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Chemistry 490AB

The following is a list of potential 490A/B projects for 2012/2013. Contact potential supervisors to discuss projects that are of interest to you.

Available Projects

Title

Radial Density Analogue of the Quantum Theory of Atoms in Molecules

Supervisors

Dr. Ray Poirier

Dr. Peter Warburton

Student

Description

Bader's Quantum Theory of Atoms in Molecules (QTAIM) partitions the electron density of a molecule into basins of regional density, from which molecular properties can be determined as a sum of that property over each regional basin. However features exist in QTAIM, such as non-nuclear attractors, where molecular density is assigned to basins that have no nucleus present, and therefore QTAIM can define basins that belong to no atom. Our previous work in defining atoms and bonds in molecules via radial densities can also partition the molecular density into regional denisites, but in this case, any regions without a nucleus can be directly associated with bonding, whereas with non-nuclear attractors this is not true.
In this project the student will implement in MUNgauss a general means of evaluating the first and second derivatives of electron density, which can be used to partition the molecular density into regional densities. Therefore we will be able to not only recreate the QTAIM method, but also do analogous partitioning via radial densities which will allow us to compare and contrast the partitoning methods. The final step will be to use the different partitioning methods to evaluate how well they recreate molecular properties as a sum of regional basin properties.

Title

1. The synthesis of a chiral [8](2,7)pyrenophane.

2. The synthesis of heterohelicenes using inverse electron demand Diels-Alder (IEDDA) chemistry.

3. An investigation of counterintuitive chemoselectivity in the SN2 reaction.

Supervisor

Dr. Graham Bodwell

Student

Description

(click here to see descriptions)

Title

Synthesis and optimization of molecularly imprinted polymers in thin-film format for analysis of caffeine in aqueous samples.

Supervisor

Dr. Christina Bottaro

Student

Description

Caffeine is an interesting analyte because it is one of the most widely consumed pharmaceuticals and is universally recognized as a indicator of wastewater contamination in surface waters. In this project, thin-film MIPs will be developed based on systems that have been previously reported for caffeine. The various systems will be tested for binding, selectivity and suitability to thin-film format. Analysis of performance will be carried out using LC-MS and methods to characterize the material properties (e.g. SEM, AFM, etc.)

Title

Studies of Monomer-Analyte Interactions by NMR Spectroscopy as a Route to New Molecularly Imprinted Polymers (MIPs)

Supervisor

Dr. Christina Bottaro

Student

Description

MIPs are polymeric systems that selectively bind only molecules used in the original templating process or compounds with a very similar shape and functionality. In this way MIP systems can be made for a wide range of analytes of interest, including those that important from an environmental or medical standpoint, including various toxins or pharmaceuticals. The versatility of MIPs is only limited by the polymer systems available and the creativity of the scientist developing the applications In this project, NMR will be used in the study of the templating process for the synthesis of molecular imprinted polymers. These systems rely on intermolecular interactions between the monomer and target analyte prior to polymerization, which must be maintained during polymerization to produce a cavity that retains the appropriate configuration once the template is removed. Factors such as solvation, nature of the monomer, temperature of polymerization, mechanism of polymerization, etc. can all be studied using the NMR. Results will allow us to optimize the conditions for production of a superior MIP system.

Title

Data-Mining as a Route to Rational Design: Structural Characterization of Crystal Packing Motifs

Supervisor

Dr. Louise Dawe and Dr. Fran Kerton

Student

Description

The emphasis of most inorganic crystal structure analysis is on the covalent metal-ligand bond distances, angles and related intramolecular properties (for example, plane calculations for metal-raft motifs.) Information “beyond the coordination sphere”, in the form of metal complex, or coordination polymer packing properties, is not always considered, and rigorous numerical documentation and analysis of motifs, other than hydrogen-bonding or pi-interactions, is not common. In this crystallographically-based project, the student will undertake the solution and refinement of metal complexes, with the goal of identifying and quantifying packing motifs through comparison with mined information from the Cambridge Structural Database. This type of analysis has been identified as essential to the rational design of new zeolites and crystal engineered materials (Wang, Z. Yu, J., Xu, R. Chem. Soc. Rev., 2012, 41, 1729–1741.)

