Theoretical Evidence for Enhanced NO Dimerization in Aromatic Hosts: Implications for the Role of the Electrophile (NO)2 in Nitric Oxide Chemistry

Nitrogen monoxide and calix[4]pyrrolato aluminate: structural constraint enabled NO dimerization

The dimerization of nitrogen monoxide (NO) is highly relevant in homo- and heterogeneous biochemical and environmental redox processes, but a broader understanding is challenged by the endergonic nature of this equilibrium. The present work describes NO-dimerization leveraged by structurally constrained aluminum and metal-ligand cooperativity at the anionic calix[4]pyrrolato aluminate(III). Quantum chemical calculations reveal the driving force for N-N bond formation, while reactivity tests shed light on subsequent redox chemistry and NO decomposition at metal surfaces. Inhibiting the dimerization pathway by saturating NO's unpaired electron with a phenyl group (nitrosobenzene) allows trapping the 1,2-adduct as a key intermediate. Elevated temperatures result in an unprecedented and high-yielding rearrangement of the calix[4]pyrrolato ligand scaffold. Kinetic and theoretical studies provide a comprehensive picture of the rearrangement mechanism and delineate systematics for ring modification of the prominent calix[4]pyrrole macrocycle.

Disproportionation of Nitric Oxide at a Surface-Bound Nickel Porphyrinoid

Uncommon metal oxidation states in porphyrinoid cofactors are responsible for the activity of many enzymes. The F430 and P450nor co-factors, with their reduced NiI - and FeIII -containing tetrapyrrolic cores, are prototypical examples of biological systems involved in methane formation and in the reduction of nitric oxide, respectively. Herein, using a comprehensive range of experimental and theoretical methods, we raise evidence that nickel tetraphenyl porphyrins deposited in vacuo on a copper surface are reactive towards nitric oxide disproportionation at room temperature. The interpretation of the measurements is far from being straightforward due to the high reactivity of the different nitrogen oxides species (eventually present in the residual gas background) and of the possible reaction intermediates. The picture is detailed in order to disentangle the challenging complexity of the system, where even a small fraction of contamination can change the scenario.

Disproportionation of Nitric Oxide at a Surface-Bound Nickel Porphyrinoid

Uncommon metal oxidation states in porphyrinoid cofactors are responsible for the activity of many enzymes. The F430 and P450nor co-factors, with their reduced NiI- and FeIII-containing tetrapyrrolic cores, are prototypical examples of biological systems involved in methane formation and in the reduction of nitric oxide, respectively. Herein, using a comprehensive range of experimental and theoretical methods, we raise evidence that nickel tetraphenyl porphyrins deposited in vacuo on a copper surface are reactive towards nitric oxide disproportionation at room temperature. The interpretation of the measurements is far from being straightforward due to the high reactivity of the different nitrogen oxides species (eventually present in the residual gas background) and of the possible reaction intermediates. The picture is detailed in order to disentangle the challenging complexity of the system, where even a small fraction of contamination can change the scenario.

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.

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.

Synthesis and activation potential of an open shell diphosphine

A paramagnetic W^III alkyne complex bearing free terminal diphenylphosphino groups at the side-on coordinated alkyne was synthesized using a stepwise template strategy. This moderately stable metal supported open shell diphosphine shows an unprecedented spontaneous splitting of nitric oxide providing a W^II-η²-C₂{P(NH₂)Ph₂}{P(O)Ph₂}⁺ complex featuring an amino phosphonium and a phosphine oxide substituent.

Nitric oxide coupling to generate N2O promoted by a single-heme system as examined by density functional theory

Bacteria utilize a heme/non-heme enzyme system to detoxify nitric oxide (NO) to N₂O. In order to probe the capacity of a single-heme system to mediate this NO-to-N₂O transformation, various scenarios for addition of electrons, protons, and a second NO molecule to a heme nitrosyl to generate N₂O were explored by density functional theory calculations. We describe, utilizing this single-heme system, several stepwise intermediates along pathways that enable the critical N-N bond formation step yielding the desired Fe-N₂O product. We also report a hitherto unreported directional second protonation that results in either productive N₂O formation with loss of water, or formation of a non-productive hyponitrous acid adduct Fe{HONNOH}.

The chemical biology of HNO signaling

Nitroxyl (HNO) is a simple molecule with significant potential as a pharmacological agent. For example, its use in the possible treatment of heart failure has received recent attention due to its unique therapeutic properties. Recent progress has been made on the elucidation of the mechanisms associated with its biological signaling. Importantly, the biochemical mechanisms described for HNO bioactivity are consistent with its unique and novel chemical properties/reactivity. To date, much of the biology of HNO can be associated with interactions and modification of important regulatory thiol proteins. Herein will be provided a description of HNO chemistry and how this chemistry translates to some of its reported biological effects.

