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.

The dissertation focuses on the temperature dependent rate coefficient measurement of reactions in the interstellar medium using a coaxial molecular beam ring electrode ion trap apparatus. The first chapter introduces the previous studies of ion-molecule reactions in the ISM, the types of instruments mainly used in the reaction rate coefficient study, the former research on the ring electrode ion trap and the gas phase reaction mechanisms. Compare to other instruments, our molecular beam - ring electrode ion trap is extremely good at ion cooling and temperature control for both ions and neutral molecules. Chapter two describes each part of the instrument used in detail. Ions produced by electron impact in the ion source chamber, are mass filtered and then reach the ring electrode ion trap. In the trap, ions collide with molecules in the molecular beam where reaction takes place. When the reaction is done, all the ions remained in the trap (the reactant and product ions) come out and move to the detector. The molecular beam terminates at residual gas analyzer which is used for the number density calibration. The third chapter shows how the temperature of ions and molecules are controlled separately in order to find the reaction mechanism. Ions are cooled by the pulsed He buffer in the ring electrode trap and a chopped beam is used to make sure the ions are cooled to the desired low temperature when the reaction takes place. Chapters four to six describe the three reactions being studied using this instrument: N₂⁺ + H₂O charge transfer reaction, H₃O⁺ + C₂H₄ proton transfer reaction and H3O⁺ + (C₂H₂)₂/C₂H₂ dimer reaction. The temperature dependent rate coefficient data of these reactions are explained by the average dipole orientation theory, statistical theory and Colussi's acetylene dimer model, respectively. Two temperatures are defined and applied in the experimental rate coefficients analysis: ion-molecule center of mass collision temperature and the reaction statistical temperature which is based on the numbers of degrees of freedom of both reactants.

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.

<p>Atomic ions trapped in microfabricated surface traps can be utilized as a physical platform with which to build a quantum computer. They possess many of the desirable characteristics of such a device, including high fidelity state preparation and readout, universal logic gates, and long coherence times, and can be readily entangled with each other through photonic interconnects. The use of optical cavities integrated with trapped ion qubits as a photonic interface presents the possibility for order of magnitude improvements in performance in several key areas for their use in quantum computation. The first part of this thesis describes the design and fabrication of a novel surface trap for integration with an optical cavity. The trap is custom made on a highly reflective mirror surface and includes the capability of moving the ion trap location along all three trap axes with nanometer scale precision. The second part of this thesis demonstrates the suitability of small microcavities formed from laser ablated, fused silica substrates with radii of curvature in the 300-500 micron range for use with the mirror trap as part of an integrated ion trap cavity system. Quantum computing applications for such a system include dramatic improvements in the photon entanglement rate of up to 10 kHz, the qubit measurement time down to 1 microsecond, and the qubit measurement error rate down to the 1e-5 range. The final part of this thesis describes a performance simulator for exploring the physical resource requirements and performance demands to scale a quantum computer to sizes capable of implementing quantum algorithms beyond the limits of classical computation.</p> / Dissertation

