2015/2016 chemistry summer scholarships



A summer scholarship in the School of Chemistry offers a unique opportunity for undergraduate students to obtain experience in chemical research and provide an insight into what it's like working with well-established researchers in high quality research facilities including: NMR Spectroscopy, Mass Spectrometry, Vibrational and Optical Spectroscopy, X-ray Crystallography, Separations, Thermophysical Properties and High-Performance Computing.

Important dates

  • Applications open: Tuesday, 23 June 2015
  • Applications close: Friday, 28 August 2015
  • Offers made: Wednesday, 30 September 2015
  • Deadline to accept offer: Wednesday, 14 October, 2015

Eligibility

The program is open to both current University of Sydney students as well as students from other Australian Universities. Applicants must be enrolled on a full time basis and be in least their second or third year of their degree program (please see "Conditions of Award" below). A summer scholarships offers:-

  • the opportunity to undertake a research project over a period of six weeks
  • supervision by well-established researchers
  • excellent research facilities
  • $497 per week in accordance with 2015 APA rate, and may be eligible for an accommodation bursary of $250 per week for recipients who live outside the Sydney metropolitan area and who are not enrolled at a University in the Sydney metropolitan area

Conditions of award

The purpose of the Division of Natural Sciences Summer Placement is to provide students with an opportunity to gain access to, and engage with academic staff and research projects over the summer holidays.

The placements will be awarded using the following conditions:

  1. Applicants will be required to submit an application.
  2. Applicants from the University of Sydney must be enrolled in a full time undergraduate degree and enrolled or successfully completed CHEM2401/2911/2915 and CHEM2402/2912/2916. In addition the applicant must be intending to proceed into Senior Chemistry at the University of Sydney. In exceptional circumstances, students who have completed or are enrolled in only one of the units above may also be considered.
  3. Applicants from other universities in Australia and New Zealand currently in 2nd or 3rd year of study are also eligible to apply.
  4. Applicants must be performing at credit level (AAM 65) or above to be considered for these placements.
  5. Applicants can only receive one Summer Scholarship per year.
  6. The placement shall be awarded on the basis of academic merit.
  7. The placement shall be awarded by the Dean of the relevant Faculty within the Division of Natural Sciences, on the recommendation of the appropriate Head of School.
  8. If a recipient is enrolled at a university other than the University of Sydney and who lives outside of the Sydney metropolitan area, and who are not enrolled at a university in the Sydney metropolitan area, they will be offered additional funds of up to $250 per week to cover accommodation/travel expenses.

How do I apply?

Please fill out an application form and ensure to add at least three projects in order of preference. Your application form can be either emailed, or submitted to Ms Dimetra Skondras-Silva by 4.00 pm on Friday, 28 August 2015. All applicants will be notified in writing of the result of their application. PLEASE NOTE THAT LATE APPLICATIONS WILL NOT BE ACCEPTED.

Contact person

Ms Dimetra Skondras-Silva
Chemistry Front Office
School of Chemistry, Building F11
The University of Sydney NSW 2006
Australia
T: +61 2 9351 4504
E:

chemistry research projects


The following research projects are on offer:-

Light-activated ruthenium(II) prodrugs

Research in my group focuses on the development of new and selective anticancer agents. Developing anticancer agents that can act on a tumour without affecting healthy cells is a major challenge in drug design. We are developing transition metal complexes as inert prodrugs of anticancer agents then using a range of methods to selectively release the anticancer agent in a tumour cell. The research projects in this area combine inorganic and organic synthesis with a range of spectroscopic and analytical techniques.

We are developing ruthenium(II) prodrugs with anticancer agents as ligands. The ruthenium complexes are stable and non-toxic in the dark, but the metal-ligand bonds are rapidly cleaved when the complex is irradiated with visible light. This project will focus on synthesising a novel series light-activated prodrugs and evaluating their stability with light using techniques such as UV-visible and 1H NMR spectroscopy, and mass spectrometry. Promising complexes will be tested against a series of tumour cell lines.

