Gamma-radiolysis DNA products: synthesis of 6-(alpha-thyminyl)-5,6-dihydro-4-thiothymine derivatives

Far-UV photolysis of 4-thiothymidylyl(3'-5')thymidine led to the formation of three stable derivatives: one resulting from a combination between a 3'-end methylene radical and a 5'-end C(4) radical [4-(alpha-thyminyl) derivative] and two formed after a combination between a 3'-end methylene radical and a 5'-end C(6) radical [6-(alpha-thyminyl) derivative]. In the latter series, two stereochemical pathways took place during the reaction between the methylene and C(6) radicals. The major pathway occurred when the 5'-base glycosidic bond had an anti conformation leading to an S configuration of the C(6) Tp-end. The minor pathway, which had never been reported before in this series, involved a 5'-base in a syn conformation leading consequently to the R configuration at the C(6) Tp-end. The 5,6-dihydrothymine moiety of these two adducts presented a 5,6-trans diaxial substitution that resulted from the epimerization, at the 5,6-dihydropyrimidine 5-position, of a less stable cis-disubstituted intermediate.     

PHOTOADDITION OF p-AMINOBENZOIC ACID TO THYMINE AND THYMIDINE

Several studies in the literature have shown that DNA is damaged after UV irradiation in the presence of the sunscreen agent p-aminobenzoic acid (PABA), both in vivo and in vitro. One type of damage has been shown to be the result of increased yields of pyrimidine cyclobutane dimer formation. However, it has been suggested that other types of lesions are produced as well. We have studied the photochemistry of the thymine-PABA and thymidine-PABA systems and report here the isolation and characterization of thymine-PABA and thymidine-PABA photoadducts. These products have been identified, respectively, as 5-(2-amino-5-carboxyphenyl)-5,6-dihydrothymine and isomeric forms of 5-(2-amino-5-carboxyphenyl)-5,6-dihydrothymine. The quantum yields for the formation of these adducts in deaerated aqueous solutions at pH 7.0 have been determined to be 9.5 x 10(-4) and 4.3 x 10(-3) for the thymine and thymidine based adducts respectively. A pH profile for the thymine-PABA system indicated a maximum quantum yield for adduct formation at pH 6.5, although it could be detected over the whole pH range studied (pH 3.5-11.0).     

Alpha'-hydroxy enones as achiral templates for Lewis acid-catalyzed enantioselective Diels-Alder reactions

alpha'-Hydroxy enones react with dienes in the presence of (S,S)-[Cu(tBu-box)](OTf)2 or (S,S)-[Cu(tBu-box)](SbF6)2 (2 to 10 mol %) to afford the corresponding Diels-Alder adducts in high yield and selectivity. Isomeric ratios (regioselectivity, endo/exo or cis/trans) of up to >99:1 and ee values of up to >99% are obtained. Significantly, difficult dienes such as isoprene, 2,3-dimethyl butadiene and piperylene behave satisfactorily. Subsequent oxidative cleavage of the ketol in the resulting cycloadducts by treatment with cerium ammonium nitrate (CAN) yields the corresponding enantiopure carboxylic acids. Alternatively, carbonyl addition and subsequent diol cleavage with CAN produces the corresponding ketone adducts.     

POTENTIAL PHOTOSENSITIZERS FOR PHOTODYNAMIC TUMOR THERAPY—I. PHOTOPHYSICAL PROPERTIES OF TWO CHLORIN DERIVATIVES

Abstract— Photophysical properties of two chlorin type molecules (CHLI) and (CHLII) were investigated in different solvents. Quantum yields of fluorescence φ_F of S, → T, intersystem crossing φ_T, and of singlet oxygen (¹Δ_g) formation φ_Δ, as well as the Stern-Volmer constants for the quenching of the S, states by oxygen and the bimolecular rate constants of quenching of ¹Δ_g by the chlorins were measured. The values of φ_T and φ_Λ can be given as 0.57 and 0.58 for CHLI and 0.69 and 0.58 for CHLII. The values of the fluorescence quantum yields, the strong absorption of the chlorins in the red (Λ > 630 nm) and the high values of the quantum yields for ¹Δ_g formation recommend the chlorin derivatives as potential markers and photosensitizers for tumor therapy.     

