Electron-transfer oxidation properties of substituted bi-, ter-, and quaterpyrroles

A set of open-chain fully substituted bi-, ter-, and quaterpyrroles bearing analogous substituents in the alpha- and beta-pyrrolic positions were studied as a function of their chain length, subunit number, and size of potential conjugation pathway by means of cyclic voltammetry, EPR, and UV-vis spectroelectrochemistry. A comparison of E1/2 values for the first one-electron abstraction of bipyrrole 1 (1.07 V), terpyrrole 2 (0.67 V), and quaterpyrrole 3 (0.44 V) demonstrate clearly that the longer oligopyrroles are easier to oxidize. A strong absorption band is observed in the visible region when terpyrrole 2 is subject to one-electron oxidation, growing in at 856 nm accompanied by a shoulder at 778 nm. These strong absorptions in the visible region of the spectrum are in sharp contrast with the absence of bands in the red region when the bipyrrole 1 is subject to a similar one-electron oxidation and this can be explained by the presence of a longer conjugation pathway in the singly oxidized forms of 2 as was confirmed by EPR spectroscopy. The EPR spectra of 1*+, 2*+, and 3*+ indicate that the unpaired electron is more delocalized on the pyrroles with a longer conjugation and that the more the unpaired electron is delocalized, the faster is the electron exchange rate.     

Electron-transfer oxidation properties of unsaturated fatty acids and mechanistic insight into lipoxygenases

Rate constants of photoinduced electron-transfer oxidation of unsaturated fatty acids with a series of singlet excited states of oxidants in acetonitrile at 298 K were examined and the resulting electron-transfer rate constants (k(et)) were evaluated in light of the free energy relationship of electron transfer to determine the one-electron oxidation potentials (E(ox)) of unsaturated fatty acids and the intrinsic barrier of electron transfer. The k(et) values of linoleic acid with a series of oxidants are the same as the corresponding k(et) values of methyl linoleate, linolenic acid, and arachidonic acid, leading to the same E(ox) value of linoleic acid, methyl linoleate, linolenic acid, and arachidonic acid (1.76 V vs SCE), which is significantly lower than that of oleic acid (2.03 V vs SCE) as indicated by the smaller k(et) values of oleic acid than those of other unsaturated fatty acids. The radical cation of linoleic acid produced in photoinduced electron transfer from linoleic acid to the singlet excited state of 10-methylacridinium ion as well as that of 9,10-dicyanoanthracene was detected by laser flash photolysis experiments. The apparent rate constant of deprotonation of the radical cation of linoleic acid was determined as 8.1 x 10(3) s(-1). In the presence of oxygen, the addition of oxygen to the deprotonated radical produces the peroxyl radical, which has successfully been detected by ESR. No thermal electron transfer or proton-coupled electron transfer has occurred from linoleic acid to a strong one-electron oxidant, Ru(bpy)3(3+) (bpy = 2,2'-bipyridine) or Fe(bpy)3(3+). The present results on the electron-transfer and proton-transfer properties of unsaturated fatty acids provide valuable mechanistic insight into lipoxygenases to clarify the proton-coupled electron-transfer process in the catalytic function.     

One-step syntheses of alkyl glycosides and alkyl-substituted DNA oligomers by chemoselective glycosidations using DNA bases

The simple and practical synthesis of alkyl glycosides by novel chemoselective glycosidations using natural resources, DNA and RNA nucleosides, was realized, and the one-step synthesis of chemoselectively modified DNA oligomers using the glycosidation method was also demonstrated.     

