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Nakao T, Takasu R, Tsuchida H, Saito M, Majima T. Delayed fragmentation of isolated nucleobases induced by MeV ions. J Chem Phys 2024; 161:054302. [PMID: 39087542 DOI: 10.1063/5.0215222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/17/2024] [Indexed: 08/02/2024] Open
Abstract
We evaluated the dissociation of isolated gas-phase nucleobase molecules induced by mega electron volt (MeV)-energy ions to gain fundamental insights into the reactions of nucleobases upon fast ion irradiation. We studied five nucleobase molecules-adenine, guanine, cytosine, thymine, and uracil-as gas-phase targets. We compared the fragmentation patterns obtained from carbon ion impacts with those obtained from proton impacts to clarify the effect of heavy ion irradiation. We also compared the results with electron impact and photoionization results. In addition, we identified several delayed fragmentation pathways by analyzing the correlation between fragment pairs generated from singly and doubly charged intermediate ions. To determine the lifetimes of delayed fragmentation from singly charged intermediate ions, we evaluated the detection efficiencies of the microchannel plate detector for the neutral fragment HCN as a function of kinetic energy using a new methodology. As the first demonstration of this method, we estimated the lifetimes of C5H5N5+ generated by 1.2-MeV C+ and 0.5-MeV H+ collisions to be 0.87 ± 0.43 and 0.67 ± 0.09 µs, respectively. These lifetimes were approximately one order of magnitude longer than those of the doubly charged intermediate ion C5H5N52+.
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Affiliation(s)
- T Nakao
- Department of Nuclear Engineering, Kyoto University, Kyoto 615-8540, Japan
| | - R Takasu
- Department of Nuclear Engineering, Kyoto University, Kyoto 615-8540, Japan
| | - H Tsuchida
- Department of Nuclear Engineering, Kyoto University, Kyoto 615-8540, Japan
- Quantum Science and Engineering Center, Kyoto University, Uji 611-0011, Japan
| | - M Saito
- Department of Nuclear Engineering, Kyoto University, Kyoto 615-8540, Japan
- Quantum Science and Engineering Center, Kyoto University, Uji 611-0011, Japan
| | - T Majima
- Department of Nuclear Engineering, Kyoto University, Kyoto 615-8540, Japan
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2
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Vetritti L, Kopyra J, Wierzbicka P, Varella MTDN. Fragmentation of the DNA Lesion 8-oxo-Guanine by Low-Energy Electrons. J Phys Chem A 2023; 127:7470-7478. [PMID: 37661383 DOI: 10.1021/acs.jpca.3c03704] [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: 09/05/2023]
Abstract
8-oxo-Guanine is a mutagenic lesion produced by reactions involving reactive oxygen species and guanine in DNA. Its production induces mispairing between the canonical nucleobases during DNA replication such that various types of cancers are associated with the DNA lesion. Since radiation therapy is used in some cases, the interaction of low-energy electrons with 8-oxo-guanine can in turn produce other reactive species, which in principle could have either a detrimental or protective effect on the organism. Motivated by these facts, we report a comparative experimental study of electron-induced fragmentation of guanine and 8-oxo-guanine, along with a theoretical study of the π* shape resonances and bound anion states, which may trigger those dissociation reactions. The electron-induced fragmentation of 8-oxo-guanine is remarkably distinct from the native form. More complex reactions were observed for the oxidized species, which may produce several anion fragments at very low energies (∼0 eV). The dehydrogenated parent anion, which is already a minor fragment in guanine, was completely suppressed in 8-oxo-guanine. The calculated thermodynamical thresholds also suggest that NH2 elimination in guanine, at sub-excitation energies, proceeds via a complex reaction involving rearrangement steps.
