Singly, doubly and triply deprotonated monosaccharide and disaccharide molecules of the Heparin family of Glycosaminoglycans (GAGs) have been studied in the gas phase to investigate their geometric structures and intrinsic stabilities. Low energy Collision Induced Dissociation (CID) in a quadrupole ion trap was used to investigate the relative stabilities of the systems along with high energy (50-150 keV) Mass Induced Kinetic Energy (MIKE) experiments. The related alkali metal cation complexes were also studied for comparison.\ud The detailed effects of the cations Li+, Na+ and K+ on the stabilities and low energy fragmentation pathways of these highly sulphated isomeric sugars have been determined, allowing suitable ionic fragments to be selected to assist in future analytical studies. High-energy MIKE experiments have provided information rich mass spectra which allow the locations of the biologically crucial sulphate groups to be unambiguously determined and are suggested as an alternative to Electron Detachment Dissociation (EDD).\ud The conformational space available to the prototypical monosaccharide residue Iduronic Acid has been investigated using a combined molecular mechanics and quantum chemical approach. Merck Molecular Force Field 94’ has been utilized to generate candidate structures for higher level B3LYP, PW91PW91, M05-2X and MP2 calculations using the 6-31++G** basis set. This method was used to explore the preferred low energy structures of this highly flexible sulphated sugar around the 1C4, 4C1, 2S0 and 1S5 sugar ring conformations and to assess the suitability of the various methods for studying this class of compounds. This work showed that M05-2X method compared very favourably to the MP2 results, and that it provided improved relative energies over B3LYP. Additionally, the results presented demonstrated the need to study the three dimensional space available to sub conformers when assessing the relative energies of ring conformations.\ud Finally, the CID technique was also used to investigate the Potential Energy Surface of two multiply charged inorganic anions. The Dichromate dianion Cr2O72- was seen to fragment via electron loss and ionic fragmentation. Density Functional Theory was used to determine that the relative barrier height for electron loss was lower than that for ionic fragmentation. The gas phase stability of the Re2X82- (X = Cl, Br) and Re2XnY8-n2- (X = Cl, Y=Br, n=1-3) metal-metal bond complexes were then studied. The ab initio calculations performed for Re2Cl82- and Re2Br82- indicated that Re2Cl82- was intrinsically stable in the gas-phase, while for Re2Br82-, loss of Br- was an exothermic process. However, gas-phase Re2Br82- was rendered metastable due to the presence of the repulsive coulomb barrier on the fragmentation potential energy surface. The intrinsic gas-phase stability displayed by the dirhenium complexes studied indicated that they could be investigated using more quantitative CID measurements to obtain accurate metal-ligand binding energies.\u
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