| 1. |
- Lindén, Fredrik
(författare)
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Anions from the lab to ionospheres
- 2016
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Anion processes have been in the focus of interest during the last decades, especially due to their importance in planetary ionospheres. Previous observations done by the Cassini Plasma Spectrometer, detected a multitude of heavy neutral and ionic molecules in the ionosphere of Saturn's moon Titan. Unfortunately, only the lighter anions could be identified as CN-, C3N- and C5N-. It has been believed that the ion-neutral reactions involving these cyano anions could explain the reaction mechanism leading to heavier negatively charged anions.In this thesis we present experimental investigations of the reaction of C3N - with C2 H2, using three different guided ion beam mass spectrometry setups. Complementary, we performed ab inito calculations at CCSD(T)/6-311++G** level of theory. These calculations provide a detailed picture of the different reaction pathways. Unfortunately our computations yielded that all these pathways possess high reaction barriers and the above-mentioned process therefore an unlikely reaction to occur in Titans atmosphere. We also performed an investigation using velocity map imaging spectrometry to study the attack mechanism of CN- on halogenated hydrocarbons. In this experiment we studied the nucleophilic substitutionThe energy distribution at low collision energies reveals isotropic scattering of I- which suggests that the process proceeds via a long-lived transition state complex, whereas at higher collision energies the backward scattering mechanism becomes more dominant. Additionally ab inito calculations were carried out, and even though the reaction energy difference between the two attack mechanisms is quite considerable (approximately 1 eV), we could not identify the ratio between the number of reactions involving an attack from the nitrogen atom leading to methylisocyanide (CH3NC) versus the one proceeding via an attack from carbon atom forming acetonitrile (CH3CN). Furthermore, I present a general semi-classical model that describes the forces and electron-transfer processes between two dielectric spheres in vacuum. The model spheres may be charged, may have different radii and different dielectric constants. Here, the model is used to calculate the so called Langevin cross sections for fusion of two spheres and charge exchange cross sections between two charged spheres. The model may be used to predict properties of reactions relevant in the chemistry of astronomical objects like dark clouds, circumstellar envelopes, protoplanetary disks and star-forming regions.
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| 2. |
- Shebanits, Oleg
(författare)
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Titan’s ionosphere and dust : – as seen by a space weather station
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Titan, the largest moon of Saturn, is the only known moon with a fully developed nitrogen-rich atmosphere, its ionosphere is detectable as high as 2200 km above its surface and hosts complex organic chemistry. Titan’s atmosphere and ionosphere has striking similarities to current theories of these regions around Earth 3.5 billion years ago. The Cassini spacecraft has been in orbit around Saturn since 2004 and carries a wide range of instruments for investigating Titan’s ionosphere, among them the Langmuir probe, a “space weather station”, manufactured and operated by the Swedish Institute of Space Physics, Uppsala.This thesis presents studies of positive ions, negative ions and negatively charged dust grains (also called aerosols) in Titan’s ionosphere using the in-situ measurements by the Cassini Langmuir probe, supplemented by the data from particle mass spectrometers. One of the main results is the detection of significant (up to about 4000 cm-3) charge densities of heavy (up to about 13800 amu/charge) negative ions and dust grains in Titan’s ionosphere below 1400 km altitude. The dust is found to be the main negative charge carrier below about 1100 km on the nightside/terminator ionosphere, forming a dusty plasma (also called “ion-ion” plasma). A new analysis method is developed using a combination of simultaneous observations by multiple instruments for a case study of four flybys of Titan’s ionosphere, further constraining the ionospheric plasma charge densities. This allows to predict a dusty plasma in the dayside ionosphere below 900 km altitude (thus declaring it a global phenomenon), as well as to empirically estimate the average charge of the negative ions and dust grains to between -2.5 and -1.5 elementary charges. The complete Cassini dataset spans just above 13 years, allowing to study effects of the solar activity on Titan’s ionosphere. From solar minimum to maximum, the increase in the solar EUV flux increases the densities by a factor of ~2 in the dayside ionosphere and, surprisingly, decreases by a factor of ~3-4 in the nightside ionosphere. The latter is proposed to be an effect of the ionospheric photochemistry modified by higher solar EUV flux. Modelling photoionization also reveals an EUV trend (as well as solar zenith angle and corotational plasma ram dependencies) in the loss rate coefficient.
