Search

Intramolecular hydrogen transfer, a reaction where donor and acceptor sites of a hydrogen atom are part of the same molecule, is a ubiquitous reaction in biochemistry and organic synthesis. In this work, we report hydronium ion (H₃O⁺) production from aminobenzoic acid (ABA) after core-level ionization with soft X-ray synchrotron radiation. The formation of H₃O⁺ during the fragmentation requires that at least two hydrogen atoms migrate to one of the oxygen atoms within the molecule. The comparison of two structural isomers, ortho- and meta-ABA, revealed that the production of H₃O⁺ depends strongly on the structure of the molecule, the ortho-isomer being much more prone to produce H₃O⁺. The isomer-dependency suggests that the amine group acts as a donor in the hydrogen transfer process. In the case of ortho-ABA, detailed H₃O⁺ production pathways were investigated using photoelectron-photoion-photoion coincidence (PEPIPICO) spectroscopy. It was found that H₃O⁺ can result from a direct two-body dissociation but also from sequential fragmentation processes.

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.

We demonstrate site-specific X-ray induced fragmentation across the sulfur L-edge of protonated cystine, the dimer of the amino acid cysteine. Ion yield NEXAFS were performed in the gas phase using electrospray ionization (ESI) in combination with an ion trap. The interpretation of the sulfur L-edge NEXAFS spectrum is supported by Restricted Open-Shell Configuration Interaction (ROCIS) calculations. The fragmentation pathway of triply charged cystine ions was modeled by Molecular Dynamics (MD) simulations. We have deduced a possible pathway of fragmentation upon excitation and ionization of S 2p electrons. The disulfide bridge breaks for resonant excitation at lower photon energies but remains intact upon higher energy resonant excitation and upon ionization of S 2p. The larger fragments initially formed subsequently break into smaller fragments.

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., Abstrakti Molekyylitasolla tapahtuvien säteilyvaurioiden ymmärrys on erittäin tärkeää säteilybiologiassa, molekyylifysiikassa ja ilmakehätieteissä. Tässä työssä on tutkittu tyhjiöolosuhteissa säteilyvaurioiden alkuaskeleita vedettömissä kaasumaisissa molekyyleissä ja vettä sisältävissä nanohiukkasissa käyttäen synkrotronisäteilypohjaista elektroni-ionikoinsidenssispektroskopiaa ja röntgenabsorptiospektroskopiaa. Elektroni-ionikoinsidenssispektroskopialla tutkittiin säteilyn aikaansaamaa hajoamista ja molekyylidynamiikkaa eristetyissä kaasumolekyyleissä. Tämän lisäksi tutkittiin, kuinka ensimmäisen ionisaatiotapahtuman paikka, molekyylin geometria ja molekyylin sisäinen kemiallinen ympäristö vaikuttaa näihin prosesseihin. Avobentsonimolekyylin sisäkuoren ionisaatio johtaa molekyylin hajoamiseen lukuisiksi eri hajoamistuotteiksi, ja hajoamistuotteiden saannin todettiin riippuvan vain vähän ionisoidusta sisäkuoresta. Orto-aminobentsoehapossa sisäkuoren ionisaation havaittiin tuottavan kahden vedyn siirtymisen vaativaa hydroniumionia, ja tuoton havaittiin riippuvan funktionaalisten ryhmien keskinäisestä paikasta. Röntgenabsorptiospektroskopiaa hyödynnettiin eri suhteellisissa ilmankosteuksissa valmistettujen nanohiukkasten tutkimuksessa. Näissä epäorgaanisissa ja saostetuissa orgaanisissa-epäorgaanisissa nanohiukkasissa veden havaittiin olevan nesteenkaltaisessa olomuodossa. Saostetuissa nanohiukkasissa nähtiin myös merkkejä orgaanisen biomolekyylin ja epäorgaanisen ja/tai veden välisestä vuorovaikutuksesta., Sammanfattning Förståelse av molekylära strålningsskador är avgörande inom radiobiologi, molekylär fysik och atmosfärsvetenskap. I denna avhandling studerades strålningsskadornas inledande steg hos gasfasmolekyler och hydratiserade nanopartiklar med hjälp av synkrotronstrålningsbaserad elektron-jon-koincidensspektroskopi och röntgenabsorptionsspektroskopi under vakuumförhållanden. Elektron-jon-koincidensspektroskopi användes för att studera fotofragmentering och molekylär dynamik hos de isolerade gasfasmolekylerna. Förutom fotofragmenteringen av gasfasmolekylerna har effekten av den initiala joniseringsplatsen i molekylen, den initiala molekylära geometrin och den intramolekyl ära kemiska miljön studerats. I avobenzon leder innerskalsjonisering till massiv fragmentering med liten platsselektivitet beträffande fragmentproduktion. I orto-aminobensoesyra leder innerskalsjonisering till produktion av en hydroniumjon, vilket pekar på vikten av funktionella gruppers position för sådan dubbel intramolekylär väteöverföring. Röntgenabsorptionsspektroskopi användes för att studera hydratiserade nanopartiklar framställda vid varierande relativa fuktighet. I hydratiserade inorganiska och blandade inorganiska-organiska nanopartiklar finns vatten i vätskeformigt tillstånd. De primära hydratiseringsskalen i de hydratiserade nanopartiklarna opåverkade av de olika relativa fuktighetsnivåerna. I blandade nanopartiklar finns det bevis för växelverkan mellan de inkluderade organiska biomolekylerna och de inorganiska jonerna och/eller vattenmolekylerna.

