Infrared multiple photon dissociation (IRMPD) spectroscopy has been coupled with electronic structure calculations in order to elucidate the structures of several small biological molecules including: uracil, 5-fluorouracil, 5-fluorocytosine, ferulic acid, and a number of their related analogs. IRMPD is a powerful technique, that when combined with electronic structure calculations can provide convincing evidence for the structural characterization of ions in the gas phase. Isomers of uracil and 5-fluorouracil (5-FU) have been characterized by calculations performed at the MP2(full)/aug-cc-pVTZ level of theory; however, infrared multiple photon dissociation spectroscopy experiments proved to be unsuccessful for these species. Geometry optimization and frequency calculations have isolated the dominant isomer(s) for neutral and deprotonated uracil and 5-fluorouracil, along with several cluster interactions involving water, methanol, ammonia, and methylamine. For both uracil and 5-FU, a single relevant neutral isomer was determined, with each isomer existing in the diketo, as opposed to the enol form. Following the deprotonation of this neutral isomer, both uracil and 5-FU were permitted to form anionic cluster ions with water, methanol, ammonia, or methylamine, and based on the relative Gibbs free energies (298 K) of the calculated isomers, relevant cluster interactions were determined. For each cluster, several sites of intramolecular interaction were found to exist; however, interaction at the site of deprotonation was the most favourable in every instance. Ionic hydrogen bond interactions have been found in several clusters formed by 5-fluorocytosine (5-FC). The chloride and trimethylammonium cluster ions, in addition to the cationic and anionic dimers have been characterized by infrared multiple photon dissociation (IRMPD) spectroscopy and electronic structure calculations performed at the B2PLYP/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. IRMPD spectra in combination with calculated spectra and relative energetics have indicated, quite conclusively, that a single isomer for each 5-FC cluster that is likely being observed experimentally except in the case of the anionic dimer, in which a combination of isomers is probable. For the 5-FC-trimethylammonium cluster specifically, the calculated spectrum of the lowest energy isomer matches the experimental spectrum remarkably well. Interestingly, the cationic dimer of 5-FC was found to have a single energetically relevant isomer (Cationic-IV) in which a unique tridentate ionic hydrogen bond interaction is formed. The three sites of intramolecular ionic hydrogen bonds in this isomer interact very efficiently, leading to a significantly large calculated enthalpy of binding of 180 kJ/mol. The magnitude of the calculated binding energy for this species, in combination with the strong correlation between the simulated and IRMPD spectra, indicates that the tridentate-bound dimer is observed predominantly in experiment. Comparison of the calculated relative Gibbs free energies (298 K) for this species with several of the other isomers considered also supports the likelihood of the dominant protonated dimer existing as Cationic-IV. Protonated ferulic acid has been characterized using infrared multiple photon dissociation spectroscopy and electronic structure calculations at the B3LYP/6-311+G(d,p) level of theory. Neutral ferulic acid has been determined to undergo protonation on the carbonyl oxygen of the acid group, forming an ion of m/z 195. Due to its extensively conjugated structure, protonated ferulic acid (m/z 195) is observed to yield three stable fragment ions in IRMPD experiments. It is proposed that two parallel fragmentation pathways of protonated ferulic acid are being observed. First, proton transfer occurs from the carbonyl oxygen to the hydroxyl oxygen within the acid group, resulting in the loss of water and subsequently carbon monoxide, forming ions of m/z 177 and 149, respectively. The second proposed fragmentation pathway undergoes proton transfer from the phenolic group to the methoxy group resulting in loss of methanol and rearrangement to a five-membered ring of m/z 163. IRMPD spectra have been obtained for the ions m/z 195 and m/z 177, and anharmonic calculations have been performed on these species at the B3LYP/6-311+G(d,p) level of theory. The calculated anharmonic spectra for these ions match the experimental spectrum exceptionally well and strongly support the proposed fragmentation mechanisms.

