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Molecular Hole Punching: Impulse Driven Reactions in Molecules and Molecular Clusters
Stockholm University, Faculty of Science, Department of Physics.ORCID iD: 0000-0003-1028-7976
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

When molecules are excited by photons or energetic particles, they will cool through the emission of photons, electrons, or by fragmenting. Such processes are often thermal as they occur after the excitation energy has been redistributed across all degrees-of-freedom in the system. Collisions with atoms or ions may also lead to ultrafast fragmentation in Rutherford-like scattering processes, where one or several atoms can literally be knocked out of the molecule by the incoming projectile before the energy can be completely redistributed. The resulting fragmentation pathways can in such knockout processes be very different from those in thermal processes.

This thesis covers extensive studies of collisions between ions/atoms and isolated Polycyclic Aromatic Hydrocarbon (PAH) molecules, isolated fullerene molecules, or clusters of these. The high stabilities and distinct fragmentation channels make these types of molecules excellent test cases for characterizing knockout-driven fragmentation and the reactions that these processes can lead to. I will present experimental measurements for a wide range of energies and compare them with my own molecular dynamics simulations and quantum chemical calculations. In this thesis, I present an in-depth study of the role of knockout in the energetic processing of molecules and clusters. The competition between knockout and thermally driven fragmentation is discussed in detail.

Knockout-driven fragmentation is shown to result in exotic fragments that are far more reactive than the intact parent molecules or fragments from thermal processes. When such reactive species are formed within molecular clusters efficient molecular growth can take place on sub-picosecond timescales. The cluster environments are crucial here because they protect the newly formed molecules by absorbing excess energy. This is a possible pathway for the growth of large PAHs, fullerenes, and similar carbonaceous complexes found in, for instance, the interstellar medium.

Place, publisher, year, edition, pages
Stockholm: Department of Physics, Stockholm University , 2016. , 74 p.
Keyword [en]
PAHs, Fullernes, Reactions, Clusters, Interstellar Medium, Fragmentation, Non-Statistical Fragmentation, Collisions, Experiments, Molecular Dynamics, Density Functional Theory
National Category
Atom and Molecular Physics and Optics
Research subject
Physics
Identifiers
URN: urn:nbn:se:su:diva-129523ISBN: 978-91-7649-436-3 (print)OAI: oai:DiVA.org:su-129523DiVA: diva2:923192
Public defence
2016-06-10, 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: Submitted.

Available from: 2016-05-18 Created: 2016-04-25 Last updated: 2017-02-17Bibliographically approved
List of papers
1. Knockout driven reactions in complex molecules and their clusters
Open this publication in new window or tab >>Knockout driven reactions in complex molecules and their clusters
(English)In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455Article in journal (Refereed) Submitted
Abstract [en]

Energetic ions lose some of their kinetic energies when interacting with electrons or nuclei in matter. Here, we discuss combined experimental and theoretical studies on such impulse driven reactions in Polycyclic Aromatic Hydrocarbons (PAHs), fullerenes, and pure or mixed clusters of these molecules. These studies show that the nature of excitation is important for how complex molecular systems respond to ion/atom impact. Rutherford-like nuclear scattering processes may lead to prompt atom knockout and formation of highly reactive fragments, while heating of the molecular electron clouds in general lead to formation of more stable and less reactive fragments. In this topical review, we focus on recent studies of knockout driven reactions, and present new calculations of the angular dependent threshold (displacement) energies for such processes in PAHs. The so formed fragments may efficiently form covalent bonds with neighboring molecules in clusters. These unique molecular growth processes may be important in astrophysical environments such as low velocity shock waves. 

