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Wei M, Zuo J, Tian G, Hua W. Simulating temperature and tautomeric effects for vibrationally resolved XPS of biomolecules: Combining time-dependent and time-independent approaches to fingerprint carbonyl groups. J Chem Phys 2024; 161:104303. [PMID: 39248239 DOI: 10.1063/5.0224090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 08/22/2024] [Indexed: 09/10/2024] Open
Abstract
Carbonyl groups (C=O) play crucial roles in the photophysics and photochemistry of biological systems. O1s x-ray photoelectron spectroscopy allows for targeted investigation of the C=O group, and the coupling between C=O vibration and O1s ionization is reflected in the fine structures. To elucidate its characteristic vibronic features, systematic Franck-Condon simulations were conducted for six common biomolecules, including three purines (xanthine, caffeine, and hypoxanthine) and three pyrimidines (thymine, 5F-uracil, and uracil). The complexity of simulation for these biomolecules lies in accounting for temperature effects and potential tautomeric variations. We combined the time-dependent and time-independent methods to efficiently account for the temperature effects and to provide explicit assignments, respectively. For hypoxanthine, the tautomeric effect was considered by incorporating the Boltzmann population ratios of two tautomers. The simulations demonstrated good agreement with experimental spectra, enabling differentiation of two types of carbonyl oxygens with subtle local structural differences, positioned between two nitrogens (O1) or between one carbon and one nitrogen (O2). The analysis provided insights into the coupling between C=O vibration and O1s ionization, consistently showing an elongation of the C=O bond length (by 0.08-0.09 Å) upon O1s ionization.
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Affiliation(s)
- Minrui Wei
- MIIT Key Laboratory of Semiconductor Microstructure and Quantum Sensing, Department of Applied Physics, School of Physics, Nanjing University of Science and Technology, 210094 Nanjing, China
| | - Junxiang Zuo
- MIIT Key Laboratory of Semiconductor Microstructure and Quantum Sensing, Department of Applied Physics, School of Physics, Nanjing University of Science and Technology, 210094 Nanjing, China
| | - Guangjun Tian
- Key Laboratory for Microstructural Material Physics of Hebei Province, School of Science, Yanshan University, Qinhuangdao 066004, China
| | - Weijie Hua
- MIIT Key Laboratory of Semiconductor Microstructure and Quantum Sensing, Department of Applied Physics, School of Physics, Nanjing University of Science and Technology, 210094 Nanjing, China
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2
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Ho J, Cheng P. Ultrafast excited‐state dynamics of gas‐phase 5‐methylcytosine tautomers. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202100254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jr‐Wei Ho
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
| | - Po‐Yuan Cheng
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
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3
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Sa'adeh H, Backler F, Wang F, Piccirillo S, Ciavardini A, Richter R, Coreno M, Prince KC. Experimental and Theoretical Soft X-ray Study of Nicotine and Related Compounds. J Phys Chem A 2020; 124:4025-4035. [PMID: 32336097 DOI: 10.1021/acs.jpca.9b11586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The valence and core electronic structure of nicotine, nicotinic acid, and nicotinamide have been studied by photoelectron and soft X-ray absorption spectroscopy, supported by theoretical calculations, which take into account conformational isomerism. The core-level photoionization spectra of all molecules have been assigned, and theory indicates that the effects of conformational differences are small, generally less than the natural line widths of the core ionic states. However, in the case of nicotinamide, the theoretical valence ionization potentials of cis and trans conformers differ significantly in the outer valence space, and the experimental spectrum is in agreement with the calculated outer valence cis conformer spectrum. In addition, the C, N, and O K edge near-edge absorption fine structure spectra are reported and interpreted by comparison with reference compounds. We find evidence at the N and O K edges of interaction between the delocalized orbitals of the pyridine ring and the substituents for nicotinic acid and nicotinamide. The strength of the interaction varies because the first is planar, while the second is twisted, reducing the extent of orbital mixing.