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Affiliation(s)
- Leonardo Vetritti
- Instituto de Física, Universidade de São Paulo, Caixa Postal 66318, 05315-970 São Paulo, São Paulo, Brazil
| | - Janina Kopyra
- Faculty of Sciences, Siedlce University of Natural Sciences and Humanities, 3 Maja 54, 08-110 Siedlce, Poland
| | - Paulina Wierzbicka
- Faculty of Sciences, Siedlce University of Natural Sciences and Humanities, 3 Maja 54, 08-110 Siedlce, Poland
| | - Márcio T do N Varella
- Instituto de Física, Universidade de São Paulo, Caixa Postal 66318, 05315-970 São Paulo, São Paulo, Brazil
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3
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Wang S, Dauletyarov Y, Krüger P, Horke DA. High-throughput UV-photofragmentation studies of thymine and guanine. Phys Chem Chem Phys 2023; 25:12322-12330. [PMID: 37083208 PMCID: PMC10155487 DOI: 10.1039/d3cp00328k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
High-throughput photofragmentation studies of thymine and guanine were performed at 257 and 343 nm and for a wide range of ionisation laser intensities. Combining a continuous laser-based thermal desorption source with femtosecond multiphoton ionisation using a 50 kHz repetition rate laser allowed us to produce detailed 2D maps of fragmentation as a function of incident laser intensity. The fragmentation was distinctly soft, the parent ions being at least an order of magnitude more abundant than fragment ions. For thymine there was a single dominant fragmentation channel, which involves consecutive HNCO and CO losses. In contrast, for guanine there were several competing ones, the most probable channel corresponding to CH2N2 loss through opening of the pyrimidine ring. The dependence of parent ion abundance on the ionisation laser intensity showed that at 257 nm the ionisation of thymine is a 1 + 1 resonance enhanced process through its open-shell singlet state.
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Affiliation(s)
- Siwen Wang
- Institute for Molecules and Materials, Radboud University, Heijendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Yerbolat Dauletyarov
- Institute for Molecules and Materials, Radboud University, Heijendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Peter Krüger
- Institute for Molecules and Materials, Radboud University, Heijendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Daniel A Horke
- Institute for Molecules and Materials, Radboud University, Heijendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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4
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Electron Impact Ionization of Adenine: Partial Cross Sections. ATOMS 2022. [DOI: 10.3390/atoms10040100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Electron ionization of a genetically important nucleobase, adenine, was investigated from threshold to 500 eV using crossed electron beam–effusive molecular beam geometry and time-of-flight mass spectrometry. We measured the complete set of absolute partial cross sections for adenine using the relative flow technique (RFT) up to an electron energy of 500 eV. Normalization to absolute values was performed using electron ionization cross sections for argon and the vapor pressure data of adenine. The total cross sections obtained by summing the partial cross sections were compared with the existing theoretical and experimental data. The appearance energies of various fragment ions were also measured and compared with the reported data. The prominence of ions with mass (HCN)n+ (n = 1 to 5) indicated a possible pathway to form adenine in the interstellar medium through aggregation of HCN units. Analysis of the partial cross sections for various groups of fragment ions as a function of electron energy was found to give insights into their composition.
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5
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Stochastic dynamic quantitative and 3D structural matrix assisted laser desorption/ionization mass spectrometric analyses of mixture of nucleosides. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Schnegotzki R, Koopman J, Grimme S, Süssmuth RD. Quantum Chemistry-based Molecular Dynamics Simulations as a Tool for the Assignment of ESI-MS/MS Spectra of Drug Molecules. Chemistry 2022; 28:e202200318. [PMID: 35235707 PMCID: PMC9325386 DOI: 10.1002/chem.202200318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Indexed: 11/08/2022]
Abstract
In organic mass spectrometry, fragment ions provide important information on the analyte as a central part of its structure elucidation. With increasing molecular size and possible protonation sites, the potential energy surface (PES) of the analyte can become very complex, which results in a large number of possible fragmentation patterns. Quantum chemical (QC) calculations can help here, enabling the fast calculation of the PES and thus enhancing the mass spectrometry-based structure elucidation processes. In this work, the previously unknown fragmentation pathways of the two drug molecules Nateglinide (45 atoms) and Zopiclone (51 atoms) were investigated using a combination of generic formalisms and calculations conducted with the Quantum Chemical Mass Spectrometry (QCxMS) program. The computations of the de novo fragment spectra were conducted with the semi-empirical GFNn-xTB (n=1, 2) methods and compared against Orbitrap measured electrospray ionization (ESI) spectra in positive ion mode. It was found that the unbiased QC calculations are particularly suitable to predict non-evident fragment ion structures, sometimes contrasting the accepted generic formulation of fragment ion structures from electron migration rules, where the "true" ion fragment structures are approximated. For the first time, all fragment and intermediate structures of these large-sized molecules could be elucidated completely and routinely using this merger of methods, finding new undocumented mechanisms, that are not considered in common rules published so far. Given the importance of ESI for medicinal chemistry, pharmacokinetics, and metabolomics, this approach can significantly enhance the mass spectrometry-based structure elucidation processes and contribute to the understanding of previously unknown fragmentation pathways.
