1
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Abid A, Veteläinen O, Boudjemia N, Pelimanni E, Kivimäki A, Alatalo M, Huttula M, Björneholm O, Patanen M. Forming Bonds While Breaking Old Ones: Isomer-Dependent Formation of H 3O + from Aminobenzoic Acid During X-ray-Induced Fragmentation. J Phys Chem A 2023; 127:1395-1401. [PMID: 36749682 PMCID: PMC9940210 DOI: 10.1021/acs.jpca.2c06869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Intramolecular hydrogen transfer, a reaction where donor and acceptor sites of a hydrogen atom are part of the same molecule, is a ubiquitous reaction in biochemistry and organic synthesis. In this work, we report hydronium ion (H3O+) production from aminobenzoic acid (ABA) after core-level ionization with soft X-ray synchrotron radiation. The formation of H3O+ during the fragmentation requires that at least two hydrogen atoms migrate to one of the oxygen atoms within the molecule. The comparison of two structural isomers, ortho- and meta-ABA, revealed that the production of H3O+ depends strongly on the structure of the molecule, the ortho-isomer being much more prone to produce H3O+. The isomer-dependency suggests that the amine group acts as a donor in the hydrogen transfer process. In the case of ortho-ABA, detailed H3O+ production pathways were investigated using photoelectron-photoion-photoion coincidence (PEPIPICO) spectroscopy. It was found that H3O+ can result from a direct two-body dissociation but also from sequential fragmentation processes.
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Affiliation(s)
- Abdul
Rahman Abid
- Nano
and Molecular Systems Research Unit, University
of Oulu, 90570 Oulu, Finland,Molecular
and Condensed Matter Physics, Uppsala University, 75120 Uppsala, Sweden
| | - Onni Veteläinen
- Nano
and Molecular Systems Research Unit, University
of Oulu, 90570 Oulu, Finland
| | - Nacer Boudjemia
- Nano
and Molecular Systems Research Unit, University
of Oulu, 90570 Oulu, Finland
| | - Eetu Pelimanni
- Nano
and Molecular Systems Research Unit, University
of Oulu, 90570 Oulu, Finland
| | - Antti Kivimäki
- Nano
and Molecular Systems Research Unit, University
of Oulu, 90570 Oulu, Finland,MAX
IV Laboratory, Lund University, 22100 Lund, Sweden
| | - Matti Alatalo
- Nano
and Molecular Systems Research Unit, University
of Oulu, 90570 Oulu, Finland
| | - Marko Huttula
- Nano
and Molecular Systems Research Unit, University
of Oulu, 90570 Oulu, Finland
| | - Olle Björneholm
- Molecular
and Condensed Matter Physics, Uppsala University, 75120 Uppsala, Sweden
| | - Minna Patanen
- Nano
and Molecular Systems Research Unit, University
of Oulu, 90570 Oulu, Finland,
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2
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Long BA, Eyet N, Williamson J, Shuman NS, Ard SG, Viggiano AA. Kinetics for the Reactions of H 3O +(H 2O) n=0-3 with Isoprene (2-Methyl-1,3-butadiene) as a Function of Temperature (300-500 K). J Phys Chem A 2022; 126:7202-7209. [PMID: 36169997 DOI: 10.1021/acs.jpca.2c05287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report kinetics studies of H3O+(H2O)n=0-3 with isoprene (2-methyl-1,3-butadiene, C5H8) as a function of temperature (300-500 K) measured using a flowing afterglow-selected ion flow tube. Results are supported by density functional (DFT) calculations at the B3LYP/def2-TZVP level. H3O+ (n = 0) reacts with isoprene near the collision limit exclusively via proton transfer to form C5H9+. The first hydrate (n = 1) also reacts at the collision limit and only the proton transfer product is observed, although hydrated protonated isoprene may have been produced and dissociated thermally. Addition of a second water (n = 2) lowers the rate constant by about a factor of 10. The proton transfer of H3O+(H2O)2 to isoprene is endothermic, but transfer of the water ligands lowers the thermicity and the likely process occurring is H3O+(H2O)2 + C5H8 → C5H9+(H2O)2 + H2O, followed by thermal dissociation of C5H9+(H2O)2. Statistical modeling indicates the amount of reactivity is consistent with the process being slightly endothermic, as is indicated by the DFT calculations. This reactivity was obscured in past experiments due to the presence of water in the reaction zone. The third hydrate is observed not to react and helps explain the past results for n = 2, as n = 2 and 3 were in equilibrium in that flow tube experiment. Very little dependence on temperature was found for the three species that did react. Finally, the C5H9+ proton transfer product further reacted with isoprene to produce mainly C6H9+ along with a small amount of clustering.
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Affiliation(s)
- Bryan A Long
- Air Force Research Laboratory, Space Vehicles Directorate, Kirtland Air Force Base, Albuquerque, New Mexico 87117, United States
| | - Nicole Eyet
- Chemistry Department, Saint Anselm College, Manchester, New Hampshire 03102, United States
| | - John Williamson
- Institute for Scientific Research, Boston College, Boston, Massachusetts 02467, United States
| | - Nicholas S Shuman
- Air Force Research Laboratory, Space Vehicles Directorate, Kirtland Air Force Base, Albuquerque, New Mexico 87117, United States
| | - Shaun G Ard
- Air Force Research Laboratory, Space Vehicles Directorate, Kirtland Air Force Base, Albuquerque, New Mexico 87117, United States
| | - Albert A Viggiano
- Air Force Research Laboratory, Space Vehicles Directorate, Kirtland Air Force Base, Albuquerque, New Mexico 87117, United States
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3
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Hemberger P, Wu X, Pan Z, Bodi A. Continuous Pyrolysis Microreactors: Hot Sources with Little Cooling? New Insights Utilizing Cation Velocity Map Imaging and Threshold Photoelectron Spectroscopy. J Phys Chem A 2022; 126:2196-2210. [PMID: 35316066 DOI: 10.1021/acs.jpca.2c00766] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Resistively heated silicon carbide microreactors are widely applied as continuous sources to selectively prepare elusive and reactive intermediates with astrochemical, catalytic, or combustion relevance to measure their photoelectron spectrum. These reactors also provide deep mechanistic insights into uni- and bimolecular chemistry. However, the sampling conditions and effects have not been fully characterized. We use cation velocity map imaging to measure the velocity distribution of the molecular beam signal and to quantify the scattered, rethermalized background sample. Although translational cooling is efficient in the adiabatic expansion from the reactor, the breakdown diagrams of methane and chlorobenzene confirm that the molecular beam component exhibits a rovibrational temperature comparable with that of the reactor. Thus, rovibrational cooling is practically absent in the expansion from the microreactor. The high rovibrational temperature also affects the threshold photoelectron spectrum of both benzene and the allyl radical in the molecular beam, but to different degrees. While the extreme broadening of the benzene TPES suggests a complex ionization mechanism, the allyl TPES is in fact consistent with an internal temperature close to that of the reactor. The background, room-temperature spectra of both are superbly reproduced by Franck-Condon simulations at 300 K. On the one hand, this leads us to suggest that room-temperature reference spectra should be used in species identification. On the other hand, analysis of the allyl iodide pyrolysis data shows that iodine atoms often recombine to form molecular iodine on the chamber surfaces. Such sampling effects may distort the chemical composition of the scattered background with respect to the molecular beam signal emanating directly from the reactor. This must be considered in quantitative analyses and kinetic modeling.
