Quinonoid Structure Research Articles

Inhibition of DNA Polymerases Used in Q-PCR by Structurally Different Soil-Derived Humic Substances

Real-time PCR for the quantitative assessment of microbial genes in DNA extracted from environmental samples is increasingly being used in microbial ecology studies. A significant problem with the quantitative aspect of the method is the possible inhibition of the PCR process by humic substances co-extracted with the DNA. A comparison of the inhibition exerted by five structurally different humic substances on six commercially available DNA polymerases revealed large differences in the resistance of the polymerases to inhibition. Depending on the DNA polymerases (or their formulation) the addition of Bovine Serum Albumin (BSA) to the mastermix reaction generally increased the resistance to the different humic substances and decreased differences between the polymerases. One of the tested polymerases was clearly hampered by the addition of BSA, indicating that BSA cannot be added to just any mastermix to improve enzyme performance. The structural differences in the tested humic acids suggest that the mechanism of the inhibition is not a feature of all organic structures, but mainly related to the presence of certain phenolic or quinonoid structures.

Role of Dihydroquinonoid Formation in Substrate Specificity of Escherichia coli Dihydrofolate Synthetase‐ Folylpolyglutamate Synthetase.

Escherichia coli dihydrofolate synthetase‐folylpolyglutamate synthetase (DHFS‐FPGS) (FolC) catalyzes the ATP‐dependent addition of glutamate to both dihydropteroate and pteroylglutamate substrates. The mechanism used by the enzyme to differentiate between folate and pteroate substrates was investigated using equilibrium binding and rapid‐reaction kinetic techniques, and structural modeling approaches. The absorbance spectrum of dihydropteroate displays a 40 nm red shift upon binding to DHFS‐FPGS· ATP, and the bound dihydropteroate exhibits increased fluorescence. Spectral and steady‐state kinetic data suggests that DHFS‐FPGS·ATP catalyzes the rapid formation of quinonoid dihydropteroate by removal of the N‐3 nitrogen proton and protonation of the C‐6 carbon of dihydropteroate. A similar spectral shift was observed for dihydrofolate when bound to enzyme in the presence of ATP or ADP. Rapid‐reaction kinetic studies demonstrate that the DHFS‐FPGS·ADP catalyzed formation of dihydrofolate quinonoid is associated with a conformational change in the enzyme. The results of this study suggest that the enzyme‐catalyzed formation of the quinonoid structure and the associated conformational change in the enzyme is required for effective DHFS activity but inhibitory for FPGS activity. These studies were supported by NIH R37DK58144 to PJS.

The bromamine acid removal from aqueous solution using electro-Fenton and Fenton systems

The bromamine acid (BA) removal is investigated in the electro-Fenton and Fenton systems. The BA is an important dye intermediate with difficult biodegradation. So removing BA with advanced oxidation processes may provide common information on anthraquinone dye wastewater treatment. BA has a typical quinonoid structure. It means that the degradation of BA may be coupled with a series of quinone–hydroquinone conversion reactions in these two systems. As a result, two distinct degradation processes for BA are shown in the electro-Fenton and Fenton systems. For a Fenton system, the BA degradation is divided into two phases: the BA quickly transforms into a hydroquinone structure (BAH) in the first few minutes probably due to the formation of a ternary HQ–Fe–H2O2 complex, and then the BAH is oxidized by the •OH; While, in the electro-Fenton system, the BAH is not accumulated during its degradation. Fenton reaction is the main reaction in the electro-Fenton system.

Optoelectronic properties of RNA–polyaniline–dendritic gold nanobiocomposite

The in situ reduction of Au+++ by aniline in the presence of RNA produces dendritic Au nanoparticles (AuNP) with the concomitant formation of doped polyaniline (PANI). FT-IR spectra indicate that the dendritic AuNPs are stabilized from the complexation of nitrogen atoms of quinonoid structure of PANI with the adsorbed Au+++ on it. CD spectrum indicates a small distortion of RNA ‘A’ helix toward ‘B’ helix. RNA–PANI–Au nanocomposite shows emission peak at 408nm with an additional peak at 579nm for the Forster resonance energy transfer (FRET) of PANI excitons to surface plasmon band of Au nanocrystals. The dendritic RNA–PANI–Au nanocomposite has three orders higher dc-conductivity compared to the spherical PANI–Au composite. Impedance data suggest that the system behaves as an equivalent parallel resistance–capacitance (R–C) circuit. The frequency dependency of ac-conductivity indicates three regions of conduction: at low frequency predominantly intrachain conduction by polarons of doped PANI, at medium frequency hopping of polarons through RNA and AuNP along with the intra-chain conduction and at very high frequency the conductivity is predominantly interchain due to localized hopping.

