1
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Moe MM, Tsai M, Liu J. Effects of Intra-Base Pair Proton Transfer on Dissociation and Singlet Oxygenation of 9-Methyl-8-Oxoguanine-1-Methyl-Cytosine Base-Pair Radical Cations. Chemphyschem 2023; 24:e202300511. [PMID: 37738022 DOI: 10.1002/cphc.202300511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 09/23/2023]
Abstract
8-Oxoguanosine is the most common oxidatively generated base damage and pairs with complementary cytidine within duplex DNA. The 8-oxoguanosine-cytidine lesion, if not recognized and removed, not only leads to G-to-T transversion mutations but renders the base pair being more vulnerable to the ionizing radiation and singlet oxygen (1 O2 ) damage. Herein, reaction dynamics of a prototype Watson-Crick base pair [9MOG ⋅ 1MC]⋅+ , consisting of 9-methyl-8-oxoguanine radical cation (9MOG⋅+ ) and 1-methylcystosine (1MC), was examined using mass spectrometry coupled with electrospray ionization. We first detected base-pair dissociation in collisions with the Xe gas, which provided insight into intra-base pair proton transfer of 9MOG⋅+ ⋅ 1MC← → ${{\stackrel{ {\rightarrow} } { {\leftarrow} } } }$ [9MOG - HN1 ]⋅ ⋅ [1MC+HN3' ]+ and subsequent non-statistical base-pair separation. We then measured the reaction of [9MOG ⋅ 1MC]⋅+ with 1 O2 , revealing the two most probable pathways, C5-O2 addition and HN7 -abstraction at 9MOG. Reactions were entangled with the two forms of 9MOG radicals and base-pair structures as well as multi-configurations between open-shell radicals and 1 O2 (that has a mixed singlet/triplet character). These were disentangled by utilizing approximately spin-projected density functional theory, coupled-cluster theory and multi-referential electronic structure modeling. The work delineated base-pair structural context effects and determined relative reactivity toward 1 O2 as [9MOG - H]⋅>9MOG⋅+ >[9MOG - HN1 ]⋅ ⋅ [1MC+HN3' ]+ ≥9MOG⋅+ ⋅ 1MC.
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Affiliation(s)
- May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Midas Tsai
- Department of Natural Sciences, LaGuardia Community College, 31-10 Thomson Ave., Long Island City, NY 11101, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
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2
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Huang JH, Zhang F, Shi YP, Cai JR, Chuang YH, Hu WP, Lee YY, Wang CC. Water Plays Multifunctional Roles in the Intervening Formation of Secondary Organic Aerosols in Ozonolysis of Limonene: A Valence Photoelectron Spectroscopy and Density Functional Theory Study. J Phys Chem Lett 2023; 14:3765-3776. [PMID: 37052309 DOI: 10.1021/acs.jpclett.3c00560] [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
Although water may affect aqueous aerosol chemistry, how it intervenes in the formation of secondary organic aerosols (SOAs) at the molecular level remains elusive. Ozonolysis of limonene is one of the most important sources of indoor SOAs. Here, we report the valence electronic properties of limonene aerosols and SOAs derived from limonene ozonolysis (Lim-SOAs) via aerosol vacuum ultraviolet photoelectron spectroscopy, with a focus on the effects of water on Lim-SOAs. The first vertical ionization energy of limonene aerosols is measured to be 8.79 ± 0.07 eV. While water significantly increases the total photoelectron yield of Lim-SOAs, three photoelectron features attributable to Lim-SOAs each exhibit distinct dependence on the fraction of water in aerosols, implying that different formation pathways and molecular origins are involved in the formation of Lim-SOAs. Combined with density functional theory calculation and mass spectrometry measurements, this study reveals that water, particularly the water dimer, enhances the formation of Lim-SOAs by altering the ozonolysis energetics and pathways by intervening in its Criegee chemistry, acting as both a catalyst and a reactant. The atmospheric implication is discussed.