 

New chemical tools to study metals in biology

Metals play many important roles in biological systems, but if levels are uncontrolled, they can cause cellular damage. It is thought that imbalances in metals play a role in neurodegenerative diseases such as Alzheimer’s. In order to better understand how metals can cause disease, it is important to be able to visualise how metal ions accumulate and move in cells. This project will involve the design of fluorescent sensors that bind selectively to biologically-important metal ions such as copper, iron and nickel, and report on the presence of the ion by a characteristic change in fluorescence emission. We will study the fluorescence behaviour of these sensors, and then measure their emission in cells by confocal microscopy.

This project will involve synthesis and fluorescence spectroscopy, with an option to observe biological studies.

Simulation of crystallization in molecular liquids

The kinetics of crystallization in a molecular liquid depends on the both the rate of molecular translations and rotations and the complexity of the crystal structure being formed. Computer simulations provide a unique insight into how these factors contribute to the rate at which a molecular crystal can grow. In this project a student will use existing software to model the crystal growth of a model molecule. Some familiarity with computer programming is helpful but not necessary.

Synthesis of block copolymers using ATRP 

Do you want to learn how to transfer liquid building blocks into solid polymer chains? During this project you will learn how to master a polymerisation technique called atom radical transfer polymerisation, short ATRP. Today, ATRP is one of the most commonly used polymerisation techniques and allows tailor-made polymer synthesis. You will polymerise monomers into block copolymers and analyse your produced macromolecules using various techniques, such as nuclear magnetic resonance (NMR) spectroscopy and size exclusion chromatography (SEC). 

pH-responsive block copolymers using RAFT 

Do you want to learn how to make micelles that respond to pH changes? During this project you will learn how to master a polymerisation technique called reversible addition-fragmentation chain-transfer (RAFT) polymerisation. Did you know that RAFT was invented in Australia? Within this project, you will polymerise monomers into block copolymers which can assemble into micelles in water. You will also analyse your produced materials using various techniques, such as nuclear magnetic resonance (NMR) spectroscopy, size exclusion chromatography (SEC), dynamic light scattering (DLS) and a Zeta sizer.

New medicines for the treatment of tuberculosis

We have discovered a new class of molecules that have potent antibiotic activity against Mycobacterium tuberculosis (M. tb.) the causative agent of tuberculosis (TB). These compounds are structurally unrelated to any other used drug in the clinic or in development for the treatment of TB. Our new compounds are macrocyclic polyamines and their metal complexes, very unusual drug candidates. We are currently investigating which parts of the molecule are required for activity, and working out how these compounds kill mycobacteria. 

As a Summer Scholar on this project, you will synthesise new molecules for testing against M. tb., gaining experience in organic synthesis, purification techniques and spectroscopy (in particular 1H and 13C NMR, IR and mass spectrometry).

Cobalt(III) complexes for drug delivery 

Research in my group focuses on the development of new and selective anticancer agents. Developing anticancer agents that can act on a tumour without affecting healthy cells is a major challenge in drug design. We are developing transition metal complexes as inert prodrugs of anticancer agents then using a range of methods to selectively release the anticancer agent in a tumour cell. The research projects in this area combine inorganic and organic synthesis with a range of spectroscopic and analytical techniques.

Certain diseases, such as cancers and tuberculosis, have regions of cells with very low oxygen concentrations (hypoxia) due to poor blood supply. These cells are some of the most difficult to treat and are resistant to most commonly used chemotherapeutics. We can take advantage of this hypoxic environment by designing prodrugs that are inert under oxygenated conditions but labile in a hypoxic, reducing environment. We are using cobalt(III) prodrugs for this purpose, which are highly inert under normal oxygenated conditions but are reduced to labile cobalt(II) in hypoxic tumour cells. Projects in this area will involve the synthesising of new cobalt-drug complexes, with particular focus on using fluorescent tags to allow the complexes to be tracked in tumour cells.

 

 

 

 

 

 

 

 

 

Figure: A fluorescent drug is released in hypoxic tumour cells by reduction of the cobalt centre.

