h-1 for NH2OH and 0.37 μg cm-2 h-1 for HNO. Potential applications of these compounds are demonstrated to make ammonia (for NH2OH), as well as to chemically react and convert cysteine, and serve as a neuroprotective agent (for HNO). The conversion of N2 into HNO and NH2OH by water plasma could offer great profitability and reduction of polluting emissions, thus giving an entirely look and perspectives to the problem of green N2 fixation.

Thermodynamic Analysis of Intermediary Metabolic Steps and Nitrous Oxide Production by Ammonium-Oxidizing Bacteria

Nitrous oxide (N₂O) is a greenhouse gas emitted from wastewater treatment, soils, and agriculture largely by ammonium-oxidizing bacteria (AOB). While AOB are characterized by being aerobes that oxidize ammonium (NH₄⁺) to nitrite (NO₂^-), fundamental studies in microbiology are revealing the importance of metabolic intermediates and reactions that can lead to the production of N₂O. These findings about the metabolic pathways for AOB were integrated with thermodynamic electron-equivalents modeling (TEEM) to estimate kinetic and stoichiometric parameters for each of the AOB's nitrogen (N)-oxidation and -reduction reactions. The TEEM analysis shows that hydroxylamine (NH₂OH) oxidation to nitroxyl (HNO) is the most energetically efficient means for the AOB to provide electrons for ammonium monooxygenation, while oxidations of HNO to nitric oxide (NO) and NO to NO₂^- are energetically favorable for respiration and biomass synthesis. The respiratory electron acceptor can be O₂ or NO, and both have similar energetics. The TEEM-predicted value for biomass yield, maximum-specific rate of NH₄⁺ utilization, and maximum specific growth rate are consistent with empirical observations. NO reduction to N₂O is thermodynamically favorable for respiration and biomass synthesis, but the need for O₂ as a reactant in ammonium monooxygenation likely precludes NO reduction to N₂O from becoming the major pathway for respiration.

Reactivity of Nitric Oxide and Nitrosonium Ion with Copper(II/I) Schiff Base Complexes: Mechanistic Aspects of Imine C═N Bond Cleavage and Oxidation of Pyridine-2-aldehyde to Pyridine-2-carboxylic Acid

Four Schiff base ligands of the general formulas [6-(R)-2-pyridyl-N-(2'-methylthiophenyl)methylenimine] (^RL1) and 6-p-chlorophenyl-2-pyridyl-N-(2'-phenylthiophenyl)methylenimine (^RL2), where R = H, Me, p-ClPh, and their bis-ligand copper(II) and copper(I) complexes, 1-4 and 1'-4', respectively, were synthesized and characterized. The reactivities of 1-4 with nitric oxide (NO) gas and of 1'-4' with solid NOBF₄ (NO⁺) were examined in dry acetonitrile in the presence and absence of water (H₂O). The results revealed that, in the absence of H₂O, complexes 1-4 (or 1'-4') reacts with NO (or NOBF₄), leading to imine C═N bond cleavage of both (or one) Schiff base(s) that generates 2 (or 1) equiv of 2-(methyl/phenyl)thiobenzenediazonium perchlorates (5/6) and the corresponding picolaldehyde (^RPial) via a copper nitrosyl of a {CuNO}¹⁰-type intermediate. In the presence of H₂O, the in situ formed ^RPial get oxidized to the corresponding picolinic acid (^RPicH) via an in situ formed LCu^IOH intermediate (LCu^I + HO-NO → LCu^IOH + NO⁺; L = ^RL1/^RL2/^RPic^- and ν_O-H of Cu^IOH = 3650 cm^-1) and subsequently produces, with the aid of NO⁺ oxidant, the picolinate-ligated copper(II) complexes (i) [(^HPic)₂Cu] (7), [(^MePic)₄Cu₃(NO₃)₂]_n·H₂O (8·H₂O), or [(^ClPhPic)₂Cu] (9) when NO reacts with 1-4 or (ii) [(^RPic)Cu^II(^RL1/^RL2)]⁺ when NO⁺ reacts with 1'-4'. The Cu^II to Cu^I reduction of [(^RPic)Cu^II(^RL1/^RL2)]⁺ is essential for C═N cleavage of the remaining ^RL1/^RL2 Schiff base; excess NO can do it. The X-ray structures (1, 1', 3', 5, 7, and 8) and spectroscopic results revealed the role of Cu^II/I, NO, NO⁺, and H₂O, shedding light on the mechanism of C═N bond cleavage and the oxidation of pyridine-2-aldehyde to pyridine-2-carboxylic acid. The reaction of 1 with ¹⁵NO revealed that the terminal N of the N₂⁺ group of 5 originates from ¹⁵NO [ν_{¹⁴N¹⁴N-} = 2248 cm^-1 and ν_{¹⁵N¹⁴N-} = 2212 cm^-1].