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Affiliation(s)
- Jhih-Hong Huang
- Department of Chemistry and Aerosol Science Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan, R.O.C. 80424
| | - Fuyi Zhang
- Department of Chemistry and Aerosol Science Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan, R.O.C. 80424
| | - Yan-Pin Shi
- Department of Chemistry and Aerosol Science Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan, R.O.C. 80424
| | - Jia-Rong Cai
- Department of Chemistry and Aerosol Science Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan, R.O.C. 80424
| | - Yu-Hsuan Chuang
- Department of Chemistry and Aerosol Science Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan, R.O.C. 80424
| | - Wei-Ping Hu
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi, Taiwan, R.O.C. 62102
| | - Yin-Yu Lee
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan, R.O.C. 30076
| | - Chia C Wang
- Department of Chemistry and Aerosol Science Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan, R.O.C. 80424
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3
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Hartweg S, Hochlaf M, Garcia GA, Nahon L. Photoionization Dynamics and Proton Transfer within the Adenine-Thymine Nucleobase Pair. J Phys Chem Lett 2023; 14:3698-3705. [PMID: 37040591 DOI: 10.1021/acs.jpclett.3c00564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Studying the stability of hydrogen-bonded nucleobase pairs, at the heart of the genetic code, is of utmost importance for an in-depth understanding of basic mechanisms of life and biomolecular evolution. We present here a VUV single photon ionization dynamic study of the nucleobase pair adenine-thymine (AT), revealing its ionization and dissociative ionization thresholds via double imaging electron/ion coincidence spectroscopy. The experimental data, consisting of cluster mass-resolved threshold photoelectron spectra and photon energy-dependent ion kinetic energy release distributions, allow the unambiguous distinction of the dissociation of AT into protonated adenine AH+ and a dehydrogenated thymine radical T(-H) from dissociative ionization processes of other nucleobase clusters. Comparison to high-level ab initio calculations indicates that our experimental observations can be explained by a single hydrogen-bonded conformer present in our molecular beam and allows the estimation of an upper limit of the barrier of the proton transfer in the ionized AT pair.
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Affiliation(s)
- Sebastian Hartweg
- Synchrotron Soleil, L'Orme des Merisiers, Départementale 128, 91190 St Aubin, France
- University of Freiburg, Institute of Physics, Hermann-Herder-Straße 3, 79104 Freiburg, Germany
| | - Majdi Hochlaf
- Université Gustave Eiffel, COSYS/IMSE, 5 Bd Descartes, 77454 Champs sur Marne, France
| | - Gustavo A Garcia
- Synchrotron Soleil, L'Orme des Merisiers, Départementale 128, 91190 St Aubin, France
| | - Laurent Nahon
- Synchrotron Soleil, L'Orme des Merisiers, Départementale 128, 91190 St Aubin, France
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4
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Bolognesi P, Avaldi L. Photoelectron-photoion(s) coincidence studies of molecules of biological interest. Phys Chem Chem Phys 2022; 24:22356-22370. [PMID: 36124990 DOI: 10.1039/d2cp03079a] [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
Photoelectron-photoion(s) coincidence, PEPICO, experiments with synchrotron radiation have become one of the most powerful tools to investigate dissociative photoionization thanks to their selectivity. In this paper their application to the study of molecular species of biological interest in the gas phase is reviewed. Some applications of PEPICO to the study of potential radiosensitizers, amino acids and small peptides and opportunities offered by the advent of novel methods for the production of beams of these molecules are discussed.
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Affiliation(s)
- P Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 00015 Monterotondo Scalo, Italy.
| | - L Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 00015 Monterotondo Scalo, Italy.
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5
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Molina F, Dezalay J, Soorkia S, Broquier M, Hochlaf M, Pino GA, Grégoire G. Cryogenic IR and UV spectroscopy of isomer-selected cytosine radical cation. Phys Chem Chem Phys 2022; 24:25182-25190. [DOI: 10.1039/d2cp03953b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
The UV photodissociation of cryogenic-cooled isomer-selected cytosine–silver complex leads to the production of cytosine radical cation without isomerization.
