1
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Wang Y, Ye Z, Han T, Du Y, Xue J. Transient spectroscopic insights into nitroindole's T 1 state: Elucidating its intermediates and unique photochemical properties. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124555. [PMID: 38823242 DOI: 10.1016/j.saa.2024.124555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/25/2024] [Accepted: 05/28/2024] [Indexed: 06/03/2024]
Abstract
Indoles are notable for their distinct photophysical and photochemical properties, making them useful indicators in biological systems and promising candidates for a variety of pharmaceutical applications. While some indoles exhibit room temperature phosphorescence, such a phenomenon has not been observed in nitroindoles. Typically, adding of a nitro group into aromatic compounds promotes ultrafast intersystem crossing and increases the formation quantum yield of the lowest excited triplet (T1). Therefore, understanding the reactivity of nitroindoles' T1 states is imperative. This study investigated the physical properties and chemical reactivities of the T1 state of 6-nitroindole (3HN-6NO2) in both polar aprotic and protic solvents, using transient absorption spectroscopy. Our results demonstrate the basicity and acidity of 3HN-6NO2, emphasizing its potential for protonation and dissociation in mildly acidic and basic conditions, respectively. Furthermore, 3HN-6NO2 has a high oxidizing capacity, participating in electron transfer reactions and proton-coupled electron transfer to produce radicals. Interestingly, in protic solvents like alcohols, 3HN-6NO2 dissociates at the -NH group and forms N-H…O hydrogen-bonded complexes with the nitro group. By identifying transient absorption spectra of intermediates and quantifying kinetic reaction rate constants, we illuminate the unique properties of the T1 state nitroindoles, enriching our understanding of their photophysical and photochemical behaviors. The results of this study have significant implications for their potential application in both biological systems and materials science.
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Affiliation(s)
- Yangxin Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Surface & Interface Science of Polymer Materials, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Zhao Ye
- School of Chemistry and Chemical Engineering, Key Laboratory of Surface & Interface Science of Polymer Materials, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Ting Han
- School of Chemistry and Chemical Engineering, Key Laboratory of Surface & Interface Science of Polymer Materials, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yong Du
- Centre for THz Research, China Jiliang University, Hangzhou, 310018, China
| | - Jiadan Xue
- School of Chemistry and Chemical Engineering, Key Laboratory of Surface & Interface Science of Polymer Materials, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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2
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Kumar G, Kellogg M, Dey S, Oliver TAA, Bradforth SE. Unraveling the Photoionization Dynamics of Indole in Aqueous and Ethanol Solutions. J Phys Chem B 2024; 128:4158-4170. [PMID: 38655896 DOI: 10.1021/acs.jpcb.4c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The photoionization dynamics of indole, the ultraviolet-B chromophore of tryptophan, were explored in water and ethanol using ultrafast transient absorption spectroscopy with 292, 268, and 200 nm excitation. By studying the femtosecond-to-nanosecond dynamics of indole in two different solvents, a new photophysical model has been generated that explains many previously unsolved facets of indole's complex solution phase photochemistry. Photoionization is only an active pathway for indole in aqueous solution, leading to a reduction in the fluorescence quantum yield in water-rich environments, which is frequently used in biophysical experiments as a key signature of the protein-folded state. Photoionization of indole in aqueous solution was observed for all three pump wavelengths but via two different mechanisms. For 200 nm excitation, electrons are ballistically ejected directly into the bulk solvent. Conversely, 292 and 268 nm excitation populates an admixture of two 1ππ* states, which form a dynamic equilibrium with a tightly bound indole cation and electron-ion pair. The ion pair dissociates on a nanosecond time scale, generating separated solvated electrons and indole cations. The charged species serve as important precursors to triplet indole production and greatly enhance the overall intersystem crossing rate. Our proposed photophysical model for indole in aqueous solution is the most appropriate for describing photoinduced dynamics of tryptophan in polypeptide sequences; tryptophan in aqueous pH 7 solution is zwitterionic, unlike in peptides, and resultantly has a competitive excited state proton transfer pathway that quenches the tryptophan fluorescence.
