Mass spectrometry of modified nucleic acid bases and nucleosides. 2. Class II mesoionic nucleosides and bases derived from thiazolo[3,2-a]pyrimidine-5,7-diones

The mass spectral characteristics of novel Class II mesoionic heterocyclic bases and nucleosides based on the thiazolo[3,2-a]pyrimidine-5,7-dione system have been examined using low and high resolution mass spectrometry and metastable ion analysis. The mass spectra of these Class II mesoionic nucleosides differ significantly from the spectra of “normal” nucleosides by the absence of fragment ions associated with the base plus portions of the sugar. The difference in fragmentation is rationalized on the basis of exclusive localization of the radical-charge site in the aglycone, a result of the mesoionic structure of these molecules. The fast atom bombardment (FAB) mass spectra of a Class I mesoionic nucleoside, 7-methylguanosine, is compared to the FAB mass spectra of the Class II mesoionic nucleosides.     

Negative-ion mass spectrometry of substituted adenine bases and adenosine nucleosides

The negative-ion chemical ionization (ammonia, 5 Pa source pressure) mass spectra of a series of substituted adenine bases, adenosine nucleosides, and the trimethylsilyl derivatives of the nucleosides are described. Selected ions from these spectra were subject to collisionally activated dissociation with mass-analysed ion kinetic energy (CAD/MIKE) analysis of the products and the spectra assessed for information content. In addition to observing strong peaks due to quasimolecular ions and heterocyclic-base ions, it proved possible to differentiate between 2'-, 3'- and 5'-deoxy and between 2'- and 3'-O-methyl isomers. The negative-ion chemical ionization spectra of four methyladenines are essentially identical, but could be clearly distinguished from each other by CAD/MIKE analysis.     

Identification of dinucleoside polyphosphates by matrix-assisted laser desorption/ionisation post-source decay mass spectrometry

Dinucleoside polyphosphates are a group of intra- and extracellular mediators controlling numerous physiological functions. In this study dinucleoside polyphosphates were examined by positive ion matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MADLI-TOFMS). 3-Hydroxypicolinic acid was used as UV-absorbing matrix. For the individual dinucleoside polyphosphates Ap(n)A (n = 2-7), Ap(n)G (n = 2-6) and Gp(n)G (n = 2-6), MALDI post-source decay (PSD) mass spectra were measured. Each mass peak in the MALDI-PSD mass spectra could be assigned to individual fragments of dinucleoside polyphosphates. The comparison of the fragmentation patterns of the dinucleoside polyphosphates presented here demonstrates that dinucleoside polyphosphates preferably cleave to fragment ions consisting of the corresponding mononucleoside polyphosphates as well as the corresponding nucleosides and bases during flight in the field-free drift path of the MALDI mass spectrometer. Therefore, the MALDI-PSD approach described here is suitable for identification of other dinucleoside polyphosphates. The present MALDI-PSD mass spectra may be used as MALDI-PSD mass reference spectra for future identification of dinucleoside polyphosphates and other nucleotides.     

Studies in organic mass spectrometry. III. Adenosine 8-Cyclonucleosides

The mass spectra of purine 8-cyclonucleosides have been determined and compared with those of purine nucleosides. The mass spectra of the former are characterized not only by the presence of an intense molecular ion but also by the presence of the peaks corresponding to 8-oxy (or 8-thio) adenine and its protonated form due to a double and triple hydrogen transfer.     

Electron impact mass spectrometry of some 6-substituted tetrazolo[1,5-c]pyrimidin-5(6H)-ones

The electron impact mass spectra of 6-methyltetrazolo[1,5-c]pyrimidin-5(6H)-one, its 7- and 8-methyl derivatives, three 8-halo derivatives and two related nucleosides are reported. On the basis of the high-resolution data and detected metastable ions, the fragmentation routes of their molecular ions are proposed. Coexistence of the tautomeric forms of the title compounds of cyclic (tetrazole) or linear (azide) structure can be suggested owing to the fragmentation pathways identified for the bases. Decomposition of the related nucleosides lies in the breaking of nucleoside bonds to produce the appropriate base and sugar fragments.     

