1
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Ferino-Pérez A, Jagau TC. Ab Initio Computation of Auger Decay in Heavy Metals: Zinc about It. J Phys Chem A 2024; 128:3957-3967. [PMID: 38742917 DOI: 10.1021/acs.jpca.4c01316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
We report the first coupled-cluster study of Auger decay in heavy metals. The zinc atom is used as a case study due to its relevance to the Auger emission properties of the 67Ga radionuclide. Coupled-cluster theory combined with complex basis functions is used to describe the transient nature of the core-ionized zinc atom. We also introduce second-order Møller-Plesset perturbation theory as an alternative method for computing partial Auger decay widths. Scalar-relativistic effects are included in our approach for computing Auger electron energies by means of the spin-free exact two-component one-electron Hamiltonian, while spin-orbit coupling is treated by means of perturbation theory. We center our attention on the K-edge Auger decay of zinc dividing the spectrum into three parts (K-LL, K-LM, and K-MM) according to the shells involved in the decay. The computed Auger spectra are in good agreement with experimental results. The most intense peak is found at an Auger electron energy of 7432 eV, which corresponds to a 1D2 final state arising from K-L2L3 transitions. Our results highlight the importance of relativistic effects for describing Auger decay in heavier nuclei. Furthermore, the effect of a first solvation shell is studied by modeling Auger decay in the hexaaqua-zinc(II) complex. We find that K-edge Auger decay is slightly enhanced by the presence of the water molecules as compared to the bare atom.
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Affiliation(s)
| | - Thomas-C Jagau
- Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium
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2
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Baweja S, Kalal B, Maity S. Spectroscopic Characterization of Hydrogen-Bonded 2,7-Diazaindole Water Complex Isolated in the Gas Phase. J Phys Chem A 2024; 128:3329-3338. [PMID: 38652167 DOI: 10.1021/acs.jpca.4c01113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
We present a systematic experimental analysis of the 1:1 complex of 2,7-diazaindole (27DAI) with water in the gas phase. The complex was characterized by using two-color-resonant two-photon ionization (R2PI), laser-induced fluorescence (LIF), single vibronic level fluorescence (SVLF), and photoionization efficiency (PIE) spectroscopic methods. The 000 band of the S1←S0 electronic transition of the 27DAI-H2O complex was observed at 33,074 cm-1, largely red-shifted by 836 cm-1 compared to that of the bare 27DAI. From the R2PI spectrum, the detected modes at 141 (ν'Tx), 169 (ν'Ty), and 194 (ν'Ry) cm-1 were identified as the internal motions of the H2O molecule in the complex. However, these modes were detected at 115 (ν″Tx), 152 (ν″Ty), and 190 (ν″Ry) cm-1 in the ground state, which suggested a stronger hydrogen bonding interaction in the photo-excited state. The structural determination was aided by the detection of νNH and νOH values in the ground and excited state complexes using the FDIR and IDIR spectroscopies. The detection of νNH at 3414 and νOH at 3447 cm-1 in 27DAI-H2O has shown an excellent correlation with the most stable structure consisting of N(1)-H···O and OH···N(7) hydrogen-bonded bridging water molecule in the ground state. The structure of the complex in the electronic excited state (S1) was confirmed by the corresponding bands at 3210 (νNH) and 3265 cm-1 (νOH). The IR-UV hole-burning spectroscopy confirmed the presence of only one isomer in the molecular beam. The ionization energy (IE) of the 27DAI-H2O complex was obtained as 8.789 ± 0.002 eV, which was significantly higher than the 7AI-H2O complex. The higher IE values of N-rich molecules suggest a higher resistivity of such molecules against photodamage. The obtained structure of the 27DAI-H2O complex has explicitly shown the formation of a cyclic one-solvent bridge incorporating N(1)-H···O and O-H···N(7) hydrogen bonds upon microsolvation. The lower excitation and higher ionization energies of the 27DAI-H2O complex compared to 7AI-H2O established higher stabilization of N-rich molecules. The solvent clusters forming a linear bridge between the hydrogen/proton acceptor and donor sites in the complex can be considered as a stepping stone to investigate the photoinduced deactivation mechanisms in nitrogen containing biologically relevant molecules.