Title

Computational Investigation of the Catalytic Deamination of the DNA Base Cytosine With Hydroxylamine and/or Bisulfite Ion

Supervisor

Dr. Chris Flinn and Dr. Peter Warburton

Students

Description
(when available)

The student involved in this project will perform geometry optimizations of possible transition states and reactant and product complexes in order to determine the reaction pathway and associated energetics for the deamination of cytosine catalyzed by hydroxylamine and bisulfite. The project calculations will be performed with the Gaussian09 software package on ACEnet computing resources. In addition to gaining insight into computational modeling of reaction energetics through geometry optimizations and frequency calculations, the student will be exposed to some of the background of computational chemistry and learn some other standard molecular modeling techniques, such as transition state calculations and intrinsic reaction coordinate (IRC) explorations of the reaction pathway to determine the reactant and product complexes connected to each transition state.

Title

Infrared spectroscopy of gaseous metal ion/biomolecule complexes by infrared multiple photon dissociation spectroscopy.

Supervisor

Dr. Travis Fridgen

Students


Description
(when available)

Infrared spectroscopy of gaseous ions has become an extremely powerful technique to determine ion structure over the past few years. It was determined recently that when Pb2+ cations complex with amino acids, they lose a proton to form [PbAA-H]+ ions. It might be expected that the amino acids deprotonate at the carboxylic acid group, however, the infrared spectra show that these ions are deprotonated at the amino group. Computational chemistry on the possible structures agree that the lowest-energy structure is indeed the one where the complex is deprotonated at the amino group. We would like to extend these studies to simple sugars, to nucleotides or nucleosides, as well as small peptides to see what mysteries we can uncover pertaining to the structures of metal/carbohydrate ion complexes. Student(s) will have a choice of simple or functionalized sugars (ie. glucoseamine, glucoronic acid), peptides, nucleobase etc. to investigate using a combination of techniques such as FTICR mass spectrometry laser spectroscopy, and computational chemistry. The goal of this research is to eventually understand, on a molecular level, how toxic or friendly metal cations interact with biological molecules such as proteins and DNA.

Title

Determination of the relative activation energies for uracil and HNCO loss from gaseous Ca(Ura-H)(Ura)+ cations (Ura=uracil) by variable-power CO2-laser infrared multiphoton dissociation (IRMPD)

Supervisor

Dr. Travis Fridgen

Student

Description

Previous work in our lab showed that collision induced dissociation (CID) of Ca(Ura-H)(Ura)+ ions resulted primarily in loss of uracil whereas IRMPD with a CO2 laser resulted primarily in HNCO loss. This was explained in terms of the IMRPD activation being a slower heating process than CID so that with IRMPD the lower-energy pathway, but with higher entropy requirement, dominated. With the faster heating CID activation ions quickly find themselves with more internal energy required for both uracil and HNCO loss so that the lower entropy process (uracil loss) dominated. The goal of this project is to determine the activation energies for both processes using IRMPD-activated rate constant determinations with varying powers of the CO2 laser. An Arrhenius-type plot with logarithm of the laser power as the ordinate will result in a measure of the activation energies for both processes. Statistical calculations of the rate constants for both processes with the known activation energies will result in a measure of the internal temperature of the ions during ion activation. Students will obtain experimental experience with the Fourier transform ion cyclotron resonance mass spectrometer, the CO2 laser as well as experience with electronic structure calculations as well as statistical calculations of rate constants and will gain a detailed understanding of unimolecular activation and dissociation processes that are common in almost all mass spectrometry experiments.

Title

Synthesis of bowl- and basket-shaped macrocycles as novel fullerene receptors.

Supervisor

Dr. Paris Georghiou

Student

Description
(when available)

Title

Determining the extent of covalent bonding between proteins and chitin in the shells of Newfoundland shrimp

Supervisor

Dr. Bob Helleur

Student

Description

Helleur’s research group has been funded to come up with a greener and less expensive way of de-proteinating chitin (a marine polysaccharide) which is a valuable biopolymer isolated from shrimp or crab shell waste. Chitin products which have very low protein content sell at a premium price as medical grade bio-compatible materials . To produce such a product (i.e., to remove the last 1% of residual protein) is very costly and uses highly caustic chemicals. Although much of the initial protein associated with the chitin macro-structure is through hydrogen bonding, another portion is associated through stronger covalent bonds, likely amide or carbon-carbon. The project will involve de-proteinating chitin isolates until only 2-3 % proteinous residue remains. The chitin polysaccharide will be then selectively hydrolyzed into mixtures of oligomers and separated by liquid chromatography (LC). The LC fractions containing amino acid residues will be further analyzed by mass spectrometry, NMR and by micro-assays including enzymatic. By determining 1) the extent of covalent bonding between carbohydrate and proteins, and, 2) the chemical nature of the amino acid linkage will assists us in designing effective de-proteination reaction conditions.