Infrared multiple photon dissociation (IRMPD) spectroscopy has been coupled with electronic structure calculations in order to elucidate the structures of several small biological molecules including: uracil, 5-fluorouracil, 5-fluorocytosine, ferulic acid, and a number of their related analogs. IRMPD is a powerful technique, that when combined with electronic structure calculations can provide convincing evidence for the structural characterization of ions in the gas phase. Isomers of uracil and 5-fluorouracil (5-FU) have been characterized by calculations performed at the MP2(full)/aug-cc-pVTZ level of theory; however, infrared multiple photon dissociation spectroscopy experiments proved to be unsuccessful for these species. Geometry optimization and frequency calculations have isolated the dominant isomer(s) for neutral and deprotonated uracil and 5-fluorouracil, along with several cluster interactions involving water, methanol, ammonia, and methylamine. For both uracil and 5-FU, a single relevant neutral isomer was determined, with each isomer existing in the diketo, as opposed to the enol form. Following the deprotonation of this neutral isomer, both uracil and 5-FU were permitted to form anionic cluster ions with water, methanol, ammonia, or methylamine, and based on the relative Gibbs free energies (298 K) of the calculated isomers, relevant cluster interactions were determined. For each cluster, several sites of intramolecular interaction were found to exist; however, interaction at the site of deprotonation was the most favourable in every instance. Ionic hydrogen bond interactions have been found in several clusters formed by 5-fluorocytosine (5-FC). The chloride and trimethylammonium cluster ions, in addition to the cationic and anionic dimers have been characterized by infrared multiple photon dissociation (IRMPD) spectroscopy and electronic structure calculations performed at the B2PLYP/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. IRMPD spectra in combination with calculated spectra and relative energetics have indicated, quite conclusively, that a single isomer for each 5-FC cluster that is likely being observed experimentally except in the case of the anionic dimer, in which a combination of isomers is probable. For the 5-FC-trimethylammonium cluster specifically, the calculated spectrum of the lowest energy isomer matches the experimental spectrum remarkably well. Interestingly, the cationic dimer of 5-FC was found to have a single energetically relevant isomer (Cationic-IV) in which a unique tridentate ionic hydrogen bond interaction is formed. The three sites of intramolecular ionic hydrogen bonds in this isomer interact very efficiently, leading to a significantly large calculated enthalpy of binding of 180 kJ/mol. The magnitude of the calculated binding energy for this species, in combination with the strong correlation between the simulated and IRMPD spectra, indicates that the tridentate-bound dimer is observed predominantly in experiment. Comparison of the calculated relative Gibbs free energies (298 K) for this species with several of the other isomers considered also supports the likelihood of the dominant protonated dimer existing as Cationic-IV. Protonated ferulic acid has been characterized using infrared multiple photon dissociation spectroscopy and electronic structure calculations at the B3LYP/6-311+G(d,p) level of theory. Neutral ferulic acid has been determined to undergo protonation on the carbonyl oxygen of the acid group, forming an ion of m/z 195. Due to its extensively conjugated structure, protonated ferulic acid (m/z 195) is observed to yield three stable fragment ions in IRMPD experiments. It is proposed that two parallel fragmentation pathways of protonated ferulic acid are being observed. First, proton transfer occurs from the carbonyl oxygen to the hydroxyl oxygen within the acid group, resulting in the loss of water and subsequently carbon monoxide, forming ions of m/z 177 and 149, respectively. The second proposed fragmentation pathway undergoes proton transfer from the phenolic group to the methoxy group resulting in loss of methanol and rearrangement to a five-membered ring of m/z 163. IRMPD spectra have been obtained for the ions m/z 195 and m/z 177, and anharmonic calculations have been performed on these species at the B3LYP/6-311+G(d,p) level of theory. The calculated anharmonic spectra for these ions match the experimental spectrum exceptionally well and strongly support the proposed fragmentation mechanisms.

In the normal operation of quadrupole ion trap mass spectrometers, the trapped ions are ejected symmetrically through both the upper (detector) and lower(source) endcap electrodes during mass selective boundary ejection experiment. This reduces the sensitivity of the instrument by almost 50%. In this preliminary study, we altered the geometry parameters of the quadrupole ion traps to introduce asymmetry. The asymmetry displaced the ion cloud towards the detector endcap which resulted in a preferential ejection through this endcap, thus imparting directionality to the ejected ions and hence to the sensitivity enhancement. Two symmetrical mass analyzers have been taken up for numerical study. They include the Paul trap(QIT) and the cylindricaliontrap(CIT). Asymmetry to these geometries is introduced in two ways, one by varying the upper endcap hole radius alone and in other by stretching the trap along the upper endcap only. The escape velocity plots and mass selective boundary ejection simulations are used to demonstrate the directionality of ion ejection for these geometries. The simulations revealed a significant increase in the number of ions getting ejected in the direction of asymmetry.

No / Two-dimensional gel electrophoresis-separated and excised haptoglobin alpha2-chain protein spots were subjected to in-gel digestion with trypsin. Previously unassigned peptide ion signals observed in mass spectrometric fingerprinting experiments were sequenced using the matrix-assisted laser desorption/ionization-quadrupole ion trap-time of flight (MALDI-QIT-TOF) mass spectrometer and showed that the haptoglobin alpha-chain derivative under study was cleaved by trypsin unspecifically. Abundant cleavages occurred C-terminal to histidine residues at H23, H28, and H87. In addition, mild acidic hydrolysis leading to cleavage after aspartic acid residues at D13 was observed. The uninterpreted tandem mass spectrometry (MS/MS) spectrum of the peptide with ion signal at 2620.19 was submitted to database search and yielded the identification of the corresponding peptide sequence comprising amino acids (aa) aa65-87 from the haptoglobin alpha-chain protein. Also, the presence of a mixture of two tryptic peptides (mass to charge ratio m/z 1708.8; aa40-54, and aa99-113, respectively), that is caused by a tiny sequence variation between the two repeats in the haptoglobin alpha2-chain protein was resolved by MS/MS fragmentation using the MALDI-QIT-TOF mass spectrometer instrument. Advantageous features such as (i) easy parent ion creation, (ii) minimal sample consumption, and (iii) real collision induced dissociation conditions, were combined successfully to determine the amino acid sequences of the previously unassigned peptides. Hence, the novel mass spectrometric sequencing method applied here has proven effective for identification of distinct molecular protein structures.

