Peter Campbell - University of Wollongong

Contents
Convenor’s Welcome 1
General Information 2
Conference Program 3
Conference Venue and Social Program 13
Pre-Conference Computational
Chemistry Workshop 14
Plenary Speakers 15
Keynote Speakers 20, 43, 89
Biographies and Abstracts 22
Poster Authors 92
Posters 104
Conference Sponsors 155
CONFERENCE ORGANISING
COMMITTEE
Dr Adam Trevitt (University of Wollongong)
A/Prof Jamie Vandenberg (Victor Chang Institute)
Prof Jeff Reimers (University of Sydney)
Dr Haibo Yu (University of Wollongong)
A/Prof Tim Schmidt (University of Sydney)
Prof Michelle Coote (Australian National University)
Dr Adam Hill (Victor Chang Institute)
Dr Ron Clarke (University of Sydney)
A/Prof Stephen Blanksby (University of
Wollongong)
Dr Meredith Jordan (University of Sydney)
CONFERENCE MANAGERS
Leishman Associates
113 Harrington Street
Hobart TAS 7000
Phone: 03 6234 7844
Fax: 03 6234 5958
Email: naomi@leishman-associates.com.au
Web: www.leishman-associates.com.au
Convenor’s
welcome
The Organising Committee welcomes
you to the inaugural BioPhysChem 2011,
a joint meeting of the RACI Physical
Chemistry Division and the Australian
Society for Biophysics.
This meeting promises to be an exciting
event, bringing together scientists from a
range of disciplines to showcase
research developments while providing a
collegial atmosphere for scientific
exchange. We have a stimulating
technical program that boasts an array of
highly regarded plenary and keynote
speakers, drawn from all across the
world, supported by a relaxed social
program.
A warm thank you must also be
extended to our sponsors and exhibitors
for your support of this important event,
your commitment to our Associations
and the chemistry community is greatly
appreciated.
We welcome you and look forward to
your participation in BioPhysChem 2011.
Dr Adam Trevitt
Conference Chair
School of Chemistry,
University of Wollongong
1

2
General Information
General Information
REGISTRATION DESK
The Registration Desk will be located in the foyer
of the McKinnon Building and will be open at the
following times:
Saturday 3 December 10:00am – 5.00pm
Sunday 4 December 8:00am – 5.30pm
Monday 5 December 8:00am – 5:30pm
Tuesday 6 December 8:00am – 5:00pm
ACCOMMODATION
If you have any queries relating to your
accommodation booking, first please see the staff
at your hotel. Your credit card details have been
passed onto the hotel to secure your booking. If
you have arrived 24 hours later than your indicated
arrival day you may find that you have been charge
one nights accommodation.
CONFERENCE NAME BADGES
All delegates and exhibitors will be provided with a
name badge, please wear your name badge at all
times as it will be your entry into all Sessions and
all Social Functions.
DISCLAIMER
The BioPhysChem 2011 Conference reserves the
right to amend or alter any advertised details
relating to dates, program and speakers if
necessary, without notice, as a result of
circumstances beyond their control. All attempts
have been made to keep any changes to an
absolute minimum.
ENTRY TO SOCIAL EVENTS
Entry to social events will not require a ticket,
attendees and additional guests will appear on a
guest list.
MOBILE PHONES
As a courtesy to other delegates, please ensure
that all mobile phones are turned off or in a silent
mode during all sessions and social functions.
SPEAKERS
Speakers will be asked to bring their presentations
with them on a CD or USB stick, then load their
presentations onto the computer in the
corresponding theatre. This must be done AT
LEAST by the break prior to your presenting time
– this may mean the day before your presentation.
There will be dedicated speakers assistants to
provide help uploading your file. All speakers are
responsible for ensuring their presentation is
uploaded and ready for their session.
Please see the staff at the Registration Desk for
further information.
SPECIAL DIETS
All catering venues have been advised of any
special diet preferences you have indicated on
your registration form. Please identify yourself to
venue staff as they come to serve you and they will
be pleased to provide you with all pre-ordered
food. For day catering, there may be a specific
area where special food is brought out, please
check with catering or Conference staff.
WEBSITE
Updated Conference information can be found at
www.biophyschem2011.net.net.au

Program
Friday 2 and Saturday 3 December 2011
Friday 2 December 2011 – Pre Conference Workshop
9:00am – 12:00pm Pre Conference Computational Chemistry Workshop
Hyperion Computer Lab - Building 17, Room 105
12:00pm – 12:45pm Lunch
12:45pm – 5:00pm Pre Conference Computational Chemistry Workshop Continues
Saturday 3 December 2011
10:00am Registration Desk Opens McKinnon Building Foyer
9:00am – 1:00pm Pre Conference Computational Chemistry Workshop
Hyperion Computer Lab - Building 17, Room 105
12:00pm – 1:15pm Lunch (workshop delegates only)
1:15pm – 1:30pm Official Conference Opening Remarks Main Theatre
Plenary Session Medalist Lectures Main Theatre
1:30pm – 2:15pm 2010 RACI Physical Chemistry Medallist Chair: Jeffrey Reimers
K.1 Adventures In Free Radical Chemistry: A Computational Approach
Professor Leo Radom, University of Sydney
2:15pm – 3:00pm 2011 Bob Robertson Medal (ASB) Chair: Jamie Vandenberg
K.2 2011 Medal Recipient
3:00pm – 3:45pm 2011 RACI Physical Chemistry Medallist Chair: Adam Trevitt
K.3 A Life in Physical Chemistry: From Fundamentals to Applications
Professor Keith King, University of Adelaide
4:30pm – 6:30pm We l c o m e M i x e r M c K i n n o n B u i l d i n g F o y e r
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Program
Sunday 4 December 2011
Sunday 4 December 2011
8:00am Registration Desk Open McKinnon Building Foyer
9:00am – 9:50am Plenary Session Main Theatre
GFP: Lighting Up Life
Professor Martin Chalfie, University of Columbia
9:50am – 10:30am Morning Refreshments McKinnon Building Foyer
10:30am – 12:00pm Concurrent Session 1
Theatre 2 Chair: Adam Trevitt Main Theatre Chair: Boris Martiniac
10:30am – 10:45am
10:30am – 10:45am
1.1.1 Density Functional Theory Studies 1.2.1 Spatial and spectral super-
of High-Oxidation State Palladium resolution – Optical imaging of
Systems
nanoscopic signalling domains in 4D
Professor Brian Yates, University of
Tasmania
Dr David Baddeley, University of Auckland
10:45am – 11:00am
1.1.2 Interpolating Molecular Potential
Energy and Property Surfaces
Dr Meredith Jordan, University of Sydney
11:00am – 11:15am
1.1.3 The Relationship Between
Intrinsic Bond Energy and Intrinsic
Radical Stability: Can This be Used to
Test the Untestable?
Professor Michelle Coote, Australian
National University
11:15am – 11:30am
1.1.4 Molecular Oxygen as Energy
Mediator for Photochemical
Upconversion of Near-Infrared Light
Dr Burkhard Fückel, The University of
Sydney
11:30am – 11:45am
1.1.5 Time Resolved Fluorescence
Imaging of Conjugated Polymer Thin
Films
Dr Xiao-Tao Hao, The University of
Melbourne
11:45am – 12:00pm
1.1.6 Quantifying cooperative
intermolecular interactions for
improved carbon dioxide capture
materials
Dr Joseph Lane, The University of Waikato
10:45am – 11:00am
1.2.2 BRET based monitoring of ligand
binding in the ODR-10 odorant
responsive G-protein coupled receptor
from Caenorhabditis elegans
Dr Helen Dacres, Food Futures Flagship @
CSIRO Ecosystem Sciences
11:00am – 11:15am
1.2.3 Photostable Fluorescent
Nanodiamond Material: Labels for
Biomolecules & FRET
Jana Say, Macquarie University
11:15am – 11:30am
1.2.4 BODIPY phosphatidylinositol
probes incorporation into the
membrane of giant unilamellar vesicles
grown in carbohydrate and
physiological buffer solutions
Dr Pierre Moens, University of New England
11:30am – 11:45am
1.2.5 Monitoring the B to A
conformation transition of DNA in
functional cells using Fourier
transform infrared spectroscopy
Donna Whelan, Monash University
11:45am – 12:00pm
1.2.6 The Structure of Mixed
Lipopolysaccharide/Porin Monolayers
at the Air-Liquid||Interface
Dr Anton Le Brun, Australian Nuclear
Science And Technology Organisation
12:00pm – 1:15pm Lunch McKinnon Building Foyer

Sunday 4 December 2011 - Continued
1:15pm – 3:00pm Concurrent Session 2
Theatre 2 Chair: Tim Schmidt Main Theatre Chair: Haibo Yu
1:15pm – 1:45pm
1:15pm – 1:30pm
2.1.1 Isomerization and Decomposition 2.2.1 Structure and dynamics of a
Chemistry of C7Hn (n = 5,7) Radicals replisomal macromolecular assembly
Dr Gabriel Da Silva, The University of Flynn Hill, University of Wollongong
Melbourne
1:30pm – 1:45pm
2.2.2 Resolving Single Molecule
Fibronectin Interactions with
Conducting Polymer Electrodes using
Atomic Force Microscopy
Dr Michael Higgins, Intelligent Polymer
Research Institute
1:45pm – 2:00pm
2.1.2 Cross-Strand Disulfides - Poised
to Act
Dr Naomi Haworth, Deakin University
2:00pm - 2:15pm
2.1.3 Computational Design of
Metal-Based Systems for the
Functionalization of Small Molecules
of Synthetic Interest
Dr Germaine Cavigliasso, Australian
National University
2:15pm - 2:30pm
2.1.4 Infrared Spectroscopy: from
Conformers to Clouds
Dr Evan Robertson, La Trobe University
2:30pm – 2:45pm
2.1.5 Photodetachment of Small
Dianions: Adventures in Mass and
Charge
Associate Professor Stephen Blanksby,
University of Wollongong
Program
Sunday 4 December 2011
2:45pm – 3:00pm
2.1.6 Laser-Based Formation and
Properties of Metal Nanoparticles in
Aqueous Solution
Professor Mark Buntine, Curtin University
1:45pm – 2:00pm
2.2.3 Engineering new catalytic
activities in enzymes through
modifying the conformational
landscape: experimental and
theoretical insights
Dr Colin Jackson, Australian National
University
2:00pm - 2:15pm
2.2.4 Towards ab initio refinement of
protein X-ray crystal structures:
interpreting and correlating structural
fluctuations
Professor Jeffrey Reimers, University of
Sydney
2:15pm - 2:30pm
2.2.5 Density Functional Theory
Calculations of Novel Silicon
Nanosheets
Dr Michelle Spencer, La Trobe University
2:30pm – 2:45pm
2.2.6 Stable Solid Supported
Membranes to probe Membrane-
Protein Interactions
Dr Ingo Koeper, Flinders University
2:45pm – 3:00pm
2.2.7 Directions and Results of OH
Attack on Nucleic Acids: a Theoretical
Study
Ganna Gryn’ova, Australian National
University
3:00pm – 3:30pm Afternoon Refreshments McKinnon Building Foyer
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Program
Sunday 4 December 2011
Sunday 4 December 2011 - Continued
3:30pm – 4:20pm Plenary Session Main Theatre
Simulating Protein-DNA Switches Chair: Meredith Jordan
Professor Tim Clark, The University of Erlangen-Nuremberg
4:20pm – 4:50pm Keynote Session Main Theatre
K.4 Using Theory to Reconcile Experiment: The Search for Certainty in an
Uncertain World Chair: Meredith Jordan
Professor Alan Mark, The University of Queensland
4:50pm – 5:10pm K.5 Towards a Unified Picture of Color and Photisomerization Behavior in
Fluorogenic Monomethine Dyes Chair: Meredith Jordan
Dr Seth Olsen, The University of Queensland
5:10pm – 5:30pm K.6 The roles of membrane deformations and electrostatics in charged
protein-lipid||interactions. Chair: Meredith Jordan
Associate Professor Toby Allen, The University of California, Davis
5:30pm – 7:30pm Poster Session 1 McKinnon Building Foyer

Program
Monday 5 December 2011
Monday 5 December 2011
8:00am Registration Desk Open McKinnon Building Foyer
9:00am – 9:50am Plenary Session Main Theatre
Seeking the Physical Basis of Receptor Tyrosine Kinase Signaling
Professor Kalina Hristova, John Hopkins University Chair: Frances Separovic
9:50am – 10:30am Morning Refreshments McKinnon Building Foyer
10:30am – 12:00pm Concurrent Session 3
Theatre 2 Chair: Irene Yarovsky Main Theatre Chair: Frances Separovic
10:30am – 10:45am
10:30am – 10:50am
3.1.1 Organic Photovoltaic Materials at 3.2.1 Copper Stabilization of Aβ42
High Spatial and Temporal Resolution Aggregation in Model Membranes
Associate Professor Trevor Smith,
Dr Marc-Antoine Sani, University of
University of Melbourne
Melbourne
10:45am – 11:00am
3.1.2 Coarse-Grained Modelling of
Morphology and Energy Transfer in
Conjugated Polymer Nanostructures
Dr David Huang, University of Adelaide
11:00am – 11:15am
3.1.3 Ultrafast Exciton Dynamics of
Conjugated Polymer Nanostructures
Dr Tak W Kee, University of Adelaide
11:15am – 11:30am
3.1.4 Structural, electronic and
transport properties of amorphous/
crystalline silicon heterojunctions
Dr Tim Schulze, Helmholtz-Zentrum Berlin
11:30am – 11:45am
3.1.5 A new understanding of
hybridization in terms of bond
strengths and resonance energies
Professor Noel Hush, The University Of
Sydney
11:45am – 12:00pm
3.1.6 Understanding electron transport
in complex systems|
Professor Gemma Solomon, University of
Copenhagen
10:50am – 11:10am
3.2.2 The enigma of the CLIC proteins:
ion channels, redox proteins, enzymes,
scaffolding proteins?
Paul Curmi, University of New South Wales
11:10am – 11:30am
3.2.3 The Advantage of Being an
Oligomer: the Trimeric Betaine Carrier
BetP
Professor Reinhard Kraemer, University Of
Cologne
11:30am – 11:45am
3.2.4 Single-Molecule View of the
Dynamics of Molecular Machines
Till Boecking, University of New South
Wales
11:45am – 12:00pm
3.2.5 The Dynamic Stator Stalk of
A-type ATPase
Alastair Stewart, The Victor Chang Cardiac
Research Institute
12:00pm – 1:15pm Lunch McKinnon Building Foyer
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Program
Monday 5 December 2011
Monday 5 December 2011 - Continued
12:15pm – 1:00pm ASSOCIATION MEETINGS
Theatre 2 RACI PChem AGM Main Theatre ASB Members Meeting
1:15pm – 3:00 pm Concurrent Session 4
Theatre 2 Chair: Tak Kee Main Theatre Chair: Alan Mark
1:15pm – 1:45pm
1:15pm – 1:30pm
4.1.1 Chemistry at the Threshold: 4.2.1 Test of a Protein Docking
Unexpected Products, Unusual Algorithm on K+ Channel Binding:
Mechanisms, and||Generally Weird Validation and Analysis
Things that Happen Near the Energetic Dr Po-Chia Chen, University of Sydney
Threshold for a Reaction.
Professor Scott Kable, The University of
Sydney
1:30pm – 1:45pm
4.2.2 Open channel structure of MscL
from restrained MD Simulations
Evelyne Deplazes, University of Western
Australia
11:45pm – 2:00pm
4.1.2 Convergent first principles
quantum dynamics: v MCG and Grow
Dr Terry Frankcombe, Australian National
University
2:00pm – 2:15pm
4.1.3 Quantum mechanical study of the
deep well reaction H+ + D2
Dr Marlies Hankel, University of Queensland
2:15pm – 2:30pm
4.1.4 Optical Spectroscopy of
Polycyclic Aromatic Nitrogen
Heterocycle Cations
Dr Viktoras Dryza, University of Melbourne
2:30pm – 2:45pm
4.1.5 Ab Initio Diabatic Potential
Energy Matrix and Dynamics for
OH(2S) + H2 /D2
Professor Michael Collins, Australian
National University
2:45pm – 3:00pm
4.1.6 G4(MP2)-6X: Accurate and
Affordable Computational Chemistry
Dr Bun Chan, University of Sydney
1:45pm – 2:00pm
4.2.3 Estimation of the pKa of
tri-peptides using Generalized
Multiplicative ANOVA of designed data
Rima Raffoul Khoury, University of New
South Wales
2:00pm – 2:15pm
4.2.4 The Fouling of Hydrophobic
Membranes by Hydrophilic Alginates:
A Molecular Dynamics Study.
Dr Matt Stewart, Victoria University
2:15pm – 2:30pm
4.2.5 HIV1-TAT Peptide modified
nanoparticles: insights from molecular
dynamics simulations
Dr Nevena Todorova, RMIT University
2:30pm – 2:45pm
4.2.6 Ion Permeation and Selectivity in
a Voltage Gated Sodium Channel
Ben Corry, University of Western Australia
2:45pm – 3:00pm
4.2.7 The Role of Molecular Strain in
Creating Ion Selectivity in Biological
Molecules
Michael Thomas, University of Western
Australia
3:00pm – 3:30pm Afternoon Refreshments McKinnon Building Foyer

Program
Monday 5 December 2011
Monday 5 December 2011 - Continued
Keynote Session Main Theatre
3:30pm – 4:00pm K.7 Molecular approaches to next generation photovoltaic energy conversion
Associate Professor Tim Schmidt, The University of Sydney Chair: Ron Clarke
4:00pm – 4.30pm K.8 Charge photo-generation and recombination in conjugated polymer donor/
fullerene acceptor bulk heterojunction solar cells
Dr Attila Janos Mozer, University of Wollongong Chair: Ron Clarke
4:30pm – 5:00pm K.9 Towards High-Efficiency Microalgae Biofuel Systems
Associate Professor Ben Hankamer, University of Queensland Chair: Ron Clarke
5:00pm – 7:00pm Poster Session 2 McKinnon Building Foyer
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10
Program
Tuesday 6 December 2011
Tuesday 6 December 2011
8.00am Registration Desk Open McKinnon Building Foyer
9.00am – 9.50am Plenary Session Main Theatre
Linking Protein Motions to Catalysis Chair: Michelle Coote
Professor Judith Klinman, University of California, Berkley
9.50am – 10.30am Morning Refreshments McKinnon Building Foyer
10:30am – 12:00pm Concurrent Session 5
Theatre 2 Chair: Michelle Coote Main Theatre Chair: Ron Clarke
10:30am – 10:45am
5.1.1 A novel Molecular Dynamics
approach for quantitative prediction of
adhesion and wettability: application
to responsive surfaces
Dr George Yiapanis, RMIT University
10:45am – 11:00am
5.1.2 What can we learn from
large-scale ab initio calculations of
ionic liquids?
Dr Ekaterina Izgorodina, Monash University
11:00am – 11:15am
5.1.3 Formation of Radical Products
From Activation of Phospholipid
Ozonides
Shane Ellis, University of Wollongong
11:15am – 11:30am
5.1.4 The Distal Effect of Electron-
Withdrawing Groups on the Stability of
Peptide Enolates and its Exploitation
in Synthesis
Junming Ho, Australian National University
11:30am – 11:45am
5.1.5 Molecular magnetic properties:
benchmarking and applications
Dr David Wilson, La Trobe University
11:45am – 12:00pm
5.1.6 Molecular Design Rules for
Frequency-Based, Universal Quantum
Computers
Laura McKemmish, University of Sydney
10:30am – 10:45am
5.2.1 Single molecule fluorescence
microscopy: visualising DNA
replication and repair dynamics within
living E. coli cells
Dr Andrew Robinson, University Of
Groningen
10:45am – 11:00am
5.2.2 Structured Illumination
Microscopy of Living Cells
Dr Liisa Hirvonen, University of Melbourne
11:00am – 11:15am
5.2.3 Differential Dynamic Microscopy
and Dynamic Light Scattering studies
of Bacterial Motility
Reece Nixon-Luke, RMIT University
11:15am – 11:30am
5.2.4 Revisiting Boltzmann:
disentangling solid-state NMR
measurements of heterogeneous
model membrane systems
Dr John Gehman, Melbourne University
11:30am – 11:45am
5.2.5 Liposomes: Stable or Kinetically
Trapped?
Dr Adam Mechler, La Trobe University
11:45am – 12:00pm
5.2.6 The Effect of Crystallization on
Protein Quaternary Structure
Dr Don Vanselow, Nativeproteins.Blogspot.
Com
12:00pm – 1:15pm Lunch McKinnon Building Foyer

Program
Tuesday 6 December 2011
Tuesday 6 December 2011 - Continued
1:15pm – 3:00pm Concurrent Session 6
Theatre 2 Chair: Stephen Blanksby Main Theatre Chair: Adam Hill
1:15pm – 1:45pm
1:15pm – 1:30pm
6.1.1 Anion Photoelectron
6.2.1 Polarization effects in ion
Spectroscopy of Ionic Complexes and channels and bulk from ab initio MD
Clusters
simulations
Assistant Professor Duncan Wild, The Associate Professor Sedar Kuyucak,
University of Western Australia
University of Sydney
1:30pm – 1:45pm
6.2.2 A critical dual role for the pore
helix in hERG K channel inactivation
Dr Mathew Perry, Victor Chang Cardiac
Research Institute
1:45pm – 2:00pm
6.1.2 Ion Mobility Mass Spectrometry
Reveals New Insights into Structure
and Assembly of Protein Complexes
Dr Tara Pukala, University of Adelaide
2:00pm – 2:15pm
6.1.3 Nanomechanics of live bacterial
cells
Associate Professor Michelle Gee,
University of Melbourne
2:15pm – 2:30pm
6.1.4 Gas-phase structures of two
isomers of deoxyguanosine radical
cation: experiments and theory
Dr Linda Feketova, University of Melbourne
2:30pm – 2:45pm
6.1.5 Attaching Molecular Hydrogen to
Atomic Ions
Professor Evan Bieske, University of
Melbourne
2:45pm – 3:00pm
6.1.6 Which Density Functionals can be
reliably applied to Main Group
Thermochemistry?
Dr Lars Goerigk, University of Sydney
1:45pm – 2:00pm
6.2.3 Bimodal Regulation of hERG
Gating by the N-Terminal Tail as
Revealed by Voltage Clamp
Fluorometry
Dr Peter Tan, Victor Chang Cardiac
Research Institute
2:00pm – 2:15pm
6.2.4 Studies of Bacterial
Mechanosensitive (MS) Channels
under High Hydrostati |Pressure
Evgeny Petrov, Victor Chang Cardiac
Research Institute
2:15pm – 2:30pm
6.2.5 SPontaneous Oscillatory
Contractions (SPOC): Assessing the
Contractile Performance of Human
Cardiomyopathies
Amy Li, Sydney University
2:30pm – 2:45pm
6.2.6 Does GLUT4 queue to get to the
plasma membrane?
Adelle Coster,University of New South
Wales
2:45pm – 3:00pm
6.2.7 Dynamics of protein hydration
water
Dr Kathleen Wood, ANSTO, Bragg Institute
3:00pm – 3:30pm Afternoon Refreshments McKinnon Building Foyer
11

12
Program
Tuesday 6 December 2011
Tuesday 6 December 2011 - Continued
3:30pm – 4:20pm Plenary Session Main Theatre
Technology that drives new science: 2D IR spectroscopy and its application to
protein aggregation and drug binding
Professor Martin Zanni, University of Wisconsin, Madison Chair: Jamie Vandenberg
4:20pm – 4.50pm K e y n o t e S e s s i o n M a i n T h e a t r e
K.10 Chair: Jamie Vandenberg
Dephosphorylation of the calcium pump – an infrared spectroscopy and density
functional theory study
Professor Andreas Barth, University of Stockholm
4:50pm – 5:10pm K.11 Chair: Jamie Vandenberg
Molecular Mechanisms of K+ Selectivity of the Na/K Pump
Haibo Yu, University of Wollongong
5:10pm – 5:30pm K.12 Chair: Jamie Vandenberg
Towards rational control of the bacterial flagellar motor
Dr Lawrence Lee, The Victor Chang Cardiac Research Institute
7:00pm – 10:30pm Farewell BBQ Novotel Wollongong
Half Page Advert - Newspec