Title

Surfactant-mediated MALDI-TOFMS in the analysis of drugs and secondary metabolites in urine

Supervisor

Dr. Bob Helleur

Student

Description

Small molecule analysis by desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) have been problematic due to the high abundance of matrix ions masking the analyte signal in the spectra. However, past studies in our lab have shown that surfactant-mediated MALDI-TOF (i.e., the use of a surfactant to suppress the matrix ions) was successfully used in the analysis of caffeine and the vitamins riboflavin, nicotinamide and pyridoxine in various energy drinks. The matrix α-cyano-4-hydroxycinnamic acid was found to be most suitable for the analysis of these high sugar-containing energy drinks and where cetyltrimethylammonium bromide (CTAB) surfactant was used as a matrix-ion suppressor. MALDI-TOFMS analysis of whole biological fluids such as urine will be even more of a challenge because of its molecular complexity. One series of experiments would be to analysis caffeine (and possibly cold medicines) in urine samples without any sample pretreatment. Other study could be analysis of urine from rats/mice which have been given drugs. In this case, the secondary metabolites could also be observed and identified using surfactant-mediated MALDI-TOFMS and TOF-TOF-MS.

Title

Synthesis of iron complexes of amine-bis(phenolate) ligands for catalytic C-C cross-coupling.

Supervisor

Dr. Chris Kozak

Student

Description

This project involves synthetic coordination and organometallic chemistry of Fe. The student will learn air-sensitive synthetic techniques involving Schlenk/vacuum lines and glove boxes. Characterization techniques include multinuclear NMR, single-crystal X-ray diffraction, UV-vis, IR, magnetochemistry, electrochemistry and other analytical methods. Catalysis studies will involve extensive use of GC-MS.

Title

Electron-poor metal complexes as catalysts for polar monomer polymerization

Supervisor

Dr. Chris Kozak

Student

Description

This project involves the preparation of Li and group 4 complexes, which will be studied for their ability to catalyze the polymerization of caprolactone and lactide. The resulting polymers will be characterized by NMR, GPC, DSC and TGA. The metal complexes will be prepared using air-free techniques (Schlenk-lines and glove boxes) and characterized by multinuclear NMR, X-ray and other methods.

Title

Modeling nanoscale materials

Supervisor

Dr. Erika Merschrod

Student

Description

Nanoscale materials can behave quite differently than their bulk counterparts with the same chemical composition. Modeling and predicting the behaviour of nanoparticles is challenging, but with recent advances in our group there are models available for study and evaluation. This project will investigate nanoparticles suitable for optically active thin films in biosensors and chemical sensors. The student will learn how to use a computational chemistry package and associated software and will design and evaluate nanoparticles for optimal optical properties. There is a possibility of experimental work related to this project as well.

Title

Artificial tissue scaffolds

Supervisor

Dr. Erika Merschrod

Student

Description

Cartilage, in contrast with bone, does not repair itself well. Artificial tissue scaffolds to promote healing in cartilage would therefore be quite useful! The student will develop composite materials from the primary components of cartilage (type-II collagen, uronic acids, etc) and evaluate their structure and mechanical properties as key indicators for biocompatibility. The student will learn protein handling techniques and, depending on progress, there may be opportunities for cell culture studies.

Title

Synthesis and reactivity of amine-bis(phenolate) Group I and II complexes

Supervisor

Dr. Chris Kozak

Student

Description

The Green Chemistry Group at MUN recently developed a method for making amine-­-phenol ligands in water (an environmentally-­friendly solvent). This 490A/B project involves studying the coordination chemistry of these ligands with alkali and alkaline earth metals using air-­free techniques (Schlenk-‐lines and glove boxes). The resulting metal complexes will be characterized by NMR spectroscopy and single crystal X-­ray diffraction. Their ability to perform (i) ring-­opening polymerization (ROP) reactions of caprolactone and lactide and (ii) carbon dioxide-­epoxide coupling/polymerization will be assessed. The complexes along with a co-­catalyst may work for CO2 activation and the alkoxides for ROP reactions. The work may be subdivided so up to two students may be accepted to work on this project.