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Affiliation(s)
- Romina Schnegotzki
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Jeroen Koopman
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115, Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115, Bonn, Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
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7
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Shafranyosh MI, Zapotokova M, Sukhoviya MI, Petrulyak VI, Shafranyosh II. Electronic Ionization of Cytosine Molecules. SURFACE ENGINEERING AND APPLIED ELECTROCHEMISTRY 2022. [DOI: 10.3103/s1068375522010100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Bandurin YA, Zavilopulo AN, Molnar S, Shpenik OO. Excitation of L-valine molecules by electrons and photons. THE EUROPEAN PHYSICAL JOURNAL. D, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 2022; 76:9. [PMID: 35069006 PMCID: PMC8761534 DOI: 10.1140/epjd/s10053-021-00331-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Excitation of L-valine molecules was studied by optical spectroscopy. Optical emission spectra of the L-valine molecule and optical excitation functions of molecular bands and the Hβ spectral line were measured in the gas phase using electron impact. In the spectra of optical emission in the wavelength range of 250-500 nm, intense emission bands were found at energies of incident electrons of 30, 50 and 70 eV. Analysis of structural features of the valine molecule suggested a fragmentation scheme with the formation of excited particles in collisions with electrons. A notable feature of the presented optical excitation functions is a different growth dynamics with an increase in the energy of exciting electrons and the presence of a number of features and kinks, which are especially pronounced for λ = 305 nm and λ = 311 nm. The excitation thresholds were determined from the initial sections of the excitation functions of the most intense spectral lines by the least-squares method. The photoluminescence spectra of L-valine were measured for the first time on a Shimadzu RF-6000 spectrofluorophotometer in the spectral range of 400-800 nm for excitation wavelengths of 250, 275, 333, 351, and 380 nm.
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Affiliation(s)
- Yu. A. Bandurin
- Institute of Electron Physics, National Academy of Sciences of Ukraine, Uzhhorod, 88017 Ukraine
| | - A. N. Zavilopulo
- Institute of Electron Physics, National Academy of Sciences of Ukraine, Uzhhorod, 88017 Ukraine
| | - Sh. Molnar
- Ukrainian-Hungarian Educational-Scientific Institute of Uzhhorod National University, Uzhhorod, 88000 Ukraine
| | - O. O. Shpenik
- Ukrainian-Hungarian Educational-Scientific Institute of Uzhhorod National University, Uzhhorod, 88000 Ukraine
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9
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de Vera P, Abril I, Garcia-Molina R. Excitation and ionisation cross-sections in condensed-phase biomaterials by electrons down to very low energy: application to liquid water and genetic building blocks. Phys Chem Chem Phys 2021; 23:5079-5095. [DOI: 10.1039/d0cp04951d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A model is presented for computing electron-impact electronic excitation and ionisation cross-sections for arbitrary condensed-phase biomaterials in a wide energy range, showing a general good agreement with the available experimental data.
