IM-MS is a 2-D technique which provides separations based on ion shape (ion-neutral collision cross-section, Ω) and mass (m/z ratio). Ion structures can be deduced from the measured collision cross-section (Ωmeas) by calculating the collision cross-sections (Ωcalc) of candidates generated by molecular dynamics (MD) and compared with the experiment results. A database of Ωs for singly-charged peptide ions is presented. Standard proteins are digested using different enzymes (trypsin, chymotrypsin and pepsin), resulting in peptides that differ in amino acid composition. The majority (63%) of the peptide ion correlates well with the globular structures, but some exhibit Ωs that are significantly larger or smaller than the average correlation. Of the peptide ions having larger Ωs, approximately 71% are derived from trypsin digestion and most of the peptide ions that have smaller Ωs are derived from pepsin digestion (90%). We use computational simulations and clustering methods to assign backbone conformations for singly-protonated ions of the model peptide (NH2-Met-Ile-Phe-Ala-Gly-Ile-Lys-COOH) formed by both MALDI and ESI and compare the structures of MIFAGIK derivatives to test the ‘sensitivity’ of the cluster analysis method. Cluster analysis suggests that [MIFAGIK + H]+ ions formed by MALDI have a predominantly turn structure even though the low energy ions prefer partial helical conformers. Although the ions formed by ESI have Ωs that are different from those formed by MALDI, the results of cluster analysis indicate that the ions backbone structures are similar. Chemical modifications (N-acetyl, methylester, as well as addition of Boc or Fmoc groups) of MIFAGIK alter the distribution of various conformers, the most dramatic changes are observed for the [M + Na]+ ion, which show a strong preference for random coil conformers owing to the strong solvation by the backbone amide groups. Ωmeas of oligodeoxynucleotides in different length have been measured in both positive and negative modes. For a given molecular weight and charge state, Ωmeas of the oligodeoxynucleotide ions are smaller than those of the peptides, indicating their different packing efficiency. A novel generalized non-Boltzman sampling MD has been utilized to investigate the gas-phase ion conformations of dGGATC based on the free energy values. Theory predicts only one low-energy conformer for the zwitterionic form of dGGATC- while dGGATC+ ions have several stable conformers in both canonical and zwitterionic form in the gas phase, in good agreement with the experiment.

Carbon nanotubes have received considerable attention since their discovery due to their novel properties. They have potential application areas in physics, chemistry and biology. Arc discharge, laser furnace, chemical vapor deposition and floating catalyst methods are the most commonly used methods to produce carbon nanotubes. Although carbon nanotubes have superior properties compared to other materials, they could not be used widely. The main reasons of this are that continuous and large scale production of carbon nanotubes could not be achieved and impurities have to be removed. To solve these problems more information about formation of carbon nanotubes has to be known. In this study concentration profiles of reactant and byproducts in a cylindrical reactor are investigated during carbon nanotube production. A special probe to collect gas samples along the reactor and samples loops to store the gas samples were designed and constructed. Gas samples were analyzed one by one in GC/MS. Experiments were done with and without catalyst at same experimental conditions. Thus, effects of catalyst on concentration profiles of chemicals were analyzed. To produce carbon nanotubes more acetylene was used compared to amount of acetylene used in pyrolysis. Increasing reaction temperature from 800&deg / C to 875&deg / C caused decomposing more acetylene and producing more carbon nanotubes. It is believed that data accumulation on the reactions involved in the gas phase will lead to large scale production and lower product costs with a large catalyst surface to be produced in the reactor.