Resonant inelastic x-ray scattering spectra excited at the fluorine K resonances of SF(6)have been recorded. While a small but significant propensity for electronically parity-allowed transitions is found, the observation of parity-forbidden electronic transitions is attributed to vibronic coupling that breaks the global inversion symmetry of the electronic wavefunction and localizes the core hole. The dependence of the scattering cross section on the polarization of the incident radiation and the scattering angle is interpreted in terms of local pi/sigma symmetry around the S-F bond. This symmetry selectivity prevails during the dissociation that occurs during the scattering process.

Hydrogen bonding leads to the formation of strong, extended intermolecular networks in molecular liquids such as water. However, it is less well-known how robust the network is to environments in which surface formation or confinement effects become prominent, such as in clusters or droplets. Such systems provide a useful way to probe the robustness of the network, since the degree of confinement can be tuned by altering the cluster size, changing both the surface-to-volume ratio and the radius of curvature. To explore the formation of hydrogen bond networks in confined geometries, here we present O 1s Auger spectra of small and large clusters of water, methanol, and dimethyl ether, as well as their deuterated equivalents. The Auger spectra of the clusters and the corresponding macroscopic liquids are compared and evaluated for an isotope effect, which is due to proton dynamics within the lifetime of the core hole (proton-transfer-mediated charge-separation, PTM-CS), and can be linked to the formation of a hydrogen bond network in the system. An isotope effect is observed in water and methanol but not for dimethyl ether, which cannot donate a hydrogen bond at its oxygen site. The isotope effect, and therefore the strength of the hydrogen bond network, is more pronounced in water than in methanol. Its value depends on the average size of the cluster, indicating that confinement effects change proton dynamics in the core ionised excited state.

The distribution and protonation states of amino acids in water droplets are of considerable concern in studies on the formation of clouds in the atmosphere as well as in many biological contexts. In the present work we use the amino acid cysteine as a prototypical example and explore the protonation states of this molecule in aqueous solution, which are strongly affected by the acidity of the environment and also can show different distributions between surface and bulk. We use a combination of X-ray photoelectron chemical shift measurements, density functional theory calculations of the shifts, and reactive force field molecular dynamics simulations of the underlying structural dynamics. We explore how the photoelectron spectra distinctly reflect the different protonation states that are generated by variation of the solution acidity and how the distribution of these protonation states can differ between bulk and surface regions. At specific pH values, we find that the distribution of the cysteine species at the surface is quite different from that in bulk, in particular, for the appearance in the surface region of species which do not exist in bulk. Some ramifications of this finding are discussed., QC 20190527

Acid–base equilibria of carboxylic acids and alkyl amines in the aqueous surface region were studied using surface-sensitive X-ray photoelectron spectroscopy and molecular dynamics simulations. Solutions of these organic compounds were examined as a function of pH, concentration and chain length to investigate the distribution of acid and base form in the surface region as compared to the aqueous bulk. Results from these experiments show that the neutral forms of the studied acid–base pairs are strongly enriched in the aqueous surface region. Moreover, we show that for species with at least four carbon atoms in their alkyl-chain, their charged forms are also found to be abundant in the surface region. Using a combination of XPS and MD results, a model is proposed that effectively describes the surface composition. Resulting absolute surface concentration estimations show clearly that the total organic mole fractions in the surface region change drastically as a function of solution pH. The origin of the observed surface phenomena, hydronium/hydroxide concentrations in the aqueous surface region and why standard chemical equations, used to describe equilibria in dilute bulk solution are not valid in the aqueous surface region, are discussed in detail. The reported results are of considerable importance especially for the detailed understanding of properties of small aqueous droplets that can be found in the atmosphere.