National Category
Atom and Molecular Physics and Optics
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-129578 (URN)
Available from: 2016-04-26 Created: 2016-04-26 Last updated: 2017-11-30Bibliographically 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, 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
Atom and Molecular Physics and Optics
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: 2017-12-06Bibliographically approved
3. 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, 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
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, 4504-4509 p.Article 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. Molecular growth inside polycyclic aromatic hydrocarbon clusters induced by ion collisions
Open this publication in new window or tab >>Molecular growth inside polycyclic aromatic hydrocarbon clusters induced by ion collisions
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2015 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 6, no 9, 1536-1542 p.Article in journal (Refereed) Published
Abstract [en]

The present work combines experimental and theoretical studies of the collision between keV ion projectiles and clusters of pyrene, one of the simplest polycyclic aromatic hydrocarbons (PAHs). Intracluster growth processes induced by ion collisions lead to the formation of a wide range of new molecules with masses larger than that of the pyrene molecule. The efficiency of these processes is found to strongly depend on the mass and velocity of the incoming projectile. Classical molecular dynamics simulations of the entire collision process-from the ion impact (nuclear scattering) to the formation of new molecular species-reproduce the essential features of the measured molecular growth process and also yield estimates of the related absolute cross sections. More elaborate density functional tight binding calculations yield the same growth products as the classical simulations. The present results could be relevant to understand the physical chemistry of the PAH-rich upper atmosphere of Saturn’s moon Titan.

Keyword
poycyclic aromatic hydrogen, ion collisions, density functional tight binding molecular dynamics simulations, classical molecular dynamics
National Category
Atom and Molecular Physics and Optics
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-117140 (URN)10.1021/acs.jpclett.5b00405 (DOI)000355014900006 ()
Available from: 2015-05-08 Created: 2015-05-08 Last updated: 2017-12-04Bibliographically approved
6. Fragmentation of anthracene C14H10, acridine C13H9N and phenazine C12H8N2 ions in collisions with atoms
Open this publication in new window or tab >>Fragmentation of anthracene C14H10, acridine C13H9N and phenazine C12H8N2 ions in collisions with atoms
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2014 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 40, 21980-21987 p.Article in journal (Refereed) Published
Abstract [en]

We report experimental total, absolute, fragmentation cross sections for anthracene C14H10, acridine C13H9N, and phenazine C12H8N2 ions colliding with He at center-of-mass energies close to 100 eV. In addition, we report results for the same ions colliding with Ne, Ar, and Xe at higher energies. The total fragmentation cross sections for these three ions are the same within error bars for a given target. The measured fragment mass distributions reveal significant contributions from both delayed (>> 10(-12) s) statistical fragmentation processes as well as non-statistical, prompt (similar to 10(-15) s), single atom knockout processes. The latter dominate and are often followed by secondary statistical fragmentation. Classical Molecular Dynamics (MD) simulations yield separate cross sections for prompt and delayed fragmentation which are consistent with the experimental results. The intensity of the single C/N-loss peak, the signature of non-statistical fragmentation, decreases with the number of N atoms in the parent ion. The fragment intensity distributions for losses of more than one C or N atom are rather similar for C14H10 and C13H9N but differ strongly for C12H8N2 where weak C-N bonds often remain in the fragments after the first fragmentation step. This greatly increases their probability to fragment further. Distributions of internal energy remaining in the fragments after knockout are obtained from the MD simulations.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-109264 (URN)10.1039/c4cp03293d (DOI)000343072800009 ()
Note

AuthorCount:16;

Available from: 2014-11-24 Created: 2014-11-17 Last updated: 2017-12-05Bibliographically approved
7. Ions colliding with mixed clusters of C-60 and coronene: Fragmentation and bond formation
Open this publication in new window or tab >>Ions colliding with mixed clusters of C-60 and coronene: Fragmentation and bond formation
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2014 (English)In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 90, no 2, 022713Article in journal (Refereed) Published
Abstract [en]

