ORCID Profile
0000-0003-1756-5449
Current Organisation
University of Melbourne
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Organic Chemistry | Organic Chemical Synthesis | Physical Organic Chemistry | Organic Chemical Synthesis | Mechanisms Of Reactions | Physical Chemistry (Incl. Structural) | Biological And Medical Chemistry | Free Radical Chemistry | Synthesis of Materials | Membrane and Separation Technologies | Physical Organic Chemistry | Macromolecular and Materials Chemistry | Soil Biology | Natural Products Chemistry | Structural Chemistry | Colloid And Surface Chemistry | Polymerisation Mechanisms | Analytical Spectrometry | Characterisation Of Macromolecules | Chemical Characterisation of Materials | Organic chemistry | Sociology and Social Studies of Science and Technology | Organometallic Chemistry | Other Chemical Sciences | Organic Chemistry Not Elsewhere Classified | Analytical Chemistry | Analytical Spectrometry | Separation Science | Physical organic chemistry | Bioinorganic Chemistry | Flow Analysis | Structural Chemistry and Spectroscopy | Industrial Chemistry | Analytical Chemistry not elsewhere classified | Plant Physiology | Theoretical And Computational Chemistry Not Elsewhere Classified | Plant cell and molecular biology | Analytical Biochemistry |
Chemical sciences | Expanding Knowledge in the Chemical Sciences | Chemical Fertilisers | Treatments (e.g. chemicals, antibiotics) | Farmland, Arable Cropland and Permanent Cropland Soils | Human Pharmaceutical Treatments (e.g. Antibiotics) | Agricultural and Environmental Standards | Management of Solid Waste from Energy Activities | Organic Industrial Chemicals (excl. Resins, Rubber and Plastics) | Prevention and treatment of pollution | Environmentally Sustainable Plant Production not elsewhere classified | Synthetic resins and rubber | Plastics in primary forms | Other | Workforce Transition and Employment | Sheet metal products | Atmospheric processes | Management of Greenhouse Gas Emissions from Plant Production | Plastic Products (incl. Construction Materials) | Polymeric materials (e.g. paints) | Environmental health | Expanding Knowledge in the Physical Sciences | Expanding Knowledge in the Biological Sciences | Food Safety
Publisher: AIP Publishing
Date: 25-04-2014
DOI: 10.1063/1.4871883
Abstract: The photophysical behaviour of the isolated retinal protonated n-butylamine Schiff base (RPSB) is investigated in the gas phase using a combination of ion mobility spectrometry and laser spectroscopy. The RPSB cations are introduced by electrospray ionisation into an ion mobility mass spectrometer where they are exposed to tunable laser radiation in the region of the S1 ← S0 transition (420–680 nm range). Four peaks are observed in the arrival time distribution of the RPSB ions. On the basis of predicted collision cross sections with nitrogen gas, the dominant peak is assigned to the all-trans isomer, whereas the subsidiary peaks are assigned to various single, double and triple cis geometric isomers. RPSB ions that absorb laser radiation undergo photoisomerization, leading to a detectable change in their drift speed. By monitoring the photoisomer signal as a function of laser wavelength an action spectrum, extending from 480 to 660 nm with a clear peak at 615 ± 5 nm, is obtained. The photoisomerization action spectrum is related to the absorption spectrum of isolated retinal RPSB molecules and should help benchmark future electronic structure calculations.
Publisher: Elsevier
Date: 2014
Publisher: Wiley
Date: 16-07-2010
Abstract: The performance of thiyl radicals RS · in “self‐terminating radical cyclisations” was explored. Using the medium‐sized cyclodecyne ( 1 ) as model system, the reaction of PhS · generated by photolysis of (PhS) 2 was used to study the intermolecular S ‐radical addition and subsequent intramolecular radical translocations. This reaction resulted in the formation of three stereoisomeric sulfides 17a in very good yield, which all possess the bicyclo[4.4.0]decane framework with either cis and trans ring fusion. The isomeric bicyclo[5.3.0]decane framework was not formed. Product identification was performed using a combination of techniques, e.g. synthesis of authentic s les, X‐ray analysis and computational studies of the potential energy surface, which also revealed valuable insight into the mechanism of this radical cyclisation cascade. The (PhS) 2 /PhS · system provides an efficient source for in situ generated thiols, which mediate reduction of the α‐thio radical, e.g., 13a → 17a . The radical cascade initiated by the addition of BnS · , t BuS · or AllylS · , respectively, to cycloalkyne 1 was typically terminated also by reduction, even in the absence of an apparent H‐donor, and resulted in formation of various bicyclic and monocyclic thioethers. The desired “self‐termination”, e.g., β‐fragmentation of the S–R bond in radical intermediate 12 / 13 and release of a stabilized radical R · , was only observed as minor reaction pathway in one particular instance where t BuS · was generated by autoxidation of t BuSH. Computional studies showed that the differentstereochemical outcome of the radical cyclizations involving S ‐radicals, compared to O ‐ or N ‐centred radicals, could be attributed to the reversibility of the initial intermolecular S ‐radical addition to the C≡C triple bond in cycloalkyne 1 .