A Cr-phthalocyanine monolayer as a potential catalyst for NO reduction investigated by DFT calculations

The reaction mechanism of nitric oxide (NO) reduction to nitrous oxide (N₂O) and N₂ catalyzed by Cr-phthalocyanine sheet (CrPc) was investigated using periodic density functional theory (DFT).

Mechanistic studies on the Rh(III)-mediated amido transfer process leading to robust C-H amination with a new type of amidating reagent

Mechanistic investigations on the Cp*Rh(III)-catalyzed direct C-H amination reaction led us to reveal the new utility of 1,4,2-dioxazol-5-one and its derivatives as highly efficient amino sources. Stepwise analysis on the C-N bond-forming process showed that competitive binding of rhodium metal center to amidating reagent or substrate is closely related to the reaction efficiency. In this line, 1,4,2-dioxazol-5-ones were observed to have a strong affinity to the cationic Rh(III) giving rise to dramatically improved amidation efficiency when compared to azides. Kinetics and computational studies suggested that the high amidating reactivity of 1,4,2-dioxazol-5-one can also be attributed to the low activation energy of an imido-insertion process in addition to the high coordination ability. While the characterization of a cationic Cp*Rh(III) complex bearing an amidating reagent was achieved, its facile conversion to an amido-inserted rhodacycle allowed for a clear picture on the C-H amidation process. The newly developed amidating reagent of 1,4,2-dioxazol-5-ones was applicable to a broad range of substrates with high functional group tolerance, releasing carbon dioxide as a single byproduct. Additional attractive features of this amino source, such as they are more convenient to prepare, store, and use when compared to the corresponding azides, take a step closer toward an ideal C-H amination protocol.

Removal of NO with silicene: a DFT investigation

NO can be adsorbed onto silicene and then reduced into N₂via a dimer mechanism.

Nitrite reduction mediated by heme models. Routes to NO and HNO?

The water-soluble ferriheme model Fe(III)(TPPS) mediates oxygen atom transfer from inorganic nitrite to a water-soluble phosphine (tppts), dimethyl sulfide, and the biological thiols cysteine (CysSH) and glutathione (GSH). The products with the latter reductant are the respective sulfenic acids CysS(O)H and GS(O)H, although these reactive intermediates are rapidly trapped by reaction with excess thiol. The nitrosyl complex Fe(II)(TPPS)(NO) is the dominant iron species while excess substrate is present. However, in slightly acidic media (pH ≈ 6), the system does not terminate at this very stable ferrous nitrosyl. Instead, it displays a matrix of redox transformations linking spontaneous regeneration of Fe(III)(TPPS) to the formation of both N2O and NO. Electrochemical sensor and trapping experiments demonstrate that HNO (nitroxyl) is formed, at least when tppts is the reductant. HNO is the likely predecessor of the N2O. A key pathway to NO formation is nitrite reduction by Fe(II)(TPPS), and the kinetics of this iron-mediated transformation are described. Given that inorganic nitrite has protective roles during ischemia/reperfusion (I/R) injury to organs, attributed in part to NO formation, and that HNO may also reduce net damage from I/R, the present studies are relevant to potential mechanisms of such nitrite protection.

Nitric oxide coupling mediated by iron porphyrins: the N-N bond formation step is facilitated by electrons and a proton

The coupling of two NO molecules catalyzed by iron porphyrins is of biological importance. We use density functional theory calculations to examine the factors that control the fundamental N-N bond formation step mediated by a single iron porphyrin. The presence of an axial Im ligand, extra electrons, and most importantly a proton, enhance the N-N bond formation step in our model.

Small molecule signaling agents: the integrated chemistry and biochemistry of nitrogen oxides, oxides of carbon, dioxygen, hydrogen sulfide, and their derived species

Several small molecule species formally known primarily as toxic gases have, over the past 20 years, been shown to be endogenously generated signaling molecules. The biological signaling associated with the small molecules NO, CO, H₂S (and the nonendogenously generated O₂), and their derived species have become a topic of extreme interest. It has become increasingly clear that these small molecule signaling agents form an integrated signaling web that affects/regulates numerous physiological processes. The chemical interactions between these species and each other or biological targets is an important factor in their roles as signaling agents. Thus, a fundamental understanding of the chemistry of these molecules is essential to understanding their biological/physiological utility. This review focuses on this chemistry and attempts to establish the chemical basis for their signaling functions.

