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Probing biomolecular fragmentation
Stockholm University, Faculty of Science, Department of Physics.
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: urn:nbn:se:su:diva-54524ISBN: 978-91-7447-228-8 (print)OAI: oai:DiVA.org:su-54524DiVA: diva2:395206
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
List of papers
1. 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
2. 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
3. Electron capture-induced dissociation of AK dipeptide dications: Influence of ion velocity, crown-ether complexation and collision gas
Open this publication in new window or tab >>Electron capture-induced dissociation of AK dipeptide dications: Influence of ion velocity, crown-ether complexation and collision gas
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2008 (English)In: International Journal of Mass Spectrometry, ISSN 1387-3806, E-ISSN 1873-2798, Vol. 276, no 2-3, 77-81 p.Article in journal (Refereed) Published
Abstract [en]

The fragmentation of doubly protonated AK dipeptide ions has been investigated after collisional electron transfer. Electron capture leads to three dominant channels, H loss, NH3 loss, and N–Cα bond breakage to give either c+ or z+ fragment ions. The relative importance of these channels has been explored as a function of ion velocity, the degree of complexation with crown ether, and collision gas. Our results indicate that H loss and NH3 loss are competing channels whereas the probability of N–Cα bond breakage is more or less constant.

Keyword
Electron capture-induced dissociation, Dipeptide, Collision gas, Electronically excited state
National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-17047 (URN)10.1016/j.ijms.2008.05.004 (DOI)000259846000002 ()
Available from: 2009-01-05 Created: 2009-01-05 Last updated: 2017-12-13Bibliographically approved
4. 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
5. Electron capture induced dissociation of doubly protonated pentapeptides: Dependence on molecular structure and charge separation
Open this publication in new window or tab >>Electron capture induced dissociation of doubly protonated pentapeptides: Dependence on molecular structure and charge separation
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2011 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 134, no 3, 035102- p.Article in journal (Refereed) Published
Abstract [en]

We have studied electron capture induced dissociation of a set of doubly protonated pentapeptides, all composed of one lysine (K) and either four glycine (G) or four alanine (A) residues, as a function of the sequence of these building blocks. Thereby the separation of the two charges, sequestered on the N-terminal amino group and the lysine side chain, is varied. The characteristic cleavage of N–Cα bonds is observed for all peptides over the whole backbone length, with the charge carrying fragments always containing K. The resulting fragmentation patterns are very similar if G is replaced by A. In the case of [XKXXX+2H]2+ (X=A or G), a distinct feature is observed in the distribution of backbone cleavage fragments and the probability for ammonia loss is drastically reduced. This may be due to an isomer with an amide oxygen as protonation site giving rise to the observed increase in breakage at a specific site in the molecule. For the other peptides, a correlation with the distance between amide oxygen and the charge at the lysine side chain has been found. This may be an indication that it is only the contribution from this site to the charge stabilization of the amide π* orbitals which determines relative fragment intensities. For comparison, complexes with two crown ether molecules have been studied as well. The crown ether provides a shielding of the charge and prevents the peptide from folding and internal hydrogen bonding, which leads to a more uniform fragmentation behavior.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-54521 (URN)10.1063/1.3533952 (DOI)000286472200071 ()
Available from: 2011-02-04 Created: 2011-02-04 Last updated: 2017-12-11Bibliographically approved
6. DESIREE as a new tool for interstellar ion chemistry
Open this publication in new window or tab >>DESIREE as a new tool for interstellar ion chemistry
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2008 (English)In: International Journal of Astrobiology, ISSN 1473-5504, E-ISSN 1475-3006, Vol. 7, no 3-4, 205-208 p.Article in journal (Refereed) Published
Abstract [en]

A novel cryogenic electrostatic storage device consisting of two ion-beam storage rings with a common straight section for studies of interactions between oppositely charged ions at low and well-defined relative velocities is under construction at Stockholm University. Here we consider the prospect of using this new tool to measure cross-sections and rate coefficients for mutual neutralization reactions of importance in interstellar ion chemistry in general and specifically in cosmic pre-biotic ion chemistry.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-32615 (URN)10.1017/S1473550408004229 (DOI)000273383100003 ()
Available from: 2009-12-15 Created: 2009-12-14 Last updated: 2017-12-12Bibliographically approved

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