Organic Host Encapsulation Effects on Nitrosobenzene Monomer-Dimer Distribution and C-NO Bond Rotation in an Aqueous Solution

The intermolecular (monomer-dimer equilibrium) and intramolecular (C-NO and C-NMe₂ rotations) dynamics of 4-nitrosocumene (1a) and 4-(N,N-dimethylamino)nitrosobenzene (1b), respectively, were found to be controlled by the medium (water) and the host environment (organic capsules and cavitands). The ability of water to shift the equilibrium toward the dimer appears to result from dipolar stabilization of the polar dimer structure and has a resemblance to water's known ability to favor organic cycloaddition reactions. In an aqueous medium, a range of organic hosts selectively include only the nitrosocumene monomer 1a. Encapsulation in the octa acid duplex (OA₂) selects two 1a monomers rather than a dimer structure. Octa acid encapsulation also results in more restricted intramolecular C-N rotations of the guest 1b.

NO Coupling by Nonclassical Dinuclear Dinitrosyliron Complexes to Form N2O Dictated by Hemilability

Selective coupling of NO by a nonclassical dinuclear dinitrosyliron complex (D-DNIC) to form N₂O is reported. The coupling is facilitated by the pyridinediimine (PDI) ligand scaffold, which enables the necessary denticity changes to produce mixed-valent, electron-deficient tethered DNICs. One-electron oxidation of the [{Fe(NO)₂}]₂^10/10 complex Fe₂(^PyrrPDI)(NO)₄ (4) results in NO coupling to form N₂O via the mixed-valent {[Fe(NO)₂]₂}^9/10 species, which possesses an electron-deficient four-coordinate {Fe(NO)₂}¹⁰ site, crucial in N-N bond formation. The hemilability of the PDI scaffold dictates the selectivity in N-N bond formation because stabilization of the five-coordinate {Fe(NO)₂}⁹ site in the mixed-valent [{Fe(NO)₂}]₂^9/10 species, [Fe₂(^Pyr2PDI)(NO)₄][PF₆] (6), does not result in an electron-deficient, four-coordinate {Fe(NO)₂}¹⁰ site, and hence no N-N coupling is observed.

Reaction between a NO2 Dimer and Dissolved SO2: A New Mechanism for ONSO3- Formation and its Fate in Aerosol

Experimental observations indicate that sulfate formation in aerosol is sensitive to the concentrations of nitric oxide (NO₂). While it also widely exists as a dimer in the gas phase, previous studies focus on the monomer of NO₂. In this study, we employ quantum chemical calculations and ab initio molecular dynamics simulations to investigate the reaction between the NO₂ dimer (ONONO₂) and sulfite (HSO₃^-/SO₃^2-) in the gas phase and in an aerosol. Gas-phase reactions turn out to be barrierless. In an aerosol, the reaction between adsorbed ONONO₂ and HSO₃^- to form ONSO₃^- follows a stepwise mechanism with proton and electron transfer processes. The reaction between ONONO₂ and SO₃^2- is more straightforward. Nevertheless, both reactions occur at a picosecond time scale. Decomposition of ONSO₃^- can form an NO molecule and SO₃^-, which gives a complementary pathway for sulfate formation in an aerosol. Hydrolysis of ONSO₃^- to form HNO and HSO₄^- is highly impossible in an aerosol, which calls for a revisit of the atmospheric N₂O formation mechanism. The results presented in this study deepen our understanding of the interaction between NO₂ and SO₂ pollutants in the atmosphere.

Solid-gas reactions for nitroxyl (HNO) generation in the gas phase

We present a novel nitroxyl (HNO) generation method, which avoids the need of using a liquid system or extreme experimental conditions. This method consists of the reaction between a gaseous base and an HNO donor (Piloty's acid) in the solid phase, allowing the formation of gaseous HNO in a fast and economical way. Detection of HNO was carried out indirectly, measuring the nitrous oxide (N₂O) byproduct of HNO dimerization using infrared spectroscopy, and directly, using mass spectrometry techniques and an electrochemical HNO sensor.

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.

ortho-Substituent effect on the crystal packing and solid state speciation of aromaticC-nitroso compounds

The solid state behaviour of a short series aromaticC-nitroso compounds has been studied as a function of the electronic and steric nature of theortho-substituent on the ring.