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Affiliation(s)
- Franco Molina
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
- INFIQC (CONICET-UNC), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
- Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Jordan Dezalay
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
| | - Satchin Soorkia
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
| | - Michel Broquier
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
| | - Majdi Hochlaf
- Université Gustave Eiffel, COSYS/IMSE, 5 Bd Descartes 77454, Champs sur Marne, France
| | - Gustavo Ariel Pino
- INFIQC (CONICET-UNC), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Gilles Grégoire
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
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6
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Benny J, Saito T, Moe MM, Liu J. Singlet O 2 Reactions with Radical Cations of 8-Bromoguanine and 8-Bromoguanosine: Guided-Ion Beam Mass Spectrometric Measurements and Theoretical Treatments. J Phys Chem A 2021; 126:68-79. [PMID: 34941276 DOI: 10.1021/acs.jpca.1c09552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
8-Bromoguanosine is generated in vivo as a biomarker for early inflammation. Its formation and secondary reactions lead to a variety of biological sequelae at inflammation sites, most of which are mutagenic and linked to cancer. Herein, we report the formation of radical cations of 8-bromoguanine (8BrG•+) and 8-bromoguanosine (8BrGuo•+) and their reactions toward the lowest excited singlet molecular oxygen (1O2)─a common reactive oxygen species generated in biological systems. This work aims to investigate synergistic, oxidatively generated damage of 8-brominated guanine and guanosine that may occur upon ionizing radiation, one-electron oxidation, and 1O2 oxidation. Capitalizing on measurements of reaction product ions and cross sections of 8BrG•+ and 8BrGuo•+ with 1O2 using guided-ion beam tandem mass spectrometry and augmented by computational modeling of the prototype reaction system, 8BrG•+ + 1O2, using the approximately spin-projected ωB97XD/6-31+G(d,p) density functional theory, the coupled cluster DLPNO-CCSD(T)/aug-cc-pVTZ and the multireference CASPT2(21,15)/6-31G**, probable reaction products, and potential energy surfaces (PESs) were mapped out. 8BrG•+ and 8BrGuo•+ present similar exothermic oxidation products, and their reaction efficiencies with 1O2 increase with decreasing collision energy. Both single- and multireference theories predicted that the two most energetically favorable reaction pathways correspond to 1O2-addition to the C8 and C5-positions of 8BrG•+, respectively. The CASPT2-calculated PES represents the best quantitative agreement with the experimental benchmark, in that the oxidation exothermicity is close to the water hydration energy of product ions and, thus, is able to eliminate a water ligand in the product ions.
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Affiliation(s)
- Jonathan Benny
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York 10016, United States
| | - Toru Saito
- Department of Biomedical Information Science, Graduate School of Information Science, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, 731-3194 Hiroshima, Japan
| | - May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York 10016, United States
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York 10016, United States
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7
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Zhou W, Liu J. Reaction mechanism and dynamics for C8-hydroxylation of 9-methylguanine radical cation by water molecules. Phys Chem Chem Phys 2021; 23:24464-24477. [PMID: 34698322 DOI: 10.1039/d1cp03884b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In contrast to their spontaneous deprotonation in aqueous solution, reactions of guanine and guanosine radical cations with water in the gas phase are exclusively initiated by hydration of the radical cations as reported in recent work (Y. Sun et al., Phys. Chem. Chem. Phys., 2018, 20, 27510). As gas-phase hydration reactions closely mimic the actual scenario for guanine radical cations in double-stranded DNA, exploration of subsequent reactions within their water complexes can provide an insight into the resulting oxidative damage to nucleosides. Herein guided-ion beam mass spectrometry experiment and direct dynamics trajectory simulations were carried out to examine prototype complexes of the 9-methylguanine radical cation with one and two water ligands (i.e., 9MG˙+·(H2O)1-2) in the gas phase, wherein the complexes were activated by collisional activation in the experiment and by thermal excitation at high temperatures in the simulations. Guided by mass spectroscopic measurements, trajectory results and reaction potential energy surface, three reaction pathways were identified. The first two reaction pathways start with H-atom abstraction from water by the O6 and N7 atoms in 9MG˙+ and are referred to as HAO6 and HAN7, respectively. The primary products of HAO6 and HAN7 reactions, including [9MG + HO6]+/[9MG + HN7]+ and ˙OH, react further to either form [8OH-9MG + HO6]˙+ and [8OH-9MG + HN7]˙+via C8-hydroxylation or form radical cations of 6-enol-guanine (6-enol-G˙+) and 7H-guanine (7HG˙+) via SN2-type methanol elimination. The third reaction pathway corresponds to the formation of 8OH-9MG+ by H elimination from the complex, referred to as HE. Among these product channels, [8OH-9MG + HN7]˙+ has the most favorable formation probability, especially in the presence of additional water molecules. This product may serve as a preceding structure to the 8-oxo-7,8-dihydroguanine lesion in DNA and has implications for health effects of radiation exposure and radiation therapy.
