Although molybdenum blue solutions have been known for more than twocenturies, an understanding of their chemical nature is only beginning to emerge.This dissertation aimed at elucidating the structural nature of the polydisperse,nanoscopic components in the solution phases and the solid states of partiallyreduced polyoxomolybdate (Mo-POM). The study offered at least fourcontributions to the area: (1) a rational protocol for the molecular recognition ofMo-POM with de novo organic hosts. (2) demonstration of kinetic precipitation ofa dynamic mixture of polyoxomolybdates and application of the technique to thestudy of the dynamic mixture by TEM (3) characterization of the Mo-POMnanostructures by an unusual combination of complementary analyticaltechniques. (4) a general approach for the synthesis of crown-ethers-containingtripodal molecules.The molecular recognition of Mo-POM with designer tripodal hexaminetris-crown ethers opened a window to the solution phase structures of Mo-POMnanoscopic components. Studies with a series of structurally analogous hostsprobed the relationship between the structure of the molecular host and theformation of nanostructures.An unusual combination of complementary analytical protocols: flow fieldflowfractionation, electron microscopy (transmission and scanning), andinductively coupled plasma – emission spectroscopy, was used to monitor thesolution-phase evolution of Mo-POM nanostructures. The crystallization – drivenformation of keplerate Mo-POM and solution-phase evolution of structurallyrelated nanoscopic species were apparent in the self-assembling process ofpartially reduced Mo-POM.

A promising new approach for studying cold ion-molecule chemical reactions is the combination of laser- or sympathetically-cooled trapped ions and slow-moving molecules from a cold molecule source, such as a quadrupole velocity selector or a Stark decelerator. Previous reaction studies using trapped atomic ions and slow molecules from a quadrupole velocity selector were able to reach average collision energies as low as 1 K. However, the guided molecules had an approximately room temperature rotational energy distribution, so the reactions studied were not truly cold. Thus, a new molecular source for producing translationally and rotationally cold molecules utilizing buffer gas cooling and quadrupole velocity selection was constructed by K. Twyman and characterized for use in cold reaction studies. This new source of cold molecules is referred to as the buffer gas guide. A new ion trap has been designed and built for use with the existing buffer gas guide. The new ion trap apparatus is compact and mechanically compatible with this new guide. It uses a linear Paul ion trap with cylindrical electrodes to trap ions. Two optical axes (one axial and one radial) enable efficient cooling of small ion crystals. A field-free time-of-flight tube and ion detection assembly are also incorporated into the apparatus. A new technique for determining the mass and quantity of trapped ions has also been developed, termed digital ion trap mass spectrometry. The new technique uses a digital RF waveform to trap ions before ejecting the ions radially from the trap using an ejection pulse applied to the trap electrodes. The ions are then detected after free flight along a time-of-flight tube. This technique was characterized by ejecting crystals of various sizes and compositions: Ca^&plus; only, Ca^&plus;/CaF^&plus;, Ca^&plus;/CaOH^&plus;/CaOD^&plus;, and Ca^&plus;/NH^&plus;<sub style='position: relative; left: -.6em;'>3</sub> /NH^&plus;<sub style='position: relative; left: -.6em;'>4</sub> /H₃O^&plus;. A linear relationship between the number of ions ejected (determined by comparing experimental and simulated crystal images) and the integral of the time-of-flight peak was observed for Ca^&plus; and Ca^&plus;/CaF^&plus;. All mass peaks were resolved. Simulations of the trapped ions and their trajectories through the time-of-flight tube were also performed, and excellent agreement between the simulated and experimental mass resolution was observed. Progress towards combining the buffer gas guide with the previously independent ion trap is also presented. It is anticipated that the combined buffer gas guide ion trap apparatus will enable the study of ion-molecule reactions at low temperatures with translationally and rotationally cold molecules. It is anticipated that the new digital ion trap mass spectrometry technique will simplify the study of reactions when multiple product ions whose masses are separated by only 1 AMU are formed. A new ion trap has been designed and built for use with the existing buffer gas guide. The new ion trap apparatus is compact and mechanically compatible with this new guide. It uses a linear Paul ion trap with cylindrical electrodes to trap ions. Two optical axes (one axial and one radial) enable efficient cooling of small ion crystals. A field-free time-of-flight tube and ion detection assembly are also incorporated into the apparatus. A new technique for determining the mass and quantity of trapped ions has also been developed, termed digital ion trap mass spectrometry. The new technique uses a digital RF waveform to trap ions before ejecting the ions radially from the trap using an ejection pulse applied to the trap electrodes. The ions are then detected after free flight along a time-of-flight tube. This technique was characterized by ejecting crystals of various sizes and compositions: Ca+ only, Ca+/CaF+, Ca+/CaOH+/CaOD+, and Ca+/NH+3/NH+4/H3O+. A linear relationship between the number of ions ejected (determined by comparing experimental and simulated crystal images) and the integral of the time-of-flight peak was observed for Ca+ and Ca+/CaF+. All mass peaks were resolved. Simulations of the trapped ions and their trajectories through the time-of-flight tube were also performed, and excellent agreement between the simulated and experimental mass resolution was observed. Progress towards combining the buffer gas guide with the previously independent ion trap is also presented. It is anticipated that the combined buffer gas guide ion trap apparatus will enable the study of ion-molecule reactions at low temperatures with translationally and rotationally cold molecules. It is anticipated that the new digital ion trap mass spectrometry technique will simplify the study of reactions when multiple product ions whose masses are separated by only 1 AMU are formed.

Mass spectrometry is a technique that analyzes the chemical compositions of compounds based on the mass-to-charge ratio of their ionized constituents. Miniaturized ion trap mass spectrometry finds application in a wide range of fields where portable, rugged, and reliable analytical instruments are required. Ion traps of various designs have been introduced over the past decades, each with their own unique advantages and capabilities. However, the process of developing a novel miniaturized ion trap mass spectrometer continues to be fraught with challenges. This dissertation discusses simulation studies pertaining to the development of a novel dual ion trap, the simplified coaxial ion trap, consisting of a simplified toroidal ion trap and a cylindrical ion trap. Ions are initially trapped in the toroidal region and the target ions are transferred to the cylindrical region where they are fragmented and mass analyzed, while the rest of the ion population remains securely trapped in the toroidal region. The compact design and extended trapping volume secure several advantages that are not available to conventional ion trap designs. The simulations were geared towards the determination of an optimized geometry and optimal operating conditions for the simplified coaxial ion trap. Four main criteria were used in the determination of the ideal geometric and operating conditions; namely, mass-selectivity of transfer from the toroidal to cylindrical traps, transfer and trapping efficiency in the cylindrical ion trap, mass resolution, and unidirectional ejection. The optimized geometry demonstrates successful trapping of ions in the toroidal region and selective transfer of target ions to the cylindrical region. Unidirectional inward ejection of ions could be achieved with a positive hexapole component in the electric field. The mass resolution under optimized conditions of the toroidal trap was 0.3 Da (FWHM), which agrees with the experimental value. The simplified coaxial ion trap yielded a total transfer and trapping efficiency of 25%. A number of suggestions to improve the efficiency are also discussed as part of this work.

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.