Selective one-electron oxidation of duplex DNA oligomers: reaction at thymines

The one-electron oxidation of duplex DNA generates a nucleobase radical cation (electron "hole") that migrates long distances by a hopping mechanism. The radical cation reacts irreversibly with H2O or O2 to form oxidation products (damaged bases). In normal DNA (containing the four common DNA bases), reaction occurs most frequently at guanine. However, in DNA duplexes that do not contain guanine (i.e., those comprised exclusively of A/T base pairs), we discovered that reaction occurs primarily at thymine and gives products resulting from oxidation of the T-C5 methyl group and from addition to its C5-C6 double bond. This surprising result shows that it is the relative reactivity, not the stability, of a nucleobase radical cation that determines the nature of the products formed from oxidation of DNA. A mechanism for reaction is proposed whereby a thymine radical cation may either lose a proton from its methyl group or H2O/O2 may add across its double bond. In the latter case, addition may initiate a tandem reaction that converts both thymines of a TT step to oxidation products.     

Chemically-modified graphenes for oxidation of DNA bases: analytical parameters

We studied the electroanalytical performances of chemically-modified graphenes (CMGs) containing different defect densities and amounts of oxygen-containing groups, namely graphite oxide (GPO), graphene oxide (GO), thermally reduced graphene oxide (TR-GO) and electrochemically reduced graphene oxide (ER-GO) by comparing the sensitivity, selectivity, linearity and repeatability towards the oxidation of DNA bases. We have observed that for differential pulse voltammetric (DPV) detection of adenine and cytosine, all CMGs showed enhanced sensitivity to oxidation, while for guanine and thymine, ER-GO and TR-GO exhibited much improved sensitivity over bare glassy carbon (GC) as well as over GPO and GO. There is also significant selectivity enhancement when using GPO for adenine and TR-GO for thymine. Our results have uncovered that the differences in surface functionalities, structure and defects of various CMGs largely influence their electrochemical behaviour in detecting the oxidation of DNA bases. The findings in this report will provide a useful guide for the future development of label-free electrochemical devices for DNA analysis.     

Synthesis and properties of DNA oligomers containing 2'-deoxynucleoside N-oxide derivatives

Cytosine and adenine N-oxide derivatives have long been known as products resulting from the oxidative damage of DNA by peroxides such as hydrogen peroxide. Although the synthesis and properties of 2'-deoxynucleoside N-oxide derivatives have been well described, little has been reported about the chemical and biochemical behavior of initially formed DNA oligomers containing these N-oxide bases. In this study, we established a convenient method for the solid-phase synthesis of oligodeoxynucleotides incorporating 2'-deoxycytidine N-oxide (dC O) or 2'-deoxyadenosine N-oxide (dA O) by using the postsynthetic oxidation of N-protected DNA oligomers except for the target dC or dA site with m-CPBA in MeOH in a highly selective manner. In this strategy, the benzoyl, phthaloyl, and (4-isopropylphenoxy)acetyl groups proved to serve as base protecting groups to avoid oxidation of adenine, cytosine, and guanine, respectively, at the unmodified sites.     

Electron-transfer oxidation of dioxenes. An example of radical cation disproportionation

Tris(p-bromophenyl ammoniumyl) tetrafluoroborate induces an easy electron-transfer process on dioxenes leading quantitatively to the corresponding α-diketones. A mechanism involving the disproportionation of the intermediate radical cations is discussed.     

Sequential electrochemical oxidation of alternating benzene-furan oligomers

Electrochemical oxidation of pentaaryl 2 containing two furan moieties occurs sequentially to give diketone 8 after two-electron transfer. Further oxidation with another two-electron transfer gives the corresponding tetraketone 9. Radical cation intermediate is detected by absorption spectroscopy. The radical intermediates of different regiochemistry have been shown to exhibit different oxidation potentials as revealed by the differential pulse voltammetry.     

Synthesis and properties of tetrazole-containing oligomers

Linear, star-shaped, and hyperbranched oligomeric compounds containing tetrazole cycles in the main chains are synthesized via the polycondensation (polyalkylation) of N-H unsubstituted bis(tetrazoles), tris(tetrazoles), and tetrakis(tetrazoles) with compounds containing mobile halogen atoms. Some properties of the oligomers are studied. Some of the oligomers are characterized by high density and a large content of nitrogen.     

