Successful methods for the separation of biomolecules like amino acids, proteins, peptides, and DNA have been developed previously using HPLC, GC, GC-MS, and CE. Recently CE has become a routine laboratory technique in the analysis of biological molecules. Even though high-resolution separations with small sample volumes is the main advantage, CE is limited by lower sensitivity detection of analytes when universal detectors like UV absorption or refractive index detectors are used. Therefore, sensitivity enhancement can be obtained by either using different detection schemes or electrophoretically based pre- or on-line concentration methods. These can be grouped into two categories. The first category includes IEF, CGF or TGF where sensitivity is achieved through equilibrium electrofocusing. In these methods, electrophoresis and bulk solution is combined in the capillary or separation column to form a null velocity point, a point at which the net velocity of the analyte is zero. Using these methods 10-10,000 fold sensitivity enhancement is achieved. The second category uses velocity gradients but not the nul velocity for the enrichment of samples. These methods include FASS, LVSS, NSM, etc., which are applied for the analysis of small molecules, and 10-10,000 fold sensitivity enhancement is reported by using these methods. In this work, first GEITP an on-line preconcentration technique is applied for the detection of amino acids (using Trp and Tyr as model analytes). This work also established the effects of different parameters on enrichment. The parameters studied include effect of current flow acceleration across capillary inner diameter, the effect of leading electrolyte (LE) concentration on current density, and the effect of applied electric fields on the current density. To explore the application of GEITP in biological fluids, optimized parameters were developed for the detection and separation of Trp and Tyr in artificial cerebrospinal fluid (aCSF). Next, GEITP was applied for enrichment and separation of physiologically relevant concentrations of chromophore-derivatized Asp and Glu in high conductivity samples like artificial cerebrospinal fluid (aCSF). It was concluded from this work that the major factors which influence the enrichment is the ratio of current density to sample conductivity. Finally, GEITP is applied as a prior step before CZE to increase the resolution between analytes without using ampholyte mixtures. In this method GEITP was combined to CZE to achieve resolution adjustment between amino acids mixture using low pressure hydrodynamic flow during CZE without changing the separation column, field strength, or electrolyte system. In this work, a rapid CE method for extraction and analysis of amino acids in planarians, labeled with 4-Fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F), was developed. This method was applied to detect the changes in the levels of amino acids when planarians were fed and starved. This method can be applied to study pharmacological effects in planaria, as it can monitor different amino acid levels with respect to feeding. Finally, ssDNA photoproducts of different lengths (11-mer and 63-mer) were separated using two different matrices, a traditional C18 and a PV/DBS (PLRP-S) matrix. A faster separation (within ~ 10 mins) was achieved for a 11-mer by the PLRP-S column. A separation was achieved in the PLRP-S column for the 63-mer while there was no separation in C18 column. Baseline resolution was not achieved. Therefore, C18 can best be used for small length DNA while PLRP-S can be applied for longer length DNA, as it is more hydrophobic than C18 column. Parameters can still be optimized for a baseline separation. / Chemistry

Electronic structure methods aim to accurately describe the behaviour of the electrons in molecules and materials. To be applicable to arbitrary systems, these methods cannot depend on observations of specific chemical phenomena and must be derived solely from the fundamental physical constants and laws that govern all electrons. Such methods are called ab initio methods. Ab initio methods directly solve the electronic Schrödinger equation to obtain the electronic energy and wavefunction. For more than one electron, solving the electronic Schrödinger equation is impossible, so it is imperative to develop approximate methods that cater to the needs of their users, which can vary depending on the chemical systems under study, the available computational resources and time, and the desired level of accuracy. The most accessible ab initio approaches, including Hartree-Fock methods and Kohn-Sham density functional theory methods, assume that only one electronic configuration is needed to describe the system. While these single-reference methods are successful when describing systems where a single electron configuration dominates, like most closed-shell ground-state organic molecules in their equilibrium geometries, single-reference methods are unreliable for molecules in nonequilibrium geometries (e.g., transition states) and molecules containing unpaired electrons (e.g., transition metal complexes and radicals). For these types of multireference systems, accurate results can only be obtained if multiple electronic configurations are accounted for. Wavefunctions that incorporate many electronic configurations are called multideterminant wavefunctions. This thesis presents a systematic approach to developing multideterminant wavefunctions. First, we establish a framework that outlines the structural components of a multideterminant wavefunction and propose several novel wavefunction ansätze. Then, we present a software package that is designed to aid the development of new wavefunctions and algorithms. Using this approach, we develop an algorithm for evaluating the geminal wavefunctions, a class of multideterminant wavefunctions that are expressed with respect to electron pairs. Finally, we explore using machine learning to solve the Schrödinger equation by presenting a neural network wavefunction ansatz and optimizing its parameters using stochastic gradient descent. / Thesis / Doctor of Science (PhD)

