School of Chemistry - Research Publications
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ItemNo Preview AvailableDeciphering the Interactions in the Root-Soil Nexus Caused by Urease and Nitrification Inhibitors: A Review(MDPI, 2023-06)Optimizing nitrogen (N) availability to plants is crucial for achieving maximum crop yield and quality. However, ensuring the appropriate supply of N to crops is challenging due to the various pathways through which N can be lost, such as ammonia (NH3) volatilization, nitrous oxide emissions, denitrification, nitrate (NO3−) leaching, and runoff. Additionally, N can become immobilized by soil minerals when ammonium (NH4+) gets trapped in the interlayers of clay minerals. Although synchronizing N availability with plant uptake could potentially reduce N loss, this approach is hindered by the fact that N loss from crop fields is typically influenced by a combination of management practices (which can be controlled) and weather dynamics, particularly precipitation, temperature fluctuations, and wind (which are beyond our control). In recent years, the use of urease and nitrification inhibitors has emerged as a strategy to temporarily delay the microbiological transformations of N-based fertilizers, thereby synchronizing N availability with plant uptake and mitigating N loss. Urease inhibitors slow down the hydrolysis of urea to NH4+ and reduce nitrogen loss through NH3 volatilization. Nitrification inhibitors temporarily inhibit soil bacteria (Nitrosomonas spp.) that convert NH4+ to nitrite (NO2−), thereby slowing down the first and rate-determining step of the nitrification process and reducing nitrogen loss as NO3− or through denitrification. This review aims to provide a comprehensive understanding of urease and nitrification inhibitor technologies and their profound implications for plants and root nitrogen uptake. It underscores the critical need to develop design principles for inhibitors with enhanced efficiency, highlighting their potential to revolutionize agricultural practices. Furthermore, this review offers valuable insights into future directions for inhibitor usage and emphasizes the essential traits that superior inhibitors should possess, thereby paving the way for innovative advancements in optimizing nitrogen management and ensuring sustainable crop production.
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ItemAssessing the Efficacy, Acute Toxicity, and Binding Modes of the Agricultural Nitrification Inhibitors 3,4-Dimethyl-1H-pyrazole (DMP) and Dicyandiamide (DCD) with Nitrosomonas europaea(American Chemical Society, 2023-01-25)Nitrification inhibitors have been coformulated with nitrogen fertilizers since the 1970s to modulate the microbiological conversion of nitrogen in agricultural soils. 3,4-Dimethyl-1H-pyrazole (DMP) and dicyandiamide (DCD) are currently the most used commercial nitrification inhibitors, but their mode of action is not well understood. This work seeks to fill this void by assessing for the first time in detail their mechanism of inhibition, efficacy, and acute toxicity with pure cell cultures of Nitrosomonas europaea. Bacterial assays based on the quantification of the nitrite (NO2–) production showed that both inhibitors reversibly target ammonia monooxygenase (AMO), which catalyzes the first step of the nitrification process. Michaelis–Menten kinetics suggest that both DMP and DCD act as uncompetitive inhibitors. Real-time measurements of the oxygen (O2) consumption confirmed the nonmechanistic mode of inhibition and showed that DMP reduced the O2 uptake rate by AMO much more at considerably lower concentrations than DCD, in line with the lower inhibitory efficiency of the latter. Acute toxicity tests revealed that DCD has a 10% higher toxicity than DMP when comparing treatments at the same inhibition efficacy (i.e., DMP at 10 ppm, DCD at 100 ppm), indicating that the inhibition of the nitrification process cannot simply be achieved by increasing the inhibitor concentration. The methods presented in this study could assist the development of more reliable nitrification inhibitors in the future.
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ItemNo Preview AvailableDamage of amino acids by aliphatic peroxyl radicals: a kinetic and computational study(ROYAL SOC CHEMISTRY, 2023-03-15)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 × 104 M-1 s-1 was obtained, whereas the reactions with Ac-Trp-OMe and Ac-Met-OMe were slower by a factor of 4 and 6, respectively. For the reaction with Ac-Pro-OMe only an upper value of 103 M-1 s-1 could be determined, suggesting that Pro residues are not effective traps for lipid peroxyl radicals. Density functional theory (DFT) calculations revealed that the reactions proceed via radical hydrogen atom transfer (HAT) from the Cα position, indicating that the rate is determined by the exothermicity of the reaction. In the case of Ac-Tyr-OMe, HAT from the phenolic OH group is the kinetically preferred pathway, which shuts down when hydrogen bonding with an amine occurs. In an alkaline environment, where the phenolic OH group is deprotonated, the reaction is predicted to occur preferably at Cβ, likely through a proton-coupled electron transfer (PCET) mechanism.