FLUORESCENCE QUANTUM YIELD DETERMINATION OF PYRIMIDINE (6-4) PYRIMIDONE PHOTOADDUCTS

Abstract An extensive study of the fluorescence characteristics of pyrimidine (6-4) pyrimidone photoadducts, a major class of far-UV-induced DNA lesions, was carried out on dinucleoside monophosphate (6-4) photoadducts, including thymidylyl-(3'→ 5')-thymidine (TpT), 2'-deoxycytidylyl-(3'-5')-thymidine, thymidylyl-(3'→ 5')-2'-deoxy-cytidine, 2'-deoxyuridylyl-(3'→ 5')-thymidine, 5-methyl-2'-deoxycytidylyl-(3'-5')-thymidine (6-4) photoadducts and the corresponding base (6-4) photoadducts, 6-4'-(5'-methylpyrimidin-2'-one) thymine (TT), 5-hydroxy-6-4'-(5'-methylpyrimidin-2'-one)-5,6-dihydrothymine (CT), 5-amino-6-4'-(pyrimidin-2'-one)-5,6-dihydrothymine (UC) obtained by mild acidic hydrolysis of the former derivatives. The fluorescence quantum yield (Φ_F) of these compounds was found to depend on one hand, on the nature of the two bases involved and the base substituent and, on the other hand, on the presence of the phosphate group. The hydrolysis of the phosphodiester bond was shown to enhance Φ_F, the larger effect being observed in the case of the thymine-thymine photoadducts with a seven-fold increase of the Φ_F value in the case of TT as compared to TpT (0.21 and 0.03, respectively). These results are discussed in terms of structural considerations.     

Direct observation of adduct formation of alkyl and aromatic iodides with cl atoms using cavity ring-down spectroscopy

The reactions of Cl atoms with RI (R = n-C3H7, n-C4H9, cyclo-C6H11, C6H5, C6F5, and p-CH3C6H4) have been studied using cavity ring-down spectroscopy at a temperature range of 233-313 K and at 100 Torr total pressure of N2 diluent. Visible absorption spectra of the RI-Cl adducts were recorded at 440-520 nm at 263 K. The yields of the adducts were temperature-dependent. There was no discernible reaction of the adducts in the presence of 100 Torr of O2 at 263 K. Theoretical calculations were performed for C4H9I-Cl and C6H5I-Cl for quantitative explanation of the absorption spectra and the strength of the I-Cl bonds in the charge-transfer complexes. Evidence for the adduct formation following the reaction of Cl with C6H5Br was sought but not found at 440 and 520 nm.     

ON THE PHOTOIONIZATION ENERGY THRESHOLD OF TRYPTOPHAN IN AQUEOUS SOLUTIONS

Abstract— To investigate the existence and energy position of a photoionization threshold. tryptophan (Trp) has been photoionized in desecrated neutral aqueous or alcoholic solution under monochromatic light of variable frequency, in presence of N₂O to scavenge the photoelectron.
Present findings and some literature data converge to show the existence of a threshold for the one photon ionization process. This threshold is located at 4.5 ± 0.1 eV and 4.85 ± 0.1 cV for Trp in aqueous and ethanol solutions. respectively, which corresponds to a lowering with respect to the gas phase ionization potential of 3.4 and 3.0 eV.
The photoionization quantum yields for Trp is found about 4 times greater at 250 nm than at Λ_cx= 265 nm, where φe^-_4M=0.080±0.025. In such spectral range. at most one photoelectron out of 4–5 escaping geminate recombination would lead to Trp photodegradation in acrated solutions.
These results also point out that the neutral radical Trp. which has been previously observed for Λ_cx > 275 nm, i.e. below the ionization threshold energy—would not necessarily derive from Trp ⁺ deprotonation or cation-electron dissociative recombination. Similarly, the opening of the indole ring with formylkynurenine (FK) formation which is observed under aerobic conditions and Λ_cx >, 280 nm would not imply an electron attachment on O₂ but reactions such as Trp +³O₂ or Trp*+³O₂ or else
     

