Determination of redox potentials for the Watson-Crick base pairs, DNA nucleosides, and relevant nucleoside analogues

Redox potentials for the DNA nucleobases and nucleosides, various relevant nucleoside analogues, Watson-Crick base pairs, and seven organic dyes are presented based on DFT/B3LYP/6-31++G(d,p) and B3YLP/6-311+G(2df,p)//B3LYP/6-31+G* levels of calculations. The values are determined from an experimentally calibrated set of equations that correlate the vertical ionization (electron affinity) energy of 20 organic molecules with their experimental reversible oxidation (reduction) potential. Our results are in good agreement with those estimated experimentally for the DNA nucleosides in acetonitrile solutions (Seidel et al. J. Phys. Chem. 1996, 100, 5541). We have found that nucleosides with anti conformation exhibit lower oxidation potentials than the corresponding syn conformers. The lowering in the oxidation potential is due to the formation of an intramolecular hydrogen bonding interaction between the 5'-OH group of the sugar and the N3 of the purine bases or C2=O of the pyrimidine bases in the syn conformation. Pairing of adenine or guanine with its complementary pyrimidine base decreases its oxidation potential by 0.15 or 0.28 V, respectively. The calculated energy difference between the oxidation potential for the G.C base pair and that of the guanine base is in good agreement with the experimental value estimated recently (0.34 V: Caruso, T.; et al. J. Am. Chem. Soc. 2005, 127, 15040). The complete and consistent set of reversible redox values determined in this work for the DNA constituents is expected to be of considerable value to those studying charge and electronic energy transfer in DNA.     

Cyclopentene carbocyclic nucleosides related to the antitumor nucleoside clitocine and their conversion to 8-Aza-neplanocin analogues. Synthesis and antiviral activity

Synthesis of the cyclopentene carbocyclic analogue of the naturally occurring nucleoside clitocine ( 1 ) is reported. Starting with racemic cyclopentenylamine ( 10 ), the heterocyclic moieties of the clitocine analogue 4 and related 1,6-dihydro-6-oxo, 5 , and 2-amino-1,6-dihydro-6-oxo, 6 , analogues were constructed. These compounds were respectively converted to 8-aza-neplanocin A (7) , 8-aza-neplanocin D ( 8 , the inosine analogue), and the corresponding 8-aza-guanosine analogue 9 after reduction of the nitro group followed by nitrous acid cyclization. Extensive antiviral evaluation revealed that only 8-aza-neplanocin A ( 7 ) had enough antiviral activity to warrant further studies. This compound showed weak antiviral activity against HSV-1, HSV-20 and the thymidine kinase deficient (TK-) HSV-1. However, it displayed good antiviral activity against human cytomegalovirus (HCMV) at a concentration of 0.40–2.50 μg/ml, well below the cytotoxicity threshold. This activity profile is consistent with a mechanism of action involving the inhibition of the enzyme adenosylhomo-cysteine hydrolase.     

Dye-sensitized photooxygenation of the C=N bond. 5. substituent effects on the cleavage of the C=N bond of C-aryl-N-aryl-N-methylhydrazones

The title compounds are cleaved cleanly at the C=N bond by singlet oxygen ((1)O(2), (1)Delta(g)) yielding arylaldehydes and N-aryl-N-methylnitrosamines. These reactions take place more rapidly at -78 degrees C than at room temperature. The effects of substituent variation at both the C-aryl and N-aryl groups were studied using a competitive method. Good correlations of the resulting rate ratios with substituent constants (sigma(-) or sigma(+)) were obtained yielding small to very small rho values indicative of small to very small changes in charge distribution between the reactant and the rate determining transition state. Electron withdrawing groups on the C-aryl moiety retard reaction somewhat by preferential stabilization of the hydrazone. Electron donors on the other hand slightly stabilize the rate determining transition state. Substituents on the N-aryl group have almost no effect. Inhibition by 3,5-di-tert-butylphenol was not observed showing that free (uncaged) radical intermediates are not involved in the mechanism. We postulate a mechanism in which the initial event is exothermic electron transfer from the hydrazone to (1)O(2) leading to an ion-radical caged pair. Subsequent covalent bond formation between the hydrazone carbon and an oxygen atom is rate controlling. The transition state for this step also has a lower enthalpy than the starting reactants, but the free energy of activation is dominated by a large negative TDeltaS++term leading to the negative temperature dependence. Direct formation of a C-O bond in the initial step is not unambiguously ruled out. Subsequent steps lead to C-N cleavage.     