Publisher: American Chemical Society (ACS)
Date: 27-08-2021
Publisher: Royal Society of Chemistry (RSC)
Date: 2023
DOI: 10.1039/D2OB02302D
Abstract: Kinetic studies revealed a moderate reactivity of a model lipid peroxyl radical towards a series of amino acids, suggesting that such radicals could damage remote cellular locations that are inaccessible for highly reactive radicals.
Publisher: American Chemical Society (ACS)
Date: 04-09-2014
DOI: 10.1021/JZ501407N
Abstract: 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. Density functional theory calculations at the M06-2X/cc-pVDZ level support a fragmentation mechanism in which RPSB undergoes an electrocyclization/fragmentation cascade with the production of protonated Schiff base of β-ionone and toluene.
Publisher: American Chemical Society (ACS)
Date: 14-04-2001
DOI: 10.1021/OL0157252
Abstract: [reaction: see text] Photochemically generated nitrate radicals (NO(3)(*)) cleave the stereoisomeric N,N-dimethyl-substituted uracil cyclobutane dimers 1a-d into the monomeric uracil derivative 2 as the major reaction pathway. A preferred splitting of the syn dimers 1a,b was observed. The reaction is expected to proceed through initial one-electron oxidation with formation of an intermediate cyclobutane radical cation 11. In addition to cycloreversion, competing reaction steps of 11, which lead to the observed byproducts, are suggested.
Publisher: No publisher found
Date: 2011
DOI: 10.1071/CH11102
Publisher: CSIRO Publishing
Date: 2007
DOI: 10.1071/CH07045
Abstract: Addition of electro- and photochemically generated nitrate radicals, NO3•, to the C≡C triple bond of aromatic alkynes 9a–9h leads to formation of 1,2-diketones 10a–10h. Surprisingly, benzophenones 11a–11h are obtained as by-products, which formally result from loss of a carbon atom. Density functional studies performed with the BHandHLYP method in combination with various basis sets revealed that 1,2-diketones result from 5-endo cyclization of the initially formed vinyl radical and loss of NO•. The key step to benzophenone formation is a γ-cleavage at the stage of the vinyl radical with release of NO2•, followed by Wolff rearrangement of the resulting α-oxo carbene.
Publisher: Elsevier BV
Date: 08-1999
Publisher: American Chemical Society (ACS)
Date: 08-12-2001
DOI: 10.1021/JA017006O
Abstract: Acyloxyl radicals RC(O)O* (with R = alkyl, aryl) could be trapped through addition to cyclic and open-chain alkynes, where they were found to act as a donor of oxygen atoms. Mechanistically, this radical oxygenation proceeded through a transannular or intramolecular, respectively, radical cyclization cascade, which was finally terminated by release of an acyl radical RC*(O). The reaction led to stereoselective formation of cyclized products, which contained a carbonyl group at the former site of the alkyne triple bond.
Publisher: Elsevier BV
Date: 10-2013
Publisher: Royal Society of Chemistry (RSC)
Date: 2019
DOI: 10.1039/C9OB01363F
Abstract: α-Cyclopropyl- N -acyliminium ions towards reaction with indoles to give 5-(3-indoyl)-5-cyclopropylpyrrolidin-2-ones and, in the case of highly electron deficient indoles and electron rich arenes, spiroheterocycles.
Publisher: Royal Society of Chemistry (RSC)
Date: 2008
DOI: 10.1039/B815358B
Abstract: Thiylperoxyl radicals are the suggested reactive key-intermediates in the oxidation of bis-aromatic alkynes to alpha-diketones using molecular oxygen "activated" by thiyl radicals.