Robust superhydrophobic surfaces 

Water repellence is important in many technological applications, such as for the design of self-cleaning and water-proof coatings, and for more efficient microfluidic devices. Nature offers fascinating examples of extreme water repellence, such as the surface of the lotus leaf, on which water flows and rolls-off easily, leaving the leaf dry and clean. In the lotus leaf, the hydrophobicity of the surface is enhanced by a special nano- and micro-scale roughness, which traps pockets of air, and leads to the beading up of water droplets. This effect leads to ‘super-hydrophobicity’, or extreme water repellence.

In this project we aim to fabricate artificial superhydrophobic surfaces using polymer layers. In this project we will combine experimental procedures already established in the group to produce new surfaces that are mechanically and thermodynamically robust.

Probes for studying carbohydrate­‐processing enzymes

Research in my group is focused on development of enzyme inhibitor probes as chemical tools to study the role of these enzymes in biology.

Glycosyltransferases are ubiquitous enzymes that have vital cellular roles in organisms found in all kingdoms of life. These bisubstrate enzymes are responsible for the biosynthesis of glycoconjugates by catalyzing the transfer of a sugar from a donor, most commonly a nucleotide sugar, to a variety of acceptors, including proteins, lipids, saccharides and metabolites.

Among them, human O-linked β-N-acetylglucosamine transferase (O-GlcNAc transferase, OGT) catalyses the transfer of β-N-acetylglucosamine (GlcNAc) from a uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) donor to specific serine and threonine residues of cytoplasmic, mitochondrial and nuclear proteins (Figure 1) Aberrant glycosylation of proteins by OGT is observed in numerous epithelial tumours and is associated with insulin resistance in diabetes. Another class of glycosyltransferase, sialyltransferases (STs), facilitate the transfer of N-acetylneuraminic acid (sialic acid, Neu5Ac) from cytidine-5’-monophospho-β-N-acetylneuraminic acid (CMP-Neu5Ac) to the terminal position of oligosaccharides of glycoproteins (Figure 1). The level of ST expression is dramatically increased during cancer transformation and therefore ST over-expression is correlated with oncogenesis and tumour progression.

In order to study OGT and STs, chemical probes that allow enzyme activity to be monitored within complex biological systems are required. To date, no such probe has been developed for these enzymes. This project will address this problem by developing enzyme inhibitors as probes for OGT and STs. These chemical probes will provide a means to analyse the activities of OGT and STs in cells, which will have direct applications in cancer diagnosis.

Design and synthesis of nucleoside analogues as novel antimycobacterial agents 

Research in my group is focused on development of enzyme inhibitor probes as chemical tools to study the role of these enzymes in biology.

Sequencing of Mycobacterium tuberculosis (Mtb) genome facilitated the identification of new targets for the design of next generation anti-TB drugs.1 Pyrimidine-nucleotide biosynthesis is an essential step in the progression of TB. There is significant difference exist in the regulatory mechanism of the pyrimidine-biosynthesis pathway in Mtb and mammals. Therefore enzymes involved in this biosynthetic pathway provide attractive targets for development of antimycobacterial agents.2

This project involves the design and synthesis of unnatural pyrimidine nucleosides. A number of pyrimidine nucleoside derivatives (1) will be synthesised in which the C5 position of uracil will be substituted with aromatic (or heteroaromatic) moiety. Project will also explore requirement of the 2’-hydroxyl group configuration (ribofuranosyl or arabinofuranosyl) for antimycobacterial activity.

References:

  1. Nature1998, 393, 537-544.
  2. J. Med. Chem. 2007, 50, 3696-3705

Synthesis and evaluation of novel tuberculosis or malarial drug candidates

Tuberculosis (TB) and malaria represent two of the most deadly infectious diseases, responsible for two million deaths per year (one death every ten seconds).  Since the determination of the Mycobacterium tuberculosis (cause of TB) and Plasmodium falciparum(cause of malaria) genome sequences, several viable drug targets have been elucidated.  This summer project will involve the synthesis of a small library of compounds that can be tested for their inhibitory properties against specific enzyme drug targets and against the causative agents of these infectious diseases. The goal of the project will be to develop a novel series of enzyme inhibitors that will serve as anti-tuberculosis and anti-malarial drug leads.

