Next-generation enhanced-efficiency fertilizers for sustained food security.

Nitrogen losses in agricultural systems can be reduced through enhanced-efficiency fertilizers (EEFs), which control the physicochemical release from fertilizers and biological nitrogen transformations in soils. The adoption of EEFs by farmers requires evidence of consistent performance across soils, crops and climates, paired with information on the economic advantages. Here we show that the benefits of EEFs due to avoided social costs of nitrogen pollution considerably outweigh their costs-and must be incorporated in fertilizer policies.

Phenylalanine Residues Are Very Rapidly Damaged by Nitrate Radicals (NO ⋅) in an Aqueous Environment.

Kinetic studies revealed that nitrate radicals (NO ⋅), which are formed through reaction of the noxious air pollutants nitrogen dioxide (NO ⋅) and ozone (O ), very rapidly oxidize phenylalanine residues in an aqueous environment, with overall rate coefficients in the 10 -10  M  s range. With amino acids and dipeptides as model systems, the data suggest that the reaction proceeds via a π-complex between NO ⋅ and the aromatic ring in Phe, which subsequently decays into a charge transfer (CT) complex. The stability of the π-complex is sequence-dependent and is increased when Phe is at the N terminus of the dipeptide.

Damage of amino acids by aliphatic peroxyl radicals: a kinetic and computational study.

Absolute second-order rate coefficients for the reaction of the N- and C-protected amino acids tyrosine (Tyr), tryptophan (Trp), methionine (Met) and proline (Pro) with triethylamine-derived aliphatic peroxyl radical TEAOO˙, which was used as a model for lipid peroxyl radicals, were determined using laser flash photolysis. For Ac-Tyr-OMe a rate coefficient of 1.4 × 10 M s was obtained, whereas the reactions with Ac-Trp-OMe and Ac-Met-OMe were slower by a factor of 4 and 6, respectively.

Oxidative Damage of Aliphatic Amino Acid Residues by the Environmental Pollutant NO: Impact of Water on the Reactivity.

The rate of oxidative damage of aliphatic amino acids and dipeptides by the environmental pollutant nitrate radical (NO) in an aqueous acidic environment was studied by laser flash photolysis. The reactivity dropped by a factor of about four for amino acid residues with secondary amide bonds and by a factor of up to nearly 20 for amino acid residues with tertiary amide bonds, compared with that in acetonitrile. According to density functional theory studies, the lower reactivity is due to protonation of the amide moiety, whereas in neutral water, hydrogen bonding with the amide should have little impact on the absolute reaction rate compared with that in acetonitrile.

Substituted 1,2,3-triazoles: a new class of nitrification inhibitors.

Nitrogen (N) fertilisers amended with nitrification inhibitors can increase nitrogen use efficiencies in agricultural systems but the effectiveness of existing commercial inhibitor products, including 3,4-dimethylpyrazole phosphate (DMPP), is strongly influenced by climatic and edaphic factors. With increasing pressure to reduce the environmental impact of large-scale agriculture it is important to develop new nitrogen-stabilising products that can give reliable and consistent results, particularly for warmer climatic conditions. We synthesised a library of 17 compounds featuring a substituted 1,2,3-triazole motif and performed laboratory incubations in two south-eastern Australian soils.

Ring Expansion of Thiolactams via Imide Intermediates: An Amino Acid Insertion Strategy.

The Ag -promoted reaction of thiolactams with N-Boc amino acids yields an N-(α-aminoacyl) lactam that can rearrange through an acyl transfer process. Boc-deprotection results in convergence to the ring-expanded adduct, thereby facilitating an overall insertion of an amino acid into the thioamide bond to generate medium-sized heterocycles. Application to the site-specific insertion of amino acids into cyclic peptides is demonstrated.

Synthesis of spirocyclic heterocycles from α,β-unsaturated -acyliminium ions.