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Affiliation(s)
- Simran Baweja
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Bhavika Kalal
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Surajit Maity
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana 502284, India
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3
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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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4
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Baweja S, Kalal B, Maity S. Laser spectroscopic characterization of supersonic jet cooled 2,7-diazaindole. Phys Chem Chem Phys 2023; 25:26679-26691. [PMID: 37772686 DOI: 10.1039/d3cp03010e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
We report the first gas phase comprehensive study of the electronic spectroscopy of 2,7-diazaindole molecule in the ground and excited states. Single vibronic level fluorescence spectroscopy (SVLF) was performed to determine the ground state vibrations of the molecule, which depicted a large Franck-Condon activity beyond 2600 cm-1. For the excited state characterization, laser-induced fluorescence (LIF) and two-color resonant two-photon ionization spectroscopy (2C-R2PI) were performed. The band origin (000) for S1 ← S0 transition appeared at 33910 ± 1 cm-1 which was red shifted by 718 cm-1 and 1322 cm-1 compared to that of 7-azaindole and indole respectively. The Franck-Condon active vibrational modes in the spectra were seen till the (000) + 1600 cm-1 region. The IR-UV hole burning spectroscopy confirmed the absence of any other isomeric species in the molecular beam. The ionization energy (IE) of the molecule was measured as 8.921 ± 0.001 eV, recorded using photoionization efficiency spectroscopy. The above IE value was significantly higher than that of the related indole derivatives, suggesting the higher photostability of the 27DAI molecule due to N(2) insertion. The ground and excited state N-H stretching frequencies of the molecule were determined using fluorescence-dip infrared spectroscopy (FDIR) and resonant ion-dip infrared spectroscopy (IDIR), and the values are 3523 and 3467 cm-1, respectively. The lower value of νNH in the electronic excited state implied the increased photoacidity of the group. A comparative analysis of the experimental LIF/2C-R2PI spectra was done against Franck-Condon simulated spectra at three different levels of theory. The vibrational frequencies calculated at B3LYP-D4/def2-TZVPP showed the most accurate prediction in comparison with the experimentally detected symmetric modes in the ground state. However, in the excited state, the lower energy asymmetric modes simulated at the B3LYP/def-SVP level of theory provided the best agreement with the experiment. This is most probably due to the distortion observed at the pyrazolyl ring leading to the appearance of asymmetric vibrational modes. The above study highlights the possibility to appropriately tune the excitation wavelengths as well as alter the photostability of the organic chromophores via additional N-insertion in the molecular systems.
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Affiliation(s)
- Simran Baweja
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana, 502284, India.
| | - Bhavika Kalal
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana, 502284, India.
| | - Surajit Maity
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana, 502284, India.
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5
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Matz F, Nijssen J, Jagau TC. Ab Initio Investigation of the Auger Spectra of Methane, Ethane, Ethylene, and Acetylene. J Phys Chem A 2023. [PMID: 37474285 DOI: 10.1021/acs.jpca.3c01649] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
We present an ab initio computational study of the Auger spectra of methane, ethane, ethylene, and acetylene. Auger spectroscopy is an established technique to probe the electronic structure of molecules and exploits the Auger-Meitner effect that core-ionized states undergo. We compute partial decay widths using coupled-cluster theory with single and double substitutions (CCSD) and equation-of-motion CCSD theory combined with complex-scaled basis functions and Feshbach-Fano projection. We generate Auger spectra from these partial widths and draw conclusions about the strength of particular decay channels and trends among the four molecules. A connection to experimental results about fragmentation pathways of the electronic states produced by Auger decay is also made.
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Affiliation(s)
- Florian Matz
- Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium
| | - Jonas Nijssen
- Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium
| | - Thomas-C Jagau
- Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium
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6
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Abad J, Martínez JI, Gómez P, Más-Montoya M, Rodríguez L, Cossaro A, Verdini A, Floreano L, Martín-Gago JA, Curiel D, Méndez J. Two-Dimensional Self-Assembly Driven by Intermolecular Hydrogen Bonding in Benzodi-7-azaindole Molecules on Au(111). THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:11591-11599. [PMID: 37377501 PMCID: PMC10291637 DOI: 10.1021/acs.jpcc.3c01640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/22/2023] [Indexed: 06/29/2023]
Abstract
The control of molecular structures at the nanoscale plays a critical role in the development of materials and applications. The adsorption of a polyheteroaromatic molecule with hydrogen bond donor and acceptor sites integrated in the conjugated structure itself, namely, benzodi-7-azaindole (BDAI), has been studied on Au(111). Intermolecular hydrogen bonding determines the formation of highly organized linear structures where surface chirality, resulting from the 2D confinement of the centrosymmetric molecules, is observed. Moreover, the structural features of the BDAI molecule lead to the formation of two differentiated arrangements with extended brick-wall and herringbone packing. A comprehensive experimental study that combines scanning tunneling microscopy, high-resolution X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure spectroscopy, and density functional theory theoretical calculations has been performed to fully characterize the 2D hydrogen-bonded domains and the on-surface thermal stability of the physisorbed material.