In this thesis we have focussed on two types of axially symmetric ion trap mass analysers viz., the quadrupole ion trap mass analyser and the toroidal ion trap mass analyser. We have undertaken three numerical studies in this thesis, one study is on the quadrupole ion trap mass analysers and two studies are on the toroidal ion trap mass analysers. The first study is related to improvement of the sensitivity of quadrupole ion trap mass analysers operated in the resonance ejection mode. In the second study we have discussed methods to determine the multipole coefficients in the toroidal ion trap mass analysers. The third study investigates the stability of ions in the toroidal ion trap mass analysers. The first study presents a technique to cause unidirectional ion ejection in a quadrupole ion trap mass spectrometer operated in the resonance ejection mode. In this technique a modified auxiliary dipolar excitation signal is applied to the endcap electrodes. This modified signal is a linear combination of two signals. The first signal is the nominal dipolar excitation signal which is applied across the endcap electrodes and the second signal is the second harmonic of the first signal, the amplitude of the second harmonic being larger than that of the fundamental. We have investigated the effect of the following parameters on achieving unidirectional ion ejection: primary signal amplitude, ratio of amplitude of second harmonic to that of primary signal amplitude, different operating points, different scan rates, different mass to charge ratios and different damping constants. In all these simulations unidirectional ejection of destabilized ions has been successfully achieved. The second study presents methods to determine multipole coefficients for describing the potential in toroidal ion trap mass analysers. Three different methods have been presented to compute the toroidal multipole coefficients. The first method uses a least square fit and is useful when we have ability to compute potential at a set of points in the trapping region. In the second method we use the Discrete Fourier Transform of potentials on a circle in the trapping region. The third method uses surface charge distribution obtained from the Boundary Element Method to compute these coefficients. Using these multipole coefficients we have presented (1) equations of ion motion in toroidal ion traps (2) the Mathieu parameters in terms of multipole coefficients and (3) the secular frequency of ion motion in these traps. It has been shown that the secular frequency obtained from our method has a good match with that obtained from numerical trajectory simulation. The third study presents stability of ions in practical toroidal ion trap mass analysers. Here we have taken up for investigation four geometries with apertures and truncation of electrodes. The stability is obtained in UDC-VRF plane and later this is converted into A-Q plane on the Mathieu stability plot. Though the plots in terms of Mathieu parameters for these structures are qualitatively similar to the corresponding plot of linear ion trap mass analysers, there is a significant difference. The stability plots of these have regions of nonlinear resonances where ion motion is unstable. These resonances have been briefly investigated and it is proposed that they occur on account of hexapole and octopole contributions to the field in these toroidal ion traps.

This thesis investigates the loss of high mass ions due to the initial thermal energy in ion trap mass analyzers. It provides an analytical expression for estimating the percentage loss of ions of a given mass at a particular temperature, in a trap operating with a set of conditions. The investigations have been carried out on quadrupole and cylindrical ion trap geometries. The three-dimensional Maxwellian velocity distribution function has been assumed to derive an expression for the percentage of ions lost. Adopting an approximation based on the observed escape velocity profiles of ions, an expression for the percentage loss of ions of a given mass has been derived as a function of the temperature for an ensemble of ions, its mass and its escape velocity. An analytical expression for the escape velocity has also been developed. It is seen that the escape velocity is a function of the trapping field, drive frequency and ion mass. Because the trapping field is determined by trap design parameters and operating conditions, it has been possible to study the influence of these parameters on ion loss. The parameters investigated include ion temperature, magnitude of the initial potential applied to the ring electrode (which determines the low mass cut-off), trap size, dimensions of apertures in the endcap electrodes and RF drive frequency. The studies demonstrate that ion loss due to initial thermal energy increases with increase in mass and that ion escape occurs in the radial direction. Reduction in the loss of high mass ions is favoured by lower ion temperatures, increasing low mass cut-off, increasing trap size, and higher RF drive frequencies. The dimensions of the apertures in the endcap electrodes do not influence ion loss in the range of aperture sizes considered.