The rate of homolysis of adducts of peroxynitrite to the C=O double bond.

Nucleophilic addition of the peroxynitrite anion, ONOO(-), to the two prototypical carbonyl compounds, acetaldehyde and acetone, was investigated in the pH interval 7.4-14. The process is initiated by fast equilibration between the reactants and the corresponding tetrahedral adduct anion, the equilibrium being strongly shifted to the reactant side. The adduct anion also undergoes fast protonation by water and added buffers. Consequently, the rate of the bimolecular reaction between ONOO(-) and the carbonyl is strongly dependent on the pH and on the concentration of the buffer. The pK(a) of the carbonyl-ONOO adduct was estimated to be approximately 11.8 and approximately 12.3 for acetone and acetaldehyde, respectively. It is shown that both the anionic and the neutral adducts suffer fast homolysis along the weak O-O bond to yield free alkoxyl and nitrogen dioxide radicals. The yield of free radicals was determined to be about 15% with both carbonyl compounds at low and high pH, while the remainder collapses to molecular products in the solvent cage. The rate constants for the homolysis of the adducts vary from ca. 3 x 10(5) to ca. 5 x 10(6) s(-1), suggesting that they cannot act as oxidants in biological systems. This small variation around a mean value of about 10(6) s(-1) suggests that the O-O bond in the adduct is rather insensitive to its protonation state and to the nature of its carbonyl precursor. An overall reaction scheme was proposed, and all the corresponding rate constants were evaluated. Finally, thermokinetic considerations were employed to argue that the formation of dioxirane as an intermediate in the reaction of ONOO(-) with acetone is an unlikely process.     

SO3-mediated addition of N-chlorourethanes to the C=C bond

Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 12, pp. 2871–2872, December, 1989.     

Free radical additions to the C=O bond of formaldehyde

The reactions between formaldehyde and n-propyl radicals were studied at 333 and 363 K. Addition to the C=O bond was found to be several times faster than abstraction of the formyl hydrogen atom. With a TST estimate of log(A/dm³ mol^–1 s^–1)=7.9±0.5, 28.0±2.1 kJ mol^–1 was obtained for the activation energy of the addition reaction.

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- 333 363 . C=O . 28.0±2.1 ^–1 , lg(A/ ^{–1 –1})=7.9±0.5 .

     

Pyrazolopyrimidine nucleosides. Part VII. The synthesis of certain pyrazolo [3,4-d] pyrimidine nucleosides related to the nucleoside antibiotics toyocamycin and sangivamycin

The condensation of 4-acetamido-3-cyanopyrazolo[3,4-d]pyrimidine ( 5 ) with crystalline 2,3,5-tri-O-acetyl-β- D -ribofuranosyl chloride ( 6 ) has furnished a good yield of nucleoside material ( 7 ) which on treatment with sodium methoxide in methanol provided a high yield of nucleoside which was subsequently established as methyl 4-amino-1-(β- D -ribofuranosyl)pyrazolo[3,4-d]-pyrimidine-3-formimidate monohydrate ( 11 ). The formimidate function of 11 was found to be highly reactive and 11 was readily converted into the corresponding carhoxamidine ( 8 ), carboxamidoxime ( 14 ) and carboxamidrazone ( 15 ) when treated with the appropriate nucleophiles. Treatment of the imidate ( 11 ) with sodium hydrogen sulfide gave a high yield of the thiocarboxamide ( 12 ) which was then readily converted into 4-amino-3-cyano-1-(β- D -ribofuranosyl)pyrazolo[3,4-d]pyrimidine ( 16 ). Aqueous base transformed 11 into 4-amino-1-(β- D -ribofuranosyl)-pyrazolo[3,4-d]pyrimidine-3-carboxamide ( 10 ) while more vigorous basic hydrolysis provided the corresponding carboxylic acid ( 9 ) in nearly quantitative yield. Decarboxylation of 9 proceeded smoothly in hot sulfolane to provide the known 4-amino-1-(β- D -ribofuranosyl)pyrazolo[3,4-d]pyrimidine ( 13 ) in 68% yield which unequivocally established the site of ribosylation and anomeric configuration for all nucleosides reported in this investigation.     