The reactions of α,β-unsaturated N-acyliminium ions, generated in situ from 4(S)-O-substitutedhydroxy-5-hydroxy-5-vinyl-N-alkylpyrrolidin-2-ones, with allylsilanes and indoles leading to the formation of spirocyclic heterocycles, are reported. Six single crystal X-ray structures and extensive 2D NMR experiments confirmed the structures and stereochemistries of these products. In addition, computational studies provided mechanistic insights and an understanding of the stereochemical outcomes of these reactions.

Oxidative damage of proline residues by nitrate radicals (NO˙): a kinetic and product study.

Tertiary amides, such as in N-acylated proline or N-methyl glycine residues, react rapidly with nitrate radicals (NO˙) with absolute rate coefficients in the range of 4-7 × 10 M s in acetonitrile. The major pathway proceeds through oxidative electron transfer (ET) at nitrogen, whereas hydrogen abstraction is only a minor contributor under these conditions. However, steric hindrance at the amide, for example by alkyl side chains at the α-carbon, lowers the rate coefficient by up to 75%, indicating that NO˙-induced oxidation of amide bonds proceeds through initial formation of a charge transfer complex.

Reactions of a distonic peroxyl radical anion influenced by SOMO-HOMO conversion: an example of anion-directed channel switching.

In free radicals the singly occupied molecular orbital (SOMO) typically has the highest energy. Recent examples of distonic radical anions were found, however, to disobey the usual orbital configuration, with the singly occupied molecular orbital buried energetically underneath doubly occupied orbitals. This unusual ordering of electrons, which contradicts the aufbau principle, has been characterized as SOMO-HOMO orbital conversion and is expected to perturb radical anion reactivity by branching toward anion-driven over radical-driven processes.

1,2-Addition versus homoconjugate addition reactions of indoles and electron-rich arenes to α-cyclopropyl N-acyliminium ions: synthetic and computational studies.

An investigation of the reactivity of α-cyclopropyl N-acyliminium ions towards indoles has resulted in the unprecedented synthesis of 5-cyclopropyl-5-(3-indoyl)pyrrolidin-2-ones via 1,2-addition reactions and, in the case of highly electron deficient indoles and electron rich arenes, spiroheterocycles via sequential homoconjugate and 1,2-addition reactions with often high diastereoselective control at the C-5 quaternary stereocentres. Computational studies provided support for the proposed mechanisms and stereochemical outcome of these reactions, clearly showing that the 1,2-addition pathway is kinetically controlled. In reactions where the 1,2-adduct is destabilised, for example when the arene ring is less nucleophilic, the 1,2-addition is reversible and the thermodynamically preferred homoconjugate addition and subsequent rearrangement and cyclisation reactions become the major pathway.

Oxidative Damage in Aliphatic Amino Acids and Di- and Tripeptides by the Environmental Free Radical Oxidant NO: The Role of the Amide Bond Revealed by Kinetic and Computational Studies.

Kinetic and computational data reveal a complex behavior of the important environmental free radical oxidant NO in its reactions with aliphatic amino acids and di- and tripeptides, suggesting that attack at the amide N-H bond in the peptide backbone is a highly viable pathway, which proceeds through a proton-coupled electron transfer (PCET) mechanism with a rate coefficient of about 1 × 10 M s in acetonitrile. Similar rate coefficients were determined for hydrogen abstraction from the α-carbon and from tertiary C-H bonds in the side chain. The obtained rate coefficients for the reaction of NO with aliphatic di- and tripeptides suggest that attack occurs at all of these sites in each individual amino acid residue, which makes aliphatic peptide sequences highly vulnerable to NO-induced oxidative damage.

Reversible Photoisomerization of the Isolated Green Fluorescent Protein Chromophore.

Fluorescent proteins have revolutionized the visualization of biological processes, prompting efforts to understand and control their intrinsic photophysics. Here we investigate the photoisomerization of deprotonated p-hydroxybenzylidene-2,3-dimethylimidazolinone anion (HBDI), the chromophore in green fluorescent protein and in Dronpa protein, where it plays a role in switching between fluorescent and nonfluorescent states. In the present work, isolated HBDI molecules are switched between the Z and E forms in the gas phase in a tandem ion mobility mass spectrometer outfitted for selecting the initial and final isomers.

