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Time Resolved Spectroscopy of Some Aromatic <i>N</i>-Oxide Triplets, Radical Anions, and Related Radicals

Laser flash photolysis (LFP) and time-resolved infrared spectroscopy (TRIR) techniques and density function theory (DFT) calculations were used to investigate the electron-transfer chemistry of the triplet excited states of isoquinoline N-oxide (1), benzocinnoline N-oxide (2), and 4-nitroquinoline N-oxide (3). It was found that neither triplet 1 nor triplet 2 undergoes electron-transfer reactions with typical donors. Rather, they undergo net hydrogen atom transfer (proton-coupled electron transfer) with hydroquinone. Triplet 4-nitroquinoline N-oxide readily undergoes electron-transfer reactions as previously reported, to form the analogous radical anion and hydroradical. The structures of these species were identified by LFP and TRIR techniques with the aid of DFT calculations. The oxygen atom on the N-oxide group was found to be the protonation site of the radical anion of 3

Lifetimes and Reactivities of Some 1,2-Didehydroazepines Commonly Used in Photoaffinity Labeling Experiments in Aqueous Solutions^†

The reactive 1,2-didehydroazepine (cyclic ketenimine) intermediates produced upon photolysis of phenyl azide, 3-hydroxyphenyl azide, 3-methoxyphenyl azide, and 3-nitrophenyl azide in water and in HEPES buffer were studied by laser flash photolysis techniques with UV−vis detection of the transient intermediates. The lifetimes of the 1,2-didehydroazepines were obtained along with the absolute rate constants of their reactions with typical amino acids, nucleosides, and other simple reagents present in a biochemical milieu. The nitro substituent greatly accelerates the bimolecular reactions of the cyclic ketenimines, and the 3-methoxy group greatly decelerates the absolute reactivity of 1,2-didehydroazepines. The intermediate produced by photolysis of 3-hydroxyphenyl azide is much more reactive than the intermediate produced by photolysis of 3-methoxyphenyl azide. We propose that the hydroxyl-substituted 1,2-didehydoazepines rapidly (<10 μs) tautomerize in water to form azepinones and much more rapidly than the corresponding 3-methoxy-substituted cyclic ketenimines undergo hydrolysis. Azepinones react more rapidly with nucleophiles than do methoxy-substituted 1,2-didehydroazepines and are the active species present upon the photolysis of 3-hydroxyphenyl azide in aqueous solution

On the Mechanism of Reaction of Radicals with Tirapazamine

Ketyl radicals produced by photolysis of ketones or di-tert-butyl peroxide (DTBP) in alcohol solvents react rapidly with tirapazamine (TPZ). The acetone ketyl radical (ACOH) reacts with TPZ with an absolute second-order rate constant of (9.7 ± 0.4) × 108 M-1 s-1. The reaction kinetics can be followed by monitoring the bleaching of TPZ absorption at 475 nm or the formation of a reaction product which absorbs at 320 and 410 nm. The ACOD radical reacts with TPZ in 2-propanol-OD with an absolute rate constant of (6.7 ± 0.5) × 108 M-1 s-1, corresponding to a kinetic isotope effect (KIE) of 1.4. Deuteration of the radical on carbon (ACOH-d6) retards the reaction of the radical with TPZ even further (absolute rate constant = (4.8 ± 0.04) × 108 M-1 s-1). This result corresponds to a KIE of 2.0. Radicals derived from dioxane and diisopropyl ether by flash photolysis of DTBP in ethereal solvent react with TPZ more slowly than do ketyl radicals. It is concluded that ketyl radicals react, in part, with TPZ in organic solvents by transfer of a hydrogen atom from the OH and CH3 groups of the ketyl radical to the oxygen atom at the N4 position of TPZ to form acetone or acetone enol and a radical derivative of TPZ (TPZH). The latter species absorbs at 320 and 405 nm, has a lifetime of hundreds of microseconds in alcohol solvents, and decays by disproportionation to form TPZ and a reduced heterocycle. The reduced heterocycle eventually forms a desoxytirapazamine by a polar mechanism. The results are supported by density functional theory calculations. It is proposed that dioxanyl radical will also react, in part, with TPZ by transfer of a hydrogen atom from the carbon adjacent to the radical center to the oxygen atom at the N4 position of TPZ. This produces the enol ether and the previously mentioned TPZH radical. It is further posited that ether radicals react a bit more slowly than ketyl radicals because they lack the second mode of hydrogen transfer (from the OH group) that is present in the ACOH radical. Our data are permissive of the possibility that ether radicals add to TPZ at a rate that is competitive with β-hydrogen atom transfer