Ion mobility-mass spectrometry (IM-MS), gas-phase hydrogen/deuterium (H/D) exchange ion molecule reactions and molecular modeling provide complimentary information and are used here for the characterization of peptide ion structure, including fine structure detail (i.e., cation-π interactions, β-turns, and charge solvation interactions). IM-MS experiments performed on tyrosine containing tripeptides show that the collision cross-sections of sodiated, potassiated and doubly sodiated species of gly-gly-tyr are smaller than that of the protonated species, while the cesiated and doubly cesiated species are larger. Conversely, all of the alkali-adducted species of try-gly-gly have collision cross-sections that are larger than that of the protonated species. The protonated and alkali metal ion adducted (Na+, K+ and Cs+) species of bradykinin and bradykinin fragments 1-5, 1-6, 1-7, 1-8, 2-7, 5-9 and 2-9 were also studied using IM-MS and the alkali metal ion adducts of these species were found to have cross-sections very close to those of the protonated species. Additionally, multiple peak features observed in the ATDs of protonated bradykinin fragments 1-5, 1-6 and 1-7 are conserved upon alkali metal ion adduction. It was observed from gas-phase H/D ion molecule reactions that alkali adducted species exchange slower and to a lesser extent than protonated species in the tyrosine- and arginine-containing peptides. Experimental and computational results are discussed in terms of peptide ion structure, specifically the intra-molecular interactions present how those interactions change upon alkali salt adduction, as well as with the sequence of the peptide. Additionally, IM-MS data suggests the presence of a compact conformation of bradykinin fragment 1-5 (RPPGF) when starting from organic solvent conditions. As water is added stepwise to methanolic solutions, a more extended conformation is populated. When the starting solution is composed of ≈90% water, two distinct mobility profiles are observed as well as a shoulder, indicating the presence of three gas-phase conformations for RPPGF. Gas-phase H/D exchange of [M+H]+ ions prepared from aqueous solvents show a bi-exponential decay, whereas samples prepared from organic solvents show a single exponential decay. The effect of solvent on gas-phase peptide ion structure, i.e., solution-phase memory effects, is discussed and gas-phase structures are compared to know solution-phase structures.

Hydrocarbon conversion and synthesis gas production are two components of the power production process that require significant development and exploration in the advanced energy arena. To remain within our current fueling infrastructure, it is imperative that an efficient and reliable mechanism to facilitate these components of the power production process is developed for automotive applications. A honeycomb monolith rhodium based catalyst has been identified as a potential fuel reformer element for use in automotive hydrocarbon fuel conversion. Using the novel and minimally invasive SpaciMS (Spatially resolved capillary inlet Mass Spectroscopy), developed at Oak Ridge National Laboratories, and an internal temperature acquisition system, the impact of fuel inlet space velocity on the operating rhodium based catalytic fuel reformer of interest was parametrically studied. In situ temperature and species profiles of the catalyst during steady state operation were produced. The data acquired through these experiments was then used to demonstrate analytic capability by conducting thermodynamic analyses on the operating fuel reformer. Experimental and analytical results can be used in development of design considerations for fuel conversion systems.

Presented in this dissertation are studies on the gas-phase structural features of peptides and peptide fragment ions using mass spectrometry (MS), hydrogen/deuterium (H/D) exchange, infrared multiphoton dissociation (IRMPD) spectroscopy, and computational modeling. Additional studies are presented on the mechanism of hydrogen/deuterium exchange using a model amino acid system. The application of chemical cross-linking to investigate the interaction between two proteins, LexA and RecA, is also presented. Gas-phase structural features can be probed using a number of techniques, and several of the studies presented in this dissertation involve the use of gas-phase H/D exchange. Although the basic mechanism for exchange has been determined, the factors that affect the rate and extent of exchange are not well understood. A computational modeling study of the exchange behavior of asparagine and its methyl ester demonstrated that exchange will occur preferentially at sites of more similar basicity. The distinctive exchange behavior of a model histidine-containing pentapeptide, HAAAA, prompted further studies into the structural features that result in five fast exchanging hydrogens and one slower exchange. Peptide analogues were used to identify the sites of exchange, and IRMPD spectroscopy combined with computational modeling indicated that exchange may occur because interaction with water at those sites results in lower energy structures compared to the other sites. Structural studies were also performed to determine whether the b₂⁺ ion from HAAAA is an oxazolone or diketopiperazine. Although the IRMPD spectrum matched that of a diketopiperazine, H/D exchange and fragmentation studies revealed the presence of both a diketopiperazine and oxazolone structure. Protein-protein interactions perform a vital role in regulating cellular processes. Despite extensive mutational analysis, the binding interaction between LexA and RecA, two proteins involved in the SOS response, is unclear. Chemical cross-linking experiments were undertaken to help target future mutational studies, and these studies identified two possible interactions. The first potential binding interaction is located in the cleft of RecA, and the second interaction may be caused by a LexA dimer binding across the RecA helical groove. The presence of two different binding interactions suggests that LexA may have redundant binding modes for RecA interaction.

