Collision-induced dissociation of uracil and its derivatives

The collision-induced dissociation of protonated uracil has been studied by tandem mass spectrometry using models extensively labeled with stable isotopes, and derivatives of the kinds found in nucleic acids. Following collisional activation at 30 eV translational energy, protonated uracil dissociates through two principal pathways which do not occur in electron ionization mass spectra: (1) elimination of NH3 almost entirely from N-3, followed by loss of CO from C-4, 0⁴; (2) loss of H2O, equally from 0² and 0⁴. Elimination of HNCO, also the principal dissociation process from odd-electron molecular ions, proceeds primarily by loss of N-3, C-Z, O² and 10% from N-l, C-Z, 0². Several secondary dissociation products are formed with quantitative site specificity of skeletal atoms: C,HO+ (4-C0, C-5, C-6); H2CN+ (N-l, C-6); C2H2+ (N-l, C-5, C-6). First-step dissociation reactions are interpreted in terms of pyrimidine ring opening at likely sites of protonation after collisional activation of MH+. Collision-induced dissociation mass spectra of uracils with structural themes common to nucleic acids (methylation, replacement of 0 by S, C-5 substitution) follow analogous reaction paths which permit assignment of sites of substitution, and exhibit ion abundance changes attributed to differences in substituent basicity and electron density.     

The (5-4) and (6-4) adducts of 1-methylthymine and their Dewar valence isomers

Previous studies of the photochemical reaction of 1-methylthymine (MeT) in frozen aqueous solution have indicated that four cyclobutane type dimers are formed. We have restudied this system and have found that, in addition to cyclobutane dimers, both a (5-4) adduct and a (6-4) adduct of MeT are formed in significant amounts. Upon standing in aqueous solution, the (5-4) adduct is susceptible to reaction to form an isomeric form of the parent adduct, possibly via ring-opening and closure reactions at C-6 of the saturated pyrimidine ring component of the adduct. Irradiation of each of these three adducts with UVB light produces a pair of Dewar-type adducts. The nine products were individually characterized by mass spectrometry, proton NMR spectroscopy and UV spectroscopy. A less comprehensive study showed that irradiation of thymidine in frozen aqueous solution produces a diastereomeric pair of (5-4) adducts, along with the previously known diastereomeric pair of (6-4) adducts.     

The photochemistry of uracil: a reinvestigation

Results from a re-examination of the photochemical reactions undergone by uracil (Ura) are presented. Irradiation of Ura in frozen aqueous solution at -78.5°C produces two diastereomeric (6-4) products, namely the cis and trans isomers of 5-hydroxy-6-4'-(pyrimidin-2'-one)-5,6-dihydrouracil. Upon heating in 0.1m HCl, each of these compounds decomposes to form 6-4'-(pyrimidin-2'-one)uracil. In addition, evidence for production of a hydrate of a trimer of Ura is presented, Irradiation of this compound at 254nm forms Ura and a (6-4) adduct as products. The compounds 5-4'-(pyrimidin-2'-one)uracil and 6-hydroxy-5,6-dihydrouracil were also present after Ura was irradiated in frozen aqueous solution. Cyclobutane dimers (CBDs) are formed when Ura is irradiated in the frozen aqueous state, in fluid aqueous and acetonitrile solution and in the presence of photosensitizers (e.g. acetone). Published information, concerning the identity and relative quantitative importance of the four CBD isomers (cis-syn, cis-anti, trans-syn and trans-anti) formed in these photochemical systems, is incomplete and often in substantial disagreement. Using chemical methods in conjunction with HPLC, the identity and relative amounts of the four dimers have been determined in each of these systems. Consequently, a number of inconsistencies found in the literature concerning dimer product identity and quantitative distribution have been resolved.     

Synthesis and biological evaluation of new bicyclic fluorinated uracils through ring-closing metathesis

Two families of bicyclic fluorinated uracils have been prepared starting from a gem-difluorinated unsaturated nitrile, by means of a ring-closing metathesis reaction to form the new ring, which is fused at the C-5/C-6 or N-1/C-6 positions of the uracil moiety. The selective formation of olefin regioisomers in the metathesis process can be controlled according to the reaction conditions (catalyst, solvent, and temperature). The acaricidal activities of the resulting compounds have also been investigated.     