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Affiliation(s)
- Wenjing Zhou
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. .,PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. .,PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
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8
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Zhao HY, Lau KC, Garcia GA, Nahon L, Carniato S, Poisson L, Schwell M, Al-Mogren MM, Hochlaf M. Unveiling the complex vibronic structure of the canonical adenine cation. Phys Chem Chem Phys 2018; 20:20756-20765. [PMID: 29989120 DOI: 10.1039/c8cp02930j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adenine, a DNA base, exists as several tautomers and isomers that are closely lying in energy and that may form a mixture upon vaporization of solid adenine. Indeed, it is challenging to bring adenine into the gas phase, especially as a unique tautomer. The experimental conditions were tuned to prepare a jet-cooled canonical adenine (9H-adenine). This isolated DNA base was ionized by single VUV photons from a synchrotron beamline and the corresponding slow photoelectron spectrum was compared to ab initio computations of the neutral and ionic species. We report the vibronic structure of the X+ 2A'' (D0), A+ 2A' (D1) and B+ 2A'' (D2) electronic states of the 9H adenine cation, from the adiabatic ionization energy (AIE) up to AIE + 1.8 eV. Accurate AIEs are derived for the 9H-adenine (X[combining tilde] 1A') + hν → 9H-adenine+ (X+ 2A'', A+ 2A', B+ 2A'') + e- transitions. Close to the AIE, we fully assign the rich vibronic structure solely to the 9H-adenine (X 1A') + hν → 9H-adenine+ (X+ 2A'') transition. Importantly, we show that the lowest cationic electronic states of canonical adenine are coupled vibronically. The present findings are important for understanding the effects of ionizing radiation and the charge distribution on this elementary building block of life, at ultrafast, short, and long timescales.
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Affiliation(s)
- Hong Yan Zhao
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong
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9
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Lin PC, Wu ZH, Chen MS, Li YL, Chen WR, Huang TP, Lee YY, Wang CC. Interfacial Solvation and Surface pH of Phenol and Dihydroxybenzene Aqueous Nanoaerosols Unveiled by Aerosol VUV Photoelectron Spectroscopy. J Phys Chem B 2017; 121:1054-1067. [PMID: 28055205 DOI: 10.1021/acs.jpcb.6b10201] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although the significance of aqueous interfaces has been recognized in numerous important fields, it can be even more prominent for nanoscaled aqueous aerosols because of their large surface-to-volume ratios and prevalent existence in nature. Also, considering that organic species are often mixed with aqueous aerosols in nature, a fundamental understanding of the electronic and structural properties of organic species in aqueous nanoaerosols is essential to learn the interplay between water and organic solutes under the nanoscaled size regime. Here, we report for the first time the vacuum ultraviolet photoelectron spectroscopy of phenol and three dihydroxybenzene (DHB) isomers including catechol, resorcinol, and hydroquinone in the aqueous nanoaerosol form. By evaluating two photoelectron features of the lowest vertical ionization energies originated from the b1(π) and a2(π) orbitals for phenolic aqueous nanoaerosols, their interfacial solvation characteristics are unraveled. Phenolic species appear to reside primarily on/near the aqueous nanoaerosol interface, where they appear only partially hydrated on the aqueous interface with the hydrophilic hydroxyl group more solvated in water. An appreciable proportion of phenol is found to coexist with phenolate at/near the nanoaerosol interface even under a high bulk pH of 12.0, indicating that the nanoaerosol interface exhibits a composition distribution and pH drastically different from those of the bulk. The surface pH of phenol-containing aqueous nanoaerosols is found to be ∼2.2 ± 0.1 units more acidic than that of the bulk interior, as measured at the bulk pH of 12.0. From the photoelectron spectra of DHB aqueous nanoaerosols, the effects of numbers/arrangements of -OH groups are assessed. This study shows that the hydration extents, pH values, deprotonation status, and numbers/relative arrangements of -OH groups are crucial factors affecting the ionization energies of phenolic aqueous nanoaerosols and thus their redox-based activities. The multifaceted implications of the present study in the aerosol science, atmospheric/marine chemistry, and biological science are also addressed.