Conference Venue and Social Program
Conference Venue & Location
The University of Wollongong has grown from a
small college of 300 students, to an international
university with over 26 000 students over the
space of 50 years.
The teaching, research and cultural life of the
University is supported by state-of-the-art facilities,
including an extensive library collection, an
interactive Science Centre, and a Recreation &
Aquatic Centre. In late 2002, the University
announced the establishment of a Wollongong
Innovation Campus on a 20 hectare site at
Brandon Park. A joint venture with the NSW
government, the private sector and local councils,
this science and technology precinct will be
developed over a ten year period commencing in
2003.
Welcome Mixer
Saturday 3 December
McKinnon Building Foyer
4:30pm – 6:30pm
Additional Tickets: $50
This is your first opportunity to catch up with
friends and network with new colleagues.
The mixer will include a relaxed canapé and
beverage service.
There will be a complimentary shuttle bus
operating between 6:00pm and 7:00pm to take
delegates from UOW to local hotels and the city.
Poster Session 1
Sunday 4 December
McKinnon Building Foyer
5:30pm – 7:30pm
Additional Tickets: $50
Join us for the first of two poster sessions for
BioPhysChem 2011.
Authors will be available to speak about their
posters during this session.
Light food and beverages will be served. There will
be a complimentary shuttle bus operating
between 7:00pm and 8:00pm pm to take
delegates from UOW to local hotels and the city.
Poster Session 2
Monday 5 December
McKinnon Building Foyer
5:00pm - 7:00pm
Additional Tickets: $50
Join us for the second poster session for
BioPhysChem 2011.
Authors will be available to speak about their
posters during this session.
Light food and beverages will be served. The
Gong Shuttle will be running its usual service until
9:00pm to take delegates from UOW to local
hotels and the city.
Farewell BBQ
Tuesday 6 December
Novotel Wollongong
7:00pm – 10:30pm
Additional Tickets: $100
Come and wind down after a full few days of
conferencing. Catch up with old friends and
colleagues and newly made acquaintances over a
drink and some scrumptious BBQ food, and be
stunned with the views that the newly built outdoor
deck at the Novotel Wollongong offer.
Please note: All social functions are included in a
full conference registration. Day registrants and
accompanying person tickets can be purchased
at an extra cost. Delegates will need to make their
own way to the Novotel Wollongong for the
Farewell BBQ.
13

14
Pre-Conference
Computational Chemistry Workshop
This workshop will provide an introduction to
computational chemistry methods including
molecular mechanics, semi-empirical theories,
molecular orbital methods and density functional
theory (DFT).
The basis sets commonly used in molecular orbital
and DFT calculations will also be introduced.
The reliability and accuracy of different methods
and/or basis sets for different applications will be
examined. The topics covered in the main part of
the workshop are:
- Classical Mechanics and Molecular Force Fields
- Semi-empirical Methods
- Hartree
- Fock Theory
- Basis Sets
- Electron Correlation
- Density Functional Theory
- Solvation
Interspersed throughout the workshop will be
“Masterclasses” of approximately 40 minutes, with
guest lecturers focussing on particular
computational problems. Concurrent with the
masterclasses will be workshops aimed at
teaching participants less familiar with
computational methods how to apply these
methods to standard problems.
The following people are contributing to the
workshop:
- Prof Tim Clarke
- Prof Michelle Coote
- Prof Leo Radom
- Prof Peter Gill
- Dr Seth Olsen
- Dr Haibo Yu
- Prof Brian Yates

Professor Martin Chalfie
University of Columbia
Sunday 4 December 9.00am – 9.50am
GFP: Lighting Up Life
Biography
Martin Chalfie is the William R. Kenan, Jr.
Professor of Biological Sciences and former chair
of the Department of Biological Sciences at
Columbia University. In 2008 he shared the Nobel
Prize in Chemistry with Osamu Shimomura and
Roger Y. Tsien for his introduction of Green
Fluorescent Protein (GFP) as a biological marker.
Dr. Chalfie was born in Chicago, Illinois. He
obtained both his A.B. and Ph.D. from Harvard
University and then did postdoctoral research with
Sydney Brenner at the MRC Laboratory of
Molecular Biology, Cambridge, England. He joined
the faculty of Columbia University as an Assistant
Professor in 1982 and has been there ever since.
He uses the nematode Caenorhabditis elegans to
investigate nerve cell development and function,
concentrating primarily on genes used in
mechanosensory neurons. His research has been
directed toward answering two quite different
biological questions: How do different types of
nerve cells acquire and maintain their unique
characteristics? and How do sensory cells
Plenary Speakers
respond to mechanical signals? In the course of
his studies, he has introduced several novel
biological methods in addition to his work with
GFP.
Dr. Chalfie is a member of the National Academy
of Sciences and the Institute of Medicine and a
fellow of the American Academy of Arts and
Sciences, the American Association for the
Advancement of Science, the Institute of Medicine,
and the Royal Society of Chemistry (Hon.). He
shared the 2006 Lewis S. Rosenstiel Award for
Distinguished Work in Basic Medical Science from
Brandeis University and the 2008 E. B. Wilson
Medal from the American Society for Cell Biology
with Roger Tsien.
Abstract
The great American baseball player Yogi Berra
once said, “You can observe a lot by watching.”
Unfortunately, before the early 1990s observations
in the biological sciences were usually done on
dead specimens that were specially prepared and
permeabilized to allow entry of reagents to stain
cell components. These methods allowed a
glimpse of what cells were doing, but they gave a
necessarily static view of life, just snapshots in
time. GFP and other fluorescent proteins
revolutionized the biological sciences because
these proteins allowed scientists to look at the
inner workings of living cells. GFP can be used to
tell where genes are turned on, where proteins are
located within tissues, and how cell activities
change over time. Once a cell can be seen, it can
be studied and manipulated. The discovery and
development of GFP also provide a very nice
example of how scientific progress is often made:
through accidental discoveries, the willingness to
ignore previous assumptions and take chances,
and the combined efforts of many people. The
story of GFP also shows the importance of basic
research on non-traditional organisms.
15

16
Plenary Speakers
Professor Tim Clarke
The University of Erlangen-Nuremberg
Sunday 4 December 2011 – 3.30pm – 4.20pm
Simulating Protein-DNA Switches
Biography
Tim Clark was born in southern England and
studied chemistry at the University of Kent at
Canterbury, where he was awarded a first class
honors Bachelor of Science in 1970. He obtained
his Ph.D. from the Queen’s University Belfast in
1973 after working on the thermochemistry and
solid phase properties of adamantane and
diamantane derivatives. After two years as an
Imperial Chemical Industries Postdoctoral Fellow
in Belfast, he moved in 1975 to Princeton
University as a NATO Postdoctoral Fellow working
for Paul Schleyer. He then followed Schleyer to the
Institut für Organische Chemie of the Universität
Erlangen-Nürnberg in 1976. He is currently
Technical Director of the Computer-Chemie-
Centrum in Erlangen and Director of the Centre for
Molecular design and Professor of Computational
Chemistry at the University of Portsmouth (UK).
His research is concentrated on the development
of calculational techniques for simulation and
cheminformatics and their use for a variety of
chemical and biological applications. Because of
the central function of CCC in Erlangen, many of
the applied research topics are interdisciplinary, in
particular with respect to signal transduction in
biological systems and catalytic reactivity for
redox-active metal complexes.
The method development currently being carried
out in the group follows two main directions.
Firstly, development of a “next generation”
semiempirical molecular orbital (MO) technique to
replace the pure NDDO-methods such as MNDO,
AM1 and PM3, which have changed little since
1977. The new technique involves new techniques
to represent the nucleus and non-valence
electrons and an additional dispersion term based
on a variational technique for calculating the
polarizability. As part of this development, a
completely new high performance semiempirical
MO-program is being developed for near-linear
scaling on highly parallel (1,024 cores and more)
computers and clusters. It has been tested for up
to 77,000 atoms.
The second method-development direction is to
use local properties at molecular surfaces for
cheminformatics and classical simulations. The
aim is to provide an alternative to the almost
universal atomistic approach, which usually suffers
from a lack of generality and very restricted
applicability. It is hoped that anisotropic unitedatom
techniques will allow us to extend the time
scale of classical simulations into the range
(microseconds) necessary to be able to study
allosteric changes, polymer and liquid-crystal
properties etc.
Other important research directions involve
calculations on enzyme reaction mechanisms,
usually using a hybrid QM/MM approach, model
CI studies on electron transfer in proteins and
organic radical ions, studies of radical reaction
mechanisms and of transition-metal complexes
with phosphorus-containing ligands.
Tim Clark is the author of over 315 articles in
scientific journals and two books, was among the
top 500 most cited chemists in the 1997
compilation and is the founding editor of the
Journal of Molecular Modeling.
Abstract
Perhaps the single most important component of

many biological control networks is the switching
of transcription by control (C) proteins that
complex specifically to promoter DNA sequences
in order to activate or repress transcription.
Whereas the repression mechanism is quite easily
visualized (the repressor protein blocks access of
the RNA polymerase to the promoter sequence
and therefore blocks transcription of the encoded
gene), activation is more difficult to understand.
Binding an activating C-protein must recruit the
sigma-subunit of the RNA-polymerase to bind to
the promoter region of the DNA.
The lecture will address two aspects of these
switching mechanisms; how do repressor proteins
that are themselves switched by small molecules
or peptides achieve this switching and how does
an activator protein recruit the sigma subunit? The
latter question is closely interlinked with that of
how C-proteins achieve their high selectivity for
specific DNA sequences.
We will discuss very extensive molecular dynamics
(MD) simulations on TetR, a repressor protein that
is switched by tetracycline antibiotics, and the
finely tuned Esp1396I bacterial restrictionmodification
(RM) system. The latter is particularly
interesting because the same C-protein acts as
promoter and repressor, depending on its
concentration. The result is a temporal control of
the RM system that is essential for it to function
correctly.
Our results will emphasize the role of MD
simulations as prospective research tools in this
area, but will also point out their limitations and the
need for exhaustive validation.
Plenary Speakers
Professor Kalina Hristova
John Hopkins University
Monday 5 December 2011 – 9.00am – 9.50am
Seeking the Physical Basis of
Receptor Tyrosine Kinase Signaling
Biography
Kalina Hristova received her B.S. degree from the
University of Sofia, Bulgaria, and her Ph.D. degree
from Duke University, USA. She did post-doctoral
work at the University of California, Irvine. She
joined the faculty at Johns Hopkins University as
an Assistant Professor in 2001. Now she is a
Professor and the Marlin U. Zimmerman Faculty
Scholar in the Departments of Materials Science
and Engineering and Biomedical Engineering at
Johns Hopkins.
Kalina Hristova is a recipient of the Margaret
Oakley Dayhoff award from the American
Biophysical Society. The main focus of the
research in her laboratory is the thermodynamic
and structural principles that underlie membrane
protein folding and signal transduction across
biological membranes. At the meeting, she will
present recent results on lateral receptor
interactions in mammalian membranes. These
studies have yielded new knowledge about the
physical principles behind human pathologies.
17

18
Plenary Speakers
Receptor tyrosine kinases (RTKs) conduct
biochemical signals via lateral dimerization in the
plasma membrane, and their transmembrane
domains play an important role in the dimerization
process. Single amino acid mutations in RTK
transmembrane domains induce unregulated
signaling and, as a consequence, pathologies.
The research in our lab is focused on the
molecular mechanism behind these pathologies,
and it suggests that RTK signaling in health and
disease can be understood based on quantitative
knowledge of receptor interaction strengths.
Professor Judith Klinman
University of California, Berkley
Tuesday 6 December 2011 – 9.00am – 9.50am
Linking Protein Motions to Catalysis
Biography
Judith Klinman received her A.B. and Ph. D.
degrees in chemistry from the University of
Pennsylvania. She was a postdoctoral fellow at the
Weizmann Institute of Science, Rehovot, Israel and
spent 10 years at the Institute for Cancer Research
in Philadelphia, first as a postdoctoral fellow with
Irwin Rose and later as a Staff Scientist. She has
been on the faculty of the University of California,
Berkeley, since 1978. During her tenure at
Berkeley, she has been a Chancellor’s Professor,
Guggenheim Fellow and Miller Fellow. She has
been elected to the National Academy of
Sciences, the American Academy of Arts and
Sciences, and the American Philosophical Society,
and has received the Repligen Award and the
Remsen Award from the American Chemical
Society; the Merck Award from the American
Advancement of Science; she is also a member of
the Royal Society of Chemistry. She was awarded
an honorary Ph. D. from the University of Uppsala,
Sweden in 2000 and an honorary degree from the
University of Pennsylvania in 2006.
Her research is currently focused on four areas: (i)
nuclear tunneling in enzyme-catalyzed reactions
and the relationship of this phenomenon to the role
of protein dynamics in catalysis; (ii) the
development of a general theory for enzyme
catalysis that utilizes protein motions to generate
active site compression; (iii) the mechanism of
dioxygen activation by enzymes; and (iv) the
biogenesis and catalytic mechanism of quinoproteins
and cofactors.
In addition to her lifelong fascination with enzymes,
Dr. Klinman enjoys adventure travel, spending time
with friends and family (especially her seven
grandchildren) and weekend retreats in Sonoma
County.
Abstract
Understanding the physical origins of the
enormous rate accelerations catalyzed by
enzymes remains a major challenge in chemistry
and biophysics. Early and persistent theories of
enzymatic rate acceleration were based on simple
transition state approximations and relied on static
three-dimensional representations of enzymes for
interpretation. Work during the past decade has
pointed increasingly toward the essential roles of
protein motion/flexibility, not only in facilitating
substrate binding and product release steps, but
also in understanding the catalysis of bond
cleavage events. This talk will focus on the
quantum properties of C-H activation in enzyme
reactions, the resulting implication of active site
compression, and the role of protein
conformational sampling in achieving such
compression. (Supported by grants from the NIH
and NSF)

Professor Martin Zanni
University of Wisconsin, Madison
Tuesday 6 December 2011 – 3:30pm – 4:20pm
Technology that drives new science:
2D IR spectroscopy and its
application to protein aggregation
and drug binding.
Biography
Martin Zanni is the Meloche-Bascom Professor of
Chemistry at the University of Wisconsin-Madison.
He was a Ph.D. student with Daniel Neumark at
the University of California-Berkeley and an NIH
postdoctoral researcher with Robin Hochstrasser
at the University of Pennsylvania. Prof. Zanni
specializes in 2D IR spectroscopy and its
application to problems in the biological and
energy sciences. He has contributed to the
technological underpinnings of the technique,
written a textbook on the subject, and uncovered
important scientific details on systems that are
very difficult to study with other techniques. He
has received much recognition for his work,
including the Presidential Early Career Award for
Scientists and Engineers, the Sackler Prize, and
the National Academy of Sciences Research
Initiatives Award.
Plenary Speakers
Abstract
2D IR spectroscopy is proving to be a very useful
tool for studying molecular structures and their
dynamics. It is now being applied in fields ranging
from biophysics to the energy sciences. In this
talk, I will present our contributions to the
technological development of this exciting
spectroscopy as well as an application to amyloid
fiber formation and drug inhibition. A few years
ago, we invented a mid-IR pulse shaper that
enabled us to computer generate the 2D IR pulse
trains. This device makes data collection faster,
more accurate, and enables new capabilities such
as phase cycling. Using this method, we can now
rapidly scan 2D IR spectra to monitor structural
kinetics, which we have done to monitor the
aggregation of amylin, which is the polypeptide
associated with type 2 diabetes. We will present
results in which we have time-resolved the
secondary structure of individual residues,
providing some of the most detailed information
available on fiber formation. Moreover, I will also
present our recent work on drug binding, in which
we have resolved the binding site and mechanism
of a peptide inhibitor that blocks fiber formation.
With 2D IR spectroscopy, we obtain an
unprecedented level of structural and kinetic detail
on systems that are traditionally difficult to study
with standard structural biology tools.
19

20
Biographies and Abstracts
Saturday 3 December - Session 1
Keynote Session - Main Theatre
K.1 - 1:30pm – 1:55pm
2010 RACI Physical Chemistry Medallist
Lecture
Adventures In Free Radical
Chemistry: A Computational
Approach
Prof Leo Radom
School of Chemistry and ARC Centre of Excellence for Free
Radical Chemistry and Biotechnology, University of
Sydney, Sydney, NSW 2006, Australia
Biography
Leo Radom is Professor of Chemistry at the
University of Sydney. After completing a PhD at
that university in 1969, he spent an extended
postdoc with John Pople at Carnegie-Mellon
University before returning to Australia with a QE II
Fellowship at the Australian National University.
He moved from the ANU to the University of
Sydney in 2003. Leo has been elected to the
Australian Academy of Science and to the
International Academy of Quantum Molecular
Science. He has been awarded the Rennie Medal
and HG Smith Medal of the RACI, the Schrödinger
Medal of WATOC, the Fukui Medal of APATCC, the
David Craig Medal of the Australian Academy of
Science, and the Centenary Medal of the
Australian Government. He has been a Named
Lecturer or Professor in Switzerland, USA, UK,
Spain, Australia, Israel and Canada. Leo’s main
research interests are concerned with the study of
the structures and stabilities of molecules and the
mechanisms of reactions in which they are
involved by use of ab initio quantum chemistry
computations. Current areas of interest include
free radical chemistry, enzyme-catalyzed reactions
and zeolite chemistry. He is currently a CI in the
ARC Centre of Excellence in Free Radical
Chemistry and Biotechnology, and the immediate
Past-President of the World Association of
Theoretical and Computational Chemists.
Abstract
Radicals are ubiquitous in chemistry and biology.
Because they are reactive species, they are often
difficult to study experimentally and therefore
theory has a potentially useful role to play in their
characterisation. In recent years, we have been
using quantum chemistry computations to
investigate the structures, stabilities and
reactivities of radicals. We have also been
examining ways to obtain improved theoretical
descriptions of radicals. Highlights from this
research will be presented.
K.2 - 1:55pm – 2:20pm
2011 Bob Robertson Medal (ASB)
The 2011 Medal Recipient
announced on the day
K.3 - 2:20pm – 2:45pm
A Life in Physical Chemistry: From
Fundamentals to Applications
Prof Keith King1 1 School of Chemical Engineering, University of Adelaide, SA
5005, keith.king@adelaide.edu.au
2011 RACI Physical Chemistry
Medallist
Biography
Keith King is currently Emeritus Professor and
Visiting Professor of Chemical Engineering at the
University of Adelaide. His areas of expertise cover
chemical kinetics, energy transfer and catalysis,
laser diagnostics, combustion and flames,
including ignition and explosions, soot formation,
and biodiesel. He is a Fellow of the Institution of
Chemical Engineers, a Fellow of the Royal
Australian Chemical Institute, a Fellow of the Royal
Society of Chemistry, and a Senior Member of the
American Institute of Chemical Engineers. He was
awarded the 1998 R. K. Murphy Medal by the
RACI Industrial Chemistry Division for ‘Outstanding
Achievements in the Practice of Chemical

Engineering and Industrial Chemistry’. He was a
senior member of the team awarded the
Engineering Excellence Award 2000 by Engineers
Australia, SA Division for ‘Design and Development
of the Fuel and Combustion System for the Sydney
2000 Olympic Torch Relay’.
Abstract
I will present a brief account with selected
highlights of my research in physical chemistry
covering chemical kinetics and energy transfer,
combustion, and laser diagnostics.
Key Words
Kinetics, energy transfer, combustion, lasers
Stanton Scientific
MASS S P E C TROME T E R S U PPOR T
A N D V A C U U M SCIE N C E PRO D U CTS
Mass Spectral data bases
N.I.S.T. (USA) and Wiley Mass Spectral Libraries
Mass Spectral Software including file conversion
Aalborg Mass Flow Meters and Controllers
Electron Multipliers and Channeltron Detectors
Mass Spectrometer Filament repair service
Representing Scientific Instrument Services New Jersey USA
Granville Phillips Vacuum Gauges
www.stantonscientific.com Email: bill@stantonscientific.com
Ph: 02 66856902 Fax: 02 85690588
21

22
Biographies and Abstracts
Sunday 4 December - Session 1
Session 1 – Theatre 2
1.1.1 10:30am – 10:45am
Density Functional Theory Studies of
High-Oxidation State Palladium
Systems
Brian F Yates 1 , Alireza Ariafard2 , Allan J
Canty3 1 University of Tasmania, Private Bag 75, Hobart TAS 7001, Brian.
Yates@utas.edu.au
2 University of Tasmania, Private Bag 75, Hobart TAS 7001,
Alireza.Ariafard@utas.edu.au
3 University of Tasmania, Private Bag 75, Hobart TAS 7001, Allan.
Canty@utas.edu.au
Biography
Professor Brian Yates heads up an active research
program in computational chemistry with
particular applications to organometallic and
organic chemistry, and his research is funded by
the Australian Research Council (ARC). He is a
current member of the ARC College of Experts
and is Chair of the Physics Chemistry and Earth
Sciences panel in 2011. He sits on the board of the
National Computational Infrastructure (NCI) and is
chair of the committee which allocates grants of
supercomputer time on the national high
performance computing facility. Brian has also
built up a strong reputation for teaching
excellence. He has been awarded competitively
funded teaching development grants at the
national (CAUT/CUTSD, ALTC) and state levels,
and he has been rewarded with local (UTAS) and
national (2006 Carrick Award, 2007 RACI
Chemical Education medal) teaching excellence
awards. He is currently a Professor in Chemistry at
the University of Tasmania and an Australian
Learning and Teaching Council (ALTC) Discipline
Scholar in Science.
Abstract
Reactions involving palladium compounds with
organic reagents are important for the synthesis of
new materials, pharmaceuticals, and biological
related molecules of value in medical research.
Recently there has been much interest in the
chemistry of high oxidation state palladium
systems because of the enhanced ability of these
systems to form new carbon-carbon bonds. In this
presentation I will discuss the computational
chemistry research in my group which is aimed at
understanding organometallic chemistry, with a
particular focus on bimetallic high oxidation state
palladium systems.
1.1.2 10:45am – 11:00am
Interpolating Molecular Potential
Energy and Property Surfaces
M. J. T. Jordan, S. J. Kolmann and M. Morris
Department of Chemistry, University of Sydney, Sydney, NSW,
2006, email: m.jordan@chem.usyd.edu.au
Biography
Meredith Jordan is currently a senior lecturer in
chemistry at the University of Sydney. She
completed a PhD at Sydney with Professor Bob
Gilbert before undertaking a postdoctoral
fellowship with Professor Mick Collins at the RSC
at the Australian National University, then being
awarded a research fellowship at Girton College,
Cambridge to work with Professor David Clary
(who promptly left for London!). Her research
focuses on the study and description of molecular
interactions.
Abstract
Over the last 15 years we have developed a
modified Shepard interpolation scheme that can
be used to iteratively construct molecular potential
energy surfaces (PES). Such surfaces have been
used in many applications, including classical
trajectory simulations, quantum dynamics and
quantum diffusion Monte Carlo simulations of
ground state wavefunctions. Some systems,
however, remain problematic and the methodology
is still not quite “black box”. Here we describe
some recent applications and modifications of the
scheme in pursuit of this goal.

