UC Riverside

Hydrogen bonds range from those observed between neutral partners (such as water molecules) to ionic hydrogen bonds (where a charge is associated with either the hydrogen bond donor or hydrogen bond acceptor). This dissertation explores the formation and stabilization of ionic hydrogen bonding species in: mono- and diprotonated polyamines, cytosine and isocytosine proton-bound dimers (PBDs), and protonated nucleosides.

Vibrational spectra of two polyamines, capable of forming N-H+…O and N-H+…N intramolecular hydrogen bonds, are recorded using IR Multiple Photon Dissociation (IRMPD) in the fingerprint and CH/NH/OH stretching domain. Density functional theory (DFT) calculations (B3LYP/6-311++G** level) were utilized to predict dissociation pathways of each charged species in the gas phase. Experimental IRMPD spectra of the two polyamines are plotted against their deuterated analogs. Bands that are present in the protonated spectrum but absent in the deuterated spectrum were assigned to be motions associated with the bridging proton.

13C and 15N solid state NMR spectra of 1-methylcytosine PBD salts suggest the bridging proton is shared unequally between the two nucleobases, resulting in an asymmetrical unit. X-ray diffraction shows two different crystal structure dimensions and morphology of 1-methylcytosine PBD iodide salt with one being identical to 1-methylcytosine PBD iodide salt-d5. Inelastic neutron scattering (INS) spectra compared completely protonated PBDs with deuterated analogs of 1-methylcytosine PBD iodide salt and revealed bands potentially corresponding to methyl torsions and N-H bends.

Proton affinities of nucleosides along with the IRMPD spectra of their protonated analogs in the CH/NH/OH domain are presented. DFT calculations (at B3LYP/6-311++G**) were utilized to predict the favored protonation sites. Partial deuteration experiments suppress combination bands and overtones of fundamental bands that are otherwise present in the CH/NH/OH domain. Conformation of the furanose ring prefers the South orientation for all three protonated nucleosides

Three target molecules are presented and their different synthetic pathways are outlined to achieve each target molecule. The three target molecules are modified cytosine and isocytosine derivatives and upon protonation, both molecules are capable of forming proton-bound dimer with either neutral or protonated cytosine and itself.