Synthesis of the TT pyrimidine (6-4) pyrimidone photoproduct-thio analogue phosphoramidite building block

The phosphoramidite building block synthesis of the thio analogue at the 5,6-dihydropyrimidine C5 position of the thymidylyl(3'-5')thymidine (6-4) photoproduct 1 is presented. This compound was readily obtained from the appropriately protected dinucleotide P-methyl-5'-O-dimethoxytritylthymidilyl(3' --> 5')-4-thiothymidine 2 after irradiation at 366 nm, then S-sulfenylmethylation of the thiol function of the resulting (6-4) adduct, and phosphitylation of the 3'-hydroxyl group.     

Asymmetric synthesis of succinic semialdehyde derivatives

The nucleophilic Michael addition of 2-(diphenylmethoxymethyl)-1-methyleneamino pyrrolidine 1Dto prochiral aliphatic and aromatic alkylidene malonates 2 takes place in the presence of MgI(2) to afford the corresponding Michael adducts 3 in excellent yields and good selectivities. In the aromatic series, optically pure (de > 98%) major diastereomers (S,S)-3 were isolated in good yields (77-93%) after chromatographic separation. Direct, racemization-free BF(3).OEt(2)-catalyzed thiolysis of compounds 3 afforded dithioacetals 7. These compounds were transformed into malonates 8 and succinic semialdehyde derivatives 9 by Raney Nickel mediated desulfuration or decarboxylation, respectively.     

Far-UV-lnduced Dimeric Photoproducts in Short Oligonucleotides: Sequence Effects

Cyclobutane pyrimidine dimers and pyrimidine(6-4)pyrimidone adducts represent the two major classes of far-UV-induced DNA photoproducts. Because of the lack of appropriate detection methods for each individual photoproduct, little is known about the effect of the sequence on their formation. In the present work, the photoproduct distribution obtained upon exposure of a series of dinucleoside monophosphates to 254 nm light was determined. In the latter model compounds, the presence of a cytosine, located at either the 5′- or the 3′- side of a thymine moiety, led to the preferential formation of (6-4) adducts, whereas the cis-syn cyclobutane dimer was the main thymine-thymine photoproduct. In contrast, the yield of dimeric photoproducts, and particularly of (6-4) photoadducts, was very low upon irradiation of the cytosine–cytosine dinucleoside monophosphate. However, substitution of cytosine by uracil led to an increase in the yield of (6-4) photoproduct. It was also shown that the presence of a phosphate group at the 5′- end of a thymine-thymine dinucleoside monophosphate does not modify the photoproduct distribution. As an extension of the studies on dinucleoside monophosphates, the trinucleotide TpdCpT was used as a more relevant DNA model. The yields of formation of the thymine-cytosine and cytosine–thymine (6-4) photoproducts were in a 5:1 ratio, very close to the value obtained upon photolysis of the related dinucleoside monophosphates. The characterization of the two TpdCpT (6-4) adducts was based on H NMR, UV and mass spectroscopy analyses. Additional evidence for the structures was inferred from the analysis of the enzymatic digestion products of the (6-4) adducts of TpdCpT with phosphodiesterases. The latter enzymes were shown to induce the quantitative release of the photoproduct as a modified dinucleoside monophosphate in a highly sequence-specific manner.     