Particle beam glow discharge mass spectrometry: spectral characteristics of nucleobases

Use of a particle beam glow discharge (PB-GD) source for mass spectrometric determinations of deoxy- and ribonucleosides and nucleotides is described. Use of this combination of sample introduction and ion source decouples the vaporization and ionization steps, leading to very simple spectral structure. The mass spectra of these compounds are EI-like in nature, with clearly identified molecular ions and fragmentation patterns that are easily rationalized. The PB-GDMS combination can be operated in a flow injection mode wherein the analyte is injected directly into the solvent flow, or can also be coupled to a high-performance liquid chromatography (HPLC) system allowing LC/MS analysis of mixtures. Mass spectra obtained for nucleic acid bases, nucleosides, and nucleotides are readily obtained with injections of low-nanomole quantities. Representative PB-GDMS spectra for deoxy- and ribonucleosides, nucleotides, and mixed-base oligonucleotides are presented to demonstrate the capabilities of the GD source. Characteristic fragmentation peaks from the spectra of adenine, cytosine, guanine, and thymine were identified in 22-base sequences of single-stranded DNA. The PB-GD source is capable of producing spectra that may be used to identify the individual bases present in mixed-base DNA and RNA fragments.     

X-ray- and U.V.-induced excitation of adenine, thymine and the related nucleosides and nucleotides in solution at 77 degrees K

Abstract— The light emitted by adenine and thymine and the related nucleosides and nucleotides in ethylene glycol/water glass during irradiation at 77°K with X-rays and 270 nm U.V. light has been studied. It was found that the same radiative levels were excited by both types of radiation. However, the phosphorescence to fluorescence ratios observed with X-rays were considerably enhanced relative to those obtained with U.V. light. This observation was taken to mean that a major fraction of the excitation results from ion recombination, although direct excitation of the triplet manifold as well as intersystem crossing between upper excited levels may have contributed to the enhancement as well. The yields of the X-ray-induced excitation of radiative levels. which were calculated by combining the yields of X-ray-induced emission and the quantum yields observed with u.v.-excitation, corresponded to: G≥ 4.0 excitations per 100 eV of dose absorbed in the solute for adenine and G≥ 1.8 for thymine. The excitation yields obtained for the nucleosides and nucleotides were somewhat smaller than those observed for the corresponding bases. It was inferred from the yields that a substantial fraction of the dose absorbed in the ribose of the nucleosides was transferred to the radiative levels of the constituent bases.     

The mass spectra of indolizines

The mass spectra of indolizine, the seven monomethylindolizines, the six 2,x-di-methylindolizines and a number of related simple indolizines are reported; the breakdown patterns are compared with those of the corresponding indoles.     

Characterization of blocked nucleosides by mass spectrometry. Benzyl derivatives

The mass spectra of eleven model monobenzylated nucleosides were studied using low and high resolution mass spectrometry. Structural assignments to the major ions were made and several decomposition mechanisms proposed, with the goal of establishing the uses and limitations of mass spectrometry for the characterization of benzylaled nucleosides. Mass spectra generally permit determination of the extent and site of benzylation, with particular regard to base vs. sugar substitution, 0–2′ vs. 0–3′ or 0–5′, and in some cases 0–5′ vs. other isomers.     

The study and characterization of nucleosides by mass spectrometry—I: The mass spectra of pyrimidine 2,2′-anhydronucleosides and their derivatives

The mass spectra of 2,2′-anhydrouridine, 2,2′-anhydrothymidine and 2,2′-anhydro-4-thiouridine are reported. The acetyl, trifluoroacetyl, trityl, pivaloyl and trimethylsilyl ether derivatives were also studied. Deuterium labeling in acetyl and trimethylsilyl groups aided characterization of many ions in the spectra, as well as helping to clarify hydrogen migration processes. The anhydronucleosides and their derivatives are readily distinguished from natural nucleosides by the presence of an ion containing the base moiety plus the anhydro-ring plus one hydrogen atom from the rest of the molecule. As for natural nucleosides the [base + H]⁺ and [base + 2H]⁺ ions are usually prominent, but in contrast to natural nucleosides, ions characteristic of the sugar moiety do not retain the 2′-oxygen atom (i.e. the oxygen atom of the anhydro-ring). The mass spectra of deuterium labeled derivatives suggest a test for the presence of a 3′-O-acetyl function (the O-acetyl group is lost from the molecular ion much more readily from the 3′- than from the 5′-carbon atom). The trimethylsilyl derivatives showed evidence in their mass spectra for migration of trimethylsilyl groups in addition to hydrogen atoms.     

Interaction of low-energy electrons with the pyrimidine bases and nucleosides of DNA

We report computed cross sections for the elastic scattering of slow electrons by the pyrimidine bases of DNA, thymine and cytosine, and by the associated nucleosides, deoxythymidine and deoxycytidine. For the isolated bases, we carried out calculations both with and without the inclusion of polarization effects. For the nucleosides, we neglect polarization effects but estimate their influence on resonance positions by comparison with the results for the corresponding bases. Where possible, we compare our results with experiment and previous calculations.     