Response of N2O production rate to ocean acidification in the western North Pacific

Ocean acidification induced by the increase of anthropogenic CO₂ emissions has a profound impact on marine organisms and biogeochemical processes.¹ The response of marine microbial activities to ocean acidification might play a crucial role in the future evolution of air-sea fluxes of biogenic gases such as nitrous oxide (N₂O), a strong greenhouse gas and the dominant stratospheric ozone-depleting substance.² Here, we examine the response of N₂O production from nitrification to acidification in a series of incubation experiments conducted in subtropical and subarctic western North Pacific. The experiments show that, when pH was reduced, the N₂O production rate during nitrification measured at subarctic stations increased significantly whereas nitrification rates remained stable or decreased. Contrary to what was previously thought, these results suggest that the effect of ocean acidification on N₂O production during nitrification and nitrification rates are likely uncoupled. Collectively these results suggest that, if seawater pH continues to decline at the same rate, ocean acidification could increase the marine N₂O production during nitrification in subarctic North Pacific by 185 to 491% by the end of the century.

Thermal Decomposition Mechanism of Aqueous Hydroxylammonium Nitrate (HAN): Molecular Simulation and Kinetic Modeling

A detailed mechanism has been developed for thermal decomposition of hydroxylammonium nitrate (HAN) solutions, based on quantum mechanical calculations using the SMD-ωB97X-D method. The mechanism describes multiple kinetic processes, including nitration and nitrosation of hydroxylamine, HNO dimerization, and HONO-regeneration pathways involving H-abstraction reactions. Rate constants of elementary reactions were estimated using transition state theory with consideration of species' diffusion effect. Kinetic modeling was performed to predict species' evolutions in 0.1 m HAN in the temperature range of 463-523 K, and results show reasonable agreement with the experimental data from flow reactor studies. For more concentrated solutions, strong autocatalytic behaviors were predicted with the late emergence of NO₂ and HONO, whose regeneration was previously considered as the major autocatalytic pathway. Sensitivity analysis results suggest an acid-catalyzed nitration-nitrosation pathway, based on which the autocatalysis should be caused by the rise of solution acidity. A linear correlation can be observed in the previously reported apparent Arrhenius parameters, which may be reconciled via a kinetic compensation effect.

Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code

In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.

Large variability in CO2 and N2 O emissions and in 15 N site preference of N2 O from reactions of nitrite with lignin and its derivatives at different pH

RATIONALE

Chemodenitrification is an important N₂ O source in soil; however, knowledge about the production of CO₂ and N₂ O from abiotic nitrite-SOM reactions, especially the N₂ O isotopic signatures (intramolecular ¹⁵ N site preference (SP), and δ¹⁵ N^bulk and δ¹⁸ O values), is quite limited at present.

METHODS

N₂ O and CO₂ emissions from chemical reactions of nitrite with lignin products were determined with gas chromatography, and their response surfaces as a function of pH from 3 to 6 and nitrite concentration from 0.1 to 0.5 mM were explored with polynomial regression. The intramolecular ¹⁵ N distribution of N₂ O, as well as δ¹⁵ N^bulk and δ¹⁸ O values, were measured with an isotope ratio mass spectrometer coupled to an online pre-concentration unit. The variability in N₂ O SP values was tested from pH 3 to 5, and for nitrite concentrations from 0.3 to 0.5 mM.

RESULTS

Both CO₂ and N₂ O emissions varied largely with pH and the structure of lignin products. The highest N₂ O emission occurred at pH 4-5 in 4-hydroxy-3,5-dimethoxybenzaldehyde and 4-hydroxy-3,5-dimethoxybenzoic acid treatments, and at pH 3 in the treatments with lignin, 4-hydroxy-3-methoxybenzaldehyde, 4-hydroxy-3-methoxybenzoic acid, 4-hydroxybenzaldehyde, and 4-hydroxybenzoic acid. A wide range of N₂ O SP values (11.9-37.4‰), which was pH dependent and not distinguishable from microbial pathways, was observed at pH 3-5. The δ¹⁵ N^bulk and δ¹⁸ O values of N₂ O were both in a similar range to that reported for fungal denitrification and bacterial denitrification.