Publisher: American Chemical Society (ACS)
Date: 20-04-2007
DOI: 10.1021/AR600015V
Abstract: Free-radical chemistry has come a long way in a relatively short period of time. The synthetic practitioner takes for granted the wealth of mechanistic and rate constant data now available and can apply free-radical techniques to the synthesis of many different classes of target molecule with confidence. Despite this, there are still mechanistic anomalies that need to be addressed. This Account highlights recent work involving nucleophilic radicals with low-lying unoccupied orbitals, such as acyl, oxyacyl, silyl, stannyl, and germyl radicals. Through interesting singly occupied molecular orbital (SOMO)-pi* and highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) interactions during these reactions, the radicals involved are able to mask as electrophiles, providing high levels of regiocontrol and efficient methods for the synthesis of important heterocycles.
Publisher: American Chemical Society (ACS)
Date: 26-01-2006
DOI: 10.1021/JP0454772
Abstract: The geometry of the nitrate radical, NO3*, for which unrestricted Hartree-Fock (HF) breaks spatial symmetry of the wave function, was optimized using hybrid density functionals that include varying fractions of Hartree-Fock exchange. Although symmetry breaking was not observed even when the functional with the highest HF exchange (BHandHLYP) was used, only B3LYP correctly describes the D(3h) symmetry of NO3* as ground-state structure with the lowest energy. Further, geometries and energies of the stationary points in the addition of NO3* to ethyne, propyne, and 2-butyne were calculated using ab initio and density functional methods. The reactions proceed through Z-configurated transition states leading to Z-configurated vinyl radicals with the activation barrier decreasing with increasing methyl substitution at the C[triple bond]C by ca. 11 kJ mol(-1) per methyl group. It was found that the results obtained at the BHandHLYP/cc-pVDZ level of theory are in good agreement with the data from single-point QCISD and CCSD(T) calculations.
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D0OB02075C
Abstract: 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.
Publisher: CSIRO Publishing
Date: 2004
DOI: 10.1071/CH04124
Abstract: Anellated pyrrolidines 19–22 were obtained through a diastereoselective self-terminating, oxidative radical cyclization cascade by treating the cis-cyclopentyl substituted alkynyl amines 14–18 with photochemically generated nitrate radicals, NO3●. A fast and modular access to the starting materials 14–18 was developed, which readily enables variation of the substitution pattern at the pyrrolidine ring formed upon radical cyclization. The diastereoselectivity of this reaction sequence was found to be strongly influenced by the nature of the substituents at the nitrogen atom. This shows that a complex interplay of both steric and stereoelectronic effects orchestrates the stereoselectivity of 5-exo radical cyclizations of highly substituted radicals.
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5CC01580D
Abstract: Highly oxidizing nitrate radicals (NO 3 ˙) 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.
Publisher: Elsevier BV
Date: 06-2007
Publisher: MDPI AG
Date: 13-06-2023
Abstract: 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.
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C0OB01186J
Abstract: Analysis of the products formed in the reaction of NO(3)˙ with the N- and C-protected aromatic amino acids 1-5, which was performed under conditions that simulate exposure of biosurfaces to environmental pollutants, revealed insight how this important atmospheric free-radical oxidant can cause irreversible damage. In general, NO(3)˙ induced electron transfer at the aromatic ring is the exclusive initial pathway in a multi-step sequence, which ultimately leads to nitroaromatic compounds. In the reaction of NO(3)˙ with tryptophan 5 tricyclic products 12 and 13 are formed through an intramolecular, oxidative cyclization involving the amide moiety. In addition to this, strong indication for formation of N-nitrosamides was obtained, which likely result from reaction with N(2)O(4) through an independent non-radical pathway.
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C1OC90007B
Publisher: Elsevier BV
Date: 08-2022
Publisher: Royal Society of Chemistry (RSC)
Date: 2006
DOI: 10.1039/B515330A
Abstract: Molecular orbital calculations reveal that acyl and silyl radicals add to numerous types of pi-systems through simultaneous SOMO-LUMO and LUMO-HOMO interactions of the radical with the radicalophile respectively.