Synthesis and biological application of pyranopyrimidine derivatives catalyzed by efficient nanoparticles and their nucleoside analogues

Abstract

Nanoparticles supply an environmentally friendly procedure for the synthesis of pyrano[2,3-d]pyrimidines by the one-pot three-component condensation reaction of thiobarbituric acid and malononitrile with pyrrol-2-carboxaldehyde. The catalyst could be easily recovered using an external magnet and reused for six cycles with almost consistent activity. A facile synthesis of a new series of cyclic and acyclic nucleosides of pyrano[2,3-d]pyrimidines derivatives was performed. The synthesis of poly heterocyclic compounds starting from pyrano[2,3-d]pyrimidines derivatives was achieved. Structures of the newly synthesized compounds were confirmed on the bases of elemental analyses and spectral data (IR, ¹H NMR, ¹³C NMR, and mass spectra). Compound 6 exhibited the most potent biological activity.     

Clustering of nucleosides in the presence of alkali metals: Biologically relevant quartets of guanosine,deoxyguanosine and uridine observed by ESI-MS/MS

Electrospray ionization (ESI) mass spectra of nucleosides, recorded in the presence of alkali metals, display alkali metal ion-bound quartets and other clusters that may have implications for understanding non-covalent interactions in DNA and RNA. The tetramers of guanosine and deoxyguanosine and also their metaclusters (clusters of clusters), cationized by alkali metals, were observed as unusually abundant magic number clusters. The observation of these species in the gas phase parallels previous condensed-phase studies, which show that guanine derivatives can form quartets and metaclusters of quartets in solution in the presence of metal cations. This parallel behavior and also internal evidence suggest that bonding in the guanosine tetramers involves the bases rather than the sugar units. The nucleobases thymine and uracil are known to form magic number pentameric adducts with K+, Cs+ and NH4+ in the gas phase. In sharp contrast, we now show that the nucleosides uridine and deoxythymidine do not form the pentameric clusters characteristic of the corresponding bases. More subtle effects of the sugars are evident in the fact that adenosine and cytidine form numerous higher order clusters with alkali metals, whereas deoxyadenosine and deoxycytidine show no clustering. It is suggested that hydrogen bonding between the bases in the tetramers of dG and rG are the dominant interactions in the clusters, hence changing the ribose group to deoxyribose (and vice versa) generally has little effect. However, the additional hydroxyl group of RNA nucleosides enhances the non-selective formation of higher-order aggregates for adenosine and cytidine and results in the lack of highly stable magic number clusters. Some clusters are the result of aggregation in the course of ionization (ESI) whereas others appear to be intrinsic to the solution being examined.     

Heterocyclic studies—XXVIII Mass spectra of some 5-trifluoromethylpyrimido-(5,4-e)as-triazines

Fragmentation of 7-substituted 5-trifluoromethylpyrimido(5,4-e)as-triazines is dominated by consecutive losses of N₂ and HCN from the triazine ring. Deuterium labelling, accurate mass measurements and spectral changes with substitution patterns confirm the fragmentation pathways. Comparison of the spectra with those of corresponding pteridines indicates that the 1,2,4-triazine ring fragments much more readily than the pyrazine ring.     

Spectral,magnetic, biological,and thermal studies of metal(II) complexes of some unsymmetrical Schiff bases

New nickel(II) and copper(II) complexes with unsymmetrical Schiff bases derived from aromatic 2-hydroxy aldehydes were synthesized and characterized by elemental analyses, melting points, ¹H-NMR, magnetic susceptibility, thermogravimetric analysis, differential scanning calorimetry (DSC), infrared (IR), and electronic spectral measurements. Comparison of IR spectra of the Schiff bases and their metal complexes indicated that the Schiff bases are tetradentate, coordinated via the two azomethine nitrogens and the two phenolic oxygens. Magnetic moments and electronic spectral data confirm square-planar geometry for the complexes. Thermal studies reveal a general decomposition pattern, whereby the complexes decomposed partially in a single step due to loss of part of the organic moiety. A single endothermic profile, corresponding to melting point, was observed from the DSC of all complexes, except those whose ligand contained the nitro group, which decomposed exothermally without melting. The Schiff bases and their complexes were screened in vitro against 10 human pathogenic bacteria. The metal(II) complexes exhibited higher antibacterial activity than their corresponding Schiff bases.     

