Polymerization of some sulfur-containing oxetanes

Polymerization under the influence of boron trifluoride of 2-oxa-6-thia[3,3]spiroheptane gives two products: a linear polyether containing oxetane groups and a crosslinked polyether polysulfide. When the polymerization was carried out at ?3°C., up to 60% of soluble polysulfide is obtained. This does not prove that the thietane group polymerizes more rapidly than the oxetane group but rather that oxetane polymerization is inhibited by the presence of thietane groups. Polymerization under the influence of boron trifluoride etherate of 3,3-bis(mercaptomethyl)oxetane leads to a polyether containing free thiol groups. The degree of polymerization of the polymer, however, is low. In order to obtain higher degrees of polymerization several compounds with masked thiol groups were polymerized. 2-Oxa-6,7-dithia-6-thio[3,4]spirooctane and 2-oxa-6,8-dithia-7,7-dimethyl[3,5]-spirononane gave crosslinked products. The diacetate of 3,3-bis(mercaptomethyl)oxetane gave a linear polyether containing thiolacetate groups. Hydrolysis of this polymer leads to poly-3,3-bis(mercaptomethyl)oxetane with a softening temperature of 125–135°C.     

Evidence that the (6-4) photolyase mechanism can proceed through an oxetane intermediate

Using the analogue of TpT methylated at the 3'-end N3 position (Tpm3T), we demonstrate that when the oxetane/(6-4) pathway is precluded, water addition occurs at the 3'-end C6 position of the oxetane intermediate to provide its opening. Photoreversal of this (6-4) photoproduct C6 hydrate brings the first experimental evidence that the (6-4) photolyase repair can proceed through an oxetane intermediate.     

Theoretical study on the repair mechanism of the (6-4) photolesion by the (6-4) photolyase

UV irradiation of DNA can lead to the formation of mutagenic (6-4) pyrimidine-pyrimidone photolesions. The (6-4) photolyases are the enzymes responsible for the photoinduced repair of such lesions. On the basis of the recently published crystal structure of the (6-4) photolyase bound to DNA [Maul et al. 2008] and employing quantum mechanics/molecular mechanics techniques, a repair mechanism is proposed, which involves two photoexcitations. The flavin chromophore, initially being in its reduced anionic form, is photoexcited and donates an electron to the (6-4) form of the photolesion. The photolesion is then protonated by the neighboring histidine residue and forms a radical intermediate. The latter undergoes a series of energy stabilizing hydrogen-bonding rearrangements before the electron back transfer to the flavin semiquinone. The resulting structure corresponds to the oxetane intermediate, long thought to be formed upon DNA-enzyme binding. A second photoexcitation of the flavin promotes another electron transfer to the oxetane. Proton donation from the same histidine residue allows for the splitting of the four-membered ring, hence opening an efficient pathway to the final repaired form. The repair of the lesion by a single photoexcitation was shown not to be feasible.     

Electron-transfer induced repair of 6-4 photoproducts in DNA: a computational study

The mechanism employed by DNA photolyase to repair 6-4 photoproducts in UV-damaged DNA is explored by means of quantum chemical calculations. Considering the repair of both oxetane and azetidine lesions, it is demonstrated that reduction as well as oxidation enables a reversion reaction by creating anionic or cationic radicals that readily fragment into monomeric pyrimidines. However, on the basis of calculated reaction energies indicating that electron transfer from the enzyme to the lesion is a much more favorable process than electron transfer in the opposite direction, it is suggested that the photoenzymic repair can only occur by way of an anionic mechanism. Furthermore, it is shown that reduction of the oxetane facilitates a mechanism involving cleavage of the C-O bond followed by cleavage of the C-C bond, whereas reductive fragmentation of the azetidine may proceed with either of the intermonomeric C-N and C-C bonds cleaved as the first step. From calculations on neutral azetidine radicals, a significant increase in the free-energy barrier for the initial fragmentation step upon protonation of the carbonylic oxygens is predicted. This effect can be attributed to protonation serving to stabilize reactant complexes more than transition structures.     