The presence of gas hydrate and free gas within marine sediments, deposited along the South Shetland margin, offshore the Antarctic Peninsula, was confirmed by low and high resolution geophysical data, acquired during three research cruises. Seismic data analysis has revealed the presence of a bottom simulating reflector that is very strong and continuous in the eastern part of the margin. This area can be considered as a useful site to study the seismic characteristics of sediments containing gas hydrate, with a particular focus on the estimation of gas hydrate and free gas amounts in the pore space. Pre-stack depth migration and tomographic inversion were performed to produce a regional velocity field of gas-phase bearing sediments and to obtain information about the average thickness of gas hydrate and free gas layers. Using these data and theoretical models, the gas hydrate and free gas concentrations can be estimated. Moreover, the common image gather semblance analysis revealed the presence of detailed features, such as layers with small thickness characterised by low velocity alternating with high velocity layers, below and above the bottom simulating reflector. These layers are associated with free gas trapped within the hydrate stability zone and deeper sediments. Thus, the use of the detailed and the regional velocity field analysis is important to give a more reliable estimate of gas content in the marine sediments.

Degassing and in situ formation of a mobile gas phase takes place when an aqueous phase equilibrated with a gas at a pressure higher than the subsurface pressure is injected in water-saturated porous media. This process, which has been termed supersaturated water injection (SWI), is a novel and hitherto unexplored means of introducing a gas phase into the subsurface. Herein is a first macroscopic account of the SWI process on the basis of continuum scale simulations and column experiments with CO2 as the dissolved gas. A published empirical mass transfer correlation (Nambi and Powers, Water Resour Res, 2003) is found to adequately describe the non-equilibrium transfer of CO2 between the aqueous and gas phases. Remarkably, the dynamics of gas-water two-phase flow, observed in a series of SWI experiments in homogeneous columns packed with silica sand or glass beads, are accurately predicted by traditional two-phase flow theory which allows the corresponding gas phase relative permeability to be determined. A key consequence of the finding, that the displacement of the aqueous phase by gas is compact at the macroscopic scale, is consistent with pore scale simulations of repeated mobilization, fragmentation and coalescence of large gas clusters (i.e., large ganglion dynamics) driven entirely by mass transfer. The significance of this finding for the efficient delivery of a gas phase below the water table in relation to the alternative process of in-situ air sparging and the potential advantages of SWI are discussed. SWI has been shown to mobilize a previously immobile oil phase in the subsurface of 3-phase systems (oil, water and gas). A macroscopic account of the SWI process is given on the basis of continuum-scale simulations and column experiments using CO2 as the dissolved gas and kerosene as the trapped oil phase. Experimental observations show that the presence of oil ganglia in the subsurface alters gas phase mobility from 2-phase predictions. A corresponding 3-phase gas relative permeability function is determined, whereas a published 3-phase relative permeability correlation (Stone, Journal of Cana Petro Tech, 1973) is found to be inadequate for describing oil phase flow during SWI. A function to predict oil phase relative permeability is developed for use during SWI at high aqueous phase saturations with a disconnected oil phase and quasi-disconnected gas phase. Remarkably, the dynamics of gas-water-oil 3-phase flow, observed in a series of SWI experiments in homogeneous columns packed with silica sand or glass beads, are accurately predicted by traditional continuum-scale flow theory. The developed relative permeability function is compared to Stone’s Method and shown to approximate it in all regions while accurately describing oil flow during SWI. A published validation of Stone’s Method (Fayers and Matthews, Soc of Petro Eng Journal, 1984) is cited to validate this approximation of Stone’s Method.

