Portable mass spectrometers provide convenience for applications where conventional mass spectrometers are not suitable. However, a series of miniaturization issues show up in small mass spectrometers, specifically mass analyzers, that need to be thoroughly addressed before further miniaturization. The work in this dissertation focuses on miniaturization issues of ion trap mass analyzers. Space-charge is one of the major issues in small ion traps affecting their analytical performance. It limits ion trapping capacity when ion-ion repulsion causes spreading of a packet of ions. Simulation studies on the relationship between different trap dimensions and trapping capacity was done on a geometry-optimized cylindrical ion trap. A reasonable way of scaling the two important operating parameters (trapping voltage and trapping frequency as functions of the trap dimension) was discussed and applied in the simulation. The trapping capacity (N) decreased with the physical trap dimension (r0) as expected, and N is scaled exponentially as r0. Scaling laws for trapping parameters are proposed, confirmed by SIMION simulations that evaluate the space charge issue in small ion traps. This effect represents a practical limit in ion trap miniaturization.Geometry deviation is another issue that cannot be neglected in miniaturized ion traps, especially in small linear ion traps (LIT). The LIT our group is working on consists of an assembly of two plates, of which each was made by lithographically patterning a series of electrodes on an insulating plate. It is a promising way of expanding the trap capacity at a small trap dimension. However, misalignment of the two plates might seriously affect its performance, specifically resolution and signal intensity. Simulations were done on the misalignment of two-plate planar LIT in the six possible degrees of freedom (DOF) of misalignment between the two plates. Each DOF's influence on the mass resolution and the ion detection efficiency were discussed. Preliminary data from a previous ceramic plate design was collected while most of the misalignment experiments were done on an improved version. A platform was designed incorporating four motorized stages to precisely control the alignment of the ion trap in vacuum. The new plate design was demonstrated to achieve a better than unit resolution for toluene and deuterated toluene after the plates were aligned. The impact on the resolution and signal intensity from pitch, x-, y- and z-displacement were also experimentally studied.

I describe the miniaturization of a linear-type ion trap mass spectrometer for possible applications in portable chemical analysis, and demonstrate the advantages of using lithographically patterned electrode plates in realizing an ion trap with dimension r0 less than 1 mm. The focus of the work was to demonstrate the viability and feasibility of the patterned electrode approach to trap miniaturization, and also to discover potential obstacles to its use. Planar ceramic substrates were patterned with metal electrodes using photolithography. Plates that were originally used in a linear trap with a half-spacing (r0) of 2.19 mm were positioned much closer together such that r0 = 0.95 mm. A capacitive voltage divider provided different radiofrequency (RF) amplitudes to each electrode, and the capacitor values were adjusted to provide the correct electric field at this closer spacing. Electron ionization mass spectra of toluene and dichloromethane demonstrate instrument performance with better than unit mass resolution. Compared with the larger plate spacing, the signal intensity is reduced, corresponding to the reduced trapping capacity of the smaller device, but the mass resolution of the larger device is retained. A further miniaturized linear ion trap with a half-spacing of 362 µm was designed and tested. A series of obstacles and troubleshooting on ion source, analytical method, and electronics were present. These experiments show promise for further miniaturization using patterned ceramic plates and provide a guide for the ion trap miniaturization. The feasibility of a wire linear ion trap was also demonstrated. Unit mass resolution was obtained, indicating a promise for further optimization and miniaturization of the wire linear ion trap. In addition to the practical experiments on the miniaturized linear ion traps, I theoretically studied ion motion in the toroidal ion trap using SIMION simulations, which show classical chaotic behavior of single ions. The chaotic motion is a result of the non-linear components of the electric fields as established by the trap electrodes, and not by Coulombic interaction from other ions. The chaotic behavior was observed specifically in the ejection direction of ions located in non-linear resonance bands within and adjacent to the region of stable trapping. The non-linear bands crossing through the stability regions correspond to hexapole resonance conditions, while the chaotic ejection observed immediately adjacent to the stable trapping region corresponds to a "fuzzy" ejection boundary. Fractal-like patterns were obtained in a series of zoomed-in regions of the stability diagram.

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.

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.