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Affiliation(s)
- Gaurav Kumar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Michael Kellogg
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Shivalee Dey
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Thomas A A Oliver
- School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, U.K
| | - Stephen E Bradforth
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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3
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Abou-Hatab S, Matsika S. Excited state hydrogen or proton transfer pathways in microsolvated n-cyanoindole fluorescent probes. Phys Chem Chem Phys 2024; 26:4511-4523. [PMID: 38240574 DOI: 10.1039/d3cp04844f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The sensitivity of the fluorescence properties of n-cyanoindole (n-CNI) fluorescent probes to the microenvironment makes them potential reporters of protein conformation and hydration. The fluorescence intensity of 5-CNI, 6-CNI, and 7-CNI is quenched when exposed to water solvent whereas substitution on position 4 of indoles dramatically increases it. A potential mechanism for this sensitivity to water may be similar to that found in indole. The fluorescence of indole is found to be quenched when interacting with water and ammonia solvent molecules via radiationless decay through an S1 (πσ*)/S0 conical intersection caused by excited state proton or hydrogen transfer to the solvent molecules. In this study we examine this fluorescence quenching mechanism along the N-H bond stretch of n-CNI probes using water cluster models and quantum mechanical calculations of the excited states. We find that n-CNI-(H2O)1-2 clusters form cyclic or non-cyclic structures via hydrogen bonds which lead to different photochemical reaction paths that can potentially quench the fluorescence by undergoing internal conversion from S1 to S0. However, the existence of a high energy barrier along the potential energy surface of the S1 state in most cases prevents this from occurring. We show that substitution on position 4 leads to the highest energy barrier that prevents the fluorophore from accessing these non-radiative channels, in agreement with its high intensity. We also find that the energy barrier in the S1 state of non-cyclic 5-CNI-(H2O)1-2 excited complexes decreases as the number of water molecules increases, which suggests great sensitivity of the fluorescence quenching on the aqueous environment.
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4
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He L, Tomaník L, Malerz S, Trinter F, Trippel S, Belina M, Slavíček P, Winter B, Küpper J. Specific versus Nonspecific Solvent Interactions of a Biomolecule in Water. J Phys Chem Lett 2023; 14:10499-10508. [PMID: 37970807 PMCID: PMC10683073 DOI: 10.1021/acs.jpclett.3c01763] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/23/2023] [Indexed: 11/19/2023]
Abstract
Solvent interactions, particularly hydration, are vital in chemical and biochemical systems. Model systems reveal microscopic details of such interactions. We uncover a specific hydrogen-bonding motif of the biomolecular building block indole (C8H7N), tryptophan's chromophore, in water: a strong localized N-H···OH2 hydrogen bond, alongside unstructured solvent interactions. This insight is revealed from a combined experimental and theoretical analysis of the electronic structure of indole in aqueous solution. We recorded the complete X-ray photoemission and Auger spectrum of aqueous-phase indole, quantitatively explaining all peaks through ab initio modeling. The efficient and accurate technique for modeling valence and core photoemission spectra involves the maximum-overlap method and the nonequilibrium polarizable-continuum model. A two-hole electron-population analysis quantitatively describes the Auger spectra. Core-electron binding energies for nitrogen and carbon highlight the specific interaction with a hydrogen-bonded water molecule at the N-H group and otherwise nonspecific solvent interactions.