Characterizing nanoparticles to be able to understand how they functions in the body is important for development of drugs. Furthermore with increasing number of nanoparticle product the nanotoxicity of nanoparticles is important to understand. This report is a part of the EU-project Nanoclassifier which purpose is to “develop a cost effective, high throughput screening platform for characterization of the bionanointerface and its cell-binding partners”. Single-cycle kinetic was used to determine the number of binding epitopes on polystyrene nanoparticle with transferrin corona. The number of available epitopes describes how active the Nanoparticle will be in the body. For this purpose Single-cycle kinetic methodology was successfully used on nanoparticles. Single-cycle kinetic methodology has great potential to become the standard method for high throughput nanoparticle epitope characterization.

Polycyclic Aromatic Hydrocarbons (PAHs) are one of the pollutants in the environment. They are organic compounds that consist of more than one aromatic ring (Kanchanamayoon & Tatrahun 2008). Due to less information forthcoming regarding the levels of PAHs in Vaal area, this study is to evaluate the levels of PAHs in the rivers around Vaal Triangle. Three river sites such as Vaal, Barrage and Klip Rivers were selected to investigate the concentration of polycyclic aromatic hydrocarbons in water. Validation of an analytical method is the process by which it is established by laboratory studies, that the performance characteristics of the method meet the requirements for the intended analytical application. (Stockl et al 2009). The validation parameters tested were, linearity detection limit of quantitation, sensitivity, accuracy, specificity, selectivity, robustness and ruggedness. PAHs can be determined using High Performance Liquid Chromatography (HPLC) which is a technique for separation, identification and quantification of components in a mixture. The following ten compounds were identified and quantified with a HPLC: naphthalene, acenaphthylene, phenanthrene, anthracene, fluoranthene, benzo(b)fluoranthene, benzo(k)fluoranthene, benzo(a)pyrene, dibenzo(a,h) anthracene and indeno(1,2,3-cd)pyrene. The linear calibration ranges from 0.1-5ppm.The linearity ranges between 0.9993-0.9999.Three reversed sorbent phases (Strata-X, MFC18 and C18) were tested for PAH retention efficiency. An optimised reverse solid phase extraction (SPE) method was used after conditioning the sorbent to extract and collect compounds of polycyclic aromatic hydrocarbons (PAHs) in river water samples. LC18 sorbent showed good recoveries after extracting PAHs standard mixture of 1 mg/l. The best performing eluting solvent was acetonitrile and very good percentage recoveries that ranged from 70% to over 100 % were obtained for eight compounds. Poor recoveries were also obtained for phenanthrene (61%) and benzo(b)fluoranthene (48%). The standard deviation ranged from 0.01 to 0.05 and the detection limits ranging from 0.01 – 0.17 mg/l were obtained. Average concentration ranges of PAHs identified within the study area were: phenanthrene (0.02 – 0.42 mg/l); anthracene (0.37 – 0.39 mg/l), fluoranthene (0.11 – 0.15 mg/l); benzo(b)fluoranthene (0.09 mg/l) and indeno(1,2,3-cd)pyrene (0.26 mg/l). However, naphthalene, acenaphthylene, benzo(k)fluoranthene, benzo(a)pyrene and dibenzo(a,h)anthracene were not detected.

