Decorated Ru/Au(111) and Os/Au(111) surfaces: An in situ STM and electrochemistry study

The structure and reactivity of bimetallic electrodes obtained by spontaneous deposition of Ru and Os on Au(111) single-crystal surfaces are studied. In situ electrochemical STM and cyclic voltammetry are used to characterize a wide range of surface morphologies thus produced. The STM results on Ru/Au(111) demonstrate a pronounced step decoration, while a random distribution of Ru nuclei, quite uniform in size, occurs on terraces. Osmium deposits show a slight preference for deposition on steps, but it also occurs readily on terraces. However, many of the Os islands grow into multilayer heights. The coverage of the Au(111) by the deposited Ru or Os islands for a particular solution concentration depends on the deposition time. Nanostructures of Ru and Os are tested for catalytic behavior and correlated to CO oxidation activity as measured by CO stripping voltammetry. Published in Russian in Elektrokhimiya, 2006, Vol. 42, No. 11, pp. 1385–1392. Based on the report delivered at the 8th International Frumkin Symposium “Kinetics of the Electrode Processes,” October 18–22, 2005, Moscow. The text was submitted by the authors in English.     

The pseudouridine synthases: revisiting a mechanism that seemed settled

RNA containing 5-fluorouridine, [f 5U]RNA, has been used as a mechanistic probe for the pseudouridine synthases, which convert uridine in RNA to its C-glycoside isomer, pseudouridine. Hydrated products of f 5U were attributed to ester hydrolysis of a covalent complex between an essential aspartic acid residue and f 5U, and the results were construed as strong support for a mechanism involving Michael addition by the aspartic acid residue. Labeling studies with [18O]water are now reported that rule out such ester hydrolysis in one pseudouridine synthase, TruB. The aspartic acid residue does not become labeled, and the hydroxyl group in the hydrated product of f 5U derives directly from solvent. The hydrated product, therefore, cannot be construed to support Michael addition during the conversion of uridine to pseudouridine, but the results do not rule out such a mechanism. A hypothesis is offered for the seemingly disparate behavior of different pseudouridine synthases toward [f 5U]RNA.     

Characterizing DNA photo-oxidation reactions by high-resolution mass measurements with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

High-resolution mass measurements by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry were employed to characterize laser-induced oxidation of guanine in a small synthetic deoxyoligonucleotide. The oligonucleotide was exposed to high-intensity UV radiation at 266 nm to produce modifications on the guanine base. The primary product showed a +16 Da mass shift relative to the original strand, whereas secondary products showed mass shifts of +32 and +34 Da. The mass shift of the primary product is consistent with an 8-oxoguanine modification. However, the reactivity of the primary product with hot piperidine and other secondary oxidizing agents was different from that of a synthetic oligonucleotide containing 7,8-dihydro-8-oxo-2'-deoxyguanine (8-oxoG). Based upon the results, a new reaction scheme involving the formation of an epoxide ring across the C-4 and C-5 positions by UV laser-induced oxidation is suggested. The results also illustrate the ability of MALDI to characterize chemical reactivity rapidly at the a low picomolar level.     

On the relationship of amino acid composition to silver staining of proteins in electrophoresis gels: II. Peptide sequence analysis.

The quantification of proteins in silver-stained electrophoresis gels has been limited by the differences in "stainability" of different proteins. Despite efforts by many researchers, the precise basis of the reaction between silver reagents and polypeptides is still unclear, and, depending on the formulation, may even differ. We have tested the hypothesis that differences in stainability among proteins can be attributed to differences in di- or tripeptide composition. The results indicate that some order of protein structure other than short peptides accounts for the staining differences observed.     

Polymerization of pyromellitic dianhydride with 3,3′-diaminobenzidine in aprotic solvents II. Dilute solution studies

Solution properties were determined for the poly(amide acid amine) obtained from the room-temperature polymerization of pyromellitic dianhydride with 3,3,-diaminobenzidine in aprotic solvents. Membrane osmometry data, viscosity studies, solution aging studies, and pH–viscosity relationships were given. Anomalous upswings in viscosity–concentration plots were attributed to absorption or capillary wall effects and not to polyelectrolyte effects, such as were induced by addition of strong bases. Similar absorption effects were found with polyamic acid solutions, in contrast to earlier reports that these polyimide precursors were polyelectrolytes. Unfavorable storage characteristics of the polymer solutions were explained by aging studies which showed that at 25°C dilute solutions exhibited a rapid drop in viscosity; in concentrated solution a slow increase to gelation was observed.     