Ab initio study of the (5R)- and (5S)-TT pyrimidine h5(6-4) pyrimidone photoproducts. Implications on the design of new biologically relevant analogues

A computational study of a series of N(1)- and/or C(6)-alkyl-5,6-dihydrothymine diastereomers at theory levels up to MP4(SDTQ)/6-31G//HF/6-31G and MP2/6-311G//HF/6-31G has demonstrated the respective importance of the substituents at positions 1, 5, and 6 on the energetically favored conformation of each isomer. Results obtained both in the gas and condensed phase indicate that unsubstitution of the N(1)-position favors a half-chair conformation with the C(5) -and C(6)-substituents in the equatorial position. On the other hand, in the case of the (6S)-1,6-dimethyl-5,6-dihydrothymine, the C(6)-substituent adopts the axial position to minimize its van der Waals interactions with the N(1)-substituent. Furthermore, if the configuration at the C(5)-dihydrothymine position has no resultant influence on the total molecular free energy, when a pyrimidone substituent is introduced at the dihydrothymine C(6)-position, additional repulsive forces between the C(5)- and C(6)-substituents make the diaxially substituted half-chair conformation the most energetically favorable one. These results indicate that the observed C(6)-axially substituted conformation of the thymine-thymine pyrimidine h(5)(6-4) pyrimidone photoproducts is not necessarily induced by the macrocyclic structure. They also nicely explain the formation mechanism of these photoproduct derivatives, and allow the prediction of the conformation of new analogues.     

Photochemically catalyzed reaction of ochratoxin A with D- and L-cysteine

The photolysis (>300 nm) of ochratoxin A (OTA, N-[[(3R)-5-chloro-8-hydroxy-3-methyl-1-oxo-7-isochromanyl]carbonyl]-3-phenyl-L-alanine, 1) in the presence of excess (2 and 12 molar equiv) cysteine (CySH) has been investigated and found to yield sulfur adducts 5 and 6 that are characterized by liquid chromatography-mass spectrometry and 1H-NMR spectroscopy. The adduct 5 was ascribed to the Michael addition conjugate resulting from covalent attachment of CySH to the ochratoxin quinone (4) generated by photooxidation of OTA. This species was also formed by photolysis of a synthetic sample of the hydroquinone of OTA (ochratoxin hydroquinone, 3) in the presence of 12 equiv L-CySH. The conjugate 5 derived from photolysis of 3 with L-CySH was used for 1H-NMR analysis. The sulfur adduct 6 was the major species detected from covalent attachment of CySH to photoactivated OTA, and it resulted from direct displacement of the OTA Cl atom by CySH. The implications of the cysteinyl adducts to the in vivo toxicity of OTA are discussed, with particular emphasis given to conjugate 5, as products from the photooxidative pathway may be of relevance to the nephrotoxic properties of OTA.     

New approaches to β-trifluoromethylated enone derivatives

β-Trifluoromethylated enaminones 1 were prepared stereospecifically or high stercoselectively in 31-92% yields from the reaction of Weinreb amides with trifluoropropynyl lithium, followed by quenching with H₂O in the presence of amine derivatives. β-Trifluoromethylated enaminone 1a was reacted with aryl or alkynyl Grignard reagents to give Michael addition products 5 at 0 °C, whereas addition-elimination adducts, β-aryl (or alkynyl)-β-trifluoromethylated enones 6, were obtained stereospecifically in 50-92% yields after stirring at room temperature for several hours.     

Spectroscopic evidence for the intermediacy of a 6-R-2,4-diazabicyclo-[3.1.0]hex-2-(3)ene in the photoisomerization of 4-R-1,4-(3,4)-dihydropyrimidines

¹H- and ¹³C-nmr spectroscopy is presented showing that photolysis of 4-(p-trifluoromethylphenyl)-1,4-(3,4)-dihydropyrimidine yields 6-(p-trifluoromethylphenyl)-2,4-diazabicyclo[3.1.0]hex-2-(3)ene.     

