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Collision- and photon-induced dynamics of complex molecular ions in the gas phase
Stockholm University, Faculty of Science, Department of Physics.ORCID iD: 0000-0003-0471-3844
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this thesis, I report experiments probing collision- and photon-induced molecular dynamics in the gas phase. Excited molecules formed in such interactions may relax by emitting electrons or photons, isomerization or fragmentation. For complex molecular systems, these processes typically occur on timescales exceeding picoseconds following statistical redistribution of the excitation energy across the internal degrees of freedom. However, energy transfer to molecules through ion/atom impact may in some cases lead to prompt atom knockout in Rutherford-type scattering processes on much faster timescales. Another example of such a non-statistical process is photon-induced excited-state proton transfer, a structural rearrangement occurring on the femtosecond timescale.

In this work, I investigate the competition between statistical and non-statistical fragmentation processes for a range of molecules colliding with He at center-of-mass energies in the sub-keV range. I show that heavy atom knockout is an important process for systems containing aromatic rings such as Polycyclic Aromatic Hydrocarbons (PAHs) or porphyrins, while statistical fragmentation processes dominate for less stable and/or smaller systems such as adenine or hydrogenated PAHs. Furthermore, I present the first measurements of the threshold energies for prompt single atom knockout from isolated molecules. The experimental results are interpreted with the aid of Molecular Dynamics (MD) simulations which allow us to extract the energy deposited into the system during a collision, knockout cross sections, fragmentation pathways and the structures of the fragments. The results presented in this work may be important for understanding the response of complex molecules to energetic processes in e.g. astrophysical environments.

Furthermore, I present the results of photodissociation and luminescence experiments probing flavin mono-anions in the gas phase. These are compared against calculations and previously measured spectra in solution. The discrepancies between the present results and the theoretical values suggest that more consideration of the vibronic structure is needed to model the photoabsorption and emission in flavins. Finally, I present the results of photoisomerisation experiments of flavin di-anions where two different isomers have been found and I discuss the proton transfer mechanisms which govern the structural changes.

Place, publisher, year, edition, pages
Stockholm: Department of Physics, Stockholm University , 2019. , p. 70
Keywords [en]
PAHs, Porphyrins, Adenine, Flavins, Biomolecules, Collisions, Experiments, Reactions, Non-Statistical Fragmentation, Molecular Dynamics, Photon-Induced Fragmentation, Luminescence, Photoisomerization, Proton Transfer
National Category
Atom and Molecular Physics and Optics
Research subject
Physics
Identifiers
URN: urn:nbn:se:su:diva-167001ISBN: 978-91-7797-632-5 (print)ISBN: 978-91-7797-633-2 (electronic)OAI: oai:DiVA.org:su-167001DiVA, id: diva2:1295747
Public defence
2019-04-25, FB42, AlbaNova universitetscentrum, Roslagstullsbacken 21, Stockholm, 13:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 1: Manuscript.

Available from: 2019-04-02 Created: 2019-03-12 Last updated: 2019-03-21Bibliographically approved
List of papers
1. Decay pathways for protonated and deprotonated Adenine molecules
Open this publication in new window or tab >>Decay pathways for protonated and deprotonated Adenine molecules
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(English)Manuscript (preprint) (Other academic)
National Category
Atom and Molecular Physics and Optics
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-166999 (URN)
Available from: 2019-03-12 Created: 2019-03-12 Last updated: 2019-03-14Bibliographically approved
2. Ion mobility action spectroscopy of flavin dianions reveals deprotomer-dependent photochemistry
Open this publication in new window or tab >>Ion mobility action spectroscopy of flavin dianions reveals deprotomer-dependent photochemistry
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2018 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 29, p. 19672-19681Article in journal (Refereed) Published
Abstract [en]

