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Zima V, Vlk M, Wan J, Cvačka J, Tureček F. Tracking Isomerizations of High-Energy Adenine Cation Radicals by UV-Vis Action Spectroscopy and Cyclic Ion Mobility Mass Spectrometry. J Phys Chem A 2023. [PMID: 37433135 DOI: 10.1021/acs.jpca.3c03179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
We report experimental and computational studies of protonated adenine C-8 σ-radicals that are presumed yet elusive reactive intermediates of oxidative damage to nucleic acids. The radicals were generated in the gas phase by the collision-induced dissociation of C-8-Br and C-8-I bonds in protonated 8-bromo- and 8-iodoadenine as well as by 8-bromo- and 8-iodo-9-methyladenine. Protonation by electrospray of 8-bromo- and 8-iodoadenine was shown by cyclic-ion mobility mass spectrometry (c-IMS) to form the N-1-H, N-9-H and N-3-H, N-7-H protomers in 85:15 and 81:19 ratios, respectively, in accordance with the equilibrium populations of these protomers in water-solvated ions that were calculated by density functional theory (DFT). Protonation of 8-halogenated 9-methyladenines yielded single N-1-H protomers, which was consistent with their thermodynamic stability. The radicals produced from the 8-bromo and 8-iodo adenine cations were characterized by UV-vis photodissociation action spectroscopy (UVPD) and c-IMS. UVPD revealed the formation of C-8 σ-radicals along with N-3-H, N-7-H-adenine π-radicals that arose as secondary products by hydrogen atom migrations. The isomers were identified by matching their action spectra against the calculated vibronic absorption spectra. Deuterium isotope effects were found to slow the isomerization and increase the population of C-8 σ-radicals. The adenine cation radicals were separated by c-IMS and identified by their collision cross sections, which were measured relative to the canonical N-9-H adenine cation radical that was cogenerated in situ as an internal standard. Ab initio CCSD(T)/CBS calculations of isomer energies showed that the adenine C-8 σ-radicals were local energy minima with relative energies at 76-79 kJ mol-1 above that of the canonical adenine cation radical. Rice-Ramsperger-Kassel-Marcus calculations of unimolecular rate constants for hydrogen and deuterium migrations resulting in exergonic isomerizations showed kinetic shifts of 10-17 kJ mol-1, stabilizing the C-8 σ-radicals. C-8 σ-radicals derived from N-1-protonated 9-methyladenine were also thermodynamically unstable and readily isomerized upon formation.
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Affiliation(s)
- Václav Zima
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Mikuláš Vlk
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - Jiahao Wan
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
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Feng E, Yu ZJ, Jiang H, Ma X, Nash JJ, Kenttämaa HI. Gas-Phase Reactivity of Phenylcarbyne Anions. J Am Chem Soc 2022; 144:8576-8590. [PMID: 35507319 DOI: 10.1021/jacs.1c13714] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gas-phase reactivities of the phenylcarbyne anion and its four derivatives were studied using a linear quadrupole ion trap mass spectrometer. The phenylcarbyne anions were calculated to have a triplet ground state (singlet-triplet splittings of 4-9 kcal mol-1), with the exception of the 4-cyanophenylcarbyne anion that has a singlet ground state (singlet-triplet splitting of -1.9 kcal mol-1). Only the phenylcarbyne anions with a triplet ground state react with acetone and dimethyl disulfide via radical mechanisms. On the other hand, only the phenylcarbyne anion with a singlet ground state abstracts H2O and H2C═C═O from acetic acid via electrophilic addition of the reagents to the anion. Finally, two hydroxy-substituted phenylcarbyne anions (with triplet ground states) partially tautomerize with the assistance of reagent molecules to the more stable distonic phenylcarbene anions. This occurs via abstraction of a proton from the reagent by the phenylcarbyne anion to generate a neutral (triplet) phenylcarbene and a reagent anion, which is followed by proton abstraction from the hydroxyl group of the neutral phenylcarbene by the reagent anion to generate the distonic phenylcarbene anion in an excited triplet state. Experiments performed on deuterated hydroxy-substituted phenylcarbyne anions verified the mechanism. The reactivities of the distonic phenylcarbene anions were found to be quite different from those of the phenylcarbyne anions. For example, they were found to abstract CH2 from acetonitrile, which is initiated by C-H insertion─typical singlet carbene reactivity.