Modified Shepard interpolation can also be used
to construct molecular property surfaces, which,
in many cases, are more straightforward than PES.
We have used a modified Shepard interpolation to
construct dipole moment surfaces (DMS) for water
and hydrogen cyanide, based on analytic DMS in
the literature. These analytic DMS allow us to
optimise the parameters and the form of the
interpolated DMS. Because the DMS is more
slowly varying than the PES we obtain accurate
results using both a standard (ie zeroth order)
Shepard expansion of each component of the
dipole moment vector and a modified Shepard
interpolation based on first order Taylor
expansions of the dipole moment. Given that our
PES interpolation method uses second derivatives
of the potential, it is straightforward to obtain the
dipole moment vector as part of the “standard”
PES interpolation, that is, to generate both the PES
and the DMS simultaneously. The PES together
with the DMS are used to predict vibrationally
averaged dipole moments and rovibrational line
strengths as well as the linear response of a
molecule to an external electric field.
1.1.3 11:00am – 11:15am
The Relationship Between Intrinsic
Bond Energy and Intrinsic Radical
Stability: Can This be Used to Test
the Untestable?
Michelle L. Coote and Ching Yeh Lin
Australian Research Council Centre of Excellence for Free Radical
Chemistry and Biotechnology,
Research School of Chemistry, Australian National University,
Canberra, ACT 0200, Australia
Biography
Professor Michelle Coote is a graduate of the
University of New South Wales, where she
completed a B.Sc. (Hons) in industrial chemistry
(1995), followed by a Ph.D. in polymer chemistry
(2000). Following postdoctoral work at the
University of Durham, UK, she joined the Research
School of Chemistry, Australian National University
in 2001, initially as a postdoctoral fellow with
Professor Leo Radom. She established her own
research group in 2004 and has recently taken up
Biographies and Abstracts
Sunday 4 December - Session 1
an ARC Future Fellowship. She has published
extensively in the fields of polymer chemistry,
radical chemistry and computational quantum
chemistry, and is a member of the ARC Centre of
Excellence for Free-Radical Chemistry and
Biotechnology. She has received many awards
including the 2001 IUPAC prize for young
scientists, the RACI Cornforth medal (2000),
Rennie medal (2006) and David Sangster Polymer
Science and Technology Achievement Award
(2010), and the Le Fevre Memorial Prize of the
Australian Academy of Science (2010).
Abstract
One of the major tasks of chemistry is structurereactivity
analysis –attempting model and explain
the mechanism, kinetics and thermodynamics of a
chemical process in terms of contributions of the
various functional groups present. This type of
analysis then allows one to make predictions
about how to manipulate chemical reactions by
changing the functional groups, and can thereby
guide reagent and catalyst design. Such studies
have proven extremely useful in radical chemistry
as such processes often involve several competing
reactions in which small changes to substitution
patterns of one or more reagents can have a major
positive or negative impact on the reaction
outcome. One the key “tools” one uses when
analysing radical reactions is radical stability.
Unfortunately, defining and measuring intrinsic
radical stability is not straightforward.1 From a
quantum mechanical perspective, the stability (or
‘propensity to react’) of any species is only
precisely definable in the context of a balanced
chemical reaction. However, this only defines the
‘stability’ of a given species relative to a particular
chemical system. It does not allow us to infer
anything about the behaviour of that molecule in
any other chemical context, thereby making this
notion of ‘stability’ virtually useless for the
purposes of chemical explanation and prediction.
It is unsurprising, then, that chemists have sought
to define a measure of stability that could be
considered an intrinsic property of a given species
— a measure of a molecule’s propensity to react
across a range of chemical reactions that could in
turn be related to the chemical structure of the
molecule using, for example, qualitative molecular
orbital theory arguments. However, the problem
23

24
Biographies and Abstracts
Sunday 4 December - Session 1
with this approach is that there is no obvious
intrinsic property of an isolated molecule definable
in quantum-mechanical terms that can provide a
guide to its propensity to react across a range of
chemical systems.
In this talk we will look at how chemists have
sought to address this problem for the case of
radical stability. We will examine some of the
leading methods for defining and measuring
radical stability, including the familiar radical
stabilization energy (RSE),2 along with some
lesser-known alternatives based on corrected
carbon-carbon bond energies,3,4 and direct
measures of the extent of radical delocalisation.
Using the results of high-level ab initio molecular
orbital theory calculations we will compare the
predictions of the various schemes with one
another, and with expectations based on
“chemical intuition”, with a view to establishing a
reliable method for measuring relative radical
stability.5 We will then examine the relationship
between intrinsic radical stability and intrinsic bond
energies, and show how “reliable” radical stability
trends can be used to evaluate the underlying
physical meaning some commonly used energy
decomposition schemes.6
1.1.4 11:15am – 11:30am
Molecular Oxygen as Energy
Mediator for Photochemical
Upconversion of Near-Infrared Light
Burkhard Fückel1 , Derrick A. Roberts1 , Yuen
Yap Cheng1 , Raphaël G. C. R. Clady1 , Roland B.
Piper2 , N. J. Ekins-Daukes 2 , Maxwell J. Crossley1 ,
Timothy W. Schmidt1 1 School of Chemistry, The University of Sydney, NSW 2006,
Australia, burkhard.fueckel@chem.usyd.edu.au, timothy.
schmidt@sydney.edu.au
2 Department of Physics and the Grantham Institute for Climate
Change, Imperial College, London, U.K.
Biography
Dr Burkhard Fückel is a postdoctoral researcher
with A/Prof Timothy Schmidt at The University of
Sydney. He has been awarded a Feodor Lynen
research fellowship of the German Alexander von
Humboldt foundation to work on “3rd generation
photovoltaics” in Sydney. Before commencing his
work in Sydney in 2010, he received his PhD from
the Gutenberg University of Mainz, where he
studied energy transfer process by single molecule
spectroscopy and quantum chemistry under
supervision of Prof Thomas Basch
Abstract
Ground state molecular oxygen (3Sg), constitutes
about 20% of the volume of air. Its chemical
reactivity increases dramatically upon electronic
excitation to the singlet (1Dg) state, leading to
spontaneous reaction with a range of unsaturated
organic compounds. Since the (1Dg) ← (3Sg)
transition of molecular oxygen can be induced by
quenching of a triplet excited state of an organic
molecule, artificial organic systems, as for example
organic photovoltaics, are generally protected from
air. Biological systems, on the contrary, have
evolved ways of handling singlet oxygen, such as
sequestration by carotenoids that protect the
sensitive pigments in the photosynthetic reaction
center of plants.
We present a strategy that employs singlet oxygen
as an energy transmitter for photochemical
upconversion (UC). Photochemical UC combines
two low energy photons into one of higher energy
by incoherent means [1] and has therefore
attracted recent interest for applications in
light-harvesting and light-emitting applications.[2]
In the employed system, singlet oxygen is
generated upon photoexcitation of the sensitizer
molecules and then acts as an energy transmitter
for the UC process. The excitation energy of two
singlet oxygen molecules is subsequently
harvested by emitter molecules, which in turn
gives rise to upconverted fluorescence of the
emitter species.[3] This process furthermore
reduces the rate of the photo-degradation of the
sensitizer molecules. We present strategies for
improvement of the currently achieved efficiencies
≤0.01% to produce excited singlet states in the
emitter molecules, which are currently under
examination.

1.1.5 11:30am – 11:45am
Time Resolved Fluorescence
Imaging of Conjugated Polymer Thin
Films
Xiao-Tao Hao1, , Trevor A Smith1, , Kenneth P.
Ghiggino2 1 School of Chemistry and ARC Centre of Excellence for Coherent
X-ray Science, The University of Melbourne, Victoria 3010,
xhao@unimelb.edu.au; trevoras@unimelb.edu.au
2 School of Chemistry, The University of Melbourne, Victoria 3010,
ghiggino@unimelb.edu.au
Biography
Dr. Xiaotao Hao is a research fellow working at
school of chemistry in the University of Melbourne.
His research interests include photophysics of light
emitting conjugated polymers, time resolved
fluorescence spectroscopy and microscopy. He
has published over 40 papers on peer-reviewed
scientific journals.
Abstract
The solid-state characteristics of conjugated
polymers are the key factors that govern the
performance of organic opto-electronic devices in
many situations. Aggregates are readily formed in
most conjugated polymer films resulting in good
charge transport via strongly interacting π-electron
systems, but these aggregates also likely induce
inhomogeneous morphologies and emission
quenching, and thereby affect device efficiency.1,2
Determining the spatial scale of the
inhomogeneities in conjugated polymer films from
nanometres to many microns, and their effect on
the dynamics of electron/hole transport, is
necessary to develop more efficient injection
processes for high performance devices.
High-resolution optical microscopy methods are a
useful tool to provide this spatial information.
Coupling ultrafast spectroscopic methods with
high spatial resolution optical techniques makes it
possible to map the dynamics of the photoinduced
charge transfer/transport processes as a
function of location in the film.
We report here the steady state and time-resolved
fluorescence emission characteristics of poly[2methoxy-5-(2-ethylhexyloxy)-1,4-phenylene
vinylene] (MEH-PPV) and a water-soluble PPV
Biographies and Abstracts
Sunday 4 December - Session 1
derivative with sulphonate-containing side chains
(DPS-PPV) thin films with different conformations
coated using various methods.3,4 We observed
inhomogeneities in the morphology and
fluorescence dynamics of thin films of the light
emitting conjugated polymer, on sub-micrometre
spatial and picosecond temporal scales using
time-resolved scanning confocal fluorescence
imaging measurements.
This work illustrates the power of time-resolved
emission imaging to identify regions of varying
degrees of aggregation, whether pre-existing
aggregates or those formed during film formation,
in MEH-PPV/PMMA films cast from a range of
solvents. Differences observed show some
correlation to the solvent from which the films are
cast. The spatiotemporal spectral behaviour can
be associated with degrees of aggregation, from a
level of “single-chain like” regions (emitting to the
blue with approximately nanosecond emission
decay components) to highly aggregated
(short-lived, red emitting) regions, within the film
morphology. The overall time-resolved behaviour
was sensitive to the degree of aggregation, which
in turn was dependent on the solvent from which
the film was cast.
In contrast, thin films of a water-soluble DPS-PPV,
formed on silica substrates by a solvent-free
friction transfer technique, were highly aggregated
producing “rods” of polymer aligned perpendicular
to the drawing direction. This “log-rolling” is in
contrast with the reported behaviour of most
comparable polymers, which tend to align along
the drawing direction. The photophysical
behaviour of the friction-transferred film is also
different compared with other film formation
techniques of the same polymer.
25

26
Biographies and Abstracts
Sunday 4 December - Session 1
1.1.6 11:45am – 12:00pm
Quantifying cooperative
intermolecular interactions for
improved carbon dioxide capture
materials
Joseph R. Lane1 1 Department of Chemistry, University of Waikato, Private Bag
3105, Hamilton 3240, New Zealand, jlane@waikato.ac.nz
Biography
Jo Lane completed his undergraduate and
graduate studies in the Department of Chemistry
at the University of Otago. He was awarded his
BSc.(Hons.) in 2005 and his PhD in 2008 under
the supervision of Prof. Henrik Kjaegaaard. Jo
then worked as a postdoctoral research fellow in
the same research group before being appointed
to a lectureship in the Department of Chemistry at
the University of Waikato in 2009
Abstract
Any serious effort to reduce anthropogenic carbon
dioxide (CO2) emissions must contend with the
geopolitical and economic reality that fossil fuels
will continue to make a dominant contribution to
the world’s energy supply for decades to come.
This makes development of scalable, costeffective
CO2 capture technologies of equal
importance to innovations in renewable energy
resources over the near future.
Nanoporous crystalline compounds such as metal
organic framework (MOF) materials have
exceptionally high surface areas and demonstrate
promising ability for the separation and capture of
CO2. However, current MOF materials do not yet
show the necessary selectivity for CO2 under
conditions relevant for fossil fuel combustion.
To better understand the fundamental
intermolecular interactions involved in CO2
adsorption, we have investigated over 100 different
complexes of CO2 with various combinations of
electron accepting (Lewis acid) and electron
donating (Lewis base) molecules. We have used
the recently developed explicitly correlated
coupled cluster singles doubles and perturbative
triples [CCSD(T)-F12] methods and the associated
VXZ-F12 (where X = D,T,Q) basis sets. We observe
only modest changes in the geometric parameters
of CO2 upon complexation, which suggests that
the geometry of CO2 adsorbed in a nanoporous
material should be similar to that of CO2 in gas
phase. For complexes that exhibit simultaneous
CO2-Lewis acid and CO2-Lewis base
intermolecular interactions, we find that the total
interaction energy is greater than the sum of the
interaction energies of the constituent complexes.
Furthermore, the intermolecular distances of the
cooperative complexes are contracted as
compared to the constituent complexes. We
suggest that MOF or similar nanoporous materials
could be designed with adsorption sites
specifically tailored for CO2 to allow cooperative
intermolecular interactions, facilitating enhanced
CO2 adsorption.
Session 1 – Main Theatre
1.2.1 10:30am – 10:45am
Spatial and spectral super-resolution
– Optical imaging of nanoscopic
signalling domains in 4D
David Baddeley1 , Isuru Jayasinghe1 , Cherrie
Kong1 , David Crossman1 , Juliette Cheyne1 ,
Johanna Montgomery1 , Mark Cannell1 , Christian
Soeller1 ,
1 Department of Physiology, University of Auckland, Private Bag
92019, Auckland, New Zealand E-mail: d.baddeley@auckland.ac.
nz
Biography
David completed a PhD at Heidelberg University in
Germany studying structured illumination and 4Pi
microscopy before returning to Auckland to work
on single molecule localisation microscopy. Since
then he has made a number of improvements to
the PALM/STORM technique and applied these to
the study of the proteins involved in excitation
contraction coupling in cardiac myocytes
Abstract
Recent single molecule localisation techniques
such as PALM and STORM have made far field
imaging with a resolution well below the diffraction
limit a reality. Optical super-resolution promises

significantly greater freedom and ease of labelling,
sample preparation and imaging than electron
microscopy and it is towards realising this potential
that we have directed our efforts. We will present
an implementation of single molecule based
localisation microscopy that puts emphasis on
making the approach as practical as possible and
culminates in a super-resolution workflow that is
no more arduous than high-quality confocal
imaging.
Our approach uses a single laser line to excite
multiple dyes which we discriminate in a
ratiometric manner offering spectral superresolution.
By using conventional dyes in the near
infra-red which are commercially available as
antibody conjugates, we both simplify labelling
procedures and minimise the contribution of
sample autofluoresence. We will also present a
novel method of extracting the z position of single
molecules based on a phase ramp in the objective
pupil plane. This method offers a modest
improvement in axial resolution over some existing
methods of 3D localisation such as astigmatism,
and is very easy to implement with components
which will already be present in a typical imaging
lab.
The distribution of proteins and their proximity on
the nanometre scale critically determines cellular
signalling responses, but could previously not be
examined with optical techniques. We have used
our super-resolution approach to investigate a
number of signalling domains and will present data
from our analysis of key Ca2+ signalling proteins in
cardiac myocytes, and from synaptic proteins in
hippocampal culture. We have already obtained a
number or surprising results such as showing that
the number of Ryanodine receptor Ca2+ channels
(RyRs) in peripheral couplons is considerably less
than initially thought, and that cluster sizes follow a
near exponential distribution compatible with a
stochastic assembly process. When performing
two colour imaging (e.g. with RyR, NCX, and
Caveolin) we consistently find much lower levels of
colocalisation than predicted from diffraction
limited imaging.
Biographies and Abstracts
Sunday 4 December - Session 1
1.2.2 10:45am – 11:00am
BRET based monitoring of ligand
binding in the ODR-10 odorant
responsive G-protein coupled
receptor from Caenorhabditis
elegans
H. Dacres, J. Wang, V. Leitch, I. Horne, A.R.
Anderson, S.C. Trowell
CSIRO Food Futures National Research Flagship & CSIRO
Ecosystem Sciences, Australia Helen.Dacres@csiro.au
Biography
Dr Helen Dacres specialises in interdisciplinary
approaches to chemical sensing and biosensing
systems. She received a PhD and MSc in
Instrumentation and Analytical Chemistry from
UMIST (Manchester, UK) for developing optical
chemical sensors to detect biologically and
environmentally relevant gases including nitric
oxide. This research made her realise the future of
chemical sensing - particularly for difficult
problems - would lie in biosensing so she looked
for a position to gain postdoctoral experience in
molecular biology and biosensing. She joined
CSIRO as a postdoctoral fellow in 2005 to work on
the development of a number of novel biosensors.
She has designed biosensors for monitoring
various disease states including blood clotting
disorders and to study the effect of cancer on cell
death. She is currently a research scientist at
CSIRO Ecosystem Sciences developing
biosensors using biological odorant receptors for
detecting volatile compounds with potential
application areas including defence, health and
biosecurity.
Abstract
Humans express over 750 G-protein coupled
receptors (GPCRs), which represent not only the
largest class of integral membrane receptors but
also the largest class of targets for therapeutic
drugs. GPCRs respond to a wide range of
ligands, including proteins peptides and small
organic molecules. GPCRs also mediate
chemosensation, the senses of taste and smell, in
vertebrates as well as in nematode worms. We set
out to develop a biosensor transduction system
27

28
Biographies and Abstracts
Sunday 4 December - Session 1
that is compatible with GPCRs generally and with
odorant receptors in particular.
Fluorescence resonance energy transfer (FRET)
has previously been used to monitor ligand binding
by secretin receptors expressed and imaged in
intact COS cells [1]. However, FRET-GPCR has
not previously been demonstrated in a cell-free
system. We recently reported that bioluminescent
resonance energy transfer (BRET) has superior
limits of detection and sensitivity in a protease
assay compared to FRET [2]. Here, for the first
time, we have inserted BRET (bioluminescence
resonance energy transfer) transduction tags in
the primary sequence of a GPCR, the nematode
ODR-10 receptor, which in vivo responds to the
odorant 2,3-butanedione (diacetyl).
In a yeast-based cell-free system, the EC50 of a
BRET2-ODR-10 biosensor was in the fM range for
2,3-butanedione. The response was ligandspecific
and was completely abolished by a single
point mutation in the receptor sequence. The
percentage change in RET ratio was several fold
higher than for an equivalent FRET-ODR-10
construct. Novel BRET-GPCR biosensors of this
type have potential application in drug discovery,
clinical diagnosis, explosive detection and quality
control of food and beverage production [3].
1.2.3 11:00am – 11:15am
Photostable Fluorescent
Nanodiamond Material: Labels for
Biomolecules & FRET
J M Say1 , L Brown2 , J R Rabeau3 1 Centre for Quantum Science and Technology and MQ Photonics
Research Centre, Department of Physics and Department of
Chemistry and Biomolecular Science, Macquarie University,
Sydney, New South Wales, 2109, jana.say@mq.edu.au
2 Department of Chemistry and Biomolecular Science, Macquarie
University, Sydney, New South Wales, 2109, louise.brown@mq.
edu.au
3 Centre for Quantum Science and Technology and MQ Photonics
Research Centre, Department of Physics, Macquarie University,
Sydney, New South Wales, 2109, james.rabeau@mq.edu.au
Biography
Jana Say is a PhD student at Macquarie University
working in the Diamond Nanoscience group. She
joined the team in March 2010 after finishing her
Honours Degree in Quantum Mechanics at the
University of British Columbia in Canada. Jana is
working jointly between the Physics and Chemistry
and Bimolecular Sciences Departments and her
PhD is focusing on the use of luminescent
nanodiamonds for biological applications. The title
of her talk today is Photostable Fluorescent
Nanodiamond Material: Labels for Biomolecules &
FRET.
Abstract
Colour centres in nanodiamonds have many
properties which make them attractive for
biological applications including their chemical and
physical stability, biocompatibility, easy surface
functionalization, near unity quantum yield,
electron and nuclear spin and stable
photoluminescence. These qualities enable
nanodiamonds to be used in a broad range of
applications including biosensing, protein
separation, drug delivery and single particle
imaging in cells. Here we propose using
fluorescent nanodiamonds as an alternative
nano-label to conventional fluorophores. We also
explore their use as a novel donor for Förster
Resonance Energy Transfer (FRET)
measurements.
Over 500 different optical centres have been
identified in diamond. Of these, the nitrogen
vacancy (NV) centre, a substitutional nitrogen atom
adjacent to a carbon vacancy, is the most widely
studied. The NV centre has a broad fluorescence
emission band, centred at approximately 685nm.
The fluorescence of an NV can therefore travel
though tissue with limited absorption and is
conveniently beyond the range of cellular
autofluorescence. However, several challenges in
using nanodiamonds for biological applications
include the size of nanodiamond particle, their
surface impurities and their tendency to aggregate.
To address these difficulties we have established a
series of chemical treatments to produce and
isolate a monodisperse population of 4nm
nanodiamond particles from material fabricated by
detonation synthesis. This process involves
successive acid washing steps, ultrasonication
and ultracentrifugation. The resulting acid treated
and oxidized nanodiamonds were covalently
attached to poly-L-lysine-FITC via carbodiimide
chemistry as a preliminary study for establishing

the conjugation of nanodiamonds to other
biomolecules of interest. Our functionalization
approach has lead to our poly-L-lysine-FITC
labeled nanodiamonds being used for labelling of
macrophage cells and also stem cells. The
long-term photostability of the nanodiamonds
provides the ability to image and track biological
cellular processes uploaded with the
nanodiamonds.
Finally, due to the photostability, long lifetime and
near unity quantum yield of the NV centre in
nanodiamonds we have been studying their use as
a donor label for FRET. We have investigated the
coupling efficiency between a single NV centre in a
nanodiamond and multiple IRDye-800CW dye
molecules absorbed onto the surface using both
fluorescence spectral intensity and lifetime
measurements. The use of the stable NV centre as
the donor molecule prevents the rapid
photobleaching of the dye molecule and allows for
distance calculations able to position the NV
centre within the nanodiamond particle.
1.2.4 11:15am – 11:30am
BODIPY phosphatidylinositol probes
incorporation into the membrane of
giant unilamellar vesicles grown in
carbohydrate and physiological
buffer solutions.
Moens, P.D.J. 2 , D. M. Gau 1,2 , Salvemini, I.L. 2 ,
Reid, J. 2
1 Department of Bioengineering, University of Pittsburgh,
Pittsburgh, PA 15213, USA, recalled@gmail.com
2 School of Science & Technology, University of New England,
Armidale, NSW 2351, Australia
Biography
David Gau, a Rotary Ambassadorial Scholar and
Whitaker Fellow, hails from Pittsburgh,
Pennsylvania, USA. Dave completed his
undergraduate career at University of Pittsburgh
completing an undergraduate thesis in
bioengineering and degrees in mathematics and
economics. While at PITT, Dave has been involved
in many student organizations and was selected
as valedictorian of the 2011 graduating class.
Biographies and Abstracts
Sunday 4 December - Session 1
Alongside, under the guidance of Dr. Partha Roy of
the Bioengineering department of PITT, David has
published a paper on identifying Pfn1 and VASP
interaction using FRET and has another paper
under review regarding effects of Pfn1-VASP
interaction in breast cancer cell migration. He is
now working under Dr. Pierre Moens of University
of New England and continuing research on Pfn1
interaction with other proteins and how it relates to
cancer invasion.
Abstract
The use of Giant Unilamellar Vesicles (GUVs)
composed of fluorescently labelled lipid analogues
has become an increasingly popular model to
study both structural and complex biophysical
properties of bilayers. However, there is a common
assumption that the number of probes
incorporated into the membrane of the GUVs is
proportional to the mole fraction (%) of these lipid
molecules in the original solvent solution. To test
this assumption, a commercial confocal laser
scanning microscope (Nikon C1) was used to
obtain single point fluorescence correlation
spectroscopy (FCS) data.
We measured the diffusion coefficient and number
of molecules incorporated into the membrane of
the GUVs for several BODIPY labelled lipid i.e.
BODIPY TMR-phosphatidylinositol (4,5)
bisphosphate, BODIPY TR- phosphatidylinositol
(4,5) bisphosphate and BODIPY (530/550)
hexadecanoyl-sn-glycero-3-phosphocholine. We
investigated the effect of various mole fraction of
these lipids and compared the results with
(1,1’-dioctadecyl-3,3,3’,3’tetramethylindocarbocyanine
perchlorate [DiIC18]
when grown in carbohydrate and physiological
buffer solutions.
We show that the number of DiIC18 molecules
incorporated into the membrane of the GUVs
(formed by the electroformation method) is in
agreement with the expected number of
molecules calculated from the mole fraction of the
organic stock solution. However, we find that the
actual proportion of β-BODIPY-HPC, TR-PI(4,5)P2,
and TMR-PI(4,5)P2 incorporated into the bilayer is
highly variable and appear significantly less than
the proportion of these lipids in the organic solvent
stock solution. This apparently low incorporation is
29