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Affiliation(s)
- José Abad
- Applied
Physics Department, Technical University
of Cartagena, c/ Dr. Fleming s/n, 30202 Cartagena, Spain
| | - José I. Martínez
- Department
of Low Dimensional Systems, Institute of
Materials Science of Madrid (ICMM-CSIC), c/ Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
| | - Paula Gómez
- Department
of Organic Chemistry, Faculty of Chemistry, University of Murcia, 30100 Murcia, Spain
| | - Miriam Más-Montoya
- Department
of Organic Chemistry, Faculty of Chemistry, University of Murcia, 30100 Murcia, Spain
| | - Luis Rodríguez
- Department
of Low Dimensional Systems, Institute of
Materials Science of Madrid (ICMM-CSIC), c/ Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
| | - Albano Cossaro
- CNR-IOM,
Laboratorio TASC, 34149 Trieste, Italy
- Department
of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste I-34149, Italy
| | | | | | - José A. Martín-Gago
- Department
of Low Dimensional Systems, Institute of
Materials Science of Madrid (ICMM-CSIC), c/ Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
| | - David Curiel
- Department
of Organic Chemistry, Faculty of Chemistry, University of Murcia, 30100 Murcia, Spain
| | - Javier Méndez
- Department
of Low Dimensional Systems, Institute of
Materials Science of Madrid (ICMM-CSIC), c/ Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
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7
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Ray S, Mondal P. Electronic Substitution Effect on the Ground and Excited State Properties of Indole Chromophore: A Computational Study. Chemphyschem 2023; 24:e202200541. [PMID: 36334020 DOI: 10.1002/cphc.202200541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/15/2022] [Indexed: 11/07/2022]
Abstract
Indole, being the main chromophore of amino acid tryptophan and several other biologically relevant molecules like serotonin, melatonin, has prompted considerable theoretical and experimental interest. The current work focuses on the investigation of substitution effect on the ground and excited electronic states of indole using computational quantum chemistry. Having three close-lying excited electronic states, the vibronic coupling effect becomes extremely important yet challenging for the photophysics and photochemistry of indole. Here, we have evaluated the performance of time-dependent density functional theory against available experimental and ab initio results from the literature. The electronic effects on the excited states of indole and indole derivatives e. g. tryptophan, serotonin and melatonin are reported. A bathochromic shift has been observed in the absorption spectrum for the La state. The absorption wavelength increases in the order of indole<tryptophan <serotonin <melatonin. While the contribution of the in-plane small adjacent groups increases the electron density of the indole ring, the out-of-plane long substituent groups have minor effect. The absorption spectra calculated including the vibronic coupling are in good agreement with experiments. These results can be used to estimate the error in photophysical observables of indole derivatives calculated considering indole as a prototypical system.
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Affiliation(s)
- Soumyadip Ray
- Department of Chemistry and Center for Atomic, Molecular and Optical Sciences and Technologies, Indian Institute of Science Education and Research (IISER) Tirupati, Karakambadi Road, Mangalam, Tirupati, 517507, Andhra Pradesh, India
| | - Padmabati Mondal
- Department of Chemistry and Center for Atomic, Molecular and Optical Sciences and Technologies, Indian Institute of Science Education and Research (IISER) Tirupati, Karakambadi Road, Mangalam, Tirupati, 517507, Andhra Pradesh, India
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8
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Jayadev NK, Ferino-Pérez A, Matz F, Krylov AI, Jagau TC. The Auger spectrum of benzene. J Chem Phys 2023; 158:064109. [PMID: 36792526 DOI: 10.1063/5.0138674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We present an ab initio computational study of the Auger electron spectrum of benzene. Auger electron spectroscopy exploits the Auger-Meitner effect, and although it is established as an analytic technique, the theoretical modeling of molecular Auger spectra from first principles remains challenging. Here, we use coupled-cluster theory and equation-of-motion coupled-cluster theory combined with two approaches to describe the decaying nature of core-ionized states: (i) Feshbach-Fano resonance theory and (ii) the method of complex basis functions. The spectra computed with these two approaches are in excellent agreement with each other and also agree well with experimental Auger spectra of benzene. The Auger spectrum of benzene features two well-resolved peaks at Auger electron energies above 260 eV, which correspond to final states with two electrons removed from the 1e1g and 3e2g highest occupied molecular orbitals. At lower Auger electron energies, the spectrum is less well resolved, and the peaks comprise multiple final states of the benzene dication. In line with theoretical considerations, singlet decay channels contribute more to the total Auger intensity than the corresponding triplet decay channels.