Covalent amination of 3,6-dinitro-1,8-naphthyridines

The preparation of 3,6-dinitro-2-R-1,8-naphthyridines ( 1 , R = OH, NH₂, OC₂H₅, Cl) is described and their addition patterns with liquid ammonia are studied. Compound 1 (R = OH, NH₂) gives with liquid ammonia at - 45° as well as at room temperature formation of the covalent ó-adduct 4-amino-1,4-dihydro-3,6-dinitro-2-R-1,8-naphthyridine ( 2 , R = OH, NH₂). Compound 1 (R = OC₂H₅) yields with ammonia at - 45° two σ-adducts, i.e. the C-4 adduct ( 2 , R = OC₂H₅) and the C-5 adduct 5-amino-5,8-dihydro-3,6-dinitro-2-R-1,8-naphthyridine ( 3 , R = OC₂H₅). The ratio is about 50:50. This ratio depends on the temperature; at room temperature the C-5 adduct is more favoured. After staying overnight the ethoxy group has been exchanged for the amino group, yielding 2 (R = NH₂). With 1 (R = Cl) both adducts 2 (R = CI) and 3 (R = CI) were formed, the C-4 adduct 2 (R = CI) is more favoured at room temperature. Prolonged treatment with liquid ammonia leads to an exchange of the chloro atom by the amino group, yielding 2 (R = NH₂).     

Synthesis of pyrene and benzo[a]pyrene adducts at the exocyclic amino groups of 2'-deoxyadenosine and 2'-deoxyguanosine by a palladium-mediated C-N bond-formation strategy

Single-electron oxidation of the carcinogenic hydrocarbon benzo[a]pyrene (BaP) is thought to result in a radical cation intermediate and this species has been proposed to cause alkylation at the nitrogens of the purine nucleobases. Although several different nucleoside adducts have been isolated as arising from this mode of metabolic activation, there are no selective, total syntheses of the stable exocyclic amino group adducts formed by the single-electron oxidation of any hydrocarbon with the purine 2'-deoxynucleosides to date. In this paper we disclose the synthesis of the model adducts N(6)-(1-pyrenyl)-2'-deoxyadenosine and N(2)-(1-pyrenyl)-2'-deoxyguanosine as well as the first synthesis of the carcinogen-linked nucleoside derivatives N(6)-(6-benzo[a]pyrenyl)-2'-deoxyadenosine and N(2)-(6-benzo[a]pyrenyl)-2'-deoxyguanosine via a palladium-mediated C-N bond formation. Two different coupling strategies were attempted: coupling of an aryl bromide with a suitably protected nucleoside and the coupling of an arylamine with a suitable halonucleoside. The former had somewhat limited applicability in that only N(6)-(1-pyrenyl)-2'-deoxyadenosine was prepared by this method; on the other hand, the latter was more general. However, there are noteworthy differences in the amination reactions at the C-6 and C-2 positions. Reactions at the C-6 resulted in the competing formation of a 1:2 amine-nucleoside adduct in addition to the desired monoaryl nucleoside. Such a dimer formation was not observed at the C-2. The C-2 adducts, however, displayed an interesting conformational behavior.     

Lithiation at the 6-position of uridine with lithium hexamethyldisilazide: crucial role of temporary silylation

Lithium hexamethyldisilazide (LiHMDS) can mediate silylation at the 6-position of uridine, although LiHMDS alone is not able to generate the C-6-lithiated uridine. Experimental results showed that temporary silylation of O-4 (or N-3) of the uracil ring triggers the C-6 lithiation with LiHMDS. This finding allowed us to develop an efficient intramolecular alkylation of 5'-deoxy-5'-iodouridine to furnish 6,5'-C-cyclouridine. [reaction--see text]     

