Mass Spectra of Nucleic Acid Derivatives. Pyrimidines

Rice, Jerry M.; Dudek, Gerald O.; Barber, Michael

doi:10.1021/ja00948a029

Cited by 231 publications

(182 citation statements)

References 0 publications

Supporting

Mentioning

154

Contrasting

Unclassified

Order By: Relevance

“…70 eV e − impact 220 nm MPI (present work) Imhoff et al 23 Rice et al 24 20 eV photo-ionization 21 Proposed ion formula a The present data columns only include peaks with count rates that are clearly greater than background measurements. In the columns summarizing the data of Jochims et al 21 and Rice et al, 24 channels with intensities <5% of the maximum peak are labeled weak.…”

Section: Methodsmentioning

confidence: 87%

“…A data acquisition system was developed to record the laser pulse energy and the number of ions detected within a given flight time range on a pulse-by-pulse basis. The system was based on a LabView application interfacing 21 by fast electrons, 23,24 and by MPI at 220 nm (Fig. 3 inset).…”

Section: Methodsmentioning

confidence: 99%

“…In the columns summarizing the data of Jochims et al 21 and Rice et al, 24 channels with intensities <5% of the maximum peak are labeled weak. Arani et al 37 reported other possible assignments but proposed those cited above as the most probable.…”

Section: Methodsmentioning

confidence: 99%

“…Table I lists the peaks observed at 220 nm. Dissociative ionization of uracil has been studied extensively by electron impact, [23][24][25][26][27][28] ion impact, [28][29][30][31][32][33][34][35] and single photon absorption. 21 Taking into account differences in energy deposition and signal/noise ratios, the previous experiments were broadly consistent in terms of the fragment ions produced and three high-resolution examples are summarized in Table I.…”

Section: A Non-dissociative Mpi Of Isolated Uracilmentioning

confidence: 99%

See 3 more Smart Citations

Multi-photon ionization and fragmentation of uracil: Neutral excited-state ring opening and hydration effects

Barc

Ryszka

Spurrell

et al. 2013

The Journal of Chemical Physics

View full text Add to dashboard Cite

Multi-photon ionization (MPI) of the RNA base uracil has been studied in the wavelength range 220–270 nm, coinciding with excitation to the S2(ππ*) state. A fragment ion at m/z = 84 was produced by 2-photon absorption at wavelengths ≤232 nm and assigned to C3H4N2O+ following CO abstraction. This ion has not been observed in alternative dissociative ionization processes (notably electron impact) and its threshold is close to recent calculations of the minimum activation energy for a ring opening conical intersection to a σ(n-π)π* closed shell state. Moreover, the predicted ring opening transition leaves a CO group at one end of the isomer, apparently vulnerable to abstraction. An MPI mass spectrum of uracil-water clusters is presented for the first time and compared with an equivalent dry measurement. Hydration enhances certain fragment ion pathways (particularly C3H3NO+) but represses C3H4N2O+ production. This indicates that hydrogen bonding to water stabilizes uracil with respect to neutral excited-state ring opening.

show abstract

Section: Methodsmentioning

confidence: 87%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: A Non-dissociative Mpi Of Isolated Uracilmentioning

confidence: 99%

See 2 more Smart Citations

Multi-photon ionization and fragmentation of uracil: Neutral excited-state ring opening and hydration effects

Barc

Ryszka

Spurrell

et al. 2013

The Journal of Chemical Physics

View full text Add to dashboard Cite

show abstract

“…For guanine, the initial expulsion of neutral cyanamide (H 2 NCN) is the dominant fragmentation (from the pyrimidine's N1-C2-NH 2 moiety), and some NH 2 group elimination was observed as well. For cytosine [31], NH 2 elimination was observed and it is followed by loss of HCN. Initial decarbonylation of the molecular ion also was observed, and the peaks at m/z 69, 68, and 67 were explained by retro-Diels-Alder reactions eliminating first ·NϭCϭO, HNCO, or H and HNCO, respectively, and subsequent HCN loss.…”