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Affiliation(s)
- Nayanthara K Jayadev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Florian Matz
- Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Thomas-C Jagau
- Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium
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9
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Salvitti G, Pizzano E, Baroncelli F, Melandri S, Evangelisti L, Negri F, Coreno M, Prince KC, Ciavardini A, Sa'adeh H, Pori M, Mazzacurati M, Maris A. Spectroscopic and quantum mechanical study of a scavenger molecule: N,N-diethylhydroxylamine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 281:121555. [PMID: 35926273 DOI: 10.1016/j.saa.2022.121555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
We report a combination of quantum mechanical calculations and a range of spectroscopic measurements in the gas phase of N,N-diethylhydroxylamine, an important scavenger compound. Three conformers were observed by pulsed jet Fourier transform microwave spectroscopy in the 6.5-18.5 GHz frequency range. They are characterized by the hydroxyl hydrogen atom being in trans orientation with respect to the bisector of the CNC angle while the side alkyl chains can be both trans (global minimum, Cs symmetry, A = 7608.1078(4), B = 2020.2988(2) and C = 1760.5423(2) MHz) or one trans and the other gauche (second energy minimum, A = 5302.896(1), B = 2395.9822(4) and C = 1804.8567(3) MHz) or gauche' (third energy minimum, A = 5960.8025(6), B = 2273.6627(4) and C = 1975.8074(4) MHz). For the global minimum, the 13Cα,13Cβ and 15N isotopologues were observed in natural abundance, allowing for an accurate partial structure determination. Moreover, several lines were detected by free jet absorption millimeter wave spectroscopy in the 59.6-74.4 GHz spectral range. The electron binding energies of the highest occupied molecular orbital and the next-to-highest occupied molecular orbital, determined by photoelectron spectroscopy, are 8.95 and 10.76 eV, respectively. Supporting calculations evidence that, (i) upon ionization of the HOMO, the molecular structure changes from an amine to an N-oxoammonium arrangement and (ii) the 0-0 of the HOMO-1 photoionization is 10.46 eV. The K-shell binding energies, determined by X-ray photoelectron spectroscopy, are 290.42 eV (Cβ), 291.45 eV (Cα), 405.98 eV (N) and 538.75 eV (O). The Fourier transform near infrared spectrum is reported and a tentative assignment is proposed. The equilibrium wavenumber (ω̃ = 3811 cm-1) and the anharmonicity constant (ω̃χ = -87.5 cm-1) of the hydroxyl stretching mode were estimated using a quadratic model.
