Reactive ion scattering spectrometry (RISS) utilizing low energy (tens of eV) polyatomic ions was employed to characterize self-assembled monolayers (SAMs) on gold. The terminal composition of halogenated SAMs, chemisorption motifs of disulfide and diselenide SAMs, and electron transfer properties of molecular wire containing SAMs were interrogated to develop the versatility of RISS as an analytical surface characterization technique.Novel halogen terminated SAMs were examined for their ability to convert translational to vibrational energy of colliding projectile ions. A general increasing energy deposition trend correlated with increasing terminal mass with the exception of the iodine functionality. Increased amounts of surface abstractions and sputtering from C12I suggest competitive ion-surface interactions account for less than predicted energy deposition results. Mixed films of CH2Br and CH3 terminal groups elucidated interfacial surface crowding discerned by energy deposition results.Thiol and disulfide based SAMs were shown by RISS comparisons to be dissimilar in structure. Terminal orientation, however, was the same based on ion-surface reactions, disproving the proposed dimer model of disulfide SAMs. Ion-surface reactions and electron transfer properties of disulfide surfaces suggested greater percentages of c(4x2) superlattice structure than in thiol SAMs. Based on increased hydrogen reactivity, decreased methyl reactivity, and increased energy deposition results, diselenide based SAMs were more disordered than S-Au based SAMs. Electron transfer results monitored through total ion currents (TIC) showed Se-Au contacts are more conductive than S-Au attachments.Molecular wire candidates whose electron transfer capabilities are difficult to characterize by traditional techniques were characterized by RISS after being doped into matrix SAMs. Electron transfer properties were dependent on the isolating SAM matrix, dipole moments of the wires, and the potential applied to the surface. Changes in surface voltage dictated molecular wire geometry and electron transfer. Wires were annealed into preferential geometries by colliding ions, but did not operate as switches.While not related to the advancement of RISS, structural elucidation of the pharmaceutical carvidioliol was investigated by collision-induced dissociation, surface-induced dissociation, sustained off-resonance irradiation, and sustained off-resonance irradiation-resonant excitation and through gas-phase hydrogen/deuterium exchange. This molecule fragmented easily by all methods and demonstrated the chemical specificity of gas-phase hydrogen/deuterium exchange experiments.

Low energy (tens of eV) polyatomic cations were used as probes for characterization of monolayers of spontaneously chemisorbed thiols on gold. Characteristics including chemical composition, surface order and orientation of the self-assembled monolayers (SAMs) can be derived by monitoring the products of projectile ion neutralization, surface-induced dissociation (SID), and ion-surface reactions.To study the influence of the terminal group chemical structures and orientations of the SAMs on ion-surface interactions, a series of semi-fluorinated alkane thiols with difluoromethylenes buried underneath hydrocarbon terminal groups were examined (CH3CF2CH2− and CH3CH2CF2−). Compared to terminally fluorinated SAMs, they showed more projectile ion neutralization and less internal to vibrational energy deposition into precursor ions. Projectile ion-hydrocarbon reactions decreased significantly when difluoromethylenes are one or two bonds away from the terminal group. Furthermore, ion-surface reaction results on surfaces with odd and even chain lengths suggested that they have similar terminal methyl orientations to their hydrocarbon counterparts.Mixed monolayers of CF3CF2(CH2)14SH (F-SAMs) and CH3(CH2)15SH (H-SAMs) with systematically changing electron transfer, energy deposition and ion-surface reaction were prepared using mixed thiols solution and micro-contact printing (μ-CP). The solution mixture system showed linear variations in electron transfer and energy deposition with different F-SAM surface concentrations, while non-linear changes occur for ion-surface reaction suggesting strong lateral interactions between the two components. These interactions are minimized in the μ-CP system containing domains of each thiol. Energy deposition on the patterned surfaces varies non-linearly with changing F-SAM concentration which differs from the homogenously mixed system.To explore SID with a 90 collision angle, eV SID of a series of protonated peptide ions were performed in an in-line sector Time-Of-Flight (TOF) mass spectrometer. The results were compared to keV collision-induced dissociation (CID) data collected with the same instrument. Fragmentation efficiency for SID was higher than CID for those peptides. In addition to the excellent control over laboratory collision energies with SID, different amount of energy deposition can be achieved when varying surface composition, e.g. using mixed F-SAM/H-SAM.Reactive ion scattering spectrometry (RISS) results provided more in-depth knowledge of low energy ion-surface interactions that will promote usage of RISS as a novel surface characterization technique.