CONCLUSIONS

These results present the first characterization of the isotopic composition of N₂ O from chemodenitrification in pure chemical assays. Chemical reactions of nitrite with lignin are pH-dependent and associated with substantial CO₂ and N₂ O emissions. The SP values of N₂ O derived from chemodenitrification were neither distinguishable from the biotic pathways nor remained stable with varying pH. Therefore, the use of N₂ O isotopic signatures for source partitioning is restricted when chemodenitrification is contributing significantly to N₂ O emission.

Sulfide Homeostasis and Nitroxyl Intersect via Formation of Reactive Sulfur Species in Staphylococcus aureus

Hydrogen sulfide (H₂S) is a toxic molecule and a recently described gasotransmitter in vertebrates whose function in bacteria is not well understood. In this work, we describe the transcriptomic response of the major human pathogen Staphylococcus aureus to quantified changes in levels of cellular organic reactive sulfur species, which are effector molecules involved in H₂S signaling. We show that nitroxyl (HNO), a recently described signaling intermediate proposed to originate from the interplay of H₂S and nitric oxide, also induces changes in cellular sulfur speciation and transition metal homeostasis, thus linking sulfide homeostasis to an adaptive response to antimicrobial reactive nitrogen species.

Staphylococcus aureus is a commensal human pathogen and a major cause of nosocomial infections. As gaseous signaling molecules, endogenous hydrogen sulfide (H₂S) and nitric oxide (NO·) protect S. aureus from antibiotic stress synergistically, which we propose involves the intermediacy of nitroxyl (HNO). Here, we examine the effect of exogenous sulfide and HNO on the transcriptome and the formation of low-molecular-weight (LMW) thiol persulfides of bacillithiol, cysteine, and coenzyme A as representative of reactive sulfur species (RSS) in wild-type and ΔcstR strains of S. aureus. CstR is a per- and polysulfide sensor that controls the expression of a sulfide oxidation and detoxification system. As anticipated, exogenous sulfide induces the cst operon but also indirectly represses much of the CymR regulon which controls cysteine metabolism. A zinc limitation response is also observed, linking sulfide homeostasis to zinc bioavailability. Cellular RSS levels impact the expression of a number of virulence factors, including the exotoxins, particularly apparent in the ΔcstR strain. HNO, like sulfide, induces the cst operon as well as other genes regulated by exogenous sulfide, a finding that is traced to a direct reaction of CstR with HNO and to an endogenous perturbation in cellular RSS, possibly originating from disassembly of Fe-S clusters. More broadly, HNO induces a transcriptomic response to Fe overload, Cu toxicity, and reactive oxygen species and reactive nitrogen species and shares similarity with the sigB regulon. This work reveals an H₂S/NO· interplay in S. aureus that impacts transition metal homeostasis and virulence gene expression.

IMPORTANCE Hydrogen sulfide (H₂S) is a toxic molecule and a recently described gasotransmitter in vertebrates whose function in bacteria is not well understood. In this work, we describe the transcriptomic response of the major human pathogen Staphylococcus aureus to quantified changes in levels of cellular organic reactive sulfur species, which are effector molecules involved in H₂S signaling. We show that nitroxyl (HNO), a recently described signaling intermediate proposed to originate from the interplay of H₂S and nitric oxide, also induces changes in cellular sulfur speciation and transition metal homeostasis, thus linking sulfide homeostasis to an adaptive response to antimicrobial reactive nitrogen species.

Solvent effects on the triplet–triplet annihilation upconversion of diiodo-Bodipy and perylene

Solvent effect plays a very important role in triplet–triplet annihilation (TTA) upconversion system and the upconversion efficiency is controlled by different solvent viscosity and polarity.

Selenols are resistant to irreversible modification by HNO

The discovery of nitric oxide (NO) as an endogenously generated signaling species in mammalian cells has spawned a vast interest in the study of the chemical biology of nitrogen oxides. Of these, nitroxyl (azanone, HNO) has gained much attention for its potential role as a therapeutic for cardiovascular disease. Known targets of HNO include hemes/heme proteins and thiols/thiol-containing proteins. Recently, due to their roles in redox signaling and cellular defense, selenols and selenoproteins have also been speculated to be additional potential targets of HNO. Indeed, as determined in the current work, selenols are targeted by HNO. Such reactions appear to result only in formation of diselenide products, which can be easily reverted back to the free selenol. This characteristic is distinct from the reaction of HNO with thiols/thiolproteins. These findings suggest that, unlike thiolproteins, selenoproteins are resistant to irreversible oxidative modification, support that Nature may have chosen to use selenium instead of sulfur in certain biological systems for its enhanced resistance to electrophilic and oxidative modification.