Model studies of the (6-4) photoproduct photoreactivation: efficient photosensitized splitting of thymine oxetane units by covalently linked tryptophan in high polarity solvents

Three covalently linked tryptophan-thymine oxetane compounds used as a model of the (6-4) photolyase-substrate complex have been prepared. Under 290 nm light, efficient splitting of the thymine oxetane with aromatic carbonyl compounds gives the thymine monomer and the corresponding carbonyl compounds by the covalently linked tryptophan via an intramolecular electron transfer, and exhibits a strong solvent dependence: the quantum yield (Phi) is ca. 0.1 in dioxane, and near 0.3 in water. Electron transfer from the excited tryptophan residue to the oxetane unit is the origin of fluorescence quenching of the tryptophan residue, and is more efficient in strong polar solvents. The splitting efficiency of the oxetane radical anion within the tryptophan.+-oxetane.- species is also solvent-dependent, ranging from ca. 0.2 in dioxane to near 0.35 in water. Thus, the back electron transfer reaction in the charge-separated species would be suppressed in water, but is still a main factor causing low splitting efficiencies in the tryptophan-oxetane systems. In contrast to the tryptophan-oxetane system, fast nonradiation processes are the main causes of low efficiency in the flavin-oxetane system. Hence, nonradiative processes of the excited FADH-, rather than electron transfer to oxetane, may be an important factor for the low repair efficiency of (6-4) photolyase.     

Electrochemical approach to the repair of oxetanes mimicking DNA (6-4) photoproducts

Electrochemical study of oxetanes mimicking DNA (6-4) photoproducts gives new insight into the repair mechanism by (6-4) photolyase. Both electrochemical oxidation and electrochemical reduction at carbon electrodes lead to the cleavage of the oxetanes in a retro-Paterno-Büchi sequence. Within the family of compounds investigated and the range of driving forces offered, transient formation of unstable radical ions is observed, for both oxidative and reductive cleavage. Taking advantage of the electrochemical signature of these mimics, enzymatic assay with Escherichia coli CPD photolyase coupled to electrochemical monitoring of the reaction brings evidence that enzymatic repair of (6-4) DNA photoproducts does involve a catalytic dissociative electron-transfer mechanism at the level of an oxetane intermediate.     

A computational study to elucidate the extraordinary reactivity of three-membered heterocycles in nucleophilic substitution reactions

The accelerated rates of small-membered heterocycles relative to acyclic analogues are typically rationalized solely in terms of relief of ring strain. The relative rates of attack of ammonia on oxirane, oxetane, thiirane, and thietane were determined computationally in the gas phase at the MP2(Full)/6-31+G(d) level with respect to the model acyclic compounds methoxyethane and thiomethylethane. Because the cyclic ether and thioether pairs have very similar strain energies, they should react at similar rates by the S(N)2 mechanism if the degree of strain energy release in the transition state is approximately equal. The reactivity of the four-membered rings could be explained almost entirely by relief of strain. The three-membered rings reacted at rates at least 10(6) times faster than calculated from ring strain considerations alone. The electronic distribution of the transition states was determined using AIM methodology and found to indicate that bond cleavage was virtually complete, while bond formation was incomplete. Calculation of atomic charges by the Mulliken, AIM, CHELPG, and NBO methods indicated that positive charge at the reaction center was significantly lower for the three-membered rings than other members of the series. A simple electrostatic model identified differences in energy sufficient to account for the observed rate acceleration. The unique topological features of a three-membered ring make it possible for the partially negatively charged oxygen or sulfur to reduce the positive charge on the reaction center.     

3, 3-不对称二取代甲基氧杂丁环的合成

以2,2-二(溴甲基)-1,3-丙二醇(1)为原料合成了3-溴甲基-3-羟甲基氧杂丁环(2)、3-乙氧甲基-3-羟甲基氧杂丁环(3)、3-叠氮甲基-3-羟甲基氧杂丁环(4)、3-叠氮甲基-3-硝酸酯甲基氧杂丁环(5)、3-溴甲基-3-硝酸酯甲基氧杂丁环(6)及3-乙氧基甲基-3-硝酸酯甲基氧杂丁环(7)共六种3,3-不对称二取代甲基氧杂丁环化合物,其中6和7的合成未见文献报道。也提出了合成5的改进路线。     