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Affiliation(s)
- Giovanna Salvitti
- Department of Chemistry "G. Ciamician", University of Bologna, I-40126 Bologna, Italy
| | - Emanuele Pizzano
- Department of Chemistry "G. Ciamician", University of Bologna, I-40126 Bologna, Italy; BASF Italia S.p.A., Pontecchio Marconi, I-40037 Bologna, Italy
| | - Filippo Baroncelli
- Department of Chemistry "G. Ciamician", University of Bologna, I-40126 Bologna, Italy
| | - Sonia Melandri
- Department of Chemistry "G. Ciamician", University of Bologna, I-40126 Bologna, Italy; Interdepartmental Centre for Industrial Aerospace Research (CIRI Aerospace), University of Bologna, I-47121 Forlì, Italy; Interdepartmental Centre for Industrial Agrifood Research (CIRI Agrifood), University of Bologna, I-47521 Cesena, Italy
| | - Luca Evangelisti
- Interdepartmental Centre for Industrial Aerospace Research (CIRI Aerospace), University of Bologna, I-47121 Forlì, Italy; Interdepartmental Centre for Industrial Agrifood Research (CIRI Agrifood), University of Bologna, I-47521 Cesena, Italy; Department of Chemistry "G. Ciamician", University of Bologna I-48123 Ravenna, Italy
| | - Fabrizia Negri
- Department of Chemistry "G. Ciamician", University of Bologna, I-40126 Bologna, Italy; INSTM, UdR Bologna, I-40126 Bologna, Italy
| | - Marcello Coreno
- CNR-ISM, Trieste LD2 Unit, I-34149 Basovizza, Trieste, Italy
| | - Kevin C Prince
- Elettra-Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy; Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Alessandra Ciavardini
- CNR-ISM, Trieste LD2 Unit, I-34149 Basovizza, Trieste, Italy; Elettra-Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy; Laboratory of Quantum Optics, University of Nova Gorica, Sl-5001 Nova Gorica, Slovenia
| | - Hanan Sa'adeh
- Elettra-Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste, Italy; Department of Physics, The University of Jordan, JO-11942 Amman, Jordan
| | - Matteo Pori
- BASF Italia S.p.A., Pontecchio Marconi, I-40037 Bologna, Italy
| | | | - Assimo Maris
- Department of Chemistry "G. Ciamician", University of Bologna, I-40126 Bologna, Italy; Interdepartmental Centre for Industrial Aerospace Research (CIRI Aerospace), University of Bologna, I-47121 Forlì, Italy.
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Ciavardini A, Galdenzi F, Coreno M, Ninno GD, Grazioli C, de Simone M, Totani R, Piccirillo S, Plekan O, Ponzi A. Valence and core-level X-ray photoemission spectroscopy of light-sensitive molecules: Lumazine and alloxazine. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Kadhane UR, Vinitha MV, Ramanathan K, S. A, Bouwman J, Avaldi L, Bolognesi P, Richter R. Comprehensive survey of dissociative photoionization of quinoline by PEPICO experiments. J Chem Phys 2022; 156:244304. [DOI: 10.1063/5.0092158] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Dissociative photoionization of quinoline induced by vacuum ultraviolet radiation is investigated using photoelectron–photoion coincidence spectroscopy. Branching ratios of all the detectable fragment ions are measured as a function of internal energy ranging from 2 to 30 eV. A specific generation hierarchy is observed in the breakdown curves of a set of dissociation channels. Moreover, a careful comparison of the breakdown curves of fragments among the successive generations allowed to establish a decay sequence in the fragmentation of quinoline cation. This enabled us to revisit and refine the understanding of the first generation decay and reassign the origin of a few of the higher generation decay products of quinoline cation. With the help of the accompanying computational work (reported concurrently), we have demonstrated the dominance of two different HCN elimination pathways over previously interpreted mechanisms. For the first time, a specific pathway for acetylene elimination is identified in quinoline+ and the role of isomerization in both acetylene as well as hydrogen cyanide loss is also demonstrated. The experiment also established that the acetylene elimination exclusively occurs from the non-nitrogen containing rings of quinoline cation. The formation of a few astronomically important species is also discussed.
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Affiliation(s)
- Umesh R. Kadhane
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | - M. V. Vinitha
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | - Karthick Ramanathan
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | - Arun S.
