An X-ray Based Spectroscopic Study of Structure Influencing Electrons : Fragmentation, Ultrafast Charge Dynamics and Surface Composition

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.    

Charge State Dependence of Amino Acid Propensity at Water Surface : Mechanisms Elucidated by Molecular Dynamics Simulations

Atmospheric aerosols contain a variety of compounds, among them free amino acids and salt ions. The pH of the aerosol droplets depends on their origin and environment. Consequently, compounds like free amino acids found in the droplets will be at different charge states, since these states to a great extent depend on the surrounding pH condition. In droplets of marine origin, amino acids are believed to drive salt ions to the water surface and a pH-dependent amino acid surface propensity will, therefore, indirectly affect many processes in atmospheric chemistry and physics such as for instance cloud condensation. To understand the surface propensity of glycine, valine, and phenylalanine at acidic, neutral, and basic pH, we used molecular dynamics (MD) simulations to investigate them at three different charge states in water. Their respective surface propensities were obtained by the means of a potential of mean force (PMF) in an umbrella sampling approach. Glycine was found to have no preference for the surface, while both valine and phenylalanine showed high propensities. Among the charge states of the surface-enriched ones, the cation, representing the amino acids at low pH, was found to have the highest affinity. Free energy decomposition revealed that the driving forces depend strongly on the nature of the amino acid and its charge state. In phenylalanine, the main factor was found to be a substantial entropy gain, likely related to the side chain, whereas in valine, hydrogen bonding to the functional groups leads to favorable energies and, in turn, affects the surface propensity. A significant gain in water-water enthalpy was seen for both valine and phenylalanine

Temperature Dependence of X-ray-Induced Auger Processes in Liquid Water

Auger spectroscopy has previously been used to study changes in the hydrogen bond network in liquid water, but to the best of our knowledge it has not been used to track such changes as a function of temperature. We show Auger spectroscopy to reflect the weakening of the hydrogen bond network upon heating. This shows that the radiation response of water, i.e., the relative propensity of the different processes occurring after radiation exposure, including femtosecond proton dynamics, depends on the temperature of the system. This proof-of-principle study further demonstrates the suitability of the technique to help elucidate information on the intermolecular structure of liquids such as water, opening the door to further temperature-dependent studies

Surface composition of size-selected sea salt particles under the influence of organic acids studied in situ using synchrotron radiation X-ray photoelectron spectroscopy

Sea spray aerosols play a key role in the climate system by scattering solar radiation and by serving as cloud condensation nuclei. Despite their importance, the impact of sea spray aerosols on global climate remains highly uncertain. One of the key knowledge gaps in our understanding of sea spray aerosol is the chemical composition of the particle surface, important for various atmospheric chemical processes, as a function of size and bulk composition. Here, we have applied X-ray photoelectron spectroscopy (XPS) to determine the surface composition of both pure inorganic sea salt aerosols and sea salt aerosols spiked with an amino acid (phenylalanine) and a straight chain fatty acid (octanoic acid). Importantly, the use of a differential mobility analyser allowed size-selection of 150, 250 and 350 nm monodisperse aerosol particles for comparison to polydisperse aerosol particles. We observed enrichment of magnesium at the particle surfaces relative to chloride in all aerosols tested, across all particle sizes. Interestingly, the magnitude of this enrichment was dependent on the type of organic present in the solution as well as the particle size. Our results suggest that the observed enrichment in magnesium is an inorganic effect which can be either enhanced or diminished by the addition of organic substances

Surface composition of size-selected sea salt particles under the influence of organic acids studied in situ using synchrotron radiation X-ray photoelectron spectroscopy

Sea spray aerosols play a key role in the climate system by scattering solar radiation and by serving as cloud condensation nuclei. Despite their importance, the impact of sea spray aerosols on global climate remains highly uncertain. One of the key knowledge gaps in our understanding of sea spray aerosol is the chemical composition of the particle surface, important for various atmospheric chemical processes, as a function of size and bulk composition. Here, we have applied X-ray photoelectron spectroscopy (XPS) to determine the surface composition of both pure inorganic sea salt aerosols and sea salt aerosols spiked with an amino acid (phenylalanine) and a straight chain fatty acid (octanoic acid). Importantly, the use of a differential mobility analyser allowed size-selection of 150, 250 and 350 nm monodisperse aerosol particles for comparison to polydisperse aerosol particles. We observed enrichment of magnesium at the particle surfaces relative to chloride in all aerosols tested, across all particle sizes. Interestingly, the magnitude of this enrichment was dependent on the type of organic present in the solution as well as the particle size. Our results suggest that the observed enrichment in magnesium is an inorganic effect which can be either enhanced or diminished by the addition of organic substances

