| 1. |
- 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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| 2. |
- Gopakumar, Geethanjali, 1992-, et al.
(författare)
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Non-local decay of highly charged aqueous inorganic ions produced by Auger decay
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- High-Z atoms are more important for biological radiation damage by photons than their low abundance due to their higher photoionization cross-section. Using the inorganic Mg 2+ and Al3+ ions in water as model systems, we have studied decay processes following deep core-level ionization. Local Auger decay rapidly produces highly charged Mg 4+and Al5+ ions, the decay of which must involve non-local processes involving the surrounding water, such as electron transfer mediated decay (ETMD). Using electron spectroscopy we observe two distinct ETMD decay steps for Al, corresponding to decay from Al5+ to Al4+, and then from Al4+ to Al3+. The ETMD energetics is discussed using both a simple model and calculations. Contrary to expectations, we do not observe any ETMD for Mg, and possible reasons for this are discussed.
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| 3. |
- Gopakumar, Geethanjali, 1992-, et al.
(författare)
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Probing Aqueous Ions with Non-local Auger Relaxation
- 2022
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 24:15, s. 8661-8671
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Tidskriftsartikel (refereegranskat)abstract
- The decay of core holes is often regarded as a local process, but in some systems, it involves the autoionization of neighbouring atoms or molecules. Here, we explore such non-local autoionization (Intermolecular Coulombic Decay, ICD) of surrounding molecules upon 1s ionization of aqueous-phase Na+, Mg2+ and Al3+ ions. The three ions are isoelectronic but differ in the strength of the ion-water interactions which is manifested in experimental Auger electron spectra by varying intensities. While for strongly interacting Mg2+ and Al3+ the non-local decay is observed, for weakly bound Na+ no signal was measured. Combined with theoretical simulations we provide a microscopic understanding of the non-local decay processes. We assigned the ICD to decay processes ending with two-hole states delocalized between the central ion and neighbouring water. The ICD process is also shown to be highly selective with respect to water molecular orbitals. The ICD lifetime was estimated to be around 40 fs for Mg and 20 fs for Al. Auger spectroscopy thus represents a novel tool for exploring molecules in the liquid phase, providing simultaneously structural and electronic information.
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| 4. |
- Gopakumar, Geethanjali, et al.
(författare)
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Probing aqueous ions with non-local Auger relaxation
- 2022
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 24:15, s. 8661-8671
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Tidskriftsartikel (refereegranskat)abstract
- Non-local analogues of Auger decay are increasingly recognized as important relaxation processes in the condensed phase. Here, we explore non-local autoionization, specifically Intermolecular Coulombic Decay (ICD), of a series of aqueous-phase isoelectronic cations following 1s core-level ionization. In particular, we focus on Na+, Mg2+, and Al3+ ions. We unambiguously identify the ICD contribution to the K-edge Auger spectrum. The different strength of the ion-water interactions is manifested by varying intensities of the respective signals: the ICD signal intensity is greatest for the Al3+ case, weaker for Mg2+, and absent for weakly-solvent-bound Na+. With the assistance of ab initio calculations and molecular dynamics simulations, we provide a microscopic understanding of the non-local decay processes. We assign the ICD signals to decay processes ending in two-hole states, delocalized between the central ion and neighbouring water. Importantly, these processes are shown to be highly selective with respect to the promoted water solvent ionization channels. Furthermore, using a core-hole-clock analysis, the associated ICD timescales are estimated to be around 76 fs for Mg2+ and 34 fs for Al3+. Building on these results, we argue that Auger and ICD spectroscopy represents a unique tool for the exploration of intra- and inter-molecular structure in the liquid phase, simultaneously providing both structural and electronic information.
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| 5. |
- Gopakumar, Geethanjali, 1992-, et al.
(författare)
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The Surface Composition of Amino Acid - Halide Salt Solutions is pH-Dependent
- 2022
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Ingår i: Environmental Science: Atmospheres. ; :3
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Tidskriftsartikel (refereegranskat)abstract
- In atmospheric aerosol particles, the chemical surface composition governs both heterogeneous chemical reactions with gas-phase species and the ability to act as nuclei for cloud droplets. The pH in aerosol droplets 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. Our findings apply to any aqueous interface at which organic species with charged functional groups are present.
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| 6. |
- Gopakumar, Geethanjali, et al.
(författare)
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The surface composition of amino acid - halide salt solutions is pH-dependent
- 2022
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Ingår i: Environmental Science: Atmospheres. - : Royal Society of Chemistry (RSC). - 2634-3606. ; 2:3, s. 441-448
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 7. |
- Gopakumar, Geethanjali, et al.
(författare)
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X-ray-induced attosecond ion-water electron dynamics of aqueous ions
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The foundation of many physical and chemical processes is the transfer of charge from one entity to another. In many cases, the charge transfer is mediated by electron transfer and due to the comparatively low mass of electrons, these processes tend to take place within a few femtoseconds or several attoseconds. We investigate the charge transfer from Na+, Mg2+ and Al3+ in an aqueous environment to neighbouring water molecules. In order to achieve this, we use the core-hole clock method and Auger spectroscopy upon 1s ionization of the respective ions. The charge transfer times range from several 100 as below the 1s ionization threshold to only 20 as far above the 1s ionization. The decrease in charge transfer times as a function of the photon energy seems to be continuous. Despite the ions being isoelectronic in our study, we nd differences in their charge transfer behaviour.
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| 8. |
- Gopakumar, Geethanjali, 1992-, et al.
(författare)
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X-ray Induced Fragmentation of Protonated Cystine
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Protein structure determination using high-intensity X-ray sources induces damage in the protein. Disulfide bridges, formed between two cysteine amino acid residues stabilize the protein structure. Owing to the higher absorption cross-section of sulfur for X-ray photons, and a large number of electrons released from sulfur atoms, these disulfide bridges are hot spots for a higher level of noise in structural studies. But it is yet to be understood how exactly the damage occurs through the interaction of the disulfide bridges with photons. Here we study the fragmentation of protonated cystine in the gas phase, which is the dimer of cysteine, by irradiation with X-rays across the sulfur L-edge using an electrospray ionization source (ESI) in combination with an ion trap. This is complemented with the calculation of the sulfur NEXAFS spectrum on the level of Restricted Open-Shell Configuration Interaction (ROCIS) and Density Functional Theory (DFT) calculations for molecular orbital visualization as well as Molecular Dynamics (MD) simulations for the fragmentation of triply charged cystine ions. We have deduced a possible pathway of fragmentation upon excitation and ionization of S 2p electrons by combining the experiments and simulations. The disulfide bridge breaks for resonant excitation at lower energies but remains intact upon higher energy resonant excitation and upon ionization of S 2p. The larger fragments formed subsequently break into smaller fragments.
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| 9. |
- Gopakumar, Geethanjali, 1992-, et al.
(författare)
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X-ray Induced Fragmentation of Protonated Cystine
- 2022
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 126:9, s. 1496-1503
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 10. |
- Herboth, Radost, et al.
(författare)
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Charge State Dependence of Amino Acid Propensity at Water Surface : Mechanisms Elucidated by Molecular Dynamics Simulations
- 2021
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 125:22, s. 4705-4714
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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