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Affiliation(s)
- Lanhai He
- Center
for Free-Electron Laser Science, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Institute
of Atomic and Molecular Physics, Jilin University, 130012 Changchun, China
| | - Lukáš Tomaník
- Department
of Physical Chemistry, University of Chemistry
and Technology, Technická 5, 16628 Prague, Czech Republic
| | - Sebastian Malerz
- Molecular
Physics, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Florian Trinter
- Molecular
Physics, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
- Institut
für Kernphysik, Goethe-Universität
Frankfurt, Max-von-Laue-Straße
1, 60438 Frankfurt
am Main, Germany
| | - Sebastian Trippel
- Center
for Free-Electron Laser Science, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Center
for Ultrafast Imaging, Universität
Hamburg, Luruper Chaussee
149, 22761 Hamburg, Germany
| | - Michal Belina
- Department
of Physical Chemistry, University of Chemistry
and Technology, Technická 5, 16628 Prague, Czech Republic
| | - Petr Slavíček
- Department
of Physical Chemistry, University of Chemistry
and Technology, Technická 5, 16628 Prague, Czech Republic
| | - Bernd Winter
- Molecular
Physics, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Jochen Küpper
- Center
for Free-Electron Laser Science, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Center
for Ultrafast Imaging, Universität
Hamburg, Luruper Chaussee
149, 22761 Hamburg, Germany
- Department
of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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5
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Chen CG, Giustini M, D'Abramo M, Amadei A. Unveiling the Excited State Dynamics of Indole in Solution. J Chem Theory Comput 2023. [PMID: 37329333 DOI: 10.1021/acs.jctc.3c00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
In this paper, we reconstruct in detail the dynamics of the emitting electronic excited state of aqueous indole, investigating its relaxation mechanism and kinetics to be related to the time-dependent fluorescence signal. Taking advantage of the results shown in a very recent paper, we were able to model the relaxation process in solution in terms of the transitions between two gas-phase singlet electronic states (1La and 1Lb), subsequently irreversibly relaxing to the gas-phase singlet dark state (1πσ*). A comparison of the results with the available experimental data shows that the relaxation mechanism we obtain by our theoretical-computational model is reliable, reproducing rather accurately all the experimental observables.
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Affiliation(s)
| | - Mauro Giustini
- Department of Chemistry, Sapienza University of Rome, Rome 00185, Italy
| | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, Rome 00185, Italy
| | - Andrea Amadei
- Department of Technological and Chemical Sciences, Tor Vergata University of Rome, Rome 00133, Italy
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6
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Onvlee J, Trippel S, Küpper J. Ultrafast light-induced dynamics in the microsolvated biomolecular indole chromophore with water. Nat Commun 2022; 13:7462. [PMID: 36460654 PMCID: PMC9718776 DOI: 10.1038/s41467-022-33901-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 10/04/2022] [Indexed: 12/05/2022] Open
Abstract
Interactions between proteins and their solvent environment can be studied in a bottom-up approach using hydrogen-bonded chromophore-solvent clusters. The ultrafast dynamics following UV-light-induced electronic excitation of the chromophores, potential radiation damage, and their dependence on solvation are important open questions. The microsolvation effect is challenging to study due to the inherent mix of the produced gas-phase aggregates. We use the electrostatic deflector to spatially separate different molecular species in combination with pump-probe velocity-map-imaging experiments. We demonstrate that this powerful experimental approach reveals intimate details of the UV-induced dynamics in the near-UV-absorbing prototypical biomolecular indole-water system. We determine the time-dependent appearance of the different reaction products and disentangle the occurring ultrafast processes. This approach ensures that the reactants are well-known and that detailed characteristics of the specific reaction products are accessible - paving the way for the complete chemical-reactivity experiment.
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Affiliation(s)
- Jolijn Onvlee
- grid.7683.a0000 0004 0492 0453Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany ,grid.9026.d0000 0001 2287 2617Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany ,grid.5590.90000000122931605Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Sebastian Trippel
- grid.7683.a0000 0004 0492 0453Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany ,grid.9026.d0000 0001 2287 2617Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Jochen Küpper
- grid.7683.a0000 0004 0492 0453Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany ,grid.9026.d0000 0001 2287 2617Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany ,grid.9026.d0000 0001 2287 2617Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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7
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Jaiswal VK, Kabaciński P, Nogueira de Faria BE, Gentile M, de Paula AM, Borrego-Varillas R, Nenov A, Conti I, Cerullo G, Garavelli M. Environment-Driven Coherent Population Transfer Governs the Ultrafast Photophysics of Tryptophan. J Am Chem Soc 2022; 144:12884-12892. [PMID: 35796759 PMCID: PMC9305959 DOI: 10.1021/jacs.2c04565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
By combining UV transient
absorption spectroscopy with sub-30-fs
temporal resolution and CASPT2/MM calculations, we present a complete
description of the primary photoinduced processes in solvated tryptophan.
Our results shed new light on the role of the solvent in the relaxation
dynamics of tryptophan. We unveil two consecutive coherent population
transfer events involving the lowest two singlet excited states: a
sub-50-fs nonadiabatic La → Lb transfer
through a conical intersection and a subsequent 220 fs reverse Lb → La transfer due to solvent-assisted adiabatic
stabilization of the La state. Vibrational fingerprints
in the transient absorption spectra provide compelling evidence of
a vibronic coherence established between the two excited states from
the earliest times after photoexcitation and lasting until the back-transfer
to La is complete. The demonstration of response to the
environment as a driver of coherent population dynamics among the
excited states of tryptophan closes the long debate on its solvent-assisted
relaxation mechanisms and extends its application as a local probe
of protein dynamics to the ultrafast time scales.