The surface composition of amino acid - halide salt solutions is pH-dependent

In atmospheric aerosol particles, the chemical surface composition governs both heterogenous chemical reactions with gas-phase species and the ability to act as nuclei for cloud droplets. The pH in aerosol particles is expected to affect these properties, but it is very challenging to measure the pH in individual droplets, precluding the investigation of its influence on the particle's surface composition. In this work, we use photoelectron spectroscopy to explore how the surface composition of aqueous solutions containing inorganic salt and amino acids changes as a function of pH. We observe a change by a factor of 4-5 of the relative distribution of inorganic ions at the surface of a liquid water jet, as a function of solution pH and type of amino acid in the solution. The driving forces for the surface enhancement or depletion are ion pairing and the formation of charged layers close to the aqueous surface

The Surface Composition of Amino Acid - KCl Solutions is pH-Dependent

The manuscript based on X-ray photoelectron spectroscopy on aqueous solutions containing KCl and different amino acids. Our analysis suggests that the presence of the inorganic ions at the surface of the liquid is strongly dependent on the pH of the solution and the type of amino acid

The surface composition of amino acid – halide salt solutions is pH-dependent

In atmospheric aerosol particles, the chemical surface composition governs both heterogenous chemical reactions with gas-phase species and the ability to act as nuclei for cloud droplets. The pH in aerosol particles is expected to affect these properties, but it is very challenging to measure the pH in individual droplets, precluding the investigation of its influence on the particle's surface composition. In this work, we use photoelectron spectroscopy to explore how the surface composition of aqueous solutions containing inorganic salt and amino acids changes as a function of pH. We observe a change by a factor of 4–5 of the relative distribution of inorganic ions at the surface of a liquid water jet, as a function of solution pH and type of amino acid in the solution. The driving forces for the surface enhancement or depletion are ion pairing and the formation of charged layers close to the aqueous surface

Radiation damage by extensive local water ionization from two-step electron-transfer-mediated decay of solvated ions

Biomolecular radiation damage is largely mediated by radicals and low-energy electrons formed by water ionization rather than by direct ionization of biomolecules. It was speculated that such an extensive, localized water ionization can be caused by ultrafast processes following excitation by core-level ionization of hydrated metal ions. In this model, ions relax via a cascade of local Auger–Meitner and, importantly, non-local charge- and energy-transfer processes involving the water environment. Here, we experimentally and theoretically show that, for solvated paradigmatic intermediate-mass Al$^{3+}$ ions, electronic relaxation involves two sequential solute–solvent electron transfer-mediated decay processes. The electron transfer-mediated decay steps correspond to sequential relaxation from Al$^{5+}$ to Al$^{3+}$ accompanied by formation of four ionized water molecules and two low-energy electrons. Such charge multiplication and the generated highly reactive species are expected to initiate cascades of radical reactions

Surface composition of size-selected sea salt particles under the influence of organic acids studied in situ using synchrotron radiation X-ray photoelectron spectroscopy

Abstract Sea spray aerosols play a key role in the climate system by scattering solar radiation and by serving as cloud condensation nuclei. Despite their importance, the impact of sea spray aerosols on global climate remains highly uncertain. One of the key knowledge gaps in our understanding of sea spray aerosol is the chemical composition of the particle surface, important for various atmospheric chemical processes, as a function of size and bulk composition. Here, we have applied X-ray photoelectron spectroscopy (XPS) to determine the surface composition of both pure inorganic sea salt aerosols and sea salt aerosols spiked with an amino acid (phenylalanine) and a straight chain fatty acid (octanoic acid). Importantly, the use of a differential mobility analyser allowed size-selection of 150, 250 and 350 nm monodisperse aerosol particles for comparison to polydisperse aerosol particles. We observed enrichment of magnesium at the particle surfaces relative to chloride in all aerosols tested, across all particle sizes. Interestingly, the magnitude of this enrichment was dependent on the type of organic present in the solution as well as the particle size. Our results suggest that the observed enrichment in magnesium is an inorganic effect which can be either enhanced or diminished by the addition of organic substances