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Ionization and Fragmentation of Complex Molecules and Clusters: Biomolecules and Polycyclic Aromatic Hydrocarbons
Stockholm University, Faculty of Science, Department of Physics.
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: urn:nbn:se:su:diva-63733ISBN: 978-91-7447-399-5 (print)OAI: oai:DiVA.org:su-63733DiVA: diva2:452046
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
List of papers
1. Electron-Capture-Induced Dissociation of Microsolvated Di- and > Tripeptide Monocations: Elucidation of Fragmentation Channels from > Measurements of Negative Ions
Open this publication in new window or tab >>Electron-Capture-Induced Dissociation of Microsolvated Di- and > Tripeptide Monocations: Elucidation of Fragmentation Channels from > Measurements of Negative Ions
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2009 (English)In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 10, no 9-10, 1619-1623 p.Article in journal (Refereed) Published
Abstract [en]

The branching ratio between ammonia loss and NCα bond cleavage of singly charged microsolvated peptides after electron capture from cesium depends on the solvent molecule attached. Density functional calculations reveal that for [GA+H]+(CE) (G=glycine, A=alanine, CE=crown ether), the singly occupied molecular orbital of the neutral radical is located mainly on the amide group (see picture).

The results from an experimental study of bare and microsolvated peptide monocations in high-energy collisions with cesium vapor are reported. Neutral radicals form after electron capture from cesium, which decay by H loss, NH3 loss, or NCα bond cleavage into characteristic z. and c fragments. The neutral fragments are converted into negatively charged species in a second collision with cesium and are identified by means of mass spectrometry. For protonated GA (G=glycine, A=alanine), the branching ratio between NH3 loss and NCα bond cleavage is found to strongly depend on the molecule attached (H2O, CH3CN, CH3OH, and 18-crown-6 ether (CE)). Addition of H2O and CH3OH increases this ratio whereas CH3CN and CE decrease it. For protonated AAA ([AAA+H]+), a similar effect is observed with methanol, while the ratio between the z1 and z2 fragment peaks remains unchanged for the bare and microsolvated species. Density functional theory calculations reveal that in the case of [GA+H]+(CE), the singly occupied molecular orbital is located mainly on the amide group in accordance with the experimental results.

Keyword
cations, electron transfer, excited states, mass spectrometry, peptides
National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-33290 (URN)10.1002/cphc.200800782 (DOI)000267928100039 ()
Available from: 2009-12-22 Created: 2009-12-22 Last updated: 2017-12-12Bibliographically approved
2. Electron capture induced dissociation of nucleotide anions in water nanodroplets
Open this publication in new window or tab >>Electron capture induced dissociation of nucleotide anions in water nanodroplets
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2008 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 7, 075102- p.Article in journal (Refereed) Published
Abstract [en]

We have studied the outcome of collisions between the hydrated nucleotide anion adenosine 5′-monophosphate (AMP) and sodium. Electron capture leads to hydrogen loss as well as water evaporation regardless of the initial number m of water molecules attached to the parent ion (m ⩽ 16). The yield of dianions with microsecond lifetimes increases strongly with m, which is explained from dielectric screening of the two charges by the water nanodroplet. For comparison, collision induced dissociation results in water losses with no or very little damage of the AMP molecule itself.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-17045 (URN)10.1063/1.2839597 (DOI)000253336800043 ()18298174 (PubMedID)
Available from: 2009-01-05 Created: 2009-01-05 Last updated: 2017-12-13Bibliographically approved
3. Collisions with biomolecules embedded in smallwater clusters
Open this publication in new window or tab >>Collisions with biomolecules embedded in smallwater clusters
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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.

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:nbn:se:su:diva-34740 (URN)10.1088/1742-6596/194/1/012053 (DOI)
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
4. Dissociation and multiple ionization energies for five polycyclic aromatic hydrocarbon molecules
Open this publication in new window or tab >>Dissociation and multiple ionization energies for five polycyclic aromatic hydrocarbon molecules
2011 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 134, no 4, 044301- p.Article in journal (Refereed) Published
Abstract [en]

We have performed density functional theory calculations for a range of neutral, singly, and multiply charged polycyclic aromatic hydrocarbons (PAHs), and their fragmentation products for H-, H+-, C2H2-, and C2H2+-emissions. The adiabatic and vertical ionization energies follow linear dependencies as functions of charge state for all five intact PAHs (naphthalene, biphenylene, anthracene, pyrene, and coronene). First estimates of the total ionization and fragmentation cross sections in ion-PAH collisions display markedly different size dependencies for pericondensed and catacondensed PAH species, reflecting differences in their first ionization energies. The dissociation energies show that the PAHq+-molecules are thermodynamically stable for q <= 2 (naphthalene, biphenylene, and anthracene), q <= 3 (pyrene), and q <= 4 (coronene). PAHs in charge states above these limits may also survive experimental time scales due to the presence of reaction barriers as deduced from explorations of the potential energy surface regions for H+-emissions from all five PAHs and for C2H2+-emission from naphthalene - the smallest PAH.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-63728 (URN)10.1063/1.3541252 (DOI)000286897600044 ()
Available from: 2011-10-27 Created: 2011-10-27 Last updated: 2017-12-08Bibliographically approved
5. Multiple ionization and fragmentation of isolated pyrene and coronene molecules in collision with ions
Open this publication in new window or tab >>Multiple ionization and fragmentation of isolated pyrene and coronene molecules in collision with ions
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2011 (English)In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 83, no 2, 022704- p.Article in journal (Refereed) Published
Abstract [en]