Stereodivergent approaches to the synthesis of isoxazolidine analogues of alpha-amino acid nucleosides. Total synthesis of isoxazolidinyl deoxypolyoxin C and uracil polyoxin C

The synthesis of new nucleoside analogues is currently of high interest. We report here full details of a study leading to the synthesis of novel isoxazolidinyl analogues of alpha-amino acid nucleosides. Three different synthetic approaches starting from L-serine have been evaluated for the construction of the isoxazolidine ring. These approaches consisted of Michael addition of N-benzylhydroxylamine to alpha,beta-unsaturated esters, nucleophilic addition of silyl ketene acetals to nitrones and 1, 3-dipolar cycloaddition of nitrones with vinyl acetate. Both Michael addition and nucleophilic addition of enolates could be carried out with stereocontrol at the newly formed stereogenic carbon. The stereocontrol observed in these reactions arises from the protecting group arrangement in the L-serine-derived substrates. Thus, whereas compounds having a diprotected nitrogen led to syn adducts, compounds having a monoprotected nitrogen gave rise to anti adducts. On the other hand, substrates having either a diprotected or monoprotected nitrogen atom led to anti adducts through the cycloaddition route. So, by choosing the appropriate route, isoxazolidinyl analogues having either syn or anti configuration with respect to the glycine unit can be prepared in enantiomerically pure form. The stereoselective synthesis of isoxazolidinyl analogues of deoxypolyoxin C and uracil polyoxin C in both D and L enantiomeric forms using these techniques has been achieved in good yields.     

MO LCAO calculation of the barrier to rotation around the C=C bond inα -nitro-β-methylaminoacrylic ester and its anion

Conclusions According to the data from MO LCAO calculations, the barrier to rotation about the C=C bond decreases by a factor of three upon passing from the-isomer of a-nitro--methylaminoacrylic ester to its anion on account of the reduction in the order of the double bond.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 1, pp. 123–126, January, 1982.     

Addition of heterocyclic CH acids to the C=N bond of azomethines

The aminomethylation of oxindole, 1-phenyl-3-methyl-5-pyrazolone, and N-phenyl-rhodanine was studied. Derivatives of these CH acids were obtained as a result of aminomethylation. The addition products were subjected to acid and base hydrolysis; the corresponding arylidene derivatives are formed in the case of the products of aminomethylation of oxindole and 1-phenyl-3-methyl-5-pyrazolone, while thioglycolic acids are formed in the case of N-phenylrhodanine derivatives.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 8, pp. 1088–1093, August, 1981.     

Comparison of the kinetics and thermodynamics for methyl radical addition to C=C, C=O, and C=S double bonds

The barriers, enthalpies, and rate constants for the addition of methyl radical to the double bonds of a selection of alkene, carbonyl, and thiocarbonyl species (CH(2)=Z, CH(3)CH=Z, and (CH(3))(2)C=Z, where Z = CH(2), O, or S) and for the reverse beta-scission reactions have been investigated using high-level ab inito calculations. The results are rationalized with the aid of the curve-crossing model. The addition reactions proceed via early transition structures in all cases. The barriers for addition of methyl radical to C=C bonds are largely determined by the reaction exothermicities. Addition to the unsubstituted carbon center of C=C double bonds is favored over addition to the substituted carbon center, both kinetically (lower barriers) and thermodynamically (greater exothermicities). The barriers for addition to C=O bonds are influenced by both the reaction exothermicity and the singlet-triplet gap of the substrate. Addition to the carbon center is favored over addition to the oxygen, also both thermodynamically and kinetically. For the thiocarbonyl systems, addition to the carbon center is thermodynamically favored over addition to sulfur. However, in this case, the reaction is contrathermodynamic, addition to the sulfur center having a lower barrier due to spin density considerations. Entropic differences among corresponding addition and beta-scission reactions are relatively minor, and the differences in reaction rates are thus dominated by differences in the respective reaction barriers.     

