1
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Affiliation(s)
- Jack P Simons
- Chemistry, University of Utah, United States of America
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2
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Liu Y, Ma C, Nováková G, Marek A, Tureček F. Charge-Tagged Nucleosides in the Gas Phase: UV-Vis Action Spectroscopy and Structures of Cytidine Cations, Dications, and Cation Radicals. J Phys Chem A 2021; 125:6096-6108. [PMID: 34240862 DOI: 10.1021/acs.jpca.1c03477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cytidine ribonucleosides were furnished at O5' with fixed-charge 6-trimethylammoniumhexan-1-aminecarbonyl tags and studied by UV-vis photodissociation action spectroscopy in the gas phase to probe isolated nucleobase chromophores in their neutral, protonated, and hydrogen-adduct radical forms. The action spectrum of the doubly charged cytidine conjugate showed bands at 310 and 270 nm that were assigned to the N3- and O2-protonated cytosine tautomers formed by electrospray, respectively. In contrast, cytidine conjugates coordinated to dibenzo-18-crown-6-ether (DBCE) in a noncovalent complex were found to strongly favor protonation at N3, forming a single-ion tautomer. This allowed us to form cytidine N3-H radicals by electron transfer dissociation of the complex and study their action spectra. Cytidine radicals showed only very weak absorption in the visible region of the spectrum for dipole-disallowed transitions to the low (A and B) excited states. The main bands were observed at 360, 300, and 250 nm that were assigned with the help of theoretical vibronic spectra obtained by time-dependent density functional theory calculations of multiple (>300) radical vibrational configurations. Collision-induced dissociations of cytidine radicals proceeded by major cleavage of the N1-C1' glycosidic bond leading to loss of cytosine and competitive loss of N3-hydrogen atom. These dissociations were characterized by calculations of transition-state structures and energies using combined Born-Oppenheimer molecular dynamics and DFT calculations. Overall, cytidine radicals were found to be kinetically and thermodynamically more stable than previously reported analogous adenosine and guanosine radicals.
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Affiliation(s)
- Yue Liu
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Congcong Ma
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Gabriela Nováková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 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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3
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Chen X, Syrstad EA, Nguyen MT, Gerbaux P, Turecek F. Adenine radicals in the gas phase: an experimental and computational study of hydrogen atom adducts to adenine. J Phys Chem A 2007; 109:8121-32. [PMID: 16834198 DOI: 10.1021/jp0529725] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The elusive hydrogen atom adduct to the N-1 position in adenine, which is thought to be the initial intermediate of chemical damage, was specifically generated in the gas phase and characterized by neutralization-reionization mass spectrometry. The N-1 adduct, 1,2-dihydroaden-2-yl radical (1), was generated by femtosecond electron transfer to N-1-protonated adenine that was selectively produced by electrospray ionization of adenine in aqueous-methanol solution. Radical 1 is an intrinsically stable species in the gas phase that undergoes specific loss of the N-1-hydrogen atom to form adenine, but does not isomerize to the more stable C-2 adduct, 1,2-dihydroaden-1-yl radical (5). Radicals 1 that are formed in the fifth and higher electronically excited states of DeltaE > or = 2.5 eV can also undergo ring-cleavage dissociations resulting in expulsion of HCN. The relative stabilities, dissociation, and transition state energies for several hydrogen atom adducts to adenine have been established computationally at highly correlated levels of theory. Transition state theory calculations of 298 K rate constants in the gas phase, including quantum tunnel corrections, indicate the branching ratios for H-atom additions to C-8, C-2, N-3, N-1, and N-7 positions in adenine as 0.68, 0.20, 0.08, 0.03, and 0.01, respectively. The relative free energies of adenine radicals in aqueous solution point to the C-8 adduct as the most stable tautomer, which is predicted to be the predominating (>99.9%) product at thermal equilibrium in solution at 298 K.
