The intrinsic stabilities and structures of alkali metal cationized guanine quadruplexes.

The structures and stabilities of self-assembled guanine quadruplexes, M(9eG)8+ (M = Na, K, Rb, Cs; 9eG = 9-ethylguanine), have been studied in the gas phase by blackbody infrared radiative dissociation to determine the difference in the stabilizing effect of the alkali metal cations. The order of stabilities to decomposition was determined to be K+ > Rb+ > Cs+ ≫ Na+, which is consistent with the observation of K+ being the ion of choice in guanine quadruplexes in nucleic acids. In the gas phase, the sodiated quadruplex was found to lose one 9eG at a time, whereas the quadruplexes of the heavier cations lost a neutral guanine tetrad. Vibrational spectroscopy on the gas-phase quadruplex ions was consistent with the structures in which the metal cations were sandwiched between two guanine tetrads. Electronic structure calculations are also used to compare with the observed stabilities and vibrational spectra.

Infrared multiphoton dissociation spectra as a probe of ion molecule reaction mechanism: the formation of the protonated water dimer via sequential bimolecular reactions with 1,1,3,3-tetrafluorodimethyl ether.

The gas-phase ion-molecule reactions of 1,1,3,3-tetrafluorodimethyl ether and water have been examined using Fourier transform ion cyclotron resonance mass spectrometry, infrared multiphoton dissociation (IRMPD) spectroscopy, and ab initio molecular orbital calculations. This reaction sequence leads to the efficient bimolecular production of the proton-bound dimer of water (H5O2+). Evidence for the dominant mechanistic pathway involving the reaction of CF2H-O=CHF+, an ion of m/z 99, with water is presented. The primary channel occurs via nucleophilic attack of water on the ion of m/z 99 (CF2H-O=CHF+), to lose formyl fluoride and yield-protonated difluoromethanol (m/z 69). Association of a second water molecule with protonated difluoromethanol generates a reactive intermediate that decomposes via a 1,4-elimination to release hydrogen fluoride and yield the proton-bound dimer of water and formyl fluoride (m/z 67). Last, the elimination of formyl fluoride occurs by the association of a third water molecule to produce H5O2+ (m/z 37). The most probable isomeric forms of the ions with m/z 99 and 69 were found using IRMPD spectroscopy and electronic structure theory calculations. Thermochemical information for reactant, transition state, and product species was obtained using MP2(full)/6-311+G**//6-31G* level of theory.

The reaction of protonated dimethyl ether with dimethyl ether: temperature and isotope effects on the methyl cation transfer reaction forming trimethyloxonium cation and methanol.

Fourier transform ion cyclotron resonance mass spectrometry has been used to study the temperature and deuterium isotope effects on the methyl cation transfer reaction between protonated dimethyl ether and dimethyl ether to produce trimethyloxonium cation and methanol. From the temperature dependence of this bimolecular reaction it was possible to obtain thermodynamic information concerning the energy barrier for methyl cation transfer for the first time. From the slope of an Arrhenius plot, a value for DeltaH(++) of -1.1 +/- 1.2 kJ mol(-1) was obtained, while from the intercept a value for DeltaS(++) of -116 +/- 15 J K(-1) mol(-1) was derived. This yields a DeltaG(++)(298) value of 33.7 +/- 2.1 kJ mol(-1). All thermodynamic values were in good agreement with ab initio calculations. Rate constant ratios for the unimolecular dissociation forming trimethyloxonium cation and the dissociation re-forming reactants were extracted from the apparent bimolecular rate constant. Attempts at modeling the temperature dependence and isotope effects of the unimolecular dissociation forming trimethyloxonium cation were also made.