Graphical illustration showing the AT- and GC-skew in the protein coding genes of the mitochondrial genome of <i>C</i>. <i>globiceps</i>.

Graphical illustration showing the AT- and GC-skew in the protein coding genes of the mitochondrial genome of C. globiceps.</p

Mass Spectral Profiling of Glycosaminoglycans from Histological Tissue Surfaces

Glycosaminoglycans (GAGs) are found in intracellular granules, cell surfaces, and extracellular matrices in a spatially and temporally regulated fashion, constituting the environment for cells to interact, migrate, and proliferate. Through binding with a great number of proteins, GAGs regulate many facets of biological processes from embryonic development to normal physiological functions. GAGs have been shown to be involved in pathologic changes and immunological responses including cancer metastasis and inflammation. Past analyses of GAGs have focused on cell lines, body fluids, and relatively large tissue samples. Structures determined from such samples reflect the heterogeneity of the cell types present. To gain an understanding of the roles played by GAG expression during pathogenesis, it is very important to be able to detect and profile GAGs at the histological scale so as to minimize cell heterogeneity to potentially inform diagnosis and prognosis. Heparan sulfate (HS) belongs to one major class of GAGs, characterized by dramatic structural heterogeneity and complexity. To demonstrate feasibility of analysis of HS, 15 μm frozen bovine brain stem, cortex, and cerebellum tissue sections were washed with a series of solvent solutions to remove lipids before applying heparin lyases I, II, and III on the tissue surfaces within 5 mm × 5 mm digestion spots. The digested HS disaccharides were extracted from tissue surfaces and then analyzed by using size exclusion chromatography/mass spectrometry (SEC-MS). The results from bovine brain stem, cortex, and cerebellum demonstrated the reproducibility and reliability of our profiling method. We applied our method to detect HS from human astrocytoma (WHO grade II) and glioblastoma (GBM, WHO grade IV) frozen slides. Higher HS abundances and lower average sulfation level of HS were detected in glioblastoma (GBM, WHO grade IV) slides compared to astrocytoma (WHO grade II) slides

Mass Spectrometric Method for Determining the Uronic Acid Epimerization in Heparan Sulfate Disaccharides Generated Using Nitrous Acid

Heparan sulfate (HS) glycosaminoglycans (GAGs) regulate a host of biological functions. To better understand their biological roles, it is necessary to gain understanding about the structure of HS, which requires identification of the sulfation pattern as well as the uronic acid epimerization. In order to model HS structure, it is necessary to quantitatively profile depolymerization products. To date, liquid chromatography–mass spectrometry (LC-MS) methods for profiling heparin lyase decomposition products have been shown. These enzymes, however, destroy information about uronic acid epimerization. Deaminative cleavage using nitrous acid (HONO) is a classic method for GAG depolymerization that retains uronic acid epimerization. Several chromatographic methods have been used for analysis of deaminative cleavage products. The chromatographic methods have the disadvantage that there is no direct readout on the structures producing the observed peaks. This report demonstrates a porous graphitized carbon (PGC)-MS method for the quantification of HONO generated disaccharides to obtain information about the sulfation pattern and uronic acid epimerization. Here, we demonstrate the separation and identification of uronic acid epimers as well as geometric sulfation isomers. The results are comparable to those expected for benchmark HS and heparin samples. The data demonstrate the utility of PGC-MS for quantification of HS nitrous acid depolymerization products for structural analysis of HS and heparin