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Affiliation(s)
- Vishal Kumar Jaiswal
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Piotr Kabaciński
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | | | - Marziogiuseppe Gentile
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Ana Maria de Paula
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte-MG, Brazil
| | - Rocio Borrego-Varillas
- Istituto di Fotonica e Nanotecnologie, CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Artur Nenov
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Irene Conti
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy.,Istituto di Fotonica e Nanotecnologie, CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Marco Garavelli
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
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8
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Lapinski L, Rostkowska H, Nowak MJ. Distinct class of photoinduced hydrogen-atom-transfer processes: phototautomerizations in molecules with no intramolecular hydrogen bond in the structure. INT REV PHYS CHEM 2022. [DOI: 10.1080/0144235x.2022.2030613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Leszek Lapinski
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Hanna Rostkowska
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Maciej J. Nowak
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
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9
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The excited state effective dipole moment of 2,3-benzofuran from thermochromic shifts in absorption and emission spectra. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2021.113476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Rostkowska H, Luchowska A, Lapinski L, Nowak MJ. Effect of a Solid-Hydrogen Environment on UV-Induced Hydrogen-Atom Transfer in Matrix-Isolated Heterocyclic Thione Compounds. J Phys Chem A 2021; 125:7437-7448. [PMID: 34406775 PMCID: PMC8419844 DOI: 10.1021/acs.jpca.1c05538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
To shed more light
on the mechanisms of UV-induced hydrogen-atom-transfer
processes in heterocyclic molecules, phototautomeric thione →
thiol reactions were investigated for thione compounds isolated in
low-temperature Ar as well as in n-H2 (normal hydrogen)
matrices. These studies concerned thione compounds with a five-membered
heterocyclic ring and thione compounds with a six-membered heterocyclic
ring. The experimental investigation of 2-thioimidazole and 3-thio-1,2,4-triazole
(thione compounds with a five-membered heterocyclic ring) revealed
that for the compounds isolated in solid n-H2 only trace
amounts of thiol photoproducts were photogenerated; even though for
the same compounds isolated in the solid Ar matrix, the thione → thiol photoconversion
was nearly
total. In contrast to that, for 3-thiopyridazine and 2-thioquinoline
(thione compounds with a six-membered heterocyclic
ring) isolated in solid n-H2, the UV-induced thione →
thiol conversion occurred with the yield reaching 25–50% of
the yield of the analogous process observed for the same species isolated
in solid Ar. The obtained experimental results allow us to conclude
that the dissociation–association mechanism nearly exclusively
governs the phototransformation in thione heterocycles with high barriers
for tautomerization (such as thione compounds with a five-membered
ring), whereas the strictly intramolecular hydrogen-atom shift contributes
to the mechanism of hydrogen-atom transfer in thione heterocycles
with lower barriers (such as thione compounds with a six-membered
ring).
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Affiliation(s)
- Hanna Rostkowska
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Anna Luchowska
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Leszek Lapinski
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Maciej J Nowak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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11
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Ponzi A, Bernes E, Toffoli D, Fronzoni G, Callegari C, Ciavardini A, Di Fraia M, Richter R, Prince KC, Sa'adeh H, Devetta M, Faccialà D, Vozzi C, Avaldi L, Bolognesi P, Castrovilli MC, Catone D, Coreno M, Plekan O. Carbon and Nitrogen K-Edge NEXAFS Spectra of Indole, 2,3-Dihydro-7-azaindole, and 3-Formylindole. J Phys Chem A 2021; 125:4160-4172. [PMID: 33961434 DOI: 10.1021/acs.jpca.1c02570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The near-edge X-ray absorption fine structure (NEXAFS) spectra of indole, 2,3-dihydro-7-azaindole, and 3-formylindole in the gas phase have been measured at the carbon and nitrogen K-edges. The spectral features have been interpreted based on density functional theory (DFT) calculations within the transition potential (TP) scheme, which is accurate enough for a general description of the measured C 1s NEXAFS spectra as well as for the assignment of the most relevant features. For the nitrogen K-edge, the agreement between experimental data and theoretical spectra calculated with TP-DFT was not quite satisfactory. This discrepancy was mainly attributed to the many-body effects associated with the excitation of the core electron, which are better described using the time-dependent density functional theory (TDDFT) with the range-separated hybrid functional CAM-B3LYP. An assignment of the measured N 1s NEXAFS spectral features has been proposed together with a complete description of the observed resonances. Intense transitions from core levels to unoccupied antibonding π* states as well as several transitions with mixed-valence/Rydberg or pure Rydberg character have been observed in the C and N K-edge spectra of all investigated indoles.