Amide Neighbouring-Group Effects in Peptides: Phenylalanine as Relay Amino Acid in Long-Distance Electron Transfer.

In nature, proteins serve as media for long-distance electron transfer (ET) to carry out redox reactions in distant compartments. This ET occurs either by a single-step superexchange or through a multi-step charge hopping process, which uses side chains of amino acids as stepping stones. In this study we demonstrate that Phe can act as a relay amino acid for long-distance electron hole transfer through peptides.

Environmental Polymer Degradation: Using the Distonic Radical Ion Approach to Study the Gas-Phase Reactions of Model Polyester Radicals.

A novel precursor to the distonic O- and C-centered radical cations OxoO and OxoC was designed and synthesized, which represents model systems for radicals produced during polyester degradation. The precursor is equipped with a nitrate functional group, which serves as a masked site for these alkoxyl and carbon radicals that are unleashed through collision-induced dissociation (CID). OxoO and OxoC feature a cyclic carboxonium ion as permanent charge tag to enable monitoring their ion-molecule reactions on the millisecond to second time scale in the ion trap of the mass spectrometer.

Oxidative Damage of Biomolecules by the Environmental Pollutants NO and NO

Air pollution is responsible for the premature death of about 7 million people every year. Ozone (O) and nitrogen dioxide (NO) are the key gaseous pollutants in the troposphere, which predominantly result from combustion processes. Their inhalation leads to reactions with constituents in the airway surface fluids (ASF) of the respiratory tract and/or lungs.

Reaction of Amino Acids, Di- and Tripeptides with the Environmental Oxidant NO : A Laser Flash Photolysis and Computational Study.

Absolute rate coefficients for the reaction between the important environmental free radical oxidant NO and a series of N- and C-protected amino acids, di- and tripeptides were determined using 355 nm laser flash photolysis of cerium(IV) ammonium nitrate in the presence of the respective substrates in acetonitrile at 298±1 K. Through combination with computational studies it was revealed that the reaction with acyclic aliphatic amino acids proceeds through hydrogen abstraction from the α-carbon, which is associated with a rate coefficient of about 1.8×10  m  s per abstractable hydrogen atom.

Oxidation of cholesterol and O-protected derivatives by the environmental pollutant NO₂.

Exposure of O-protected and free cholesterol to NO2˙ under exclusion of water leads to nitroimine nitrates through a non-radical mechanism, which reveals the high susceptibility of the π system to oxidative damage. In the presence of moisture the reaction leads to 6-nitrocholesterols , which result from hydrolysis and oxidation of 2.

Synthesis of Bridged Heterocycles via Sequential 1,4- and 1,2-Addition Reactions to α,β-Unsaturated N-Acyliminium Ions: Mechanistic and Computational Studies.

Novel tricyclic bridged heterocyclic systems can be readily prepared from sequential 1,4- and 1,2-addition reactions of allyl and 3-substituted allylsilanes to indolizidine and quinolizidine α,β-unsaturated N-acyliminium ions. These reactions involve a novel N-assisted, transannular 1,5-hydride shift. Such a mechanism was supported by examining the reaction of a dideuterated indolizidine, α,β-unsaturated N-acyliminium ion precursor, which provided specifically dideuterated tricyclic bridged heterocyclic products, and from computational studies.

Synthesis of Peptides by Silver-Promoted Coupling of Carboxylates and Thioamides: Mechanistic Insight from Computational Studies.