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Affiliation(s)
- Patrick Hemberger
- Paul Scherrer Insitute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - Xiangkun Wu
- Paul Scherrer Insitute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - Zeyou Pan
- Paul Scherrer Insitute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
| | - Andras Bodi
- Paul Scherrer Insitute, Forschungsstrasse 111, CH-5232 Villigen PSI, Switzerland
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4
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Rösch D, Almeida R, Sztáray B, Osborn DL. High-Resolution Double Velocity Map Imaging Photoelectron Photoion Coincidence Spectrometer for Gas-Phase Reaction Kinetics. J Phys Chem A 2022; 126:1761-1774. [PMID: 35258948 DOI: 10.1021/acs.jpca.1c10293] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present a new photoelectron photoion coincidence (PEPICO) spectrometer that combines high mass resolution of cations with independently adjustable velocity map imaging of both cations and electrons. We photoionize atoms and molecules using fixed-frequency vacuum ultraviolet radiation. Mass-resolved photoelectron spectra associated with each cation's mass-to-charge ratio can be obtained by inversion of the photoelectron image. The mass-resolved photoelectron spectra enable kinetic time-resolved probing of chemical reactions with isomeric resolution using fixed-frequency radiation sources amenable to small laboratory settings. The instrument accommodates a variety of sample delivery sources to explore a broad range of physical chemistry. To demonstrate the time-resolved capabilities of the instrument, we study the 193 nm photodissociation of SO2 via the C̃(1B2) ← X̃(1A1) transition. In addition to the well-documented O(3Pj) + SO(3Σ-) channel, we observe direct evidence for a small yield of S(3Pj) + O2(3Σg-) as a primary photodissociation product channel, which may impact sulfur mass-independent fractionation chemistry.
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Affiliation(s)
- Daniel Rösch
- Combustion Research Facility, Sandia National Laboratories, Mail Stop 9055, Livermore, California 94551-0969, United States
| | - Raybel Almeida
- Combustion Research Facility, Sandia National Laboratories, Mail Stop 9055, Livermore, California 94551-0969, United States
| | - Bálint Sztáray
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
| | - David L Osborn
- Combustion Research Facility, Sandia National Laboratories, Mail Stop 9055, Livermore, California 94551-0969, United States.,Department of Chemical Engineering, University of California, Davis, Davis, California 95616, United States
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5
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Wu X, Zhou X, Bjelić S, Hemberger P, Sztáray B, Bodi A. A plethora of isomerization processes and hydrogen scrambling in the fragmentation of the methanol dimer cation: a PEPICO study. Phys Chem Chem Phys 2022; 24:1437-1446. [PMID: 34984425 DOI: 10.1039/d1cp05155e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The valence photoionization of light and deuterated methanol dimers was studied by imaging photoelectron photoion coincidence spectroscopy in the 10.00-10.35 eV photon energy range. Methanol clusters were generated in a rich methanol beam in nitrogen after expansion into vacuum. They generally photoionize dissociatively to protonated methanol cluster cations, (CH3OH)nH+. However, the stable dimer parent ion (CH3OH)2+ is readily detected below the dissociation threshold to yield the dominant CH3OH2+ fragment ion. In addition to protonated methanol, we could also detect the water- and methyl-loss fragment ions of the methanol dimer cation for the first time. These newly revealed fragmentation channels are slow and cannot compete with protonated methanol cation formation at higher internal energies. In fact, the water- and methyl-loss fragment ions appear together and disappear at a ca. 150 meV higher energy in the breakdown diagram. Experiments with selectively deuterated methanol samples showed H scrambling involving two hydroxyl and one methyl hydrogens prior to protonated methanol formation. These insights guided the potential energy surface exploration to rationalize the dissociative photoionization mechanism. The potential energy surface was further validated by a statistical model including isotope effects to fit the experiment for the light and the perdeuterated methanol dimers simultaneously. The (CH3OH)2+ parent ion dissociates via five parallel channels at low internal energies. The loss of both CH2OH and CH3O neutral fragments leads to protonated methanol. However, the latter, direct dissociation channel is energetically forbidden at low energies. Instead, an isomerization transition state is followed by proton transfer from a methyl group, which leads to the CH3(H)OH+⋯CH2OH ion, the precursor to the CH2OH-, H2O-, and CH3-loss fragments after further isomerization steps, in part by a roaming mechanism. Water loss yields the ethanol cation, and two paths are proposed to account for m/z 49 fragment ions after CH3 loss. The roaming pathways are quickly outcompeted by hydrogen bond breaking to yield CH3OH2+, which explains the dominance of the protonated methanol fragment ion in the mass spectrum.
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Affiliation(s)
- Xiangkun Wu
- Paul Scherrer Institute, 5232 Villigen, Switzerland.
| | - Xiaoguo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Saša Bjelić
- Paul Scherrer Institute, 5232 Villigen, Switzerland.
| | | | - Bálint Sztáray
- University of the Pacific, Department of Chemistry, Stockton, CA 95211, USA
| | - Andras Bodi
- Paul Scherrer Institute, 5232 Villigen, Switzerland.