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Affiliation(s)
| | | | | | | | | | - Tzu-Ping Huang
- National Synchrotron Radiation Research Center , Hsinchu, Taiwan 30076, ROC
| | - Yin-Yu Lee
- National Synchrotron Radiation Research Center , Hsinchu, Taiwan 30076, ROC
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10
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Chen Z, Lau KC, Garcia GA, Nahon L, Božanić DK, Poisson L, Al-Mogren MM, Schwell M, Francisco JS, Bellili A, Hochlaf M. Identifying Cytosine-Specific Isomers via High-Accuracy Single Photon Ionization. J Am Chem Soc 2016; 138:16596-16599. [DOI: 10.1021/jacs.6b10413] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Ziyong Chen
- Department
of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Kai-Chung Lau
- Department
of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Gustavo A. Garcia
- Synchrotron SOLEIL, L’orme des
Merisiers, Saint-Aubin
- BP 48, 91192 Gif-sur-Yvette Cedex, France
| | - Laurent Nahon
- Synchrotron SOLEIL, L’orme des
Merisiers, Saint-Aubin
- BP 48, 91192 Gif-sur-Yvette Cedex, France
| | - Dušan K. Božanić
- Synchrotron SOLEIL, L’orme des
Merisiers, Saint-Aubin
- BP 48, 91192 Gif-sur-Yvette Cedex, France
| | - Lionel Poisson
- LIDYL,
CEA, CNRS, Université Paris-Saclay, CEA Saclay, F-91191 Gif-sur-Yvette, France
| | - Muneerah Mogren Al-Mogren
- Chemistry
Department, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Martin Schwell
- Laboratoire
Interuniversitaire des Systèmes Atmosphériques (LISA),
UMR 7583 CNRS, Universités Paris-Est Créteil et Paris Diderot, 61 Avenue du Général de Gaulle, 94010 Créteil, France
| | - Joseph S. Francisco
- Department
of Chemistry, University of Nebraska-Lincoln. 433 Hamilton Hall, Lincoln, Nebraska 68588-0304, United States
| | - Ayad Bellili
- Laboratoire
Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est. 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - Majdi Hochlaf
- Laboratoire
Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est. 5 bd Descartes, 77454 Marne-la-Vallée, France
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11
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Sadr-Arani L, Mignon P, Chermette H, Abdoul-Carime H, Farizon B, Farizon M. Fragmentation mechanisms of cytosine, adenine and guanine ionized bases. Phys Chem Chem Phys 2016; 17:11813-26. [PMID: 25869111 DOI: 10.1039/c5cp00104h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The different fragmentation channels of cytosine, adenine and guanine have been studied through DFT calculations. The electronic structure of bases, their cations, and the fragments obtained by breaking bonds provides a good understanding of the fragmentation process that can complete the experimental approach. The calculations allow assigning various fragments to the given peaks. The comparison between the energy required for the formation of fragments and the peak intensity in the mass spectrum is used. For cytosine and guanine the elimination of the HNCO molecule is a major route of dissociation, while for adenine multiple loss of HCN or HNC can be followed up to small fragments. For cytosine, this corresponds to the initial bond cleavage of N3-C4/N1-C2, which represents the main dissociation route. For guanine the release of HNCO is obtained through the N1-C2/C5-C6 bond cleavage (reverse order also possible) leading to the largest peak of the spectrum. The corresponding energies of 3.5 and 3.9 eV are typically in the range available in the experiments. The loss of NH3 or HCN is also possible but requires more energy. For adenine, fragmentation consists of multiple loss of the HCN molecule and the main route corresponding to HC8N9 loss is followed by the release of HC2N1.