Publisher: Elsevier BV
Date: 1995
DOI: 10.1016/0024-3205(95)00010-4
Abstract: The affinity of morphine, codeine, dihydrocodeine and their glucuronides for mu-, delta-, and kappa-opioid receptors was investigated. Binding was studied on guinea-pig brain homogenates with [3H]DAMGO, [3H]DPDPE, and [3H]U69593. The substitution of the free phenolic group of morphine caused a decrease in binding at opioid receptors without affecting the mu/delta-ratio nor that of mu/kappa. Glucuronidation of the 6-hydroxyl group of morphine, codeine or dihydrocodeine did not affect the affinity to mu-receptors, slightly increased the affinity for delta-receptors and reduced the affinity for kappa-receptors. The 6-glucuronides possess a decreased selectivity for mu-receptors over delta-receptors whereas that for mu- over kappa-receptors was increased. It is concluded that chemical variations at 3- and 6-position of morphine independently affect the affinity to opioid receptor subtypes.
Publisher: American Chemical Society (ACS)
Date: 30-05-2014
DOI: 10.1021/ES500319Q
Abstract: Enols are emerging as trace atmospheric components that may play a significant role in the formation of organic acids in the atmosphere. We have investigated the hydroxyl radical ((•)OH) initiated oxidation chemistry of the simplest enol, vinyl alcohol (ethenol, CH2═CHOH), using quantum chemical calculations and energy-grained master equation simulations. A lifetime of around 4 h was determined for vinyl alcohol in the presence of tropospheric levels of (•)OH. The reaction proceeds by (•)OH addition at both the α (66%) and β (33%) carbons of the π-system, yielding the C-centered radicals (•)CH2CH(OH)2, and HOCH2C(•)HOH, respectively. Subsequent trapping by O2 leads to the respective peroxyl radicals. About 90% of the chemically activated population of the major peroxyl radical adduct (•)O2CH2CH(OH)2 is predicted to undergo fragmentation to produce formic acid and formaldehyde, with regeneration of (•)OH. The minor peroxyl radical HOCH2C(OO(•))HOH is even less stable and undergoes almost exclusive HO2(•) elimination to form glycolaldehyde (HOCH2CHO). Formation of the latter has not been proposed before in the oxidation of vinyl alcohol. A kinetic mechanism for use in atmospheric modeling is provided, featuring phenomenological rate coefficients for formation of the three main product channels ((•)O2CH2CH(OH)2 [8%] HC(O)OH + HCHO + (•)OH [56%] HOCH2CHO + HO2(•) [37%]). Our study supports previous findings that vinyl alcohol should be rapidly removed from the atmosphere by reaction with (•)OH and O2 with glycolaldehyde being identified as a previously unconsidered product. Most importantly, it is shown that direct chemically activated reactions can lead to (•)OH and HO2(•) (HOx) recycling.
Publisher: American Chemical Society (ACS)
Date: 03-10-2023
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/D0OB01337D
Abstract: Kinetic studies in acetonitrile revealed that proline residues in peptides are considerably protected against radical-induced oxidative damage by the neighbouring peptide bonds, compared with the single amino acid.
Publisher: American Chemical Society (ACS)
Date: 08-02-2016
Abstract: 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. In contrast, the corresponding pyrrolo[1,2-a]azepine system did not provide the corresponding tricyclic bridged heterocyclic product and gave only a bis-allyl adduct, while more substituted versions gave novel furo[3,2-d]pyrrolo[1,2-a]azepine products. Such heterocyclic systems would be expected to be useful scaffolds for the preparation of libraries of novel compounds for new drug discovery programs.
Publisher: No publisher found
Date: 2008
DOI: 10.1021/JO702261U
Abstract: Intermolecular addition of photochemically generated N-centered aminium and amidyl radicals 13a-d and 16a,b, respectively, to the cyclic alkyne 1 initiates a radical translocation/cyclization cascade, followed by an oxidative termination step that eventually leads to formation of the bicyclic ketones 7a and 8a. Computational studies were performed to gain insight into the mechanism of these reactions, which are an interesting modification of the recently discovered concept of self-terminating radical cyclizations.
Publisher: Royal Society of Chemistry (RSC)
Date: 2020
DOI: 10.1039/C9CP05989J
Abstract: Deprotonation of a remote site in a peroxyl radical energetically buries the singly occupied molecular orbital, suppressing radical-driven oxidation and promoting reactions involving the anion site.