Photophysics of DNA staining dye Propidium Iodide encapsulated in bio-mimetic micelle and genomic fish sperm DNA

Photophysical processes in Propidium Iodide (PI), the well known DNA staining dye, have been exploited in homogeneous as well as heterogeneous medium by steady state and time resolved spectroscopy. The DNA staining dye PI exhibits intermolecular proton transfer reaction in aqueous and hydrogen-bonding acceptor solvents due to the formation of quinonoid structure which is acidic in nature. Time resolved emission spectroscopy also predicts the hydrogen bond donor ability of PI. The target dye interacts only with anionic surfactant sodium dodecylsulphate but not with cationic surfactant cetyltrimethylammonium bromide and neutral surfactant Triton X-100 and this interaction is found to be electrostatic in nature. We have further scrutinized the mode of binding of PI with fish sperm DNA. The effect of addition of urea, fluorescence quenching phenomenon, CD measurements reveal that the probe binds to DNA through intercalative style.

Dye-incorporated water-soluble polymer via click triazole formation

A click triazole-polymerization is proposed for the synthesis of a water-soluble polymer dye. 4,4′-Diazidostilbene-2,2′-disulfonate (DASS) sodium salt reacted with a diacetylenic derivative of para-methyl red (PMR) in water, which was catalyzed by copper (I) ion or accelerated under ultrasound irradiation. DASS formed a soluble polymer with a carboxylate salt of PMR showing a water solubility of 120 g/100 mL but it generated an insoluble polymer with an alkyl ammonium salt. The prepared polymeric dye underwent color transition at pH 5–6, which is higher than that of PMR and similar to that of ortho-methyl red (OMR). The quinonoid canonical structure of PMR generated a purple water solution and was dominant in the polymer solution at pH below 5. Intra-molecular hydrogen bonding between the triazoles and azo nitrogens was presumed to have induced the formation of the quinonoid structure. The color change of the polymer was reproducible during successive up/down pH cycles.

Solvation in aqueous binary mixtures: consequences of the hydrophobic character of the ionic liquids and the solvatochromic probes

Information on the solvation in mixtures of water, W, and the ionic liquids, ILs, 1-allyl-3-R-imidazolium chlorides; R = methyl, 1-butyl, and 1-hexyl, has been obtained from the responses of the following solvatochromic probes: 2,6-dibromo-4-[(E)-2-(1-R-pyridinium-4-yl)ethenyl] phenolate, R = methyl, MePMBr2; 1-octyl, OcPMBr2, and the corresponding quinolinium derivative, MeQMBr2. A model developed for solvation in binary mixtures of W and molecular solvents has been extended to the present mixtures. Our objective is to assess the relevance to solvation of hydrogen-bonding and the hydrophobic character of the IL and the solvatochromic probe. Plots of the medium empirical polarity, ET(probe) versus its composition revealed non-ideal behavior, attributed to preferential solvation by the IL and, more efficiently, by the IL–W hydrogen-bonded complex. The deviation from linearity increases as a function of increasing number of carbon atoms in the alkyl group of the IL, and is larger than that observed for solvation by W plus molecular solvents (1-propanol and 2-(1-butoxy)ethanol) that are more hydrophobic than the ILs investigated. This enhanced deviation is attributed to the more organized structure of the ILs proper, which persists in their aqueous solutions. MeQMBr2 is more susceptible to solvent lipophilicity than OcPMBr2, although the former probe is less lipophilic. This enhanced susceptibility agrees with the important effect of annelation on the contributions of the quinonoid and zwitterionic limiting structures to the ground and excited states of the probe, hence on its response to both medium composition and lipophilicity of the IL.

Degradation of 248 nm Deep UV Photoresist by Ion Implantation

Wet processes are gaining a renewed interest for removal of high dose ion implanted photoresist (II-PR) in front-end-of-line semiconductor manufacturing because of their excellent selectivity towards the wafer substrate and gate materials. The selection of wet chemistries is supported by an insight into the resist degradation by ion implantation. In this work, different analytical techniques have been applied for in-depth characterization of the chemical changes in 248 nm DUV PR after arsenic implantation. A radical mechanism of resist degradation is proposed involving cross-linking and chain scission reactions. The cross-linking of the resist is dominant especially for high doses and energies. It leads to significant depletion of hydrogen and formation of carbon macroradicals that recombine to form C-C cross-linked crust. Moreover, formation of αβ-unsaturated ketonic and/or quinonoid structures by cross-linking reactions is suggested. In addition, the dopant species may provide rigid points in the PR matrix by chemical bonding with the resist. For higher doses and energies further dehydrogenation occurs, which leads to formation of triple bonds in the crust. Different π-conjugated structures are formed in the crust by cross-linking and dehydrogenation reactions. No presence of amorphous carbon in the crust is revealed.