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Affiliation(s)
- Xiaohong Chen
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, WA 98195-1700, USA
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4
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Yao C, Tureček F. Hypervalent ammonium radicals. Competitive N–C and N–H bond dissociations in methyl ammonium and ethyl ammonium. Phys Chem Chem Phys 2005; 7:912-20. [DOI: 10.1039/b414764b] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Tam F, Syrstad EA, Chen X, Turecek F. Electron-rich radicals by neutralizationreionization mass spectrometry. Generation, dissociations and energetics of the hydrogen atom adduct to acetamide. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2004; 10:869-880. [PMID: 15775047 DOI: 10.1255/ejms.680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protonated acetamide exists as two planar conformers, the more stable anti-form (anti-1(+)) and the syn-form (syn-1(+)), DeltaG(degree) (298) (anti-->syn) = 10.8 kJ mol(-1). Collisional neutralization of 1(+) produces 1-hydroxy-1-amino-1-ethyl radicals (anti-1 and syn-1) which in part survive for 3.7 micros. The major dissociation of 1 is loss of the hydroxyl hydrogen atom (approximately 95%) which is accompanied by loss of one of the methyl hydrogen atoms (approximately 3%) and loss of the methyl group (approximately 2%). The most favorable dissociation of the OH bond is calculated to be only 34 kJ mol(1) endothermic but requires 88 kJ mol(-1) in the transition state. Other dissociations of 1, e.g., loss of one of the amide hydrogens, methyl hydrogens, and loss of ammonia are calculated to proceed through higher- energy transition states and are not kinetically competitive if proceeding from the ground doublet electronic state of 1. The unimolecular dissociation of 1 following collisional electron transfer is promoted by large Franck-Condon effects that result in 8090 kJ mol(-1) vibrational excitation in the radicals. Radicals 1 are calculated to exoergically abstract hydrogen atoms from acetamide in water, but not in the gas phase. The different reactivity is due to solvent effects that favor the products, (.)CH(2)CONH(2) and CH(3)CH(OH)NH(2), over the reactants.
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Affiliation(s)
- Francis Tam
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, WA 98195-1700, USA
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6
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Srikanth R, Srinivas R, Bhanuprakash K, Vivekananda S, Syrstad EA, Turecek F. Generation and characterization of ionic and neutral P(OH)2+/* in the gas phase by tandem mass spectrometry and computational chemistry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:250-264. [PMID: 11908805 DOI: 10.1016/s1044-0305(01)00360-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The bicoordinated dihydroxyphosphenium ion P(OH)2+ (1+) was generated specifically by charge-exchange dissociative ionization of triethylphosphite and its connectivity was confirmed by collision induced dissociation and neutralization-reionization mass spectra. The major dissociation of 1+ forming PO+ ions at m/z 47 involved another isomer, O=P-OH2+ (2+), for which the optimized geometry showed a long P-OH2 bond. Dissociative 70-eV electron ionization of diethyl phosphite produced mostly 1+ together with a less stable isomer, HP(O)OH+ (3+). Ion 2+ is possibly co-formed with 1+ upon dissociative 70-eV electron ionization of methylphosphonic acid. Neutralization-reionization of 1+ confirmed that P(OH)2* (1) was a stable species. Dissociations of neutral 1, as identified by variable-time measurements, involved rate-determining isomerization to 2 followed by fast loss of water. A competitive loss of H occurs from long-lived excited states of 1 produced by vertical electron transfer. The A and B states undergo rate-determining internal conversion to vibrationally highly excited ground state that loses an H atom via two competing mechanisms. The first of these is the direct cleavage of one of the O-H bonds in 1. The other is an isomerization to 3 followed by cleavage of the P-H bond to form O=P-OH as a stable product. The relative, dissociation, and transition state energies for the ions and neutrals were studied by ab initio and density functional theory calculations up to the QCISD(T)/6-311+G(3df,2p) and CCSD(T)/aug-cc-pVTZ levels of theory. RRKM calculations were performed to investigate unimolecular dissociation kinetics of 1. Excited state geometries and energies were investigated by a combination of configuration interaction singles and time-dependent density functional theory calculations.