Mar. Drugs 2013, 11(7), 2382-2397; ChemMedChem. 2010, 5, 1067; Chem. Commun. 2011,47, 5166; ChemMedChem. 2012, 7, 1031

Synthesis of glycopeptides as cancer vaccine and diagnostic candidates 

Over 50% of all proteins in our bodies are glycosylated, however, a rational explanation of why nature expends so much energy to decorate our proteins with carbohydrates is largely unknown. In cancer cells there is a significant increase in the expression of a number of glycoproteins (glycosylated proteins), which is combined with incomplete carbohydrtate assembly.  This aberrant glycosylation results in the exposure of additional peptide epitopes, which therefore become accessible to the immune system.  The aim of this project will use a combination of solution and solid phase peptide synthesis to synthesise defined glycopeptide segments of a number of cancer-associated cell-surface glycoproteins (one target compound is shown below). The synthetic glycopeptides will be used to generate tumour-selective immunostimulating antigens followed by evaluation as cancer vaccines.

Chem. Eur. J. 2012, 18(51), 16540-16548; Angew. Chem. Int. Ed. 2011, 50, 1635-1639; Chem. Commun. 2010, 46, 6249-6251.

Probing the cause of multiple sclerosis

There is growing evidence to support the hypotheses that the majority of neurodegenerative diseases may be initiated by a combination of pollutant-induced damage to neurons in the locus ceruleus (LC) and dietary factors, such as sugar intake.  In the first ever study of this type, we undertook elemental maps from frozen brain sections of patients who had suffered multiple sclerosis to show at least 50% have Hg in specific neurons in the LC and all have a range of heavy metals.  This project aims to use chemometrics to mine the information-rich images to learn more about how these metals and others, such as Fe and Cu may have contributed to the disease  (Prof. Peter Lay and Dr Rachel Mak, in collaboration with Professor Roger Pamphlett, Brain and Mind Research Institute and Dr Joonsup Lee, Vibrational Spectroscopy Core Facility).

Are microparticles released from cancer and normal cells key players in disease pathology?

Microparticles (MPs) are microvesicles within the size of 100 nm to one micron that contain RNA, DNA, proteins and lipids and are released from all human cells and function to control cell-cell signaling under normal conditions, however, under disease conditions the number and composition of microparticles released changes and these “disease microparticles” act like human viruses to infect and damage healthy cells or promote cancers.  The aim of this project is to use biospectroscopies to probe differences in biochemical content in disease vs normal MPs and to examine how they change the biochemistry of target cells.  (Prof. Peter Lay, and Dr Aviva Levina in collaboration with Drs Elizabeth Carter and Joonsup Lee, Vibrational Spectroscopy Core Facility, and Professors Georges Grau and Nick King, Pathology, School of Medical Sciences).

Fabrication of 3D printed optical fibre preforms

3D printing is revolutionizing the way we undertake manufacturing and research. Recently we recognized the potential of this technology to completely revolutionize optical fibre fabrication and we demonstrated the worlds first structured optical fibre drawing from a 3D printed preform. This project will continue with that, looking to optimise and characterise annealing of polymers for improving transmission.

Fabrication of exotic filaments for 3D printing

3D printing is revolutionizing the way we undertake manufacturing and research. This project will examine the fabrication of filaments for 3D printing with customized dopants for specific applications aiming to expanding the reach of 3D printing technology.

Smartphone sensors

This project will continue the pioneering work we have undertaken in developing smartphone based instrumentation and sensors. The detection of important biomedical and environmental species such as glucose, Zn and porphyrins will be explored depending on particular interests at the time with the students.