Highly stereoselective and stereodivergent synthesis of four types of THF cores in acetogenins using a C4-chiral building block

[reaction: see text] Four stereoisomers of the THF cores, synthetic intermediates of acetogenins, have been synthesized with high diastereoselectivity by asymmetric alkynylation and subsequent stereodivergent THF ring formation. The asymmetric alkynylation of alpha-oxyaldehyde with (S)-3-butyne-1,2-diol derivatives (C4-unit) gave good yields of syn and anti adducts with >97:3 dr and 94:6 dr, respectively. These adducts were converted into the four types of THF compounds via one-pot THF formation or via intramolecular Williamson synthesis.     

PHOTOREACTIONS OF 5-BROMOURACIL IN THE PRESENCE OF CYSTEINE AND GLUTATHIONE

Abstract —Sulfhydryl compounds such as cysteine and glutathione enhance the photochemical reactivity of 5-bromouracil irradiated in aqueous solution with ultraviolet light (Λ > 240 nm). Production of uracil and addition of the sulfhydryl compound to the 5-bromouracil residue are the major photoreactions.     

Synthesis of 2,5-disubstituted thienosultines and their thermal reactions with dienophiles and nucleophiles

The 2,5-disubstituted thienosultines (5,7-disubstituted 1,4-dihydro-1H-3lambda(4)-thieno[3,4-d][2,3]oxathiin-3-oxides) 5a-d were prepared from the corresponding dichlorides 4a-d with the commercially available Rongalite (sodium formaldehyde sulfoxylate) in 17-60% yields. When heated in the presence of electron-poor dienophiles, sultines 5a-d underwent elimination of SO(2), and the resulting non-Kekulé biradicals 7a-d were intercepted as the 1:1 adducts 8-12 in good to excellent yields. The pyrolysis of sultines and sulfolenes with different concentrations of dienophiles revealed that either a preequilibrium between starting reagents and biradical species or Diels-Alder and retro-Diels-Alder reaction mechanisms may be involved; however, more work is necessary to establish the proposed mechanisms. Reaction of sultine 5b with nBuLi was found to undergo a nucleophilic ring-opening reaction to give sulfinyl alcohol 17 after H(2)O workup. When sultine 5a was heated in benzene in a sealed tube in the presence of methanol, methanol-d(4), or 2-mercaptoethanol, the respective 1:1 trapping adducts 19-21 as well as the rearranged sulfolene 6a were isolated in similar amounts. The isolation of adducts 19-21 may be explained by the involvement of either biradical or ionic intermediates during the pyrolysis.     

SPECTRAL PROPERTIES OF THE RHODOPSIN-SYSTEM OF THE CRAYFISH Astacus leptodactylus

Abstract— The absorption spectra of the membrane-bound and of the digitonin-solubilized visual pigment of crayfish Astacus leptodactylus were investigated by conventional spectrophotometry. A method was developed to isolate purified rhabdoms almost entirely free from screening pigments from a single retina. The quantity of isolated and purified rhabdoms from a single retina was sufficient to measure the absorption spectra of the visual pigment.
The absorption spectra of the chromoprotein system (R and M) show that both the membrane-bound and the digitonin-solubilized visual pigment isomers are stable at 0°C and pH 7.0. Rhodopsin and metarhodopsin are photoreversible under these conditions without any light-induced denaturation. The difference spectra for the chromoprotein isomers and those of different photostationary states yield maximal values for ΔE at 570 and 485 nm.
At neutral pH, 0°C, Λ_max of rhodopsin is 530 nm. Irradiation with light of Λ= 630 to 640 nm isomerizes rhodopsin nearly quantitatively to metarhodopsin with Λ_max, of 500 nm. The molar extinction coefficient of metarhodopsin is greater than that of rhodopsin by a factor of ˜ 1.41. each measured at its respective Λ_max Metarhodopsin can be isomerized to rhodopsin by irradiating at Λ > 630 nm. As the absorption spectra of the two chromoprotein isomers overlap, only part of the metarhodopsin can be reversed to rhodopsin. The maximal photoreversion can be achieved by irradiating at 460 nm. The stability of the digitonin-solubilized chromoprotein is remarkably dependent on temperature. Warming the digitonin extract of rhabdoms from 0 to 20 or 30°C caused a shift of the rhodopsin spectrum to shorter wavelengths (Λ_max= 485 nm) accompanied by a decrease of E_Λmax by about 30%.     