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6
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Giustini A, Winfough M, Czekner J, Sztáray B, Meloni G, Bodi A. Photoionization of Two Potential Biofuel Additives: γ-Valerolactone and Methyl Butyrate. J Phys Chem A 2021; 125:10711-10724. [PMID: 34918933 DOI: 10.1021/acs.jpca.1c08033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photoionization of two potential biofuel additives, γ-valerolactone (GVL, C5H8O2) and methyl butyrate (MB, C5H10O2) has been studied by imaging photoelectron photoion coincidence spectroscopy (iPEPICO) at the VUV beamline of the Swiss Light Source (SLS). The vibrational fine structure in the photoelectron spectrum is compared with a Franck-Condon simulation for the electronic ground-state band of the GVL cation. In the lowest energy dissociative photoionization channel of GVL, CO2 is lost, resulting in a 1-butene fragment ion with a 0 K appearance energy of E0 = 10.35 ± 0.01 eV. A newly calculated 1-butene ionization energy of 9.595 ± 0.015 eV establishes the reverse barrier height to CO2 loss as 66.6 ± 4.3 kJ mol-1. Methyl butyrate cations undergo McLafferty rearrangement, which explains the missing ion signal at the computed adiabatic ionization energy of 9.25 eV. After H transfer, ethylene is lost in the lowest energy dissociation channel to yield the methyl acetate enol ion at E0 = 10.24 ± 0.04 eV. This value connects the energetics of methyl butyrate with that of methyl acetate enol ion, which is established at ΔfHo0K[CH2C(OH)OCH3+] = 502 ± 6 kJ mol-1. Parallel to ethylene loss, methyl loss is also observed from the enol tautomer of the parent ion. Both samples exhibit low-energy nonstatistical dissociative ionization channels. In GVL, the methyl-loss abundance rises quickly but levels off suddenly in the energy range of the first electronically excited states, indicating nonstatistical competition between CH3 and CO2 loss. In MB, the major parallel dissociation channel is the loss of a methoxy radical. Calculations indicate that McLafferty rearrangement is inhibited on the excited-state surface. Indeed, breakdown curve modeling of this and a sequential CO-loss channel confirms a second statistical regime in dissociative photoionization, decoupled from ethylene loss.
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Affiliation(s)
- Andrea Giustini
- Dipartimento di Scienze Fisiche e Chimiche, University of L'Aquila, 67100 L'Aquila, Italy
| | - Matthew Winfough
- Department of Chemistry, University of San Francisco, 2130 Fulton Street, San Francisco, California 94117-1080, United States
| | - Joseph Czekner
- Institut für Physikalische Chemie II, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Bálint Sztáray
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, California 95211, United States
| | - Giovanni Meloni
- Dipartimento di Scienze Fisiche e Chimiche, University of L'Aquila, 67100 L'Aquila, Italy.,Department of Chemistry, University of San Francisco, 2130 Fulton Street, San Francisco, California 94117-1080, United States
| | - Andras Bodi
- Laboratory for Femtochemistry and Synchrotron Radiation, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland
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7
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Abstract
![]()
Cluster-size-resolved
ultrafast dynamics of the solvated electron
in neutral water clusters with n = 3 to ∼200
molecules are studied with pump–probe time-of-flight mass spectrometry
after below band gap excitation. For the smallest clusters, no longer-lived
(>100–200 fs) hydrated electrons were detected, indicating
a minimum size of n ∼ 14 for being able to
sustain hydrated electrons. Larger clusters show a systematic increase
of the number of hydrated electrons per molecule on the femtosecond
to picosecond time scale. We propose that with increasing cluster
size the underlying dynamics is governed by more effective electron
formation processes combined with less effective electron loss processes,
such as ultrafast hydrogen ejection and recombination. It appears
unlikely that any size dependence of the solvent relaxation dynamics
would be reflected in the observed time-resolved ion yields.
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Affiliation(s)
- Loren Ban
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Bruce L Yoder
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Ruth Signorell
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
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8
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Hartweg S, Garcia GA, Nahon L. Photoelectron Spectroscopy of the Water Dimer Reveals Unpredicted Vibrational Structure. J Phys Chem A 2021; 125:4882-4887. [PMID: 34028282 DOI: 10.1021/acs.jpca.1c03201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen bonds and proton transfer reactions can be considered as being at the very heart of aqueous chemistry and of utmost importance for many processes of biological relevance. Nevertheless, these processes are not yet well understood, even in seemingly simple model systems like small water clusters. We present a study of the photoelectron spectrum of the water dimer, revealing previously unresolved vibrational structure with 10-30 meV (80-242 cm-1) typical splitting, in disagreement with a previous theoretical photoionization study predicting an apparent main vibrational progression with an ∼130 meV spacing [Kamarchik et al.; J. Chem. Phys. 2010, 132, 194311]. The observed vibrational structure and its deviation from the theoretical prediction is discussed in terms of known difficulties with calculations of strongly coupled anharmonic systems involving large amplitude motions. Potential contributions of the nonzero vibrational energy of the neutral water dimer at a finite experimental internal temperature are addressed. The internal temperature is estimated from the breakdown diagram associated with the dissociative ionization of the water dimer to be around to 130 K. This analysis also provides two additional, independently measured values for the 0 K appearance energy of the hydronium ion (H3O+) from dissociative ionization of the water dimer.
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Affiliation(s)
- Sebastian Hartweg
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin BP 48, 91192 Gif sur Yvette Cedex, France
| | - Gustavo A Garcia
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin BP 48, 91192 Gif sur Yvette Cedex, France
| | - Laurent Nahon
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin BP 48, 91192 Gif sur Yvette Cedex, France
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9
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Bodi A, Hemberger P, Tuckett RP. From Energetics to Intracluster Chemistry: Valence Photoionization of Trifluoromethylsulfur Pentafluoride (CF 3SF 5) by Double Velocity Map Imaging. J Phys Chem A 2021; 125:2601-2611. [PMID: 33729793 DOI: 10.1021/acs.jpca.1c00918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Trifluoromethylsulfur pentafluoride (CF3SF5) was valence threshold photoionized in a double imaging photoelectron photoion coincidence spectrometer using vacuum ultraviolet synchrotron radiation. In the 12.5-16.4 eV photon energy range, CF3+, SF5+, and SF3+ cations were observed in both room temperature (RT) and molecular beam (MB) experiments. Their fractional abundances exhibited differences beyond the sample temperature. Kinetic energy analysis of the fragment ions confirmed the difference in the dissociative photoionization mechanism. In the RT experiment, the CF3+ kinetic energies were extrapolated to a 11.84 ± 0.15 eV threshold, which was used in an ion cycle to determine the enthalpy of formation of CF3SF5 as ΔfH°298K(CF3SF5) = -1593 ± 16 kJ mol-1. We also updated the enthalpy of formation of the sulfur pentafluoride radical as ΔfH°298K(SF5) = -854 ± 7 kJ mol-1 and discuss the discrepancy between the CF3 ionization energy based on the Active Thermochemical Tables and the value anchored to the CF ionization energy. A computed reaction enthalpy network optimization resulted in ΔfH°298K(CF3SF5) = -1608 ± 20 kJ mol-1. Both values for ΔfH°298K(CF3SF5) agree with previous ab initio ones in contrast to the original, experimental determination. SF3+ is formed by F-transfer processes both in the RT and MB experiments. Although the same peaks were observed in both experiments, the lower SF3+ onset energy and the more slowly rising CF3+ kinetic energy release in the MB experiment revealed clustering and intracluster F-transfer reactions upon ionization. The monomer and dimer cation potential energy surfaces were explored to rationalize the observations. In the dimer cation, the observer CF3SF5 catalyzes fluorine transfer and promotes CF4 formation, which ultimately leads to the SF3+ fragment ion.
