Master of Chemical Sciences Capstone Research Paper
The MCS Capstone is an independent research project that integrates what the student has learned in the program and contributes to the advancement of Chemistry. If you are a MCS graduate and would like to have your capstone project uploaded to this site, please submit your capstone. Your decision to upload the document will serve as your agreement to the terms, both for individual authors and multiple authors. If you have a question about this collection, please contact Tina Morgan Ross.
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Publication Molecular Analysis of Copper Binding to the Bacterial MFS-type Copper Importer CcoA(2019-05-15) Zhao, WenchuMany enzymes require copper (Cu) as a cofactor in proceeding their role in different biological pathways. Copper’s oxidative and reductive abilities make it a good cofactor to accomplish the electron transfer process in reactions. CcoA was discovered in the Gram-negative, facultative photosynthetic model organism Rhodobacater capsulatus. It was found to belong to the Major Facilitator Superfamily (MFS) group of transporter proteins and since then had become the prototype of the newly defined copper uptake porter family. In this capstone project, an antibody that specifically targets the CcoA protein was screened in order to contribute to future molecular analysis of copper binding of the CcoA in the Rhodobacater capsulatus. Different antibody and sample preparation methods were tested in order to optimize the western blot recognition results. Additionally, in order to further investigate the function of the conserved residues in CcoA-like-Transporter family, another aim of the study was focused on the study of the activity of the ccb3-type cytochrome oxidases in a mutant lacking the CcoA homolog protein of the Agrobacterium tumefaciens (fabrum). The study gives insights to the Cu uptake and delivery pathways of the CcoA-like-Transporter in a different bacterial species, and the role of this oxidase on tumor formation in plants. It also emphasizes the function of the conserved histidine residue in these transporters.Publication Synthesis and Biological Evaluation of Biliatresone Analogs and its Photoaffinity Probe(2019-07-25) Lin, ShengPublication Oxidative Coupling of Phenols(2018-05-19) Sreevatsan, PrasannaNature makes extensive use of oxidative reactions to generate bonds between carbons, particularly in the coupling of phenols, which is a striking feature in many biosynthetic pathways. The coupled phenols may exhibit the phenomenon called axial “chirality” or handedness. The Kozlowski group uses the atom economical oxidant O2 and metal-based catalysts which, developed in-house, mimic the active sites of the enzymes to bring about these transformations. Vanadium catalysts have been extensively applied to the coupling of phenols and carbazoles with great efficiency and results. Here, this method is applied to the synthesis of bismurrayaquinone-A, an antitumor compound that occurs naturally in the roots of the curryleaf tree, Murraya koenigii. In this report, the routes for synthesis of the coupled phenol and carbazoles are highlighted. In the scaleup synthesis, 515 mg of the coupled carbazole was synthesized with an overall of 68% yield and 91% ee. A key oxidative coupling intermediate in the synthesis of bismurrayaquinone-A was afforded in 51% ee.Publication Synthesis and Optical Properties of Rare Earth Doped Fluorides Nanoparticles Via Enhanced Absorption(2019-05-19) Wu, YupengRare-earth elements are strong candidates for upconverting materials due to their relatively long-lived excited states.1-3 However, they are generally not efficient light absorbers.4-6 One of the approaches to enhance the optical absorption is adding a sensitizer layer (i.e.an extra semiconductor layer or using organic dyes as sensitizer with stronger absorption properties).7 On the other hand, the surface quenching effect decreases the efficiency of optical emission. This project explores the creation of undoped shells, sensitizer shells on rare earth nanoparticles and studies the effect of the size of the shell, semiconductor shells and dyes on the optical properties.NaYF4:Yb0.20, Er0.02 nanoparticlesare investigated specifically to reveal the effect of sensitizers on the absorption and emission properties. A solvothermal method is used to synthesize core NaYF4:Yb0.20, Er0.02 nanoparticles and NaYF4doped core-undoped shell particles.8-13 XRD and TEM indicated that pure β-NaYF4nanoparticles were synthesized. The size of NaYF4nanoparticles was monitored using reaction time. The emission spectrum revealed that growth of undoped NaYF4shells enhanced the emission intensity of doped core-undoped shell particles. This is presumably because the shell inhibits the nonradiative transition and the surface quenching on the surface ofNaYF4:Yb0.20, Er0.02core nanoparticles. CdS shells and ligand exchange with a dye absorbing in NIR were investigated as potential