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Affiliation(s)
- Erlu Feng
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Zaikuan J Yu
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Hanning Jiang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Xin Ma
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - John J Nash
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Hilkka I Kenttämaa
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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Ding D, Feng E, Kotha RR, Chapman NC, Jiang H, Nash JJ, Kenttämaa HI. Spin-Spin Coupling Controls the Gas-Phase Reactivity of Aromatic σ-Type Triradicals. Chemistry 2021; 28:e202102968. [PMID: 34786768 DOI: 10.1002/chem.202102968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Indexed: 11/11/2022]
Abstract
Examination of the reactions of σ-type quinolinium-based triradicals with cyclohexane in the gas phase demonstrated that the radical site that is the least strongly coupled to the other two radical sites reacts first, independent of the intrinsic reactivity of this radical site, in contrast to related biradicals that first react at the most electron-deficient radical site. Abstraction of one or two H atoms and formation of an ion that formally corresponds to a combination of the ion and cyclohexane accompanied by elimination of a H atom ("addition-H") were observed. In all cases except one, the most reactive radical site of the triradicals is intrinsically less reactive than the other two radical sites. The product complex of the first H atom abstraction either dissociates to give the H-atom-abstraction product and the cyclohexyl radical or the more reactive radical site in the produced biradical abstracts a H atom from the cyclohexyl radical. The monoradical product sometimes adds to cyclohexene followed by elimination of a H atom, generating the "addition-H" products. Similar reaction efficiencies were measured for three of the triradicals as for relevant monoradicals. Surprisingly, the remaining three triradicals (all containing a meta-pyridyne moiety) reacted substantially faster than the relevant monoradicals. This is likely due to the exothermic generation of a meta-pyridyne analog that has enough energy to attain the dehydrocarbon atom separation common for H-atom-abstraction transition states of protonated meta-pyridynes.
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Affiliation(s)
- Duanchen Ding
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Erlu Feng
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Raghavendhar R Kotha
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Nathan C Chapman
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Hanning Jiang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - John J Nash
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Hilkka I Kenttämaa
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
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Huang SR, Nováková G, Marek A, Tureček F. The Elusive Noncanonical Isomers of Ionized 9-Methyladenine and 2′-Deoxyadenosine. J Phys Chem A 2020; 125:338-348. [DOI: 10.1021/acs.jpca.0c10293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Shu R. Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Gabriela Nováková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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Shi G, Zhou J, Li Z, Sun Y, Kantorovich LN, Fang Q, Besenbacher F, Yu M. Graphene‐Like Covalent Organic Framework with a Wide Band Gap Synthesized On Surface via Stepwise Reactions. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006176] [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)
- Guoqiang Shi
- State Key Laboratory of Urban Water Resource and Environment School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
| | - Junfeng Zhou
- Shanghai Institute of Organic Chemistry Chinese Academy of Sciences Shanghai 200032 China
| | - Zhuo Li
- State Key Laboratory of Urban Water Resource and Environment School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
| | - Ye Sun
- Condensed Matter Science and Technology Institute Harbin Institute of Technology Harbin 150001 China
| | - Lev N. Kantorovich
- Department of Physics King's College London The Strand London WC2R 2LS UK
| | - Qiang Fang
- Shanghai Institute of Organic Chemistry Chinese Academy of Sciences Shanghai 200032 China
| | - Flemming Besenbacher
- Interdisciplinary Nanoscience Center (iNANO) and Department of Physics and Astronomy Aarhus University Aarhus 8000 Denmark
| | - Miao Yu
- State Key Laboratory of Urban Water Resource and Environment School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
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Shi G, Zhou J, Li Z, Sun Y, Kantorovich LN, Fang Q, Besenbacher F, Yu M. Graphene-Like Covalent Organic Framework with a Wide Band Gap Synthesized On Surface via Stepwise Reactions. Angew Chem Int Ed Engl 2020; 59:15958-15962. [PMID: 32516498 DOI: 10.1002/anie.202006176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Indexed: 11/10/2022]
Abstract
Developing graphene-like two-dimensional materials naturally possessing a band gap has sparked enormous interest. Thanks to the inherent wide band gap and high mobility in the 2D plane, covalent organic frameworks containing triazine rings (t-COFs) hold great promise in this regard, whilst the synthesis of single-layer t-COFs remains highly challenging. Herein, we present the fabrication of a well-defined graphene-like t-COF on Au(111). Instead of single/multiple-step single-type reactions commonly applied for on-surface synthesis, distinct stepwise on-surface reactions, including alkynyl cyclotrimerization, C-O bond cleavage, and C-H bond activation, are triggered on demand, leading to product evolution in a controlled step-by-step manner. Aside from the precise control in sophisticated on-surface synthesis, this work proposes a single-atomic-layer organic semiconductor with a wide band gap of 3.41 eV.
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Affiliation(s)
- Guoqiang Shi
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Junfeng Zhou
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhuo Li
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Ye Sun
- Condensed Matter Science and Technology Institute, Harbin Institute of Technology, Harbin, 150001, China
| | - Lev N Kantorovich
- Department of Physics, King's College London, The Strand, London, WC2R 2LS, UK
| | - Qiang Fang
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Flemming Besenbacher
- Interdisciplinary Nanoscience Center (iNANO) and Department of Physics and Astronomy, Aarhus University, Aarhus, 8000, Denmark
| | - Miao Yu
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
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