Mass spectra of nucleic acid derivatives.  II.  Guanine, adenine, and related compounds

Rice, Jerry M.; Dudek, Gerald O.

doi:10.1021/ja00987a039

Cited by 177 publications

(162 citation statements)

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“…It is also important to note that the mass spectra arising from fragmentation at 10 eV are mostly due to thermal energy bond breaking in contrast to dissociative ionization, hence the results are reflective of neutral cytosine. m/z 95 originates from NH 2 elimination, and Rice et al 58 suggested that m/z 68 could be due to the further HCN elimination from this fragment. This channel can operate at higher temperatures employed in our work.…”

Section: Experimental Mass Spectrum and Thermal Fragmentationmentioning

confidence: 99%

Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations

Kostko

Bravaya

Krylov

et al. 2010

Phys. Chem. Chem. Phys.

124

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Photoionization of the cytosine dimer 2 SummaryWe report a combined theoretical and experimental study of ionization of cytosine monomers and dimers.Gas-phase molecules are generated by thermal vaporization of cytosine followed by expansion of the vapor in a continuous supersonic jet seeded in Ar. The resulting species are investigated by single photon ionization with tunable vacuum-ultraviolet (VUV) synchrotron radiation and mass analyzed using reflectron mass spectrometry. Energy onsets for the measured photoionization efficiency (PIE) spectra are 8.60±0.05 eV and 7.6±0.1 eV for the monomer and the dimer, respectively, and provide an estimate for the adiabatic ionization energies (AIE). The first AIE and the ten lowest vertical ionization energies (VIEs) for selected isomers of cytosine dimer computed using equation-of-motion coupled-cluster (EOM-IP-CCSD) method are reported. The comparison of the computed VIEs with the derivative of the PIE spectra, suggests that multiple isomers of the cytosine dimer are present in the molecular beam. The calculations reveal that the large red shift (0.7 eV) of the first IE of the lowest-energy cytosine dimer is due to strong inter-fragment electrostatic interactions, i.e., the hole localized on one of the fragments is stabilized by the dipole moment of the other. A sharp rise in the CH + signal at 9.20±0.05 eV is ascribed to the formation of protonated cytosine by dissociation of the ionized dimers. The dominant role of this channel is supported by the computed energy thresholds for the CH + appearance and the barrierless or nearly barrierless ionization-induced proton transfer observed for five isomers of the dimer.3

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Section: Experimental Mass Spectrum and Thermal Fragmentationmentioning

confidence: 99%

Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations

Kostko

Bravaya

Krylov

et al. 2010

Phys. Chem. Chem. Phys.

124

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“…The mass spectra of the nucleobases have been studied using electron-impact ionization many years ago [28]. The EI study of adenine showed that the major fragmentation path involves successive loss of HCN molecules.…”

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.

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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...

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“…The fragmentation patterns of methylated purines have been investigated. 8,9) The initial expulsion of neutral cyanamide fragments consisting of N-1, C-2, and their attached substituents is a very characteristic fragmentation of the molecular ion peak of these compounds. Since guanines contain an imino substituent and isoguanines have an oxygen substitution at the C-2 position, they can be easily distinguished by EI-MS due to a one mass-unit difference.…”

Section: -7)mentioning

confidence: 99%

“…In our continuing search for new bioactive marine natural products, we have isolated a new purine base from a Philippine sponge, Zyzzya fuliginosa (CARTER, 1879), together with the known metabolites makaluvamines A (2), C (3), and K (4) as well as 4-hydroxyphenylacetic acid (5), methyl ester of 4-hydroxyphenylacetic acid (6), 4-hydroxyphenethyl alcohol (7), L-phenylalanine (8) and L-tryptophan (9). In this paper, we describe the isolation and characterization of the new compound, 3,7-dimethylguanine (1).…”

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confidence: 99%

3,7-Dimethylguanine, a New Purine from a Philippine Sponge Zyzzya fuliginosa.

et al. 2001

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Marine organisms have proven to be a valuable source of modified purine bases and nucleosides. A number of methylated guanine or isoguanine derivatives have been reported from marine sponges [1][2][3][4] and also from some ascidians. 5-7)In our continuing search for new bioactive marine natural products, we have isolated a new purine base from a Philippine sponge, Zyzzya fuliginosa (CARTER, 1879), together with the known metabolites makaluvamines A (2), C (3), and K (4) as well as 4-hydroxyphenylacetic acid (5), methyl ester of 4-hydroxyphenylacetic acid (6), 4-hydroxyphenethyl alcohol (7), L-phenylalanine (8) and L-tryptophan (9). In this paper, we describe the isolation and characterization of the new compound, 3,7-dimethylguanine (1). Compound 1 was isolated as an amorphous white powder. N-9) suggested that the second methyl group resided on the imidazole ring, either on N-7 or N-9. Crucial long range 1 H-13 C couplings from this methyl group to C-8 (d 145.3), C-5 (d 110.5), and C-6 (d 154.6) unambiguously located it at N-7. The latter correlation (N-7-CH 3 /C-6) was also indicative of a guanine ring. Distinction between the two possible structures, 3,7-dimethylguanine (1) and 3,7-dimethylisoguanine (10) was made by MS. The fragmentation patterns of methylated purines have been investigated. 8,9) The initial expulsion of neutral cyanamide fragments consisting of N-1, C-2, and their attached substituents is a very characteristic fragmentation of the molecular ion peak of these compounds. Since guanines contain an imino substituent and isoguanines have an oxygen substitution at the C-2 position, they can be easily distinguished by EI-MS due to a one mass-unit difference.1,3) Thus, 1 showed a diagnostic ion at m/z 137.0595 due to loss of CH 2 N 2 (m/z 42) via a retro-Diels-Alder pathway. The positive mode tandem ESI- * To whom correspondence should be addressed. A new purine 3,7-dimethylguanine (1) has been isolated from the marine sponge Zyzzya fuliginosa, along with the known metabolites, makaluvamines A, C, K (2-4), 4-hydroxyphenylacetic acid (5), methyl ester of 4-hydroxyphenylacetic acid (6), 4-hydroxyphenethyl alcohol (7), L-phenylalanine (8) and L-tryptophan (9). The structure of 3,7-dimethylguanine (1) was elucidated by analysis of 1D and 2D (one-and two-dimensional) NMR [HMQC (heteronuclear multiple quantum coherence), gHMBC (heteronuclear multiple bond connectivity), 1 H-15 N gHMBC] data, mass spectroscopy data, and by comparison with 3,7-dimethylisoguanine (10).

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Mass spectra of nucleic acid derivatives. II. Guanine, adenine, and related compounds

Cited by 177 publications

References 0 publications

Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations

Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations

Ammonia elimination from protonated nucleobases and related synthetic substrates

3,7-Dimethylguanine, a New Purine from a Philippine Sponge Zyzzya fuliginosa.

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