Synthetic utility of an isolable nucleoside phosphonium salt

The reaction of O6-benzyl-3',5'-bis- O-( tert-butyldimethylsilyl)-2'-deoxyxanthosine with 1H-benzotriazol-1-yloxy-tris(dimethylamino)phosphonium hexafluorophosphate (BOP) yielded the nucleoside C-2 tris(dimethylamino)phosphonium hexafluorophosphate salt as a stable, isolable species. This is in contrast to reactions of inosine nucleosides with BOP, where the in situ formed phosphonium salts undergo subsequent reaction to yield O6-(benzotriazol-1-yl)inosine derivatives. The phosphonium salt obtained from the 2'-deoxyxanthosine derivative can be effectively used to synthesize N2-modified 2'-deoxyguanosine analogues. Using this salt, a new synthesis of an acrolein-2'-deoxyguanosine adduct has also been accomplished.     

Adenine radicals in the gas phase: an experimental and computational study of hydrogen atom adducts to adenine

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.     

Nucleoside synthesis from 3-alkylated sugars: role of 3beta-oxy substituents in directing nucleoside formation

Using Vorbrüggen's protocol, reaction of persilylated uracil with xylofuranose derivatives having 3beta-oxy-3alpha-alkyl substitution produced both alpha- and beta-nucleosides. Only the beta-nucleosides were formed from substrates having the reverse stereochemistry at C-3 or lacking the 3-alkyl substituent. Participation of the 3beta-oxy substituent in stabilizing the incipient C-1 carbonium ion (or oxonium ion) intermediate has been suggested from analysis of energy-minimized conformations.     

The addition of hydroxylamine to the halogenated uracils

Hydroxylamine adds reversibly to C-6 of uracil bases via a multistep mechanism. Equilibrium constants measured at several pH values, 25°, μ = 3.0 M are: uracil, 0.25 M^?1; 5-iodouracil, 0.30 M^?1, 5-bromouracil, 0.24 M^?1, 5-chlorouracil, 0.06 M^?1 and 5-fluorouracil, 5.11 M^?1. The kinetics of hydroxylamine addition to both 5-bromo-and 5-iodouracil are complex. At low hydroxylamine buffer concentrations, the rate constants are second-order with respect to hydroxylamine buffer but at higher concentration a first-order dependence is approached. Hydroxylamine elimination from 5-iodo-6-hydroxylamino-5,6-dihydrouracil is subject to general base catalysis by tris(hydroxy-methyl)aminomethane but at higher concentrations the rate constants are not proportional to the concentration of general base. This reaction is subject to solvent effects where increasing ethanol concentration depresses the rate when measured at constant pH. These kinetics can be rationalized in terms of a multistep reaction pathway in which hydroxylamine addition to C-6 of the halogenated uracil precedes general acid catalyzed proton transfer to C-5 yielding the final 6-hydroxylaminodihydropyrimidine product.     

Equilibrium of formation of the 6-carbanion of UMP,a potential intermediate in the action of OMP decarboxylase

There has been some speculation that the C-6 position in UMP may be unusually acidic, stabilizing a carbanion that is generated at this position during OMP decarboxylation. On the basis of the rate of OH- catalyzed deuterium exchange at elevated temperatures we estimate that the pKa value for ionization at C-6 of dimethyl uracil is 34 +/- 2 in water. The same method yields a value of 37 +/- 2 for ionization at C-2 of thiophene in good agreement with the value determined by polarographic methods. The barrier to proton release (46 kcal/mol) is even higher than that for CO2 release from orotic acid derivatives.     

Desulfurizative stannylation of uracil derivatives

Phenylthio group in the C-6 or C-5 position of uracil moiety can be removed by radical mediated stannylation with tributyltin hydride followed by protonolysis, providing a new route to 5-substituted uridines.     

Proton affinity of uracil. A computational study of protonation sites

Relative stabilities of uracil tautomers and cations formed by gas-phase protonation were studied computationally with the B3LYP, MP2, QCISD, and QCISD(T) methods and with basis sets expanding from 6-31G(d,p) to 6-311+G(3df,2p). In accordance with a previous density functional theory study, the dioxo tautomer 1a was the most stable uracil isomer in the gas phase. Gibbs free energy calculations using effective QCISD(T)/6-311+G(3df,2p) energies suggested >99.9% of 1a at equilibrium at 523 K. The most stable ion isomer corresponded to N-1 protonated 2,4-dihydroxypyrimidine, which however is not formed by direct protonation of 1a. The topical proton affinities in 1a followed the order O-8 > O-7 > C-5 > N-3 > N-1. The thermodynamic proton affinity of 1a was calculated as 858 kJ mol⁻¹ at 298 K. A revision is suggested for the current estimate included in the ion thermochemistry database.     