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Affiliation(s)
- Andras Bodi
- Laboratory for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Patrick Hemberger
- Laboratory for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Richard P Tuckett
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
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10
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Photobiomodulation and Oxidative Stress: 980 nm Diode Laser Light Regulates Mitochondrial Activity and Reactive Oxygen Species Production. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6626286. [PMID: 33763170 PMCID: PMC7952159 DOI: 10.1155/2021/6626286] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/09/2021] [Accepted: 02/17/2021] [Indexed: 12/20/2022]
Abstract
Photobiomodulation with 808 nm laser light electively stimulates Complexes III and IV of the mitochondrial respiratory chain, while Complexes I and II are not affected. At the wavelength of 1064 nm, Complexes I, III, and IV are excited, while Complex II and some mitochondrial matrix enzymes seem to be not receptive to photons at that wavelength. Complex IV was also activated by 633 nm. The mechanism of action of wavelengths in the range 900–1000 nm on mitochondria is less understood or not described. Oxidative stress from reactive oxygen species (ROS) generated by mitochondrial activity is an inescapable consequence of aerobic metabolism. The antioxidant enzyme system for ROS scavenging can keep them under control. However, alterations in mitochondrial activity can cause an increment of ROS production. ROS and ATP can play a role in cell death, cell proliferation, and cell cycle arrest. In our work, bovine liver isolated mitochondria were irradiated for 60 sec, in continuous wave mode with 980 nm and powers from 0.1 to 1.4 W (0.1 W increment at every step) to generate energies from 6 to 84 J, fluences from 7.7 to 107.7 J/cm2, power densities from 0.13 to 1.79 W/cm2, and spot size 0.78 cm2. The control was equal to 0 W. The activity of the mitochondria's complexes, Krebs cycle enzymes, ATP production, oxygen consumption, generation of ROS, and oxidative stress were detected. Lower powers (0.1–0.2 W) showed an inhibitory effect; those that were intermediate (0.3–0.7 W) did not display an effect, and the higher powers (0.8–1.1 W) induced an increment of ATP synthesis. Increasing the power (1.2–1.4 W) recovered the ATP production to the control level. The interaction occurred on Complexes III and IV, as well as ATP production and oxygen consumption. Results showed that 0.1 W uncoupled the respiratory chain and induced higher oxidative stress and drastic inhibition of ATP production. Conversely, 0.8 W kept mitochondria coupled and induced an increase of ATP production by increments of Complex III and IV activities. An augmentation of oxidative stress was also observed, probably as a consequence of the increased oxygen consumption and mitochondrial isolation experimental conditions. No effect was observed using 0.5 W, and no effect was observed on the enzymes of the Krebs cycle.
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11
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Weidner P, Ray AW, Bodi A, Sztáray B. Dissociative Photoionization of Methyl Vinyl Ketone-Thermochemical Anchors and a Drifting Methyl Group. J Phys Chem A 2021; 125:848-856. [PMID: 33464085 DOI: 10.1021/acs.jpca.0c10665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dissociative photoionization of methyl vinyl ketone (MVK), an important intermediate in the atmospheric oxidation of isoprene, has been studied by photoelectron photoion coincidence spectroscopy. In the photon energy range of 9.5-13.8 eV, four main fragment ions were detected at m/z 55, 43, 42, and 27 aside from the parent ion at m/z 70. The m/z 55 fragment ion (C2H3CO+) is formed from ionized MVK by direct methyl loss, while breaking the C-C bond on the other side of the carbonyl group results in the acetyl cation (CH3CO+, m/z 43) and the vinyl radical. The m/z 42 fragment ion is formed via a CO-loss from the molecular ion after a methyl shift. The lightest fragment ion, the vinyl cation (C2H3+ at m/z 27), is produced in two different reactions: acetyl radical loss from the molecular ion and CO-loss from C2H3CO+. Their contributions to the m/z 27 signal are quantified based on the acetyl and vinyl fragment thermochemical anchors and quantum chemical calculations. Based on the experimentally derived appearance energy of the m/z 43 fragment ion, a new, experimentally derived heat of formation is proposed herein for gaseous methyl vinyl ketone (ΔfH0K = -94.3 ± 4.8 kJ mol-1; ΔfH298K = -110.5 ± 4.8 kJ mol-1), together with cationic heats of formation and bond dissociation energies.
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Affiliation(s)
- Peter Weidner
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
| | - Amelia W Ray
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
| | - Andras Bodi
- Laboratory for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Bálint Sztáray
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
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12
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Artemov VG, Uykur E, Roh S, Pronin AV, Ouerdane H, Dressel M. Revealing excess protons in the infrared spectrum of liquid water. Sci Rep 2020; 10:11320. [PMID: 32647228 PMCID: PMC7347896 DOI: 10.1038/s41598-020-68116-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 06/17/2020] [Indexed: 11/30/2022] Open
Abstract
The most common species in liquid water, next to neutral [Formula: see text] molecules, are the [Formula: see text] and [Formula: see text] ions. In a dynamic picture, their exact concentrations depend on the time scale at which these are probed. Here, using a spectral-weight analysis, we experimentally resolve the fingerprints of the elusive fluctuations-born short-living [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text] ions in the IR spectra of light ([Formula: see text]), heavy ([Formula: see text]), and semi-heavy (HDO) water. We find that short-living ions, with concentrations reaching [Formula: see text] of the content of water molecules, coexist with long-living pH-active ions on the picosecond timescale, thus making liquid water an effective ionic liquid in femtochemistry.