Chromatographic analysis of sagebrush monoterpenes in blood plasma

An analytical method is required for the analysis of monoterpenes in animal plasma to support a pharmacokinetic study. Monoterpenes common to sagebrush are extracted from sheep plasma by employing solid-phase extraction (SPE), followed by analysis of the extracts by gas chromatography with flame ionization detection. The analytes are quantitated versus an external standard and by comparison with a surrogate standard added to the sample prior to extraction. In addition to comparing the two quantitative methods, the storage stability of the analytes in plasma and SPE columns is evaluated. Both methods employed for quantitation yield precision suitable for pharmacokinetic studies. However, determination of monoterpenes residues versus external standards produces improved accuracy as compared with use of the surrogate standard. Some analyte loss is observed from plasma samples stored for five weeks at -12 degrees C. However, storage of extracts on the SPE columns affords excellent stability.     

Two new octahedral/pyramidal frameworks containing both cation channels and lone-pair channels: syntheses and structures of Ba2MnMn2(SeO3)6 and PbFe2(SeO3)4

The hydrothermal syntheses, single crystal structures, and some properties of Ba₂Mn^IIMn₂^III(SeO₃)₆ and PbFe₂(SeO₃)₄ are reported. These related phases contain three-dimensional frameworks of vertex (FeO₆) and vertex/edge linked (MnO₆) octahedra and SeO₃ pyramids. In each case, the MO₆/SeO₃ framework encloses two types of 8 ring channels, one of which encapsulates the extra-framework cations and one of which provides space for the Se^IV lone pairs. Crystal data: Ba₂Mn₃(SeO₃)₆, M_r=1201.22, monoclinic, P2₁/c (No. 14), a=5.4717 (3) Å, b=9.0636 (4) Å, c=17.6586 (9) Å, β=94.519 (1)°, V=873.03 (8) Å³, Z=2, R(F)=0.031, wR(F²)=0.070; PbFe₂(SeO₃)₄, M_r=826.73, triclinic, (No. 2), a=5.2318 (5) Å, b=6.7925 (6) Å, c=7.6445 (7) Å, α=94.300 (2)°, β=90.613 (2)°, γ=95.224 (2)°, V=269.73 (4) Å³, Z=1, R(F)=0.051, wR(F²)=0.131.     

Structure and behavior of organic analytical reagents : Stability of chelates of 2-(o-hydroxyphenyl)-benzimidazole and analogous reagents1

Stabilities of chelates of 2-(o-hydroxyphenyl)-pyridine, 2-(o-hydroxyphenyl)-quinoline, 1-(o-hydroxyphenyl)-isoquinoline, 2-(o-hydroxyphenyl)-benzimidazole, and 2-(o-hydroxyphenyl)-imidazoline were determined by the Calvin-Bjerrum potentiometric titration technique. The results have been interpreted in terms of steric considerations.     

Sequence-specific fragmentation of benzyloxycarbonyl dipeptides by resonance-enhanced multiphoton ionization

The mechanism of fragment ion formation in resonance-enhanced multiphoton ionization (REMPI) of benzyloxycarbonyl (CBZ)-derivitized dipeptides is presented. At 266 nm, the entire multiphoton process can be thought of as a two-part scheme where ionization occurs by resonant two-photon ionization followed by photodissociation of the created ions. When the energy of two photons exceeds the molecular ionization energy by a significant amount, REMPI has the advantage of producing both parent ions and low appearance energy fragments in large amounts. For CBZ dipeptides, resonant two-photon ionization at 266 nm produces parent ions as well as A type sequence ions with high abundance. On the other hand, a three-photon process (resonant two-photon ionization followed by parent ion photodissociation) forms sequence-related ions which also involve complex fragmentations of the CBZ chromophore. These results are compared to mass spectra obtained by other ionization/dissociation methods and to REMPI mass spectra of related compounds. Factors related to molecular structure elucidation based upon REMPI mass spectra are discussed. Enhanced isomer distinction is demonstrated for CBZ-leu-ala-OCH₃ and CBZ-ile-ala-OCH₃ based upon REMPI fragmentation.     

CHARACTERIZATION OF THE PHOTOREACTION BETWEEN DNA AND AMINOMETHYL-TRIMETHYLPSORALEN USING ABSORPTION AND FLUORESCENCE SPECTROSCOPY

–The use of absorption and fluorescence spectroscopy for following the progress of the photo-reaction between DNA and 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT) has been investigated. Absorption at long wavelengths and fluorescence both decline upon intercalation of AMT into the DNA helix. The loss of fluorescence from AMT and the accompanying appearance of monoadduct fluorescence upon irradiation by UV light can be easily followed by using the excitation beam of a spectro-fluorometer as the source of irradiation and monitoring the changing emission spectrum. Where cross-link formation is possible, the subsequent decline of monoadduct fluorescence is seen as well. This suggests that the 4,5-tnonoadduct is a precursor of cross-links. Both monoaddition and cross-linking are more rapid with poly d(A·T) than with calf thymus DNA or poly d(A·T). Excitation spectra can be helpful in resolving the levels of AMT and 4',5'-monoadduct when both are contributing to the emission spectrum. Some changes are observed in the emission spectrum of AMT–poly d(A·T) monoadducts after prolonged irradiation which indicate further photoreaction.