30
Biographies and Abstracts
Sunday 4 December - Session 1
observed regardless of the solutions (carbohydrate
or physiological buffer) used when growing the
GUVs. These variations in incorporation can be
explained by the formation of a blue fluorescent
species which is probably due to the formation of
dimers of the BODIPY labelled lipids.
1.2.5 11:30am – 11:45am
Monitoring the B to A conformation
transition of DNA in functional cells
using Fourier transform infrared
spectroscopy
Donna R. Whelan1 , Keith R. Bambery 1 , Philip
Heraud1,2 , Mark J. Tobin 3 , Don McNaughton 1 and
Bayden R. Wood1 .
1 Center for Biospectroscopy and School of Chemistry, Monash
University, Clayton, Victoria, 3800
2 Monash Immunology and Stem Cell Laboratories, Monash
University, Clayton, Victoria, 3800
3 Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria
3168, Australia
Biography
Donna Whelan is currently completing a PhD with
the School of Chemistry at Monash University
concentrating on the elucidation of DNA
conformation and architecture within live cells
using Fourier transform infrared spectroscopy and
fluorescence microscopy methods. In 2010 she
successfully completely her Honours year and
published her research on the B to A transition of
DNA in cells in ‘Nucleic Acids Research’. She has
recently returned from a visit to Imperial College in
London where she conducted further research on
this topic under Prof. Sergei Kazarian.
Abstract
The structure of DNA inside cells is a central
aspect of research into the normal and diseased
state. In the past, the conformation of DNA inside
cells has been hypothesized as predominantly
B-like with temporary transitions of small sections
to alternate conformations. Using Fourier transform
infrared (FTIR) spectroscopy we have been able to
detect the conformation of DNA within live cells
and monitor an overall B- to A-like transition during
the dehydration of several cell types including
avian erythrocytes, mammalian fibroblasts and
bacterial strains. Upon rehydration the A-like DNA
reverts to the B-like conformation observed in live
cells. Changes in band profile to both the
symmetric phosphate stretch (1087 cm-1) and the
C-O stretch (1052 cm-1), and shifts in the
antisymmetric phosphate stretch (1225 – 1237
cm-1) and the C-C stretch (970 – 966 cm-1)
among others, were identified as diagnostic of this
conformational transition. This indicates an
important step forward in understanding the role
of A-like DNA inside cells and the mechanism by
which some dehydrated cells, including the
bacteria examined, can return to a functional state.
Furthermore, we demonstrate that by applying
FTIR spectroscopy to hydrated samples, sharp
DNA bands can be used to approximate DNA
concentration. This is anticipated as enabling
differentiation of cancerous from non-cancerous
cells based on the increased DNA content inherent
to dysplastic and neoplastic tissue.
1.2.6 11:45am – 12:00pm
The Structure of Mixed
Lipopolysaccharide/Porin
Monolayers at the Air-Liquid
Interface
Anton P. Le Brun1 , Luke A. Clifton2 ,
Christopher L. Johnson3 , Jeremy H. Lakey3 and
Stephen A. Holt1 1 Bragg Institute, Australian Nuclear Science and Technology
Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232,
Australia.
2 ISIS Neutron Facility, STFC Rutherford Appleton Laboratory,
Harwell Science and Innovation Campus, Didcot, Oxfordshire,
OX11 0QX, United Kingdom.
3 Institute for Cell and Molecular Biosciences, The Medical School,
University of Newcastle upon Tyne, Framlington Place,
Newcastle upon Tyne, NE2 4HH, United Kingdom.
Biography
Anton Le Brun is a post-doctorial research fellow
in the Bragg Institute and National Deuteration
Facility, ANSTO. His research interests are in
membrane structural biology with a particular
focus for studying membrane proteins and lipid
bilayers using neutron reflectometry. He completed
his bachelors and masters degrees in

iochemistry at the University of York. Anton went
onto study for a PhD in biophysics in Professor
Jeremy Lakeyâ€s laboratory at the University of
Newcastle upon Tyne. His thesis describes
characterising model membranes based on the
outer membrane of the bacterial Gram-negative
cell envelope, work which he now continues to
further at ANSTO.
Abstract
The Gram-negative bacterial cell envelope is a
complex structure. It consists of a cytoplasmic
inner membrane, the periplasm and an outer
membrane. The outer membrane composes of a
phospholipid inner leaflet and an outer leaflet of
lipopolysaccharide as well as integral membrane
proteins. The challenge in studying the structures
and functions at the outer membrane is in creating
simple, but yet representative models of the
membrane. Current models consist of solidsupported
bilayers containing the lipid and protein
components of the bacterial outer membrane [1].
Although this makes for a good representation of a
bilayer the fluidity of the lipid layers is not truly
represented. By depositing mixed monolayers of
lipid and protein at the air-liquid interface on a
Langmuir trough, a monolayer that represents the
fluidity and outer surface of a membrane can be
achieved. Monolayers of the anionic lipid DPPG
and outer membrane protein F (OmpF) from E. coli
have been successfully deposited and
characterised [2]. Whilst these monolayers model
the negative charge characteristics and fluidity of a
bacterial outer membrane, DPPG is not a
representative lipid of the outer membrane
surface. This work has been extended to make a
more representative outer membrane surfaces by
using lipopolysaccharide (LPS) as the lipid
component. Monolayers of LPS and OmpF were
deposited onto an aqueous surface using a vesicle
rupture method first described by Schindler and
colleagues [3]. The layers were characterised
using neutron reflectometry. The ability to
discriminate between hydrogen (a weak scatter)
and its isotope deuterium (a strong scatter) in
neutron scattering makes neutron reflectometry a
powerful tool for probing the layers along the axis
perpendicular to the plane of the membrane.
Production of deuterated versions of the
molecules to be studied allows the lipid, protein
Biographies and Abstracts
Sunday 4 December - Session 1
and solvent components of the membrane layer to
be deduced. In this case we used bio-deuteration
methods to produce deuterated OmpF and
deuterated LPS from E. coli. The deposited
material forms stable monolayers as shown by
reproducible pressure-area isotherms. By using
different combinations of deuterated and
hydrogenated material a detailed picture of the
monolayer is achieved. Finally, colicin N is a
pore-forming E. coli toxin produced by E. coli cells
to kill competing cells when nutrients are scarce.
Colicin N uses OmpF as it receptor and
translocator to cross the outer membrane. The
translocation of colicin N is tracked across the
LPS/OmpF monolayer using neutron reflectometry.
References
1. S. A. Holt et al (2009) Soft Matter 5:2576-2586.
2. L. A. Clifton et al (2011) Structure submitted.
3. H. Schindler et al (1978) Proc. Natl. Acad. Sci. USA
75:3751-3755.
31

32
Biographies and Abstracts
Sunday 4 December - Session 2
Session 2 – Theatre 2
2.1.1 1:15pm – 1:45pm
Isomerization and Decomposition
Chemistry of C7Hn (n = 5, 7)
Radicals
Gabriel da Silva
Chemical and Biomolecular Engineering, The University of
Melbourne, Parkville 3010, Australia
Biography
Dr. Gabriel da Silva is a Lecturer in the Department
of Chemical and Biomolecular Engineering at the
University of Melbourne. After completing a Ph.D.
in Chemical Engineering at the University of
Newcastle, Gabriel worked as a postdoctoral
scholar in Chemistry and Enviornmental Science
at NJIT, before moving to Melbourne in 2007.
Abstract
Benzyl is a cyclic C7H7 resonance-stabilized
radical (RSR) that is widely encountered in flames
and in numerous other reacting systems. In
combustion, reaction chemistry of the benzyl
radical plays a key role in the oxidation of aromatic
fuels (such as toluene) and in the formation of
polycyclic aromatic hydrocarbon (PAH) pollutants
and soot particles. Computational chemistry and
statistical reaction rate theory have been used to
model the mechanism and kinetics of benzyl
radical decomposition, suggesting that the
predominant reaction products are the C7H6
species fulvenallene (+H) and the RSR
cyclopentadienyl (+ HCCH). Benzyl can also
isomerize to form the RSRs tropyl and
vinylcyclopentadienyl; the latter is almost as stable
as tropyl but much less widely known. Chemically
activated bimolecular reactions on the C7H7
surface, relevant to combustion and atmospheric
chemistry, will also be discussed. The effect of
methyl substitution in benzyl (resulting in C8H9
methyl-benzyl radicals) is also examined.
The benzyl decomposition product fulvenallene is
shown to readily decompose at flame
temperatures to yield the fulvenallenyl radical
(C7H5), a novel RSR that shares properties of
cyclopentadienyl and propargyl. Rate constant
calculations for fulvenallenyl decomposition
identify a large overall reaction barrier, making the
closed-shell species fulvenallene approximately as
stable as its open-shell parent (C7H7) and
daughter (C7H5) radicals. Fulvenallenyl
decomposition proceeds via a complex reaction
mechanism, forming the i/n-C5H3 (+ HCCH) and
C3H3 (+ C4H2) RSRs as the major products. The
theoretically proposed reaction products are
consistent with products identified in threhold
photoionization mass spectra for C7H5 radical
pyrolysis obtained using VUV synchrotron
radiation. The C7H5 energy surface can also be
accessed via the reverse C5H3 + C2H2 and C3H3
+ C4H2 reactions, as well as the near-barrierless
reactions of several C7H4 polyynes with H,
reactions which are, again, of interest to
combustion scientists and astrochemists. Finally,
incorporating the theoretical results presented
here into a detailed kinetic model for toluene
pyrolysis is shown to result in significant
improvements in predicted radical concentrations,
as well as pointing to a role for fulvenallenyl in PAH
chemistry.
2.1.2 1:45pm - 2:00pm
Cross-Strand Disulfides - Poised to
Act
Naomi L Haworth 1 , Merridee A Wouters2 1 School of Life and Environmental Sciences, Deakin University,
Geelong, Victoria, 3217, naomi.haworth@deakin.edu.au
2 School of Life and Environmental Sciences, Deakin University,
Geelong, Victoria, 3217, m.wouters@deakin.edu.au
Biography
Dr Haworth completed her BSc (Hons) in
Chemistry and Quantum Physics at the University
of Melbourne. Her PhD in Theoretical Chemistry
followed. This was under Dr George Bacskay at
the University of Sydney and focussed on highly
accurate calculations of the thermochemistry of
small molecules. After a post-doc in the same field
with Professor Leo Radom, she changed direction
to look at quantum chemical and biophysical
studies of proteins. This has included a Humboldt
Fellowship under Prof Tim Clarke at Erlangen and
her current position at Deakin University in
Melbourne.

Abstract
Cross-strand disulfides (CSDs) link cysteine (Cys)
residues across adjacent strands of b-sheets. As
the strands are already linked by H-bonding, CSDs
appear at best to be redundant. Initially the
formation of such disulfides was predicted to be
forbidden, producing too much strain in the protein
fold.(1) Nevertheless, CSDs do exist in nature.(2)
As disulfides in strained environments have the
potential to be involved in redox processes, CSDs
may perform important biological roles.
There are three protein environments in which a
CSD can form. In antiparallel b-sheet, the two Cys
can be in a non-H-bonding site (aCSDn) or in an
H-bonding site (aCSDn). CSDs can also be found
in parallel b-sheet (pCSD).
Almost all CSDs adopt one of two disulfide
conformations: the right-handed staple (RHSt) and
the left-handed saddle/cis (LHC). When the Cys
residues are involved in H-bonding across the
b-ladder (aCSDhs) an LHC conformation is usually
seen, whereas when the Cys do not form H-bonds
with their b-partners (aCSDns) an RHSt
conformation is almost always formed. In pCSDs,
only one Cys forms H-bonds across the b-ladder
while the other is non-H-bonding. This results in a
mix between RHSt and LHC conformations.
The CSD types and conformations interact
differently with the surrounding b-sheet.
Antiparallel b-sheets have positive sheet twist and
shear. Parallel sheets also have positive twist but
are not sheared. aCSDns with RHSt
conformations generate positive twist and shear
between the two Cys. The values match well with
the natural sheet deformation, thus condensation
of these disufides does not cause significant
additional strain. In contrast, aCSDhs with LHC
conformations generate positive twist but negative
shear. The sheet must therefore experience
significant disruption to allow the disulfide to form.
This involves buckling and tilting of the b-strands
as well as breaking of H-bonds in some cases.
pCSDs of either conformation generate positive
twist as well as large positive shear. Thus oxidation
of pCSDs also results in significant sheet strain.
One of the most important CSDs in nature is an
aCSDh found in ribonuclease reductases of all
organisms (including viruses). This highly strained
Biographies and Abstracts
Sunday 4 December - Session 2
disulfide is responsible for the reduction of
ribonucleotides to deoxyribonucleotides and is
therefore essential for all life.(3)
1. Richardson, JS (1981) Adv. Protein Chem. 34, 167.
2. Wouters, MA, George, RA, Haworth, NL (2007) Curr.
Prot. Pept. Sci. 8, 484.
3. Eriksson, M, et al. (1997) Structure 5, 1077.
2.1.3 2:00pm – 2:15pm
Computational Design of Metal-
Based Systems for the
Functionalization of Small Molecules
of Synthetic Interest
Germán E Cavigliasso 1 , Robert Stranger1 ,
Brian F Yates 2
1 Research School of Chemistry, Australian National University,
Canberra, Australia
2 School of Chemistry, University of Tasmania, Hobart, Australia
Biography
Germán E Cavigliasso is currently a research
fellow and lecturer at the Australian National
University, with principal interests in computational
chemistry and transition metal systems. He carried
out undergraduate studies in engineering,
physical, and chemical sciences in Argentina, and
postgraduate and doctoral work in computational
chemistry at the University of British Columbia, the
University of Hull, and the University of Cambridge.
He was a postdoctoral fellow at the Australian
National University and University College London.
Abstract
Cleavage of cyanide is more difficult to achieve
compared to dinitrogen and carbon monoxide,
even though these species contain triple bonds of
greater strength. In this work, we have used
computational methods to investigate
thermodynamic and mechanistic aspects of the
C-N bond cleavage process in [L3M-CN-M’L3]
systems consisting of a central cyanide unit bound
in an end-on fashion to two terminal metal
tris-amide complexes. The general structural,
bonding, and thermochemical trends across the
transition metal series investigated indicate that
the systems exhibiting the greatest degree of C-N
activation, and most favourable energetics for C-N
33

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Biographies and Abstracts
Sunday 4 December - Session 2
cleavage, also possess the most favourable
electronic properties, namely, a close match
between the relevant p-like orbitals on the
metal-based and cyanide fragments. Therefore,
metal-based systems with high-lying dp orbitals
are best suited to C-N cleavage. In terms of
chemical periodicity, these systems can be
identified as the heavier members within a group
and the earlier members within a period. As a
consequence, Mo complexes (which under
experimental conditions have been successfully
used for N-N bond scission in dinitrogen, but have
failed in the case of cyanide) are not well suited to
cleaving the C-N bond, whereas the Ta analogues
are the most favourable systems and should, in
principle, be capable of cleaving cyanide under
relatively mild conditions. An important conclusion
from this work is that a successful strategy for
achieving cleavage of multiply-bonded, and
relatively unreactive, molecular fragments, may lie
in tuning the electronic structures and orbital
interactions by judicious choice of metal sites and
ligand groups.
2.1.4 2:15pm – 2:30pm
Infrared Spectroscopy: from
Conformers to Clouds
Evan G Robertson 1 , Isabella Antony Lobo1 ,
Chris Medcraft 2 , Chris Thompson2 , Don
McNaughton2 , Dominique Appadoo3 .
1 Department of Chemistry, La Trobe University, Bundoora,
Victoria, 3086. e.robertson@latrobe.edu.au, ialobo@student.
latrobe.edu.au,
2 School of Chemistry, Monash University, Victoria, 3800. chris.
medcraft@monash.edu, chris.thompson@monash.edu, Donald.
mcnaughton@monash.edu
3 Australian Synchrotron, Blackburn Rd, Clayton, Victoria 3168,
Australia. Dominique.Appadoo@synchrotron.org.au
Biography
Evan Robertson studied for his PhD with Don
McNaughton at Monash university, before a 5 year
post-doctoral stint with John Simons at the
University of Oxford. He returned to Monash
University, working first as an ARC fellow from
2001 and then as lecturer from 2006. In 2009, he
moved to La Trobe University where he has
continued to pursue his research interests as a
colour blind spectroscopist.
Abstract
IR spectroscopy, with its exquisite sensitivity to
molecular structure and the intramolecular
bonding environment, is ideally suited to
investigating a range of chemical and physical
problems. Some diverse applications arising from
specialised techniques used in our research group
will be highlighted:
1. Conformational studies of neurotransmitters
have been conducted using IR-UV ion depletion
technique experiments based on nanosecond
pulsed lasers. E.g. Conformer-selective IR spectra
measured for amino-p-phenethylamine (APEA)
allow the two most populated conformers to be
unambiguously identified as those having a
gauche arrangement of the side chain which
facilitates an NH…p type hydrogen bond.
The pharmaceutical tranylcypromine is another
subject for these studies.
2. Rotationally resolved, high resolution FTIR
spectroscopy has been applied to molecules of

atmospheric relevance such as CFC pollutant
dichlorodifluoromethane (R12) or interstellar
interest such as propynal. Some samples requires
cooling in order to obtain spectra suitable for
rovibrational analysis, and a specialised collisional
cooling cell has been employed to this end.
Measurements in the far-IR region benefit
considerably from synchrotron source radiation.
3. Atmospheric aerosols scatter and absorb
radiation, influence cloud formation and play a role
in heterogeneous chemical reactions in the
atmosphere, affecting the concentration and
distribution of atmospheric trace gases. Also, from
the perspective of climate science and modelling
the far IR region is very important yet has been
relatively little studied. Combining these two
elements, a collisional cooling cell capable of
generating aerosols has been modified from the
design of Bauerecker to extend its optical range
into the far-infrared where the synchrotron source
has the greatest advantage over thermal sources.
This unique facility has been used to measure the
first far IR spectra of water aerosols, accessing
spectral bands with implications that extend to
non-terrestrial environments.
Biographies and Abstracts
Sunday 4 December - Session 2
2.1.5 2:30pm – 2:45pm
Photodetachment of Small Dianions:
Adventures in Mass and Charge
Stephen J. Blanksby1 , Celli Lloyd1 ,
Pramesh I. Hettiarachachi 1 , Benjamin B. Kirk1 ,
Adam J. Trevitt 1
1. ARC Centre of Excellence for Free Radical Chemistry and
Biotechnology, School of Chemistry, University of Wollongong
NSW, Australia.
Biography
Dr Blanksby received his PhD from the University
of Adelaide (1999) in the field of organic mass
spectrometry before undertaking postdoctoral
research at the University of Colorado (Boulder) in
gas phase ion chemistry and spectroscopy. He
returned to Australia in 2002 to commence his
academic appointment at the University of
Wollongong.
Abstract
The advent of electrospray ionisation mass
spectrometry has allowed the routine generation of
multiply charged anions. Coupling of electrospray
ionisation sources with negative ion photoelectron
spectroscopy has given deep insight into the
intrinsic stabilisation of dianions; most notably
characterisation of the contribution of the reverse
Coulomb barrier to electron binding in such
systems [1]. Another related but less well
understood phenomenon is the observation of
zero-kinetic energy electrons arising from the
photodetachment of small dicarboxylate dianions.
Intriguingly, this electron population is found to be
largely independent of both (i) the energy of the
incident photon (provided it is greater than the
electron detachment threshold) and (ii) the
separation of the charged moieties (e.g., it is
observed for a range of dicarboxylate dianions of
the form -O2C(CH2)nCO22-, where n ≥ 2). It has
been suggested that following photodetachment
of the first electron the nascent radical anion
undergoes facile free radical decomposition
resulting in thermal ejection of the second electron
and stable even-electron neutrals (e.g., alkenes
and carbon dioxide). One exception to this pattern
has been noted. The photodetachment of
acetylene dicarboxylate dianion (O2CCCCO2•-)
35

36
Biographies and Abstracts
Sunday 4 December - Session 2
does not give rise to zero-kinetic energy electrons
suggesting that the corresponding radical anion is
stable on the timescale of the experiment. We
have recently modified an electrospray ionisation
linear ion-trap mass spectrometer
(ThermoFinnigan LTQ) to allow irradiation of
mass-selected ions with both fixed frequency
(Continuum, Minilite II) and tuneable (GWU
Versascan) laser sources. Using this platform we
have photodetached a wide range of dicarboxylate
dianions and, by measuring the mass-to-charge
ratio of the resulting ions, found that
decarboxylation and subsequent free radical
rearrangements of the resulting radical anions is
facile. Consistent with predictions based on
photoelectron spectroscopy, the acetylene
dicarboxylate dianion is the one of a limited
number of systems thus far identified where an ion
corresponding to the residual radical anion is
detected (m/z 112 in the Figure below). Isolation of
this species for varying increments of time reveals
its unimolecular decomposition via loss of carbon
dioxide (to form m/z 68) over several hundred
milliseconds. The unique stabilisation of this radical
anion relative to other aliphatic and even aromatic
systems will be discussed along with results from
recent investigations of photodetachment from
amino acid and small peptide-based dianions
where intact radical anions have also been
observed.
[1] WANG X. B. and WANG L. S., Photoelectron Spectroscopy of
Multiply Charged Anions. Annual Review of Physical Chemistry,
2009. 60: p. 105-126.
2.1.6 2:45pm – 3:00pm
Laser-Based Formation and
Properties of Metal Nanoparticles in
Aqueous Solution
Mark A. Buntine1,2 , Yuen-Yang Fong2 , Jason
R. Gascooke 3 , Gregory F. Metha2 , Hugh Harris2 ,
Ashley Mulder1 , Aidon Slaney1 , Sean Long1 , Franca
Jones1 , Max Massi1 , Mark Ogden1 , Bruce Cowie4 ,
Lars Thompson4 1 Department of Chemistry, Curtin University, GPO Box U1987
Perth WA 6845
2 School of Chemistry and Physics, The University of Adelaide,
Adelaide SA 5005
3 School of Chemical and Physical Sciences, The Flinders
University of South Australia, GPO Box 2100 Adelaide SA 5001
4 Australian Synchrotron, 800 Blackburn Road, Clayton VIC 3168
Biography
Mark Buntine undertook undergraduate studies at
Monash University in Melbourne, Australia, and his
Ph.D. with Richard Zare at Stanford University,
graduating in 1992. He undertook postdoctoral
studies with Mark Johnson at Yale University,
before commencing an independent academic
career at The University of Adelaide in 1994. He
moved through the ranks to become a full
professor in 2007, and was Head of Chemistry
from 2003. In 2009 Buntine moved to Curtin
University in Perth where he is Head of the
Chemistry Department and maintains an active
research program focussed on the use of liquid
beam methodologies to explore the molecular
dynamics of liquid-vapour phase transitions via
electronic spectroscopy. More recent
experimental work has focussed on exploring the
mechanistic aspects of the in situ laser-based
production of metal nanoparticles in aqueous
solution. Buntine is a former Chair of the RACI
Physical Chemistry Division and President of the
South Australian Branch. He is currently
President-Elect of the RACI and serves on the
Executive Committee of the Australian and New
Zealand Society for Mass Spectrometry.
Abstract
We report on the production and time evolution of
metal nanoparticle optical properties and size
distributions as a function of laser irradiation in

pure water samples and in the presence of anionic
and cationic surfactants and ‘encapsulation’
ligands. Our investigations provide a mechanistic
insight into the laser-induced formation kinetics
involved in the in situ metal nanoparticle
production, as well as the electronic structure of
the surface atoms. Early studies explored the role
of surfactant type and concentration on the
longer-term stability of metal nanoparticles. More
recent studies employing ligands to encapsulate
the nanoparticles highlight how the electronic
structure of the particle surface can be
manipulated. Implications of this work in a variety
of possible application areas will be discussed.
Session 2 – Main Theatre
2.2.1 1:15pm – 1:30pm
Structure and dynamics of a
replisomal macromolecular
assembly
Flynn R. Hill1 , Charikleia Ioannou1 , Marek M.
Koza2 , Agata Rekas3 , Peter J. Holden3 , Nigel M.
Kirby4 , Kathleen Wood5 , Nicholas E. Dixon1 ,
Moeava Tehei 1,6 ,
1 School of Chemistry, University of Wollongong, Wollongong,
NSW.
2 Institut Laue Langevin, Grenoble, France.
3 National Deuteration Facility, Australian Nuclear Science and
Technology Organisation, Menai, NSW.
4 Australian Synchrotron, Clayton, VIC.
5 Bragg Institute, Australian Nuclear Science and Technology
Organisation, Menai, NSW.
6 Australian Institute of Nuclear Science and Engineering, Menai,
NSW.
Biography
Flynn is a PhD student at the University of
Wollongong’s School of Chemistry working on
proteins involved in bacterial DNA replication. He is
co-supervised by Prof Nick Dixon and Dr Moeava
Tehei.
Abstract
The replication of genetic material for passing
down from parent to progeny is the most essential
process for the continued existence of life on
Earth. Double-stranded DNA is the genetic
material in the majority of lifeforms and the two
Biographies and Abstracts
Sunday 4 December - Session 2
parental strands must be separated ahead of the
catalytic elongation of the complementary
daughter strands. We have investigated the DnaB
helicase enzyme responsible for this strand
separation in Gram-positive bacteria and the DnaI
protein which complexes with DnaB to assist in
loading of the helicase onto parental DNA.
Differential deuterium labelling and quasielastic
neutron spectroscopy (QENS) with an instrument
sensitive to hydrogen motions at time scales of
~10 ps was used to probe the dynamics of DnaB,
DnaI and the DnaB-DnaI complex. In this
incoherent scattering technique, the deuterated
protein is effectively invisible and the dynamical
contribution of each protein to the complex can be
isolated. Similarly, solvent contrast variation and
deuterium labeling are planned for measurement
of the shape-dependent coherent small angleneutron
scattering (SANS) of these proteins in
solution, to allow separation of the structural
contribution of each protein within the complex. To
complement these SANS experiments, we have
performed synchrotron small-angle X-ray
scattering (SAXS) in the presence and absence of
nucleotide cofactors to probe conformational
transitions of the helicase ATPase cycle.
The helicase shows high elasticity within the fast
motion time-scale investigated, while its solution
small-angle scattering suggests a structure with
low conformational flexibility at the whole-domain
level and a narrower central channel than is
present in the crystal structure. Taken together,
our results suggest that fast small-scale motions of
residues lining the DnaB central channel through
which DNA is fed are responsible for its rapid
translocation, rather than large-scale
conformational transitions. These results and
others concerning the mechanism of helicase
loading will be presented along with an
introduction to the biophysical techniques
involved.
37