methods to enhance the absorption properties of NaYF4:Yb0.20, Er0.02 nanoparticles. TEM revealed that CdS segregated to form heterostructurewith NaYF4:Yb0.20, Er0.02 core nanoparticlesinstead of core-shell structure. This is likely due to the mismatch of CdS lattice to β-NaYF4.A NIR absorbing dye was coated to the NaYF4:Yb0.20, Er0.02 corenanoparticles via ligand exchange method. A color change was noticed after the ligand exchange with the nanoparticles. However, the emission properties and energy transfer process need further studies since the intensity at 542 nm and 660 nm are not pronounced under 806 nm excitation and 980 nm excitation.Publication Synthesis of Au-Ag Alloy Nanoparticles and Characterization of Nanoparticle-Anthracene Hybrid Materials(2020-01-01) ZHOU, XIANGIn this work, the optical properties of Au-Ag alloys with an anthracene ligand grafter to their surfaces was examined. Structurally and chemically homogeneous Au-Ag alloy NPs were synthesized by a seed-mediated method with the Ag precursor reduced and grown onto the prepared Au seeds. The alloy NPs were formed after inter-diffusion of Au and Ag and protected using oleylamine. Functionalization of the metal NPs with the anthracene-incorporated ligands was conducted via a simple ligand exchange protocol. The morphological information and chemical composition of the resulting NPs were confirmed by transmission electron microscopy and energy dispersive X-ray spectroscopy, respectively. The plasmonic effect of the metal NPs on the fluorescence was examined using Ultraviolet-visible and fluorescence spectroscopy. The plasmonic enhancement of the fluorescence was found to be varied among different compositions of the alloy NPs.Publication Synthesis and photochemical studies of two p-hydroxyphenacyl derived photocages(2020-05-01) Deng, ChangfengThe synthesis of new p-hydroxyphenylacyl(pHP) derived photocages containing either coumarin or benzothiazole fluorophore cores is described. The newly synthesized photocages exhibit absorption spectra extending beyond 400 nm and good photolysis efficiency. The pHP inspired design, with the insertion of a carbonyl group, provides a 50-60 nm bathochromic shift and efficient photo-cleavage. Caged chemical probes for controlled protein dimerization were prepared containing the newly developed pHP photocages. In vitro experiments verified efficient photochemical uncaging of the newly developed pHP chemical probes. Cell imaging experiments utilizing the new pHP caged probes are currently in progress.Publication Peptide Synthesis and Modification as a Versatile Strategy for Probes Construction(2017-08-11) Wang, JieliangPeptide synthesis and modification is a versatile chemical biology strategy to construct probes and sensors of a variety of types of biological activity, including protein/protein interactions, protein localization, and proteolysis. In my thesis work, I have made probes for three distinct biological applications. To do so, I have used a combination of solid phase peptide synthesis (SPPS), native chemical ligation (NCL), protein expression, and S-alkylation to construct probes with desired functional groups, while minimizing the perturbation to the native structure. In the first project, I constructed photo-crosslinking probes to study the difference in protein-protein interactions of N-terminal acetylated (N-ac) histone H4 peptide versus non-acetylated histone H4 peptide. One protein was identified by Western blot with binding preference to N-Ace histone H4 peptide. In the second separate project, I constructed probes to study the toxicity mechanism of proline/arginine dipeptide PRx from amyotrophic lateral sclerosis (ALS) associated gene C9ORF72. The preliminary result suggested the PRx peptide toxicity on proteasome depends on the length of the (PR)x peptide. In the third project, I synthesized fluorescence sensors to study the positional effects of thioamide on the proteolysis process of chymotrypsin. From hydrolysis studies, my coworkers and I determined that thioamide incorporation at the P1 or P2 positions can greatly inhibit chymotrypsin proteolysis.Publication Formation of nanoparticles for the oral delivery of small molecules by Flash Nanoprecipitation(2020-05-07) Lo, Jing ZhiNanoparticles have shown considerable potential in many biological applications including drug delivery, bio-imaging, and medical diagnostics. Specifically, the development of nanoparticle-based drug formulations holds opportunities to improve the dissolution rate and oral availability of poorly water-soluble drugs. The goal of this project is to improve oral bioavailability of a small molecule drug (“G-1”) through the formation of nanoparticles using the flash nanoprecipitation (FNP) process. Interestingly, “G-1” formed ~80 nm particles that are electrostatically stabilized without the use of stabilizing polymers and concentration as high as 160 mg/mL of “G-1” formed nanoparticles. Additionally, trehalose was found to be an effective