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Collisions with biomolecules embedded in smallwater clusters
Stockholm University, Faculty of Science, Department of Physics. (Atomic Physics)
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2009 (English)Conference paper, Published paper (Refereed)
Abstract [en]

We have studied fragmentation of water embedded adenosine 5’-monophosphate(AMP) anions after collisions with neutral sodium atoms. At a collision energy of 50 keV,loss of water molecules from the collisionally excited cluster ions is the dominant process andfragmentation of the AMP itself is almost completely prohibited if the number of attachedwater molecules is larger than 13. However, regardless of the initial number of water moleculesattached to the ion, capture of an electron, i.e. formation of a dianion, always leads to loss ofa single hydrogen atom accompanied by evaporation of water molecules. This damaging effectbecomes more important as the size of the water cluster increases, which is just the oppositeto the protective behavior observed for collision induced dissociation (CID) without electrontransfer. For both cases, the loss of water molecules within the experimental time frame isqualitatively well described by means of a common model of an evaporative ensemble. Thesesimulations, however, indicate that characteristically different distributions of internal energyare involved in CID and electron capture induced dissociation.

Place, publisher, year, edition, pages
2009. 012053- p.
Series
Journal of Physics: Conference Series, ISSN 1742-6596 ; 194
National Category
Atom and Molecular Physics and Optics Physical Sciences
Research subject
Biophysics; Physics
Identifiers
URN: urn:nbn:se:su:diva-34740DOI: 10.1088/1742-6596/194/1/012053OAI: oai:DiVA.org:su-34740DiVA: diva2:285372
Conference
XXVI International Conference on Photonic, Electronic and Atomic Collisions
Available from: 2010-01-11 Created: 2010-01-11 Last updated: 2011-10-27Bibliographically approved
In thesis
1. Fragmentation of Amino Acids and Microsolvated Peptides and Nucleotides using Electrospray Ionization Tandem Mass Spectrometry
Open this publication in new window or tab >>Fragmentation of Amino Acids and Microsolvated Peptides and Nucleotides using Electrospray Ionization Tandem Mass Spectrometry
2010 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis presents three different series of high energy (keV) collision experiments as well as a brief scientific introduction to the field. In the first series, protonated glycine and leucine were collided with carbon dioxide and a beam attenuation method was applied to determine their total fragmentation cross sections. A technique was also presented for how to restore the resolution in mass spectra obtained with a hemispherical electrostatic analyzer followed by a position sensitive detector (micro-channel plate equipped with a resistive anode). In the second series of experiments, Collision Induced Dissociation (CID) and Electron Capture Induced Dissociation (ECID) studies were performed on the nucleotide adenosine 5'-monophosphate anion (AMP-) in water complexes.  The two dissociation techniques revealed different fragmentation patterns and a numerical solvent evaporation model was used to interpret the spectra. It was then found that the CID and ECID processes were associated with different internal energy distributions. The third experiment concerned ECID of the protonated dipeptide glycine-alanine ([GA+H]+) in complexes with water, methanol, acetonitrile or crown ether. Depending on the attached molecular species, different ratios between the two competing channels ammonia loss and N-Cα bond cleavage were observed. Quantum chemical calculations revealed that a notable shift in the location of the captured electron occurred for the case of two acetonitriles and one crown ether compared to the bare ion and the ion in complexes with either water or methanol. Finally, this thesis will discuss developments of the electrospray ionization platform as well as the new Double ElectroStatic IonRing ExpEriment (DESIREE) facility.