Ion traps can easily be miniaturized to become portable mass spectrometers. Trapped ions can be ejected by adjusting voltage settings of the radiofrequency (RF) signal applied to the electrodes. Several ion trap designs include the quadrupole ion trap (QIT), cylindrical ion trap (CIT), linear ion trap (LIT), rectilinear ion trap (RIT), toroidal ion trap, and cylindrical toroidal ion trap. Although toroidal ion traps are being used more widely in miniaturized mass spectrometers, there is a lack of fundamental understanding of how the toroidal electric field affects ion motion, and therefore, the ion trap's performance as a mass analyzer. Simulation programs can be used to discover how traps with toroidal geometry can be optimized. Potential mapping, field calculations, and simulations of ion motion were used to compare three types of toroidal ion traps: a symmetric and an asymmetric trap made using hyperbolic electrodes, and a simplified trap made using cylindrical electrodes. Toroidal harmonics, which represent solutions to the Laplace equation in a toroidal coordinate system, may be useful to understand toroidal ion traps. Ion trapping and ion motion simulations were performed in a time-varying electric potential representing the symmetric, second-order toroidal harmonic of the second kind—the solution most analogous to the conventional, Cartesian quadrupole. This potential distribution, which we call the toroidal quadrupole, demonstrated non-ideal features in the stability diagram of the toroidal quadrupole which were similar to that for conventional ion traps with higher-order field contributions. To eliminate or reduce these non-ideal features, other solutions to the Laplace equation can be added to the toroidal quadrupole, namely the toroidal dipole, toroidal hexapole, toroidal octopole, and toroidal decapole. The addition of a toroidal hexapole component to the toroidal quadrupole provides improvement in ion trapping, and is expected to play an important role in optimizing the performance of all types of toroidal ion trap mass spectrometers.The cylindrical toroidal ion trap has been miniaturized for a portable mass spectrometer. The first miniaturized version (r0 and z0 reduced by 1/3) used the same central electrode and alignment sleeve as the original design, but it had too high of capacitance for the desired RF frequency. The second miniaturized version (R, r0, and z0 reduced by 1/3) was designed with much less capacitance, but several issues including electrode alignment and sample pressure control caused the mass spectra to have poor resolution. The third miniaturized design used a different alignment method, and its efficiency still needs to be improved.

Mass measurements provide important information concerning nuclear structure. This work presents results from the pioneering Penning trap spectrometer Isoltrap at CERN-ISOLDE. High-precision mass measurements of neutron-rich manganese (58−66Mn) and krypton isotopes (96,97Kr) are presented, of which the 66Mn and 96,97Kr masses are measured for the first time. In particular, the mass of 97Kr was measured using the preparation trap and required the definition of a new fit function. In the case of the manganese isotopes, the N = 40 shell closure is addressed. The two-neutron-separation energies calculated from the new masses show no shell closure at N = 40 but give an estimation of the proton-neutron interaction (around 0.5 MeV) responsible for the increase of collectivity and nuclear deformation in this mass region. The new krypton masses show behavior in sharp contrast with heavier neighbors where sudden and intense deformation is present, interpreted as the establishment of a nuclear quantum shape/phase transition critical-point boundary. The new masses confirm findings from nuclear mean-square charge-radius measurements up to N = 60 but are at variance with conclusions from recent gamma-ray spectroscopy. Another part of this work was the design of new decay spectroscopy system behind the Isoltrap mass spectrometer. The beam purity achievable with Isoltrap will allow decay studies with and detection coupled to a tape-station. This system has been mounted and commissioned with the radioactive beam 80Rb.

GnRH peptides have been discovered in a wide variety of vertebrate and invertebrate organisms, and work is ongoing to characterize additional unique isoforms. This dissertation describes the investigation of reversed-phase chromatographic and mass spectrometric behavior of GnRH peptides, the development and application of an LC-MS/MS method for qualitative identification of GnRH peptides, and the comprehensive validation of an LC-MS/MS method for simultaneous, quantitative measurement of hydroxyproline9GnRH (Hyp9GnRH) and mammalian GnRH (mGnRH) in rat brain tissues. Chromatographic and mass spectrometric behavior of GnRH isoforms was characterized for six GnRH model peptides. Using reversed-phase high performance liquid chromatography (HPLC), nearly complete separation of the model GnRH peptides was achieved. Evaluation of electrospray source conditions indicated that certain parameters can be adjusted to affect the abundance of selected charge states and improve response. Using the conditions found to be optimal for GnRH peptides in general, a method was developed to facilitate characterization of novel GnRH isoforms or confirm the identity of known isoforms. Fragmentation patterns for six model GnRH isoforms were examined to determine what portion of the primary sequence could be elucidated by de novo sequencing, and a simple solid phase extraction protocol was developed to isolate the model GnRH compounds from tissue samples. Application of the method to rat brain samples resulted in successful isolation and structural confirmation of hydroxyproline9GnRH and mammalian GnRH. A quantitative method for the determination of concentrations of hydroxyproline9GnRH and mammalian GnRH in rat brain tissue was developed and rigorously validated. Guinea pig brains were found to be a suitable substitute matrix for rat brains, and accuracy and precision were determined after four validation runs. Stability of both peptides in samples over long-term storage and under experimental conditions were evaluated, and the LC-MS/MS method was compared to an enzyme-linked immunoassay. Thirty-one brains from Sprague-Dawley rats were analyzed using the LC-MS/MS procedure and compared to published results for Hyp9GnRH and mGnRH.