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Affiliation(s)
- Leila Sadr-Arani
- Université de Lyon, Université Claude Bernard Lyon1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de la Doua, 69100 Villeurbanne, France.
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12
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Fulfer KD, Hardy D, Aguilar AA, Poliakoff ED. High-resolution photoelectron spectra of the pyrimidine-type nucleobases. J Chem Phys 2015; 142:224310. [DOI: 10.1063/1.4922310] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- K. D. Fulfer
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - D. Hardy
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - A. A. Aguilar
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - E. D. Poliakoff
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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13
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Itälä E, Kooser K, Rachlew E, Levola H, Ha DT, Kukk E. Gas-phase study on uridine: Conformation and X-ray photofragmentation. J Chem Phys 2015; 142:194303. [PMID: 26001457 DOI: 10.1063/1.4919878] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Fragmentation of RNA nucleoside uridine, induced by carbon 1s core ionization, has been studied. The measurements by combined electron and ion spectroscopy have been performed in gas phase utilizing synchrotron radiation. As uridine is a combination of d-ribose and uracil, which have been studied earlier with the same method, this study also considers the effect of chemical environment and the relevant functional groups. Furthermore, since in core ionization the initial core hole is always highly localized, charge migration prior to fragmentation has been studied here. This study also demonstrates the destructive nature of core ionization as in most cases the C 1s ionization of uridine leads to concerted explosions producing only small fragments with masses ≤43 amu. In addition to fragmentation patterns, we found out that upon evaporation the sugar part of the uridine molecule attains hexagonal form.
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Affiliation(s)
- Eero Itälä
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Kuno Kooser
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Elisabeth Rachlew
- Royal Institute of Technology KTH, Physics department, S-10691 Stockholm, Sweden
| | - Helena Levola
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Dang Trinh Ha
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Edwin Kukk
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
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14
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Raczyńska ED, Makowski M, Hallmann M, Kamińska B. Geometric and energetic consequences of prototropy for adenine and its structural models – a review. RSC Adv 2015. [DOI: 10.1039/c4ra17280a] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Prototropy for adenine and its convenient models causes parallel changes of geometric (HOMED) and energetic (ΔE) parameters for neutral tautomers.
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Affiliation(s)
- Ewa D. Raczyńska
- Department of Chemistry
- Warsaw University of Life Sciences (SGGW)
- 02-776 Warszawa
- Poland
| | | | - Małgorzata Hallmann
- Department of Chemistry
- Warsaw University of Life Sciences (SGGW)
- 02-776 Warszawa
- Poland
| | - Beata Kamińska
- Department of Chemistry
- Warsaw University of Life Sciences (SGGW)
- 02-776 Warszawa
- Poland
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15
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Dossmann H, Schwarzenberg A, Lesage D, Pérot-Taillandier M, Afonso C, Cunha de Miranda B, Garcia GA. Vacuum Ultraviolet Photoionization Study of Gas Phase Vitamins A and B1 Using Aerosol Thermodesorption and Synchrotron Radiation. J Phys Chem A 2014; 118:11185-92. [DOI: 10.1021/jp507050y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Héloïse Dossmann
- Université Pierre et Marie Curie, IPCM/CSOB UMR 8232, 4, Place Jussieu BP 45, 75252 Paris, France
| | - Adrián Schwarzenberg
- Université Pierre et Marie Curie, IPCM/CSOB UMR 8232, 4, Place Jussieu BP 45, 75252 Paris, France
| | - Denis Lesage
- Université Pierre et Marie Curie, IPCM/CSOB UMR 8232, 4, Place Jussieu BP 45, 75252 Paris, France
| | - Marie Pérot-Taillandier
- Université Pierre et Marie Curie, IPCM/CSOB UMR 8232, 4, Place Jussieu BP 45, 75252 Paris, France
| | - Carlos Afonso
- Normandie Université, COBRA, UMR6014 and FR3038, Université de Rouen; INSA de Rouen; CNRS, IRCOF, 76821 Mont-Saint-Aignan