We have studied collisions between 22.5 keV He2+ ions and mixed clusters [(C-60)(m)(C24H12)(n)] of m C-60 and n coronene molecules where m and n range up to about ten. Surprisingly, the cluster fragmentation behavior in distant collisions is dramatically different for pure coronene clusters (m = 0) and clusters containing a single C-60 molecule (m = 1). In the latter case, the clusters may be ionized without also being fragmented on the experimental time scale of tens of microseconds. This does not occur for pure coronene clusters, but is a main characteristic of pure fullerene clusters. For ion trajectories penetrating the mixed cluster, we observe covalent bond formations between C-59 or C-58 and C-60, but not between coronene fragments and C-60, or between C-60 fragments and coronene. These results are explained by means of classical molecular dynamics simulations of collisions inside the fragmenting mixed clusters.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-108022 (URN)10.1103/PhysRevA.90.022713 (DOI)000341233200006 ()
Note

AuthorCount:13;

Available from: 2014-10-07 Created: 2014-10-06 Last updated: 2017-12-05Bibliographically approved
8. Absolute fragmentation cross sections in atom-molecule collisions: Scaling laws for non-statistical fragmentation of polycyclic aromatic hydrocarbon molecules
Open this publication in new window or tab >>Absolute fragmentation cross sections in atom-molecule collisions: Scaling laws for non-statistical fragmentation of polycyclic aromatic hydrocarbon molecules
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2014 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 140, no 22, 224306Article in journal (Refereed) Published
Abstract [en]

We present scaling laws for absolute cross sections for non-statistical fragmentation in collisions between Polycyclic Aromatic Hydrocarbons (PAH/PAH(+)) and hydrogen or helium atoms with kinetic energies ranging from 50 eV to 10 keV. Further, we calculate the total fragmentation cross sections (including statistical fragmentation) for 110 eV PAH/PAH(+) + He collisions, and show that they compare well with experimental results. We demonstrate that non-statistical fragmentation becomes dominant for large PAHs and that it yields highly reactive fragments forming strong covalent bonds with atoms (H and N) and molecules (C6H5). Thus nonstatistical fragmentation may be an effective initial step in the formation of, e. g., Polycyclic Aromatic Nitrogen Heterocycles (PANHs). This relates to recent discussions on the evolution of PAHNs in space and the reactivities of defect graphene structures.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-106342 (URN)10.1063/1.4881603 (DOI)000337806100023 ()
Note

AuthorCount:15;

Available from: 2014-08-08 Created: 2014-08-04 Last updated: 2017-12-05Bibliographically approved
9. Nonstatistical fragmentation of large molecules
Open this publication in new window or tab >>Nonstatistical fragmentation of large molecules
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2014 (English)In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 89, no 3, 032701Article in journal (Refereed) Published
Abstract [en]

We present experimental evidence for the dominance of prompt single-atom knockout in fragmenting collisions between large polycyclic aromatic hydrocarbon cations and He atoms at center-of-mass energies close to 100 eV. Such nonstatistical processes are shown to give highly reactive fragments. We argue that nonstatistical fragmentation is dominant for any sufficiently large molecular system under similar conditions.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-102212 (URN)10.1103/PhysRevA.89.032701 (DOI)000332340800004 ()
Funder
Swedish Research Council, 621-2012-3662, 621-2012-3660, 621-2011-4047
Note

AuthorCount: 18;

Available from: 2014-03-28 Created: 2014-03-28 Last updated: 2017-12-05Bibliographically approved
10. Non-statistical fragmentation of PAHs and fullerenes in collisions with atoms
Open this publication in new window or tab >>Non-statistical fragmentation of PAHs and fullerenes in collisions with atoms
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2014 (English)In: International Journal of Mass Spectrometry, ISSN 1387-3806, E-ISSN 1873-2798, Vol. 365, 260-265 p.Article in journal (Refereed) Published
Abstract [en]

Non-statistical fragmentation processes may be important when Polycyclic Aromatic Hydrocarbon molecules (PAHs), fullerenes, or other large complex molecules collide with atoms and atomic ions. For collisions with hydrogen or helium this occurs for center-of-mass energies between a few tens to a few hundreds of electron volts and typically results in losses of single atoms. In such processes one forms much more reactive fragments than in statistical fragmentation, which instead are dominated by losses of C2- or C2H2-molecules (H-atoms) from fullerenes and PAHs, respectively. An enhanced reactivity has recently been demonstrated for van der Waals clusters of C60 molecules where prompt knockouts of single C-atoms from one of the fullerenes yield highly reactive C59+ fragments, which easily form covalent bonds with a C60 molecule inside the clusters

