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Chemistry

The Use of Chemical Vapor Deposition and Precursor Chemistry in Selective Sensing Applications

Chaimowitz, Adam ('10);  Davis-Van Atta, Casey ('10);  Taylor, Charles;  Haley, David;  Tanenbaum, David;  Montgomery, Chip*;  Afridi, Yaqub*
*NIST

Chemical vapor deposition (CVD) may be used to prepare thin films of a variety of materials. This work uses microhotplate arrays to investigate the application of CVD precursor chemistry for preparing thin film sensors based on vanadium oxide. Since precursors with different chemical structures may yield thin films with vastly different microstructures, we have explored the selectivity in the response of sensors prepared using two dramatically different CVD precursors: vanadium oxytrinitrate (VO(NO3)3) and vanadium oxytripropoxide (VO(OPr)3). We tested sensing films towards a variety of analytes including NO2, NO, NH3, isopropanol, n-PrOH, and hydrogen using an automated vapor sensor test system. The microhotplate platform enables us to simultaneously test several films with the same concentration of analyte present. Sensing film microstructure was characterized using field emission scanning electron microscopy. Using this approach for preparing selective chemical sensors, we will work towards creating application specific sensor arrays based on the microhotplate platform.
Funding provided by: Rose Hills Foundation (AC)

Method Development for the Analysis of Biodiesel From Waste Vegetable Oil

Diep, Bonnie ('09);  Taylor, Charles

The Claremont Biodiesel Initiative aims to convert waste vegetable oil produced by the Claremont Colleges to biodiesel for use on campus. Currently, however, the content of the biodiesel produced is not determined, and especially because biodiesel composition varies depending on the waste oil, it is important to have quality assurance to prevent the presence of unreacted triglycerides or fatty acids, which can be detrimental to diesel engines. The objective of this project is to develop a methodology, one that chemistry students can perform in laboratory experiments, to analyze the biodiesel to provide a means of quality control. Fatty acid methyl esters, fatty acids, and glycerides will be examined using gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry.
Funding provided by: Rose Hills Foundation

Synthesis and Structural Analysis of Hydrocarbon Stapled Peptides

Farkas, Catherine ('09);  O'Leary, Daniel;  Nevarez, Zulimar;  Toniolo, Claudio*
*University of Padova, Padua, Italy

The function of a protein or peptide is strongly dependent on its structure;  thus it is advantageous to understand the structural consequences of chemically modifying a peptide. This study focuses on the effects of modifying 310-helical peptides using ring-closing metathesis (RCM). Previously, RCM has been used to link two allylated serine resides from position i to i + 3 on a 310-helical octapeptide in a reaction that was highly trans-selective and helix preserving. The pentapeptides and hexapeptides studied were analogous systems, also having allylated serine residues in positions i and i+3. Infrared spectroscopy, circular dichroism, and nuclear magnetic resonance experiments were conducted to determine the secondary structure of the linear peptides, the ring-closed peptides, and the ring-closed and reduced peptides. The hexapeptides have more 310-helical structure than the pentapeptides, and both linear peptides are helical. X-ray crystallography and mass spectrometry experiments will be done to confirm these results.
Funding provided by: The Paul K. Richter and Evalyn E. Cook Richter Award

Expression of PELF, a Protein Involved in Biofilm Formation in Pseudomonos Aeruginosa

Gucinski, Grant ('10);  Giliam, Amanda ('09);  Kotwani, Prashant ('09);  Sazinsky, Matthew

Abstract removed upon request

Overexpression and Purification of PsrB

Huang, Grace ('09);  Crane, E.J.;  Lopez, Karlo*
*HHMI Post Doc

Shewanella oneidensis MR-1 is a thermophilic bacterium that is able to reduce a variety of different substrates. To reduce sulfur, it uses a complex known as polysulfide reductase, which is known to consist of three subunits, A, B, and C. The gene for PsrB was isolated using PCR and ligated into the pET 21b vector, which contains a His tag. It was then overexpressed in Escherichia coli. Ferrous ammonium sulfate was added during the overexpression process to try to obtain PsrB with its four 4Fe-4S clusters. Fast protein liquid chromatography with a nickel column, which binds the His tag, was used to purify PsrB but the purification process caused the iron clusters to fall apart thus resulting in the apoenzyme. In the future, instead of trying to express PsrB with the iron clusters, the apoenzyme will be used in an attempt reconstitute the iron clusters anaerobically after purification.
Funding provided by: Pomona College SURP (GH);  Howard Hughes Medical Insitute (KL)