The intrinsic optical properties and photochemistry of flavin adenine dinucleotide (FAD) dianions are investigated using a combination of tandem ion mobility spectrometry and action spectroscopy. Two principal isomers are observed, the more stable form being deprotonated on the isoalloxazine group and a phosphate (N-3,PO4 deprotomer), and the other on the two phosphates (PO4,PO4 deprotomer). Ion mobility data and electronic action spectra suggest that photo-induced proton transfer occurs from the isoalloxazine group to a phosphate group, converting the PO4,PO4 deprotomer to the N-3,PO4 deprotomer. Comparisons of the isomer selective action spectra of FAD dianions and flavin monoanions with solution spectra and gas-phase photodissociation action spectra suggests that solvation shifts the electronic absorption of the deprotonated isoalloxazine group to higher energy. This is interpreted as evidence for significant charge transfer in the lowest optical transition of deprotonated isoalloxazine. Overall, this work demonstrates that the site of deprotonation of flavin anions strongly affects their electronic absorptions and photochemistry.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-162058 (URN)10.1039/c8cp03244k (DOI)000448132600043 ()30014081 (PubMedID)
Available from: 2018-11-28 Created: 2018-11-28 Last updated: 2019-03-14Bibliographically approved
3. Absorption and luminescence spectroscopy of mass-selected flavin adenine dinucleotide mono-anions
Open this publication in new window or tab >>Absorption and luminescence spectroscopy of mass-selected flavin adenine dinucleotide mono-anions
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2018 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 148, no 21, article id 214309Article in journal (Refereed) Published
Abstract [en]

We report the absorption profile of isolated Flavin Adenine Dinucleotide (FAD) mono-anions recorded using photo-induced dissociation action spectroscopy. In this charge state, one of the phosphoric acid groups is deprotonated and the chromophore itself is in its neutral oxidized state. These measurements cover the first four optical transitions of FAD with excitation energies from 2.3 to 6.0 eV (210-550 nm). The S-0 -> S-2 transition is strongly blue shifted relative to aqueous solution, supporting the view that this transition has a significant charge-transfer character. The remaining bands are close to their solution-phase positions. This confirms that the large discrepancy between quantum chemical calculations of vertical transition energies and solution-phase band maxima cannot be explained by solvent effects. We also report the luminescence spectrum of FAD mono-anions in vacuo. The gas-phase Stokes shift for S-1 is 3000 cm(-1), which is considerably larger than any previously reported for other molecular ions and consistent with a significant displacement of the ground and excited state potential energy surfaces. Consideration of the vibronic structure is thus essential for simulating the absorption and luminescence spectra of flavins.

National Category
Physical Sciences
Identifiers
urn:nbn:se:su:diva-158273 (URN)10.1063/1.5024028 (DOI)000434837600018 ()29884035 (PubMedID)
Available from: 2018-08-03 Created: 2018-08-03 Last updated: 2019-03-12Bibliographically approved
4. DESIREE electrospray ion source test bench and setup for collision induced dissociation experiments
Open this publication in new window or tab >>DESIREE electrospray ion source test bench and setup for collision induced dissociation experiments
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2018 (English)In: Review of Scientific Instruments, ISSN 0034-6748, E-ISSN 1089-7623, Vol. 89, no 7, article id 075102Article in journal (Refereed) Published
Abstract [en]

In this paper, we give a detailed description of an electrospray ion source test bench and a single-pass setup for ion fragmentation studies at the Double ElectroStatic Ion Ring ExpEriment infrastructure at Stockholm University. This arrangement allows for collision-induced dissociation experiments at the center-of-mass energies between 10 eV and 1 keV. Charged fragments are analyzed with respect to their kinetic energies (masses) by means of an electrostatic energy analyzer with a wide angular acceptance and adjustable energy resolution.

National Category
Accelerator Physics and Instrumentation Atom and Molecular Physics and Optics
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-156241 (URN)10.1063/1.5030528 (DOI)000440590200049 ()
Funder
Swedish Research Council, 2017-00621Swedish Research Council, 2014-4501Swedish Research Council, 2015-04990Swedish Research Council, 2016-03675Swedish Research Council, 2016-04181Swedish Research Council, 2016-06625
Available from: 2018-05-14 Created: 2018-05-14 Last updated: 2019-03-12Bibliographically approved
5. Knockout driven fragmentation of porphyrins
Open this publication in new window or tab >>Knockout driven fragmentation of porphyrins
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2017 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 30, p. 19750-19755Article in journal (Refereed) Published
Abstract [en]