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Affiliation(s)
- Vasily G Artemov
- Center for Energy Science and Technology, Skolkovo Institute of Science and Technology, Moscow, Russia, 121205.
| | - Ece Uykur
- 1. Physikalisches Institut, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Seulki Roh
- 1. Physikalisches Institut, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Artem V Pronin
- 1. Physikalisches Institut, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Henni Ouerdane
- Center for Energy Science and Technology, Skolkovo Institute of Science and Technology, Moscow, Russia, 121205
| | - Martin Dressel
- 1. Physikalisches Institut, Universität Stuttgart, 70569, Stuttgart, Germany
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13
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Torma KG, Voronova K, Sztáray B, Bodi A. Dissociative Photoionization of the C7H8 Isomers Cycloheptatriene and Toluene: Looking at Two Sides of the Same Coin Simultaneously. J Phys Chem A 2019; 123:3454-3463. [DOI: 10.1021/acs.jpca.9b00936] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Krisztián G. Torma
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
| | - Krisztina Voronova
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - Bálint Sztáray
- Department of Chemistry, University of the Pacific, Stockton, California 95211, United States
| | - Andras Bodi
- Laboratory for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, Villigen PSI CH-5232, Switzerland
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14
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Bodi A, Hemberger P. Low-Energy Photoelectron Spectrum and Dissociative Photoionization of the Smallest Amides: Formamide and Acetamide. J Phys Chem A 2018; 123:272-283. [DOI: 10.1021/acs.jpca.8b10373] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andras Bodi
- Laboratory for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Patrick Hemberger
- Laboratory for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
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15
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West B, Rodriguez Castillo S, Sit A, Mohamad S, Lowe B, Joblin C, Bodi A, Mayer PM. Unimolecular reaction energies for polycyclic aromatic hydrocarbon ions. Phys Chem Chem Phys 2018; 20:7195-7205. [PMID: 29480289 PMCID: PMC6031295 DOI: 10.1039/c7cp07369k] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Imaging photoelectron photoion coincidence spectroscopy was employed to explore the unimolecular dissociation of the ionized polycyclic aromatic hydrocarbons (PAHs) acenaphthylene, fluorene, cyclopenta[d,e,f]phenanthrene, pyrene, perylene, fluoranthene, dibenzo[a,e]pyrene, dibenzo[a,l]pyrene, coronene and corannulene. The primary reaction is always hydrogen atom loss, with the smaller species also exhibiting loss of C2H2 to varying extents. Combined with previous work on smaller PAH ions, trends in the reaction energies (E0) for loss of H from sp2-C and sp3-C centres, along with hydrocarbon molecule loss were found as a function of the number of carbon atoms in the ionized PAHs ranging in size from naphthalene to coronene. In the case of molecules which possessed at least one sp3-C centre, the activation energy for the loss of an H atom from this site was 2.34 eV, with the exception of cyclopenta[d,e,f]phenanthrene (CPP) ions, for which the E0 was 3.44 ± 0.86 eV due to steric constraints. The hydrogen loss from PAH cations and from their H-loss fragments exhibits two trends, depending on the number of unpaired electrons. For the loss of the first hydrogen atom, the energy is consistently ca. 4.40 eV, while the threshold to lose the second hydrogen atom is much lower at ca. 3.16 eV. The only exception was for the dibenzo[a,l]pyrene cation, which has a unique structure due to steric constraints, resulting in a low H loss reaction energy of 2.85 eV. If C2H2 is lost directly from the precursor cation, the energy required for this dissociation is 4.16 eV. No other fragmentation channels were observed over a large enough sample set for trends to be extrapolated, though data on CH3 and C4H2 loss obtained in previous studies is included for completeness. The dissociation reactions were also studied by collision induced dissociation after ionization by atmospheric pressure chemical ionization. When modeled with a simple temperature-based theory for the post-collision internal energy distribution, there was reasonable agreement between the two sets of data.
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Affiliation(s)
- Brandi West
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada.
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16
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Voronova K, Ervin KM, Torma KG, Hemberger P, Bodi A, Gerber T, Osborn DL, Sztáray B. Radical Thermometers, Thermochemistry, and Photoelectron Spectra: A Photoelectron Photoion Coincidence Spectroscopy Study of the Methyl Peroxy Radical. J Phys Chem Lett 2018; 9:534-539. [PMID: 29290108 DOI: 10.1021/acs.jpclett.7b03145] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We investigated the simplest alkylperoxy radical, CH3OO, formed by reacting photolytically generated CH3 radicals with O2, using the new combustion reactions followed by photoelectron photoion coincidence (CRF-PEPICO) apparatus at the Swiss Light Source. Modeling the experimental photoion mass-selected threshold photoelectron spectrum using Franck-Condon simulations including transitions to triplet and singlet cationic states yielded the adiabatic ionization energy of 10.265 ± 0.025 eV. Dissociative photoionization of CH3OO generates the CH3+ fragment ion at the appearance energy of 11.164 ± 0.010 eV. Combining these two values with ΔfH0K°(CH3) yields ΔfH0K°(CH3OO) = 22.06 ± 0.97 kJ mol-1, reducing the uncertainty of the previously determined value by a factor of 5. Statistical simulation of the CH3OO breakdown diagram provides a molecular thermometer of the free radical's internal temperature, which we measured to be 330 ± 30 K.
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Affiliation(s)
- Krisztina Voronova
- Department of Chemistry, University of the Pacific , Stockton, California 95211, United States
| | - Kent M Ervin
- Department of Chemistry, University of Nevada, Reno , Reno, Nevada 89557-0216, United States
| | - Krisztián G Torma
- Department of Chemistry, University of the Pacific , Stockton, California 95211, United States
| | | | - Andras Bodi
- Paul Scherrer Institute , CH-5232 Villigen PSI, Switzerland
| | - Thomas Gerber
- Paul Scherrer Institute , CH-5232 Villigen PSI, Switzerland
| | - David L Osborn
- Combustion Research Facility, Sandia National Laboratories , Livermore, California 94551, United States
| | - Bálint Sztáray
- Department of Chemistry, University of the Pacific , Stockton, California 95211, United States
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17
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Covert KJ, Voronova K, Torma KG, Bodi A, Zádor J, Sztáray B. Thermochemistry of the smallest QOOH radical from the roaming fragmentation of energy selected methyl hydroperoxide ions. Phys Chem Chem Phys 2018; 20:21085-21094. [DOI: 10.1039/c8cp03168a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
PEPICO spectroscopy and quantum-chemical calculations, including BOMD simulations, reveal the importance of dynamic effects in methyl hydroperoxide dissociative photoionization.