Convenient synthesis of nucleoside and isonucleoside analogues

[reaction: see text]. A very simple methodology to stereoselectively achieve tricyclic isonucleosides (nucleobase = thymine, uracil, and 5-fluoruracil) and 3'-C-branched nucleosides (nucleobase = theophylline) was performed by means of a DBU-mediated addition process using a readily available 2-bromo sugar. The mechanism for these transformations implies the loss of both substituents at C-2 and C-3 on the sugar moiety, and although it seems that DBU is probably involved, its involvement has not yet been ascertained. Cytosine did not react under these conditions.     

Reactions of OH* and eaq − with uracil and thymine in the presence of Cu(II) ions in dilute aqueous solutions: A pulse radiolysis study

The reactions of OH^* and e_aq ^? adducts of uracil and thymine with Cu(II) ions in aqueous solutions were followed by pulse radiolysis. The transient absorption spectra of the OH^* adducts of uracil when followed in the presence of Cu(II) ions show growth in absorption at wavelengths 420 and 350 nm at 15 μs and 65 μs after the pulse respectively. Similar transient absorption spectra of thymine showed growth in absorption at wavelengths 390 and 320 nm at 38 μs and 65 μs after the pulse respectively. The rates of electron transfer from the OH^* adducts of uracil and thymine to various Cu(II) compounds when monitored at 360 nm lie between 10⁶ and 10⁸ mol^?1 dm³ s^?1 this implies that the electron transfer process is not an efficient process. Low rate constants coupled with the spectral changes suggest formation of a radical copper adduct which decays by water insertion to give cis-glycols as the major product. The electron transfer from the electron adducts of uracil and thymine to various copper(II) compounds takes place more efficiently (rate constants of the order of 10⁸ and 10⁹ mol^?1 dm³ s^?1) compared with that from the OH^* adducts. The t-butanol radicals formed on scavenging the OH^* radicals also produce adducts with Cu(I) ions which are formed on oxidation of the electron adducts by Cu(II) ions. This adduct has absorption around 400 nm both in the case of uracil and thymine.     

Methoxymethyl (MOM) group nitrogen protection of pyrimidines bearing C-6 acyclic side-chains

Novel N-methoxymethylated (MOM) pyrimidine (4-13) and pyrimidine-2,4-diones (15-17) nucleoside mimetics in which an isobutyl side-chain is attached at the C-6 position of the pyrimidine moiety were synthesized. Synthetic methods via O-persilylated or N-anionic uracil derivatives have been evaluated for the synthesis of N-1- and/or N-3-MOM pyrimidine derivatives with C-6 acyclic side-chains. A synthetic approach using an activated N-anionic pyrimidine derivative afforded the desired N,N-1,3-diMOM and N-1-MOM pyrimidines 4 and 5 in good yield. Introduction of fluorine into the side-chain was performed with DAST as the fluorinating reagent to give a N,N-1,3-diMOM pyrimidine 13 with a 1-fluoro-3-hydroxyisobutyl moiety at C-6. Conformational study of the monotritylated N-1-MOM pyrimidine 12 by the use of the NOE experiments revealed the predominant conformation of the compound to be one where the hydroxymethyl group in the C-6 side-chain is close to the N-1-MOM moiety, while the OMTr is in proximity to the CH(3)-5 group. Contrary to this no NOE enhancements between the N-1-MOM group and hydroxymethyl or fluoromethyl protons in 13 were observed, which suggested a nonrestricted rotation along the C-6 side-chain. Fluorinated N,N-1,3-diMOM pyrimidine 13 emerged as a model compound for development of tracer molecules for non-invasive imaging of gene expression using positron emission tomography (PET).     