Le profilage d’impuretés de candidats médicaments est une préoccupation majeure des industries pharmaceutiques. L’identification et la quantification des impuretés doivent être strictement contrôlées pour assurer l’efficacité et la toxicité limitée du principe actif. Il est donc nécessaire de disposer de méthodes analytiques performantes afin de s’assurer que l’ensemble des impuretés est identifié. L’HPLC phase inverse sur phase C18 reste aujourd’hui la méthode de choix pour cette tâche. Cependant, il arrive que cette méthode échoue, notamment lorsque le principe actif n’est pas suffisamment retenu sur la colonne ou que les impuretés ne sont pas parfaitement séparées du composé principal. Il est alors essentiel de pouvoir se tourner vers des méthodes analytiques alternatives et complémentaires.Ce travail de recherche traite du développement et de l’évaluation de méthodes analytiques alternatives à l’HPLC phase inverse sur phase C18 pour le profilage d’impuretés de principes actifs pharmaceutiques. L’HPLC phase inverse sur d’autres phases stationnaires, l’HPLC mixed-mode ainsi que la SFC ont été explorées et leurs performances chromatographiques comparées. La comparaison et l’étude des différentes méthodes ont permis de proposer une stratégie d’analyse du candidat médicament. / Impurity profiling of drug candidates is a significant concern of pharmaceutical industries. The identification and quantification of impurities must be strictly controlled to ensure the efficacy and limited toxicity of the active ingredient. It is therefore necessary to have efficient analytical methods to ensure that all impurities are identified. Today, reversed-phase HPLC with C18 column remains the method of choice for this task. However, this method sometimes fails, particularly when the active pharmaceutical ingredient is not sufficiently retained on the column or when the impurities are not resolved from the main compound. It is therefore essential to turn to alternative and complementary analytical methods.This work deals with the development and evaluation of alternative analytical methods to reversed-phase HPLC on C18 phase for impurity profiling of pharmaceuticals. Reversed-phase HPLC on other stationary phases, mixed-mode HPLC as well as SFC were explored and their chromatographic performances compared. The comparison and the study of the different methods allowed proposing a strategy of analysis of the drug candidate.

This study developed a GC-MS method for the simultaneous detection of piperazines and congeners in street samples of amphetamine type stimulants. This research investigated the clandestine routes of synthesis and chemical profiles of phenylpiperazines, represented by 1- (4-fluorophenyl)piperazine (4-FPP) and 1-(3-trifluoromethylphenyl)piperazine (3-TFMPP). These drugs are part of the increasingly prevalent illicit new psychoactive substances. The presence of (2, 3, 4) FPP and (2, 3, 4) TFMPP positional isomers has been identified by other researchers as a limitation due to their similar chemical profiles. The method was optimized and confirmed as compliant with the International Conference on Harmonisation and the Center for Drug Evaluation and Research guidelines on validation. 4- FPP and 3-TFMPP were synthesised using potential routes for clandestine laboratories. Simple extraction and analysis of 11 street samples was conducted using the method developed. Furthermore, the stability of 22 drugs during analysis was investigated. Limits of detection were in the range 5 – 1.95ng/mL free base on column. The synthesised samples were identified as 4-FPP and 3-TFMPP. Several impurities were observed in the synthesised samples, which were identified and categorised as residual reactants, isomers of 4-FPP and of 3-TFMPP and by-products of synthesis. The percentage yields of the synthesised samples obtained were up to 82.4% 4-FPP and 78.7% 3-TFMPP. The street samples were found to contain MDMA, 3-TFMPP, BZP, caffeine, ephedrine and other impurities. The analytical method simultaneously separates 19 of the most common drugs found in piperazine samples and achieves for the first time the GC-MS separation of (i) 2-FPP, 3-FPP and 4-FPP and (ii) 2-TFMPP, 3-TFMPP and 4-TFMPP at the same time from a sample matrix containing all the 19 compounds. This method provides operational laboratories with a more effective method for the chemical characterisation of street samples of piperazines and also provides novel stability data.

<p>In the development of turbo machinery components it's desirable to not spend more time than necessary when setting up aero-thermal calculations to investigate uncertainties in the design. This report aims to describe general thoughts used in the development of an ICEM-mesh script and the possible configurations in the script file which enables the user to build mesh-grids with/without clearance gap at the hub and/or shroud for different blade geometries. It also aims to illustrate the performance analysis made on the Vinci LH2 turbine, a next generation upper stage engine to the Ariane 5 rocket, in which the effect of the tip gap size on the efficiency has been studied.</p><p>The calculations made have shown good agreement with experimental data. The efficiency loss due to the mixing of fluid where leakage flow passes the tip gap, which results in growth of a strong vortex, and the fluid passing the blade tip, with almost no work extracted from it, has shown a quite linear efficiency dependence depending on the tip gap size.</p>

