The effect of impurities on the analysis of single-stranded DNA oligomers by the technique of matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry has been studied using the matrix 3-hydroxypicolinic acid and 355-nm pulsed light. By mixing the DNA oligomers with different concentrations of impurities and recording mass spectra, limits are set on the tolerable level of a given impurity in a sample. The tolerance limits for sodium chloride, potassium chloride, sodium acetate, sodium fluoride, sodium dodecyl sulfate (SDS), and manganese(II) chloride were found to be approximately 10(-2) M. It was found that magnesium salts degraded the mass spectrum at much lower levels of 10(-4) M. The organic compounds tris(hydroxymethyl)aminomethane (Tris), urea, dithiothreitol (DTT), glycerol, and ethylenediaminetetraacetic acid (EDTA), when present as its ammonium salt, were tolerable at concentrations into the range of 0.25-0.5 M, while the organic polyamine compound spermine substantially degraded the mass spectrum at concentrations above 10(-2) M. When comparing these results for DNA analysis with previously reported limits for protein analysis, large differences are seen for some of the impurities tested.

The product branching ratios from the infrared multiple-photon dissociation (IRMPD) of a series of tertiary alkoxides are examined and an overall order for the relative acidities of several alkyl groups is inferred. Comparison with the order of acidities derived from a similar silane system reveals an overall similarity, although small differences exist. A model system, the reaction of phenyltrimethylsilane plus hydroxide to give either benzene or methane, is studied more closely. Analysis of the energetics of the alkoxide system and the silane system using statistical reaction rate theory (RRK and RRKM) reveals differences between the mechanisms of decomposition for the systems. These discrepancies between the known, experimental product ratio and the energetics suggest that the transition state of pentacoordinate hydroxysilane anion decomposition has concerted, albeit polar character. Decomposition of the pentacoordinate adduct formed by the reaction of methoxide plus phenyltrimethylsilane is consistent with this suggestion. Caution should be used when inferring the relative acidities of alkyl groups from kinetic methods when assumptions of the decomposition mechanism have not been validated.

The unimolecular rearrangement reactions of the isomeric enolate ions of 2-butanone have been investigated using Fourier transform ion cyclotron resonance mass spectrometry and infrared multiple photon activation techniques. The individual isomers of 2-butanone enolate ions were generated from the corresponding trimethylsilyl enol ethers and photodissociated independently. Infrared multiple photon activation of the 2-butanone enolate ions induces a 1,3-hydrogen rearrangement which interconverts the individual isomers. Because infrared multiple photon activation only involves vibrational excitation, the 1,3-hydrogen rearrangement must be a thermal reaction and occur on the ground electronic state potential energy surface. The observation of a 1,3-hydrogen rearrangement is unexpected and appears to violate the Woodward-Hoffmann symmetry rules. Orbital correlation diagrams show, however, that thermal suprafacial 1.3-hydrogen rearrangements are allowed for enolic systems. Nevertheless, a more probable reaction mechanism involves the rotation of the methylene groups so that the 1,3-hydrogen rearrangement corresponds to a simple proton transfer between two unsaturated carbons.

No abstract