School of Chemistry - Research Publications
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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 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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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.
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ItemReaction of Amino Acids, Di- and Tripeptides with the Environmental Oxidant NO3•: A Laser Flash Photolysis and Computational Study(WILEY-V C H VERLAG GMBH, 2016-11-22)Absolute rate coefficients for the reaction between the important environmental free radical oxidant NO3. 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 1.8×106 m-1 s-1 per abstractable hydrogen atom. The considerably faster reaction with phenylalanine [k=(1.1±0.1)×107 m-1 s-1 ] is indicative for a mechanism involving electron transfer. An unprecedented amplification of the rate coefficient by a factor of 7-20 was found with di- and tripeptides that contain more than one phenylalanine residue. This suggests a synergistic effect between two aromatic rings in close vicinity, which makes such peptide sequences highly vulnerable to oxidative damage by this major environmental pollutant.
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ItemAmide Neighbouring-Group Effects in Peptides: Phenylalanine as Relay Amino Acid in Long-Distance Electron Transfer(WILEY-V C H VERLAG GMBH, 2018-05-04)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. The considerably increased susceptibility of the aromatic ring to oxidation is caused by the lone pairs of neighbouring amide carbonyl groups, which stabilise the Phe radical cation. This neighbouring-amide-group effect helps improve understanding of the mechanism of extracellular electron transfer through conductive protein filaments (pili) of anaerobic bacteria during mineral respiration.
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ItemOxidative Repair of Pyrimidine Cyclobutane Dimers by Nitrate Radicals (NO3•): A Kinetic and Computational Study(MDPI, 2020-06)Pyrimidine cyclobutane dimers are hazardous DNA lesions formed upon exposure of DNA to UV light, which can be repaired through oxidative electron transfer (ET). Laser flash photolysis and computational studies were performed to explore the role of configuration and constitution at the cyclobutane ring on the oxidative repair process, using the nitrate radical (NO3•) as oxidant. The rate coefficients of 8–280 × 107 M−1 s−1 in acetonitrile revealed a very high reactivity of the cyclobutane dimers of N,N’-dimethylated uracil (DMU), thymine (DMT), and 6-methyluracil (DMU6-Me) towards NO3•, which likely proceeds via ET at N(1) as a major pathway. The overall rate of NO3• consumption was determined by (i) the redox potential, which was lower for the syn- than for the anti-configured dimers, and (ii) the accessibility of the reaction site for NO3•. In the trans dimers, both N(1) atoms could be approached from above and below the molecular plane, whereas in the cis dimers, only the convex side was readily accessible for NO3•. The higher reactivity of the DMT dimers compared with isomeric DMU dimers was due to the electron-donating methyl groups on the cyclobutane ring, which increased their susceptibility to oxidation. On the other hand, the approach of NO3• to the dimers of DMU6-Me was hindered by the methyl substituents adjacent to N(1), making these dimers the least reactive in this series.
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ItemReaction of Distonic Aryl and Alkyl Radical Cations with Amines: The Role of Charge and Spin Revealed by Mass Spectrometry, Kinetic Studies, and DFT Calculations(Wiley, 2020-01-01)Gas‐phase reaction of the aromatic distonic radical cations 4‐Pyr+. and 3‐Pyr+. with amines led to formation of the corresponding amino pyridinium ions 4‐Pyr+NR2 and 3‐Pyr+NR2 through amine addition at the site of the radical, followed by homolytic β‐fragmentation. The reaction efficiencies range from 66–100 % for 4‐Pyr+. and 57–86 % for 3‐Pyr+., respectively, indicating practically collision‐controlled processes in some cases. Computational studies revealed that the combination of positive charge and spin makes nucleophilic attack by the amine at the site of the radical barrierless and strongly exothermic by about 175±15 kJ mol−1, thereby rendering ‘conventional’ radical pathways through hydrogen abstraction or addition onto π systems less important. Exemplary studies with 4‐Pyr+. showed that this reaction can be reproduced in solution. A similar addition/radical fragmentation sequence occurs also in the gas‐phase reaction of amines with the aliphatic distonic radical cation Oxo+C., showing that the observed charge‐spin synergism is not limited to aromatic systems.