Optical spectroscopy combined with mass spectrometry provides a unique opportunity to probe the intrinsic properties of biologically-relevant ions in the gas phase, free from the interfering effects of solvent interactions in the condensed phase. Electrospray ionization allows large biomolecules to be transferred intact into the gas phase for mass analysis. Modern mass spectrometers provide excellent sensitivity, mass-resolution and can efficiently isolate a single ionic species from a complex mixture. However, the extent to which biomolecules retain their solution-phase conformations in the gas phase is largely unknown. Therefore, there is considerable interest in applying spectroscopic methods to biological ions in vacuuo. Due to the low number densities of ions in storage devices, traditional absorption measurements are not feasible, requiring more sensitive analytical methods. Two such techniques are laser-inducedfluorescence (LIF) and photo-dissociation (PD) action spectroscopy, both of which measure the consequence of absorption. The work in this dissertation describes applications of optical spectroscopic methods to interrogate mass-selected ions using a variety of ion storage apparatus including a Fourier transform ion cyclotron resonance mass spectrometer, a quadrupole ion trap and an electrostatic ion storage ring. First, the conformations of small cationized arginine complexes have been investigated using infrared multiple-photon dissociation (IRMPD) action spectroscopy in the IR fingerprint region of the spectrum (200-1800 cm-1). Second, an apparatus incorporating a quadrupole ion trap has been constructed in our laboratory to perform LIF and PD-action spectroscopy. The gas-phase fluorescence and photodissociation properties of three Rhodamine dyes have been investigated including fluorescence excitation and dispersed fluorescence spectra. Finally, the latter chapters describe the use of electronic action spectroscopy to investigate a model chromophore of the green fluorescent protein (GFP), p-hydroxybenzylidene-2,3-dimethylimidazolone (HBDI). The body of work in this dissertation highlights the integration of gas-phase spectroscopy and mass spectrometry to elucidate the fundamental photophysical properties of biological and related ions.

In the production of boron fibers using CVD technique, boron deposition and dichloroborane formation reactions take place in a reactor. Boron deposition reaction occurs at the surface while formation of dichloroborane is the result of both gas phase and surface reactions. A CSTR type of reactor was designed and constructed from stainless steel to investigate the gas phase reaction kinetics and kinetic parameters of boron fibers produced from the reaction of boron trichloride and hydrogen gases in a CVD reactor. The gases were heated by passing through the two pipes which were located into the ceramic furnace and they were mixed in the CSTR. The effluent gas mixture of the reactor was quenched by passing through a heat exchanger. An FT-IR spectrophotometer was connected to the heat exchanger outlet stream to perform on-line chemical analysis of the effluent gas mixture. Experiments were carried out at atmospheric pressure and a reactor temperature range of 300-600 &ordm / C with different inlet reactant concentrations. The analysis of the FT-IR spectra indicated that the gas phase reaction and the surface reaction started at reactor temperatures above 170 &ordm / C and 500&ordm / C, respectively. It was concluded that reaction rate of the product increased with an increase in the inlet concentration of both reactants (BCl3 and H2) and with an increase in the reactor temperature. The gas phase reaction rate was expressed in terms of a th and b th orders with respect to the inlet concentrations of BCl3 and H2. The activation energy of the gas phase reaction, a and b were found to be 30.156 , 0.54 and 0.64, respectively. The correlation coefficient was 0.9969.

Although the native environment of the vast majority of proteins is a complex aqueous solution, like the interior of a cell, many analysis methods for assessing chemical and physical properties of biomolecules require the sample to be aerosolized; that is, transferred to the gas-phase. An important example is electrospray-ionization mass spectrometry, which can provide a wide range of information about e.g. biomolecules. That includes structural features, charged sites, and gas-phase equilibrium constants of reactions. To date much of the microscopic detail about the aerosolization process remains beyond the limits of experimental observation. How is the gas-phase structure of a protein related to the solution-phase structure? How transferable are observations done in the gas phase to solution? On the basis of classical molecular-dynamics simulations this thesis reveals important features of gas-phase biomolecular structure near the end of the the aerosolization process, the relation between gas-phase structure and native structure, microscopic detail about the de-wetting of gas-phase biomolecules, and the impact of temperature and residual solvent on structure preservation. Residual solvent on proteins is shown to have a stabilizing effect on proteins, in part because it allows the scarcely hydrated protein to cool through solvent evaporation, but also because part of the solvent provides structural support by hydrogen bonding to the protein. The gas-phase structure of micellar aggregates is seen to depend on composition, where some types of lipids cause rapid micelle inversion, whereas others maintain much of their collective structure when transferred to the gas phase. The thesis also addresses proton-transfer reactions, which have an impact on the biophysical aspects of proteins, both in the gas phase and in solution. The thesis presents a computationally efficient method for including proton-transfer reactions in classical molecular-dynamics simulations, which expands the range of scientific problems that can be addressed with molecular dynamics.