Ion traps used in mass spectrometers are of two classes. One class consists of traps having three electrode geometries which have rotational symmetry about central axis. They are called axially symmetric ion traps. Paul trap, Cylindrical Ion Trap(CIT) are examples in this class. Other class of traps contain 2D electric field inside them which has same profile along the central axis due to translational symmetry. Linear Ion Trap(LIT) and Rectilinear Ion Trap(RIT) are examples in this class. In the ideal hyperbolic geometries of Paul trap and LIT, electric field is a perfectly linear function of distance from the center of the trap. But when these ideal geometries are simplified in to simpler geometries of the CIT and the RIT for ease in machining, linearity of field, which is a specialty of Paul trap and LIT is lost. In this thesis, an effort is made to optimize the field within the traps by using split electrodes. The ring electrode of the CIT and both pairs of electrodes in the RIT are divided into more number of parts. Suitable voltages are applied on these parts to improve the linearity of the field. This thesis contains six chapters. Chapter 1 contains a background information about mass spectrometry. Chapter 2 discusses the Boundary Element Method (BEM) used to calculate charge distribution and Nelder-Mead method used for optimization. It also shows the calculation of multipoles. In Chapter 3, two new geometries namely split-electrode RIT and split-electrode CIT are considered with the objective of improving the linearity of electric field inside them. It is shown here that by applying certain external potential on various parts of split electrodes of these geometries, it is possible to improve the linearity of electric field inside them. In Chapter 4, capacitor models of new geometries proposed in chapter 3 are discussed. The use of external capacitors as a replacement to external power supply is also discussed in this chapter. InChapter5, study similar to that ofChapter3is carried out by splitting the geometries in more number of parts. The possibility of improved field profile is investigated by applying full potential to some of these parts and keeping other parts at ground potential. In Chapter 6, concluding remarks are discussed.

Since the tragedy of the drug Thalidomide® in the late 1950 to early 1960’s, chirality has been recognized as an important aspect that must be controlled in the drug development process in the pharmaceutical industry. Since then, there has been a considerable movement towards single enantiomer drugs. This demand has presented many challenges for the synthetic organic chemist. Chiral catalysts offer one solution to this problem, as they afford the unique ability to preferentially synthesize one enantiomer. Unfortunately, the design of new chiral catalysts is often empirical, with luck and trial and error necessary due to factors that govern enantioselectivity. Therefore, it would be highly beneficial to develop a method that is capable of screening multiple chiral catalysts early in the catalyst development cycle. Using a modified ion-trap mass spectrometer, the chiral environment of various chiral catalysts may be examined, free from solvent and ion-pairing affects. Thus, the catalyst’s inherent asymmetric environment (enantioselectivity) may be probed using simple chiral molecules, including alcohols, ethers, and epoxides of various steric demands. Using these probes, various C2-symmetric bis-oxazolines and di-imines catalysts were examined. Use of the binaphthyl-based diamine, BINAM, condensed with various 3,5-disubstituted benzaldehydes, provided selectivity close to the privileged catalyst, bis-oxazoline. In general, the chiral probes 1-phenyl-2-propanol, 1-mehtoxyethylbenzene, and styrene oxide offer the best look at the catalyst’s enantioselectivity potential. With the use of the ion-trap mass spectrometer as a mass filter, the purity of the catalyst is not paramount, thus, multiple catalysts may be screened simultaneously, with the constraint that the catalysts must be of different m/z. This thesis presents results found during the exploration of various C2 and C1-symmetric chiral catalysts, in the development of the new chiral screening method utilizing various chiral probes.

Developing portable mass spectrometry systems is an active area of research due to its broad range of useful applications, including environmental monitoring, threat detection, and space exploration. The mass analyzer is one of the key elements of the mass spectrometry system to develop for a portable system. Ion traps are a good candidate for the mass analyzer in a portable mass spectrometry system because the operating pressure scales with size. This allows for scaling down the other components of the system including the vacuum and electrical systems. Researchers at BYU are making an effort to develop miniature ion traps based on a planar geometry. The ion traps are made using microfabrication processes. A summary of the plates developed at BYU is presented in this work. Results from experiments to test the effects of pitch alignment on one design of planar ion trap plates are also presented. Conventional ion traps use a sinusoidal waveform to drive them. Driving the ion trap with a digital waveform has many benefits including extended mass range, lower voltage, and more control over the waveform. One of the difficulties involved in using a digital waveform is creation of a high voltage, high frequency waveform. This work details the design of a digital circuit capable of outputting a waveform with an amplitude of 100 VP-P at a frequency of 5 MHz and lower. This waveform was applied to a new ion trap design based on wire electrodes instead of planar electrodes. This trap offers many benefits over the planar ion traps developed at BYU. This work presents mass spectra obtained using a square digital waveform applied to the wire ion trap.