Keyword
Fullerene, PAH, Knockout, Ion collisions, Molecular fusion, Non-statistical fragmentation
National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-102211 (URN)10.1016/j.ijms.2013.12.013 (DOI)000338622200042 ()
Available from: 2014-03-28 Created: 2014-03-28 Last updated: 2017-12-05Bibliographically approved
11. Ions colliding with clusters of fullerenes-Decay pathways and covalent bond formations
Open this publication in new window or tab >>Ions colliding with clusters of fullerenes-Decay pathways and covalent bond formations
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2013 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 139, no 3, 034309Article in journal (Refereed) Published
Abstract [en]

We report experimental results for the ionization and fragmentation of weakly bound van der Waals clusters of n C-60 molecules following collisions with Ar2+, He2+, and Xe20+ at laboratory kinetic energies of 13 keV, 22.5 keV, and 300 keV, respectively. Intact singly charged C-60 monomers are the dominant reaction products in all three cases and this is accounted for by means of Monte Carlo calculations of energy transfer processes and a simple Arrhenius-type [C-60](n)(+) -> C-60(+) + (n - 1)C-60 evaporation model. Excitation energies in the range of only similar to 0.7 eV per C-60 molecule in a [C-60](13)(+) cluster are sufficient for complete evaporation and such low energies correspond to ion trajectories far outside the clusters. Still we observe singly and even doubly charged intact cluster ions which stem from even more distant collisions. For penetrating collisions the clusters become multiply charged and some of the individual molecules may be promptly fragmented in direct knock-out processes leading to efficient formations of new covalent systems. For Ar2+ and He2+ collisions, we observe very efficient C-119(+) and C-118(+) formation and molecular dynamics simulations suggest that they are covalent dumb-bell systems due to bonding between C-59(+) or C-58(+) and C-60 during cluster fragmentation. In the Ar2+ case, it is possible to form even smaller C-120-2m(+) molecules (m = 2-7), while no molecular fusion reactions are observed for the present Xe20+ collisions.

National Category
Atom and Molecular Physics and Optics
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-92922 (URN)10.1063/1.4812790 (DOI)000322203000028 ()
Funder
Swedish Research Council, 621-2008-3773Swedish Research Council, 621-2009-3468Swedish Research Council, 621-2011-4047EU, European Research Council, 246976
Note

AuthorCount:23;

Available from: 2013-08-30 Created: 2013-08-26 Last updated: 2017-12-06Bibliographically approved
12. Formations of Dumbbell C-118 and C-119 inside Clusters of C-60 Molecules by Collision with alpha Particles
Open this publication in new window or tab >>Formations of Dumbbell C-118 and C-119 inside Clusters of C-60 Molecules by Collision with alpha Particles
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2013 (English)In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 110, no 18, 185501Article in journal (Refereed) Published
Abstract [en]

We report highly selective covalent bond modifications in collisions between keV alpha particles and van der Waals clusters of C-60 fullerenes. Surprisingly, C-119(+) and C-118(+) are the dominant molecular fusion products. We use molecular dynamics simulations to show that C-59(+) and C-58(+) ions-effectively produced in prompt knockout processes with He2+-react rapidly with C-60 to form dumbbell C-119(+) and C-118(+). Ion impact on molecular clusters in general is expected to lead to efficient secondary reactions of interest for astrophysics. These reactions are different from those induced by photons.

National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:su:diva-91298 (URN)10.1103/PhysRevLett.110.185501 (DOI)000319019300008 ()
Funder
Swedish Research Council, 621-2008-3773, 621-2009-3468, 621-2011-4047EU, European Research Council, 246976
Note

AuthorCount:22;

Available from: 2013-06-27 Created: 2013-06-24 Last updated: 2017-12-06Bibliographically approved

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