- Indian Institute of Space Science and Technology, Thiruvananthapuram 695547, Kerala, India
| | - Jordy Bouwman
- Laboratory for Atmospheric and Space Physics, University of Colorado, Boulder, Colorado 80303, USA
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Monterotondo, Roma 00015, Italy
| | - Paola Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Monterotondo, Roma 00015, Italy
| | - Robert Richter
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163, 5 in AREA Science Park, Basovizza TS 34149, Italy
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12
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Baweja S, Chowdhury PR, Maity S. Excited state hydrogen atom transfer pathways in 2,7-diazaindole - S 1-3 (S = H 2O and NH 3) clusters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 265:120386. [PMID: 34560582 DOI: 10.1016/j.saa.2021.120386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/17/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
The photoinduced tautomerization reactions via hydrogen atom transfer in the excited electronic state (ESHT) have been computationally investigated in 2,7-diazaindole (27DAI) - (H2O)1-3 and 27DAI - (NH3)1-3 isolated clusters to understand the role of various solvent wires. Two competing ESHT reaction pathways originating from the N(1)-H group to the neighbouring N(7) (R(1H-Sn-7H)) and N(2) (R(1H-Sn-2H)) atoms were rigorously examined for each system. Both one- and two-dimensional potential energy surfaces have been calculated in the excited state to investigate the pathways. The R(1H-Sn-7H) was found to be the dominant route with reaction barriers ranging from 26-40 kJmol-1 for water clusters, and 14-26 kJmol-1 for ammonia clusters. The barrier heights for ammonia clusters were found to be nearly half of the that observed for the water systems. The lengthening of the solvent chain up to two molecules resulted in a drastic decrease in the barrier heights for R(1H-Sn-7H). The barriers of the competing reaction channel R(1H-Sn-2H) were found to be significantly higher (31-127 kJmol-1) but were observed to be decreasing with the lengthening of the solvent wire as in the R(1H-Sn-7H) pathway. In both the reactions, the angle strain present in the transition state structures was dependent upon the solvent chain's length and was most likely the governing factor for the barrier heights in each solvent cluster. The results have also affirmed that the ammonia molecule is a better candidate for hydrogen transfer than water because of its higher gas-phase basicity. The results delineated from this investigation can pave the way to unravel the excited-state hydrogen atom transfer pathways in novel N-H bearing molecules.
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Affiliation(s)
- Simran Baweja
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | | | - Surajit Maity
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana 502285, India.
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13
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Molteni E, Mattioli G, Alippi P, Avaldi L, Bolognesi P, Carlini L, Vismarra F, Wu Y, Varillas RB, Nisoli M, Singh M, Valadan M, Altucci C, Richter R, Sangalli D. A systematic study of the valence electronic structure of cyclo(Gly-Phe), cyclo(Trp-Tyr) and cyclo(Trp-Trp) dipeptides in the gas phase. Phys Chem Chem Phys 2021; 23:26793-26805. [PMID: 34816853 DOI: 10.1039/d1cp04050b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The electronic energy levels of cyclo(glycine-phenylalanine), cyclo(tryptophan-tyrosine) and cyclo(tryptophan-tryptophan) dipeptides are investigated with a joint experimental and theoretical approach. Experimentally, valence photoelectron spectra in the gas phase are measured using VUV radiation. Theoretically, we first obtain low-energy conformers through an automated conformer-rotamer ensemble sampling scheme based on tight-binding simulations. Then, different first principles computational schemes are considered to simulate the spectra: Hartree-Fock (HF), density functional theory (DFT) within the B3LYP approximation, the quasi-particle GW correction, and the quantum-chemistry CCSD method. Theory allows assignment of the main features of the spectra. A discussion on the role of electronic correlation is provided, by comparing computationally cheaper DFT scheme (and GW) results with the accurate CCSD method.
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Affiliation(s)
- Elena Molteni
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy. .,Dipartimento di Fisica, Universita' degli Studi di Milano, via Celoria 16, I-20133 Milano, Italy
| | - Giuseppe Mattioli
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Paola Alippi
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Lorenzo Avaldi
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Paola Bolognesi
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Laura Carlini
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy.