Investigation of the pathways of excess electron transfer in DNA with flavin-donor and oxetane-acceptor modified DNA hairpins

Oxetane is a potential intermediate that is enzymatically formed during the repair of (6-4) DNA lesions by special repair enzymes (6-4 DNA photolyases). These enzymes use a reduced and deprotonated flavin to cleave the oxetane by single electron donation. Herein we report synthesis of DNA hairpin model compounds containing a flavin as the hairpin head and two different oxetanes in the stem structure of the hairpin. The data show that the electron moves through the duplex even over distances of 17 A. Attempts to trap the moving electron with N2O showed no reduction of the cleavage efficiency showing that the electron moves through the duplex and not through solution. The electron transfer is sequence dependent. The efficiency is reduced by a factor of 2 in GC rich DNA hairpins.     

Quantum mechanical study of energetics and mechanisms of cis–trans isomerization of some four-membered heterocycles

Ab initio quantum mechanical calculations using density functional (B3LYP) method and 6-311G** basis set have been performed on two cis and trans conformers of 2,4-diphenyl thietane dioxide (DPTD), 2,4-diphenyl thietane (DPT), 2,4-diphenyl azetidine (DPA) and 2,4-diphenyl oxetane (DPO). The calculated stability energy for cis–trans isomerization in gas phase and in different solvents such as benzene, DMSO, water and methanol indicated that the cis conformer is more stable than trans in all above-mentioned compounds about 11–2 kcal mol^?1. In the next step, a transition states for cis–trans inter-conversion for all four-membered heterocycles (DPTD, DPT, DPA and DPO) were proposed in methanol as solvent. Thermodynamic functions such as standard enthalpies of isomerization (?Hº_iso), standard entropy of isomerization (?Sº_iso) and standard Gibbs free energy of isomerization (?Gº_iso) for all studied compounds were also evaluated. The calculation showed that the conversion of trans to cis isomer is exothermic and spontaneous. In all calculations, solvent effects were considered using a polarized continuum model.     

Characterization of the Intermediate in and Identification of the Repair Mechanism of (6‐4) Photolesions by Photolyases

Quantum mechanics/molecular mechanics calculations are employed to assign previously recorded experimental spectroscopic signatures of the intermediates occurring during the photo‐induced repair of (6‐4) photolesions by photolyases to specific molecular structures. Based on this close comparison of experiment and theory it is demonstrated that the acting repair mechanism involves proton transfer from the protonated His365 to the N3′ nitrogen of the lesion, which proceeds simultaneously with intramolecular OH transfer along an oxetane‐like transition state.     

Quantum Chemical Study of the Enzymatic Repair of T(6‐4)C/C(6‐4)T UV‐Photolesions by DNA Photolyases

Several strategies have evolved to repair one of the abundant UV radiation‐induced damages caused to DNA, namely the mutagenic pyrimidine (6‐4) pyrimidone photolesions. DNA (6‐4)‐photolyases are enzymes repairing these lesions by a photoinitiated electron transfer. An important aspect of a possible repair mechanism is its generality and transferability to different (6‐4) lesions. Therefore, previously suggested mechanisms for the repair of the T(6‐4)T lesion are here transferred to the T(6‐4)C and C(6‐4)T lesions and investigated theoretically using quantum chemical methods. Despite the different functional groups of the pyrimidine bases involved, a general valid molecular mechanism was identified, in which the initial step is an electron transfer coupled to a proton transfer from the protonated HIS365 to the N3^′ nitrogen of the 3^′ pyrimidine, followed by an intramolecular OH/NH₂ transfer in one concerted step, which does not require an oxetane/azetidine or isolated water/ammonia intermediate.     

Umpolung Asymmetric 1,5-Conjugate Addition via Palladium Hydride Catalysis

Electronically matched nucleophilic 1,6-conjugate addition has been well studied and widely applied in synthetic areas. In contrast, nucleophilic 1,5-conjugate addition represents an electronically forbidden process and is considered unfeasible. Here, we describe modular protocols for 1,5-conjugate addition reactions via palladium hydride catalysis. Both palladium and synergistic Pd/organocatalyst systems are developed to catalyze 1,5-conjugate reaction, followed by inter- or intramolecular [3+2] cyclization. A migratory 1,5-addition protocol is established to corroborate the feasibility of this umpolung concept. The 1,5-addition products are conveniently transformed into a series of privileged enantioenriched motifs, including polysubstituted tetrahydrofuran, dihydrofuran, cyclopropane, cyclobutane, azetidine, oxetane, thietane, spirocycle and bridged rings. Preliminary mechanistic studies corroborate the involvement of palladium hydride catalysis.     