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Affiliation(s)
| | - Elisa Bernes
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, via L. Giorgieri 1, I-34127 Trieste, Italy
| | - Daniele Toffoli
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, via L. Giorgieri 1, I-34127 Trieste, Italy
| | - Giovanna Fronzoni
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, via L. Giorgieri 1, I-34127 Trieste, Italy
| | | | | | | | - Robert Richter
- Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy
| | - Kevin C Prince
- Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy
| | - Hanan Sa'adeh
- Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy.,Department of Physics, The University of Jordan, Amman 11942, Jordan
| | - Michele Devetta
- CNR-Istituto di Fotonica e Nanotecnologie (CNR-IFN), 20133 Milano, Italy
| | - Davide Faccialà
- CNR-Istituto di Fotonica e Nanotecnologie (CNR-IFN), 20133 Milano, Italy
| | - Caterina Vozzi
- CNR-Istituto di Fotonica e Nanotecnologie (CNR-IFN), 20133 Milano, Italy
| | - Lorenzo Avaldi
- Istituto di Struttura della Materia-CNR (ISM-CNR), 00133 Rome, Italy
| | - Paola Bolognesi
- Istituto di Struttura della Materia-CNR (ISM-CNR), 00133 Rome, Italy
| | | | - Daniele Catone
- Istituto di Struttura della Materia-CNR (ISM-CNR), 00133 Rome, Italy
| | - Marcello Coreno
- Istituto di Struttura della Materia-CNR (ISM-CNR), 00133 Rome, Italy
| | - Oksana Plekan
- Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy
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12
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Lopes Jesus AJ, Rosado MTS, Fausto R, Reva I. UV-induced radical formation and isomerization of 4-methoxyindole and 5-methoxyindole. Phys Chem Chem Phys 2020; 22:22943-22955. [PMID: 33026378 DOI: 10.1039/d0cp04354k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Monomers of 4-methoxyindole and 5-methoxyindole trapped in low-temperature xenon matrices (15-16 K) were characterized by IR spectroscopy, in separate experiments. Each compound was shown to adopt the most stable 1H-tautomeric form. The photochemistry of the matrix-isolated compounds was then investigated by exciting the matrices with narrowband UV light with λ ≤ 305 nm. Two main photoproducts, similar for each compound, have been detected: (1) 4-methoxy- or 5-methoxy-indolyl radical, resulting from cleavage of the N-H bond; (2) 3H-tautomers (4-methoxy- or 5-methoxy-) with the released hydrogen atom reconnected at the C3 ring carbon atom. The presence of the two types of photoproducts in the UV-irradiated matrices was confirmed by comparison of their B3LYP/6-311++G(d,p) calculated IR spectra with the experimental spectra emerging upon the irradiations. The mechanism of the observed phototransformations was elucidated by Natural Bond Orbital and Natural Resonance Theory computations on the methoxy-substituted indolyl radicals resulting from the N-H bond cleavage. The highest natural atomic spin densities were predicted at the C3 and N1 positions of the indolyl ring, corresponding to a predominance of the resonance structures with the radical centres located at these two atoms. As a whole, the obtained experimental and theoretical data allowed establishing a general pattern for the photochemistry of methoxyindoles under matrix-isolation conditions.
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Affiliation(s)
- A J Lopes Jesus
- University of Coimbra, CQC, Department of Chemistry, 3004-535, Coimbra, Portugal.