Cedex, France
| | | | - Gustavo A. Garcia
- Synchrotron SOLEIL, L’Orme des Merisiers, St Aubin, BP 48, 91192 Gif-sur-Yvette Cedex, France
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16
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Dawley MM, Tanzer K, Cantrell WA, Plattner P, Brinkmann NR, Scheier P, Denifl S, Ptasińska S. Electron ionization of the nucleobases adenine and hypoxanthine near the threshold: a combined experimental and theoretical study. Phys Chem Chem Phys 2014; 16:25039-53. [DOI: 10.1039/c4cp03452j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Tia M, Cunha de Miranda B, Daly S, Gaie-Levrel F, Garcia GA, Nahon L, Powis I. VUV photodynamics and chiral asymmetry in the photoionization of gas phase alanine enantiomers. J Phys Chem A 2014; 118:2765-79. [PMID: 24654892 DOI: 10.1021/jp5016142] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The valence shell photoionization of the simplest proteinaceous chiral amino acid, alanine, is investigated over the vacuum ultraviolet region from its ionization threshold up to 18 eV. Tunable and variable polarization synchrotron radiation was coupled to a double imaging photoelectron/photoion coincidence (i(2)PEPICO) spectrometer to produce mass-selected threshold photoelectron spectra and derive the state-selected fragmentation channels. The photoelectron circular dichroism (PECD), an orbital-sensitive, conformer-dependent chiroptical effect, was also recorded at various photon energies and compared to continuum multiple scattering calculations. Two complementary vaporization methods-aerosol thermodesorption and a resistively heated sample oven coupled to an adiabatic expansion-were applied to promote pure enantiomers of alanine into the gas phase, yielding neutral alanine with different internal energy distributions. A comparison of the photoelectron spectroscopy, fragmentation, and dichroism measured for each of the vaporization methods was rationalized in terms of internal energy and conformer populations and supported by theoretical calculations. The analytical potential of the so-called PECD-PICO detection technique-where the electron spectroscopy and circular dichroism can be obtained as a function of mass and ion translational energy-is underlined and applied to characterize the origin of the various species found in the experimental mass spectra. Finally, the PECD findings are discussed within an astrochemical context, and possible implications regarding the origin of biomolecular asymmetry are identified.
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Affiliation(s)
- Maurice Tia
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin BP 48, 91192 Gif sur Yvette Cedex, France
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18
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Schwell M, Hochlaf M. Photoionization Spectroscopy of Nucleobases and Analogues in the Gas Phase Using Synchrotron Radiation as Excitation Light Source. Top Curr Chem (Cham) 2014; 355:155-208. [DOI: 10.1007/128_2014_550] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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19
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Janssen MHM, Powis I. Detecting chirality in molecules by imaging photoelectron circular dichroism. Phys Chem Chem Phys 2014; 16:856-71. [DOI: 10.1039/c3cp53741b] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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20
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Méjean M, Giuliani A, Brunelle A, Touboul D. Determination of ionization energies of a monoterpene series by atmospheric pressure photoionization using tunable vacuum ultraviolet synchrotron radiation. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2014; 20:403-407. [PMID: 25707130 DOI: 10.1255/ejms.1291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Monoterpenes are the main class of biogenic volatile organic compounds. They promptly react with oxygen and nitrogen species, leading to the formation of secondary aerosols. The determination of their physicochemical properties, such as their ionization energies (IEs), is crucial to understand better their reactivity. We previously introduced a modified atmospheric pressure photoionization source coupled to a tunable vacuum ultraviolet source at the SOLEIL synchrotron radiation facility. Here, this set-up is employed to determine IEs of ten monoterpenes with a good precision (±50 meV) and a small sample consumption limited to 10 μg.
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