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C4CP02981J
Abstract: The study of unimolecular isomerization and decomposition of a charge-tagged β-hydroxyperoxyl radical anion ˙CH 2 C(OH)(CH 3 )CH 2 C(O)O − using mass spectrometry, quantum mechanical calculations and master equation kinetic simulations.
Publisher: American Chemical Society (ACS)
Date: 11-09-2015
Abstract: 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. This barrier lies below the energy of the UV/vis absorption band of glycolaldehyde and is also considerably below the energy of the products resulting from photolytic decomposition. The subsequent atmospheric oxidation of 1,2-ethenediol by (•)OH is initiated by addition of the radical to the π system to give the (•)CH(OH)CH(OH)2 radical, which is subsequently trapped by O2 to form the peroxyl radical (•)O2CH(OH)CH(OH)2. According to kinetic simulations, collisional deactivation of the latter is negligible and cannot compete with rapid fragmentation reactions, which lead to (i) formation of glyoxal hydrate [CH(OH)2CHO] and HO2(•) through an α-hydroxyl mechanism (96%) and (ii) two molecules of formic acid with release of (•)OH through a β-hydroxyl pathway (4%). Phenomenological rate coefficients for these two reaction channels were obtained for use in atmospheric chemical modeling. At tropospheric (•)OH concentrations, the lifetime of 1,2-ethenediol toward reaction with (•)OH is calculated to be 68 h.
Publisher: Wiley
Date: 11-11-2010
DOI: 10.1002/POC.1808
Publisher: American Chemical Society (ACS)
Date: 02-11-2012
DOI: 10.1021/CR100359D
Publisher: American Chemical Society (ACS)
Date: 11-02-2019
Abstract: Kinetic and computational data reveal a complex behavior of the important environmental free radical oxidant NO
Publisher: Wiley
Date: 20-01-2009
Publisher: Beilstein Institut
Date: 20-09-2013
DOI: 10.3762/BJOC.9.225
Abstract: Manufactured polymer materials are used in increasingly demanding applications, but their lifetime is strongly influenced by environmental conditions. In particular, weathering and ageing leads to dramatic changes in the properties of the polymers, which results in decreased service life and limited usage. Despite the heavy reliance of our society on polymers, the mechanism of their degradation upon exposure to environmental oxidants is barely understood. In this work, model systems of important structural motifs in commercial high-performing polyesters were used to study the reaction with the night-time free radical oxidant NO 3 • in the absence and presence of other radical and non-radical oxidants. Identification of the products revealed ‘hot spots’ in polyesters that are particularly vulnerable to attack by NO 3 • and insight into the mechanism of oxidative damage by this environmentally important radical. It is suggested that both intermediates as well as products of these reactions are potentially capable of promoting further degradation processes in polyesters under environmental conditions.
Publisher: Wiley
Date: 10-2006
Publisher: Wiley
Date: 11-10-2016
Abstract: Absolute rate coefficients for the reaction between the important environmental free radical oxidant NO
Publisher: Wiley
Date: 15-02-2010
Abstract: Electrons with virtually no kinetic energy (close to 0 eV) trigger the decomposition of cytotoxic cyclobutane-pyrimidine dimer (CPD) into a surprisingly large variety of fragment ions plus their neutral counterparts. The response of CPD to low energy electrons is thus comparable to that of explosives like trinitrotoluene (TNT). The dominant unimolecular reaction is the splitting into two thymine like units, which can be considered as the essential molecular step in the photolyase of CPD. We find that CPD is significantly more sensitive towards low energy electrons than its thymine building blocks. It is proposed that electron attachment at very low energy proceeds via dipole bound states, supported by the large dipole moment of the molecule (6.2 D). These states act as effective doorways to dissociative electron attachment (DEA).
Publisher: The Chemical Society of Japan
Date: 02-2007
DOI: 10.1246/CL.2007.300
Publisher: American Chemical Society (ACS)
Date: 13-06-2018
Publisher: Wiley
Date: 09-2015
Abstract: 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. The relative rate of the fragmentation-rearrangement depends on the nature of the amino acids and decreases with increasing steric bulk at the α carbon in the order Gly>Ala>Val. Peptides that possessed consecutive aromatic side chains only gave products that resulted from nitrosation of the sterically less congested N-terminal amide. Such backbone fragmentation-rearrangement occurs under physiologically relevant conditions and could be an important reaction pathway for peptides, in which sections without readily oxidizable side chains are exposed to the air pollutant NO2 (.) . In addition to NO2 (.) -induced radical oxidation processes, this outcome shows that ionic reaction pathways, in particular nitrosation, should be factored in when assessing NO2 (.) reactivity in biological systems.