13C?13C spin–spin coupling constants and 13C isotope effects on 13C chemical shifts in some 4-membered rings

The ¹³C? ¹³C spin–spin coupling constants in natural abundance oxetane, thietane, cyclobutanone, bromo-and chlorocyclobutane have been measured. Furthermore, the ¹³C isotope-induced changes in the chemical shifts of the different ¹³C nuclei in the molecules mentioned above are reported. These shifts are normally to higher magnetic field; in cyclobutanone, however, the resonance of the carbonyl carbon has shifted to lower field because of the substitution of ¹³C?3 for ¹²C?3.     

Preparation and polymerization of the two isomeric (chloromethyl)oxetanes

2-(Chloromethyl)oxetane was prepared in 8% overall yield from 2-propen-1-ol by protection of the alcohol with dihydropyran, epoxidation, ring expansion with dimethylsulfoxonium methylide, acid deprotection, and chlorination with triphenylphosphine in CCl₄. 3-(Chloromethyl)oxetane was prepared in 22% overall yield by hydroboration-oxidation of 3-chloro-2-chloromethyl-1-propene followed by base-catalyzed cyclization. Each of the oxetanes was converted to the corresponding elastomeric homopolymer by treatment with a triethylaluminum–acetylacetone–water mixture. Poly[2-(chloromethyl)oxetane] was found to be similar to polyepichlorophydrin in reactivity toward benzoate ion, whereas poly[3-(chloromethyl)oxetane] is more reactive by a factor of 2.     

(6-4)-photolyase activity requires a charge shift reaction

A model compound containing a thymine oxetane moiety linked to a flavin chromophore was investigated regarding (6-4)-photolyase activity. The need for a charge shift reaction was demonstrated by a detailed pH-dependent kinetic analysis.     

Crystal Structure of the T(6‐4)C Lesion in Complex with a (6‐4) DNA Photolyase and Repair of UV‐Induced (6‐4) and Dewar Photolesions

UV‐light irradiation induces the formation of highly mutagenic lesions in DNA, such as cis‐syn cyclobutane pyrimidine dimers (CPD photoproducts), pyrimidine(6‐4)pyrimidone photoproducts ((6‐4) photoproducts) and their Dewar valence isomers ((Dew) photoproducts). Here we describe the synthesis of defined DNA strands containing these lesions by direct irradiation. We show that all lesions are efficiently repaired except for the T(Dew)T lesion, which cannot be cleaved by the repair enzyme under our conditions. A crystal structure of a T(6‐4)C lesion containing DNA duplex in complex with the (6‐4) photolyase from Drosophila melanogaster provides insight into the molecular recognition event of a cytosine derived photolesion for the first time. In light of the previously postulated repair mechanism, which involves rearrangement of the (6‐4) lesions into strained four‐membered ring repair intermediates, it is surprising that the not rearranged T(6‐4)C lesion is observed in the active site. The structure, therefore, provides additional support for the newly postulated repair mechanism that avoids this rearrangement step and argues for a direct electron injection into the lesion as the first step of the repair reaction performed by (6‐4) DNA photolyases.     

Oxidation and isomerism of thietane-containing heterocycles

Oxidation of 6-methyl-1-(thiethan-3-yl)pyrimidine-2,4(1H,3H)-dione, 5(6)-nitro-1-(thiethan-3-yl)-benzimidazole, 2-methyl-4-nitro-1-(thiethan-3-yl)- and 5-bromo-2-methyl-4-nitro-1-(thiethan-3-yl)imidazoles was examined. Corresponding 1-oxothietan-3-yl- and 1,1-dioxothietan-3-yl derivatives were synthesized for the first time. Some factors affecting the quality of the final products and optimal conditions of the oxidation of thietanyl derivatives of pyrimidine-2,4(1H,3H)-dione, nitrobenzimidazole, and nitroimidazole were found. According to 1H NMR spectroscopy data, the obtained sulfoxides are mixtures of cis/trans isomers, the diastereomers ratio determined by the substituent at position 3 of thietane ring.     