Mass spectrometric investigation of N-sulfonylated purine nucleic bases and nucleosides

The gas/phase behaviour of N-sulfonylated purine nucleic bases and nucleosides towards electron impact (EI) and matrix-assisted laser desorption/ionization (MALDI) occurring in a ion trap of a Fourier transform ion cyclotron resonance mass spectrometer is investigated. The influence of the storage time on the protonated molecule ([M+H](+)) abundance under EI conditions confirms that the formation of these ions proceeds through ion/molecule reactions. Using stored-waveform inverse Fourier transform (SWIFT) selective isolation of M(+.) or H(3)O(+), self-chemical ionization, M(+.)/M, and chemical ionization, H(3)O(+)/M, are detected. Investigation of specific EI expulsion of SO(2), SO(2)H and/or SO(2)H(2) from M(+.) and/or [M+H](+) shows that oxygen protonation in bond;SO(2)bond; proceeds faster than nitrogen protonation. Expulsion of SO(2) from molecular ions is not observed in MALDI mass spectra of nucleosides.     

Migration mechanism of bases and nucleosides in oil-in-water microemulsion capillary electrophoresis.

The electrophoretic behaviors of five bases and corresponding nucleosides in the oil in water (o/w) microemulsion capillary electrophoresis, microemulsion electrokinetic chromatography (MEEKC), were examined in comparison with those in normal capillary zone electrophoresis (CZE). The microemulsion systems were composed of heptane, sodium dodecyl sulfate (SDS), 1-butanol and 10 mM phosphate buffer (pH 7.0) or toluene, SDS, 1-butanol and 5 mM carbonate buffer (pH 10.0). CZE was carried out in the range of pH 9.7-10.9, and the dissociation constants, pKa, of the bases and nucleosides and the electrophoretic mobilities of the anionic forms were determined. The electrophoretic behaviors of the solutes in the microemulsion systems were analyzed from their pKa, the electrophoretic mobilities of the anions determined by CZE, and the distribution constants, K(D), of the neutral forms between the microemulsion droplets and the outer aqueous phase. The importance of adsorption mechanism in MEEKC system was suggested from the correlation between log K(D) and log P.     

Interaction of low-energy electrons with the purine bases, nucleosides, and nucleotides of DNA

The authors report results from computational studies of the interaction of low-energy electrons with the purine bases of DNA, adenine and guanine, as well as with the associated nucleosides, deoxyadenosine and deoxyguanosine, and the nucleotide deoxyadenosine monophosphate. Their calculations focus on the characterization of the pi* shape resonances associated with the bases and also provide general information on the scattering of slow electrons by these targets. Results are obtained for adenine and guanine both with and without inclusion of polarization effects, and the resonance energy shifts observed due to polarization are used to predict pi* resonance energies in associated nucleosides and nucleotides, for which static-exchange calculations were carried out. They observe slight shifts between the resonance energies in the isolated bases and those in the nucleosides.     

Electron-impact induced fragmentation of 2-substituted pyridines and picolines

The fragmentation patterns obtained upon electron impact on 2-nitro-, 2-chloro, and 2-aminopyridines, as well as those of the corresponding 3-, 4-, 5- and 6-picolines were examined. There was considerable departure from those patterns reported for the corresponding benzenoid derivatives. Although the molecular ion from 2-nitro-3-picoline did not show fragment ions attributable to an “ortho-effect” (unlike o-nitrotoluene), those from 2-chloro- and 2-amino-3-picolines did show a loss of HCl and NH₃, respectively. Quite unexpectedly the ions from 2-chloro- and 2-amino-6-picolines also lost HCl and NH₃. Such meta-eliminations for the 2-substituted-6-picolines are postulated to be preceeded by either hydrogen or methyl migration. The mass spectra of 2-pyridone, 2-pyridthione and their respective 3-, 4-, 5- and 6-methyl analogs were also studied. The primary fragmentations of the 2-pyridones were as expected from those reported in the literature. The ions from 3- and 6-methyl-2-pyridones lost water also, the former being another example of an “ortho-effect” observed in this series. Of the thiones, the fragmentations of 3-methyl-2-pyridthione proved most unique since its molecular ion showed besides the loss of HS, the pronounced elimination of H₂S, the latter presumably due to an “ortho-effect.” Figures are presented to illustrate the patterns and metastable ions are indicated when found for the transitions discussed.     

Novel bile acid derived H‐phosphonate conjugates: Synthesis and spectroscopic characterization

The H‐phosphonate bioconjugates of bile acids, conjugated with various alcohols and nucleosides, were obtained in one pot by a tandem transesterification with diphenyl phosphite (DPP). The synthesis of cholic acid derived phosphoramide from the corresponding H‐phosphonate was also demonstrated. The structures of these novel conjugates were confirmed on the basis of IR,³¹P NMR, ¹H NMR, and mass spectra. The synthesized bile acid conjugates were mixtures of diastereoisomers due to the chirality of the phosphorus. © 2008 Wiley Periodicals, Inc. Heteroatom Chem 19:402–407, 2008; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20447