A multiplexed method for performing MS/MS on multiple ions simultaneously in a miniature rectilinear ion trap (RIT) mass spectrometer has been developed. This method uses an ion encoding procedure that relies on the mass bias that exists when ions are externally injected into an RIT operated with only a single phase RF applied to one pair of electrodes. The ion injection profile under such conditions ions is Gaussian-like over a wide range of RF amplitudes, or low mass cutoff (LMCO) values, during ion accumulation. We show that this distribution is related to ion m/z, and is likely caused by ions having an optimal range of pseudo-potential well depths for efficient trapping. Based on this observation, precursor ion intensity changes between two different injection LMCO values can be predicted, and these ion intensity changes are found to be carried through to their corresponding product ions, enabling multiplexed MS/MS spectra to be deconvoluted. The gas-phase reactions of a series of coordinatively unsaturated [Ni(L) n]y+ complexes, where L is a nitrogen-containing ligand, with chemical warfare agent (CWA) simulants in a miniature rectilinear ion trap mass spectrometer were investigated as part of a new approach to detect CWA. Results show that the metal complex ions can react with low concentrations of several CWA simulants, including dipropyl sulfide (simulant for mustard gas), acetonitrile (simulant for the nerve agent tabun), and diethyl phosphite (simulant for nerve agents sarin, soman, tabun, and VX), thereby providing a sensitive means of detecting these compounds. The [Ni(L)n] 2+ complexes are found to be particularly reactive with the simulants of mustard gas and tabun, allowing their detection at low parts-per-billion (ppb) levels. These detection limits are well below the median lethal doses for these CWAs, which indicates the applicability of this new approach, and are about two orders of magnitude lower than electron ionization detection limits on the same mass spectrometer. The use of coordinatively unsaturated metal complexes as reagent ions offers the possibility of further tuning the ion-molecule chemistry so that desired compounds can be detected selectively or at even lower concentrations. Mass spectrometry has become a tool for studying noncovalently bound complexes. Specifically, electrospray ionization mass spectrometry (ESI-MS) has found increasing use for the determination of affinity (Ka) or dissociation (Kd) constants. Direct measurement of the equilibrium components by ESI-MS is the most straightforward approach for determining binding equilibrium constants, but this approach is prone to error and has some inherent limitations. Transferring complexes from solution to the gas phase may perturb the equilibrium concentrations and/or different ionization efficiencies may cause the resulting ion signals not to reflect actual solution concentrations. Furthermore, ESI only works under a limited range of solvent conditions (i.e. low ionic strengths), which limits the broad applicability of this approach. We propose an approach based on covalent labeling in the context of metal-catalyzed oxidation (MCO) reactions that, when combined with MS, overcomes such limitations when determining metal-ligand binding constants. The MCO-MS approach will provide concurrent information regarding metal binding site and metal-protein binding affinity. Optimization of the MCO reaction through isotopic mass tags will permit enhanced identification of modified residues. Application of this method to study the affinity and binding interactions of other divalent metals with β2m are likely to provide insight into the specificity of copper for causing β2m amyloid formation.

<p> Nanomaterials are the focus of intense research efforts in a variety of fields because of dramatic differences in properties when compared to the corresponding bulk materials. Catalysis is one material property that can become more pronounced at the nanoscale. By lowering energy requirements for chemical reactions, catalysts reduce production costs in diverse sectors of the economy, including medicine, transportation, environmental protection, oil and gas, food, and synthetic materials. Transition metals are an important class of catalysts capable of facilitating reduction and oxidation of molecular species. Since the discovery of transition metal catalysts nearly 200 years ago, certain metals were considered more active as catalysts (i.e., Pt, Pd, and Ru), while others (Au) appeared to have negligible catalytic activity as bulk materials. In recent years, gold nanoparticles (AuNPs) have become a fast-growing field of research owing to their unexpected catalytic properties not present in the bulk material. However, unsupported AuNPs are highly prone to flocculation and subsequent reduced catalytic activity. The choice of an appropriate aggregation-resistant stabilizing ligand for these nanoparticles is an important part of maintaining nanoscale catalytic properties. Additional stability is provided by anchoring AuNPs to support materials, allowing for dramatic improvements in catalyst lifetimes. This work discusses the development of novel diamond support materials for improving the stability of catalytically active AuNPs. Synthetic nanodiamond is a widely available, inexpensive, and robust material that has found applications in a wide range of commercial abrasives, lubricants, and composite materials. By exploiting the rich surface chemistry of nanodiamond, we have developed versatile catalyst support materials that offer unrivaled chemical and mechanical stability. Various nanodiamond surface modifications are readily prepared using a combination of chemical vapor deposition, photo-active polymer chemistry, and synthetic organic chemistry techniques. Control over the surface chemistry and properties of the resulting nanodiamond allow for increased stability of AuNPs via surface anchored thiol and amine moieties. The use of diamond as a support material should allow a wide variety of noble and nonprecious metal composite materials to be used as catalysts in harsh chemical environments not suitable for existing support materials.</p><p>