Reaction of Hydroxyl Radical with Aromatic Hydrocarbons in Nonaqueous Solutions: A Laser Flash Photolysis Study in Acetonitrile

Laser flash photolysis (LFP) of acetonitrile solutions of N-hydroxypyridin-2-thione in the presence of trans-stilbene generates a transient absorbance at 392 nm, attributed to the addition of hydroxyl radical to stilbene. The observed transient absorbance was used in competitive LFP experiments to determine relative rates of reaction for hydroxyl radical with a range of aromatic hydrocarbons in acetonitrile. Structure−reactivity relationships for the reaction of hydroxyl radical with arenes are derived. With these aromatic hydrocarbons, we observe a good correlation between the rates of hydroxyl-radical reaction and the ionization potential of the arene. Kinetic isotope effects are consistent with hydroxyl-radical addition being the dominant reaction pathway with the arene

Surface Tension and Dilational Viscoelasticity of Water in the Presence of Surfactants Tyloxapol and Triton X-100 with Cetyl Trimethylammonium Bromide at 25 °C

Surface tension and dilational viscoelasticity of water in the presence of surfactants Tyloxapol and Triton X-100 with cetyl trimethylammonium Bromide (CTAB) at 25 °C are investigated. The results show that there is synergistic behavior in both the mixtures at higher mole fraction of nonionic surfactant. According to the Rubingh and Rosen theory, the results predict nonideal mixing and attractive interaction between the constituent surfactants in the mixed micelle and layer. By using the Maeda theory, the results suggest the chain−chain interaction among surfactants does not seem to be high. The surface dilational viscoelasticity results show that the Tyloxapol adsorption layer has the highest dilational modulus |ε| value among three single surfactants. Also, it indicates the |ε| maximum values of surfactant mixtures are usually between that of the single surfactant. Moreover, it is worth noting that the |ε| maximum values of Tyloxapol/CTAB mixtures are always higher than those of TX-100/CTAB ones

Characterization of the Complete Mitochondrial Genome Sequence of the Globose Head Whiptail <i>Cetonurus globiceps</i> (Gadiformes: Macrouridae) and Its Phylogenetic Analysis

<div><p>The particular environmental characteristics of deep water such as its immense scale and high pressure systems, presents technological problems that have prevented research to broaden our knowledge of deep-sea fish. Here, we described the mitogenome sequence of a deep-sea fish, <i>Cetonurus globiceps</i>. The genome is 17,137 bp in length, with a standard set of 22 transfer RNA genes (tRNAs), two ribosomal RNA genes, 13 protein-coding genes, and two typical non-coding control regions. Additionally, a 70bp tRNA^Thr-tRNA^Pro intergenic spacer is present. The <i>C</i>. <i>globiceps</i> mitogenome exhibited strand-specific asymmetry in nucleotide composition. The AT-skew and GC-skew values in the whole genome of <i>C</i>. <i>globiceps</i> were 0 and -0.2877, respectively, revealing that the H-strand had equal amounts of A and T and that the overall nucleotide composition was C skewed. All of the tRNA genes could be folded into cloverleaf secondary structures, while the secondary structure of tRNA^Ser(AGY) lacked a discernible dihydrouridine stem. By comparing this genome sequence with the recognition sites in teleost species, several conserved sequence blocks were identified in the control region. However, the GTGGG-box, the typical characteristic of conserved sequence block E (CSB-E), was absent. Notably, tandem repeats were identified in the 3' portion of the control region. No similar repetitive motifs are present in most of other gadiform species. Phylogenetic analysis based on 12 protein coding genes provided strong support that <i>C</i>. <i>globiceps</i> was the most derived in the clade. Some relationships however, are in contrast with those presented in previous studies. This study enriches our knowledge of mitogenomes of the genus <i>Cetonurus</i> and provides valuable information on the evolution of Macrouridae mtDNA and deep-sea fish.</p></div