Publisher: Royal Society of Chemistry (RSC)
Date: 2008
DOI: 10.1039/B803456G
Abstract: Reaction of nitrate radicals, NO*3 , with aromatic amino acids leads to irreversible oxidative functionalization at the beta-position or at the aromatic ring, suggesting that this important atmospheric oxidant could potentially cause damage to peptides lining the respiratory tract and may contribute to pollution-derived diseases.
Publisher: Wiley
Date: 27-01-2016
Abstract: 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). The proposed mechanism clearly emphasises the requirement of two equivalents of Ag(I) and basic reaction conditions, which is in full agreement with the experimental findings. Alternative rearrangement pathways involving only one equivalent of Ag(I) or through O-sp(3) N 1,3-acyl migration can be excluded. The computations further revealed that peptide couplings involving thioformamides require significant conformational changes in the intermediate isoformimide, which slow down the rearrangement process.
Publisher: Wiley
Date: 22-12-2020
Publisher: CSIRO Publishing
Date: 2012
DOI: 10.1071/CH11446
Abstract: Analysis of the products formed in the reaction of the environmental free radical oxidant NO3• with permethylated uridine 1 and thymidine 2 in solution revealed highly complex reaction pathways following initial NO3• induced oxidative electron transfer at the pyrimidine ring. Product formation was found to depend not only on the nature of the nucleobase, but also on the presence of other free radical oxidants, namely NO2•. In the reaction of 1 with NO3•, which was generated through CAN photolysis, apart from formation of the highly oxidized nucleoside derivative 4 as the major product, cleavage of the C–N glycosidic bond did also occur, resulting in formation of ribolactone 5 and the free nucleobase 6. The suggested mechanism involves in situ generation of NO2• during the course of the reaction, which promotes conversion of the initially formed radical cation 7 to 4 in an autocatalytic fashion.When the reaction of NO2• with O3 was used to generate NO3•, the initially formed radical cation 7 in the reaction with permethylated uridine 1 is rapidly trapped by NO2• to give 5-nitrouridine 18 in a radical mediated vinylic substitution reaction. In contrast to this, under similar conditions in the reaction involving thymidine 2 the highly oxidized products 20 and 21 are obtained as major compounds, which result from addition to the C5–C6 double bond. No direct reaction between NO3• and the carbohydrate moiety in 1 and 2 was found. Also, no reaction occurred between the nucleosides and mixtures of NO2•/N2O4 and O3/O2, respectively.
Publisher: Royal Society of Chemistry (RSC)
Date: 2016
DOI: 10.1039/C5CC09663D
Abstract: Exposure of O -protected and free cholesterol to NO 2 ˙ leads to oxidation of the alkene moiety through non-radical pathways, demonstrating that ionic processes must be considered when assessing NO 2 ˙ toxicity.
Publisher: MDPI AG
Date: 09-05-2020
Abstract: 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.
Publisher: Wiley
Date: 2020
Publisher: American Chemical Society (ACS)
Date: 25-06-2008
DOI: 10.1021/JO800750A
Abstract: BHandHLYP/6-311G** and BHandHLYP/DZP computations of the potential surface of Si-, Ge-, and Sn-radical cyclizations onto the imine double bond reveal that these reactions proceed through simultaneous SOMO --> pi*, LP(N) --> SOMO, and LP(N) --> sigma* interactions. Such multicomponent orbital interactions are responsible for the regioselectivity in these radical cyclizations, where the nucleophilic radical unexpectedly attacks the more electron-rich end of the pi system. Less nucleophilic heteroatoms, for ex le, the nitrogen atom in nitriles or the oxygen atom in carbonyl compounds, show reduced LP interactions with the radical center in the respective transition states, so that these reactions predominantly occur in the "classical" fashion and with the expected regioselectivities of nucleophilic radicals through SOMO --> pi* interactions. This supports the hypothesis that Si-, Ge- and, to a lesser extent, Sn-radicals are ambiphilic in nature and that the unpaired electron is not necessarily the most reactive site in a radical but can act as an observer of a nucleophilic attack at the radical center.