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13
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Paterson MJ, Townsend D. Rydberg-to-valence evolution in excited state molecular dynamics. INT REV PHYS CHEM 2020. [DOI: 10.1080/0144235x.2020.1815389] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Dave Townsend
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, UK
- Institute of Photonics & Quantum Sciences, Heriot-Watt University, Edinburgh, UK
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14
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Plekan O, Sa'adeh H, Ciavardini A, Callegari C, Cautero G, Dri C, Di Fraia M, Prince KC, Richter R, Sergo R, Stebel L, Devetta M, Faccialà D, Vozzi C, Avaldi L, Bolognesi P, Castrovilli MC, Catone D, Coreno M, Zuccaro F, Bernes E, Fronzoni G, Toffoli D, Ponzi A. Experimental and Theoretical Photoemission Study of Indole and Its Derivatives in the Gas Phase. J Phys Chem A 2020; 124:4115-4127. [PMID: 32329341 DOI: 10.1021/acs.jpca.0c02719] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The valence and core-level photoelectron spectra of gaseous indole, 2,3-dihydro-7-azaindole, and 3-formylindole have been investigated using VUV and soft X-ray radiation supported by both an ab initio electron propagator and density functional theory calculations. Three methods were used to calculate the outer valence band photoemission spectra: outer valence Green function, partial third order, and renormalized partial third order. While all gave an acceptable description of the valence spectra, the last method yielded very accurate agreement, especially for indole and 3-formylindole. The carbon, nitrogen, and oxygen 1s core-level spectra of these heterocycles were measured and assigned. The double ionization appearance potential for indole has been determined to be 21.8 ± 0.2 eV by C 1s and N 1s Auger photoelectron spectroscopy. Theoretical analysis identifies the doubly ionized states as a band consisting of two overlapping singlet states and one triplet state with dominant configurations corresponding to holes in the two uppermost molecular orbitals. One of the singlet states and the triplet state can be described as consisting largely of a single configuration, but other doubly ionized states are heavily mixed by configuration interactions. This work provides full assignment of the relative binding energies of the core level features and an analysis of the electronic structure of substituted indoles in comparison with the parent indole.
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Affiliation(s)
- Oksana Plekan
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Hanan Sa'adeh
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy.,Department of Physics, The University of Jordan, Amman 11942, Jordan
| | | | - Carlo Callegari
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Giuseppe Cautero
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Carlo Dri
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy.,IOM-CNR Laboratorio TASC, Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Michele Di Fraia
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Kevin C Prince
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy.,Centre for Translational Atomaterials, Swinburne University of Technology, Melbourne 3122, Australia
| | - Robert Richter
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Rudi Sergo
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Luigi Stebel
- Elettra-Sincrotrone Trieste S.C.p.A., in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Michele Devetta
- Istituto di Fotonica e Nanotecnologie, CNR, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Davide Faccialà
- Istituto di Fotonica e Nanotecnologie, CNR, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Caterina Vozzi
- Istituto di Fotonica e Nanotecnologie, CNR, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Lorenzo Avaldi
- CNR - Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo, 00133 Rome, Italy
| | - Paola Bolognesi
- CNR - Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo, 00133 Rome, Italy
| | - Mattea Carmen Castrovilli
- CNR - Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo Scalo, 00133 Rome, Italy
| | - Daniele Catone
- CNR - Istituto di Struttura della Materia (CNR-ISM), Area della Ricerca di Tor Vergata, 00133 Rome, Italy
| | - Marcello Coreno
- CNR - Istituto di Struttura Della Materia (CNR-ISM), Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Fabio Zuccaro
- CNR - Istituto di Struttura Della Materia (CNR-ISM), Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Elisa Bernes
- Dipartimento di Scienze Chimiche, Università degli Studi di Trieste, 34127 Trieste, Italy
| | - Giovanna Fronzoni
- Dipartimento di Scienze Chimiche, Università degli Studi di Trieste, 34127 Trieste, Italy
| | - Daniele Toffoli
- Dipartimento di Scienze Chimiche, Università degli Studi di Trieste, 34127 Trieste, Italy
| | - Aurora Ponzi
- Institut Ruđer Bošković, Bijenička cesta 54, 10000 Zagreb, Croatia
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15
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Crane SW, Ghafur O, Saalbach L, Paterson MJ, Townsend D. The influence of substituent position on the excited state dynamics operating in 4-, 5- and 6-hydroxyindole. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2019.136870] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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16
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Intersystem crossing dynamics in singly substituted thiouracil studied by time-resolved photoelectron spectroscopy: Micro-environmental effects due to sulfur position. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.08.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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17