Linkage isomerization in heme-NOx compounds: understanding NO, nitrite, and hyponitrite interactions with iron porphyrins

Nitric oxide (NO) and its derivatives such as nitrite and hyponitrite are biologically important species of relevance to human health. Much of their physiological relevance stems from their interactions with the iron centers in heme proteins. The chemical reactivities displayed by the heme-NOx species (NOx = NO, nitrite, hyponitrite) are a function of the binding modes of the NOx ligands. Hence, an understanding of the types of binding modes extant in heme-NOx compounds is important if we are to unravel the inherent chemical properties of these NOx metabolites. In this Forum Article, the experimentally characterized linkage isomers of heme-NOx models and proteins are presented and reviewed. Nitrosyl linkage isomers of synthetic iron and ruthenium porphyrins have been generated by photolysis at low temperatures and characterized by spectroscopy and density functional theory calculations. Nitrite linkage isomers in synthetic metalloporphyrin derivatives have been generated from photolysis experiments and in low-temperature matrices. In the case of nitrite adducts of heme proteins, both N and O binding have been determined crystallographically, and the role of the distal H-bonding residue in myoglobin in directing the O-binding mode of nitrite has been explored using mutagenesis. To date, only one synthetic metalloporphyrin complex containing a hyponitrite ligand (displaying an O-binding mode) has been characterized by crystallography. This is contrasted with other hyponitrite binding modes experimentally determined for coordination compounds and computationally for NO reductase enzymes. Although linkage isomerism in heme-NOx derivatives is still in its infancy, opportunities now exist for a detailed exploration of the existence and stabilities of the metastable states in both heme models and heme proteins.

The SNO-proteome: causation and classifications

Cell signaling is a complex and highly regulated process. Post-translational modifications of proteins serve to sense and transduce cellular signals in a precisely coordinated manner. It is increasingly recognized that protein S-nitrosylation, the addition of a nitric oxide group to cysteine thiols, serves an important role in a wide range of signaling pathways. In spite of the large number of SNO-proteins now identified (∼1000), the observed specificity of S-nitrosylation in terms of target proteins and specific cysteines within modified proteins is incompletely understood. Here we review the progress made in S-nitrosylation detection methods that have facilitated the study of the SNO-proteome under physiological and pathophysiological conditions, and some factors important in determining the SNO-proteome. Classification schemes for emergent denitrosylases and prospective 'protein S-nitrosylases' are provided.

Mechanism of pH-dependent decomposition of monoalkylamine diazeniumdiolates to form HNO and NO, deduced from the model compound methylamine diazeniumdiolate, density functional theory, and CBS-QB3 calculations

Isopropylamine diazeniumdiolate, IPA/NO, the product of the reaction of isopropylamine and nitric oxide, NO, decomposes in a pH-dependent manner to afford nitroxyl, HNO, in the pH range of 13 to above 5, and NO below pH 7. Theoretical studies using B3LYP/6-311+G(d) density functional theory, the polarizable continuum and conductor-like polarizable continuum solvation models, and the high-accuracy CBS-QB3 method on the simplified model compound methylamine diazeniumdiolate predict a mechanism involving HNO production via decomposition of the unstable tautomer MeNN+(O-)NHO-. The production of NO at lower pH is predicted to result from fragmentation of the amide/NO adduct upon protonation of the amine nitrogen.

A Computational Study on the Interaction of the Nitric Oxide Ions NO+ and NO- with the Side Groups of the Aromatic Amino Acids

The interaction of the nitric oxide ions NO+ and NO- with benzene (C6H6) and the aromatic R-groups of the amino acids phenylalanine (Phe), tyrosine (Tyr), histidine (His), and tryptophan (Trp) have been examined using the DFT method B3LYP and the conventional electron correlation method MP2. In particular, the structures and complexation energies of the resulting half-sandwich Ar...NO+/- and sandwich [Ar...NO...Ar]+/- complexes have been considered. For the Ar...NO+ complexes, the presence of an electron rich heteroatom within or attached to the ring is found to not preclude the cation...pi bound complex from being the most stable. Furthermore, unlike the anionic complexes, the pi...cation...pi ([Ar...NO...Ar]+) complexes do not correspond to a "doubling" of the parent half-sandwich.

Chemistry of the potassium, silver, and tetra(n-butyl)ammonium salts of sydnone N-oxide (Traube's anion)