Identification of Benzenoid and Quinonoid Structures by Through-Space NMR Shieldings (TSNMRS)

The spatial magnetic properties (through-space NMR shieldings (TSNMRS)) of benzenoid and quinonoid structures (hydroquinone/p-benzoquinone, p-phenylendiamine/p-phenylendiimine, pentacene, and N-containing heteropentacenes) have been calculated by the GIAO perturbation method employing the nucleus-independent chemical shift (NICS) concept of Paul von Rague Schleyer and visualized as isochemical shielding surfaces (ICSS) of various size and direction. The TSNMRS values, thus obtained, can be successfully employed to quantify and visualize the (anti)aromaticity of the compounds studied and to identify readily the existence of benzenoid and quinonoid structures, respectively. As an alternative, computed (as compared with experimental) (1)H chemical shifts can be employed.

Acid‐dyes as corrosion inhibitors for mechanically pretreated aluminum

PurposeThe purpose of this paper is to provide acid‐dyes, known for the dyeing of porous aluminum oxide films, as inhibitors of the corrosion of aluminum in neutral chloride solutions.Design/methodology/approachPotentiodynamic polarization plots are recorded on mechanically pretreated aluminum using a three‐electrode cell containing 0.01 M NaCl solution with or without 0.025 mM of the acid‐dyes monosulfonic methyl orange (MO), disulfonic chromotrop RR (CH), disulfonic alphazurine A (AZ) and trisulfonic light green SF yellowish (LG). The X‐ray fluorescence technique is used in certain cases for the estimation of sulfur net content of the surface of the probes and thus of the concentration of the adsorbed dye.FindingsThe inhibition efficiency of acid dyes on corrosion of mechanically pretreated aluminum seems to be related more to the presence of a following quinonoid structure which probably contributes more to the formation of mono‐ or bi‐dentate compounds with the aluminum cations in the substrate than to the number of sulfonic groups in their molecule. Thus, the triphenylmethane dyes LG and, to a greater extent AZ, having this quinonoid structure means they are more efficient as corrosion inhibitors in near‐neutral chloride solution than the azo dyes MO and CH, that do not have it.Practical implicationsSelected acid‐dyes such as triphenylmethane sulfonic‐dyes, which have found wide application in the dyeing industry, seem to protect aluminum against the corrosive action of chlorides.Originality/valueThis paper is intended to be the nucleus for the electrochemical studies of the effectiveness of acid dyes as corrosion inhibitors for aluminum.

Effect of photoirradiation on the antioxidant properties of secondary resins and asphaltenes

The consequences of photoirradiation of resins and asphaltenes from the heavy catalytically cracked gas oil fraction of a vacuum distillate and heavy pyrolysis tar of straight-run gasoline from Baku crude oil were studied by IR spectroscopy. It was found that exposure to light results in intramolecular rearrangement, leading to the formation of stable polycondensed aromatic functional quinonoid and phenolic structures which exhibit an antiradical activity. The effect of enhancement of the inhibiting activity of resins and asphaltenes as a result of photoirradiation is illustrated by the model test reaction of polystyrene oxidation.

The chemical oxidative polymerization of aniline in water: Raman spectroscopy

AbstractThe structural changes of aniline oligomers and polyaniline, associated with oxidation of aniline with ammonium peroxydisulfate in aqueous solutions without any added acid, were studied. The reaction was quenched at various times and the films deposited on silicon windows have been studied in detail by Raman spectroscopy, at excitation wavelengths 633 and 514 nm. The presence of substituted phenazine structural units, in addition to ordinary benzenoid, quinonoid, and semiquinonoid structures, has been proved by the appearance of characteristic Raman bands at 1645–1630, 1420–1400, 1380–1365, ∼575, and ∼415 cm−1. The remarkable differences of the Raman spectra of oligoanilines, precipitated in the first phase of oxidative polymerization, and polyaniline nanotubes and nanorods, formed in the second stage of reaction, are discussed. Copyright © 2008 John Wiley & Sons, Ltd.