38
Biographies and Abstracts
Sunday 4 December - Session 2
2.2.2 1:30pm – 1:45pm
Resolving Single Molecule
Fibronectin Interactions with
Conducting Polymer Interfaces
using Atomic Force Microscopy
Michael Higgins, Amy Gelmi, Gordon
Wallace
Intelligent Polymer Research Institute (IPRI), University of
Wollongong.
Biography
Dr Michael Higgins is an ARC Australian Research
Fellow in the Intelligent Polymer Research Institute,
University of Wollongong. Dr Higgins’s main
interest is on the application of Atomic Force
Microscopy to biological systems, including living
cells, model lipid membranes, single ligandreceptor
interactions, individual protein unfolding
and fundamental surface-force interactions. He
has unique skills in instrument development, probe
modifications and their use in imaging and probing
biomolecular and cellular interaction forces.
Abstract
In this presentation, we focus on biomedical
applications involving the emerging use of
conducting polymers as electrodes for controlling
in vitro cell culture systems (e.g. enhanced cell
proliferation and differentiation) or in vivo
implantation for neural prosthesis applications.
Conducting polymers represent a new generation
of neural electrodes that can uniquely operate by
simultaneously delivering bioregulative cues (e.g.
expulsion of drugs) and electrical stimulation. For
example, neurite outgrowth on these polymers can
be dramatically enhanced by applying a voltage to
modulate the redox state of the polymer. At
present, the underlying mechanisms for the
cell-material interactions are unknown and require
extensive characterization in order to develop
these polymers for use as implantable electrodes
and drug release devices.
We have recently incorporated extracellular matrix
(ECM) components into a conducting polymer with
the aim of improving electrode biocompatibility
through the exposure of RGD peptide cell binding
regions. Another important focus of our research
is the adsorption of fibronectin, a major cell
adhesion molecule which binds to the ECM and is
critical for mediating cellular interactions with our
materials. The presence of ECM and/or accretion
of cell adhesion molecules at these polymer
surfaces are very important for conditioning the
electrode-cell interface to promote favourable
interactions such as intimate contact with nerve
cells while avoiding unwanted foreign body
responses.
To understand the interaction of fibronectin with
conducting polymers, we have functionalized
Atomic Force Microscopy (AFM) probes to directly
measure the interaction forces between fibronectin
and conducting polymers-ECM (hyaluronic acid
and chondroitin sulfate) composites. We will
demonstrate the use of in situ electrochemical
AFM to study the fibronectin-polymer interaction in
response to electrical stimulation applied through
the polymer. The presentation will highlight several
major findings including the ability to resolve single
fibronectin protein interactions with the polymer.
We will show differences in the conformation,
unfolding force profiles and binding probabilities of
the protein as a function of the polymer surface
chemistries. The ability to reversibly modulate the
fibronectin adhesion by applying electrical
stimulation to the polymer electrode will also be
presented. We will finally give insight into the
possible mechanisms and implications of the
fibronectin-conducting polymer interactions.
2.2.3 1:45pm – 2:00pm
Engineering new catalytic activities
in enzymes through modifying the
conformational landscape:
experimental and theoretical
insights
Colin J Jackson1 1 Research School of Chemistry, Australian National University,
ACT, 0200, cjackson@rsc.anu.edu.au
Biography
Colin Jackson received a Bsc (Hons) in
biochemistry from the University of Otago, New
Zealand, before completing his PhD at the

Australian National University. From 2008 he
worked at the CSIRO as a research team leader.
He has recently finished a Marie Curie research
fellowship at the Institut de Biologie Structurale in
Grenoble, France where he has continued to use
laboratory evolution and structural biology to
understand the how new catalytic functions can
evolve in enzymes. He now leads an independent
research group at the Australian National
University that uses a range of techniques to
investigate molecular evolution and catalysis.
Abstract
Conformational plasticity is known to be an integral
aspect of enzyme function, allowing enzymes to
meet the different demands of substrate binding,
catalysis and product release. Now that advances
in computational and experimental structural
biology has made characterization of
conformational fluctuations considerably more
accurate, we seek to understand how
conformational landscapes can be engineered to
suit our needs as designer enzymes. The bacterial
phosphotriesterase serves as an excellent model
system to study conformational sampling: it
catalyzes a simple one-step (SN2) hydrolysis of a
phosphotriester, it has been extensively
characterized and a large library of mutant
enzymes is available. Our results suggest that
mutations many angstroms from the active site
can modulate activity by changing the relative
energies of different conformations, thereby
changing the populations of states associated with
different steps in the catalytic cycle. Furthermore,
the sequence of mutations that change the
function of phosphotriesterase to an arylesterase
involves an initial mutation within the active site
that generates a rare, but highly efficient catalytic
conformation, followed by a series of outer-shell
mutations that fine-tune the free-energy landscape
to stabilize this conformation.
Biographies and Abstracts
Sunday 4 December - Session 2
2.2.4 2.00pm – 2.15pm
Towards ab initio Refinement of
Protein X-ray Crystal Structures:
Interpreting and Correlating
Structural Fluctuations
Jeffrey R. Reimers 3 ,Olle Falklöf1 , Charles
Collyer2 ,
1 School of Chemistry, The University of Sydney, Sydney, New
South Wales 2006, Australia, and Department of Chemistry,
The University of Gothenburg, Sweden
2 School of Molecular Bioscience, The University of Sydney,
Sydney, New South Wales 2006, Australia
3 School of Chemistry, The University of Sydney, Sydney, New
South Wales 2006, Australia
Biography
Jeffrey Reimers studied spectroscopy under Ian
Ross, thermodynamics under Bob Watts, and
semiclassical dynamics under Eric Heller and Kent
Wilson before starting his career as a research
scientist at The University of Sydney in 1985. Since
then he has worked extensively with Noel Hush
and Max Crossley studying molecular electronics,
natural and artificial photosynthesis, and chemical
theory, establishing an interdisciplinary research
team studying biochemical processes, scanningtunnelling
microscopy, quantum chemistry, the
quantum mechanics of electron-vibration
interactions, nanoparticle and surface structure,
quantum computing, and consciousness
research. His research has received many
distinctions including the award of H.G. Smith
Medal of the RACI and admission as a Fellow of
the Australian Academy of Science.
Abstract
The refinement of protein crystal structures
currently involves the use of empirical restraints
and force fields that are known to work well in
many situations but nevertheless yield structural
models with some features that are inconsistent
with detailed chemical analysis and therefore
warrant further improvement. Ab initio electronic
structure computational methods have now
advanced to the point at which they can deliver
reliable results for macromolecules in realistic
times using linear-scaling algorithms. The
replacement of empirical force fields with ab initio
39

40
Biographies and Abstracts
Sunday 4 December - Session 2
methods in a final refinement stage could allow
new structural features to be identified in complex
structures, reduce errors and remove
computational bias from structural models. In
contrast to empirical approaches, ab initio
refinements can only be performed on models that
obey basic qualitative chemical rules, imposing
constraints on the parameter space of existing
refinements, and this in turn inhibits the inclusion
of unlikely structural features. Here we focus on
methods for determining an appropriate ensemble
of initial structural models for an ab initio X-ray
refinement, modeling as an example the highresolution
single-crystal X-ray diffraction data
reported for the structure of lysozyme (PDB entry
“2VB1”). The AMBER force field is used in a Monte
Carlo calculation to determine an ensemble of 8
structures that together embody all of the partial
atomic occupancies noted in the original
refinement, correlating these variations into a set of
feasible chemical structures while simultaneously
retaining consistency with the X-ray diffraction
data. Subsequent analysis of these results
strongly suggests that the occupancies in the
empirically refined model are inconsistent with
protein energetic considerations, thus depicting
the 2VB1 structure as a deep-lying minimum in its
optimized parameter space that actually embodies
chemically unreasonable features. Indeed,
density-functional-theory calculations for one
specific nitrate ion with an occupancy of 62%
indicate that water replaces this ion 38% of the
time, a result confirmed by subsequent
crystallographic R-factor analysis. It is foreseeable
that any subsequent ab initio refinement of the
whole structure would need to locate a globally
improved structure involving significant changes to
2VB1 which correct these identified local structural
inconsistencies.
2.2.5 2.15pm – 2.30pm
Density Functional Theory
Calculations of Novel Silicon
Nanosheets
Michelle J.S. Spencer1 , Tetsuya Morishita 2 ,
Masuhiro Mikami2 , Ian K. Snook3 , Yusuke
Sugiyama4 , Hideyuki Nakano4 1 Department of Chemistry, La Trobe Institute for Molecular
Science, La Trobe University, Bundoora, Victoria 3086, Australia
m.spencer@latrobe.edu.au
2 Nanosystem Research Institute (NRI), National Institute of
Advanced Industrial Science and Technology (AIST), Central 2,
1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan,
t-morishita@aist.go.jp
3 Applied Physics, School of Applied Sciences, RMIT University,
Melbourne, Victoria 3001, Australia
4 Toyota Central R&D Labs., Inc., 41-1 Yokomichi, Nagakute, Aichi
480-1192, Japan
Biography
Dr Spencer is leader of the computational
materials chemistry group at La Trobe University.
Her expertise is in using density functional theory
calculations, and ab initio molecular dynamics
simulations to investigate the chemistry of a wide
variety of materials. In particular her research
focuses on surface reactions of metals, oxides and
semiconductors, with an emphasis on
nanomaterials which have applications as gas
sensors and electronic devices.
Abstract
Silicon is one of the most important elements is
our current society, forming the basis of most
semiconducting electronic devices. As the drive
intensifies to enhance our current technological
capabilities and miniaturize device sizes, it is
imperative to find materials and structures that
meet the new demands. Nanosheets of silicon are
one of the more recently discovered
nanostructured morphologies (see for example
[1,2]). The unique properties of these quasi 2D
materials make them ideal for a variety of
applications, including electronic devices, batteries
and sensors. In order for their full potential to be
realised their properties and structural details need
to be determined.
We are using density functional theory calculations
to provide critical information about the structure

and chemistry of clean and functionalised
nanosheets (see Fig. 1). Such information is being
used in conjunction with experimental synthesis
[1,3] to tailor the growth and development of these
materials.
Fig. 1. Phenyl modified Si nanosheet [6].
Our calculations have shown that the structure of
clean silicon nanosheets changes as a function of
thickness. For very thin Si(111) oriented
nanosheets, we have discovered a novel surface
reconstruction classified as Si(111)-2x2 that forms
on the nanosheet surface layers [4]. Functionalising
the nanosheet surface with different atomic or
molecular species has also resulted in varying
structural and electronic properties. In particular,
by varying the surface termination or substitutional
dopant [5], the nanosheet can be changed to a
p- or an n-type semiconductor. For phenyl
modified nanosheets [6] our calculations have
shown that this material retains the sp3 structure
after functionalisation, resulting in a wide (direct)
band gap. Overall these novel materials possess
the unique characteristic that the electronic
properties can be easily altered by exchanging the
molecules or atoms that functionalise the
nanosheet.
1. Y. Sugiyama, H. Okamoto, T. Mitsuoka, T. Morikawa, K.
Nakanishi, T. Ohta, H. Nakano, J. Am. Chem. Soc. 132 (2010)
5946.
2. T. Morishita, K. Nishio, M. Mikami, Phys. Rev. B 77 (2008)
081401(R).
3. H. Okamoto, Y. Kumai, Y. Sugiyama, T. Mitsuoka, K. Nakanishi,
T. Ohta, H. Nozaki, S. Yamaguchi, S. Shirai, H. Nakano, J. Am.
Chem. Soc. 132 (2010) 2710.
4. T. Morishita, M.J.S. Spencer, S.P. Russo, I.K. Snook, M. Mikami,
Chem. Phys. Lett. 506 (2011) 221.
5. T. Morishita, S.P. Russo, I.K. Snook, M.J.S. Spencer, K. Nishio,
M. Mikami, Phys. Rev. B 82 (2010) 045419.
6. M.J.S. Spencer, M. Morishita, M. Mikami, I.K. Snook, Y.
Sugiyama, H. Nakano, Phys. Chem. Chem. Phys. 13 (2011)
15418.
Biographies and Abstracts
Sunday 4 December - Session 2
2.2.6 2:30pm – 2:45pm
Stable Solid Supported Membranes
to probe Membrane-Protein
Interactions
Ingo Koeper1 1 Flinders University, School of Chemical and Physical Sciences,
GPO Box 2100, Adelaide, SA 5011, inog.koeper@flinders.edu.
au
Biography
Ingo Koeper studied chemistry at the University of
Dortmund. In 2002 he received his PhD from the
University of Paris VIIn 2002 he joined the
Materials Science Department at the Max Planck
Institute for Polymer Research, Mainz, Germany.
After one year as a post-doc, he became a project
leader, leading an independent research team
working on biofunctional surfaces.
In September 2009, he followed a call to become
lecturer in the School of Chemical and Physical
Sciences at Flinders University, Adelaide, Australia
Abstract
The tethered bilayer membrane has been shown
to provide an ideal platform to study membrane
related processes. The architecture consists of a
lipid bilayer, where the proximal leaflet is covalently
coupled to a solid substrate via a spacer unit. The
solid substrate allows for the use of various
surface analytical techniques such as surface
plasmon spectroscopy, impedance spectroscopy,
neutron reflectometry, quartz crystal microbalance
or atomic force microscopy.
We have performed extensive structural
investigations of the membrane and probed the
influence of the molecular structure of the lipids
used on the overall membrane structure and its
functionality.
Furthermore, the platform has been used to probe
the function of embedded membrane proteins,
e.g. ion channels as well as the interaction of
proteins with the lipid bilayer. Here, the tethered
membrane architecture has proven to provide a
very robust system, allowing extensive systematic
studies.
In this presentation, I will summarize finding on the
41

42
Biographies and Abstracts
Sunday 4 December - Session 2
interaction between small globular proteins and
lipid membrane of different composition as well as
highlight some new finding on the effect of small
molecules on the membrane structure and
function.
2.2.7 2:45pm – 3:00pm
Directions and Results of OH Attack
on Nucleic Acids: a Theoretical
Study
Ganna Gryn’ova, Michelle Coote
Biography
PhD Candidate
ARC Centre of Excellence for Free-Radical
Chemistry and Biotechnology, Research
School of Chemistry, Australian National
University, Canberra, ACT 0200, Australia
Phone: +61 2 6125 5411 E-mail: agrynova@rsc.
anu.edu.au
Personal History
2004-2008 B.Sc. in chemistry at the
Dnepropetrovsk National University, Ukraine
2008-2009 M.Sc. in chemistry at the
Dnepropetrovsk National University, Ukraine
Since 2010 Ph.D. candidate in chemistry at the
Australian National University
Research interests: computational chemistry,
mechanisms of polymer/biopolymer degradation
and their stabilisation
Abstract
Radiation damage to cellular nucleic acids is a
major deleterious event resulting in a cascade of
harmful consequences. Sources of such damage
are very diverse, however hydroxyl radical, being
the most abundant and extremely reactive, is
considered to be one of the main degradation
agents.7
Experimental studies show, that hydroxyl radical
reacts with DNA/RNA bases at almost diffusion
controlled rates, and approximately 5-10 times
slower with the sugar moiety. Whereas it can only
abstract hydrogen from (deoxy)ribose ring, various
pathways are suggested for its interaction with the
base moiety: addition to double bonds,
abstraction of hydrogen atoms from both ring
atoms and substituents, and finally sequential
electron proton transfer.8 These mechanistic
pathways were intensively investigated both
experimentally and theoretically (Monte Carlo
simulations and quantum chemical calculations),
however the resulting trends in site reactivity in
sugars and in bases are often quite different.9
Moreover, to the best of our knowledge, there is
no evidence in literature for the high-level
computational study of the kinetics of sugar radical
formation, and available theoretical studies on
bases are conducted with either insufficiently
accurate methodology or inconsistent models.
Present study focuses on the kinetics and
thermodynamics of the OH• attack on DNA/RNA.
We apply two levels of modelling – free sugars and
bases, as well as nucleotide 3’,5’-diphosphates,
and use G3(MP2)-RAD level of theory. Our results
reveal a number of interesting trends, including
remarkable correlation between kinetics,
thermodynamics and electronic structure of
attacked substrates (for example, see Fig. 1).
Comparison of the obtained site reactivity trends
with the experimental/MD ones gives a deeper
insight into the protective mechanisms that nature
applies.
Fig. 1 - Calculated reaction Gibbs free energies (kJ mol-1, aqueous
solution, 298.15 K) and rate constants (logarithms) for the
reactions of hydroxyl radical with free pyrimidine bases.

Keynote Session
- Main Theatre
K.4 4:20pm – 4:50pm
Using Theory to Reconcile
Experiment: The Search for
Certainty in an Uncertain World
Alan E. Mark1 ,
1 School of Chemistry and Molecular Biosciences (SCMB) and
Institute for Molecular Biosciences (IMB), University of
Queensland, Brisbane, QLD 4072, Australia. Email: a.e.mark@
uq.edu.au
Biography
Professor Alan Mark originally studied Chemistry/
Biochemistry at Sydney University. He obtained his
Ph.D in physical biochemistry at the JCSMR, ANU.
He went on to hold positions at RSC, ANU,
University of Groningen, The Netherlands and at
ETH-Zurich, Switzerland. In 1998 he was
appointed Prof. Molecular Simulation University of
Groningen. In 2005 he moved to the University of
Queeensland as a Federation Fellow. His primary
interests are in understanding the dynamic and
thermodynamic properties of biomolecular
systems at an atomic level. He is associated with
the development of the GROMOS and GROMACS
simulation packages as well as the associated
force fields. His group have also performed
pioneering simulations of a wide range of
biological phenomena. He was awarded the
Ruzicka prize in 1998 for his work on peptide
folding, In 2005 he was awarded an honorary
personal Chair at the University of Groningen.
Abstract
Despite continuing advances in structural biology it
is still not possible to directly observe the energetic
and dynamic properties of individual atoms in
biomolecular systems using currently available
experimental techniques. In fact, everything we
know (or think we know) regarding biomolecular
systems is to some degree based on a theoretical
or structural model. The question is to what extent
can these models be trusted? For example, while
the overall structure of a protein may be resolved in
near atomic detail, the position, orientation and/or
conformation of a small molecular ligand (cofactor,
Biographies and Abstracts
Sunday 4 December - Session 2
substrate, inhibitor etc.) bound to such a protein is
often much less certain.1 Electrostatics will often
determine the interaction between a protein and its
ligand but are generally ignored in structure
refinement. In other cases there is evidence of
systematic bias in how data is interpreted. The
variation in the area per lipid in theoretical
calculations of membrane systems is much less
than the variation in the experimental data on
which they are based.2 This is not only a problem
for experimentalists but represent a fundamental
challenge to theoreticians attempting to validate
computational models.3 The talk will illustrate how
the models we use can bias our interpretation of
experimental data and how atomistic simulations
can be used to identify and correct common
errors is in structural models of protein ligand
complexes.
1. Malde, A.K. and Mark, A.E. (2011) Challenges in the
determination of the binding modes of non-standard ligands in
X-ray crystal complexes. J. Comp. Aided Mol. Des. 25, 1-12.
2. Poger, D. and Mark, A. E. (2010)
On the Validation of Molecular Dynamics Simulations of Saturated
and cis-Monounsaturated Phosphatidylcholine Lipid Bilayers: A
Comparison with Experiment.
J. Chem. Theory Comput. 6, 325-336.
3. Nair, P,C., Malde, A.K. and Mark, A.E. (2011)
Using theory to reconcile experiment: the structural and
thermodynamic basis of ligand recognition by Phenylethanolamine
N-Methyl Transferase (PNMT). J. Chem. Theory Comput. 7,
1458-1468
K.5 4:50pm – 5:10 pm
Towards a Unified Picture of Color
and Photisomerization Behavior in
Fluorogenic Monomethine Dyes
Seth Olsen1 The University of Queensland
Biography
Seth Olsen was born February 8, 1975 in New
York City. His early years were spent growing up
at a series of US Coast Guard bases distributed
across the United States; after his father left the
service his family settled in Maryland (in the center
of the US Atlantic coast). He obtained his BSc
with Honors in Physics at the College of William &
Mary in Virginia (Williamsburg, VA, USA),
completing his undergraduate thesis in solid state
43

44
Biographies and Abstracts
Sunday 4 December - Session 2
biomolecular NMR spectroscopy. He went on to
obtain his PhD at the Center for Biophysics and
Computational Biology at the University of Illinois,
Urbana-Champaign. Seth’s career has been
marked by a strong interdisciplinary focus that
spans all three of the natural sciences of Biology,
Chemistry and Physics. He has worked in
departments of chemistry and physics, and
publishes in journals devoted to biology, chemistry
and physics. His research interests are focussed
on the development of models to explain
molecular photochemical and photobiological
processes - problems that lie at the intersection of
all three natural sciences.
Abstract
Many techniques for biological fluorescence
imaging rely on dyes that are non-fluorescent in
fluid solution (quantum yield ϕ ~10-5), but become
f
highly fluorescent (ϕ ~1) upon binding to
f
biomolecules. Interestingly, many of these dyes
also share a common charge-resonant electronic
structure, wherein the ground state of the dye can
be written as a superposition of Lewis structures
with opposing bond alternation and formal charge
localization. A well-known example is the
chromophore of the green fluorescent protein[1]:
Other dyes for which display both chargeresonance
and binding-dependent fluorescence
enhancement include di- and tri-arylmethanes and
monomethine cyanines. These dyes are venerable
molecules, some of them dating to the dawn of
industrial chemistry itself.
In all these cases, the mechanism of fluorescence
enhancement is attributed to suppression of a
competing double bond photoisomerization
reaction. In the case of resonant dyes, this raises
an obvious question: if there are multiple bonding
schemes superimposed, which bonds are most
likely to twist?
In this talk, I will describe how the pathway
ambiguity can be addressed with high-level
computational quantum chemistry[2]. Furthermore
I will show that the electronic structure describing
the photoisomerization reaction can be rationalized
and described using a simple resonance-theoretic
model that was proposed decades ago to
describe the color of charge-resonant dyes[3]. I
will argue that the commonly invoked mechanism
of steric hindrance is incomplete. I will suggest
methods of further investigation, all of which
proceed naturally from the chemically motivated
concept of resonance, illustrated above.
[1] M. Chalfie, Angew. Chem. Int. Ed. 48 5603 (2009).
[2] S. Olsen et al., J. Chem. Phys. 130 184302 (2009).
[3] S. Olsen, J. Chem. Theory. Comput. 6 1089 (2010).
[4] S. Olsen et al., J. Chem. Phys. 134 114520 (2011).
K.6 5:10pm – 5:30pm
The roles of membrane deformations
and electrostatics in charged
protein-lipid interactions
Toby W. Allen 3 ,Igor Vorobyov1 , Libo Li2 ,
1 Department of Chemistry, University of California, Davis, One
Shields Avenue, CA, 95616, USA. ivorobyov@ucdavis.edu
2 Department of Chemistry, University of California, Davis, One
Shields Avenue, CA, 95616, USA. lili@ucdavis.edu
3 School of Applied Science, RMIT University, GPO Box 2476V,
Melbourne, VIC, 3001, Australia; Department of
Chemistry, University of California, Davis, One Shields Avenue, CA,
95616, USA. toby.allen@rmit.edu.au
Biography
Prof. Allen is a computational biophysicist carrying
out research into membranes, protein-lipid
interactions and ion channel function. His group is
known for its contributions to understand how
charged proteins interact with membranes, and
the mechanisms of permeation and selectivity in
ion channels. Prof. Allen received his Ph.D. from
the Australian National University, carried out
postdoctoral work at the ANU and then at Cornell
University in the USA, after which he became
Assistant and then Associate Professor at the
University of California, Davis. He is the recipient
of awards including a National Science Foundation
Career award (USA), Philippe foundation award
(France), Keck Fellowship (USA), Revson
Fellowship (USA), Alberta Heritage Foundation
lecturer award (Canada) and several competitive
funding and supercomputing grants in the USA.
This year he returned to Australia to take up a Vice