Mechanistic studies of the reactions of the reduced vitamin B12 derivatives with the HNO donor Piloty's acid: further evidence for oxidation of cob(I)alamin by (H)NO

There is accumulating evidence for the existence of HNO in biological systems. Compared with NO (˙NO), much less is known about the chemical and biochemical reactivity of HNO. Kinetic and mechanistic studies have been carried out on the reaction between the vitamin B12-derived radical complex cob(II)alamin (Cbl(II)˙, Cbl(II)) with the widely used HNO donor Piloty's acid (PA). A stoichiometry of 1 : 2 Cbl(II) : PA was obtained and PA decomposition to HNO and benzenesulfinate (C6H5SO2(-)) is the rate-determining step. No evidence was found for nitrite (Griess assay), ammonia (Nessler's test) or NH2OH (indooxine test) in the product solution, and it is likely that HNO is instead reduced to N2. A mechanism is proposed in which reduction of Cbl(II) by (H)NO results in formation of cob(I)alamin (Cbl(I)(-)) and ˙NO. The Cbl(I)(-) intermediate is subsequently oxidized back to Cbl(II) by a second (H)NO molecule, and Cbl(II) reacts rapidly with ˙NO to form nitroxylcobalamin (NOCbl). Separate studies on the reaction between Cbl(I)(-) and PA shows that this system involves an additional step in which Cbl(I)(-) is first oxidized by (H)NO to Cbl(II), which reacts further with (H)NO to form NOCbl, with an overall stoichiometry of 1 : 3 Cbl(I)(-) : PA. Experiments in the presence of nitrite for both systems support the involvement of a Cbl(I)(-) intermediate in the Cbl(II)/PA reaction. These systems provide the second example of oxidation of cob(I)alamin by (H)NO.

Nitroxyl as a ligand in ruthenium tetraammine systems: a density functional theory study

The properties of the free nitroxyl molecule and the nitroxyl ligand in Ru(ii) tetraammines (trans-[Ru(NH₃)₄(nitroxyl)ⁿ(L)]²⁺ⁿ (n = nitroxyl charge; L = NH₃, py, P(OEt)₃, H₂O, Cl⁻ and Br⁻)) were studied using density functional theory.

Predicting pKa in Implicit Solvents: Current Status and Future Directions

Computational prediction of condensed phase acidity is a topic of much interest in the field today. We introduce the methods available for predicting gas phase acidity and pKas in aqueous and non-aqueous solvents including high-level electronic structure methods, empirical linear free energy relationships (LFERs), implicit solvent methods, explicit solvent statistical free energy methods, and hybrid implicit–explicit approaches. The focus of this paper is on implicit solvent methods, and we review recent developments including new electronic structure methods, cluster-continuum schemes for calculating ionic solvation free energies, as well as address issues relating to the choice of proton solvation free energy to use with implicit solvation models, and whether thermodynamic cycles are necessary for the computation of pKas. A comparison of the scope and accuracy of implicit solvent methods with ab initio molecular dynamics free energy methods is also presented. The present status of the theory and future directions are outlined.

Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

Nitrous oxide (N(2)O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N(2)O is formed biologically from the oxidation of hydroxylamine (NH(2)OH) or the reduction of nitrite (NO(-) (2)) to NO and further to N(2)O. Our review of the biological pathways for N(2)O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO(-) (2) to NO and the further reduction of NO to N(2)O, while N(2)O formation from NH(2)OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N(2)O formation due to the reactivity of NO(-) (2), NH(2)OH, and nitroxyl (HNO). Moreover, biological N(2)O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N(2)O build-up are key to understand mechanisms of N(2)O release. Here, we discuss novel technologies that allow experiments on NO and N(2)O formation at high temporal resolution, namely NO and N(2)O microelectrodes and the dynamic analysis of the isotopic signature of N(2)O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N(2)O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N(2)O build-up.

Computational investigations of HNO in biology

HNO (nitroxyl) has been found to have many physiological effects in numerous biological processes. Computational investigations have been employed to help understand the structural properties of HNO complexes and HNO reactivities in some interesting biologically relevant systems. The following computational aspects were reviewed in this work: 1) structural and energetic properties of HNO isomers; 2) interactions between HNO and non-metal molecules; 3) structural and spectroscopic properties of HNO metal complexes; 4) HNO reactions with biologically important non-metal systems; 5) involvement of HNO in reactions of metal complexes and metalloproteins. Results indicate that computational investigations are very helpful to elucidate interesting experimental phenomena and provide new insights into unique structural, spectroscopic, and mechanistic properties of HNO involvement in biology.