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Affiliation(s)
- Kyle J. Covert
- Department of Chemistry
- University of the Pacific
- Stockton
- USA
| | | | | | - Andras Bodi
- Laboratory of Synchrotron Radiation and Femtochemistry
- Paul Scherrer Institute
- Villigen
- Switzerland
| | - Judit Zádor
- Combustion Research Facility
- Sandia National Laboratories
- Livermore
- USA
| | - Bálint Sztáray
- Department of Chemistry
- University of the Pacific
- Stockton
- USA
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18
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Steglich M, Custodis VBF, Trevitt AJ, daSilva G, Bodi A, Hemberger P. Photoelectron Spectrum and Energetics of the meta-Xylylene Diradical. J Am Chem Soc 2017; 139:14348-14351. [DOI: 10.1021/jacs.7b06714] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Victoria B. F. Custodis
- Department
of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, HCI D 130, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Adam J. Trevitt
- School
of Chemistry, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Gabriel daSilva
- Department
of Chemical and Biomolecular Engineering, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Andras Bodi
- Paul Scherrer Institute, CH-5232 Villigen-PSI, Switzerland
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19
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Ganyecz Á, Kállay M, Csontos J. Moderate-Cost Ab Initio Thermochemistry with Chemical Accuracy. J Chem Theory Comput 2017; 13:4193-4204. [DOI: 10.1021/acs.jctc.7b00607] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ádám Ganyecz
- MTA-BME Lendület Quantum
Chemistry Research Group, Department of Physical Chemistry and Materials
Science, Budapest University of Technology and Economics, Budapest, P.O. Box 91, H-1521 Hungary
| | - Mihály Kállay
- MTA-BME Lendület Quantum
Chemistry Research Group, Department of Physical Chemistry and Materials
Science, Budapest University of Technology and Economics, Budapest, P.O. Box 91, H-1521 Hungary
| | - József Csontos
- MTA-BME Lendület Quantum
Chemistry Research Group, Department of Physical Chemistry and Materials
Science, Budapest University of Technology and Economics, Budapest, P.O. Box 91, H-1521 Hungary
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20
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Daly S, Powis I, Garcia GA, Tia M, Nahon L. An imaging photoelectron-photoion coincidence investigation of homochiral 2R,3R-butanediol clusters. J Chem Phys 2017; 147:013937. [PMID: 28688422 DOI: 10.1063/1.4983139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report an experimental investigation of homochiral cluster formation in seeded molecular beam expansions of (2R,3R)-butanediol. Synchrotron radiation vacuum ultraviolet photoionization measurements have been performed using a double imaging electron-ion spectrometer in various configurations and modes of operation. These include measurements of the cluster ion mass spectra, wavelength scanned ion yields, and threshold electron spectra. Protonated cluster ions ranging up to n = 7 have been observed and size-selected photoelectron spectra and photoelectron circular dichroism (PECD) have been recorded by velocity map imaging, recorded in coincidence with ions, at a number of fixed photon energies. Translation temperatures of the cluster ions have been further examined by ion imaging measurements. As well as the sequence of protonated clusters with integral numbers of butanediol monomer units, a second series with half-integral monomer masses is observed and deduced to result from a facile cleavage of a butanediol monomer moiety within the nascent cluster. This second sequence of half-integral masses displays quite distinct behaviours. PECD measurements are used to show that the half-integral mass cluster ions do not share a common parentage with whole integer masses. Using an analogy developed with simple theoretical calculations of butanediol dimer structures, it is inferred that the dissociative branching into integral and half-integral ion mass sequences is controlled by the presence of different butanediol monomer conformations within the hydrogen bonded clusters.
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Affiliation(s)
- Steven Daly
- School of Chemistry, University of Nottingham, University Park NG7 2RD, Nottingham, United Kingdom
| | - Ivan Powis
- School of Chemistry, University of Nottingham, University Park NG7 2RD, Nottingham, United Kingdom
| | - Gustavo A Garcia
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP 48, 91192 Gif sur Yvette Cedex, France
| | - Maurice Tia
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP 48, 91192 Gif sur Yvette Cedex, France
| | - Laurent Nahon
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP 48, 91192 Gif sur Yvette Cedex, France
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21
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Hartweg S, Yoder BL, Garcia GA, Nahon L, Signorell R. Size-Resolved Photoelectron Anisotropy of Gas Phase Water Clusters and Predictions for Liquid Water. PHYSICAL REVIEW LETTERS 2017; 118:103402. [PMID: 28339280 DOI: 10.1103/physrevlett.118.103402] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Indexed: 05/05/2023]
Abstract
We report the first measurements of size-resolved photoelectron angular distributions for the valence orbitals of neutral water clusters with up to 20 molecules. A systematic decrease of the photoelectron anisotropy is found for clusters with up to 5-6 molecules, and most remarkably, convergence of the anisotropy for larger clusters. We suggest the latter to be the result of a local short-range scattering potential that is fully described by a unit of 5-6 molecules. The cluster data and a detailed electron scattering model are used to predict the anisotropy of slow photoelectrons in liquid water. Reasonable agreement with experimental liquid jet data is found.
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Affiliation(s)
- Sebastian Hartweg
- Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Bruce L Yoder
- Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Gustavo A Garcia
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP 48, 91192 Gif sur Yvette, France
| | - Laurent Nahon
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP 48, 91192 Gif sur Yvette, France
| | - Ruth Signorell
- Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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22
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Bodi A, Hemberger P, Tuckett RP. Coincident velocity map image reconstruction illustrated by the single-photon valence photoionisation of CF3SF5. Phys Chem Chem Phys 2017; 19:30173-30180. [DOI: 10.1039/c7cp05576e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoion–photoelectron kinetic energy and angular anisotropy correlation maps reveal new details about the ionization mechanism.