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Affiliation(s)
- Hanan Sa'adeh
- Department of Physics, The University of Jordan, 11942 Amman, Jordan.,Elettra Sincrotrone Trieste, in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Frederick Backler
- Centre for Translational Atomaterials and Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Feng Wang
- Centre for Translational Atomaterials and Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Susanna Piccirillo
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", 00133 Rome, Italy
| | | | - Robert Richter
- Elettra Sincrotrone Trieste, in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Marcello Coreno
- ISM-CNR, in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Kevin C Prince
- Elettra Sincrotrone Trieste, in Area Science Park, 34149 Basovizza, Trieste, Italy.,Centre for Translational Atomaterials and Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
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4
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Yang D, Liu W, Kong L, Zhang Q, Liu Y. Ultrafast excited state intramolecular proton transfer (ESIPT) mechanism for 2,6-bis(benzothiazolyl-2-yl)phenol: A theoretical investigation. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137226] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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5
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Feketeová L, Plekan O, Goonewardane M, Ahmed M, Albright AL, White J, O’Hair RAJ, Horsman MR, Wang F, Prince KC. Photoelectron Spectra and Electronic Structures of the Radiosensitizer Nimorazole and Related Compounds. J Phys Chem A 2015; 119:9986-95. [DOI: 10.1021/acs.jpca.5b05950] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Linda Feketeová
- School
of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, 30 Flemington Road, 3010 Parkville, Victoria, Australia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, Parkville, Victoria 3010, Australia
- Institut
de Physique Nucléaire de Lyon, Université Claude Bernard
Lyon1, Université de Lyon, CNRS/IN2P3 UMR 5822, 43 Bd du 11
novembre 1918, 69622 Villeurbanne Cedex, France
| | - Oksana Plekan
- Elettra-Sincrotrone Trieste, in Area Science
Park, 34149 Basovizza,
Trieste, Italy
| | - Mayanthi Goonewardane
- Molecular
Model Discovery Laboratory, Department of Chemistry and Biotechnology,
Faculty of Science, Engineering and Technology, Swinburne University of Technology, 3122 Hawthorn, Victoria, Australia
| | - Marawan Ahmed
- Molecular
Model Discovery Laboratory, Department of Chemistry and Biotechnology,
Faculty of Science, Engineering and Technology, Swinburne University of Technology, 3122 Hawthorn, Victoria, Australia
| | - Abigail L. Albright
- School
of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, 30 Flemington Road, 3010 Parkville, Victoria, Australia
| | - Jonathan White
- School
of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, 30 Flemington Road, 3010 Parkville, Victoria, Australia
| | - Richard A. J. O’Hair
- School
of Chemistry and Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, 30 Flemington Road, 3010 Parkville, Victoria, Australia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, Parkville, Victoria 3010, Australia
| | - Michael R. Horsman
- Department
of Experimental Clinical Oncology, Aarhus University Hospital, Nørrebrogade 44, 8000 Aarhus C, Denmark
| | - Feng Wang
- Molecular
Model Discovery Laboratory, Department of Chemistry and Biotechnology,
Faculty of Science, Engineering and Technology, Swinburne University of Technology, 3122 Hawthorn, Victoria, Australia
| | - Kevin C. Prince
- Elettra-Sincrotrone Trieste, in Area Science
Park, 34149 Basovizza,
Trieste, Italy
- Molecular
Model Discovery Laboratory, Department of Chemistry and Biotechnology,
Faculty of Science, Engineering and Technology, Swinburne University of Technology, 3122 Hawthorn, Victoria, Australia
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6
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Nakayama A, Yamazaki S, Taketsugu T. Quantum Chemical Investigations on the Nonradiative Deactivation Pathways of Cytosine Derivatives. J Phys Chem A 2014; 118:9429-37. [DOI: 10.1021/jp506740r] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Akira Nakayama
- Catalysis
Research Center, Hokkaido University, Sapporo 001-0021, Japan
| | - Shohei Yamazaki
- Department
of Frontier Materials Chemistry, Graduate School of Science and Technology, Hirosaki University, Hirosaki 036-8561, Japan
| | - Tetsuya Taketsugu
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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7
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Lapinski L, Reva I, Rostkowska H, Fausto R, Nowak MJ. Near-IR-Induced, UV-Induced, and Spontaneous Isomerizations in 5-Methylcytosine and 5-Fluorocytosine. J Phys Chem B 2014; 118:2831-41. [DOI: 10.1021/jp411423c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Leszek Lapinski
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Igor Reva
- Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Hanna Rostkowska
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Rui Fausto
- Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Maciej J. Nowak
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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8
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Frey JA, Ottiger P, Leutwyler S. Watson–Crick and Sugar-Edge Base Pairing of Cytosine in the Gas Phase: UV and Infrared Spectra of Cytosine·2-Pyridone. J Phys Chem B 2014; 118:682-91. [DOI: 10.1021/jp409660b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jann A. Frey
- Department
of Chemistry and
Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Philipp Ottiger
- Department
of Chemistry and
Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Department
of Chemistry and
Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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9
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Galvão TLP, Rocha IM, Ribeiro da Silva MDMC, Ribeiro da Silva MAV. From 2-Hydroxypyridine to 4(3H)-Pyrimidinone: Computational Study on the Control of the Tautomeric Equilibrium. J Phys Chem A 2013; 117:12668-74. [DOI: 10.1021/jp410004x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tiago L. P. Galvão
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007, Porto, Portugal
| | - Inês M. Rocha
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007, Porto, Portugal
| | - Maria D. M. C. Ribeiro da Silva
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007, Porto, Portugal
| | - Manuel A. V. Ribeiro da Silva
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007, Porto, Portugal
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10
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Trachsel MA, Lobsiger S, Leutwyler S. Out-of-Plane Low-Frequency Vibrations and Nonradiative Decay in the 1ππ* State of Jet-Cooled 5-Methylcytosine. J Phys Chem B 2012; 116:11081-91. [DOI: 10.1021/jp305688m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria A. Trachsel
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Simon Lobsiger
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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