Publisher
80 p.
National Category
Atom and Molecular Physics and Optics
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-37202 (URN)
Presentation
2010-02-15, FA31, Albanova universitetscentrum, Roslagstullsbacken 21, Stockholm, 13:15 (English)
Opponent
Supervisors
Available from: 2011-02-18 Created: 2010-02-17 Last updated: 2011-02-18Bibliographically approved
2. Probing biomolecular fragmentation
Open this publication in new window or tab >>Probing biomolecular fragmentation
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis deals with fragmentation of complex molecular ions, especially biomolecules, in gas phase collision experiments. The aim is to investigate the relations between energy deposition and fragmentation and to shed light on the mechanisms behind energy and charge transfer processes in collisions involving the building blocks of life. Further, the question how a solvent environment influences the dissociation behavior is elucidated. In the first part of the thesis, results from different collision experiments with biomolecular ions are presented, focusing on electron capture induced dissociation of hydrated nucleotides and small peptides. The investigated processes may be relevant for the understanding of radiation damage and the optimization of sequencing methods used in protein research. Our results clearly demonstrate that effects due to surrounding solvent molecules are substantial. While the dissipation of internal energy by evaporation of the loosely bound solvent molecules may protect the biomolecule, the influence which this environment has on the electronic structure may lead to an enhancement or suppression of certain dissociation channels. The second part of the thesis focuses on recent instrumental developments. Here, the aim was to optimize and complement the techniques used in the experiments above and to have versatile tools available for different kinds of gas phase collision studies involving complex molecular ions. Therefore, we have constructed an electrospray ion source platform for the preparation of intense beams, with options of accumulation and cooling of mass selected ions, allowing for a large variety of experiments. This device is also intended to serve as an ion source for the new storage ring facility DESIREE (DoubleElectroStatic Ion Ring ExpEriment), which is currently under construction at Stockholm University. In these unique storage rings, oppositely charged ions may interact at very low relative velocities in a cryogenically cooled and ultrahigh vacuum environment.

Place, publisher, year, edition, pages
Stockholm: Department of Physics, Stockholm University, 2011. 124 p.
National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-54524 (URN)978-91-7447-228-8 (ISBN)
Public defence
2011-03-11, FB55, AlbaNova universitetscentrum, Roslagstullsbacken 21, Stockholm, 13:00 (English)
Opponent
Supervisors
Available from: 2011-02-17 Created: 2011-02-04 Last updated: 2011-02-07Bibliographically approved
3. Ionization and Fragmentation of Complex Molecules and Clusters: Biomolecules and Polycyclic Aromatic Hydrocarbons
Open this publication in new window or tab >>Ionization and Fragmentation of Complex Molecules and Clusters: Biomolecules and Polycyclic Aromatic Hydrocarbons
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This work deals with ionization and fragmentation of biomolecules and polycyclic aromatic hydrocarbon (PAH) molecules. They are studied in the gas phase both as isolated molecules and as weakly bound clusters. The purpose of the experimental and theoretical investigations are to elucidate charge and energy transfer and related redistribution processes, as well as fragmentation behaviors.

The first part of this thesis presents results from studies on biomolecular ions, in particular nucleotides and peptides, which are primarily examined in electron capture induced dissociation processes. These investigations are relevant for the better understanding of radiation damage to DNA and processes involved in the sequencing of proteins. It is found that the immediate environment have a decisive influence on the fragmentation behaviors. Evaporation of surrounding molecules protect the biomolecules, but their effect on the electronic structure may also enhance or suppress different fragmentation channels.

In the second part of the thesis, results from studies on PAH molecules are presented. Experimentally, their properties are mainly probed through collisions with atomic ion projectiles having kilo-electronvolt kinetic energies. As a widespread pollutant on Earth, and as a family of abundant molecules in space, PAHs are not only relevant from an environmental and health perspective, but they are also important for the understanding of the universe. The present results relate to the stabilities of these molecules, both in isolated form and in clusters, when heated or multiply ionized. It is found to be easier to remove several electrons from clusters of PAH molecules than from isolated PAHs, and fission processes determine their ultimate stabilities. Heated low-charge state clusters of PAHs undergo long evaporation sequences once these have started. For isolated and heated PAHs, internal structural rearrangements are demonstrated to be important in the fragmentation processes.

Place, publisher, year, edition, pages
Stockholm: Department of Physics, Stockholm University, 2011. 168 p.
National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-63733 (URN)978-91-7447-399-5 (ISBN)
Public defence
2011-12-02, lecture room FB53, AlbaNova universitetscentrum, Roslagstullsbacken 21, Stockholm, 13:00 (English)
Opponent
Supervisors
Available from: 2011-11-10 Created: 2011-10-27 Last updated: 2011-11-01Bibliographically approved

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