Effect of changing electrophilic center from C=O to C=S on rates and mechanism: pyridinolyses of O-2,4-dinitrophenyl thionobenzoate and its oxygen analogue

Second-order rate constants have been measured spectrophotometrically for the reactions of O-2,4-dinitrophenyl thionobenzoate (1) and 2,4-dinitrophenyl benzoate (2) with a series of substituted pyridines in 80 mol % H(2)O/20 mol % DMSO at 25.0 +/- 0.1 degrees C. The Br?nsted-type plots obtained are nonlinear with beta(1) = 0.26, beta(2) = 1.07, and pK(a) degrees = 7.5 for the reactions of 1 and beta(1) = 0.40, beta(2) = 0.90, and pK(a) degrees = 9.5 for the reactions of 2, suggesting that the pyridinolyses of 1 and 2 proceed through a zwiterionic tetrahedral intermediate T(+/-) with a change in the rate-determining step at pK(a) degrees = 7.5 and 9.5, respectively. The thiono ester 1 is more reactive than its oxygen analogue 2 except for the reaction with the strongest basic pyridine studied (pK(a) = 11.30). The k(1) value is larger for the reactions of 1 than for those of 2 in the low pK(a) region, but the difference in the k(1) value becomes negligible with increasing the basicity of pyridines. On the other hand, 1 exhibits slightly larger k(2)/k(-1) ratio than 2 in the low pK(a) region but the difference in the k(2)/k(-1) ratio becomes more significant with increasing the basicity of pyridines. Pyridines are more reactive than alicyclic secondary amines of similar basicity toward 2 in the pK(a) above ca. 7.2 but less reactive in the pK(a) below ca. 7.2. The k(1) value is slightly larger, but the k(2)/k(-1) ratio is much smaller for the reactions of 2 with pyridines than with isobasic secondary amines in the low pK(a) region, which is responsible for the fact that the weakly basic pyridines are less reactive than isobasic secondary amines.     

An original way to use a β-cyclodextrin-bonded silica stationary phase in electrochromatography. Application to the achiral separation of nucleobases and nucleosides

Summary Although β-cyclodextrin-bonded silica stationary phases are usually dedicated to the separation of enantiomers, they can also be used for achiral purposes, taking advantage of the complex interactions between the solutes and the cyclodextrins. The work described in this paper was intended to show how such stationary phases can be used in short-end injection capillary electrochromatography (CEC) for rapid (<6 min) resolution of a mixture of purines and pyrimidines. Several experimental conditions (mobile-phase composition, voltage and temperature) were investigated to determine the optimum operating conditions for the method, which can also be applied to the analysis of nucleosides. Quantitative analysis was also performed; theophylline was used as internal standard to assess the linearity and the repeatability of the method. Limits of detection ranged from 4 to 13 μm and repeatability was good (RSD never exceeded 2.6%).     

A concerted mechanism for uncatalysed transfer of carbon substituents from diimides to C = C and C[triple bond]C

We present high-level computational predictions regarding a novel uncatalysed, yet feasible, C-C bond forming reaction.     

Synthesis of nine-, ten-, and fifteen-membered alkenolides by the oxidative cleavage of the bridging C=C bond in 2-oxabicycloalkenes

Hydroperoxidation of C=C-bridged 2-oxabicycloalkenes in which the five- or six-membered oxacycle is fused with the five-, six-, or twelve-membered hydrocarbon ring was studied. The Cu(OAc)₂-catalyzed decomposition of the resulting hydroperoxides afforded nine-, ten-, or fifteen-membered trans-alkenolides, respectively. The latter compounds were obtained as pairs of regioisomers, with the isomers in which the double bond is more remote from the ether oxygen atom predominating.