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Affiliation(s)
- R Srikanth
- National Center for Mass Spectrometry, Indian Institute of Chemical Technology, Hyderabad
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7
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Syrstad EA, Tureček F. Hydrogen Atom Adducts to the Amide Bond. Generation and Energetics of the Amino(hydroxy)methyl Radical in the Gas Phase. J Phys Chem A 2001. [DOI: 10.1021/jp012931i] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Erik A. Syrstad
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
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8
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Polášek M, Tureček F. Nitromethyl Radical, Cation, and Anion. A Neutralization and Electron Photodetachment−Reionization Mass Spectrometric and ab Initio Computational Study of [C,H2,N,O2] Isomers. J Phys Chem A 2001. [DOI: 10.1021/jp002758a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miroslav Polášek
- Department of Chemistry, Bagley Hall, University of Washington, Box 351700, Seattle, Washington 98195-1700
| | - František Tureček
- Department of Chemistry, Bagley Hall, University of Washington, Box 351700, Seattle, Washington 98195-1700
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Polasek M, Turecek F. Protonation sites in methyl nitrate and the formation of transient CH4NO3 radicals. A neutralization-reionization mass spectrometric and computational study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2000; 11:380-392. [PMID: 10790841 DOI: 10.1016/s1044-0305(00)00106-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Protonation sites in methyl nitrate (1) were evaluated computationally at the Gaussian 2(MP2) level of ab initio theory. The methoxy oxygen was the most basic site that had a calculated proton affinity of PA = 728-738 kJ mol-1 depending on the optimization method used to calculate the equilibrium geometry of the CH3O(H)-NO2+ ion (2+). Protonation at the terminal oxygen atoms in methyl nitrate was less exothermic; the calculated proton affinities were 725, 722, and 712 kJ mol-1 for the formation of the syn-syn, anti-syn, and syn-anti ion rotamers 3a+, 3b+, and 3c+, respectively. Ion 2+ was prepared by an ion-molecule reaction of NO2+ with methanol and used to generate the transient CH3O(H)-NO2. radical (2) by femtosecond collisional electron transfer. Exothermic protonation of 1 produced a mixture of 3a(+)-3c+ with 2+ that was used to generate transient radicals 3a-3c. Radical 2 was found to be unbound and dissociated without barrier to methanol and NO2. Radicals 3a-3c were calculated to be weakly bound. When formed by vertical neutralization, 3a-3c dissociated completely on the 4.2 microseconds time scale of the experiment. The main dissociations of 3a-3c were formations of CH3O. + HONO and CH3ONO + OH.. The gas-phase chemistry of radicals 3a-3c and their dissociation products, as studied by neutralization-reionization mass spectrometry, was dominated by Franck-Condon effects on collisional neutralization and reionization. The adiabatic ionization energies of 3a-3c were calculated as 7.54, 7.57, and 7.66 eV, respectively.
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Affiliation(s)
- M Polasek
- Department of Chemistry, University of Washington, Seattle 98195-1700, USA
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10
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Polášek M, Tureček F. Direct Observation of Hydrogen Atom Adducts to Nitromethane and Methyl Nitrite. A Variable-Time Neutralization−Reionization Mass Spectrometric and ab Initio/RRKM Study. J Phys Chem A 1999. [DOI: 10.1021/jp991984l] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miroslav Polášek
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
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Frank AJ, Turecek F. Methylsulfonyl and Methoxysulfinyl Radicals and Cations in the Gas Phase. A Variable-Time and Photoexcitation Neutralization−Reionization Mass Spectrometric and ab Initio/RRKM Study. J Phys Chem A 1999. [DOI: 10.1021/jp990946z] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aaron J. Frank
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
| | - Frantisek Turecek
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
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Schalley CA, Hornung G, Schrdder D, Schwarz H. Mass spectrometry as a tool to probe the gas-phase reactivity of neutral molecules. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0168-1176(97)00115-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Frank AJ, Sadílek M, Ferrier JG, Tureček F. Sulfur Oxyacids and Radicals in the Gas Phase. A Variable-Time Neutralization−Photoexcitation−Reionization Mass Spectrometric and Ab Initio/RRKM Study. J Am Chem Soc 1997. [DOI: 10.1021/ja972602x] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Hornung G, Schalley CA, Dieterle M, Schröder D, Schwarz H. A Study of the Gas-Phase Reactivity of Neutral Alkoxy Radicals by Mass Spectrometry: α-Cleavages and Barton-type Hydrogen Migrations. Chemistry 1997. [DOI: 10.1002/chem.19970031120] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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15
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Nguyen VQ, Sadilek M, Ferrier J, Frank AJ, Tureček F. Metastable States of Dimethylammonium, (CH3)2NH2•. J Phys Chem A 1997. [DOI: 10.1021/jp964077e] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Viet Q. Nguyen
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
| | - Martin Sadilek
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
| | - Jordan Ferrier
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
| | - Aaron J. Frank
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
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Nguyen VQ, Tureček F. Protonation Sites in Pyrimidine and Pyrimidinamines in the Gas Phase. J Am Chem Soc 1997. [DOI: 10.1021/ja9634785] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Viet Q. Nguyen
- Contribution from the Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
| | - František Tureček
- Contribution from the Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
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