Ab Initio Molecular Dynamics Simulations Of O^- Reaction With CH₄, Dissociative Ionization And Electron Attachment

The genetic toxicity effects of ionizing radiations can cause the living body potentially lethal DNA lesions, such as single- and double-strand breaks (SSBs and DSBs), transcription of genetic information, gene expression, gene mutation and so on. The ionizing radiation damages to biological organisms are mainly categorized into direct damage and indirect damage. After ionizing radiation energy deposition in organisms, the low-energy free secondary electron can cause a series of secondary reactions, which is usually referred to as low energy electron dissociative electron attachment process of indirect radiation damage. And high-energy particle or photon can directly make organism ionization to the free radicals state. So the main contents of the dissertation is to simulate the dissociative electron attachment and photoionization process of dialanine, dissociative electron attachment process of chlorobenzene and its derivatives, and ion-molecule reaction of oxygen anion with methane by using ab initio molecular dynamics simulations.Firstly, dissociative electron attachment (DEA) processes of six low-lying conformers (1-6) of dialanine in gas phase are investigated by using ab initio molecular dynamics simulations. The incoming electron is captured and primarily occupied at the virtual molecular orbital Ï€*, which is followed by the different dissociation processes. The electron attachments to the conformers 1 and 2 having the stronger N-H…N and O-H…O intramolecular hydrogen bonds do not lead to fragmentations; but two different backbone bonds are broken in the DEAs to conformers 3 (or 4) and 6, respectively. It is interesting that the hydrogen abstraction of -NH from the terminal methyl group -CH3 is found in the roaming dissociation of the temporary anion of conformer 3. The present simulations enable us to have more insights into the peptide backbone bond breaks in the DEA process, and demonstrate a promising way toward understanding the radiation damages of complicated biological system.Secondly, the DEA processes of C6Hs(CH2)nCl (n=0,1,2,3,4) are investigated with ab initio molecular dynamics simulations. The fragment Cl- is generated and the C-Cl bond cleavage time decreases with the increasing of the length of the alkyl chain. In the DEA processes, the incoming electron is initially captured by the local Ï€* virtual orbital of the phenyl group and then transfers to the anti-bond a* orbital of the remote C-Cl moiety; while the variation of the C-Cl bond cleavage times are closely related to the dissociation thresholds of C6H5(CH2)nCl+e-â†'C6H5(CH2)n’+Cl-. From theoretical calculation we have shown that the electron auto-detachment process cannot be ignored in the experiment. The yield of Cl- decreases with the growth of the alkyl chain, which is mainly caused by the electron auto-detachment.Thirdly, photoionization processes of seven low-lying conformers (1-7) of dialanine in gas phase are investigated by using ab initio molecular dynamics simulations. The photoionization evolvement processes to conformers 1,2,3,4,6 all lead to the Cα’-C4 cleavages of the peptide backbone bonds with C2H6N(m/z=44) cation fragment and C4H6NO3(m=116) free radical fragment. Conformer 5 having a stronger steric hindrance does not lead to fragmentations, and one can observe the rotations of the terminal groups with respect to bond axis by the internal energy dissipation. Conformer 7 leads to the Cα-C1 cleavages of the peptide backbone bonds with CO2 (m=44) neutral fragment. And it is interesting that the hydrogen abstraction of C4=O from the terminal methyl group -N6H3 is found in the roaming dissociation of the temporary anion of conformer 7. The present simulations provide more insights into the peptide backbone bond breaks in the photoionization process, and demonstrate a promising way toward understanding the radiation damages of complicated biological system.In addition, stationary transition state calculations and ab initio molecular dynamics simulations for the new H-atom abandoned reaction O-+CH4â†'H’+OCH3-, endothermic by 0.20 eV. We performed stationary and vibrational ab initio molecular dynamics simulations with an attack models. O- attacks methane along the vertex model and the IRC transition state barrier height is 0.40 eV, which is the lowest barrier height of the OH-+CH3 product channel. O attacks methane along the center of plane and the center of edge angle model with H and OCH3- products and the IRC transition state barrier height is 2.54 eV, which is the new endothermic product channel. The present dynamic simulations enable us to have more insights into the OH-+CH3’ product channel.