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Affiliation(s)
- Pablo de Vera
- Departamento de Física – Centro de Investigación en Óptica y Nanofísica
- Universidad de Murcia
- Murcia
- Spain
- Currently at European Centre for Theoretical Studies in Nuclear Physics and Related Areas (ECT*)
| | - Isabel Abril
- Departament de Física Aplicada
- Universitat d’Alacant
- Alacant
- Spain
| | - Rafael Garcia-Molina
- Departamento de Física – Centro de Investigación en Óptica y Nanofísica
- Universidad de Murcia
- Murcia
- Spain
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10
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11
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Petrenko A, Leitonas K, Volyniuk D, Baryshnikov GV, Belyakov S, Minaev BF, Ågren H, Durgaryan H, GraŽulevičius JV, Arsenyan P. Benzoselenophenylpyridine platinum complexes: green versus red phosphorescence towards hybrid OLEDs. Dalton Trans 2020; 49:3393-3397. [PMID: 32129412 DOI: 10.1039/d0dt00214c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first examples of phosphorescent platinum complexes bearing 2- and 3-(2-pyridyl)benzo[b]selenophenes (PyBSe) were synthesized and fully characterized. Almost identical ionization potential values (5.6 and 5.58 eV) of the solid samples of the Pt complexes were obtained by electron photoemission spectroscopy. Having slightly different molecular design, the solid solutions of the complexes emitted efficient green and red phosphorescence with absolute quantum yields of 52% (for green) and 11.6% (for red). It is demonstrated that the platinum complexes synthesized can be used as phosphorescent dopants for hybrid solution-processable OLEDs.
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Affiliation(s)
- Alla Petrenko
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006, Riga, Latvia.
| | - Karolis Leitonas
- Kaunas University of Technology, Department of Polymer Chemistry and Technology, Radvilenu pl. 19, LT-50254, Kaunas, Lithuania.
| | - Dmytro Volyniuk
- Kaunas University of Technology, Department of Polymer Chemistry and Technology, Radvilenu pl. 19, LT-50254, Kaunas, Lithuania.
| | - Gleb V Baryshnikov
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 10691, Stockholm, Sweden and Department of Chemistry and Nanomaterials Science, Bohdan Khmelnytsky National University, 18031, Cherkasy, Ukraine
| | - Sergey Belyakov
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006, Riga, Latvia.
| | - Boris F Minaev
- Department of Chemistry and Nanomaterials Science, Bohdan Khmelnytsky National University, 18031, Cherkasy, Ukraine
| | - Hans Ågren
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 10691, Stockholm, Sweden and College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, P. R. China
| | - Hranush Durgaryan
- Kaunas University of Technology, Department of Polymer Chemistry and Technology, Radvilenu pl. 19, LT-50254, Kaunas, Lithuania.
| | - Juozas Vidas GraŽulevičius
- Kaunas University of Technology, Department of Polymer Chemistry and Technology, Radvilenu pl. 19, LT-50254, Kaunas, Lithuania.
| | - Pavel Arsenyan
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006, Riga, Latvia.
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12
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Pal S, Kumar M, Singh R, Kumar N. Evaluation of Electron-Impact Ionization Cross Sections for Molecules. J Phys Chem A 2019; 123:4314-4321. [DOI: 10.1021/acs.jpca.9b02021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Satyendra Pal
- Department of Physics, M.M.H. College, Ghaziabad 201001, UP, India
| | - Manoj Kumar
- Department of Physics, M.M.H. College, Ghaziabad 201001, UP, India
| | - Rajbeer Singh
- Department of Physics, M.M.H. College, Ghaziabad 201001, UP, India
| | - Neeraj Kumar
- Department of Physics, M.M.H. College, Ghaziabad 201001, UP, India
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13
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Zhang Y, Xie P, Yang S, Han K. Ionization and Electron Attachment for Nucleobases in Water. J Phys Chem B 2019; 123:1237-1247. [DOI: 10.1021/acs.jpcb.8b09435] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yan Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao, Binhai Road 72, Qingdao 266237, China
| | - Peng Xie
- School of Chemistry & Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Songqiu Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
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14
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Molecule Relaxation. RADIATION 2019. [DOI: 10.1016/b978-0-444-63979-0.00013-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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15
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Cunha T, Mendes M, Ferreira da Silva F, Eden S, García G, Bacchus-Montabonel MC, Limão-Vieira P. Electron transfer driven decomposition of adenine and selected analogs as probed by experimental and theoretical methods. J Chem Phys 2018; 148:134301. [PMID: 29626890 DOI: 10.1063/1.5021888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report on a combined experimental and theoretical study of electron-transfer-induced decomposition of adenine (Ad) and a selection of analog molecules in collisions with potassium (K) atoms. Time-of-flight negative ion mass spectra have been obtained in a wide collision energy range (6-68 eV in the centre-of-mass frame), providing a comprehensive investigation of the fragmentation patterns of purine (Pu), adenine (Ad), 9-methyl adenine (9-mAd), 6-dimethyl adenine (6-dimAd), and 2-D adenine (2-DAd). Following our recent communication about selective hydrogen loss from the transient negative ions (TNIs) produced in these collisions [T. Cunha et al., J. Chem. Phys. 148, 021101 (2018)], this work focuses on the production of smaller fragment anions. In the low-energy part of the present range, several dissociation channels that are accessible in free electron attachment experiments are absent from the present mass spectra, notably NH2 loss from adenine and 9-methyl adenine. This can be understood in terms of a relatively long transit time of the K+ cation in the vicinity of the TNI tending to enhance the likelihood of intramolecular electron transfer. In this case, the excess energy can be redistributed through the available degrees of freedom inhibiting fragmentation pathways. Ab initio theoretical calculations were performed for 9-methyl adenine (9-mAd) and adenine (Ad) in the presence of a potassium atom and provided a strong basis for the assignment of the lowest unoccupied molecular orbitals accessed in the collision process.