Dual-Beam Polarization Interferometry Resolves Mechanistic Aspects of Polyelectrolyte Adsorption

Lane, Thomas J. ('10);  Fletcher, Will ('11);  Gomally, Michael V. ('11);  Johal, Malkiat

The electrostatically driven binding dynamics of a polyelectrolyte multilayer (PEMU) film was investigated in real-time using dual-beam polarization interferometry (DPI) and quartz crystal microbalance with dissipation monitoring (QCM-D) studies. Multilayer assemblies of the polyanions poly[1-[4[(3-carboxy-4-hydroxyphenylazo) benzenesulfonamido]-1,2-ethanediyl, sodium salt] (PAZO) and polystyrene sulfonate (PSS) were constructed with the polycation polyethylenimine (PEI) on anionic functionalized substrates. DPI measurements indicate that polyelectrolyte adsorption occurs in three distinct stages. In the first stage, coil-like segments of polyanion partially tether to the surface of the oppositely charged PEI. In the second stage, these coils unfurl to cover the surface resulting in an increase in average density of the film. During the final adsorption step, the surface-bound polyelectrolyte diffuses into the multilayer assembly exposing the surface to further deposition. This last step occurs over a much longer time period and results in a highly interpenetrated film containing a charge-overcompensated region at the film surface.
Funding provided by: Arnold and Mabel Beckman Foundation (TJL);  The Paul K. Richter and Evalyn E. Cook Richter Award (WF);  Pomona College Chemistry Dept (MG)

The Design of a Novel System for Engineering of Aromatic Hydroxylases

Lawson, Michael ('09);  Sazinsky, Matthew

Abstract removed upon request

FeoB

Lee, Jessica ('09);  Sazinsky, Matthew;  Elles, Lisa

Abstract removed upon request.

Correlation of the Structure and Toxicities of Derivatives of Trichothecene Mycotoxins

Lin, Alvin ('09);  Steinmetz, Wayne

In a continuing attempt to correlate toxicity to structure of a class of tricothecene mycotoxins -which include derivatives of roridin A, verrucarin A, and the baccharinoids - SYBYL a powerful modeling package was used to generate the 3D structures of a select set of these mycotoxins. The application of CoMFA, a sophisticated 3D QSAR procedure, will allow a rigorous analysis of any relationship between the physical properties of this set of mycotoxins and their toxicities.
Funding provided by: Pomona College Chemistry Dept.

Versatile Aromatic Amine Oxidations by Di-Iron Metalloproteins

Marsh, Christopher ('10);  Sazinsky, Matthew H.

Abstract removed upon request.

Binding Affinities Between Various Drug Compounds and Bovine Serum Albumin

Myers, Kathryn ('09);  Selassie, Cynthia;  Johal, Malkiat;  Rawle, Robert ('08)

The binding kinetics between a series of drugs and bovine serum albumin (BSA) were investigated using the quartz crystal microbalance with dissipation monitoring (QCM-D). The affinity of a drug for BSA gives important information about the drug1s pharmacokinetic profile and physiological activity. To create a model platform of non-specific drug binding in vivo, gold substrates were functionalized with 11-mercaptoundecanoic acid, and activated with N-hydroxysuccinimide and EDC for attachment to BSA. BSA deposition was monitored in real time using the QCM-D. A set of drugs with varying hydrophobicities were run over the BSA surface, allowing for the extraction of the Kon, Koff, and Kd values for each drug using non-linear regression in Excel. We will present 5-10 graphical representations of drug binding to BSA surfaces from the QCM-D, in addition to Kon, Koff, and Kd values obtained from analysis.
Funding provided by: The Paul K. Richter and Evalyn E. Cook Richter Award