Thermal desorption behavior and binding properties of DNA bases and nucleosides on gold

A comparison of the binding of DNA bases (adenine, cytosine, guanine, and thymine) and nucleosides (2'deoxyadenosine, 2'deoxycytidine, 2'deoxyguanosine, and thymidine) to gold thin films is presented. Desorption of monolayer/submonolayer and multilayer films of the adsorbates on gold studied via temperature-programmed desorption (TPD) and reflection-absorption infrared (RAIR) spectroscopy reveals that there are major differences in the binding affinities of the different bases to gold, for example, thymine DeltaHdes = 111 +/- 2 kJ/mol compared to guanine DeltaHdes = 146 +/- 2 kJ/mol. The differences can be rationalized by molecular structures of the bases and their binding modes to gold surfaces deduced from IR data. Similar trends in desorption energies, shifted to lower desorption energy by more than 10 kJ/mol, are observed for deoxynucleoside layers on gold thin films.     

Liquid properties of oligomers. Comparison of relaxational properties of propylene glycol oligomers with those of ethylene glycol oligomers

Liquid properties such as dielectric relaxation and viscous flow of the two structurally homologous propylene glycol oligomers HO(CH(CH₃)CH₂O)_nH (n=1, 2, 3, 4, 5 and 34) and ethylene glycol oligomers HO(C₂H₄O)_nH (n=1, 2, 3, 4, 5 and 6) are studied in pure liquid state to clarify the degree of polymerization dependences of chain molecules on their liquid properties. These oligomers are, at room temperature, viscous liquid which shows dielectric relaxations in the frequency range from 10 Hz to 3 MHz. Propylene glycol oligomers (n=from 1 to 5) show the Davidson-Cole-type relaxations, but the higher glycol (n=34) shows superposition of the two different relaxations, i. e., small Debye-type relaxation in the lower-frequency region and large principal Havriliak-Negami-type relaxation in the higher-frequency region. Relaxation times vs. degree of polymerization do not increase linearly, but vary in zigzag lines. Above all, the dimers (dipropylene glycol and diethylene glycol) show longer relaxation times than the other glycols. This dielectric result does not agree with the degree of polymerization dependence of viscous flow.     

Conformational properties of thiophene oligomers

The molecular geometries and the torsional potentials about the inter‐ring C‐C bond in α‐oligothiophenes (α‐nTh, n=2–4) have been calculated by means of conventional ab initio and density functional theory (DFT) calculations employing the hybrid B3LYP and BH&HLYP functionals. The position and the energetics of the critical points in the potential energy curve generated by rotation about the inter‐ring C? C bond are shown to be dependent on the computational method. DFT calculations, in comparison with MP2 calculations, favour conjugative interactions, while steric and coulombic interactions are equally treated by both methods. On oligomerization the electron delocalisation increases slightly, the p‐charge being preferentially confined within the rings, although it is sufficient to move the molecular structure towards co‐planarization and to increase the barrier through the perpendicular conformation. The IR and Raman spectra on the relevant rotamers of α‐2Th have been computed at HF/6–31G* and B3LYP/6–31G* levels. The comparison with the experiment is excellent. It has been found that small twisting from the planar conformation has no apparent effects, while 90° twisting and isomerization to the syn‐gauche form produce significant frequency and intensity variations which could be useful probes in conformational studies. The simulated IR and Raman spectra of the α‐2Th rotamers are consistent with a smallπ‐electron delocalisation between the rings.     

Number of graphene layers exhibiting an influence on oxidation of DNA bases: Analytical parameters

This article investigates the analytical performance of double-, few- and multi-layer graphene upon oxidation of adenine and guanine. We observed that the sensitivity of differential pulse voltammetric response of guanine and adenine is significantly higher at few-layer graphene surface than single-layer graphene. We use glassy carbon electrode as substrate coated with graphenes. Our findings shall have profound influence on construction of graphene based genosensors.     