We have studied collisions between tetraphenylporphyrin cations and He or Ne at center-of-mass energies in the range 50-110 eV. The experimental results were interpreted in view of density functional theory calculations of dissociation energies and classical molecular dynamics simulations of how the molecules respond to the He/Ne impact. We demonstrate that prompt atom knockout strongly contributes to the total destruction cross sections. Such impulse driven processes typically yield highly reactive fragments and are expected to be important for collisions with any molecular system in this collision energy range, but have earlier been very difficult to isolate for biomolecules.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-147092 (URN)10.1039/c7cp01583f (DOI)000407053000024 ()28627574 (PubMedID)
Available from: 2017-10-12 Created: 2017-10-12 Last updated: 2019-03-14Bibliographically approved
6. Hydrogenated pyrene: Statistical single-carbon loss below the knockout threshold
Open this publication in new window or tab >>Hydrogenated pyrene: Statistical single-carbon loss below the knockout threshold
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2016 (English)In: European Physical Journal D: Atomic, Molecular and Optical Physics, ISSN 1434-6060, E-ISSN 1434-6079, Vol. 70, no 4, article id 85Article in journal (Refereed) Published
Abstract [en]

An ongoing discussion revolves around the question of what effect hydrogenation has oncarbon backbone fragmentation in polycyclic aromatic hydrocarbons (PAHs). In order to shedmore light on this issue, we have measured absolute single carbon loss cross sections incollisions between native or hydrogenated pyrene cations (C16H+ 10+m , m = 0, 6, 16) and He as functions of center-of-massenergies down to 20 eV. Classical molecular dynamics (MD) simulations give further insightinto energy transfer processes and also yield m-dependent threshold energies for prompt(femtoseconds) carbon knockout. Such fast, non-statistical fragmentation processesdominate CH x -loss for native pyrene (m = 0), while much slowerstatistical fragmentation processes contribute significantly to single-carbon loss for thehydrogenated molecules (m =6 and m =16). The latter is shown by measurements of large CH x -loss crosssections far below the MD knockout thresholds for C16H+ 16 and C16H+ 26.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-129527 (URN)10.1140/epjd/e2016-60735-3 (DOI)000375296200002 ()
Available from: 2016-04-26 Created: 2016-04-25 Last updated: 2019-03-12Bibliographically approved
7. Threshold Energies for Single-Carbon Knockout from Polycyclic Aromatic Hydrocarbons
Open this publication in new window or tab >>Threshold Energies for Single-Carbon Knockout from Polycyclic Aromatic Hydrocarbons
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2015 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 6, no 22, p. 4504-4509Article in journal (Refereed) Published
Abstract [en]

We have measured absolute cross sections for ultrafast (femtosecond) single-carbon knockout from polycyclic aromatic hydrocarbon (PAR) cations as functions of He-PAR center-of-mass collision energy in the 10-200 eV range. Classical molecular dynamics (MD) simulations cover this range and extend up to 105 eV. The shapes of the knockout cross sections are well-described by a simple analytical expression yielding experimental and MD threshold energies of E-th(Exp) = 32.5 +/- 0.4 eV and E-th(MD) = 41.0 +/- 0.3 eV, respectively. These are the first measurements of knockout threshold energies for molecules isolated in vacuo. We further deduce semiempirical (SE) and MD displacement energies, i.e., the energy transfers to the PAH molecules at the threshold energies for knockout, of T-disp(SE) = 23.3 +/- 0.3 eV and T-disp(MD) = 27.0 +/- 0.3 eV. The semiempirical results compare favorably with measured displacement energies for graphene (T-disp = 23.6 eV).

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-124747 (URN)10.1021/acs.jpclett.5b02080 (DOI)000365460700010 ()
Available from: 2016-01-12 Created: 2016-01-04 Last updated: 2019-03-12Bibliographically approved
8. Failure of hydrogenation in protecting polycyclic aromatic hydrocarbons from fragmentation
Open this publication in new window or tab >>Failure of hydrogenation in protecting polycyclic aromatic hydrocarbons from fragmentation
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2015 (English)In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 92, no 5, article id 050702Article in journal (Refereed) Published
Abstract [en]

A recent study of soft x-ray absorption in native and hydrogenated coronene cations, C24H12+m + m = 0-7, led to the conclusion that additional hydrogen atoms protect (interstellar) polycyclic aromatic hydrocarbon (PAH) molecules from fragmentation [Reitsma et al., Phys. Rev. Lett. 113, 053002 (2014)]. The present experiment with collisions between fast (30-200 eV) He atoms and pyrene (C16H10+m +, m = 0, 6, and 16) and simulations without reference to the excitation method suggests the opposite. We find that the absolute carbon-backbone fragmentation cross section does not decrease but increases with the degree of hydrogenation for pyrene molecules.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-124759 (URN)10.1103/PhysRevA.92.050702 (DOI)000364807900001 ()
Available from: 2016-01-12 Created: 2016-01-04 Last updated: 2019-03-12Bibliographically approved

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