cryoprotectant for lyophilization of “G-1” nanoparticles suspension into stable dried powders. Unexpectedly, the release kinetics of “G-1” in its free powder form exhibit rapid dissolution rate in the modified biorelevant media (FaSSIF with 1.5% Tween 20). Further formulations with “G-1” were conducted to generate ~300 nm particles with PS-b-PEG as stabilizing polymer. Through the use of a tangential flow filtration (TFF) system, drug loading (wt%) of the lyophilized “G-1” nanoparticles were increased by nearly 2-fold (30.5% versus 16.7%). These lyophilized nanoparticles were introduced to Genentech’s in vivo and in vitro studies and have provided more insight in the bioavailability and pharmacokinetics properties of this drug.Publication Electronic Spectroscopy and Photochemistry of Methacrolein Oxide: A Four Carbon Criegee Intermediate from Isoprene Ozonolysis(2019-01-01) BHAGDE, TRISHAIsoprene is an unsaturated hydrocarbon and the most abundant non-methane hydrocarbon in Earth’s atmosphere. Atmospheric oxidation of isoprene via reaction with ozone leads to formation of carbonyl oxide intermediates, known as Criegee intermediates. Methacrolein oxide (MACR-oxide, (CH2=C(CH3))CHOO), is a four carbon unsaturated Criegee intermediate produced in isoprene ozonolysis. The aim of this study is to obtain the UV-Visible absorption spectrum of MACR-oxide on a strong π*¬π electronic transition associated with the conjugated carbonyl oxide and vinyl groups. MACR-oxide is synthesized in the laboratory by photolyzing a diiodo alkene precursor (1,3-diiodo-2- methylprop-1-ene) followed by reaction with oxygen that transiently forms a iodoalkene peroxy radical. Subsequent loss an iodine atom yields MACR-oxide in four conformational forms. MACR-oxide is produced in a quartz capillary reactor tube and cooled in a pulsed supersonic jet expansion. MACR-oxide is detected by photoionization using 118 nm VUV radiation on the m/z = 86 mass channel of a time of flight mass spectrometer. UV-Visible radiation is absorbed and promotes MACR-oxide from its ground state to an excited 11ππ* electronic state. This results in a ground state depletion that is detected as a reduction in the 118 nm photoionization signal. The UV-Visible spectrum of MACR-oxide is observed from 315 to 500 nm and peaks at 380 nm. Weak oscillatory structure is found in the long wavelength region of the spectrum, which can be attributed to vibrational resonances. Complementary Velocity Map Imaging experiments show that MACR-oxide dissociates rapidly upon UV-Visible excitation. This assures that the UV-Visible spectrum of MACR-oxide obtained by the depletion method is equivalent to a direct absorption measurement. The UV-visible spectrum of MACR-oxide is expected to have broad applicability as a sensitive probe of its unimolecular decay and bimolecular reactions with trace species relevant in the atmosphere.Publication Synthesis of Dendritic Ligands Containing Ferrocene for Quantum Dots (QDs) and Characterization of QD-ligands Hybrid System(2019-05-20) Park, Jung MiLigands for nanocrystals (NCs) have been widely studied beyond its role as a capping agent to applications such as tuning self-assembled properties of nanocrystals. Recent studies show that functionalized ligands can introduce precise control over charge and energy transfer of semiconductor NCs, or quantum dots (QDs). This can be used in various applications in optoelectronic devices, such as solar cells and light emitting diodes, or even further photocatalysis, and biological imaging. Herein, this project describes the design and synthesis of a series of novel dendritic ligands containing active moiety with efficient synthetic route for developing dendron series to graft onto the surface of CdSe/CdS core shell QDs. For active site in the ligand, ferrocene (Fc) was used because of its chemical stability and the ease of the Fc/Fc+ redox couple. To characterize the series of ligands, Nuclear magnetic resonance (NMR) spectroscopy and mass spectroscopy studies were performed to analyze and confirm molecular structure of compounds. In addition, the synthesized ligands were grafted onto QDs and self-assembly of NCD. For characterization of this hybrid system, the changes of energy dynamics were studied by Ultraviolet-visible spectroscopy (UV-Vis) and Fluorescence spectrometer. As a result, the quenching effect was observed as placed Fc near QDs and degree of quenching also varies. This study reveals that active moiety Fc introduced optical dynamic changes in absorbance and fluorescence when anchored on QDs surfaces compared to QD-as synthesized. This project will be a capstone for enhancing mechanistic understanding of how charge transfers between active moiety and QDs. The series of samples of ligands and QD-Fc ligand hybrids were successfully made as a part of collaboration work with Prof. Baxter group at Drexel University, for ultrafast spectroscopic analysis which will enable ultimate understanding of direct charge and energy flow.