Chancellor’s Senior Research Fellowship at RMIT
University in Melbourne.
Abstract
Biological membranes are both the gateways into
cells and home to a range of proteins that play
essential roles in the body. These membranes
exhibit wide-ranging compositions that influence
their topology, mechanical and electrostatic
properties, which in turn govern protein function
and transport. Using molecular dynamics
simulations, we have uncovered a new theoretical
description of the interactions of charged
molecules with membranes, with implications for
the actions of antimicrobial and viral peptides,
toxins, integral and peripheral membrane proteins.
These studies were motivated by a controversial
model of voltage-gated ion channels that assumed
lipid-exposed arginine side chain movement, as
well as cell biological experiments that inferred
small energetic costs for incorporating charged
protein groups into membranes, opposing
long-standing views. Using trans-membrane
protein segment and simple analogue models, we
reveal that the process of an ion or charged
protein group crossing a membrane is very
different to that depicted by traditional membrane
models. We demonstrate that the membrane
deforms to such an extent that the dehydration
energy and the membrane electrostatic (dipole)
potential are not determining factors, contrary to
prevailing theory. As a consequence, we observe
almost identical membrane translocation
energetics for a range of charged protein groups,
physiological ions, and even ion pairs and
zwitterions. We use this insight to make
predictions for uncatalysed ion permeation,
membrane interactions with highly charged
peptides, and the effects of different lipid
components (in particular charged lipids and lipids
of varying chain length). We also explore the
competition of defect-driven and solubilitydiffusion
mechanisms of permeation to allow for
better predictions of membrane transport
phenomena.
Biographies and Abstracts
Sunday 4 December - Session 2
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45

World class
research leadership
Geoff Cohen
Professor Infrastructure Governance
Peter Campbell
Professor Infrastructure Systems
Pascal Perez
Professor Infrastructure Modelling & Simulation
Henry Ergas
Professor Infrastructure Economics
Andrew McCusker
Director, Rail Logistics Research
smart.uow.edu.au

Session 3 – Theatre 2
3.1.1 10:30am – 10:45am
Organic Photovoltaic Materials at
High Spatial and Temporal
Resolution
Trevor A. Smith1 and Xiaotao Hao2 1 Ultrafast and Microspectroscopy Laboratories, School of
Chemistry, and ARC Centre of Excellence for Coherent X-Ray
Science, University of Melbourne, Vic. 3010, trevoras@unimelb.
edu.au
2 Ultrafast and Microspectroscopy Laboratories, School of
Chemistry, and ARC Centre of Excellence for Coherent X-Ray
Science, University of Melbourne, Vic. 3010, xhao@unimelb.
edu.au
Biography
Trevor Smith heads the Ultrafast and
Microspectroscopy Labs in the School of
Chemistry at the University of Melbourne. He has
worked previously in laboratories at Imperial
College, London and Osaka & Tohoku Universities,
Japan, and held a number of competitive research
fellowships, including an ARC QEII Fellowship. His
current research involves the development and
application of techniques with femtosecond
time-resolution and sub-diffraction limit optical
resolution, and the combination of these two
regimes. He is also a member of the ARC Centre
of Excellence for Coherent X-Ray Science, using
ultrafast lasers to generate coherent XUV and soft
X-Ray sources for coherent imaging applications.
Abstract
The efficiency of photovoltaic devices based on
photo- and electro-luminescent polymeric and
small molecule materials is critically dependent on
the morphology of the films produced from these
molecules. Structures can form from the 10s of
nanometre scale to several microns, dependent on
the materials themselves, the solvent from which
they are cast and the film casting method used.
This is particularly the case in bulk heterojunction
electron/hole donor/acceptor blend systems.
It is therefore necessary to fully characterise such
films on the sub-micron scale, and a range of
optical microscopy techniques can be applied to
investigate these films. Emission spectroscopic
information can also be gained at the sub-micron
Biographies and Abstracts
Monday 5 December - Session 3
level and provides detail relating to the polymer
conformation, aggregation and energy
redistribution within these films. Many of the
photochemical/photophysical processes that
occur following excitation of the films occur on the
femtosecond to nanosecond time scales.
Time-resolved emission measurements at these
spatial scales can provide an additional level of
information relating to aggregation of the film
components and electron-hole separation
dynamics.
We will discuss the application of a range of
high-resolution optical microscopy techniques,
coupled with emission spectroscopy and ultrafast
time-resolved measurements to elucidate the
morphological variability of the characteristics of
films of conjugated molecules and polymers.
3.1.2 10:45am – 11:00am
Coarse-Grained Modelling of
Morphology and Energy Transfer in
Conjugated Polymer Nanostructures
David M. Huang 5 , Ming Chiu1 , Kyra N.
Schwarz2 , Scott N. Clafton3 , Tak W. Kee4 1 School of Chemistry & Physics, The University of Adelaide, SA,
5005, ming.chiu@student.adelaide.edu.au
2 School of Chemistry & Physics, The University of Adelaide, SA,
5005, kyra.schwarz@student.adelaide.edu.au
3 School of Chemistry & Physics, The University of Adelaide, SA,
5005, scott.clafton@adelaide.edu.au
4 School of Chemistry & Physics, The University of Adelaide, SA,
5005, tak.kee@adelaide.edu.au
5 School of Chemistry & Physics, The University of Adelaide, SA,
5005, david.huang@adelaide.edu.au
Biography
Dr David Huang is a Lecturer in Chemistry at The
University of Adelaide. He has a BSc (Hons)
degree in Physical Chemistry from the University of
Sydney and a PhD in Theoretical Chemistry from
the University of California, Berkeley, which he
carried out as a Fulbright Scholar under the
supervision of Prof David Chandler. He worked as
a postdoc with Prof Lyderic Bocquet at the
University of Lyon and then with Prof Adam Moule
at the University of California, Davis, before taking
up his current position.
47

48
Biographies and Abstracts
Monday 5 December - Session 3
Abstract
Self-assembled conjugated polymer
nanostructures such as nanoparticles and
nanowires show promise in applications like
biological imaging and organic photovoltaics. One
useful property of these nanostructures is the
highly efficient energy transfer that they exhibit
upon photoexcitation. Computational modelling
can shed light on the molecular-scale mechanism
of energy transfer, but modelling conjugated
polymers in atomistic detail is not feasible for
nanostructures of the size studied experimentally.
We develop coarse-grained simulation models of
two widely used conjugated polymers, MEH-PPV
and P3HT, in solution. In the parameterisation of
these models, collections of atoms from an
atomistic model are mapped on to a smaller
number of coarse-grained sites such that the
coarse-grained models accurately reproduce the
local fluid structure of the atomistic models and
retain all relevant molecular details. We use these
models to study the dynamics of self-assembly of
conjugated polymer nanostructures as a function
of solvent quality and temperature. We investigate
the dependence of energy transfer on
experimental conditions and conjugated polymer
morphology by simulating exciton migration
dynamics upon photoexcitation in the resulting
nanostructures using a Förster line-dipole
approach. The simulated energy transfer
dynamics is compared with time-resolved
measurements of polarisation anisotropy decay in
MEH-PPV and P3HT nanostructures.
3.1.3 11:00am – 11:15am
Ultrafast Exciton Dynamics of
Conjugated Polymer Nanostructures
Tak W. Kee6 , Scott N. Clafton1 , Kyra N.
Schwarz2 , William R. Massey3 , Ming Chiu4 , David
M. Huang5 1 School of Chemistry & Physics, The University of Adelaide, SA,
5005, scott.clafton@adelaide.edu.au
2 School of Chemistry & Physics, The University of Adelaide, SA,
5005, kyra.schwarz@student.adelaide.edu.au
3 School of Chemistry & Physics, The University of Adelaide, SA,
5005,
william.massey@student.adelaide.edu.au
4 School of Chemistry & Physics, The University of Adelaide, SA,
5005, ming.chiu@student.adelaide.edu.au
5 School of Chemistry & Physics, The University of Adelaide, SA,
5005, david.huang@adelaide.edu.au
6 School of Chemistry & Physics, The University of Adelaide, SA,
5005, tak.kee@adelaide.edu.au
Biography
Dr Tak W. Kee is a senior lecturer at the University
of Adelaide. He received his PhD from the
University of Texas at Austin, USA in 2003. From
2003 to 2006, he was a postdoctoral fellow at the
National Institute of Standards and Technology
(NIST) at Gaithersburg, USA. He began his
position with the University of Adelaide in 2006.
His current research interests include the studies
of energy and charge transfer of conjugated
polymer nanostructures and investigations of
molecular processes in naturally occurring
medicinal pigments. He uses time resolved
spectroscopic techniques including fluorescence
upconversion and femtosecond transient
absorption spectroscopy in his work.
Abstract
Conjugated polymer nanostructures are attracting
significant attentions owing to their applications in
light emitting devices, fluorescence imaging and
organic photovoltaics. In this presentation, recent
results from a femtosecond fluorescence
upconversion study on conjugated two polymer
nanostructures, nanoparticles and nanowires, will
be presented. Conjugated polymer nanoparticles
offer colloidal stability in aqueous solution, good
photostability, and tunable luminescence
properties. Conjugated polymer nanowires are
elongated nanostructures that provide efficient
energy transport over a distance of microns.
Comparison of the time-resolved fluorescence
results of these nanostructures to those of
conjugated polymer in a “good” solvent reveals the
dependence of exciton dynamics on polymer
conformation. In addition, results on fluorescence
anisotropy are presented to show fluorescence
depolarization of conjugated polymer
nanoparticles and nanowires, which offer further
insight into the exciton dynamics.

3.1.4 11:15am – 11:30am
Structural, electronic and transport
properties of amorphous/crystalline
silicon heterojunctions
Tim F. Schulze1 ,*, Caspar Leendertz 1 , Lars
Korte1 , Nicola Mingirulli1 , Bernd Rech1 1 Helmholtz-Zentrum Berlin, Insitute Silicon Photovoltaics,
Kekuléstraße 5, D-12489 Berlin, Germany
* corresponding author, e-mail: tim.schulze@helmholtz-berlin.de
Biography
Tim Schulze was born in Berlin in 1979. He studied
Mechanical Engineering and Physics in Berlin, La
Laguna (Spain) and Zurich (Switzerland). In 2007,
he graduated at the Swiss Federal Institute of
Technology Zurich with a diploma on stronglycorrelated
electron physics. Afterwards, he
conducted his PhD work at the Helmholtz-Zentrum
Berlin on silicon-based heterojunction solar cells.
He was awarded a PhD by the Technical University
Berlin in 2011. As an Alexander-von-Humboldt
visiting fellow he is currently working on
photochemical upconversion of photons for solar
cell applications in Timothy Schmidtâs group at
the University of Sydney.
Abstract
Despite the widespread application in diodes and
high-efficiency solar cells, fundamental aspects
concerning the physics of amorphous/crystalline
silicon (a-Si:H/c-Si) heterojunctions remain under
dispute. This e.g. concerns the line-up of the
electronic bands, the charge carrier transport
across the heterojunction, or the outstandingly
effective passivation of c-Si surface states by
undoped a-Si:H.
In the present study, these aspects are tackled by
linking the microscopic properties of thin undoped
a-Si:H layers with the resulting behaviour of the
a-Si:H/c-Si heterojunction. Employing infrared
spectroscopy, spectroscopic ellipsometry,
photoelectron spectroscopy and secondary ion
mass spectroscopy, the structural, electronic and
optical properties of (i)a-Si:H are analysed.
Then, these properties are linked with the resulting
passivation of c-Si surface states, which limit the
obtainable open-circuit-voltage in a heterojunction
Biographies and Abstracts
Monday 5 December - Session 3
solar cell. It is found that in case of ideal
processing, the heterojunction does not possess
particular properties but can be described by the
a-Si:H bulk properties projected onto the actual
heterojunction. Based on this conclusion it is
possible to comprehend the complex
phenomenology of c-Si surface passivation by
a-Si:H from the properties of the amorphous
silicon passivation layer [1]. The principal limit of
c-Si surface passivation follows naturally from the
metastability inherent to a-Si:H, as does the
explanation of passivation degradation effects. The
amorphous network has the propensity to adapt
upon changes in externally controllable
parameters like the Fermi energy, which was
seldom taken into account so far when interpreting
phenomena of the a-Si:H/c-Si heterojunction.
Next, the line-up of the electronic bands at the
heterojunction is elucidated in device-relevant
a-Si:H/c-Si heterostructures. To this end, a novel
method combining photoelectron spectroscopy
and surface photovoltage measurements is
developed and employed. It is found that upon
widening the a-Si:H optical band gap by
controlling its hydrogen content, predominantly the
valence band offset is increasing while the
conduction band offset stays constant [2]. This
result is consistent with established theories on
the a-Si:H electronic structure, but was not
experimentally observed to date. The significance
of the valence band offset for solar cell operation
and possible pathways for tailoring the electronic
properties of the heterojunction are discussed.
Thus, insight is gained in the dependence of
heterojunction band line-up, c-Si surface
passivation, electronic transport and ultimately
solar cell device performance on the structural and
electronic properties of the thin a-Si:H layers.
49

50
Biographies and Abstracts
Monday 5 December - Session 3
3.1.5 11.30am – 11.45am
A new understanding of
hybridization in terms of bond
strengths and resonance energies
Prof Noel Hush
The University of Sydney
Biography
Noel Hush was educated at the University of
Sydney from which he graduated as Bachelor and
Master of Science in 1946 and 1948, respectively.
After two decades working in the United Kingdom
he returned to Sydney in 1971 and became the
Foundation Professor of Theoretical Chemistry,
setting up a new department that had a profound
impact on the development of the fiels in Australia.
He is most known for the theory of electron
transfer processes, a theory developed for
electrochemical processes and inorganic
complexes that is now very widely applied
throughout biochemistry and nanotechnology.
This rapidly attracted very talented staff and
developed a flourishing widely-based research
programme including the introduction of
experimental Photoelectron Spectroscopy to
Australia. He continued quantum chemical studies
on molecular response functions, including Stark
electronic and vibrational effects. In the area of
electron transfer he studied inter alia basic rate
formalisms, long range bridged transfer, soliton
theory, photosynthetic reaction-centre structure
and function and applications of Stark
spectroscopy to properties of mixed-valence
systems. His interests drew him naturally towards
Molecular Electronics, and to basic work on
conductivity of molecular ‘wires’, switches and
logic assemblies. Following formal retirement in
1989 he works largely in this area, and is currently
Convenor of the University of Sydney Molecular
Electronics Group. There he undertakes basic
theoretical work on molecular conductance,
nanowire-molecule structure and interpretation of
scanning probe images, including those generated
in the Group’s laboratory. This group is now well
funded by the ARC and major international
industry. He is a Fellow of the Royal Australian
Chemical Institute and of the Australian Academy
of Science, a Fellow of the Royal Society of
London, a Foreign Member of the American
Academy of Arts and Sciences, and a Fellow of
the USA National Academy of Sciences. He has
received many distinguished awards including the
RACI Phys Chem Division Medal, the Centenary
Medal of the Royal Society of Chemistry, the
Flinders and inaugural David Craig Medals of the
Australian Academy of Science, the Welch Prize,
and election as Officer of the Order of Australia
(AO).
Abstract
Ammonia has a HNH bond angle close to that for
sp hybridization rather than the 120 3 o angle
expected for a planar sp structure and a 90 2 o
angle typical of say unhybridized orbitals in BiH . 3
We introduce a simple description of this
phenomenon in terms of coupled diabatic
surfaces representing the two localized potentialwells
of ammonia. This approach links to general
theories of chemical reaction dynamics including
proton transfer, aromaticity, and electron transfer.
Standard approaches for interpreting electrontransfer
reactions are then applied and it is found
that a fundamental difference arises: electrontransfer
reactions involve one electron moving
between two orbitals whereas in ammonia two
electrons in the HOMO orbital interact with the
molecules lowest-energy valence unoccupied
orbital. The intrinsic involvement of two electrons
in the process causes the singly excited state to
interact strongly with its corresponding doubly
excited state. Hence three states are required in
the fundamental description of the chemistry, not
two. However, we describe a transformation
which maps this full problem onto an effective
two-state problem with renormalized parameters.
This explains why 2-state diabatic approaches
have in the past been applied with some success
as well as significant failings- the parameters
previously deduced had no apparent physical
meaning. Our renormalized multi-state approach
also applies to benzene and allows, for the first
time, quantification of the interactions between its
Kekulé structures. Hence we determine the
chemical features that control hybridisation in
ammonia using a general chemical theory that can
be used to compare and contrast reactions of
dramatically different apparent character.

3.1.6 11:45am – 12:00pm
Understanding electron transport in
complex systems
Gemma C. Solomon1 1 Nano-Science Center and Department of Chemistry, University
of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø,
Denmark
Biography
Gemma completed her PhD in Chemistry at the
University of Sydney in 2006 under the supervision
of Jeff Reimers. After that she moved to Chicago
where she postdoc’d at Northwestern with Mark
Ratner. In 2010 she received a European Research
Council Starting Grant and joined the faculty at the
University of Copenhagen as an Assistant
Professor.
Abstract
As system complexity increases, in either
biological or synthetic molecules, understanding of
structure-function relationships makes it possible
to identify the essential functional units controlling
physical properties from what may be a vast sea of
spectator components. Until recently, the range of
theoretical tools that have been implemented for
elucidating structure-function relationships in
molecular electron transport have been limited and
consequently the ability to build chemical intuition
for the behaviour of complex systems has been
hindered.
Here we present our efforts developing a local
description of molecular electron transport1, which
has allowed us to map the interactions in a
molecule that mediate the tunnelling current, as
shown in Figure 1. With this description of the local
transport we can understand the behaviour of a
complex, fluctuating system2 as a force is applied
that induces conformational change. We can
isolate the interactions in the molecule responsible
for high currents in both the folded and unfolded
conformations and can use this information to
refine the system design.
Biographies and Abstracts
Monday 5 December - Session 3
Figure 1 The local transmission through a complex molecule,
showing the interactions in the molecule that mediate the
tunnelling current.
We illustrate how the combination of conductance
and force spectroscopy can provide a large
amount of information about the folded structure
of a complex system, providing a model for future
experiments integrating these two techniques for
studying biological systems.
1. G. C. Solomon, C. Herrmann, T. Hansen, V. Mujica and M. A.
Ratner, Nature Chem. (2010), 2, 223-228
2. I. Franco, C. B. George, G. C. Solomon, G. C. Schatz and M. A.
Ratner, J. Am. Chem. Soc. (2011) 133, 2242-2249
Session 3 – Main Theatre
3.2.1 10.30am – 10.50am
Copper Stabilization of Aβ42
Aggregation in Model Membranes
Marc-Antoine Sani1 , Daniel K. Weber1 ,
John D. Gehman1 and Frances Separovic1 1 School of Chemistry, Bio21 Institute, University of Melbourne,
VIC 3010
Biography
“Marco” graduated with a Masters of Science with
distinctions from the University of Bordeaux 1. He
then tested his cold resistance by moving for his
PhD training to the University of Umeå in far north
Sweden. His interest in the fascinating role of lipids
started with his PhD thesis investigating the
regulation of apoptosis via interaction between
mitochondrial membranes and peptides from the
Bcl protein family. After spending four years
between 24H of beautiful sun and 22H of complete
darkness, the now-Dr. Sani challenged himself
again by travelling to the antipodes where he
51

52
Biographies and Abstracts
Monday 5 December - Session 3
honed skills in microbiology at the University of
Technology Sydney on gene cassette-based
resistance in bacteria. From here, he felt in love
with Australia and moved to Melbourne to fulfill his
passion of biophysics in the laboratory of Prof.
Frances Separovic and Dr. John Gehman at the
University of Melbourne. He currently works on
Alzheimer diseases and antimicrobial peptides,
where his goal is to link peptide/protein interaction
to lipid membrane structure and dynamics.
Abstract
The amyloid-beta (Aß) peptide is associated with
Alzheimer’s disease (AD). Evidence suggests that
Aß interaction with neuronal cell membranes
correlates strongly with neurodegeneration but
understanding the molecular mechanism remains
a challenge. The role of heavy metals often found
in amyloid plaques from AD brain patients is
another path for investigation. Our recent findings
support the role of lipid membrane composition as
crucial in many biological mechanisms. We
observed that different lipids promote different
fibril morphologies and aggregation kinetics and
are now facing the following conundrum: how
does copper mediate Aß42 aggregation and how
do membranes interact with Aß42-Cu complexes?
ThT fluorescence and circular dichroism showed
that increasing copper concentration above
equimolar ratio stabilized Aß42 into nonamyloidogenic
beta-sheet structures with or
without the presence of lipids. 31P and 2H
solid-state NMR revealed that equimolar Aß42-Cu
complexes had some effect on lipid membrane
structure and dynamics while the hydrophobic
core remained unperturbed and that Aß42
peptides did not scavenge copper from the lipid
headgroup. However, copper-free samples
showed a net reduction in the headgroup
dynamics, with the chemical shift anisotropy, T1
and T2 relaxation values being strongly reduced
and again lacked evidence of hydrophobic core
perturbations. The data supports a periperipheral
interaction of A←42 and peptide-Cu complexes
with phospholipid membranes.
3.2.2 10:50am – 11:10am
The enigma of the CLIC proteins: ion
channels, redox proteins, enzymes,
scaffolding proteins?
Paul M.G Curmi1,3 , Dene R. Littler 1 , Stephen
J. Harrop 1 , Sophia C. Goodchild 2 , Juanita M.
Phang1 , Andrew V. Mynott1 , Lele Jiang3 , Louise J.
Brown2 , Samuel N. Breit3 1 School of Physics, University of New South Wales, Sydney
NSW 2052, Australia
2 Department of Chemistry and Biomolecular Sciences,
Macquarie University, Sydney, New South Wales 2109,
Australia.
3 St Vincent’s Centre for Applied Medical Research, St Vincent’s
Hospital and University of New South Wales, Sydney NSW 2010
Australia
Biography
Professor Paul Curmi leads the Protein Structure
group in the School of Physics, University of New
South Wales. His research focuses on the
structure and function of proteins as determined
by x-ray crystallography. Key areas of his research
include: the CLIC proteins that undergo radical
structural changes including membrane insertion;
cryptophyte light harvesting proteins, where
quantum coherence may play a role in biological
function; and higher order organization of protein
systems within cells including biological pattern
formation
Abstract
Chloride intracellular channel proteins (CLICs) are
distinct from most ion channels in that they have
both soluble and integral membrane forms. CLICs
are highly conserved in chordates, with six
vertebrate paralogues. CLIC-like proteins are
found in other metazoans. The crystal structures
of the soluble form of CLIC proteins shows that
they belong to the GST fold family. They differ
from the GSTs in having a glutaredoxin(Grx)-like
redox active site centred on a conserved cysteine.
In this form, the CLIC proteins do not bind GSH
strongly and yet portions of the GSH binding site
are preserved. CLICs form channels in artificial
bilayers in a process favoured by oxidising
conditions and low pH. They are structurally
plastic, with CLIC1 adopting two distinct soluble
conformations that have been characterised at