The interaction of multiply charged ions (He2+, O3+, and Xe20+) with gas-phase pericondensed polycyclic aromatic hydrocarbon (PAH) molecules of coronene (C24H12) and pyrene (C16H10) is studied for low-velocity collisions (v <= 0.6 a.u.). The mass spectrometric analysis shows that singly and up to quadruply charged intact molecules are important reaction products. The relative experimental yields are compared with the results of a simple classical over-the-barrier model. For higher molecular charge states, the experimental yields decrease much more strongly than the model predictions due to the instabilities of the multiply charged PAH molecules. Even-odd oscillations with the number of carbon atoms, n, in the intensity distributions of the CnHx+ fragments indicate a linear chain structure of the fragments similar to those observed for ion-C60 collisions. The latter oscillations are known to be due to dissociation energy differences between even-and odd-n Cn-chain molecules. For PAH molecules, the average numbers of H atoms attached to the CnHx chains are larger for even-n reflecting acetylenic bond systems.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-63730 (URN)10.1103/PhysRevA.83.022704 (DOI)000287076800006 ()
Available from: 2011-10-27 Created: 2011-10-27 Last updated: 2017-12-08Bibliographically approved
6. Unimolecular dissociation of anthracene and acridine cations: The importance of isomerization barriers for the C2H2 loss and HCN loss channels
Open this publication in new window or tab >>Unimolecular dissociation of anthracene and acridine cations: The importance of isomerization barriers for the C2H2 loss and HCN loss channels
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2011 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 135, 084304- p.Article in journal (Refereed) Published
Abstract [en]

The loss of C2H2 is a low activation energy dissociation channel for anthracene (C14H10) and acridine (C13H9N) cations. For the latter ion another prominent fragmentation pathway is the loss of HCN. We have studied these two dissociation channels by collision induced dissociation experiments of 50 keV anthracene cations and protonated acridine, both produced by electrospray ionization, in collisions with a neutral xenon target. In addition, we have carried out density functional theory calculations on possible reaction pathways for the loss of C2H2 and HCN. The mass spectra display features of multi-step processes, and for protonated acridine the dominant first step process is the loss of a hydrogen from the N site, which then leads to C2H2/HCN loss from the acridine cation. With our calculations we have identified three pathways for the loss of C2H2 from the anthracene cation, with three different cationic products: 2-ethynylnaphthalene, biphenylene, and acenaphthylene. The third product is the one with the overall lowest dissociation energy barrier. For the acridine cation our calculated pathway for the loss of C2H2 leads to the 3-ethynylquinoline cation, and the loss of HCN leads to the biphenylene cation. Isomerization plays an important role in the formation of the non-ethynyl containing products. All calculated fragmentation pathways should be accessible in the present experiment due to substantial energy deposition in the collisions.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-63731 (URN)10.1063/1.3626792 (DOI)
Available from: 2011-10-27 Created: 2011-10-27 Last updated: 2017-12-08Bibliographically approved
7. Ions Colliding with Cold Polycyclic Aromatic Hydrocarbon Clusters
Open this publication in new window or tab >>Ions Colliding with Cold Polycyclic Aromatic Hydrocarbon Clusters
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2010 (English)In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 105, no 21, 213401- p.Article in journal (Refereed) Published
Abstract [en]

We report the first experimental study of ions interacting with clusters of polycyclic aromatic hydrocarbon (PAH) molecules. Collisions between 11.25 keV He-3(+) or 360 keV Xe-129(20+) and weakly bound clusters of one of the smallest PAH molecules, anthracene, show that C14H10 clusters have much higher tendencies to fragment in ion collisions than other weakly bound clusters. The ionization is dominated by peripheral collisions in which the clusters, very surprisingly, are more strongly heated by Xe20+ collisions than by He+ collisions. The appearance size is k = 15 for [C14H10](k)(2+).

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-51342 (URN)10.1103/PhysRevLett.105.213401 (DOI)000284407400012 ()
Note
authorCount :16Available from: 2011-01-11 Created: 2011-01-10 Last updated: 2017-12-11Bibliographically approved
8. Ionization and fragmentation of polycyclic aromatic hydrocarbon clusters in collisions with keV ions
Open this publication in new window or tab >>Ionization and fragmentation of polycyclic aromatic hydrocarbon clusters in collisions with keV ions
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2011 (English)In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 84, no 4, 043201- p.Article in journal (Refereed) Published
Abstract [en]

We report on an experimental study of the ionization and fragmentation of clusters of k polycyclic aromatic hydrocarbon (PAH) molecules using anthracene, C14H10, or coronene, C24H12. These PAH clusters are moderately charged and strongly heated in small impact parameter collisions with 22.5-keV He2+ ions, after which they mostly decay in long monomer evaporation sequences with singly charged and comparatively cold monomers as dominating end products. We describe a simple cluster evaporation model and estimate the number of PAH molecules in the clusters that have to be hit by He2+ projectiles for such complete cluster evaporations to occur. Highly charged and initially cold clusters are efficiently formed in collisions with 360-keV Xe20+ ions, leading to cluster Coulomb explosions and several hot charged fragments, which again predominantly yield singly charged, but much hotter, monomer ions than the He2+ collisions. We present a simple formula, based on density-functional-theory calculations, for the ionization energy sequences as functions of coronene cluster size, rationalized in terms of the classic electrostatic expression for the ionization of a charged conducting object. Our analysis indicates that multiple electron removal by highly charged ions from a cluster of PAH molecules rapidly may become more important than single ionization as the cluster size k increases and that this is the main reason for the unexpectedly strong heating in these types of collisions.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-63732 (URN)10.1103/PhysRevA.84.043201 (DOI)000295712700013 ()
Available from: 2011-10-27 Created: 2011-10-27 Last updated: 2017-12-08Bibliographically approved

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