Stabilizing Small 310-Helical Peptides Through RCM Between Constituent Amino Acid Side Chains

Nyabanga, Custon Tafadzwa ('09);  O'Leary, Daniel

Following previously reported conformational study on 310-helical octapeptides cross-linked through allyl residues at positions i and i+3 through ring closing metathesis (RCM) reaction, we intend to investigate the conformational stability of a tetrapeptide containing ?-aminoisobutiric acid (Aib) andallylated serine residues. Small chains of amino acids are known to easily conform to 310-helical motifs. Herein we intend to investigate conformational stability of the tetrapeptide with the sequence Boc-Ser(Al)-Aib-Aib-Ser(Al)-OMe, and in similar fashion link the allylatedserines through RCM. During the synthesis of the tetrapeptide we observed racemization of the allylated serine residues which required us to devote a synthesis and cyclization of this tetrapeptide, we intend to further stabilize the olefin RCM product by forming its dihyd.
Funding provided by: The Paul K. Richter and Evalyn E. Cook Richter Award

Engineering Terminal Hydroxylation of Alkanes by Toluene Monooxygenase

Ornelas, Jennifer ('09);  Sazinsky, Matthew

Abstract removed upon request.

Reaction Efficiency of Diffusion-Controlled Processes on Planar Arrays

Raju, Swaroop ('10);  Low, Daniel ('11);  Coreas, Bryan ('11);  Gómez, Ulysses ('11);  Shapiro, Bryan ('11);  Garza Lopez, Roberto

By modeling diffusion processes through the construction and coding of Euclidean and fractal lattices, the utilization of Walsh and Kozak’s algorithm (1981) enables us to observe the effects of differing dimensionality and valence on average random walk-lengths <n>. The underlying purpose of our research lies in using said procedure to explore correlation between symmetrical sites on d=2 and d=3 arrays and their corresponding average walk-length <n>. Manipulation of a simple matrix inversion process in Maple 11 allows for a time-efficient means of solving the system of equations needed to obtain the desired random walk-lengths. Current results confirm that the configuration of a planar array, as illustrated in Figure 1, produces a constant value for the random walk-length <n> for sites that are symmetrical. Finally, future progress in this experiment includes various calculations of <n> with respect to dipole-dipole, ion-dipole, and ion-ion interactions using eigenvalues to generate a characteristic equation that would facilitate the comparison of different structures.
Funding provided by: The Elgin Fund for Summer Student Research (SR);  Howard Hughes Medical Institute (UG);  Pomona College Chemistry Dept. (BC, DL)

Tandem Pinacol-Rearrangement Radical Cyclization: Carbocyclic Skeletons Via Radical Cations

Ramirez, Vanessa ('10);  Nevarez, Zulimar

This project is intended to expand the chemistry of radical cations in a tandem Pinacol-rearrangement radical cyclization reaction to provide synthetically relevant structures. Such methodology requires homolytic cleavage of a radical precursor followed by heterolytic fragmentation of an α-leaving group to generate a radical cation/anion pair such as 2. The in situ generated intermediate may undergo [1,2]-migration of an R substituent followed by a radical cyclization to yield a carbocyclic skeleton resembling 4. The design and progress of the syntheses of the phosphorylated nitro alcohol substrates needed to test the tandem strategy will be presented as well as future plans to overcome synthetic challenges.
Funding provided by: Rose Hills Foundation

QSAR and CoMFA Studies on Trichothecene Mycotoxin

Rodarte, Cezar (UR '09)*;  Steinmetz, Wayne;  Murray, Barbara*

*University of Redlands, Redlands CA

Trichothecene mycotoxins are a large class of compounds produced by several species of mold including Fusarium and Myrotecium. In this study, two data sets of trichothecene mycotoxins were studied to develop a quantitative relationship between their toxicities and their 3D structure using what is known as the Comparative Molecular Field Analysis (CoMFA) method. In the CoMFA method, molecular interaction (electrostatic and steric) fields are calculated on the set of modeled and superimposed compounds using the software package SYBYL. The values of these fields around each molecule are then correlated to the observed toxicity in order to build a statistical model. If the model is successful, it can be used to predict the toxicity of closely related analogues. The statistical results of the model produced in this study (Q2= .633 R2=.901) showed that it was an excellent fit of the data and did well in predicting toxicities.
Funding provided by: University of Redlands Chemistry Dept.