Section: Initial Expulsion Of Nitrile or Ammoniamentioning

confidence: 99%

Ammonia elimination from protonated nucleobases and related synthetic substrates

Qian

Yang

et al. 2007

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

The results are reported of mass-spectrometric studies of the nucleobases adenine 1h (1, R ϭ H), guanine 2h, and cytosine 3h. The protonated nucleobases are generated by electrospray ionization of adenosine 1r (1, R ϭ ribose), guanosine 2r, and deoxycytidine 3d (3, R ϭ deoxyribose) and their fragmentations were studied with tandem mass spectrometry. In contrast to previous EI-MS studies of the nucleobases, NH 3 elimination does present a major path for the fragmentations of the ions [1h ϩ H] ϩ , [2h ϩ H] ϩ , and [3h ϩ H] ϩ . The ion [2h ϩ H Ϫ NH 3 ] ϩ also was generated from the acyclic precursor 5-cyanoamino-4-oxomethylenedihydroimidazole 13h and from the thioether derivative 14h of 2h (NH 2 replaced by MeS). The analyses of the modes of initial fragmentation is supported by density functional theoretical studies. Conjugate acids 15-55 were studied to determine site preferences for the protonations of 1h, 2h, 3h, 13h, and 14h. The proton affinity of the amino group hardly ever is the substrate's best protonation site, and possible mechanisms for NH 3 elimination are discussed in which the amino group serves as the dissociative protonation site. The results provide semi-direct experimental evidence for the existence of the pyrimidine ring-opened cations that we had proposed on the basis of theoretical studies as intermediates in nitrosative nucleobase deamination. [1,2]. This chemistry has been studied extensively because of the dietary and environmental exposure of humans to these substances [3][4][5]. Toxicological studies of deamination became more significant when it was recognized that endogenous nitric oxide [6,7] causes nitrosation [8,9], and that this process is accelerated by chronic inflammatory diseases [10,11]. It has been known for a long time that deamination of adenine 1, guanine 2, and cytosine 3 (Scheme 1) results in the formation of hypoxanthine, xanthine, and uracil, respectively, and these products are thought to result from DNA base diazonium ions 4-6, respectively, by direct nucleophilic dediazoniation. The discovery of oxanine formation [12][13][14] in the nitrosative deamination of guanine challenged the generality and completeness of this mechanism. Theoretical studies revealed that unimolecular dediazoniation of guaninediazonium ion 5 is accompanied or immediately followed by pyrimidine ringopening [15,16] and that cytosine-catalysis promotes the process [17,18]. The resulting 5-cyanoimino-4-oxomethylene-4,5-dihydroimidazole is a highly reactive intermediate and undergoes acid-catalyzed 1,4-addition via cyano-N or imino-N protonated 5-cyanoimino-4-oxomethylene-4,5-dihydroimidazoles, 9 and 10, respectively [19].Labeling studies support this reaction mechanism for oxanine formation [20]. Moreover, we synthesized 5-cyanoamino-4-imidazolecarboxamide and studied its cyclization chemistry [21] and its proficiency for cross-link formation [22]. The unimolecular dediazoniation of the diazonium ions of adenine and cytosine can proceed without ring-opening but the cations 7 and 11 formed in this...

show abstract

Acetone chemical ionization studies. Acetone chemical ionization studies—IX: amino acids and nucleobases

Prabhakar

Krishna

Vairamani

1997

Rapid Commun. Mass Spectrom.

View full text Add to dashboard Cite

Received 30 August 1997; Revised 20 October 1997; Accepted 21 October 1997 Rapid Commun. Mass Spectrom. 11, 1945-1952(1997 Amino acids and nucleobases are the building blocks for proteins and nucleic acids, respectively, and are important synthetic intermediates for many biologically active compounds. The characterization of free amino acids by mass spectrometry using the electron ionization technique is difficult. However, soft ionization techniques such as chemical ionization (CI), and desorption techniques like field desorption (FD), fast atom bombardment (FAB) or liquid-assisted secondary ion mass spectrometry (LSIMS) and matrix-assisted laser desorption/ionization (MALDI), have allowed the extension of mass spectrometry to the analysis of such nonvolatile biomolecules. The analysis of free and protected amino acids under CI conditions, using methane, 1,2 hydrogen, 3 isobutane, 4 ammonia 5 and ethyleneglycol 6 as reagent gases, is known in the literature. However, free nucleobases are known to give abundant molecular ions under EI conditions. 7-9 Acetone, which was introduced by Wang et al. 10 as a CI reagent gas, is being extensively investigated in our laboratory on a variety of substrates for solving regio-and stereoselective problems due to the interesting ion-molecule reactions between the substrate molecules and the reagent ions.11-18 Moreover, the results obtained using acetone/CI are very similar to those obtained with isobutane/CI for many substrates due to the closeness of the proton affinity of acetone (824 kJ/mol) to that of isobutene (823 kJ/mol).19 Acetone is also being used as a CI reagent not only to study ion-molecule reactions with different substrates, but also to determine the site of protonation and proton affinities of substrates in addition to the normal CI reagents like methane, isobutane and ammonia. [20][21][22][23][24][25] In continuation of our studies on acetone/CI, we have investigated free amino acids and free nucleobases, and the results are presented here. RESULTS AND DISCUSSION Amino acidsUnder CI conditions, the acetone plasma mainly contains ions of protonated acetone (m/z 59), its dimer (m/z 117), acetylated acetone (m/z 101) and acetyl ion (m/z 43). In the acetone/CI mass spectra of the natural α-amino acids studied here (1-16) (Table 1). Similar types of adducts characteristic of the CI reagent have been reported in the isobutane/CI of some amino acids. 4 Protonation of the amino acid is the dominant process (base peak) for most of the amino acids studied under acetone/CI conditons, due to the higher proton affinity of amino acids ( > 885 kJ/ mol) 19 as compared to acetone (823 kJ/mol). The protonation of amino acids under acetone/CI conditions could be by the reagent ions at m/z 59, and also by the ion at m/z 117. However, the acetyl cation of the reagent plasma might also contribute to the formation of [M + H] + , as the proton affinity of ketene (828 kJ/ mol) 19 is close to that of acetone. In general it is known that the extent of protonation and of adduct ...

show abstract

Mass Spectra of Nucleic Acid Derivatives. Pyrimidines

Cited by 231 publications

References 0 publications

Multi-photon ionization and fragmentation of uracil: Neutral excited-state ring opening and hydration effects

Multi-photon ionization and fragmentation of uracil: Neutral excited-state ring opening and hydration effects

Ammonia elimination from protonated nucleobases and related synthetic substrates

Acetone chemical ionization studies. Acetone chemical ionization studies—IX: amino acids and nucleobases

Contact Info

Product

Resources

About