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Affiliation(s)
- Andras Bodi
- Laboratory for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute
- Villigen 5232
- Switzerland
| | - Patrick Hemberger
- Laboratory for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute
- Villigen 5232
- Switzerland
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23
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Bodi A, Sigurdardottir KL, Kvaran Á, Bjornsson R, Arnason I. Dissociative Photoionization of 1-Halogenated Silacyclohexanes: Silicon Traps the Halogen. J Phys Chem A 2016; 120:9188-9197. [DOI: 10.1021/acs.jpca.6b09195] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andras Bodi
- Laboratory
for Femtochemistry and Synchrotron Radiation, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | | | - Ágúst Kvaran
- Science
Institute, University of Iceland, Dunhaga 3, 107 Reykjavík, Iceland
| | - Ragnar Bjornsson
- Science
Institute, University of Iceland, Dunhaga 3, 107 Reykjavík, Iceland
| | - Ingvar Arnason
- Science
Institute, University of Iceland, Dunhaga 3, 107 Reykjavík, Iceland
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24
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Osborn DL, Hayden CC, Hemberger P, Bodi A, Voronova K, Sztáray B. Breaking through the false coincidence barrier in electron–ion coincidence experiments. J Chem Phys 2016; 145:164202. [DOI: 10.1063/1.4965428] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- David L. Osborn
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551, USA
| | - Carl C. Hayden
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551, USA
| | - Patrick Hemberger
- Laboratory for Femtochemistry and Synchrotron Radiation, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Andras Bodi
- Laboratory for Femtochemistry and Synchrotron Radiation, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Krisztina Voronova
- Department of Chemistry, University of the Pacific, Stockton, California 95211, USA
| | - Bálint Sztáray
- Department of Chemistry, University of the Pacific, Stockton, California 95211, USA
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25
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Raczyńska ED, Gal JF, Maria PC. Enhanced Basicity of Push-Pull Nitrogen Bases in the Gas Phase. Chem Rev 2016; 116:13454-13511. [PMID: 27739663 DOI: 10.1021/acs.chemrev.6b00224] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogen bases containing one or more pushing amino-group(s) directly linked to a pulling cyano, imino, or phosphoimino group, as well as those in which the pushing and pulling moieties are separated by a conjugated spacer (C═X)n, where X is CH or N, display an exceptionally strong basicity. The n-π conjugation between the pushing and pulling groups in such systems lowers the basicity of the pushing amino-group(s) and increases the basicity of the pulling cyano, imino, or phosphoimino group. In the gas phase, most of the so-called push-pull nitrogen bases exhibit a very high basicity. This paper presents an analysis of the exceptional gas-phase basicity, mostly in terms of experimental data, in relation with structure and conjugation of various subfamilies of push-pull nitrogen bases: nitriles, azoles, azines, amidines, guanidines, vinamidines, biguanides, and phosphazenes. The strong basicity of biomolecules containing a push-pull nitrogen substructure, such as bioamines, amino acids, and peptides containing push-pull side chains, nucleobases, and their nucleosides and nucleotides, is also analyzed. Progress and perspectives of experimental determinations of GBs and PAs of highly basic compounds, termed as "superbases", are presented and benchmarked on the basis of theoretical calculations on existing or hypothetical molecules.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW) , ul. Nowoursynowska 159c, 02-776 Warszawa, Poland
| | - Jean-François Gal
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
| | - Pierre-Charles Maria
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
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26
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Kostko O, Bandyopadhyay B, Ahmed M. Vacuum Ultraviolet Photoionization of Complex Chemical Systems. Annu Rev Phys Chem 2016; 67:19-40. [DOI: 10.1146/annurev-physchem-040215-112553] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Oleg Kostko
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
| | - Biswajit Bandyopadhyay
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
| | - Musahid Ahmed
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720;
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27
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Heringa MF, Slowik JG, Prévôt ASH, Baltensperger U, Hemberger P, Bodi A. Dissociative Ionization Mechanism and Appearance Energies in Adipic Acid Revealed by Imaging Photoelectron Photoion Coincidence, Selective Deuteration, and Calculations. J Phys Chem A 2016; 120:3397-405. [DOI: 10.1021/acs.jpca.6b00908] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maarten F. Heringa
- Laboratory
of Atmospheric Chemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
- Laboratory
for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, Villigen
PSI, Switzerland
| | - Jay G. Slowik
- Laboratory
of Atmospheric Chemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - André S. H. Prévôt
- Laboratory
of Atmospheric Chemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Urs Baltensperger
- Laboratory
of Atmospheric Chemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Patrick Hemberger
- Laboratory
for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, Villigen
PSI, Switzerland
| | - Andras Bodi
- Laboratory
for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, Villigen
PSI, Switzerland
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28
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Arruda MS, Medina A, Sousa JN, Mendes LAV, Marinho RRT, Prudente FV. Ionization and Fragmentation of DCOOD Induced by Synchrotron Radiation at the Oxygen 1s Edge: The Role of Dimer Formation. J Phys Chem A 2016; 120:5325-36. [DOI: 10.1021/acs.jpca.6b01714] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manuela S. Arruda
- Instituto
de Física, Universidade Federal da Bahia, 40170-115 Salvador, BA, Brazil
- Centro
de Ciências Exatas e Tecnológicas, Universidade Federal do Recôncavo da Bahia, 44380-000 Cruz das Almas, BA, Brazil
| | - Aline Medina
- Instituto
de Física, Universidade Federal da Bahia, 40170-115 Salvador, BA, Brazil
| | - Josenilton N. Sousa
- Instituto
de Física, Universidade Federal da Bahia, 40170-115 Salvador, BA, Brazil
| | - Luiz A. V. Mendes
- Instituto
de Física, Universidade Federal da Bahia, 40170-115 Salvador, BA, Brazil
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29
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Burgess DR. An Evaluation of Gas Phase Enthalpies of Formation for Hydrogen-Oxygen (H xO y) Species. JOURNAL OF RESEARCH OF THE NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY 2016; 121:108-138. [PMID: 34434616 PMCID: PMC7339710 DOI: 10.6028/jres.121.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/11/2016] [Indexed: 06/13/2023]
Abstract
We have compiled gas phase enthalpies of formation for nine hydrogen-oxygen species (HxOy) and selected recommended values for H, O, OH, H2O, HO2, H2O2, O3, HO3, and H2O3. The compilation consists of values derived from experimental measurements, quantum chemical calculations, and prior evaluations. This work updates the recommended values in the NIST-JANAF (1985) and Gurvich et al. (1989) thermochemical tables for seven species. For two species, HO3 and H2O3 (important in atmospheric chemistry) and not found in prior thermochemical evaluations, we also provide supplementary data consisting of molecular geometries, vibrational frequencies, and torsional potentials which can be used to compute thermochemical functions. For all species, we also provide supplementary data consisting of zero point energies, vibrational frequencies, and ion reaction energetics.