<p>We have found that calixarenes are good receptors of choline (trimethylammonium group) and they have strong affinity to form host-guest complexes with a variety of molecules carrying this moiety. Furthermore, the ability of lower rim carboxylic acid calix[n]arenes and upper rim phosphonic acid functionalized calix[4]arene to transport choline-conjugated drugs through a liquid membrane was discovered. The results demonstrate that these systems are highly efficient toward transporting choline-conjugated targets, as well as neurotransmitters that possess ionizable amine termini. The breadth of compounds that are transported is significant, facing limitations only when the payloads become extremely lipophilic. These developments reveal new approaches towards attempting synthetic receptor mediated selective small molecule transport in vesicular and cellular systems.

<p> Metal containing complexes have been used to catalyze various organic transformations for the past few decades. The success of several mononuclear catalysts led to transition metal catalysts used in pharmaceuticals, environmental, and industrial processes. While mononuclear complexes have been used extensively, bimetallic systems have received far less attention. Bimetallic or polynuclear sites are commonly found in metalloenzymes that perform elegant transformation in biological systems, underlying their significance. Inorganic chemists take inspiration from nature and design model bimetallic complexes to further study this cooperativity effect. A bimetallic platform offers many structural and functional differences such as the identity of the metal atoms and the bonding interactions between metals, which have been reflected in their unique catalytic ability and reactivity. </p><p> This dissertation encompasses work related to the computational study of metal-metal interactions of bimetallic systems, the ¹H NMR study of stereochemical and conformational changes in solution of <i> N,N'</i>-diarylformamidines, the synthesis of dizinc formamidinate complexes, and the synthesis and catalytic ability of dicopper formamidinate complexes. </p><p> In the first part, DFT calculations are used to study factors that influence metal-metal bond lengths in various complexes. Several experimentally obtained X-ray crystal structures were used as the basis for the study. Differences in metal-metal separations were investigated through various functionals, indicating the importance of charge, orbital interactions, and formal bond order. BH&amp;HLYP SDD/aug-CC-PVDZ geometry optimizations of octahalodimetalate anions Tc₂X₈^n- (X = Cl, Br; n=2, 3), Re₂X₈^2- (X = Cl, Br), and Mo₂Cl₈^4- reproduced M-M bond distance trends observed experimentally. The study demonstrated that the increase in &sigma; and &pi; bond strength resulted in the shortening in Tc-Tc bond distance from Tc₂X₈^2- to Tc₂X₈^3-, which was further supported by the short Mo-Mo bond in the Mo₂Cl₈^4- ion. This study was expanded further through the inclusion of [M₂Cl₄(PMe₃)₄]ⁿ⁺ (M = Tc, Re, n = 0-2) and [Mo₂E₄]^n- (E = HPO₄ or SO₄, n = 2-4), allowing a systematic study on the role of charge on the metal atoms. PBEO SDD/aug-CC-PVDZ calculations revealed that both formal bond order and formal charge on the metal atoms dictate the trends in M-M bond strength. </p><p> The second half of this dissertation focuses on the synthesis and characterization of bimetallic Zn- and Cu-formamidinate complexes. The stereochemical exchange of substituted <i>N,N'</i>-diarylformamidines were studied through ¹H NMR in various solvents. Alkyl substituents placed on the ortho positions were found to shift the isomeric equilibrium in solution through destabilization of the hydrogen-bond dimer evident in X-ray crystal structures. The Z-isomer of substituted <i>N,N'</i>-diarylformamidines is observed in CDCl₃, C₆D₆, and DMSO-d₆ when the ligands feature significant steric hinderance. Similar ortho substituted <i> N,N'</i>-diarylformamidines were also used to enforce steric interactions to limit the nuclearity of Zn-formamidinate complexes. Various dizinc formamidinate complexes were synthesized through direct and transmetalation routes. NMR and mass spectrometry were used alongside X-ray crystal structures to fully characterize the dizinc complexes. Dicopper formamidinates formed through a transmetallation route were synthesized and feature distinct short Cu^&hellip;Cu separations thought to be brought about by metalophillic interactions. Preliminary results suggest catalytic ability of dicopper formamidinates in cyclopropanation and aziridination of styrene with various diazo compounds. The catalytic activity suggests the formation of dicopper carbene and nitrene intermediates, of which only few published experimentally observed examples exist in the literature.</p><p>