Light-activated MOFs for CO2 Capture

The development of more efficient processes for carbon dioxide (CO2) capture is considered a key to the reduction of greenhouse gas emissions implicated in global warming. Highly porous three-dimensional solids known as metal-organic frameworks (MOFs) have enormous potential for use as CO2 capture materials. Recently, methodologies for the postsynthetic covalent functionalisation of MOFs have opened up fascinating prospects for building complexity into the pores. This project will involve the synthesis of materials as “photoswitchable molecular sieves” in which light can be used to modulate the size and polarity of the pores. The structural and physical characteristics of the materials will be interrogated using novel techniques to probe the light-activated gas permeation properties. The ultimate goal is the realisation of economically-viable materials which can be readily integrated into industrial platforms.

Selective detection of anions using peptide derived sensors

Anions are ubiquitous and they have major roles in a wide range of chemical, biological and environmental processes. The ability to discriminate between anions in real time will lead to many potential applications but particularly in medical diagnostics and devices. The aim of this project is to design sensors for a variety of target anions that are suitable for use in biological systems. This will involve the design and synthesis of a number of small peptide based anion receptors and subsequent measurement of their anion selectivity using numerous techniques (NMR, UV/Vis absorption and fluorescence spectroscopy).

Structure search for crystalline ground states

This project will develop a tool to computationally search for the minimum energy crystal structures of model atomic systems.  Many computational models of liquids and glasses are widely used without ever identifying the relevant crystal structures for the model potential.  A general method to identify these crystals will find wide application for this and other crystal-structure-prediction purposes.  We have a method in mind, and some promising early results for you to expand on. The project will involve programming, so some experience would be beneficial.

Stimulus-Responsive Self-Assembly Structures (2 projects)

We are interested in stimulus-responsive molecules that have reversible self-assembly at nanometre length scales.  Because the nanometre scale structure ultimately controls bulk properties, these materials can be used in applications that range from the controlled release of molecular drugs to the bulk viscosity modification of solutions.  In these project you will prepare new, thermo- and pH-responsive surfactants using controlled radical polymerization, or co-assemble photo- and pH-responsive components into surfactant systems, and then characterize their self-assembly and response to external stimuli.

Device physics of organic solar cells

π-conjugated polymers (CPs) are proven to be cheap, easily processible and flexible alternatives to silicon for sustainable energy applications like organic solar cells. Similar to photosynthesis, CPs funnel the absorbed sunlight to a reaction centre creating opposite free charges – electrons (-ve) and holes (+ve). These free charges must be transported to the respective electrodes and extracted to yield a flow of current in a solar cell. However, these opposite charges can also recombine before reaching the electrodes due to Columbic attraction between them resulting in a loss of current. This tussle between charge transport and recombination influences the device efficiency drastically. In this project, you will perform numerical simulations to (1) understand device physics of an organic solar cell, and (2) figure out strategies to reduce charge recombination thereby providing design rules for highly efficient solar cells.

Probing structure-property relationships of conducting polymers

π-conjugated polymers (CPs), also known as conducting polymers, are large organic molecules with alternate single and double bond character that provide for their semiconducting properties. CPs are proven to be cheap, easily processible and flexible alternatives to silicon for sustainable energy applications like thin film solar cells and light emitting diodes. However, the optical and electronic properties of CPs depend strongly on the polymer structure organization within the film. Structure-property relationships in CPs are very complicated and not well understood. Circular Dichroism spectroscopy has been used to study molecular organization of chiral materials by measuring difference in absorbance of left- and right- circularly polarised light. In this project, you will experimentally study structure-property relationships of chiral analogues of CPs using Circular Dichroism spectroscopy and characterize their organization in thin films.

Assembly of nanorods at interfaces for solar energy applications

Among the barriers to making solar cells cheaper and more efficient is the high energy cost of the crystalline silicon and vapor deposition methods commonly used today. One possible solution is to print solar cells using an ink of semiconducting nanoparticles. In this project you will explore how interfaces (fluid-fluid and liquid-solid) affect the self-assembly of nanorods using models that we have recently developed. This will yield design rules that can be used by experimental collaborators to make desired assemblies in the laboratory for testing in solar cells.