Proton-Coupled Electron Transfer in Ruthenium(II)−Pterin Complexes: Formation of Ruthenium-Coordinated Pterin Radicals and Their Electronic Structures

Ruthenium(II)-pterin complexes were prepared using tetradentate and tripodal tris(2-pyridylmethyl)amine (TPA) and tris(5-methyl-2-pyridylmethyl)amine (5-Me3-TPA) as auxiliary ligands together with 2-(N,N-dimethyl)-6,7-dimethylpterin (Hdmdmp) and 6,7-dimethylpterin (Hdmp) as pterin derivatives for ligands. Characterization was made by spectroscopic methods, X-ray crystallography, and electrochemical measurements. The pterin ligands coordinated to the ruthenium centers as monoanionic bidentate ligands via the 4-oxygen of the pyrimidinone moiety and the 5-nitrogen of the pyrazine parts. The striking feature is that the coordinated dmp- ligand exhibits a quinonoid structure rather than a deprotonated biopterin structure, showing a short C-N bond length for the 2-amino group. Those complexes exhibit reversible two-step protonation for both pterin derivatives coordinated to the ruthenium centers to give a drastic spectral change in the UV-vis spectroscopy. Doubly protonated Ru(II)-pterin complexes were stabilized by pi-back-bonding interaction and exhibited clear and reversible proton-coupled electron transfer (PCET) to give ruthenium-coordinated neutral monohydropterin radicals as intermediates of PCET processes. Those ESR spectra indicate that the unpaired electron delocalizes onto the PCET region (N5-C6-C7-N8) of the pyrazine moiety.

Mn Quinonoid Core‐Rh Quinonoid Shell Organometallic Nanospheres as Atom Economical Semiheterogeneous Catalysts in Carbene Transfer Reactions

Mn quinonoid core/Rh quinonoid shell structures are prepared in a step-by-step manner and characterized by a variety of instrumental analysis techniques. The core/shell nanospheres show better catalytic activities in carbene transfer reaction of EDA than Rh quinonoid nanospheres, because more catalysts can be prepared using the same amount of rhodium metal.

SERS and DFT study of nitroarenes adsorbed on metal nanoparticles

A combined SERS and DFT investigation has been performed for 2-amino,5-nitropyridine (ANP) adsorbed on silver colloidal nanoparticles in order to get a better insight into the adsorption mechanism of ANP on the silver surface. Both B3LYP and B3PW91 functionals were used in the DFT calculations on ANP in the anionic form (ANP −) and on different models of ANP −/silver surface complexes. A mixed basis set 6-311++G **/LANL2DZ was used in the case of the ANP −/Ag + complexes. From the comparison between the experimental and the computational data, it was evinced that ANP is adsorbed on the silver surface in the anionic form with a quinonoid electronic structure through the nitrogen atom of the imino group.

Copolymerization of aniline and 4,4′-diaminodiphenyl sulphone and characterization of formed nano size copolymer

Aniline was copolymerized chemically in presence of five different concentrations of 4,4′-diaminodiphenyl sulphone using potassium persulphate. The copolymer exhibited good solubility in DMF and DMSO. Copolymers were characterized by UV–VIS, FTIR, XRD and SEM studies. The formation of polymer through N–H group was understood from the single N–H stretching vibrational frequency at 3378 cm −1 and bands at 1630 and 1494 cm −1 for quinonoid and benzenoid structures, respectively. The stretching vibration of sulphone S O at 1115 cm −1 clearly indicated the presence of DDS in the copolymer. The X-ray diffraction studies revealed the formation of nano sized crystalline copolymer. When more DDS was incorporated in the copolymer the crystalline nature changed from less to more. The grain size of the copolymer calculated from Scherrer's formula was 83 nm. The nano size copolymer formation was also confirmed through surface morphology (100 nm) studies. The electrical property of the copolymer was studied by four-probe conductivity meter. The synthesized polymers have conductivity of 7.21 × 10 −3 to 2.07 × 10 −3 S cm −1. The voltammetric and spectroelectrochemical results were also presented.