Axial mole-fraction profiles were measured in a low-pressure reactive flow of propylene/chlorine and a low-pressure, fuel-rich ethylene flame doped with allene. The purpose was to generate data and test models for improving allyl chloride production and pollutant-related C3 flame chemistry. Molecular-beam mass spectrometry was the principal analytical technique. The propylene/chlorine system had feed conditions of 71.2% propylene and 28.8% chlorine, 76.00 ± 0.01 Torr, and 17.5 cm/s burner-surface gas velocity (298 K). Because propylene and chlorine could pre-react, a novel multidiffusion burner was developed. Mole fraction profiles were mapped for seven stable species. Temperature measurements were made using a K-type thermocouple, and the constant flow cross-section was determined visually. By modeling as a plug-flow reactor with literature rate constants and data and rate constants determined here, a self-consistent reaction mechanism was constructed and used to predict concentration profiles for unmeasured species. Predicted profiles were consistent with measured data. Thus, by also accounting for pressure effects, the new model provides a sound basis for modeling the industrial process. The allene-doped ethylene flame had a fuel equivalence ratio of 1.9 and feed gas composition of 0.5% allene, 18.9% C2H4, 30.9% O 2, and 49.7% Ar. It was operated at 20.00 ± 0.01 Torr with a burner surface gas velocity at 298 K of 62.5 cm/s. Mole fraction profiles were measured for 41 stable and radical species. Data from this allene-doped ethylene flame were compared to the data of Bhargava's (1997) nearly identical fuel-rich undoped ethylene flame. Addition of allene enhanced the production of phenyl and benzene, supporting the arguments that C3 species play a very important role in the formation of phenyl and benzene. Using the data and reaction path analysis, Bhargava's (1997) reaction set was improved. New rate constants were determined, incorrect reactions were removed, and new chemistry was added, improving many of the model predictions. Modeling suggested that the major reaction responsible for increased production of phenyl and benzene was 2C3H3 = phenyl +H. Identification and analysis of an important error in Bhargava's reaction set suggest that a reactive boundary condition at the burner surface may be necessary for improved modeling of this flame.

Thesis (Ph.D.)--Lehigh University, 2009. / Adviser: Tianbo Liu.

<p> The development of better energy conversion and storage devices, such as fuel cells and batteries, is crucial for reduction of our global carbon footprint and improving the quality of the air we breathe. However, both of these technologies face important challenges. The development of lower cost and better electrode materials, which are more durable and allow more control over the electrochemical reactions occurring at the electrode/electrolyte interface, is perhaps most important for meeting these challenges. Hence, full characterization of the electrochemical processes that occur at the electrodes is vital for intelligent design of more energy efficient electrodes. </p><p> X-ray absorption spectroscopy (XAS) is a short-range order, element specific technique that can be utilized to probe the processes occurring at operating electrode surfaces, as well for studying the amorphous materials and nano-particles making up the electrodes. It has been increasingly used in recent years to study fuel cell catalysts through application of the &Delta;&mgr; XANES technique, in combination with the more traditional X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) techniques. The &Delta;&mgr; XANES data analysis technique, previously developed and applied to heterogeneous catalysts and fuel cell electrocatalysts by the GWU group, was extended in this work to provide for the first time space resolved adsorbate coverages on both electrodes of a direct methanol fuel cell. Even more importantly, the &Delta;&mgr; technique was applied for the first time to battery relevant materials, where bulk properties such as the oxidation state and local geometry of a cathode are followed.</p>

