Theoretical Studies of Radical Reactions for Selected Biological and Atmospheric Related Chemical Systems: 1. Peptide Radical Cations, 2. Carbonate Radical Anion and 3. Hydrated Electron

生物體及大氣化學系統特定自由基反應的理論研究。1. 多肽自由基陽離子 2. 碳酸自由基陰離子3.水合電子

Student thesis: Doctoral Thesis

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Award date3 Aug 2017

Abstract

Mechanisms of unimolecular dissociations and ion-molecule reactions of some gas-phase radical peptides and atmospheric species were studied by means of molecular orbitals and molecular dynamics simulations performed using quantum chemistry packages, including Gaussian 09 and CP2K. Unravelling the mechanistic basis of electron transfers of radical peptides and atmospheric molecules is able to improve our understanding toward the factors governing radical migrations during various molecular transformations as well as the fate of the radical species. This thesis had focused on four chemical systems: 1) Selective backbone cleavages of β-radical peptides; 2) Radical recombination of NO2● with tyrosine-containing radical peptides; 3) Reactions of CO3●– with three atmospheric acids (hydrogen chloride, formic acid and acrylic acid); 4) Electron transfers between a hydrated electron and small sulphur-containing molecules (CH3SH and CH3SSCH3) in water clusters. Most of the theoretical results are in good agreement with the mass spectrometric data acquired by our collaborators.

Gas-phase dissociations of peptide ions in a mass spectrometer form the scientific basis of mass spectrometry-based proteomics. Here, we had performed mechanistic studies for cleavages of N–C or C–C bonds along the peptide backbone of β-radical peptides, which contains an unpaired electron at the β-carbon of the cleaving amino-acid residue. Their bond dissociation energies had been examined by a few levels of density functional theory (DFT), coupled cluster theory and G3X (MP2)-Rad theory. Among these theories, M06-2X can be an effective alternative to evaluate the electronic energy of β-radical peptide backbone dissociation with accuracy comparable with higher level, but more computationally costly, ab initio theories. The selectivity of N–C or C–C bonds cleavages induced by the β-radical was evaluated by comparing the energy barriers of both bond dissociations. It was found that the Cα–C bond cleavage is homolytic and is favorable with or without the presence of a labile proton. However, the N–Cα bond cleavage gains the priority in backbone fragmentation if an electron-donating group is directly attached to the β-carbon (e.g. threonine and serine) resulting in a captodative stabilization. Cleavages of the N–Cα bond at the β-radical of aromatic amino acids are also more favorable when a proton is available near the cleaving site and their cleavages show heterolytic character.

To further elucidate intra molecular transfers of the radical sites, an oligopeptide radical cation containing four amino-acid residues, namely [GGYG]●+, was employed as the model system to perform ion-molecule reactions with NO2●. Detail experimental and DFT studies suggested that the ion-molecule reaction between [GGYG]●+ and NO2● was attributed to the radical recombination process of NO2● toward the locations of the unpaired electron in different [GGYG]●+ tautomers, such as [GGYπ●G]+ (π-radical), [GGYβ●G]+ (β-radical) and [GGYo●G]+ (phenoxy-radical). The energy barriers for the interconversions of these tautomers are low. Interestingly, the ion-molecule reaction between [GGYβ●G]+ and NO2● will generate NO2[GGYG]+ in which the NO2 moiety is labile that can easily fall off as a NO2H molecule upon collision-induced dissociations. By contrast, [GGYo●G]+ can also react with NO2● to form NO2[GGYG]+, subsequent dissociations of which can result in fragment ions containing a stable tagged NO2 group. In combination with isotope-labeling experiments and theoretical calculations, these results suggest that a 3-nitrotyrosine residue is formed, which is analogous to the protein tyrosine nitration processes in biological systems.

Reactions of atmospheric molecule CO3●– with various organic molecules display diverse radical chemistry especially in generating neutral carbon dioxide and OH●. Despite the fact that CO3●– is abundant in the troposphere as well as a potential source of atmospheric OH●, its reactions were not much reported, probably because its reactions always led to signal loss inside a mass spectrometer, making detail investigations challenging. Gas-phase intermolecular radical reactions of CO3●– with inorganic and organic acids, including HCl, formic acid and acrylic acid, were demonstrated by combination of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry and quantum chemical calculations. Both FT-ICR and DFT studies suggested that the reactions could release a free electron, explaining the common signal loss. This free electron could behave as a catalysis and close the catalytic cycle for the oxidation of these acids with ozone. The theoretical potential energy surface also provided reaction paths for the formation of neutral carbon dioxide and OH● as the thermochemically favored products.

DFT-based molecular dynamics methods were employed to model gas-phase intermolecular electron transfer from a hydrated electron to small sulphur-containing molecules (CH3SH and CH3SSCH3) in water clusters. DFT-MD simulations clearly revealed that two dynamics electron transfer processes had occurred, resulting in reductive dissociations of CH3SH and CH3SSCH3, yielding CH3SH●- and CH3SSCH3●- respectively. The S–H and S–S bonds were dissociated upon the reduction process due to the reductive electron transfer from hydrated electron to the * orbital of the dissociating bond. Interestingly, the electron transfer process was facilitated by the structural change of the clusters, for instance, hydrogen bond formation, which in turn reduced the HOMO-LUMO gap. The predicted reaction energies were in reasonable good agreement with experimental values estimated from nanocalorimetric technique measured by FT-ICR mass spectrometer.