The mechanism of the recently described N→C direction peptide synthesis through silver-promoted coupling of N-protected amino acids with thioacetylated amino esters was explored by using density functional theory. Calculation of the potential energy surfaces for various pathways revealed that the reaction proceeds through silver-assisted addition of the carboxylate to the thioamide, which is followed by deprotonation and silver-mediated extrusion of sulfur as Ag2 S. The resulting isoimide is the key intermediate, which subsequently rearranges to an imide through a concerted pericyclic [1,3]-acyl shift (O-sp(2) N 1,3-acyl migration).

What Are the Potential Sites of Protein Arylation by N-Acetyl-p-benzoquinone Imine (NAPQI)?

Acetaminophen (paracetamol, APAP) is a safe and widely used analgesic medication when taken at therapeutic doses. However, APAP can cause potentially fatal hepatotoxicity when taken in overdose or in patients with metabolic irregularities. The production of the electrophilic and putatively toxic compound N-acetyl-p-benzoquinone imine (NAPQI), which cannot be efficiently detoxicated at high doses, is implicated in APAP toxicity.

A Theoretical Study of the Photoisomerization of Glycolaldehyde and Subsequent OH Radical-Initiated Oxidation of 1,2-Ethenediol.

It has recently been discovered that carbonyl compounds can undergo UV-induced isomerization to their enol counterparts under atmospheric conditions. This study investigates the photoisomerization of glycolaldehyde (HOCH2CHO) to 1,2-ethenediol (HOCH═CHOH) and the subsequent (•)OH-initiated oxidation chemistry of the latter using quantum chemical calculations and stochastic master equation simulations. The keto-enol tautomerization of glycolaldehyde to 1,2-ethenediol is associated with a barrier of 66 kcal mol(-1) and involves a double-hydrogen shift mechanism to give the lower-energy Z isomer.

Fragmentation-Rearrangement of Peptide Backbones Mediated by the Air Pollutant NO2 (.).

The fragmentation-rearrangement of peptide backbones mediated by nitrogen dioxide, NO2 (.) , was explored using di-, tri-, and tetrapeptides 8-18 as model systems. The reaction, which is initiated through nonradical N-nitrosation of the peptide bond, shortens the peptide chain by the expulsion of one amino acid moiety with simultaneous fusion of the remaining molecular termini through formation of a new peptide bond.

Ion Mobility Unlocks the Photofragmentation Mechanism of Retinal Protonated Schiff Base.

Retinal protonated Schiff base (RPSB) is a key molecular component of biological photoreceptors and bacterial photosynthetic structures, where its action involves photoisomerization around bonds in the polyene chain. In a vacuum environment, collisional activation or exposure to visible light causes the RPSB molecule to disintegrate, producing charged molecular fragments with m/z = 248 Da that cannot be formed by simple cleavage of the polyene chain. Photofragments resulting from laser excitation of RPSB at a wavelength of 532 nm are analyzed in an ion mobility mass spectrometer (IMMS) and found to be the protonated Schiff base of β-ionone.

Visible light photooxidation of nitrate: the dawn of a nocturnal radical.

Highly oxidizing nitrate radicals (NO3˙) are easily accessed from readily available nitrate salts by visible light photoredox catalysis using a purely organic dye as the catalyst and oxygen as the terminal oxidant. The interaction of the excited catalyst and nitrate anions was studied by spectroscopic methods to elucidate the mechanism, and the method was applied to the NO3˙ induced oxidation of alkynes and alcohols.

The role of peroxyl radicals in polyester degradation--a mass spectrometric product and kinetic study using the distonic radical ion approach.

Mass spectrometric techniques were used to obtain detailed insight into the reactions of peroxyl radicals with model systems of (damaged) polyesters. Using a distonic radical ion approach, it was shown that N-methylpyridinium peroxyl radical cations, Pyr(+)OO˙, do not react with non-activated C-H bonds typically present in polyesters that resist degradation. Structural damage in the polymer, for example small amounts of alkene moieties formed during the manufacturing process, is required to enable reaction with Pyr(+)OO˙, which proceeds with high preference through addition to the π system rather than via allylic hydrogen atom abstraction (kadd/kHAT > 20 for internal alkenes).