Publisher: Royal Society of Chemistry (RSC)
Date: 1991
DOI: 10.1039/FT9918702141
Publisher: American Chemical Society (ACS)
Date: 20-04-2012
DOI: 10.1021/OL300831T
Abstract: The first total synthesis of mycocyclosin, a diketopiperazine natural product isolated from M. tuberculosis, is described. While direct oxidative coupling of tyrosine phenolic groups was unsuccessful, construction of the highly strained bicyclic framework was successfully accomplished through an intramolecular Miyaura-Suzuki cross-coupling to generate the biaryl linkage.
Publisher: American Chemical Society (ACS)
Date: 02-11-2015
DOI: 10.1021/ACS.CHEMRESTOX.5B00373
Abstract: 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. Numerous studies have identified that excess NAPQI can form covalent linkages to the thiol side chains of cysteine residues in proteins however, the reactivity of NAPQI toward other amino acid side chains is largely unexplored. Here, we report a survey of the reactivity of NAPQI toward 11 N-acetyl amino acid methyl esters and four peptides. (1)H NMR analysis reveals that NAPQI forms covalent bonds to the side-chain functional groups of cysteine, methionine, tyrosine, and tryptophan residues. Analogous reaction products were observed when NAPQI was reacted with synthetic model peptides GAIL-X-GAILR for X = Cys, Met, Tyr, and Trp. Tandem mass spectrometry peptide sequencing showed that the NAPQI modification sites are located on the "X" residue in each case. However, when APAP and the GAIL-X-GAILR peptide were incubated with rat liver microsomes that contain many metabolic enzymes, NAPQI formed by oxidative metabolism reacted with GAIL-C-GAILR exclusively. For the peptides where X = Met, Tyr, and Trp, competing reactions between NAPQI and alternative nucleophiles precluded arylation of the target peptide by NAPQI. Although Cys residues are favorably targeted under these conditions, these data suggest that NAPQI can, in principle, also damage proteins at Met, Tyr, and Trp residues.
Publisher: American Chemical Society (ACS)
Date: 29-04-2006
DOI: 10.1021/JO0520543
Abstract: The 1,2-nitroxyl and 1,2-acetoxyl rearrangement in beta-(nitroxy)vinyl and beta-(acetoxy)vinyl radicals 13a and 13b, respectively, has been studied for the gas phase with various ab initio and density functional methods. The energetically most favorable pathway for 13a is calculated to proceed via reversible fragmentation/radical addition through transition state I-19a. In the case of 13b, rearrangement through a five-membered ring transition state III-16b and the fragmentation/radical addition pathway via transition state I-19b are competing processes. Mulliken and natural population analysis reveal a certain degree of charge separation in III-16a/b that may indicate a potential solvent effect on the rearrangement rate. A stepwise group migration through a cyclic radical intermediate V-18a/b or rearrangement through a three-membered ring transition state II-15a/b can be ruled out for both vinyl radicals. A comparison of the results of the calculations with experimental findings provides important insights into the kinetics of "self-terminating radical oxygenations". A significant method dependence on the outcome of the calculations was observed, which revealed the unsuitability of the UHF, MP2, B3LYP, and mPW1PW91 methods for computing these radical rearrangement processes. The results from BHandHLYP/cc-pVDZ calculations showed the best agreement with single-point energy calculations performed at the QCISD and CCSD(T) levels of theory.
Publisher: American Chemical Society (ACS)
Date: 03-05-2018
DOI: 10.1021/ACS.JPCLETT.8B01201
Abstract: 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
Publisher: Wiley
Date: 12-05-2021
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 (NO 3 . ) with rate coefficients of 7.7×10 9 , 3.4×10 9 and 2.0×10 9 M −1 s −1 , respectively, in acetonitrile. Methionine (Ac−Met−OMe) is successively oxidized via the sulfoxide (Ac−MetO−Me) to the sulfone (Ac−MetO 2 −OMe), with the latter step being also extremely fast with a rate coefficient of 1.2×10 9 M −1 s −1 . Computations predict formation of an initial charge transfer complex between NO 3 . 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 NO 2 . expulsion. Calculations for the reaction of cysteine (Ac‐Cys‐OMe) with NO 3 . revealed side‐chain oxidation to give a thiyl radical or a sulfenic acid as likely pathways. These findings highlight the potential harmful impact of NO 2 . /O 3 pollution on S‐containing amino acid residues in peptides.