Mechanistic insight into the initiation step of the coupling reaction of oxetane or epoxides and CO2 catalyzed by (salen)CrX complexes

The most active and robust current catalysts for the copolymerization of carbon dioxide and epoxides or oxetanes, (salen)CrX in conjunction with PPNX (PPN(+) = (Ph3P)2N(+)) or n-Bu4NX (X = Cl, N3, CN, NCO), are characterized both in solution by infrared spectroscopy and in the solid-state by X-ray crystallography. All anions (X) afford six-coordinate chromium(III) PPN(+) or n-Bu4N(+) salts composed of trans-(salen)CrX2(-) species. Of the X groups investigated in (salen)CrX, chloride is easily displaced by the others, that is, the reaction of (salen)CrCl with 2 equiv of N3(-), CN(-), or NCO(-) quantitatively provide (salen)Cr(N3)2(-), (salen)Cr(CN)2(-), and (salen)Cr(NCO)2(-), respectively. On the other hand, addition of less than 2 equiv of azide to (salen)CrCl leads to a Schlenk (ligand redistribution) equilibrium of the three possible anions both in solution and in the solid-state as shown by X-ray crystallography and electrospray ionization mass spectrometry. It was further demonstrated that all trans-(salen)CrX2(-) anions react with the epoxide or oxetane monomers in TCE (tetrachloroethane) solution to afford an equilibrium mixture containing (salen)CrX x monomer, with the oxetane adduct being thermodynamically more favored. The ring-opening steps of the bound cyclic ether monomers by X(-) were examined, revealing the rate of ring-opening of the epoxides (cyclohexene oxide and propylene oxide) to be much faster than of oxetane, with propylene oxide faster than cyclohexene oxide. Furthermore, both X anions in (salen)CrX2(-) were shown to be directly involved in monomer ring-opening.     

O(4)-Alkyl-2'-deoxythymidine cross-linked DNA to probe recognition and repair by O(6)-alkylguanine DNA alkyltransferases

DNA duplexes containing a directly opposed O(4)-2'-deoxythymidine-alkyl-O(4)-2'-deoxythymidine (O(4)-dT-alkyl-O(4)-dT) interstrand cross-link (ICL) have been prepared by the synthesis of cross-linked nucleoside dimers which were converted to phosphoramidites to produce site specific ICL. ICL duplexes containing alkyl chains of four and seven methylene groups were prepared and characterized by mass spectrometry and nuclease digests. Thermal denaturation experiments revealed four and seven methylene containing ICL increased the T(m) of the duplex with respect to the non-cross-linked control with an observed decrease in enthalpy based on thermodynamic analysis of the denaturation curves. Circular dichroism experiments on the ICL duplexes indicated minimal difference from B-form DNA structure. These ICL were used for DNA repair studies with O(6)-alkylguanine DNA alkyltransferase (AGT) proteins from human (hAGT) and E. coli (Ada-C and OGT), whose purpose is to remove O(6)-alkylguanine and in some cases O(4)-alkylthymine lesions. It has been previously shown that hAGT can repair O(6)-2'-deoxyguanosine-alkyl-O(6)-2'-deoxyguanosine ICL. The O(4)-dT-alkyl-O(4)-dT ICL prepared in this study were found to evade repair by hAGT, OGT and Ada-C. Electromobility shift assay (EMSA) results indicated that the absence of any repair by hAGT was not a result of binding. OGT was the only AGT to show activity in the repair of oligonucleotides containing the mono-adducts O(4)-butyl-4-ol-2'-deoxythymidine and O(4)-heptyl-7-ol-2'-deoxythymidine. Binding experiments conducted with hAGT demonstrated that the protein bound O(4)-alkylthymine lesions with similar affinities to O(6)-methylguanine, which hAGT repairs efficiently, suggesting the lack of O(4)-alkylthymine repair by hAGT is not a function of recognition.