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Affiliation(s)
- T Cunha
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - M Mendes
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - F Ferreira da Silva
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - S Eden
- School of Physical Sciences, The Open University, Walton Hall, MK7 6AA Milton Keynes, United Kingdom
| | - G García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006 Madrid, Spain
| | - M-C Bacchus-Montabonel
- Institut Lumiére Matiére, Université Lyon, Université Claude Bernard Lyon 1, CNRS, 69622 Villeurbanne, France
| | - P Limão-Vieira
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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Fennimore MA, Matsika S. Electronic Resonances of Nucleobases Using Stabilization Methods. J Phys Chem A 2018; 122:4048-4057. [DOI: 10.1021/acs.jpca.8b01523] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Mark A. Fennimore
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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17
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Francés-Monerris A, Segarra-Martí J, Merchán M, Roca-Sanjuán D. Complete-active-space second-order perturbation theory (CASPT2//CASSCF) study of the dissociative electron attachment in canonical DNA nucleobases caused by low-energy electrons (0-3 eV). J Chem Phys 2016; 143:215101. [PMID: 26646889 DOI: 10.1063/1.4936574] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Low-energy (0-3 eV) ballistic electrons originated during the irradiation of biological material can interact with DNA/RNA nucleobases yielding transient-anion species which undergo decompositions. Since the discovery that these reactions can eventually lead to strand breaking of the DNA chains, great efforts have been dedicated to their study. The main fragmentation at the 0-3 eV energy range is the ejection of a hydrogen atom from the specific nitrogen positions. In the present study, the methodological approach introduced in a previous work on uracil [I. González-Ramírez et al., J. Chem. Theory Comput. 8, 2769-2776 (2012)] is employed to study the DNA canonical nucleobases fragmentations of N-H bonds induced by low-energy electrons. The approach is based on minimum energy path and linear interpolation of internal coordinates computations along the N-H dissociation channels carried out at the complete-active-space self-consistent field//complete-active-space second-order perturbation theory level. On the basis of the calculated theoretical quantities, new assignations for the adenine and cytosine anion yield curves are provided. In addition, the π1 (-) and π2 (-) states of the pyrimidine nucleobases are expected to produce the temporary anions at electron energies close to 1 and 2 eV, respectively. Finally, the present theoretical results do not allow to discard neither the dipole-bound nor the valence-bound mechanisms in the range of energies explored, suggesting that both possibilities may coexist in the experiments carried out with the isolated nucleobases.