Publisher: Wiley
Date: 16-05-2023
Abstract: Kinetic studies revealed that nitrate radicals (NO 3 ⋅), which are formed through reaction of the noxious air pollutants nitrogen dioxide (NO 2 ⋅) and ozone (O 3 ), very rapidly oxidize phenylalanine residues in an aqueous environment, with overall rate coefficients in the 10 8 –10 9 M −1 s −1 range. With amino acids and dipeptides as model systems, the data suggest that the reaction proceeds via a π‐complex between NO 3 ⋅ 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. Computations revealed that the considerably more rapid radical‐induced oxidation of Phe residues in both neutral and acidic aqueous environments, compared to acetonitrile, can be attributed to stabilization of the CT complex by the protic solvent this clearly highlights the health‐damaging potential of exposure to combined NO 2 ⋅ and O 3 .
Publisher: Elsevier BV
Date: 09-1999
Publisher: Royal Society of Chemistry (RSC)
Date: 02-09-2014
DOI: 10.1039/C4OB01577K
Abstract: Irreversible oxidative damage at both aromatic side chains and dipeptide linkage occurs in the aromatic N- and C-protected dipeptides 7-11 upon exposure to the environmental pollutants NO2˙ and O3. The reaction proceeds through initial oxidation of the aromatic ring by in situ generated NO3˙, or by NO2˙, respectively, which leads to formation of nitroaromatic products. The indole ring in Phe-Trp undergoes oxidative cyclization to a pyrroloindoline. An important reaction pathway for dipeptides with less oxidisable aromatic side chains proceeds through fragmentation of the peptide bond with concomitant acyl migration. This process is likely initiated by an ionic reaction of the amide nitrogen with the NO2˙ dimer, N2O4.
Publisher: Wiley
Date: 14-04-2018
Abstract: 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.
Publisher: Elsevier BV
Date: 02-2002
Publisher: American Chemical Society (ACS)
Date: 25-01-2023
Publisher: Wiley
Date: 19-09-2019
DOI: 10.1002/POC.3896
Publisher: American Chemical Society (ACS)
Date: 06-07-2017
Abstract: A novel precursor to the distonic O- and C-centered radical cations Oxo
Publisher: American Chemical Society (ACS)
Date: 20-02-2023
Publisher: Royal Society of Chemistry (RSC)
Date: 2012
DOI: 10.1039/C2OC90015G
Publisher: Georg Thieme Verlag KG
Date: 2005
Publisher: Springer Science and Business Media LLC
Date: 08-1991
DOI: 10.1007/BF00115972
Publisher: Royal Society of Chemistry (RSC)
Date: 2009
DOI: 10.1039/B920282J
Abstract: Crossed-beam experiments revealed that attachment of a free electron to the cyclobutane pyrimidine dimers c,s-DMT<>DMT and c,a-DMT<>DMT leads to the formation of dimer radical anions with the lifetime of at least 80 micros, thus showing that the latter are much more stable than previously believed.
Publisher: Royal Society of Chemistry (RSC)
Date: 2004
DOI: 10.1039/B406923D
Publisher: American Chemical Society (ACS)
Date: 07-06-2022
Abstract: The rate of oxidative damage of aliphatic amino acids and dipeptides by the environmental pollutant nitrate radical (NO
Publisher: Springer Berlin Heidelberg
Date: 2000
DOI: 10.1007/10722280_29
Publisher: Royal Society of Chemistry (RSC)
Date: 2013
DOI: 10.1039/C3CC44784G
Abstract: The synthesis of the first members of a new class of cyclic peptide-containing hemicryptophanes is described. Synthesis was achieved through attachment of veratryl groups to the L-tyrosine side chains of a cyclic hexapeptide, c(YG)3, followed by intramolecular cyclodehydration to generate the CTV unit. The diastereomeric P- and M-hemicryptophanes were generated in a 2 : 1 ratio and were separated by chromatography. The enantioselective binding properties of the hemicryptophanes were investigated by complexation with carnitine. Both isomers were found to have significant selectivity for binding (R)-carnitine.
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