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Excited states dissociation dynamics of indole-x-carboxaldehyde (x = 4, 5, 6, 7): Theoretical and experimental study. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.09.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Mai S, Mohamadzade A, Marquetand P, González L, Ullrich S. Simulated and Experimental Time-Resolved Photoelectron Spectra of the Intersystem Crossing Dynamics in 2-Thiouracil. Molecules 2018; 23:E2836. [PMID: 30388739 PMCID: PMC6278540 DOI: 10.3390/molecules23112836] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 11/16/2022] Open
Abstract
We report time-dependent photoelectron spectra recorded with a single-photon ionization setup and extensive simulations of the same spectra for the excited-state dynamics of 2-thiouracil (2TU) in the gas phase. We find that single-photon ionization produces very similar results as two-photon ionization, showing that the probe process does not have a strong influence on the measured dynamics. The good agreement between the single-photon ionization experiments and the simulations shows that the norms of Dyson orbitals allow for qualitatively describing the ionization probabilities of 2TU. This reasonable performance of Dyson norms is attributed to the particular electronic structure of 2TU, where all important neutral and ionic states involve similar orbital transitions and thus the shape of the Dyson orbitals do not strongly depend on the initial neutral and final ionic state. We argue that similar situations should also occur in other biologically relevant thio-nucleobases, and that the time-resolved photoelectron spectra of these bases could therefore be adequately modeled with the techniques employed here.
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Affiliation(s)
- Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.
| | - Abed Mohamadzade
- Department of Physics and Astronomy, University of Georgia, Athens, GA 30602, USA.
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.
| | - Susanne Ullrich
- Department of Physics and Astronomy, University of Georgia, Athens, GA 30602, USA.
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19
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Picconi D, Grebenshchikov SY. Photodissociation dynamics in the first absorption band of pyrrole. I. Molecular Hamiltonian and the Herzberg-Teller absorption spectrum for the A21(πσ*)←X̃1 A1(ππ) transition. J Chem Phys 2018; 148:104103. [DOI: 10.1063/1.5019735] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- David Picconi
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Sergy Yu. Grebenshchikov
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany
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20
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Kierspel T, Bomme C, Di Fraia M, Wiese J, Anielski D, Bari S, Boll R, Erk B, Kienitz JS, Müller NLM, Rolles D, Viefhaus J, Trippel S, Küpper J. Photophysics of indole upon X-ray absorption. Phys Chem Chem Phys 2018; 20:20205-20216. [DOI: 10.1039/c8cp00936h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A photofragmentation study of gas-phase indole (C8H7N) upon single-photon ionization at a photon energy of 420 eV is presented.
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21
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Reva I, Lapinski L, Lopes Jesus AJ, Nowak MJ. Photoinduced transformations of indole and 3-formylindole monomers isolated in low-temperature matrices. J Chem Phys 2017; 147:194304. [DOI: 10.1063/1.5003326] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Igor Reva
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Leszek Lapinski
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - A. J. Lopes Jesus
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- CQC, Faculty of Pharmacy, University of Coimbra, 3004-295 Coimbra, Portugal
| | - Maciej J. Nowak
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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22
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Safko TM, Kertesz M, Weiss RG. Photophysics of N,N-dimethyl-3-(1-indolyl)propan-1-ammonium chloride and related derivatives. Photochem Photobiol Sci 2017; 16:1546-1555. [PMID: 28876020 DOI: 10.1039/c7pp00199a] [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 photophysical properties of two new indole derivatives have been examined by steady-state and dynamic spectroscopic methods. The ground-state structures and conformations of 3-(1-indolyl)-N,N-dimethylpropan-1-ammonium chloride (InCl) and 3-(1-indolyl)-N,N,N-trimethylpropan-1-ammonium chloride (MeInCl) have been examined through density functional theory calculations. These calculations reveal a preference for a 'closed' conformation which places the cationic ammonium group in proximity to the π-electron cloud in low polarity environments. This interaction is best described as an intramolecular hydrogen-π bond in the case of InCl and a cation-π interaction for MeInCl. The ground-state conformational equilibria are influenced by changes in the dielectric constant of the solvent, resulting in a variety of photophysical behaviors. The excitation/emission spectra, fluorescence quantum yields, and excited-state lifetimes, are reported for InCl, MeInCl, and a reference compound, 1-methylindole, in 1,4-dioxane (ε = 2), acetonitrile (ε = 37), and water (ε = 78) where solubility allows. Data from these solvents provide evidence for independent fluorescence quenching pathways for InCl and MeInCl. In addition, they lead to insights into the complexities of indole photophysics by demonstrating the sensitivity of the locally-excited states to changes in charge-density and solvent environment.