Axially symmetric rf ion traps consists of a mass analyser having three electrodes, one of which is a central ring electrode and the other two are endcap electrodes. In the ideal Paul trap mass spectrometer, the electrodes have hyperboloidal shape (March and Hughes, 1989) and in mass analyser with simplified geometry, such as the cylindrical ion trap (Wu et al.,2005) the central electrode is a cylinder and the two endcap electrode and flat plates. rf-only or rf/dc potential is applied across the ring electrode and the grounded endcap electrodes for conducting the basic experiments of the mass spectrometer. In recent times, the miniaturisation of ion trap is one of the research interests in the field of mass spectrometry. The miniaturisation has the advantages of compactness, low power consumption and portability. However, this is achieved at the cost of the overall performance of the mass spectrometer with its deleterious effect on resolution. Research groups study the field distribution in the trap for better understanding of ion dynamics in the direction of achieving improved performance with the miniaturised traps. One aspect which has not received any attention in research associated with quadrupole ion traps is the possible role of the magnetic field in improving performance of these traps. Since in the quadrupole ion trap mass analyser ion is confined by an oscillating (rf) field, magnetic fields have been considered superfluous. The motivation of the thesis is to understand the dynamics of ions in axially symmetric rf ion traps, in the presence of the magnetic field. The axially symmetric rf ion trap geometries considered in this thesis are the Paul trap and the cylindrical ion trap (CIT). The changes incurred to the ion motion and Mathieu stability diagram in the presence of magnetic field is observed in this work. Also, the relation between the magnetic field and the Mathieu parameter is shown. The thesis contains 4 chapters: Chapter 1 provides the basic back ground of mass spectrometry and the operating principles. The equations of ion motion in the Paul trap is derived and also the solution to Mathieu equation is provided. The solution to the Mathieu equation are the Mathieu parameters and , when plotted with on the x-axis and on the y-axis, results in the Mathieu stability plot, the explanation of which is also given in the chapter. A brief description of the secular frequency associated with the ion dynamics is given in this chapter. The popular experiments conducted (i.e. the mass selective boundary ejection and resonance ejection) with a mass spectrometer is described here. Finally at the end of the chapter is the scope of the thesis. Chapter 2 facilitates with the preliminary study required fort he accomplishment of the task. The Paul trap and the CIT are the rf ion traps considered in this work. The geometries of these two traps are described in this chapter. The computational methods used for the analysis of various aspects of mass spectrometer is introduced. The computational methods used involve the methods used for calculating the charge distribution on the electrodes, potentials, multipole co-efficients and trajectory calculations. The boundary element method(BEM), calculation for Potentials and the Runge-Kutta method used for the trajectory calculations are introduced in this chapter. The expressions for calculating the multipole co-efficients are also specified. Chapter 3 presents the results obtained. The equations of ion motion in a quadrupole ion trap in the presence of magnetic field is derived here. Verification of numerical results with and without the magnetic field are presented at the end of this chapter. The chapter also presents various graphs showing the impact of magnetic field on the ion dynamics in the Paul trap and the CIT. The impact of the presence of magnetic field on the micro motion in -, -and -directions of the rf ion traps are shown in this chapter. Also the figures showing the variation in the Mathieu stability plots, with varying magnetic field intensity are presented in the chapter. At the end of this chapter the relation between the magnetic field and the Mathieu parameter is derived and plotted. Chapter 4 explains the various observations made from the results obtained. This chapter also highlights the future scope of the work for making this a more applicable one. References in the text have been given by quoting the author’s name and year of publication. Full references have been provide, in an alphabetic order, at the end of the thesis.

<p>Crude oil is a mixture of hydrocarbons so complex that it is predicted to comprise as many compounds as there are genes in the human genome. Developing methods to not only recover crude oil from the ground but also to convert crude oil into desirable products is challenging due to its complex nature. Thus, the petroleum industry relies heavily on analytical techniques to characterize the oil in reservoirs prior to enhanced oil recovery efforts and to evaluate the chemical compositions of their crude oil based products. Mass spectrometry (MS) is the only analytical technique that has the potential to provide elemental composition as well as structural information for the individual compounds that comprise petroleum samples. The continuous development of ionization techniques and mass analyzers, and other instrumentation advances, have primed mass spectrometry as the go-to analytical technique for providing solutions to problems faced by the petroleum industry. The research discussed in this dissertation can be divided into three parts: developing novel mass spectrometry-based methods to characterize mixtures of saturated hydrocarbons in petroleum products (Chapters 3 and 5), exploring the cause of fragmentation of saturated hydrocarbons upon atmospheric pressure chemical ionization to improve the analysis of samples containing these compounds (Chapter 4), and developing a better understanding of the chemical composition of crude oil that tightly binds to reservoir surfaces to improve chemically enhanced oil recovery (Chapter 6). </p>