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Affiliation(s)
- Donald R Burgess
- National Institute of Standards and Technology, Gaithersburg, MD 20899
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30
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Rossini E, Knapp EW. Proton solvation in protic and aprotic solvents. J Comput Chem 2016; 37:1082-91. [DOI: 10.1002/jcc.24297] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 10/08/2015] [Accepted: 12/17/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Emanuele Rossini
- Institute of Chemistry and Biochemistry, Freie Universität Berlin; Fabeckstr. 36a Berlin D-14195 Germany
| | - Ernst-Walter Knapp
- Institute of Chemistry and Biochemistry, Freie Universität Berlin; Fabeckstr. 36a Berlin D-14195 Germany
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31
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Yoder BL, Bravaya KB, Bodi A, West AHC, Sztáray B, Signorell R. Barrierless proton transfer across weak CH⋯O hydrogen bonds in dimethyl ether dimer. J Chem Phys 2015; 142:114303. [DOI: 10.1063/1.4914456] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Bruce L. Yoder
- Laboratory of Physical Chemistry, ETH Zürich, Zürich 8093, Switzerland
| | - Ksenia B. Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215-2521, USA
| | - Andras Bodi
- Molecular Dynamics Group, Paul Scherrer Institut, Villigen 5232, Switzerland
| | - Adam H. C. West
- Laboratory of Physical Chemistry, ETH Zürich, Zürich 8093, Switzerland
| | - Bálint Sztáray
- Department of Chemistry, University of the Pacific, Stockton, California 95211, USA
| | - Ruth Signorell
- Laboratory of Physical Chemistry, ETH Zürich, Zürich 8093, Switzerland
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32
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Bekçioğlu G, Allolio C, Sebastiani D. Water Wires in Aqueous Solutions from First-Principles Calculations. J Phys Chem B 2015; 119:4053-60. [DOI: 10.1021/jp5121417] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Gül Bekçioğlu
- Physics Department, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Christoph Allolio
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám 2, CZ-16610 Prague 6, Czech Republic
| | - Daniel Sebastiani
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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Ganyecz Á, Csontos J, Nagy B, Kállay M. Theoretical and thermochemical network approaches to determine the heats of formation for HO2 and its ionic counterparts. J Phys Chem A 2015; 119:1164-76. [PMID: 25611209 DOI: 10.1021/jp5104643] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ádám Ganyecz
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics , P.O. Box 91, H-1521 Budapest, Hungary
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Bodi A, Baer T, Wells NK, Fakhoury D, Klecyngier D, Kercher JP. Controlling tunnelling in methane loss from acetone ions by deuteration. Phys Chem Chem Phys 2015; 17:28505-9. [DOI: 10.1039/c5cp02944a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Methane loss is predominantly a result of quantum tunnelling in acetone cations, and it can be suppressed quantitatively by deuteration.
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Affiliation(s)
- Andras Bodi
- Molecular Dynamics Group
- Paul Scherrer Institute
- Villigen 5232
- Switzerland
| | - Tomas Baer
- Department of Chemistry
- University of North Carolina
- Chapel Hill
- USA
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Samanta AK, Czakó G, Wang Y, Mancini JS, Bowman JM, Reisler H. Experimental and theoretical investigations of energy transfer and hydrogen-bond breaking in small water and HCl clusters. Acc Chem Res 2014; 47:2700-9. [PMID: 25072730 DOI: 10.1021/ar500213q] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water is one of the most pervasive molecules on earth and other planetary bodies; it is the molecule that is searched for as the presumptive precursor to extraterrestrial life. It is also the paradigm substance illustrating ubiquitous hydrogen bonding (H-bonding) in the gas phase, liquids, crystals, and amorphous solids. Moreover, H-bonding with other molecules and between different molecules is of the utmost importance in chemistry and biology. It is no wonder, then, that for nearly a century theoreticians and experimentalists have tried to understand all aspects of H-bonding and its influence on reactivity. It is somewhat surprising, therefore, that several fundamental aspects of H-bonding that are particularly important for benchmarking theoretical models have remained unexplored experimentally. For example, even the binding strength between two gas-phase water molecules has never been determined with sufficient accuracy for comparison with high-level electronic structure calculations. Likewise, the effect of cooperativity (nonadditivity) in small H-bonded networks is not known with sufficient accuracy. An even greater challenge for both theory and experiment is the description of the dissociation dynamics of H-bonded small clusters upon acquiring vibrational excitation. This is because of the long lifetimes of many clusters, which requires running classical trajectories for many nanoseconds to achieve dissociation. In this Account, we describe recent progress and ongoing research that demonstrates how the combined and complementary efforts of theory and experiment are enlisted to determine bond dissociation energies (D0) of small dimers and cyclic trimers of water and HCl with unprecedented accuracy, describe dissociation dynamics, and assess the effects of cooperativity. The experimental techniques rely on IR excitation of H-bonded X-H stretch vibrations, measuring velocity distributions of fragments in specific rovibrational states, and determining product state distributions at the pair-correlation level. The theoretical methods are based on high-level ab initio potential energy surfaces used in quantum and classical dynamical calculations. We achieve excellent agreement on D0 between theory and experiments for all of the clusters that we have compared, as well as for cooperativity in ring trimers of water and HCl. We also show that both the long-range and the repulsive parts of the potential must be involved in bond breaking. We explain why H-bonds are so resilient and hard to break, and we propose that a common motif in the breaking of cyclic trimers is the opening of the ring following transfer of one quantum of stretch excitation to form open-chain structures that are weakly bound. However, it still takes many vibrational periods to release one monomer fragment from the open-chain structures. Our success with water and HCl dimers and trimers led us to embark on a more ambitious project: studies of mixed water and HCl small clusters. These clusters eventually lead to ionization of HCl and serve as prototypes of acid dissociation in water. Measurements and calculations of such ionizations are yet to be achieved, and we are now characterizing these systems by adding monomers one at a time. We describe our completed work on the HCl-H2O dimer and mention our recent theoretical results on larger mixed clusters.
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Affiliation(s)
- Amit K. Samanta
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Gábor Czakó
- Laboratory
of Molecular Structure and Dynamics, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518 Budapest 112, Hungary
| | - Yimin Wang
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - John S. Mancini
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Joel M. Bowman
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Hanna Reisler
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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Harvey J, Tuckett RP, Bodi A. Shining new light on the multifaceted dissociative photoionisation dynamics of CCl4. Phys Chem Chem Phys 2014; 16:20492-9. [DOI: 10.1039/c4cp03009e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Statisticality restored: high internal energy CCl4+ dissociates mostly according to statistical theory, and an intersystem crossing path precludes fluorescence.
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Affiliation(s)
- Jonelle Harvey
- School of Chemistry
- University of Birmingham
- Birmingham B15 2TT, UK
| | | | - Andras Bodi
- Molecular Dynamics Group
- Swiss Light Source
- Paul Scherrer Institut
- Villigen 5232, Switzerland
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