An investigation of the sympathetic cooling method for the studies of large ultra-cold molecular ions in a quadrupole ion trap has been conducted.Molecular dynamics simulations are performed to study the rf heating mechanisms in the ion trap. The dependence of rf heating rates on the ion temperature, trapping parameters, and the number of ions is obtained. New rf heating mechanism affecting ultra-cold ion clouds exposed to laser radiation is described.The saturation spectroscopy setup of the hyperfine spectra of the molecular iodine has been built to provide an accurate frequency reference for the laser wavelength. This reference is used to obtain the fluorescence lineshapes of the laser cooled Mg$^+$ ions under different trapping conditions.The ion temperatures are deduced from the measurements, and the influence of the rf heating rates on the fluorescence lineshapes is also discussed. Cooling of the heavy ($m=720$a.u.) fullerene ions to under 10K by the means of the sympathetic cooling by the Mg$^+$ ions($m=24$a.u.) is demonstrated. The single-photon imaging system has been developed and used to obtain the images of the Mg$^+$ ion crystal structures at mK temperatures.

Cold trapped ions have many applications in quantum information science and precision metrology. In this thesis, we present progress toward two objectives involving ions confined to linear RF traps: the strong coupling of Ba+ ions with a high finesse optical cavity, and the observation of an optical nuclear transition in 229Th3+. In pursuit of the first objective, a novel high-temperture vapor cell for the spectroscopy of neutral barium was constructed. Using this vapor cell, a new technique for isotope-selective photoionization loading of Ba+ in an ion trap was developed. In pursuit of the second objective, techniques ultimately to be used in creating, trapping, and observing 229Th3+ are studied using 232Th3+. Ion traps are loaded with 232Th3+ via laser ablation of thorium targets. 232Th3+ is detected optically using laser-induced fluorescence and electronically using a channel electron multiplier. A technique for creating ablation targets from trace quantities of thorium nitrate is presented. The primary loss mechanisms of Th3+, charge exchange and chemical reactions, are studied.

Universal quantum computation requires precision control of the dynamics of qubits. Frequently accurate quantum control is impeded by systematic drifts and other errors. Compensating composite pulse sequences are a resource efficient technique for quantum error reduction. This work describes compensating sequences for ion-trap quantum computers. We introduce a Lie-algebraic framework which unifies all known fully-compensating sequences and admits a novel geometric interpretation where sequences are treated as vector paths on a dynamical Lie algebra. Using these techniques, we construct new narrowband sequences with improved error correction and reduced time costs. We use these sequences to achieve laser addressing of single trapped 40Ca+ ions, even if neighboring ions experience significant field intensity. We also use broadband sequences to achieve robust control of 171Yb+ ions even with inhomogeneous microwave fields. Further, we generalize compensating sequences to correct certain multi-qubit interactions. We show that multi-qubit gates may be corrected to arbitrary accuracy if there exists either two non-commuting controls with correlated errors or one error-free control. A practical ion-trap quantum computer must be extendible to many trapped ions. One solution is to employ microfabricated surface-electrode traps, which are well-suited for scalable designs and integrated systems. We describe two novel surface-electrode traps, one with on-chip microwave waveguides for hyperfine 171Yb+ qubit manipulations, and a second trap with an integrated high numerical aperture spherical micromirror for enhanced fluorescence collection.