Some Specific Features of Acid Nitration of 2-Substituted 4,6-Dihydroxypyrimidines. Nucleophilic Cleavage of the Nitration Products

The nitration of 2-substituted 4,6-dihydroxypyrimidines in concentrated sulfuric acid yields the corresponding 5,5-dinitro derivatives. When the substituent in position 2 is an alkyl group, the nitration occurs both at position 5 and at the -carbon atom of the side chain. Hydrolysis of 2-substituted 4,6-dihydroxy-5,5-dinitropyrimidines leads to formation of 1,1-diamino-2-R-2-nitroethylene derivatives. 1,1-Diamino-2,2-dinitro-ethylene was obtained by nitration of 4,6-dihydroxy-2-methylpyrimidine and subsequent hydrolysis of 4,6-dihydroxy-5,5-dinitro-2-(dinitromethylene)-2,5-dihydropyrimidine.     

Structure of molybdenum and tungsten sulfide M(x)S(y)+ clusters: experiment and DFT calculations

A combination of experiment and density functional theory was used to investigate the energetics of CO adsorption onto several small M(x)S(y)(+) (M = Mo, W; x/y = 2/6, 3/7, 5/7, 6/8) clusters as a probe of their atomic and electronic structure. Experimentally, tandem mass spectrometry was used to measure the relative yields of M(x)S(y)(+)(CO)(n) cluster adducts formed by collisions between a beam of mass-selected M(x)S(y)(+) cluster ions and CO molecules in a high-pressure collision cell (hexapole ion guide). The most probable M(x)S(y)(+)(CO)(n) adducts observed are those with n < or = x, that is, only one CO molecule bound to each metal site. The notable exception is the M(5)S(7)(+) cluster, for which the n = 6 adduct is found to have nearly the same intensity as the n = x = 5 adduct. Density functional calculations were used to search for the lowest energy structures of the bare M(x)S(y)(+) clusters and to obtain their relative stability for sequential CO binding. The calculated trends in CO binding energies were then compared to the experimental adduct distributions for assigning the ground-state structures. In this way, it was possible to distinguish between two nearly isoenergetic ground-state isomers for the M(2)S(6)(+) and M(3)S(7)(+) clusters, as only one isomer gave a calculated CO stabilization energy trend that was consistent with the experimental data. Similar comparisons of predicted and observed CO adsorption trends also provide evidence for assigning the ground-state structures of the M(5)S(7)(+) and M(6)S(8)(+) clusters. The latter contain metallic cores with most of the sulfur atoms bonded along the edges or in the faces of the metal core structure. The n = 6 and 7 adducts of M(5)S(7)(+) are predicted to be more stable than the n = x = 5 adduct, but only the n = 6 adduct is observed experimentally. The DFT calculations show that the n = 7 adduct undergoes internal bond breaking whereas the n = 6 framework is stable, albeit highly distorted. For the M(6)S(8)(+) cluster, the calculations predict that the two lowest energy isomers can bind more than six CO molecules without fragmentation; however, the apparent binding energy drops significantly for adducts with n > 6. In general, the ability of these small M(x)S(y)(+) clusters to bind more CO molecules than the number of metal atoms is a balance between the gain in CO adsorption energy versus the strain introduced into the cluster structure caused by CO crowding, the consequences of which can be fragmentation of the M(x)S(y)(+)(CO)(n) cluster adduct (n > x).