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ItemNo Preview AvailableRapid and Inexpensive Assay for Testing the Efficiency of Potential New Synthetic Nitrification Inhibitors(AMER CHEMICAL SOC, 2023-03-20)
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ItemNo Preview AvailableOxidative Damage of Aliphatic Amino Acid Residues by the Environmental Pollutant NO3.: Impact of Water on the Reactivity(AMER CHEMICAL SOC, 2022-06-21)The rate of oxidative damage of aliphatic amino acids and dipeptides by the environmental pollutant nitrate radical (NO3·) 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. This finding can be rationalized by the high reactivity and broad reaction pattern of NO3·. Although hydrogen bonding involving the amide group raises the energies associated with some electron transfer processes, alternative low-energy pathways remain available so that the overall reaction rate is barely affected. The undiminished high reactivity of NO3· toward aliphatic amino acid residues in a neutral aqueous environment highlights the health-damaging potential of exposure to the combined air pollutants nitrogen dioxide (NO2·) and ozone (O3).
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ItemSurface modification of coal tailings by thermal air oxidation for ammonia capture(Elsevier, 2022-08-15)Utilization of coal tailings (CTs) to enable ammonia (NH3) capture is of interest from pollution control and waste management perspectives. In this work, CTs were surface modified by air oxidation at different temperatures and varying duration to increase the uptake of NH3. The CTs treated at 300 and 250 °C for 5 h achieved an NH3 uptake of 52.5 and 45.3 mg g−1, respectively, which was significantly higher than that of the untreated CT (2.1 mg g−1). A linear relationship between NH3 uptake and concentration of acidic surface functional groups was found (R2 = 0.99). Spectroscopic analysis showed that NH3 can be retained on the oxidized CT through chemisorption involving carboxylic groups, leading to the formation of amides. Kinetic studies in the temperature range of 200–300 °C revealed an activation energy of 50.2 kJ mol−1 for the formation of acidic surface functional groups on CTs. These comparably mild conditions for the oxidative surface modification make CTs versatile and readily available materials for reducing agricultural NH3 emissions.
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Item1,2-Addition versus homoconjugate addition reactions of indoles and electron-rich arenes to α-cyclopropyl N-acyliminium ions: synthetic and computational studies(ROYAL SOC CHEMISTRY, 2019-08-07)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.
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ItemOxidative damage of proline residues by nitrate radicals (NO3): a kinetic and product study(ROYAL SOC CHEMISTRY, 2020-09-21)Tertiary amides, such as in N-acylated proline or N-methyl glycine residues, react rapidly with nitrate radicals (NO3˙) with absolute rate coefficients in the range of 4-7 × 108 M-1 s-1 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 NO3˙-induced oxidation of amide bonds proceeds through initial formation of a charge transfer complex. Furthermore, the rate of oxidative damage of proline and N-methyl glycine is significantly influenced by its position in a peptide. Thus, neighbouring peptide bonds, particularly in the N-direction, reduce the electron density at the tertiary amide, which slows down the rate of ET by up to one order of magnitude. The results from these model studies suggest that the susceptibility of proline residues in peptides to radical-induced oxidative damage should be considerably reduced, compared with the single amino acid.
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ItemOxidative Damage of S-Containing Amino Acids by the Environmental Radical NO3.: A Kinetic, Product and Computational Study(WILEY-V C H VERLAG GMBH, 2021-05-14)Abstract Methionine, cysteine and cystine, which were acetylated at the N‐terminus and methylated at the C‐terminus, react rapidly with the environmental nitrate radical (NO3.) with rate coefficients of 7.7×109, 3.4×109 and 2.0×109 M−1 s−1, respectively, in acetonitrile. Methionine (Ac−Met−OMe) is successively oxidized via the sulfoxide (Ac−MetO−Me) to the sulfone (Ac−MetO2−OMe), with the latter step being also extremely fast with a rate coefficient of 1.2×109 M−1 s−1. Computations predict formation of an initial charge transfer complex between NO3. and the S or SO moiety in Ac‐Met‐OMe, Ac‐MetO‐OMe and cystine (Ac−Cys(S−S)Cys‐OMe), respectively, which is followed by simultaneous S−O bond formation and NO2. expulsion. Calculations for the reaction of cysteine (Ac‐Cys‐OMe) with NO3. revealed side‐chain oxidation to give a thiyl radical or a sulfenic acid as likely pathways. These findings highlight the potential harmful impact of NO2./O3 pollution on S‐containing amino acid residues in peptides.