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| 3. |
- Ottosson, Niklas, 1981-
(författare)
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Aqueous Solutions as seen through an Electron Spectrometer : Surface Structure, Hydration Motifs and Ultrafast Charge Delocalization Dynamics
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In spite of their high abundance and importance, aqueous systems are enigmatic on the microscopic scale. In order to obtain information about their geometrical and electronic structure, simple aqueous solutions have been studied experimentally by photo- and Auger electron spectroscopy using the novel liquid micro-jet technique in conjunction with synchrotron radiation. The thesis is thematically divided into three parts. In the first part we utilize the surface sensitivity of photoelectron spectroscopy to probe the distributions of solutes near the water surface. In agreement with recent theoretical predictions we find that large polarizable anions, such as I- and ClO4-, display enhanced surface propensities compared to smaller rigid ions. Surface effects arising from ion-ion interactions at higher electrolyte concentrations and as function of pH are investigated. Studies of linear mono-carboxylic acids and benzoic acid show that the neutral molecular forms of such weak acids are better stabilized at the water surface than their respective conjugate base forms. The second part examines what type of information core-electron spectra can yield about the chemical state and hydration structure of small organic molecules in water. We demonstrate that the method is sensitive to the protonation state of titratable functional groups and that core-level lineshapes are dependent on local water hydration configurations. Using a combination of photoelectron and X-ray absorption spectroscopy we also show that the electronic re-arrangement upon hydrolysis of aldehydes yields characteristic fingerprints in core-level spectra. In the last part of this thesis we study ultrafast charge delocalization dynamics in aqueous solutions using resonant and off-resonant Auger spectroscopy. Intermolecular Coulombic decay (ICD) is found to occur in a number of core-excited solutions where excess energy is transferred between the solvent and the solute. The rate of ultrafast electron delocalization between hydrogen bonded water molecules upon oxygen 1s resonant core-excitation is found to decrease upon solvation of inorganic ions. The presented work is illustrative of how core-level photoelectron spectroscopy can be valuable in the study of fundamental phenomena in aqueous solutions.
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| 4. |
- Zhang, Chaofan
(författare)
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Multicomponent Clusters/Nanoparticles : An Investigation of Electronic and Geometric Properties by Photoelectron Spectroscopy
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Clusters/nanoparticles are aggregates of a “small” number of building blocks, atoms or molecules, ranging from two up to millions of atoms. Two main groups of clusters have been studied using photoelectron spectroscopy based on synchrotron radiation. They are dry/wet alkali-halide clusters, including pure water clusters, and metal-based nanoparticles.For the dry alkali halide clusters, analysis of the data and theoretical modeling has allowed us insights into the local electronic properties at nanoscale: a change of polarizability of ions in the alkali-halide clusters due to the varying environment has been suggested. The study of the wet salt clusters shows that the alkali-halides are already solvated at the nanoscale reached by water clusters doped with salt vapor.The photoelectron angular distribution of water cluster shows lower anisotropy parameters as compared to the separate monomers. A model based on intracluster scattering has been built to partly explain the reduction.In the last part of the thesis, metal-based multi-component nanoparticles have been produced by self-assembly processes using reactive magnetron sputtering. Depending on the specific metal element, oxidation processes have been applied before or after the aggregation. Clearly radial distributions such as core-shell and “sandwich-like” structures have unambiguously determined by photoelectron spectroscopy.
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| 5. |
- 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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| 6. |
- 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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| 7. |
- Ekholm, Victor, 1989-
(författare)
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Ion pairing and Langmuir-like adsorption at aqueous surfaces studied by core-level spectroscopy
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Surface-bulk equilibria for solutes in aqueous solutions are studied using X-ray Photoelectron Spectroscopy (XPS) with high surface and chemical sensitivity. In the first part, the results show a reduction of the biochemically relevant guanidinium ions’ surface propensity with the addition of disodium sulphate due to ion pairing with the strongly hydrated sulphate ion, which could have implications for protein folding. Thereafter, the work considers amphiphilic organic compounds related to atmospheric science where the surface propensities, orientations at the surface and solute-solute and solute-solvent interactions are investigated. In the second part, two linear organic ions are investigated both as single solutes and in mixture. Both organic ions are surface enriched on their own and even more in the mixed solute solution. Due to hydrophobic expulsion of the alkyl chains, ion pairing between the organic ions and van der Waals interaction, the organic ions seem to assemble in clusters with their alkyl chains pointing out of the surface. The third part also covers linear organic compounds but one at a time probing the surface concentration as a function of bulk concentration. A Langmuir-like adsorption behavior was observed and Gibb’s free energy of surface adsorption (ΔGAds) values were extracted. An empiric model for deriving values for ΔGAds is proposed based upon the seemingly linear change in ΔGAds per carbon when comparing alcohols of different chain lengths. The fourth part investigates the acid/base fraction at the surface as function of bulk pH. The most important factor for this fraction seems to be how the surface propensity varies with the charge state of the acid or base instead of a possible difference in pH or pKa value at the surface. In the fifth part the oxygen K-edge of aqueous carbonate and bicarbonate is probed with the bulk-sensitive Resonant Inelastic X-ray Scattering (RIXS) technique.