high resolution by x-ray crystallography. This is a
very dramatic structural transition with a complete
refolding of the Grx-like N-domain of CLIC1.
Phylogenetic and structural data indicate that
CLICs are likely to have enzymatic function. The
physiological role of CLICs appears to be
maintenance of intracellular membranes, which is
associated with tubulogenesis but may involve
other substructures.
3.2.3 11:10am – 11:30am
The Advantage of Being an
Oligomer: the Trimeric Betaine
Carrier BetP
Reinhard Kraemer1 ,Markus Becker1 , Camilo
Perez2 , Christine Ziegler2 1 Institute of Biochemistry, University of Cologne, Zuelpicher Str.
47, 50674 Cologne, Germany.
2 Dep. Of Structural Biology, Max Planck Institute of Biophysics,
Frankfurt, Germany. r,kraemer@unikoeln.de; markus.becker@
uni-koeln.de; Camilo.Perez@mpibp-frankfurt.mpg.de; Christine.
Ziegler@mpibpfrankfurt.mpg.de
Biography
Reinhard Kraemer studied Biochemistry at the
Universities of Tuebingen and Munich, Germany.
His PhD thesis (1978, Institute of Physical
Biochemistry, LMU Munich) focused on
membrane protein reconstitution. As a postdoc,
he worked on energetics and regulation of
mitochondrial transporters. In 1987 he was jointly
appointed associate professor at the University of
Düsseldorf and the Institute of Biotechnology
(Research Center Juelich). There he switched to
the study of bacterial transport systems and
discovered active mechanisms of amino acid
export. After becoming chair in Biochemistry at
Koeln University in 1997, his major interest is
currently bacterial stress response and signal
transduction, as well as microbial biotechnology.
He has published more than 200 scientific
publications in peer reviewed journals.
Abstract
Solute carriers occur in various states of
oligomerization, frequently in monomeric, dimeric,
or trimeric state. So far, in not a single case, the
functional significance of the oligomeric state of a
Biographies and Abstracts
Monday 5 December - Session 3
particular transporter has been elucidated. We
describe here structural (X-ray and electron
crystallography) and functional studies (solute
transport in intact cells and in reconstituted
proteoliposomes) of the osmoregulated,
secondary active, glycine betaine uptake system
of the grampositive soil bacterium
Corynebacterium glutamicum. The homotrimeric
carrier BetP is a unique transport system in
harboring three independent functions, (a) sensing
of hyperosmotic stress (stimulus perception), (b)
intramolecular signal transduction from the
sensory to the catalytic domain, and (c) Na+coupled
uptake of betaine (transport catalysis). On
the basis of the X-ray structure, the contact site
between the three identical monomers were
identified. Site-specific replacement of three amino
acids in the contact site led to a stable monomeric
form of BetP. Monomeric BetP turned out to be
still transport competent, albeit at low activity
(function c), but has lost its regulatory competence
(functions a and b). Consequently, transport does
not require the trimeric state whereas regulation
does. By constructing artificial heterotrimeric forms
of BetP, we currently try to elucidate the
conformational crosstalk between the individual
BetP monomers on a molecular level.
3.2.4 11:30am – 11:45am
Single-Molecule View of the
Dynamics of Molecular Machines
Till Böcking1 1 Centre for Vascular Research, UNSW, Sydney 2052, till.
boecking@unsw.edu.au
Biography
ARC Future Fellow Till Böcking is the leader of the
Molecular Machines Unit in the Centre for Vascular
Research. Originally trained in biochemistry at the
University of Bonn in Germany, he crossed
disciplines and completed a PhD in Biophysics at
UNSW with Hans Coster and Kevin Barrow in
2004. During his doctoral and subsequent
postdoctoral research with Justin Gooding and
Michael Gal, he developed self-assembly
chemistries to assemble biomolecules on
surfaces. This work lead to the development of
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Biographies and Abstracts
Monday 5 December - Session 3
biosensors and the discovery of fundamental
principles that govern the performance of these
devices. In 2006 he joined the group of Tomas
Kirchhausen at Harvard Medical School to
elucidate the mechanism of the chaperonemediated
disassembly of the protein coat
surrounding endocytic vesicles. Till was awarded a
Cross-Disciplinary Fellowship of the Human
Frontier Science Program in 2007. Since returning
to Australia, Till leads independent research
focused on understanding biological processes at
the molecular level using approaches from the
physical sciences. In particular his team uses
single-molecule techniques to resolve
mechanistsic questions inaccessible with
traditional approaches.
Abstract
Single-molecule approaches have had a huge
impact on our understanding of molecular
processes because they provide insight into the
dynamics of biomolecular interactions that are
inaccessible with traditional techniques. The
advantage of single molecule measurements is
that they can resolve the kinetics of processes
without the need for synchronization and permit
the detection of short-lived intermediates in the
reaction pathways that are otherwise averaged out
in classical ensemble measurements. Here we
integrate surface chemistry approaches and
microfluidics with fluorescence microscopy to
visualise the dynamic interactions between protein
machines and their substrates at the singlemolecule
level. Glass coverslips are chemically
modified with self-assembled monolayers
designed to capture fluorescence labelled
biomolecules while resisting the non-specific
adsorption of other species. We then use
fluorescence imaging to record at high temporal
resolution the interactions of individual immobilised
biomolecules with their interaction partners in real
time. The utility of the approach is demonstrated
by following in real time the kinetics of the
assembly and disassembly of macromolecular
complexes.
3.2.5 11:45am – 12:00pm
The Dynamic Stator Stalk of A-type
ATPase
Alastair G. Stewart 1,2 , Lawrence K. Lee1,2 ,
Mhairi Donohoe3 and Daniela Stock1,2 1 The Victor Chang Cardiac Research Institute, Darlinghurst, NSW
2010
2 Faculty of Medicine, University of New South Wales, Sydney,
NSW 2053
3 National Neuroscience Facility, Melbourne, Vic 3053
Biography
After obtaining a Bachelor of Arts from the
University of Cambridge in England, Alastair
emigrated to Australia to train in crystallography
under the supervision of Daniela Stock at the
Victor Chang Cardiac Research Institute. Alastair’s
PhD project has been to investigate proton
translocating ATPases via X-ray crystallography.
He is now in his final year, and has been able to
obtain two crystal structures of a sub complex of
this biological rotary motor, which has lead to a
new hypothesis of how these complex nano
machines function.
Abstract
Rotary ATPases couple ATP hydrolysis/synthesis
with proton translocation across biological
membranes. The peripheral stalks are essential
components of these rotary ATPases and function
to counteract torque generated by rotation of the
central stalk during proton translocation. The
peripheral stalks have been proposed to form rigid
scaffolds that prevent rotation of the soluble head
domain relative to the ion channel anchored in the
membrane. We have solved a 2.25 Å resolution
crystal structure of the peripheral stalk from
Thermus thermophilus H+-ATPase/synthase.
Comparison with a different crystal form identifies
a bending and twisting motion inherent within the
peripheral stalk that can accommodate and
complement the wobbling motion of rotary
ATPases as they progress through different states
of their catalytic cycle. Transitions observed
between different conformations of the peripheral
stalk in crystal structures and in low-resolution
electron micrographs can be simulated by normal
mode analysis. This motion changes the

orientation of the head of the peripheral stalk
relative its coiled-coil domain, coupled with
bending the coiled-coil itself. This analysis also
shows that the novel right-handed coiled-coil of
the peripheral stalk can accommodate radial
fluctuations associated with nucleotide binding
states of the subunits as they move between
catalytic states, while retaining the stiffness
needed to restrain azimuthal movement generated
by the rotation of the central stalk.
Biographies and Abstracts
Monday 5 December - Session 3
Notes
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56
Biographies and Abstracts
Monday 5 December - Session 4
Session 4 – Theatre 2
4.1.1 1:15pm – 1:45pm
Chemistry at the Threshold:
Unexpected Products, Unusual
Mechanisms, and Generally Weird
Things that Happen Near the
Energetic Threshold for a Reaction
Scott H. Kable, Alan T. Maccarone, Klaas
Nauta, Gabrielle de Wit, Mitchell Quinn, Scott A.
Reid, Klaas Nauta, and Meredith J.T. Jordan
School of Chemistry, University of Sydney, Sydney, NSW, 2006
Biography
Scott Kable is a professor of chemistry at the
University of Sydney. He earned his PhD at Griffith
University and did 3 years post-doctoral research
at Cornell University before returning to Australia at
the University of Sydney in 1992. His research has
been recognised by the Le Fevre Award of the
Australian Academy of Science, a JILA Fellowship,
and a Fulbright Senior Fellowship in 2010. He is
also a committed teacher who has been awarded
a Carrick Award and Citation, and several
University Teaching Awards.
Abstract
Reactions that occur near the energetic threshold
can be very different to those where energy is in
excess. In a series of experiments, we have used a
narrow linewidth laser to provide a small organic
molecule, acetaldehyde (CH3CHO), with a precise
amount of energy, and used spectroscopic and
imaging based techniques to probe the reaction
products. In this paper I shall present two different
examples of “weird chemistry” that happens at
threshold: i) fragments of acetaldehyde, CH3 and
HCO, or CH3CO and H, almost separate but are
trapped in their mutual van der Waals well. Here
they orbit each other and produce different
chemical products; ii) selectively deuterated
acetaldehyde is observed to undergo facile and
unexpected H/D exchange before the reaction is
complete. Near-threshold chemistry is not an
esoteric, narrow window, but one that is prevalent
in chemistry more generally. Examples in
atmospheric and combustion chemistry will be
presented.
4.1.2 1:45pm – 2:00pm
Convergent first principles quantum
dynamics: vMCG and Grow
Terry J. Frankcombe
Research School of Chemistry, Australian National University, ACT
0200, tjf@rsc.anu.edu.au
Biography
Terry Frankcombe (born 1975, Tasmania) received
his BSc(Hons) with a University Medal from the
Australian National University in 1997, which
included a period conducting research with Prof.
Sture Nordholm at Göteborgs Universitet. He
completed his PhD in 2001 under the supervision
of Prof. Sean Smith at the University of
Queensland. This was followed by postdoctoral
work at the University of Queensland
(2002--2003) and with Prof. Geert-Jan Kroes at
the University of Leiden (2004--2006). He spend a
year at Göteborgs Universitet as a Marie Currie
Fellow working with Prof. Gunnar Nyman before
returning to the Australian National University to
work with Prof. Michael Collins. In
2010 he was awarded a Future Fellowship by the
Australian Research Council. His theoretical and
computational research interests are diverse, from
modelling solid state materials to astrochemistry
and quantum scattering methodology.
Abstract
Performing accurate quantum dynamics
calculations requires two things: a method to
simulate the properties of the nuclear wave
function, and an accurate potential energy surface
(or set of coupled surfaces) that determines these
properties. Moving beyond a few atoms using
traditional grid-based
methods is extremely computationally onerous on
both counts, with the configuration space grid
getting very large very quickly.
A novel approach is being developed to
counteract both of these issues at once. The
dynamics calculations are performed using a
variational time-dependent wave packet approach
(vMCG) that only depends on the potential and its
derivatives at a reasonably small number of

configurations along non-classical trajectories.
The potential is expressed as a modified Shepard
interpolation of scattered ab initio data. The key
idea in the overall approach is that these two areas
of the calculation must be tightly coupled in an
iterative process, so that the dynamics calculations
specify where ab initio calculations must be
performed and one gets the most “value for
money” out of each ab initio calculation.
In this presentation the methodology will be
described in detail, along with demonstrations that
the approach not only works, but that the method
has the unique feature that explicit assessment of
the convergence of the dynamics results
(demonstrable convergence) is inherently built in.
4.1.3 2:00pm – 2:15pm
Quantum mechanical study of the
deep well reaction H2+ / D2
M.Hankel 1
1 Centre for Computational Molecular Science, Australian Institute
for Bioengineering and Nanotechnology, The University of
Queensland, Brisbane QLD 4072, Australia
Biography
Marlies Hankel obtained her first degree in
Mathematics in her home country of Germany.
She then moved to the University of Bristol in the
UK for her PhD in Physical Chemistry with Prof.
Gabriel Balint-Kurti to work on the development of
the real wavepacket approach. After a postdoc in
Manchester with Prof. Jonathan Connor she
moved to the University of Queensland in 2004.
Since then she has worked in the group of Prof.
Sean Smith investigating the reaction dynamics of
gas phase reactions and further developing her
own reactive scattering code. Apart from her
research Marlies Hankel is also the manager of the
local high performance computer cluster with
300+ CPUs.
Abstract
We present integral and differential cross sections
as well as product state distributions for the H+ +
D2 reaction obtained from quantum mechanical
calculations employing the DIFFREALWAVE (DRW)
code [1,2]. We employ the ground adiabatic
Biographies and Abstracts
Monday 5 December - Session 4
electronic state potential energy surface of
Kamisaka et al. [3]. The integral cross sections
decrease with energy and we find cold vibrational
distributions and highly inverted rotational
distributions. The differential cross sections
oscillate strongly with energy.
We also employ an adapted DRW code where we
can restrict the helicity states to a fixed kmax and
with this the Coriolis couplings involved in the
dynamics [4]. This introduces a significant saving
in the computational effort required for these
demanding calculations which, in the present
case, is about 2/3 compared to the fully coupled
calculations. Coriolis coupling is found to be
important in the H+ + D2 reaction dynamics and
truncating the couplings leads to an overestimation
of the exact results. However, we also find that the
features of the integral cross section are well
reproduced as well as the product rotational state
distributions if the maximum helicity state is
chosen carefully [4].
References:
[1] M. Hankel, S. C. Smith, R. J. Allan, S. K. Gray and G. G.
Balint-Kurti, J. Chem. Phys. 125, 164303 (2006).
[2] M. Hankel, S. C. Smith, S. K. Gray and G. G. Balint-Kurti,
Comput. Phys. Commun. 179, 569 (2008).
[3] H. Kamisaka, W. Bian, K. Nobusada and H. Nakamura, J.
Chem. Phys. 116, 654 (2002).
[4] M. Hankel, Phys. Chem. Chem. Phys. 13, 7948 (2011).
4.1.4 2:15pm – 2:30pm
Optical Spectroscopy of Polycyclic
Aromatic Nitrogen Heterocycle
Cations
Viktoras Dryza 1 , Evan Robertson 2 , Evan
Bieske3 1 School of Chemistry, University of Melbourne, Parkville 3010,
vdryza@unimelb.edu.au
2 Department of Chemistry, La Trobe University, Bundoora,
Victoria, 3086, e.robertson@latrobe.edu.au
3 School of Chemistry, University of Melbourne, Parkville 3010,
evanjb@unimelb.edu.au
Biography
Viktoras Dryza received his PhD from the
University of Adelaide in 2008, under the
supervision of Gregory Metha, for elucidating the
structures of gas-phase metal-carbide clusters via
photoionization efficiency spectroscopy. Currently
57

58
Biographies and Abstracts
Monday 5 December - Session 4
he is a postdoctoral fellow in the research group of
Evan Bieske at the University of Melbourne,
characterizing gas-phase molecular ions of
technological and astrophysical relevance using
infrared and optical photodissociation
spectroscopy.
Abstract
Polycyclic Aromatic Hydrocarbons (PAHs) in their
neutral or ionized forms are believed by some to
be constituents of the interstellar medium and
perhaps associated with the diffuse interstellar
bands [1]. An important variation of PAHs entails
the incorporation of nitrogen atoms to form
Polycyclic Aromatic Nitrogen Heterocycles
(PANHs). To develop a better understanding of the
optical properties of PANHs we have investigated
the D3 ← D0 and D4 ← D0 transitions of the
quinoline and isoquinoline radical cations,
structural isomers of the simplest PANH member
C9H7N+. The spectra are obtained by massselecting
quinoline+-Ar and isoquinoline+-Ar
complexes in a tandem mass spectrometer and
monitoring the photo-induced Ar loss channel. The
D3 ← D0 bands of quinoline+-Ar and isoquinoline+-
Ar feature origin transitions at 16050 and 15245
cm-1, respectively, and display several strong
vibronic progressions. The analogous transition for
the isoelectronic naphthalene+-Ar complex occurs
at a slightly lower energy (14863 cm-1 [2]). To aid
spectroscopic assignments, the resolved vibronic
structure is modelled by performing timedependent
density functional theory calculations in
conjunction with Franck-Condon simulations.
FIG. 1: Resonance enhanced photodissociation spectrum of the
isoquinoline+-Ar complex.
References:
[1] PAHs and the Universe, edited by C. Joblin and A.G.G.M.
Tielens, EAS Publication Series Vol. 46 (2011).
[2] T. Pino, N. Boudin, P. Bréchignac, J. Chem. Phys. 111, 7337
(1999).
4.1.5 2:30pm – 2:45pm
Ab Initio Diabatic Potential Energy
Matrix and Dynamics for OH(2S) +
H2 /D2
Michael A. Collins1 , Oded Godsi2 , Shu Liu
and Dong H. Zhang3 1 Research School of Chemistry, Australian National
University,Canberra. ACT 0200. Australia
2 Research School of Chemistry, Australian National
University,Canberra. ACT 0200. Australia
3 Dalian Institute of Chemical Physics, Chinese Academy of
Sciences, Dalian 116023, People’s Republic of China
Biography
Mick Collins is a professor of chemistry at the ANU
Abstract
This talk will briefly review the methodology for
constructing an ab initio quasi-diabatic potential
energy matrix (DPEM) that governs nonadiabatic
chemical dynamics in multiple electronic states. A
DPEM for three electronic states of OH3 has been
constructed by interpolation of multi-reference
configuration interaction electronic structure data.
The reactive, OH(2S) + H2 ← H2O + H, exchange,
and non-reactive quenching dynamics have been
investigated using surface hopping classical
trajectories and time dependent wavepacket
calculations. The most recent results of these
dynamical studies on OH3 and deuterated
analogues will be reported.
4.1.6 2:45pm – 3:00pm
G4(MP2)-6X: Accurate and
Affordable Computational Chemistry
Bun Chan1 , Jia Deng2 , Leo Radom3 1 ARC Centre of Excellence for Free Radical Chemistry and
Biotechnology and School of Chemistry, University of Sydney,
Sydney, NSW 2006, Australia
2 Research School of Chemistry, Australian National University,
Canberra, ACT 0200, Australia
3 ARC Centre of Excellence for Free Radical Chemistry and
Biotechnology and School of Chemistry, University of Sydney,
Sydney, NSW 2006, Australia

Biography
Bun Chan was trained as an experimental organic
chemist in Otago, New Zealand. During his PhD
he also did molecular modeling to complement his
experimental studies, which triggered his interest
in theoretical chemistry. After graduation, he
spent a year in Academia Sinica as a postdoctoral
experimental chemist. He then moved to the
University of Sydney to embark on a career as a
computational chemist, where he remains to this
date
Abstract
Computational chemistry is nowadays an
indispensable tool to chemists. Nonetheless,
theoretical methods that are of chemical accuracy
are still costly in terms of computational resource,
thus rendering them applicable only to small
molecules (up to ~ 10 atoms). The Gn series of
composite procedures has been offering an
excellent solution to this dilemma. The latest in the
series, G4,1 offers chemical accuracy for a diverse
set of energies, and can be applied to larger
chemical systems (up to ~ 20 atoms). Its less
expensive cousin, G4(MP2)2 is applicable to even
larger molecules containing ~40–50 atoms. It
shows good performance but has not yet reached
the same level of accuracy. Our new procedure,
G4(MP2)-6X,3 is an alternative to G4(MP2) of
similar cost but with a performance approaching
that for G4. It achieves chemical accuracy for a
diverse set of thermochemical properties including
reaction energies, barriers and weak interactions,
thus it is broadly applicable in chemistry.
1 Curtiss, L. A.; Redfern, P. C.; Raghavachari, K. J. Chem. Phys.
2007, 126, 084108.
2 Curtiss, L. A.; Redfern, P. C.; Raghavachari, K. J. Chem. Phys.
2007, 127, 124105.
3 Chan, B.; Deng, J.; Radom, L. J. Chem. Theory Comput. 2011, 7,
112.
Biographies and Abstracts
Monday 5 December - Session 4
Session 4 – Main Theatre
4.2.1 1:15pm – 1:30pm
Test of a Protein Docking Algorithm
on K+ Channel Binding: Validation
and Analysis
Po-chia Chen1 , Serdar Kuyucak 2
1 School of Physics, University of Sydney, NSW, Australia 2006.
poker@physics.usyd.edu.au
2 School of Physics, University of Sydney, NSW, Australia 2006.
serdar@physics.usyd.edu.au
Biography
Po-chia is a long-time resident of Sydney
University who has recently finished his PhD thesis
on potassium channel binding. This thesis process
has brought Po-chia through multiple aspects of
biophysical simulation, from ab-initio through
classical dynamics and molecular docking. While
aware of the likelihood that his new work is old-hat
to researchers in private pharmaceutical
development, he dreams of a day when these
corporations can afford to share their knowledge
with academia at large.
Aside from his day-job running biophysical
simulations, Po-chia also thinks about
incorporating computer simulation and
visualisation into science education. He would
particularly like to devise an effective method to
teach organic chemistry.
Abstract
The active components of animal venoms have
historically been used to identify channel
expressions in electro-physiology, and is currently
a prospective candidate for related pharmaceutical
applications. The fitness of a particular toxin for
these tasks is determined by its selectivity profile
over a range of target channels. However,
comprehensive affinity data is not always available,
and are time-consuming to produce.
We present a preliminary method to deduce the
selectivity profile of a peptide toxin against related
channels by means of docking simulations. This is
tested on the family of ←-KTx scorpion toxins
versus the Shaker-type potassium channels (Kv1),
for which both structural and affinity data are
available to validate predictions. A total of ~25
59

60
Biographies and Abstracts
Monday 5 December - Session 4
toxins were docked to Kv1.1, Kv1.2 and Kv1.3,
resulting in ~75 total docking simulations in the
program
The performance of HADDOCK will first be
evaluated, followed by an analysis of a selection of
toxins for which validation can be best provided.
The general selectivity profiles of toxin-subfamilies
can be deduced by a consensus between closely
related toxin-channel pairings, while individual
selectivity profiles can be identified by comparison
of docked-complex quality and program
performance. In particular, HADDOCK was able to
classify αKTX2 toxins as universal binders and
αKTX3 toxins as Kv1.3-selective binders. It was
also able to reproduce the differing characteristics
of αKTX6-toxins, which depend on sequence and
di-sulphide patterns. Distinct binding orientations
can be observed between the channels (an
example is shown in the included figure).
4.2.2 1:30pm – 1:45pm
Open channel structure of MscL
from restrained MD Simulations
Evelyne Deplazes1, Dylan, Jayatilaka1 , Martti
Louhivuori2 , Siewert J. Marrink 2 , Ben Corry1 .
1 The University of Western Australia, Perth, ben.corry@uwa.edu.
au
2 University of Groningen, Groningen, Netherlands
Biography
Evelyne Deplazes is a PhD student at the
University of Western Australia. Her project
focused on using a combination of molecular
dynamics simulations and experimental data to
investigate the structure of the mechanosensitive
channel of large conductance. In addition she has
used simulations to simulate the behavior of
fluorescent molecules and to better understand
FRET at the molecular level.
Abstract
Mechanosensitive channels are membrane
proteins that have evolved for osmoregulation in
bacteria and function as mechano-electrical
switches in many physiological processes such as
hearing and touch sensation. The
mechanosensitive channel of large conductance
(MscL) is the most studied mechanosensitive
channel and often serves as a model system to
study mechanosensory transduction. Although a
detailed structure of the closed state is known,
many questions about the open pore structure
and the gating mechanism are yet to be answered.
The MscL protein has been characterized using
EPR [1] and FRET [2] spectroscopy providing a
large set structural data. In this study we
incorporate inter-subunit distances and solvent
accessibility data in to coarse grained molecular
dynamics simulations to model the open pore
structure of MscL. A series of simulations with
different combinations of restraints and membrane
tension were carried out to produce a set of
potential open channel structures.
The open structures show a pore diameter
between 26Å and 32Å and TM1 and TM2 tilts of
~60º and ~46º, respectively. These
measurements are in good agreement with data
from recent all-atoms restrained simulations [3] as
well as previously reported open pore models. In
all our structures the N-terminal lie along the
membrane surface and is therefore unlikely to
serve as a second gate. The C-terminals does not
dissociate during gating but stays as a helical
bundle pointing into the cytoplasm.
Furthermore, the results suggests that an outward
motion of the periplasmic loop in combination with
a change in the relative orientation of TM1 and the
periplasmic loop are associated the formation of
the open pore. The results also indicate that
tension induced thinning of the lipid bilayer is
necessary for these structural changes to occur.
These results are consistent with data from
experiments of MscL in thinner membranes. To
further investigate these effects we carried out
simulations of MscL in short-chain lipids.
[1] Perozo E et al. (2002). Open channel structure
of MscL and the gating mechanism of
mechanosensitive channels. Nature, 418, 942-948
[2] Corry B et al. (2005). Conformational changes
involved in MscL channel gating measured using
FRET spectroscopy, Biophysical Journal, 89,
L49-L51
[3] Corry B et al. (2010). An improved openchannel
structure of MscL determined from FRET
confocal microscopy and simulation. Journal of
General Physiology, 136, 483-494