| | - Federico Vismarra
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milano, Italy.,CNR-Istituto di Fotonica e Nanotecnologie, Piazza Leonardo da Vinci, 32, Milano, Italy
| | - Yingxuan Wu
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milano, Italy.,CNR-Istituto di Fotonica e Nanotecnologie, Piazza Leonardo da Vinci, 32, Milano, Italy
| | | | - Mauro Nisoli
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milano, Italy.,CNR-Istituto di Fotonica e Nanotecnologie, Piazza Leonardo da Vinci, 32, Milano, Italy
| | - Manjot Singh
- Dipartimento di Scienze Biomediche Avanzate, Universita' degli Studi di Napoli Federico II, via Pansini 5, I-80131, Napoli, Italy
| | - Mohammadhassan Valadan
- Dipartimento di Scienze Biomediche Avanzate, Universita' degli Studi di Napoli Federico II, via Pansini 5, I-80131, Napoli, Italy.,Istituto Nazionale Fisica Nucleare (INFN), Sezione di Napoli, Napoli, Italy
| | - Carlo Altucci
- Dipartimento di Scienze Biomediche Avanzate, Universita' degli Studi di Napoli Federico II, via Pansini 5, I-80131, Napoli, Italy.,Istituto Nazionale Fisica Nucleare (INFN), Sezione di Napoli, Napoli, Italy
| | - Robert Richter
- Sincrotrone Trieste, Area Science Park, Basovizza, Trieste, Italy
| | - Davide Sangalli
- Istituto di Struttura della Materia-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, CP 10, Monterotondo Scalo, Roma, Italy. .,Dipartimento di Fisica, Universita' degli Studi di Milano, via Celoria 16, I-20133 Milano, Italy
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14
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Hill A, Sa'adeh H, Cameron D, Wang F, Trofimov AB, Larionova EY, Richter R, Prince KC. Positional and Conformational Isomerism in Hydroxybenzoic Acid: A Core-Level Study and Comparison with Phenol and Benzoic Acid. J Phys Chem A 2021; 125:9877-9891. [PMID: 34752704 DOI: 10.1021/acs.jpca.1c07523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three positional isomers of hydroxybenzoic acid, as well as phenol and benzoic acid, were studied using core-level photoemission and X-ray absorption spectroscopies, supported by quantum chemical calculations. While 2-hydroxybenzoic (salicylic) acid exists as a single conformer with an internal hydrogen bond, 3- and 4-hydroxybenzoic acids are mixtures of multiple conformers. The effects due to isomerism are clearly seen in the C 1s and O 1s photoelectron spectra, whereas the conformational effects on the binding energies are less pronounced. The O 1s photoelectron spectrum of salicylic acid is significantly different from that of the other two isomers, providing a signature of the hydrogen bond. In contrast, the oxygen K edge X-ray absorption spectra of the three hydroxybenzoic acids show only minor differences. The salicylic acid absorption spectrum at the carbon K edge shows a more resolved vibrational structure than the spectra of the other molecules, which can be explained in part by the existence of a single conformer. Our theoretical study of vibrational excitations in the lowest C 1s absorption bands of salicylic and 4-hydroxybenzoic acids indicates that the observed structure can be assigned to 0-0 lines of various electronic transitions since most of the totally symmetric vibrational modes with sufficiently large frequencies to be resolved are predicted to be inactive. Significant sensitivity of the C 1s excitations in 3-hydroxybenzoic acid to rotational conformerism was predicted but not observed due to spectral crowding.
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Affiliation(s)
- Alexander Hill
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technology, Swinburne University of Technology, Melbourne 3122, Australia
| | - Hanan Sa'adeh
- Department of Physics, The University of Jordan, Amman 11942, Jordan.,Elettra Sincrotrone Trieste, in Area Science Park, Basovizza, Trieste 34149, Italy
| | - David Cameron
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technology, Swinburne University of Technology, Melbourne 3122, Australia
| | - Feng Wang
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technology, Swinburne University of Technology, Melbourne 3122, Australia
| | - Alexander B Trofimov
- Laboratory of Quantum Chemistry, Irkutsk State University, Karl Marx Str. 1, Irkutsk 664003, Russia.,A. E. Favorsky Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky Str. 1, Irkutsk 664033, Russia
| | - Elena Yu Larionova
- Laboratory of Quantum Chemistry, Irkutsk State University, Karl Marx Str. 1, Irkutsk 664003, Russia.,East-Siberian Institute of the MIA of Russia, Lermontov Str. 110, Irkutsk 664074, Russia
| | - Robert Richter
- Elettra Sincrotrone Trieste, in Area Science Park, Basovizza, Trieste 34149, Italy
| | - Kevin C Prince
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technology, Swinburne University of Technology, Melbourne 3122, Australia.,Elettra Sincrotrone Trieste, in Area Science Park, Basovizza, Trieste 34149, Italy
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15
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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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16
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Chong DP. Computational Study of the Electron Spectra of Vapor-Phase Indole and Four Azaindoles. Molecules 2021; 26:1947. [PMID: 33808397 PMCID: PMC8037839 DOI: 10.3390/molecules26071947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 11/19/2022] Open
Abstract
After geometry optimization, the electron spectra of indole and four azaindoles are calculated by density functional theory. Available experimental photoemission and excitation data for indole and 7-azaindole are used to compare with the theoretical values. The results for the other azaindoles are presented as predictions to help the interpretation of experimental spectra when they become available.
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Affiliation(s)
- Delano P Chong
- Department of Chemistry, University of British Columbia, 2016 Main Mall, Vancouver, BC V6T 1Z1, Canada
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17
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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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