Characterization of hte PSRABC Membrane Protein of the Bacteria Shewanella Oneidensis

Trang, Johnson ('11);  Lee, Kelvin (‘11);  Crane, E.J.;  Lopez, Karlo*
*HHMI Post Doc

Research was done to further characterize the polysulfide reductase membrane complex (PsrABC) of Shewanella oneidensis MR-1. The bacteria were harvested and lysed via French Press to obtain a crude extract containing membranes for assays. The crude extract was used to reduce sulfur to sulfide using hydrogen as the electron donor. An assay which uses the formation of methylene blue was used to measure the concentration of sulfide. Despite being a commonly used sulfide assay, in our hands the assay produced erratic results despite numerous attempts and variations. The assay does not seem to work as intended when biological components are involved. Due to its inaccurate nature, we must do further research to find a more efficient assay. Attempts to assay the complex in the reverse direction (using sulfide to reduce the complex and assaying for the ability of the bound quinone to reduce the sodium dithionite) produced an unexpected result.

Funding provided by: The Paul K. Richter and Evalyn E. Cook RichterAward (JT);  Pomona College Chemistry Dept (KL);  Howard Hughes Medical Institute (KL)

Controlling Layer Thickness and Photostability ofa Water-Soluble Cationic PPV in Multilayer Thin Films by Surfactant Complexation

Treger, Jeremy ('09);  Lin, Jenny ('11);  Johal, Malkiat;  Wang, Hsing-Lin*
*Chemistry Div. Los Alamos National Laboratory, Los Alamos NM

In this work we build on prior studies of the novel water-soluble cationic conjugated polymer known as “P2” – poly{2,5-bis[3-(N,N,N-triethylammonium bromide)-1- oxapropyl]-1,4-phenylenevinylene} – with a focus on its incorporation into thin films for such applications as photovoltaics or electroluminescent devices. Multilayer assemblies were constructed using P2, the anionic surfactant sodium dodecylsulfate (SDS), and the polyanion poly(sodium 4-styrene-sulfonate) (PSS) using the technique of layer-by-layer electrostatic self-assembly (LBL-ESA). SDS was observed to affect the layer thicknesses and absorbance characteristics of the films. We show that the optical properties and photo-oxidative resistance can be improved by varying the SDS content in the assemblies. Specifically, the surfactant-complexed PPV shows an enhanced absorption at longer wavelengths as well as improved photostability. Therefore, our work may have broad implications on the development of stable PPV-based materials in general, and their efficient integration into thin films technologies.
Funding provided by: Arnold and Mabel Beckman Foundation (JT);  Pomona College Chemistry Dept (JL);  Dept. of Energy (HW)

Characterization and Mutant Formation of the Enzyme NADH-Dependent Polysulfide Reductase (Npsr)

Warner, Megan ('10);  Crane, E.J.;  Lukose, Vinita ('08);  Lopez, Karlo*
*HHMI Post Doc

NADH-dependent Polysulfide Reductase (Npsr) is an enzyme from the microorganism Shewanella loichia PV-4. Under anaerobic conditions, this organism shows the ability to use a wide variety of materials as electron acceptors, including sulfur. Npsr has two domains, a flavoprotein domain which appears to be homologous to the NAD(P)H-dependent coenzyme A disulfide reductase/sulfur reductase (CoADR) from Pyrococcus and a smaller domain similar to rhodanese or the Sud polysulfide carrier protein of Wolinella succinogenes. This project looked to further characterize this enzyme through uv-visible spectroscopy, fluorescence, titrations and crystallization as well as to make mutants of key amino acid residues conserved in enzymes homologous to the various domains of Npsr in order to determine their role in enzyme function and sulfur reduction in later experiments.
Funding provided by: Pomona College SURP (MW);  Howard Hughes Medical Institute (KL)

Research at Pomona