Effects of chain flexibility and cationizing agent on the gas-phase conformations of a series of polyethers were studied. Collision cross-sections of poly(propylene glycol) (PPG) and poly(tetramethylene glycol) (PTMEG) oligomers (from the 5-mer to 14-mer) cationized by sodium were measured using ion mobility methods and compared to earlier work on sodiated poly(ethylene glycol) (PEG). Molecular mechanics/dynamics calculations show that all three polyethers form a ring of oxygen atoms around Na+, coordinating additional oxygens to the cation from above and/or below this ring. However, the number and arrangement of these oxygens are system dependent. Up to 8 oxygens in PEG coordinate Na+, but that number drops to 7 for PPG and 6 for PTMEG. The difference is attributed to changes in the structural details of the ring as well as the position of the Na+ ion in that ring. Molecular mechanics/dynamics calculations were also used to investigate the structures of neutral PPG and PTMEG oligomers. In these cases, the oligomers are relatively compact below 200 K but they suddenly unfold into more extended structures between 200 and 300 K.

The gas-phase conformations of a series of cytosine/guanine DNA duplexes were examined by ion mobility and molecular dynamics methods. Deprotonated duplex ions were formed by electrospray ionization, and their collision cross sections measured in helium were compared to calculated cross sections of theoretical models generated by molecular dynamics. The 4-mer (dCGCG) and 6-mer (dCGCGCG) duplexes were found to have globular conformations. Globular and helical structures were observed for the 8-mer (dCGCGCGCG) duplex, with the globular form being the more favored conformer. For the 10-mer (dCGCGCGCGCG), 14-mer (dCGCGCGCGCGCGCG), and 18-mer (dCGCGCGCGCGCGCGCGCG) duplexes, only helical structures were observed in the ion mobility measurements. Theory predicts that the helical structures are less stable than the globular forms in the gas phase and should collapse into the globular form given enough time. However, molecular dynamics simulations at 300 K indicate the helical structures are stable in aqueous solution and will retain their conformations for a limited time in the gas phase. The presence of helical structures in the ion mobility experiments indicates that the duplexes retain "solution structures" in the gas phase on the millisecond time scale.

Lipids in Escherichia coli and Bacillus subtilis were analyzed by matrix-assisted laser desorption/ ionization time-of-flight (MALDI-TOF) mass spectrometry and TOF/TOF tandem mass spectrometry. Lipids were extracted from bacterial cells using an equal volume mixture of dichloromethane, ethanol, and water, which formed a biphasic system with the lipids in the organic layer. The resulting mass spectra of the extracts from both bacteria showed a series of peaks corresponding to sodiated phospholipids -primarily phosphatidylethanolamines (PE) and phosphatidylglycerols (PG). The relative amounts of the phospholipids and the fatty acid compositions inferred from the spectra were in good agreement with previously reported values from GC/MS and thin-layer chromatography studies. E. coli and B. subtilis were easily differentiated by dissimilarities in the composition and relative amounts of the phospholipids present as well as by the presence of lysyl-phosphatidylglycerol and diglucosyl diglycerides solely in the B. subtilis mass spectra. Changes in lipid content in the bacteria during their growth phases were also monitored. In E. coli, the spectra indicated an increase in the amount of the unique C cy-17 fatty acid (in which the fatty acid chain contains a cyclopropane ring) formed during exponential growth. During stationary growth, the spectra indicated an increase in the amount of saturated fatty acids. In B. subtilis, the phospholipid composition remained relatively unchanged during exponential growth, but the amount of PG slightly decreased while the amount of PE slightly increased during stationary growth. No significant changes were observed for the lysyl-phosphatidylglycerols or glycolipids during the exponential or stationary growth phases.

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