Traube's dianion, 4-methylcarboxysydnone-3-hydroxylate (2), and its monomethyl ester (1) are readily isolated as their di- and mono-potassium salts from the reaction of nitric oxide with dimethylmalonate and potassium methoxide in methanol. Metathesis reactions of 1 with silver nitrate and tetra(n-butyl)ammonium bromide yield the silver and tetra(n-butyl)ammonium salts of 4-methylcarboxysydnone-3-hydroxylate. In contrast to other known sydnone derivatives, the present sydnones are stable in both acidic and basic solutions. Single crystal X-ray diffraction data obtained for 2 and the silver salt (3) reveal planarity and delocalization of double bonds in the sydnone ring, indicating aromatic behavior. The tetra(n-butyl)ammonium salt (4) is soluble in a range of organic compounds. Cyclic voltammetric data measured for 4 in acetonitrile reveal an irreversible oxidation peak at +1.09 V vs. Fc–Fc+ couple suggesting that the sydnone derivatives can be oxidized with an appropriate oxidizing agent. Differential scanning calorimetry data reveal thermal stability at ambient conditions and exothermic decomposition at high temperatures (>229 °C). The sydnone derivatives are characterized by two strong electronic absorptions in the UV region and rich vibrational (IR and Raman) spectra in the 1800–1500 cm–1 region. Density functional theory (B3LYP/6-311+++G**) is applied to estimate the aromaticity of the sydnone ring and to assign the vibrational spectral data.Key words: sydnone, trans-diazeniumdiolate, N-oxide.

N+NO Reaction on Rh(111) Surfaces Studied with Fast Near-Edge X-ray Absorption Fine Structure Spectroscopy: Role of NO Dimer as an Extrinsic Precursor

We studied the mechanism of the N+NO reaction on Rh(111) surfaces by means of fast near-edge X-ray absorption fine structure spectroscopy. This reaction is important as a basis of NOx reduction reactions on platinum-group metal surfaces. Atomic nitrogen layers on Rh(111) were titrated with NO at various temperatures. N2O is exclusively formed and desorbs into the gas phase below 350 K. The consumption rate of atomic nitrogen exhibits strange temperature dependence between 100 and 350 K; the reaction proceeds slower with increasing temperature. Reaction kinetics analyses and isotope-controlled experiments have revealed that the surface N atoms do not react with chemisorbed NO molecules but with NO dimers weakly bound on top of the chemisorbed layer, which play a role as an extrinsic precursor. The present results may support the possibility that NO dimers participate in various NO-related synthetic, biochemical, and surface reactions as an intermediate.

Noncovalent interactions of molecules with single walled carbon nanotubes

In this critical review we survey non-covalent interactions of carbon nanotubes with molecular species from a chemical perspective, particularly emphasising the relationship between the structure and dynamics of these structures and their functional properties. We demonstrate the synergistic character of the nanotube-molecule interactions, as molecules that affect nanotube properties are also altered by the presence of the nanotube. The diversity of mechanisms of molecule-nanotube interactions and the range of experimental techniques employed for their characterisation are illustrated by examples from recent reports. Some practical applications for carbon nanotubes involved in non-covalent interactions with molecules are discussed.

S-nitrosothiol signaling in respiratory biology

Genetic and biochemical data demonstrate a pivotal role for S-nitrosothiols (SNOs) in mediating the actions of nitric oxide synthases (NOSs). SNOs serve to convey NO bioactivity and to regulate protein function. This understanding is of immediate interest to the pulmonary clinical and research communities. This article reviews the following: (1) biochemical and cellular evidence that SNOs in amino acids, peptides, and proteins elicit NOS-dependent signaling in the respiratory system and (2) studies that link SNO signaling to pulmonary medicine. SNO-mediated signaling is involved in the regulation of minute ventilation, ventilation-perfusion matching, pulmonary arterial pressure, basal airway tone, and respiratory and peripheral muscle function. Derangements in SNO signaling are implicated in many disorders relevant to pulmonary and critical care medicine, including apnea, hypoxemia, pulmonary hypertension, asthma, cystic fibrosis, pneumonia, and septic shock.

Thionitroxides, RSNHO*: the structure of the SNO moiety in "S-Nitrosohemoglobin", a possible NO reservoir and transporter

Nitric oxide (NO) plays important roles in many biological processes. S-Nitrosothiols have long been believed to have significant roles in NO biochemistry. The modified cysteine residue of hemoglobin was previously identified as a distorted S-nitrosothiol (RSNO) or an S-hydroxyamino radical (RSN*OH). Here we show that a thionitroxide (RSNHO*, S-aminyloxyl radical) is likely the observed species. Computational studies show that the thionitroxide is the only structure consistent with the electron density in the hemoglobin Cysbeta93-SNO structure previously reported. Although a metastable adduct, the thionitroxide in a hydrogen-bonding environment can form readily and release NO upon exposure to an aqueous environment. The thionitroxides could be responsible for the biological effects attributed to S-nitrosothiols or could serve as precursors to S-nitrosothiols in oxidative conditions.

Competitive photoinduced electron transfer by the complex formation of porphyrin with cyclodextrin bearing viologen

Photoinduced electron transfer between a porphyrin and a new guest cyclodextrin bearing viologen occurs by a supramolecular formation with conformational change of a guest molecule.