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Affiliation(s)
| | - Javier Segarra-Martí
- Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, 46071 València, Spain
| | - Manuela Merchán
- Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, 46071 València, Spain
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, 46071 València, Spain
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18
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Bauer CA, Grimme S. How to Compute Electron Ionization Mass Spectra from First Principles. J Phys Chem A 2016; 120:3755-66. [DOI: 10.1021/acs.jpca.6b02907] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christoph Alexander Bauer
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie
der Rheinischen Friedrich-Wilhelms, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie
der Rheinischen Friedrich-Wilhelms, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
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19
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Rahman MA, Krishnakumar E. Communication: Electron ionization of DNA bases. J Chem Phys 2016; 144:161102. [PMID: 27131520 DOI: 10.1063/1.4948412] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
No reliable experimental data exist for the partial and total electron ionization cross sections for DNA bases, which are very crucial for modeling radiation damage in genetic material of living cell. We have measured a complete set of absolute partial electron ionization cross sections up to 500 eV for DNA bases for the first time by using the relative flow technique. These partial cross sections are summed to obtain total ion cross sections for all the four bases and are compared with the existing theoretical calculations and the only set of measured absolute cross sections. Our measurements clearly resolve the existing discrepancy between the theoretical and experimental results, thereby providing for the first time reliable numbers for partial and total ion cross sections for these molecules. The results on fragmentation analysis of adenine supports the theory of its formation in space.
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Affiliation(s)
- M A Rahman
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - E Krishnakumar
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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20
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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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Chen B, Zhou L. Computational study on mechanisms of the anticancer drug: Cisplatin and novel polynuclear platinum(II) interaction with sulfur-donor biomolecules and DNA purine bases. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.09.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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22
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Dawley MM, Tanzer K, Carmichael I, Denifl S, Ptasińska S. Dissociative electron attachment to the gas-phase nucleobase hypoxanthine. J Chem Phys 2015; 142:215101. [DOI: 10.1063/1.4921388] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. Michele Dawley
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Katrin Tanzer
- Institut für Ionenphysik und Angewandte Physik, and Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens Universität Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Ian Carmichael
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik, and Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens Universität Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Sylwia Ptasińska
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
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Cole CA, Wang ZC, Snow TP, Bierbaum VM. Deprotonated Purine Dissociation: Experiments, Computations, and Astrobiological Implications. J Phys Chem A 2015; 119:334-43. [DOI: 10.1021/jp509012s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Callie A. Cole
- Department
of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, United States
| | - Zhe-Chen Wang
- Department
of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, United States
| | - Theodore P. Snow
- Department
of Astrophysical and Planetary Sciences, University of Colorado, 391 UCB, Boulder, Colorado 80309, United States
- Center
for Astrophysics and Space Astronomy, University of Colorado, 389 UCB, Boulder, Colorado 80309, United States
| | - Veronica M. Bierbaum
- Department
of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, United States
- Center
for Astrophysics and Space Astronomy, University of Colorado, 389 UCB, Boulder, Colorado 80309, United States
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Grimme S, Bauer CA. Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases Uracil, Thymine, Cytosine, and Guanine. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:125-140. [PMID: 26307693 DOI: 10.1255/ejms.1313] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich- Wilhelms-Universität Bonn, Beringstr. 4, D-53115, Bonn, Germany. - bonn.de
| | - Christopher Alexander Bauer
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, D-53115, Bonn, Germany.
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Bauer CA, Grimme S. Elucidation of Electron Ionization Induced Fragmentations of Adenine by Semiempirical and Density Functional Molecular Dynamics. J Phys Chem A 2014; 118:11479-84. [DOI: 10.1021/jp5096618] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph Alexander Bauer
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn, Beringstrasse 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn, Beringstrasse 4, D-53115 Bonn, Germany
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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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Baryshnikov GV, Valiev RR, Karaush NN, Minaev BF. Aromaticity of the planar hetero[8]circulenes and their doubly charged ions: NICS and GIMIC characterization. Phys Chem Chem Phys 2014; 16:15367-74. [DOI: 10.1039/c4cp00860j] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
All hetero[8]circulenes represent nonaromatic species because the paratropic internal currents (red colour) substantially cancel out the diatropic contribution on the outside edge (blue colour).
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Affiliation(s)
| | - R. R. Valiev
- Tomsk State University
- Tomsk, Russian Federation
- National Research Tomsk Polytechnic University
- Tomsk, Russian Federation
| | - N. N. Karaush
- Bohdan Khmelnytsky National University
- Cherkassy, Ukraine
| | - B. F. Minaev
- Bohdan Khmelnytsky National University
- Cherkassy, Ukraine
- Tomsk State University
- Tomsk, Russian Federation
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