Montmorillonite Clay Nanocomposites of Sulfonic Acid Doped Thermoreversible Polyaniline Gel: Physical and Mechanical Properties

Polyaniline (PANI)−dinonylnaphthalene disulfonic acid (DNNDSA) form a thermoreversible gel when prepared from formic acid medium. Mixing of organically modified montmorillonite (om-MMT) clay during PANI−DNNDSA gel preparation produces the PANI−DNNDSA gel nanocomposites (GNCs). WAXS and TEM pictures indicate GNC-1 (number indicates percentage (w/w) of om-clay in the nanocomposite) has an exfoliated structure, whereas GNC-3 and GNC-5 have an intercalated structure. FTIR spectra indicate an interaction between om-clay and PANI−DNNDSA shifting the QN+H−B or B−N+H−B (Q = quinonoid and B = benzonoid unit of PANI) vibration of quinonoid structure to lower energy. The exfoliated GNC-1 has higher thermal stability than that of the intercalated GNC-3 and GNC-5 samples. The storage modulus (G‘) has increased dramatically on addition of clay to the gel and its relative increase is larger with increase in temperature until the gel melts. The highest increase (445%) of G‘ is observed for GNC-1 at 60 °C. The π band−polaron band position remains unaffected by the addition of clay in the gel and so also the dc conductivity. PANI−DNNDSA gel shows emission at 353 nm when excited with a radiation of 262 nm. But in the GNCs, fluorescence quenching occurs and it is maximum for the exfoliated GNC-1 sample. These GNCs of PANI are easily processable due to its thermoreversible nature.

Application of UV-Vis and resonance Raman spectroscopy to study bleaching and photoyellowing of thermomechanical pulps

Abstract The chemistry of thermomechanical pulp bleaching and brightness reversion was studied. First, UV-Vis reflectance spectroscopy was used to obtain information on the reactive structures in pulp. Based on these data, a Raman excitation wavelength was chosen close to the absorption bands of the chromophores formed to take advantage of the resonance enhancement (resonance Raman spectroscopy). Fluorescence was rejected with a picosecond Kerr gate. The results revealed that coniferyl aldehyde structures were partly removed by alkaline peroxide bleaching and these structures were further degraded during light exposure. However, this reaction was obviously not responsible for chromophore formation in the pulp. On the other hand, based on the resonance Raman spectra, formation of quinonoid structures, possibly para-quinones, was a more prominent explanation for the brightness reversion.

Water-Soluble Multiwalled Carbon Nanotubes Functionalized with Sulfonated Polyaniline

Multiwalled carbon nanotubes (MWNTs) functionalized with a water-soluble conducting polymer, sulfonated polyaniline (SPAN), were prepared by in situ polymerization of aniline followed by sulfonation with chlorosulfonic acid in an inert solvent and by hydrolysis in water. Electron microscopy, laser Raman spectroscopy, X-ray photoelectron spectroscopy, and UV-vis absorption spectroscopy were employed to characterize the morphology and chemical structure of the resulting product. The results show that the quinonoid structure of SPAN preferentially interacts with the nanotubes and is stabilized by strong pi-pi interaction between two components. The structure of MWNTs was not perturbed by the incorporation of SPAN, since the pi-pi interaction between MWNTs and SPAN is much weaker in comparison to that of the carbon covalent bond. The SPAN functionalized MWNTs are highly dispersible in water, thus opening new possibilities for their prospective technological applications.

Koopmans-Based Analysis of the Optical Spectra of p-Phenylene-Bridged Intervalence Radical Ions

[Figure: see text]. The optical spectra of 10 p-phenylene-bridged delocalized intervalence compounds MC6H4M*- or *+ are analyzed using the Koopmans-based method, which considers only transitions from filled orbitals to the singly occupied orbital (SOMO), called Hoijtink type A transitions, and from the SOMO to unoccupied orbitals, Hoijtink type B transitions, and ignores configuration interaction. The radical ions with quinonoid structures, those that form ring-M double bonds with M = C(CN)2, NMe2, 3-oxo-9-azabicyclo[3.3.1], NPPh3, and O when the odd electron of the intervalence oxidation level is removed, are calculated to have the lowest-allowed type B transition lying mostly above the lowest-allowed A transition, with B(i)- A(j) decreasing in the order shown from +14 370 to -1390 cm(-1), and the more intense second-lowest-allowed type B transition B(i) - A(j) from +14 940 to +7070 cm(-1). The five radical anions with benzenoid structures, which form ring-M single bonds with X = CN, CO2Me, CHO, C3HMeBF2O2, and NO2 when the odd electron of the intervalence oxidation level is removed, have a B(i)- A(j) value of the opposite sign that increases in magnitude from -2880 to -17 050 cm(-)(1) in the order shown. Configuration interaction is of course present in the observed spectra, and the predictions ignoring it mostly overestimate transition energies by 1900-2600 cm(-1) for the quinonoid compounds (but by 450 cm(-1) for the M = C(CN)2 radical anion), and by 1000-1400 cm(-1) for the benzenoid compounds (2500 cm(-1) for the M = CN radical anion). The very simple Koopmans-based model is useful for considering the optical spectra of these radical ions.