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| 8. |
- 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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| 9. |
- Jönsson, H. Olof, 1985-
(författare)
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Femtosecond Dynamics in Water and Biological Materials with an X-Ray Laser
- 2016
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Using high intensity ultrashort pulses from X-ray free electron lasers to investigate soft matter is a recent and successful development. The last decade has seen the development of new variant of protein crystallography with femtosecond dynamics, and single particle imaging with atomic resolution is on the horizon. The work presented here is part of the effort to explain what processes influence the capability to achieve high resolution information in these techniques. Non-local thermal equilibrium plasma continuum modelling is used to predict signal changes as a function of pulse duration, shape and energy. It is found that ionization is the main contributor to radiation damage in certain photon energy and intensity ranges, and diffusion depending on heating is dominant in other scenarios. In femtosecond protein crystallography, self-gating of Bragg diffraction is predicted to quench the signal from the latest parts of an X-ray pulse. At high intensities ionization is dominant and the last part of the pulse will contain less information at low resolution. At lower intensities, displacement will dominate and high resolution information will be gated first. Temporal pulse shape is also an important factor. The difference between pulse shapes is most prominent at low photon energy in the form of a general increase or decrease in signal, but the resolution dependance is most prominent at high energies. When investigating the X-ray scattering from water a simple diffusion model can be replaced by a molecular dynamics simulation, which predicts structural changes in water on femtosecond timescales. Experiments performed at LCLS are presented that supports the simulation results on structural changes that occur in the solvent during the exposure.
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| 10. |
- Jönsson, Olof, 1985-
(författare)
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Ultrafast Structural and Electron Dynamics in Soft Matter Exposed to Intense X-ray Pulses
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Investigations of soft matter using ultrashort high intensity pulses have been made possible through the advent of X-ray free-electrons lasers. The last decade has seen the development of a new type of protein crystallography where femtosecond dynamics can be studied, and single particle imaging with atomic resolution is on the horizon. The pulses are so intense that any sample quickly turns into a plasma. This thesis studies the ultrafast transition from soft matter to warm dense matter, and the implications for structural determination of proteins. We use non-thermal plasma simulations to predict ultrafast structural and electron dynamics. Changes in atomic form factors due to the electronic state, and displacement as a function of temperature, are used to predict Bragg signal intensity in protein nanocrystals. The damage processes started by the pulse will gate the diffracted signal within the pulse duration, suggesting that long pulses are useful to study protein structure. This illustrates diffraction-before-destruction in crystallography.The effect from a varying temporal photon distribution within a pulse is also investigated. A well-defined initial front determines the quality of the diffracted signal. At lower intensities, the temporal shape of the X-ray pulse will affect the overall signal strength; at high intensities the signal level will be strongly dependent on the resolution.Water is routinely used to deliver biological samples into the X-ray beam. Structural dynamics in water exposed to intense X-rays were investigated with simulations and experiments. Using pulses of different duration, we found that non-thermal heating will affect the water structure on a time scale longer than 25 fs but shorter than 75 fs. Modeling suggests that a loss of long-range coordination of the solvation shells accounts for the observed decrease in scattering signal.The feasibility of using X-ray emission from plasma as an indicator for hits in serial diffraction experiments is studied. Specific line emission from sulfur at high X-ray energies is suitable for distinguishing spectral features from proteins, compared to emission from delivery liquids. We find that plasma emission continues long after the femtosecond pulse has ended, suggesting that spectrum-during-destruction could reveal information complementary to diffraction.
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