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Affiliation(s)
- Trevor M Safko
- Department of Chemistry, Georgetown University, 37th and O Streets, NW, Washington, DC 20057-1227, USA
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23
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Couch DE, Kapteyn HC, Murnane MM, Peters WK. Uncovering Highly-Excited State Mixing in Acetone Using Ultrafast VUV Pulses and Coincidence Imaging Techniques. J Phys Chem A 2017; 121:2361-2366. [PMID: 28267341 DOI: 10.1021/acs.jpca.7b01112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the ultrafast dynamics of highly excited electronic states of small molecules is critical for a better understanding of atmospheric and astrophysical processes, as well as for designing coherent control strategies for manipulating chemical dynamics. In highly excited states, nonadiabatic coupling, electron-electron interactions, and the high density of states govern dynamics. However, these states are computationally and experimentally challenging to access. Fortunately, new sources of ultrafast vacuum ultraviolet pulses, in combination with electron-ion coincidence spectroscopies, provide new tools to unravel the complex electronic landscape. Here we report time-resolved photoelectron-photoion coincidence experiments using 8 eV pump photons to study the highly excited states of acetone. We uncover for the first time direct evidence that the resulting excited state consists of a mixture of both ny → 3p and π → π* character, which decays with a time constant of 330 fs. In the future, this approach can inform models of VUV photochemistry and aid in designing coherent control strategies for manipulating chemical reactions.
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Affiliation(s)
- David E Couch
- JILA and Department of Physics, University of Colorado , Boulder, Colorado 80309, United States
| | - Henry C Kapteyn
- JILA and Department of Physics, University of Colorado , Boulder, Colorado 80309, United States
| | - Margaret M Murnane
- JILA and Department of Physics, University of Colorado , Boulder, Colorado 80309, United States
| | - William K Peters
- JILA and Department of Physics, University of Colorado , Boulder, Colorado 80309, United States
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24
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Nowak MJ, Reva I, Rostkowska H, Lapinski L. UV-induced hydrogen-atom transfer and hydrogen-atom detachment in monomeric 7-azaindole isolated in Ar and n-H2 matrices. Phys Chem Chem Phys 2017; 19:11447-11454. [DOI: 10.1039/c7cp01363a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Upon UV excitation, the N1H form of 7-azaindole isolated in an Ar matrix transforms into N7H, C3H tautomers and the 7-azaindolyl radical; whereas only C3H and 7-azaindolyl radical products are photogenerated in solid H2 environment.
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Affiliation(s)
- Maciej J. Nowak
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
| | - Igor Reva
- CQC
- Department of Chemistry
- University of Coimbra
- 3004-535 Coimbra
- Portugal
| | - Hanna Rostkowska
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
| | - Leszek Lapinski
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
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25
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Zawadzki MM, Thompson JOF, Burgess EA, Paterson MJ, Townsend D. Time-resolved photoionization spectroscopy of mixed Rydberg-valence states: indole case study. Phys Chem Chem Phys 2015; 17:26659-69. [DOI: 10.1039/c5cp04645a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Time-resolved photoelectron imaging reveals subtle new mechanistic insight into the ultraviolet relaxation dynamics of gas-phase indole.
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Affiliation(s)
| | | | - Emma A. Burgess
- Institute of Photonics & Quantum Sciences
- Heriot-Watt University
- Edinburgh
- UK
| | | | - Dave Townsend
- Institute of Photonics & Quantum Sciences
- Heriot-Watt University
- Edinburgh
- UK
- Institute of Chemical Sciences
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