The thesis aims at building an experimental setup for conducting the boundary ejection and resonance ejection experiments on wide variety of ion trap mass analyzers. The experimental setup has two parts namely power electronics circuits and mechanical assembly. The focus of the thesis is on the electronics hardware which provides various power sources required for the operation of ion trap mass spectrometer. The electronics circuits discussed in the thesis have better performance, flexibility and ruggedness compared to the existing setup. The traditional power supplies used in ion trap mass spectrometers are all linear supplies. But one major drawback of these supplies is the high power dissipation and consequently, the power efficiency degrades. We are trying to introduce switch mode power supplies to reduce the power dissipation loss and eventually increase the power efficiency. In the course of the work the following power supplies have been developed. The supplies are - 1.Constant current source, 2.Filament base, 3.gating power supply and pulsing circuit, 4.High voltage DC power supply and 5. High voltage RF generator.

Mass selective axial ejection of ions and mass analysis with a stability island with linear quadrupoles with added octopole fields are described. With mass selective axial ejection, quadrupoles with 2.0% and 2.6% added octopole fields have been tested and compared to a conventional quadrupole. The effects of trapping ions at different q values, excitation voltage, scan direction, balanced and unbalanced rf voltages on the rods, and dc applied between the rods have been investigated. The highest scan speeds and highest resolution are obtained with resonant excitation and ejection at high q (q = 0.8). With axial ejection, the quadrupole with a 2.0% added octopole field provides mass resolution and ejection efficiencies similar to a conventional rod set. Quadrupole, dipole and simultaneous dipole-dipole excitation between the x and y rod pairs were compared and no advantage was found with quadrupole or dipole-dipole excitation. The effects of scan speed were investigated and a resolution at half height of about 1600 is possible at scan speeds up to 5000 Th/s. Mass analysis using islands of stability was investigated with a quadrupole with2.0% added octopole field. The island of stability is formed with auxiliary excitation. The experiments confirm the predictions of the simulations. With the resolving dc applied to the quadrupole so that the Mathieu parameter a>0, conventional mass analysis with applied rf and dc and no auxiliary excitation is possible. In this case use of an island of stability yields similar peak shape and resolution. However with the polarity of the resolving dc reversed so that a<0, only very low resolution can be obtained; the added octopole prevents conventional mass analysis. By using a stability island when a<0, the resolution is substantially improved.

The purpose of the SCRIT project is to determine size and shape of short-lived and rarely-produced nuclei by elastic electron scattering, which is the best probe for the structure studies, for the first time. In traditional electron scattering, a solid target having an order of 1023 nuclei/cm^2 is normally used, which is not possible for short-lived and rarely-produced nuclei. In this project a Self Containing Radioactive Isotope Target scheme (SCRIT) is going to be employed. This innovative ion-trap method is shown to be a way to make measurements with a very small amount of nuclei, an order of only 106 nuclei. In order to determine the absolute cross section for elastic electron scattering for structure study, the simulates measurement of the bremsstrahlung from the trapped nuclei is required. Since the bremsstrahlung cross section for a nucleus of the atomic number Z is well know, the precise measurement of the bremsstrahlung provides the luminosity. My theme in this SCRIT project was a construction of a bremsstrahlung luminosity monitor. It consists of a position monitor for measuring the spatial distribution of bremsstrahlung and a Pb-glass Cerenkov detector for energy measurement. My efforts have been mainly devoted to the construction of a position monitor system using fiber scintillators. The construction of the position monitor was divided into five parts; detector construction, support construction, trigger detector construction, software programming, software testing and detector tests. The position monitor consists of two sets of fiber scintillation detectors. Each of them uses 16 fibers, Bicron BCF-10 with a cross section of 2x2mm^2, optically coupled to a multi-anode photomultiplier, (Hamamatsu H6568-10). The position monitor can measure the XY distribution of bremsstrahlung. Strictly speaking, the fiber detector detects not bremsstrahlung directly but electrons and/or positrons by pair creation of bremsstrahlung in a materials. The data acquisition system has been programmed in NI LabVIEW. The software is an advanced X/Y-coordinate counting system, which can additionally preform functions as save data to file and 3D-plot to determine the spreading of the bremsstrahlung luminosity. The results can be saved and transferred online to a server so that is possible to access the data from anywhere. The system has been tested using beta rays from 90Sr source. The results of the test shown that the detectors can detect minimum ionizing particle, i.e. electrons and positrons. The detector and software testings shows that the system is ready to use for luminosity measurements at SCRIT experiment. This system I constructed surely provides a new and useful information for the SCRIT experiments. / SCRIT Project