Advances in protein topology mapping methods are urgently needed to complement the wealth of interactome data that is presently being generated at a rapid pace. Chemical crosslinking followed by mass spectrometry (MS) has evolved over the last decade as an attractive method for protein topology and interface mapping, and holds great promise as a counterpart to modern interactome studies in the field of proteomics. Furthermore, stabilization of proteins and protein complexes with crosslinking offers many advantages over high-resolution structural mapping methods, including the ability to study protein topologies in vivo. The reliance on direct detection of crosslinked peptides, however, continues to pose challenges to protein topology and interface mapping with chemical crosslinking plus MS. The present body of work aimed to develop a novel generic methodology that utilizes chemical crosslinking, cyanogen bromide (CNBr) cleavage and MS for the low-resolution mapping of protein topologies and interfaces. Through such low-resolution mapping of crosslinked regions, this novel strategy overcomes limitations associated with the direct detection of crosslinked peptides. Following optimization of various steps, the present method was validated with the bacterial DNA-directed RNA polymerase core complex and was subsequently applied to probe the tetrameric assembly of yeast Skp1p-Cdc4p heterodimers. Further improvements were made through the enrichment of crosslinked CNBr-cleaved protein fragments prior to their identification via MS. Two enrichment strategies were developed which depended upon the conjugation of tags to CNBr-cleaved peptide C-termini followed by either tandem affinity purification or tandem reversed-phase HPLC purification. These strategies were successfully applied for the efficient purification of disulfide-linked peptides from peptide mixtures. It is expected that the potential to achieve sensitive mapping of topologies and interfaces of multi-subunit protein complexes in vivo, in combination with further enhancements to permit studies on complex protein samples, will extend the utility of this method to complement large-scale interactome studies.

The alternative fuel biodiesel is produced from the transesterification of vegetable oils or animal fat to fatty acid methyl esters. Pomona has a reactor on campus that can be used to run this reaction and produce biodiesel. The use of biodiesel has been found to lower air pollutant and greenhouse gas emissions, but can be potentially harmful to the engines if it contains impurities. This paper proposes a method using high-performance liquid chromatography to test the quality of biodiesel. This method utilizes instrumentation and materials that are available in Pomona College's Chemistry Department, requires very little sample preparation, and is relatively safe, as long as general lab safety practices are followed. This method can also be used to optimize the procedure used to make the biodiesel. An optimized production procedure and a test method to assess the final product will ensure high quality fuel that can be used with confidence in diesel engines. This will likely add strength to proposals to increase the use of the on-campus reactor and produce biodiesel for campus grounds equipment from waste vegetable oil.

Advances in protein topology mapping methods are urgently needed to complement the wealth of interactome data that is presently being generated at a rapid pace. Chemical crosslinking followed by mass spectrometry (MS) has evolved over the last decade as an attractive method for protein topology and interface mapping, and holds great promise as a counterpart to modern interactome studies in the field of proteomics. Furthermore, stabilization of proteins and protein complexes with crosslinking offers many advantages over high-resolution structural mapping methods, including the ability to study protein topologies in vivo. The reliance on direct detection of crosslinked peptides, however, continues to pose challenges to protein topology and interface mapping with chemical crosslinking plus MS. The present body of work aimed to develop a novel generic methodology that utilizes chemical crosslinking, cyanogen bromide (CNBr) cleavage and MS for the low-resolution mapping of protein topologies and interfaces. Through such low-resolution mapping of crosslinked regions, this novel strategy overcomes limitations associated with the direct detection of crosslinked peptides. Following optimization of various steps, the present method was validated with the bacterial DNA-directed RNA polymerase core complex and was subsequently applied to probe the tetrameric assembly of yeast Skp1p-Cdc4p heterodimers. Further improvements were made through the enrichment of crosslinked CNBr-cleaved protein fragments prior to their identification via MS. Two enrichment strategies were developed which depended upon the conjugation of tags to CNBr-cleaved peptide C-termini followed by either tandem affinity purification or tandem reversed-phase HPLC purification. These strategies were successfully applied for the efficient purification of disulfide-linked peptides from peptide mixtures. It is expected that the potential to achieve sensitive mapping of topologies and interfaces of multi-subunit protein complexes in vivo, in combination with further enhancements to permit studies on complex protein samples, will extend the utility of this method to complement large-scale interactome studies.