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Energetic processing of complex molecules in the gas phase
Stockholm University, Faculty of Science, Department of Physics.
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Collisions between molecules and gas phase targets often lead to various intriguing processes. Such collisions may induce fragmentation of molecules that can be divided into different subsets depending on the projectile, target, and collision energy. One major part of the present research is the exploration of astrophysical relevant collision mechanisms. In collisions between polycyclic aromatic hydrocarbon (PAH) molecules or fullerenes with, for example, helium, nuclear stopping can lead to the prompt knockout of a carbon atom from the molecule. Such a vacancy in the molecular carbon backbone can be highly reactive, and lead to the formation of larger molecules. The energy dependencies of such processes are important for the understanding of astrochemical molecular growth processes, which in turn may lead to the formation of larger and more complex molecules in space. In addition, hydrogenation of PAHs changes their structures and internal properties, including their resistance against fragmentation. To better understand the effects of hydrogenation on the fragmentation of PAHs, low energy photofragmentation experiments are presented along with the collision experiments, and a detailed comparison is made between the effects of these different types of energy transfer processes.

Besides astrophysically relevant research, studies on the response of biomolecules to collisions with gas phase targets are presented. Here, the energy dependence for formation of the protonated n-butyl β-ionone Schiff base through electrocyclization of the protonated n-butylamine Schiff base of all-trans-retinal in collisions is presented. The latter is a model compound for all-trans-retinal, the chromophore of the light sensitive opsin proteins, and such studies are essential for the understanding of the operation of mammal vision.

While our collision studies are very successful, they are sometimes also limited by the experimental timescale. Therefore, we have constructed an experimental setup for ion storage and fragmentation analysis. The goal of this new experiment is to store internally hot fragments to investigate their behavior on extended timescales and as functions of internal excitation energies.

Place, publisher, year, edition, pages
Department of Physics, Stockholm University , 2018.
National Category
Physical Sciences
Research subject
Physics
Identifiers
URN: urn:nbn:se:su:diva-149602ISBN: 978-91-7797-083-5 (print)ISBN: 978-91-7797-084-2 (electronic)OAI: oai:DiVA.org:su-149602DiVA, id: diva2:1163284
Public defence
2018-01-31, FB52, AlbaNova Universitetscentrum, Roslagstullsbacken 21, Stockholm, 13:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 5: Submitted. Paper 6: Submitted.

Available from: 2018-01-08 Created: 2017-12-06 Last updated: 2018-01-10Bibliographically approved
List of papers
1. 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: 2017-12-06Bibliographically approved
2. 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: 2017-12-14Bibliographically approved
3. PHOTO-STABILITY OF SUPER-HYDROGENATED PAHs DETERMINED BY ACTION SPECTROSCOPY EXPERIMENTS
Open this publication in new window or tab >>PHOTO-STABILITY OF SUPER-HYDROGENATED PAHs DETERMINED BY ACTION SPECTROSCOPY EXPERIMENTS
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2016 (English)In: Astrophysical Journal, ISSN 0004-637X, E-ISSN 1538-4357, Vol. 832, no 1, article id 24Article in journal (Refereed) Published
Abstract [en]

We have investigated the photo-stability of pristine and super-hydrogenated pyrene cations (C16H10+m+, m = 0, 6, or 16) by means of gas-phase action spectroscopy. Optical absorption spectra and photoinduced dissociation mass spectra are presented. By measuring the yield of mass-selected photo-fragment ions as a function of laser pulse intensity, the number of photons (and hence the energy) needed for fragmentation of the carbon backbone was determined. Backbone fragmentation of pristine pyrene ions (C16H10+) requires absorption of three photons of energy just below 3 eV, whereas super-hydrogenated hexahydropyrene (C16H16+) must absorb two such photons and fully hydrogenated hexadecahydropyrene (C16H26+) only a single photon. These results are consistent with previously reported dissociation energies for these ions. Our experiments clearly demonstrate that the increased heat capacity from the additional hydrogen atoms does not compensate for the weakening of the carbon backbone when pyrene is hydrogenated. In photodissociation regions, super-hydrogenated Polycyclic Aromatic Hydrocarbons (PAHs) have been proposed to serve as catalysts for H-2 formation. Our results indicate that carbon backbone fragmentation may be a serious competitor to H-2 formation at least for small hydrogenated PAHs like pyrene.

Keyword
ISM: molecules, photon-dominated region (PDR)
National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-137722 (URN)10.3847/0004-637X/832/1/24 (DOI)000388603600006 ()
Available from: 2017-01-17 Created: 2017-01-10 Last updated: 2017-12-14Bibliographically approved
4. 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: 2017-12-06Bibliographically approved
5. The threshold displacement energy of buckminsterfullerene and formation of endohedral defect fullerenes
Open this publication in new window or tab >>The threshold displacement energy of buckminsterfullerene and formation of endohedral defect fullerenes
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(English)In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114Article in journal (Refereed) Submitted
Abstract [en]

We have measured the threshold center-of-mass energy for knocking out a single carbon atom from C60 in C60-+He collisions.  Combining this experimental result with classical molecular dynamics simulations of such collisions we deduce a semi-empirical value of 24.1±0.5 eV for the C60 → C59+C threshold displacement energy, the minimum energy needed to remove a single carbon atom from the C60 cage. In addition, we oberserve the formation of the endohedral defect fullerene complex He@C59- and its decay product He@C58-.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-149589 (URN)
Funder
Swedish Research Council, 2016-03675Swedish Research Council, 2016-06625
Available from: 2017-12-06 Created: 2017-12-06 Last updated: 2017-12-22Bibliographically approved
6. Collision Induced Dissociation of the retinal chromophore Schiff base from sub-eV to keV collision energies
Open this publication in new window or tab >>Collision Induced Dissociation of the retinal chromophore Schiff base from sub-eV to keV collision energies
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(English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215Article in journal (Refereed) Submitted
Abstract [en]

The gas-phase fragmentation of the protonated n-butylamine Schiff base of all-trans-retinal (NB-RPSB) was measured in low- and high-energy collisional activation modes. The protonated n-butyl β-ionone Schiff base (NB-BISB) peak at m/z = 248, known to be formed as a result of a complex gas-phase rearrangement reaction, has been reported to dominate in mass spectra of NB-RPSB after photo- and collisionally activated fragmentation processes. Earlier reported high-energy collision (50 keV) mass spectra have shown a broad distribution of the fragments with the peak at m/z = 248 present but not dominating. We observed the formation of a peak at m/z = 248 only in collisional activation of NB-RPSB parent ion below a few eV, which shows that the rearrangement process is extremely efficient and happens in a very narrow energy range. On the other hand, our high-energy collision induced dissociation experiments yielded fragmentation patterns, which are fully accounted for simple bond cleavages of the NB-RPSB molecular backbone. We do not observe any peak corresponding to the formation of NB-BISB in the 10 eV – 1 keV collision energy range. This leaves the question open why this fragment reappears in the mass spectra at much higher energies.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-149529 (URN)
Funder
Swedish Research Council, 2015-04990Swedish Research Council, 2014-04501Swedish Research Council, 2016-06625Swedish Research Council, 2016-04181
Available from: 2017-12-06 Created: 2017-12-06 Last updated: 2017-12-22Bibliographically approved

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