Synthesis and paramagnetic properties of polytelluride oligomers

Organotellurium oligomers with different lengths of the telluride fragments and hydrocarbon chains were synthesized by reactions of tellurium with organic dihalogen derivatives in the system hydrazine hydrate-KOH. Oligomers containing two and three contiguous tellurium atoms in the solid state give rise to strong ESR signals with a g value of 2.005–2.030 and a line width of 180–290 Oe. The possibility for formation of tellurium-centered radicals is discussed. Nitrosodurene as radical scavenger in chloroform solution trapped neither primary radical species nor radical products derived therefrom.     

The metal complexes of new Schiff bases containing phosphonate groups and catalytic properties for alkane oxidation

In this study, two new salicylidene phosphonate ligands (HL¹ and HL²) and their metal complexes (Cu²⁺, VO²⁺ and La³⁺) were synthesized and characterized by spectroscopic and analytical methods. The molecular structure of the ligand HL¹ was determined by single‐crystal X‐ray diffraction study. In the structure of the ligand, there is an intramolecular phenol‐imine hydrogen bond. The synthesized compounds exhibit only one emission maximum upon excitation at 270–295  nm range. Complexation of the Schiff base ligands with metal ions did not cause a considerable quenching effect. Finally, the complexes prepared were used as catalysts in cyclohexane oxidation under microwave irradiation. The complexes showed high conversion rates (> 90%) for cyclohexane oxidation; however, poor selectivity was observed for all complexes. The La³⁺ complexes showed better selectivity for cyclohexane → cyclohexanol transformation with about 45% selectivity.     

On-chip electrophoretic accumulation of DNA oligomers and streptavidin

A micro-chamber for electrophoretic accumulation of charged biomolecules has been designed and evaluated. The system is based on a chip with an array of planar focusing electrodes. Particular attention was devoted to a design which enables penetration of a large sample volume by the electric field of the focusing electrodes. General design principles for a cylindrically symmetrical arrangement of the focusing electrodes were derived. Accumulation of DNA oligomers and streptavidin in aqueous solution was demonstrated. The concentration of biomolecules in the centre of the chip was enhanced by up to a factor of 200. The major fraction of the total charge delivered during electrophoretic accumulation results from Faradaic processes. The maximum charge density deliverable without visible gas formation was determined. By careful control of the voltage and current density applied to the electrodes, evolution of gas bubbles could be avoided for the time required to accumulate analyte molecules in the centre of the micro-chamber. On-chip electrophoretic accumulation of biomolecules can be applied to sample pre-conditioning in lab-on-a-chip devices for analysis of DNA and protein samples.     

Efficient and improved synthesis of triazole-linked DNA (DNA) oligomers

A method for the synthesis of triazole-linked DNA oligomers has been revisited to incorporate a reliable protective group and linker for solid-phase synthesis. The new solid-phase synthesis allowed the preparation of oligomers with the efficiency of elongation reaching over 90%.     

Size-expanded DNA bases: an ab initio study of their structural and electronic properties

The size-expanded DNA bases, xA, xC, xG, and xT, are benzo-homologue forms of the natural DNA bases; i.e., their structure can be seen as the fusion of a natural base and a benzene ring. Recently, a variety of DNAs, known as xDNAs, have been synthesized in which size-expanded and natural bases are paired. In this paper we use second-order M?ller-Plesset perturbation theory and density functional theory to investigate the structural and electronic properties of xA, xC, xG, and xT and their natural counterparts. We find that whereas natural and size-expanded bases have both nonplanar amino groups the latter have also nonplanar aromatic rings. When density functional theory is used to investigate the electronic properties of size-expanded and natural bases, it is found that the HOMO-LUMO gap of the size-expanded bases is smaller than that of the natural bases. Also, xG should be easier to oxidize than G.