| 1. |
- Abid, Abdul Rahman
(författare)
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X-ray Absorption and Fragmentationas Initial Steps of Radiation Damage in Free Organic Molecules and Nanoparticles
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Understanding the molecular radiation damage is crucial in radiobiology, molecular physics, and atmospheric science. In this thesis, the initial steps of radiation damage of anhydrous gas-phase molecules and hydrated nanoparticles were studied using synchrotron radiation based electron-ion coincidence spectroscopy and X-ray absorption spectroscopy under vacuum conditions. Electron - ion coincidence spectroscopy was used to study the photofragmentation and molecular dynamics of the isolated gas-phase molecules. In addition to the photofragmentation of the gas-phase molecules, the effect of the initial ionization site, initial molecular geometry, and the intramolecular chemical environment has been studied. In avobenzone, core ionization leads to massive fragmentation, with a slight site-selectivity concerning fragment production. In ortho-aminobenzoic acid, core ionization leads to the production of a hydronium ion, indicating that the importance of functional group's position for double intramolecular hydrogen transfer. X-ray absorption spectroscopy was used to probe hydrated nanoparticles prepared at different relative humidities. In hydrated inorganic and mixed inorganic-organic nanoparticles, water is present in a liquid-like state. With different ranges of relative humidity, the primary hydration layers of the hydrated nanoparticles stays the same. In mixed nanoparticles, there is evidence for interaction between the included organic biomolecule with the inorganic and/or water molecules.
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| 2. |
- Akiyama, Tomoko
(författare)
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Ionization Influence on the Dynamics of Simple Organic Molecules
- 2023
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This licentiate thesis is devoted to the investigation of how bonding in simple organic molecules are affected by X-ray beam irradiation. The investigation targets molecules with three carbons as their main-chain structure. The stability of the bonds under ionization are simulated using the SIESTA package. SIESTA is a simulation package that provides molecular dynamics simulations based on density functional theory within the Born-Oppenheimer approximation. The aim of this study is to understand statistically the damaging process and selectivity among different types of bond. As the first targets, 4 hydrocarbons are investigated. They are propane, propene, propyne and propadiene, which have different combinations of single, double and triple bonds as their main-chain structures. Depending on the combinations, the structures can be either symmetric around the central atom or not. The structure of the symmetric molecules propane and propadiene are stable until charge +3. In contrast, the asymmetric molecules propene and propyne, the main-chain bonds show a tendency towards a more similar bond-distance as the level of ionization increases. In addition, hydrogens relocation occurs in propene, leading to a symmetric structure. Secondly, the bond fluctuations are investigated among 4 types of three-carbon molecules which have functional parts. Alcohol and carboxyl groups molecules show the stable bond integrities at charging 0 to +2. On the other hand, the carbon-carbon bonds in molecules with acetyl and ketone groups are broken by ionization. Comparing the 8 kinds of bond breaking processes in these molecules, this statistical study gives an insight to organic molecules bonding systems.
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| 3. |
- Gopakumar, Geethanjali, 1992-
(författare)
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An X-ray Based Spectroscopic Study of Structure Influencing Electrons : Fragmentation, Ultrafast Charge Dynamics and Surface Composition
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The structure of biomolecules, such as proteins, is intimately connected to the function of the molecules. These structures are often studied using X-ray diffraction. However, the interaction of the X-ray photons with the molecule can excite or ionize its electrons which in turn can causes changes in the molecular structure. Getting a better understanding of the radiation damage induced by the X-rays, will lead to higher resolution molecular imaging. In proteins, sulfur bridges stabilize the structure, but sulfur is relatively more susceptible to X-ray photon-induced dynamics. The first section of the thesis presents results obtained by fragment mass spectroscopy using an ion trap on the X-ray induced dynamics leading to breakage in the smallest unit containing sulfur bridge in proteins, cystine. The fragmentation of the bridge is seen to depend on the photon energy used.Molecular damage is not always undesirable. The radiation-induced damage of DNA of cancer cells is an aspired outcome of radiation therapy treatment. Along with the direct damaging effect of the radiation, the surrounding water and metal ions also play a role in indirectly destroying the DNA structure. The X-rays ionize the metal ions and water molecules, which relaxes via different processes, producing water radicals and slow electrons. Both are agents of the destruction of DNA strands. The second section of the thesis reports on results obtained by electron spectroscopy on ultrafast electron dynamics originating from the relaxation of core-excited and ionized aqueous ions, which can result in slow electrons and water radicals. To understand the damages in the system of aqueous ions and biomolecules, one needs to understand the interaction between the organic-inorganic species. Using surface sensitive X-ray photoelectron spectroscopy on such a sample mixture of potassium chloride and amino acids is explained in the last section of the thesis. It is seen that changing the chemical environment in the solution (pH), affects both the protonation of the functional group of amino acids and the surface distribution of solvated counter ions. The interaction between organic biomolecules and inorganic ions can be ensured by controlling the chemical environment. This thesis puts forward the study of electrons that influences the molecular structure using various X-ray based spectroscopy techniques.
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