Title

Electrochemical formation of biomembranes

Supervisor

Dr. Erika Merschrod and Dr. Kris Poduska

Student

Description

Proteins, being polyelectrolytes, will move in an applied electric field. Other, more complicated phenomena can arise from using the field to "focus" or confine protein molecules to a quasi-2D space. We have found interesting current signatures of this confinement process, and we would like to understand these characteristic changes in current in terms of the mobility and rearrangements of ions and proteins in solution. At a practical level, the student will explore the effect of different electrode geometries on protein focusing and current response. This project could involve nanofabrication and/or micro-particle imaging velocimetry (fluorescence microscopy), depending on the inclination of the student.

Title

Asymmetric Synthesis of Aryl Quinolizidine Alkaloids and their Analogs

Supervisor

Dr. Sunil Pansare

Student

Description

Aryl quinolizidines, and the related phenanthroquinolizidines, form an important group of alkaloids with interesting biological activity. Recent studies in our group have established an enantioselective route to functionalized quinolizidines from chiral gamma-nitroketones which are obtained from an organocatalytic ketone-nitroalkene conjugate addition reaction. This methodology will be applied to the synthesis of naturally occuring quinolizidine alkaloids and their synthetic analogs. The focus of these studies is the synthesis of libraries of structurally related aryl quinolizidines which will be screened for anticancer activity.

Title

Catalysts for the electrochemical oxidation of organic fuels

Supervisor

Dr. Peter Pickup

Student

Description

Honours project involving fundamental studies of the effects of polymer and/or metal oxide supports on the activities of Pt or Pd based catalysts. The electrochemical oxidation of a fuel that can be used in a fuel cell (e.g. formic acid, methanol, ethanol, ethylene glycol) will be studied. The work will involve the synthesis and characterization (X-ray diffraction; electron and atomic force microscopy) of metal particle colloids, coating electrodes with the support material and colloid, and electrochemical measurements of electrocatalytic activity by cyclic voltammetry and constant potential experiments.

Title

Finding order within structural disorder

Supervisor

Dr. Kristin Poduska

Student

Description

Infrared spectroscopy provides information about bond energies in a material, and we exploit this fact to learn about the differences in structural perfection that result from different ways of synthesizing the same solid material. This offers the possibility of identifying the production method used to prepare a material based on its infrared spectral features. For example, earlier work in my group uncovered disorder signatures in carbonate materials to differentiate between samples with archaeological or geological origins. We are now expanding this to look at marine-based carbonates, such as those found in sea urchins or produced by sea cucumbers. An Honours student with an interest in spectroscopic measurements and analysis could help us address this question.

Title

The Polarized Electrostatic Potential of Molecules

Supervisor

Dr. Chris Rowley

Student

Description
(when available)

The electrostatic potential provides one of the most powerful tools for understanding intermolecular interactions as it provides a simple description of the electrostatic interactions experienced when two molecules interact. A failing of this description is that the polarization of the electron density by the presence of the external molecule is ignored. In this project, the student will perform computational chemistry calculations to determine the most accurate electrostatic potential of a molecule and how it can be polarized by its environment. We will use these results to develop more realistic models in simulations of ionic liquids.

Title

The structure and Dynamics of Viruses Affecting Aquaculture

Supervisor

Dr. Chris Rowley

Student

Description
(when available)

Fish farming has emerged as a major industry in Newfoundland and Labrador, with the value of production reaching $116 million in 2010. Salmonid species such as Atlantic salmon and Steelhead trout account for a large part of this production. This industry must contend the threat of outbreaks of viruses such as the Infectious Salmon Anemia Virus (ISAV) and the Infectious Pancreatic Necrosis Virus (IPNV), which have had serious impacts on the aquaculture industries in other parts of the world. Recently, crystallographic structures of important viral proteins have been reported, providing new insights into the life cycle of these viruses. In this project, we will use computer simulations to model the structure and dynamics of these proteins in solution with the aim of developing treatments for managing outbreaks of these viruses.