<p> This dissertation describes metabolic engineering of cyanobacterium <i> Synechococcus elongatus</i> PCC7942 as a photosynthetic host for the conversion of CO₂ into 2,3-butanediol. Current advances in pathway design, genetic tool development, and yield improvement are described (Chapter 1). A pathway for the synthesis of 2,3-butanediol is designed based on collective concepts of pathway strength, robustness, and irreversibility, and extensively tested through the generation of mutants (Chapter 2). This pathway is then optimized through modulation of translation by combinatorial mixing of ribosome binding sites (Chapter 3). Finally, photosynthetic productivity is investigated through expression of an exogenous pathway targeting every step between fixation and product (Chapter 4). All materials and methods are given separately for easy reference (Chapter 5).</p>

<p> Heavy metal pollution is a growing concern as growing worldwide population and industrial processes increase pollution levels in most environments. High metal concentrations throughout ecosystems pose a serious threat to wild-life and human health. Methods to monitor rising threat levels of metals are a primary concern for monitoring overall ecosystem health. Mechanisms which spread pollution must be intimately understood because of the persistence of heavy metals. Heavy metal contamination in the Tar Creek superfund site provides a great case study to selectively observe differences in heavy metals concentrations both upstream and downstream of mining activity. Thus, research is able to identify natural and man-made point sources of pollution. </p><p> The abilities of bivalves to filter-feed and sediment-feed provide a unique monitoring tool for analyzing heavy metals. Mussels are constantly filtering the environment around them. A mussel's seasonal and annual growth layers provide an excellent sample media for obtaining historical records of environmental data. Many species of mussels are found in most freshwater ecosystems throughout the United States. Mussels have low migration rates, live for a suitable amount of time, and leave relic shells. These features make mussels very practical for monitoring heavy metal pollution. </p><p> Various studies were conducted to obtain insight into developing methods for using LA-ICP-MS as a tool for monitoring heavy metals in mussel shells. Surface laser ablations, compared at additional depths, resulted in a more than 20% increase in signal intensity. Theoretical and experimental designs show signal changes as a function of depth. Mussel tissue and shell digestions were found to be best when using approximately 1.0 mL of hydrogen peroxide and 1.0 mL of nitric acid for each 0.1 grams of sample. Mussel tissue was found to have greater heavy metal concentrations than shells. Shells were found to average a 96% weight of calcium carbonate; however, the organic layers contained the greatest concentrations of heavy metals per weight. </p>

<p> The objective in this thesis is to study the structure of peptides using molecular spectroscopy. Molecular spectroscopy, both vibrational and electronic, can be used as a sensitive tool to study molecular structure. Since it is an inherently low resolution method, theoretical calculations are essential for a complete understanding of vibrational and electronic spectra. The first part of this thesis contains quantum chemical calculations of the molecular spectra of several small peptide systems with different secondary structures. Optical trapping is a method that allows for the manipulation of sub-micron scale objects using tightly focused laser light. Raman spectroscopy, which is sensitive to molecular vibrations also requires intense laser light. Combined with optical tweezing, Raman spectroscopy can prove to be a very powerful tool to study small sample volumes and probe single living cells. In the second part of this thesis, I detail the construction an such an instrument, an optical trapping Raman spectrometer (OTRS). Our OTRS can measure Raman spectra from sub micron systems while at the same time quantifying the mechanical forces that are acting upon them. Thus the OTRS can give insight into the relationship between mechanical forces acting upon cells and their molecular structure. </p>