Covalent amination of 1-alkyl- and 1-aryl-3-carbamoylpyridinium chlorides as “model” for enzymic activity of rabbit liver aldehyde oxidase

The site of animation for 1-alkyl-3-carbamoylpyridinium chlorides in liquid ammonia is dependent on the identity of the 1-alkyl substituent. For the methyl, ethyl and n-propyl derivatives exclusively 6-adducts are found. Adduct formation takes place at C-6 and C-4, when the 1-substituent is an i-propyl or t-butyl group. The adduct ratio for the latter compounds is determined by the size of the substituent. 1-Aryl derivatives exhibit amination at C-2 and C-6 and the adduct ratios are dependent on the temperature. When the aryl substituent is a 2,4,6-trimethylphenyl group the 4-adduct is detected as well. A comparison is made between the sites of oxidation of these compounds by rabbit liver aldehyde oxidase and the covalent amination pattern in liquid ammonia. It is shown that covalent animation as a “model” for the enzymic activity of aldehyde oxide1 is particularly valuable in cases where the enzyme reaction is controlled by steric factors.     

Analysis of MS/MS fragmentation of taxoids

The fragmentation pathways of seven types of taxoids were investigated by using a LC-MS/MS method, namely: (1) neutral taxoids with a C-4(20) double bond; (2) taxoids with a C-4(20) double bond and oxygenation at C-14; (3) 5-cinnamoyl taxoids with a C-4(20) double bond; (4) a basic taxoid with a C-4(20) double bond; (5) a taxoid with a C-4(20) epoxide; (6) taxoids with an oxetane ring; and (7) taxoids with an oxetane ring and a phenylisoserine C-13 side chain. Depending on the class of core structure and the substitution pattern, each taxoid gave either the molecular adduct ion [M+NH4]+ or [M+H]+. In the MS/MS, the molecular adduct ion gave characteristic product ions corresponding to the loss of water, acetic acid, benzoic acid, and cinnamic acid or the phenylisoserine group. These could reflect the difference of the substitutions and structural modifications and should be utilized for the structure elucidation oftaxoids by LC-MS.     

Palladium-catalyzed synthesis of nucleoside adducts from bay- and fjord-region diol epoxides

Palladium-catalyzed C-N bond formation has been utilized to synthesize covalent 2'-deoxyadenosine (dA) and 2'-deoxyguanosine (dG) adducts of benzo[a]pyrene (BaP) series 1 (syn) and benzo[c]phenanthrene (BcPh) series 2 (anti) diol epoxides. For this, (+/-)-10 alpha-amino-7 beta,8 alpha,9 beta-trisbenzoyloxy-7,8,9,10-tetrahydro BaP and (+/-)-1 beta-amino-2 alpha,3 alpha,4 beta-trisbenzoyloxy-1,2,3,4-tetrahydro BcPh were coupled with 6-halo-9-[3,5-bis-O-(tert-butyldimethylsilyl)-beta-D-erythro-pentofuranosyl]purine and O6-benzyl-3',5'-bis-O-(tert-butyldimethylsilyl)-2-bromo-2'-deoxyinosine, using a (+/-)-BINAP-Pd complex and Cs2CO3. For the synthesis of the dA adducts, both the 6-chloro- as well as the 6-bromopurine nucleoside derivatives were analyzed for the C-N coupling reaction with the hydrocarbon amino tribenzoates. With the BaP amino tribenzoate, the 6-chloronucleoside provided satisfactory results, whereas the 6-bromo analogue proved to be superior with the BcPh amino tribenzoate. Overall, lower yields of the dA adducts were obtained with the more hindered fjord-region BcPh amino tribenzoate as compared to the bay-region BaP amino tribenzoate. In contrast to reactions leading to the dA adducts, the C-N reactions of both BaP and BcPh amino tribenzoates with the 2-bromo-2'-deoxyinosine derivative proceeded in comparable yields. This seems to indicate that such Pd-catalyzed adduct forming reactions at the C-6 position may be influenced by steric constraints of the amine component, whereas those at the C-2 position are less sensitive. Diastereomeric adduct pairs were separated and characterized by spectral methods and by comparisons to adducts produced by direct displacement reactions as well as those formed from DNA alkylation by diol epoxides.