4.2.3 1:45pm – 2:00pm
Estimation of the pKa of tri-peptides
using Generalized Multiplicative
ANOVA of designed data
Rima Raffoul Khoury 1 , Diako Ebrahimi2 , D.
Brynn Hibbert1 1 School of Chemistry, The University of New South Wales, NSW,
2052, s3213363@unsw.edu.au
2 Faculty of Medicine, Centre of Vascular Research, The University
of New South Wales, NSW, 2052, diako@unsw.edu.
au
1 School of Chemistry, The University of New South Wales, NSW,
2052, b.hibbert@unsw.edu.au
Biography
Rima Raffoul Khoury is a current PhD student at
the University of New South Wales, in the
Chemometrics group under the supervision of
Prof. Hibbert and Dr. Ebrahimi. Rima is working on
modelling the multi-way interactions between
metal ions and oligopeptides systems using
Generalised Multiplicative Analysis of Variance
GEMANOVA. Her research tackles two problems:
the requirements of experimental design and the
correct modelling of data obtained from complex
systems where the measured response is
dominated by high order interaction between the
influencing factors. Rima is using GEMANOVA to
model data obtained from Potentiometry,
Spectroscopy and Electrochemistry.
Previously, she has completed an Honours degree
from UNSW 2008, where she investigated the
degradation of Fatty acids methyl esters in
Biodiesels, under bio-degradation and photooxidation
conditions. More details can be found:
Fuel, Volume 90, Issue 8, August 2011, Pages
2677-2683
Rima has obtained double degrees: Maitrise-es in
Biochemistry, 2004 and General Chemistry, 2003
from the National Lebanese University, Lebanon.
Abstract
In chemistry, there are many cases in which the
response of a process is affected by the
interaction between the influencing factors rather
than only by the individual and independent
factors. The classical methods for modelling
chemical systems have mainly focussed on the
Biographies and Abstracts
Monday 5 December - Session 4
effects of individual factors by assuming that the
interaction effects (in particular high order effects)
are insignificant. This is partly because the
inclusion of high order interaction terms in classic
models such as ANOVA requires the estimation of
a large number of parameters, which in turn
makes the interpretation of the results very difficult.
When the measured response is mainly affected
by the interactions among factors, disregarding
these interactions leads to erroneous models and
inhibits understanding of correct mechanisms.
In this work we use a generalized multiplicative
analysis of variance (GEMANOVA) to efficiently
model the interactions among amino acid residues
of a tri-peptide system in a designed experiment.
A full factorial design of a tri-peptide system
containing Glutamic acid (Glu, E), Glycine (Gly, G)
and Histidine (His, H) was investigated. In this
study the three positions of amino acid residues
are considered as three factors each having three
instances of E, G and H, thus forming a 33 design.
Each of 27 different tri-peptide (GGG, GGE, GGH
...HHH) was subjected to an alkali titration under a
specific experimental condition. The HyperQuad
2008 software was used to estimate the pKa
values of tripeptides from the titration data
obtained from potentiometry experiments. The
estimated pKa data was then modelled using
GEMANOVA.
The results indicate that the position and the type
of amino acid have strong influence on the acidity
of the terminal carboxylic acid of the tripeptides.
To investigate whether it is possible to predict the
pKa of tripeptides using GEMANOVA model, we fit
GEMANOVA models on the data with missing pKa
of up to 18 tripeptides. The results indicated that
GEMANOVA is a robust method for modelling the
amino acid interactions of peptides as well as for
prediction of pKa of peptides. The tripeptides
EHH, GHH and HHH which have H at position 2
and 3 had the lowest measured pKa for their
terminal carboxylic acid (pKa = 1.905, 1.93 and
2.05, respectively). The peptides which do not
have a terminal H and contain E (especially at
position 1) were found to have relatively high pKa
values; for example the measured pKa for EEG,
EGE, EHE were 3.480, 3.840 and 3.735,
respectively.
61

62
Biographies and Abstracts
Monday 5 December - Session 4
4.2.4 2:00pm – 2:15pm
The Fouling of Hydrophobic
Membranes by Hydrophilic
Alginates: A Molecular Dynamics
Study.
Matthew B. Stewart 1 , Darli Theint Myat1 ,
Stephen R Gray1 and John D. Orbell1,2 1 Institute for Sustainability and Innovation, Victoria University, PO
Box 14428, Melbourne, Victoria, 8001, matthew.stewart@vu.
edu.au
2 School of Engineering and Science, Victoria University, PO Box
14428, Melbourne, Victoria, 8001, john.orbell@vu.edu.au
Biography
Dr. Matthew Stewart is a current postdoctoral
fellow at Victoria University in Melbourne. Under
Prof. Orbell, he was awarded his PhD in 2009 for a
thesis which focused on the reconciliation of
experimental and computational data to provide
insights into the behaviours of biologically
interesting molecules. This work included
antioxidant activities, nucleotide-metal interactions
and iron-based radical complexes. His current
work involves computational support for
researchers within the Institute for Sustainability
and Innovation at Victoria University, which
includes membrane fouling mechanisms,
shear-induced protein conformation changes and
the development of approaches towards the
modelling of advanced oxidation processes. He
also enjoys AFL football, cricket, traveling and long
walks on the beach.
Abstract
Natural Organic Matter (NOM) is the collective
name for a wide range of compounds routinely
found in surface and waste waters. Many
studies1-5 have found that the hydrophilic fraction
of NOM is the most significant with respect to the
fouling of hydrophobic microfiltration membranes.
Whilst there is no definable hydrophilic NOM
structure, there are a number of molecules that
effectively mimic the general properties of NOM.
These compounds are used as analogues for the
study of the NOM fouling of a number of
membranes used in water treatment - the most
common model compound being sodium alginate.
Alginate (also known as Alginic acid) is an ionic
polyuronic acid naturally found in a number of
algae (including seaweed) and bacteria species.
Alginate is a polymer consisting of linked
←-D-mannuronic acid (M) and ←-L-guluronic acid
(G) monomers. The general structure of algaederived
alginates exhibit ordered sequences of
poly-G, poly-M and alternating GM6. The lengths
and order of these sections are highly variable. In
this regard, the composition of alginate chains is
most accurately expressed by the G/M ratio,
which is species dependent. Whilst this structural
uncertainty can be an issue in experimental
investigations of alginates, especially from a
mechanistic point-of-view, it can be used to
advantage in computational studies of these
polymeric molecules. Each section (poly-G,
poly-M and alternating GM) can be individually
studied and combined to infer the behaviour of
longer chains of alginates.
This approach has been used in this study, where
decamers of G, M and GM were subjected to
molecular dynamics calculations under a variety of
conditions that reflect the experimental conditions
of membrane fouling experiments currently being
carried out within the research group. Thus, the
effect of pH and ionic strength on the
conformation of the individual alginate chains, the
interactions between the chains and the
interaction of the chains with the membrane
surface have been simulated. This work provides
insights into the solution chemistry of alginate
molecules, as well as their specific interactions
with cations (mono- and divalent) and polymer
surfaces. Such insights may also be useful to the
food processing and cosmetics industries, as
alginate is a commonly used constituent.
1. S. R Gray, C. B. Ritchie, T. Tran, B. A. Bolto, P. Greenwood, F.
Busetti, B. Allpike, Effect of membrane character and solution
chemistry on microfiltration performance, Water Research, 42
(2008) 743-753
2. L. Fan, L. J. Harris, F. A. Roddick, A. N. Booker, Influence of
characteristics of natural organic matter on the fouling of
microfiltration membranes, Water Research, 35 (2001)
4455-4463
3. T. Carroll, S. King, S. R. Gray, B. Bolto, A. N. Booker, The fouling
of microfiltration membranes by NOM after coagulation
treatment, Water Research, 34 (2000) 2861-2868
4. Jarusutthirak. C, A. Gary, Fouling characteristics of wastewater
effluent organic matter (EfOM) isolates on NF and UF
membranes, Desalination, 145 (2002) 247-255
5. S.R. Gray, N. Dow, J.D. Orbell, T. Tran and B.A. Bolto, The
significance of interactions between organic compounds and
low pressure membrane fouling, Water Science and

Technology, 64 (2011), 632-639
6. I. Donati and S. Paoletti, Material Properties of Alginates, In:
Alginates: Biology and Applications, B.H.A. Rehms (Ed.) (2009)
Springer; Dordrecht, Germany
4.2.5 2:15pm – 2:30pm
HIV1-TAT Peptide modified
nanoparticles: insights from
molecular dynamics simulations.
Nevena Todorova1 , Morgan Mager2 , Molly
Stevens2 , Irene Yarovsky1 1 Health Innovations Research Institute, School of Applied
Sciences, RMIT University, GPO Box 2476 V, Melbourne, VIC,
Australia.
2 Department of Materials, Department of Bioengineering, and
Institute for Biomedical Engineering, Imperial College London,
London, U.K., SW7 2AZ
Biography
Nevena Todorova completed her PhD in 2009 at
RMIT University, where she investigated the effects
of environment on protein folding, misfolding and
aggregation using a range of computational
modelling techniques. She is now a post-doctorate
fellow in the Materials Modelling and Simulations
group of Prof. Irene Yarovsky at RMIT. Her current
projects involve studies on the effects of
nanoparticles on protein structure and dynamics
and the application of bio-inspired nanomaterials
for drug-delivery, sensing and diagnostics. At the
conference she will present her findings from her
recent work on peptide functionalised
nanoparticles titled “HIV1-TAT Peptide modified
nanoparticles: insights from molecular dynamics
simulations”.
Abstract
Nanoparticle functionalisation with peptides has
been shown to be a good strategy to inhibit
particle aggregation, increase nanoparticle
solubility and develop potential nanocarriers [1]. A
biologically-inspired set of peptides collectively
known as cell-penetrating peptides (CPPs) has
become an increasingly popular tool for
transfection and other types of cellular delivery [2].
One such example is a peptide derived from the
transcription transactivation (TAT) protein from
human HIV-1 virus (residues 48-60,
GRKKRRQRRRPPQ) [3]. Experimental studies
Biographies and Abstracts
Monday 5 December - Session 4
have shown that TAT-peptide functionalized gold
nanoparticles have the ability to penetrate the cell
membrane and localize in the nucleus [4].
However, the peptides’ behaviour with respect to
their immediate environment and the nanoparticle
surface prior to contact with a membrane is not
well understood. In this work we employed fully
atomistic Molecular Dynamics simulations to shed
some light on the structure and dynamics of the
TAT functionalized nanoparticles in solution.
We developed the TAT and CALNN peptide
functionalised nanoparticle models at varying
grafting density. The effect of TAT:CALNN surface
ratio on the peptide’s structure and dynamics was
investigated for the 3nm nanoparticle coated with
1.82%, 3.71%, 5.66%, 7.69%, 9.81% of TAT, the
concentrations close to those used in experiments
[5]. The nanoparticle-peptide systems were
simulated at 285K, 288K, 296K and 308K to
investigate the effects of temperature. For each
concentration, the peptide structure, dynamics
and interactions with the nanoparticle surface and
the environment will be discussed. Our results
identified specific properties that may be
necessary for membrane activity of the TAT
modified nanoparticles.
Figure showing the 9.8% TAT coated nanoparticle; starting
structure (TAT expanded) and final conformation (TAT collapsed).
[1] A. Makarucha, N. Todorova, I. Yarovsky “Nanomaterials in
biological environment: a review of computer modelling studies”
European Biophysical Journal, 40(2):103 (2011).
[2] N.A. Brooks, et al. “Cell-penetrating peptides: Application in
vaccine delivery”, Biochemica et Biophysica Acta, 1805:25 (2010)
[3] A.D. Frankel and C.O. Pabo “Cellular uptake of the tat protein
from human immunodeficiency virus”, Cell, 55(6):1189 (1988)
[4] J.M de la Fuente and C.C. Berry “Tat peptide as an efficient
molecule to translocate gold nanoparticles into the cell nucleus”,
Bioconjugate Chem. 16:1176 (2005)
[5] Unpublished results, Prof. Molly Stevens, Dr. Morgan Mager,
Imperial College, London.
63

64
Biographies and Abstracts
Monday 5 December - Session 4
4.2.6 2:30pm – 2:45pm
Ion Permeation and Selectivity in a
Voltage Gated Sodium Channel
Ben Corry1 , Michael Thomas1 1 School of Biomedical, Biomolecular and Chemical Sciences,
The University of Western Australia, Crawley WA 6009, ben.
corry@uwa.edu.au
Biography
Associate Professor Ben Corry has focused his
research on studying ion transport in pores,
particularly in biological ion channels. After gaining
his PhD at the ANU, he has been based at the
University of Western Australia and during this time
has been awarded the 2005 Young Biophysicist
Award from the Australian Society for Biophysics
and the 2008 Young Scientist of the Year at the
WA Premier’s Science Awards.
Abstract
Ion channels regulate electrical signalling in cells
by opening and closing selective pores across the
membrane in response to stimuli. In order to carry
out their function, such channels must be able to
rapidly transport ions at the same time as
effectively discriminating between different ion
types so that the correct signal can be passed
without destroying the electrochemical gradients
across the membrane. Investigations into how ions
permeate through membrane channels have been
focussed on K+ selective channels due to the
availability of a number of high resolution crystal
structures. The recent publication of the first high
resolution crystal structure of a voltage gated
sodium channel,1 however, opens the door to
understanding how sodium ions permeate into the
cell and how Na+ can be transported while
blocking the passage of K+.
Using molecular dynamics simulations we are able
to demonstrate the multi-ion knock-on basis of ion
permeation through the channel and identify the
major binding sites for ions. The nature of these
binding sites, and the ability of ions to pass
through the channel with the majority of their
hydration shell is very different to the situation in
potassium channels. Using free energy
calculations we elucidate the mechanism of ion
selectivity in the sodium channel and contrast this
to how K+ selectivity is obtained in potassium
channels.
1. J Payandeh, T Scheuer, N Zheng & WA Catterall,
Nature, 475, 353–358 (2011)
4.2.7 2:45pm – 3:00pm
The Role of Molecular Strain in the
Ion Selectivity of Biological
Molecules
M. Thomas1 , M. J. Turner 1 , D. Jayatilaka1, B.
Corry1 1 School of Biomedical, Biomolecular and Chemical Science,
University of Western Australia, M313 35 Stirling Hwy Crawley,
WA 6009, thomam05@student.uwa.edu.au
Biography
Michael is a PhD student in the school of
Biomedical, Biomolecular and Chemical Sciences
at the University of Western Australia under the
supervisor of Dr Ben Corry and A/Prof Dylan
Jayatilaka. He is investigating the mechanisms that
lead to ion selectivity in biological molecules using
computational approaches. Hopefully by now he
has submitted his thesis and is enjoying life to the
fullest.
Abstract
Many biological molecules are able to differentiate
between two extremely similar ions, Na+ and K+.
Different molecules are able to achieve this
remarkable feat by using a combination of different
mechanisms.[1] However, these mechanisms
focus on the interactions occuring at the ion
binding site and do not take into account
interactions that may be induced away from the
binding site, such as strain in the molecular
scaffold or induced conformational changes.
These changes may contribute to the selectivity of
an ion binding site but are difficult to predict
without prior knowledge of the structure and
dynamics of the molecule. As such, a general
model of the role of strain in ion selectivity will be
difficult, if not impossible, to construct. [2]
The role of strain and conformational changes can
be characterised in specific cases so as to obtain
an understanding of what may be occuring in
other molecules. In this investigation, this role is

elucidated for two ion selective bacterial
ionophores: valinomycin and nonactin. Several
intramolecular hydrogen bonds hold valinomycin in
a rigid structure, thought to be necessary for
achieving ion selectivity. Nonactin, on the other
hand, lacks these bonds, making the comparison
between the two particularly interesting.
[1] Thomas, M., Jayatilaka, D., Corry, B., Biophys. J, 2011, 100,
60-69
[2] Bostick, D.L., Brooks, C.L., Biophys. J., 2009, 96, 4470-4492
Keynote Session - Main Theatre
K.7 3:30 – 4:00 pm
Molecular approaches to next
generation photovoltaic energy
conversion
Timothy W. Schmidt1 ,Yuen Yap Cheng1 ,
Burkhard Fückel1 , Murad Tayebjee1 , Raphaël
Clady1 , Nicholas J. Ekins-Daukes 2 , Maxwell J.
Crossley1 , Klaus Lips3 ,
1 School of Chemistry, The University of Sydney, NSW 2006
2 Department of Physics and Grantham Centre for Climate
Change, Imperial College, London
3 Institut für Silizium-Photovoltaik, Helmholtz Zentrum-Berlin für
Energie und Materialen
Biography
Tim Schmidt gained his BSc (Hons) from this
university in 1998 winning the University Medal in
theoretical chemistry. He then studied at Churchill
College, Cambridge, gaining a PhD in chemistry
from the University of Cambridge in 2001 for work
on the femtosecond dynamics of molecules in
intense laser field under the supervision of Dr
Gareth Roberts. Postoctoral work was performed
in the group of Professor John Paul Maier in Basel
on the electronic spectroscopy of highly
unsaturated hydrocarbons of astrophysical
relevance. Tim returned to Australia in 2003 to
work at the CSIRO (CTIP, Lindfield) on modelling of
the rubsico enzyme. He commenced as a lecturer
in chemistry in April 2004. From January 2011, Tim
is appointed as Associate Professor. He was the
2010 recipient of the Coblentz Award, and the
inaugural recipient of the Lecturership of the
Physical Chemistry Division of the RACI.
Biographies and Abstracts
Monday 5 December - Session 4
Abstract
Single threshold solar cells, by their design, are
limited to a maximum energy conversion efficiency
of 33% under the standard AM1.5G spectrum.
While this number depends on the absorption
threshold of the material, many first generation
technologies such as crystalline silicon are
approaching this limit. By sacrificing efficiency,
cost savings can be made by using cheaper
processing methods and a smaller amount of
photoactive material. These cheaper cells, referred
to as second generation solar cells, include
technologies such as thin-film silicon and organic
(plastic) photovoltaics. The field of third generation
photovoltaics seeks to build on the cost savings of
the second generation cells while circumventing
the single threshold limit. One strategy in this
direction is to transform the solar spectrum by
upconversion, where long wavelength light used
poorly by a single threshold solar cell is converted
to a shorter wavelength of more utility to the cell.
In our laboratory, we have been investigating the
phenomenon known as triplet-triplet annihilation
upconversion (TTA-UC), an upconversion
technology which uses organic molecules to
harvest low energy light, and conjoin the energy of
two photons to bring about higher energy
radiation. This technique is extremely flexible with
regard to wavelength: Using a range of porphyrin
molecules, we have succeeded in upconverting
red to blue, red to green, red to yellow and green
to blue. Experiments have shown that TTA-UC can
proceed with high efficiency. In the tens of
microseconds following laser excitation, we find as
many as 33% of the absorbed quanta take part in
the TTA-UC process, with instantaneous
efficiencies exceeding 40%.[1,2] Moreover, kinetic
analysis reveals that the process would reach its
maximum at a value exceeding 60% (where 100%
represents the maximum quantum efficiency of
50%). I will present experiments demonstrating
enhancements in the energy conversion of an
amorphous silicon solar cell, due to the
upconversion unit.
1. Y. Y. Cheng, T. Khoury, R. Clady, M. J. Y. Tayebjee, N. J.
Ekins-Daukes, M. J. Crossley, and T. W. Schmidt, “On the
efficiency limit of triplet-triplet annihilation for photochemical
upconversion,” Physical Chemistry Chemical Physics 12(1), 66-71
(2010).
2. Y. Y. Cheng, B. Fückel, T. Khoury, R. l. G. C. R. Clady, M. J. Y.
Tayebjee, N. J. Ekins-Daukes, M. J. Crossley, and T. W. Schmidt,
65

66
Biographies and Abstracts
Monday 5 December - Session 4
“Kinetic Analysis of Photochemical Upconversion by Triplet-Triplet
Annihilation: Beyond Any Spin Statistical Limit,” The Journal of
Physical Chemistry Letters 1(12), 1795-1799 (2010).
3. N. J. Ekins-Daukes and T. W. Schmidt, “A molecular approach
to the intermediate band solar cell: The symmetric case,” Applied
Physics Letters 93(6)(2008).
K.8 4:00pm – 4:30pm
Charge photo-generation and
recombination in conjugated
polymer donor/ fullerene acceptor
bulk heterojunction solar cells
Attila J. Mozer, Tracey M. Clarke
ARC Centre of Excellence for Electromaterials Science, Intelligent
Polymer Research Institute, University of Wollongong, AIIM
Building, Innovation Campus, Squires way, North Wollongong,
NSW 2500, Australia,
attila@uow.edu.au, tclarke@uow.edu.au
Biography
Dr Mozer is an Australian Research Fellow (2011 -)
and a Senior Research Fellow (2010 -) at the
Intelligent Polymer Research Institute at the
University of Wollongong. Dr Mozer is the lead
chief investigator of three Australian Research
Council grants focused on developing costefficient
solar energy conversion systems using
organic solar cell technology. His main expertise is
studying solar cell efficiency-determining charge
photo-generation and recombination reactions
using time-resolved optical and electronic probes.
Dr Mozer has a significant track record in two of
the major organic solar cell architectures: donor /
acceptor polymer bulk heterojunction solar cells
and dye-sensitised photo-electrochemical solar
cells.
He has an h index of 14, and has published (since
2004) three book chapters and 33 publications
with total citations exceeding 600. He has
obtained his PhD from Prof. Serdar Sariciftci, the
invertor of polymer solar cell technology at the Linz
Institute for Organic Solar Cells, Johannes Kepler
University, Linz, Austria in 2004. He has obtained
his MSc in Chemical Engineering from the
Budapest University of Technology and
Economics in 2002. Dr Mozer has received
research fellowships including the Australian
Research Council ARF Fellowship (2011 -), the
Japanese Society for the Promotion of Science
Short-Term Visiting Fellowship (2011 -) and
Postdoctoral Fellowship (2005). He is the Team
Leader of the Solar Energy Research Strength at
the Intelligent Polymer Research Institute, and the
member of the ARC Centre of Excellence for
Electromaterials Science (ACES) Centre Executive.
Abstract
Ultrafast photo-induced electron transfer between
a photo-excited conjugated polymer (electron
donor) and fullerene (acceptor) was first reported
in 1992 by Sariciftci et al.1 This initial discovery has
led to a number of important applications in photodetectors,
bio-sensors, light-sensitive field-effect
transistors and plastic solar cells.2 The efficiency
of the first bulk-heterojunction (plastic) solar cells,
where an intimate mixing of the electron donor /
electron acceptor phases created large surface
area for efficient charge separation, was < 1%.
This year, the best reported certified efficiencies
surpassed 8%3 making this low-cost technology
commercially viable. Two of the most
fundamentally important questions still unresolved
are (i) “What is the minimum thermodynamic
driving force (approximately corresponding to the
potential difference between the ionisation
potential of photo-excited donor and the electron
affinity of the acceptor) required for efficient charge
separation?”; (ii) “What governs charge
recombination of the photo-induced charge
carriers and how to minimise charge
recombination in a well-intermixed donor/acceptor
blend with high internal surface area?” Relevant to
answering both of these questions is determining
the optimum donor/acceptor domain size leading
to high charge separation yield and slow
recombination.
In this presentation we will show that relatively
large driving force is required for efficient charge
separation in the benchmark regioregular
poly-3-hexylthiophene / PCBM bulk
heterojunction.4 Using sub-ns and femtosecond
transient absorption spectroscopy, the kinetics of
charge photo-generation in a series of low
bandgap polymers with deep lying LUMO energy
and thus small thermodynamic driving force will be
presented.
Furthermore, in 2005 we have shown using
integral mode time-of-flight and photo-induced

charge extraction by linearly increasing voltage
(photo-CELIV) techniques that bimolecular
recombination is significantly reduced in
regioregular P3HT/PCBM mixture compared to the
widely-accepted diffusion-controlled Langevin
recombination model.5 This observation was
attributed to the highly ordered, nanofibre-like
morphology of P3HT in annealed P3HT/PCBM
blends, reducing the chance for the electron and
hole to meet and recombine. This year, we have
reported reduced recombination in a novel
silole-based low bandgap polymer/PCBM blend,6
which enables the fabrication of relatively thick (up
to 300 nm) photoactive layers without a significant
drop in charge collection efficiency. A chemically
very similar polymer mixed with PCBM shows the
typically observed Langevin recombination
kinetics, yet its morphology is virtually identical to
the reduced recombination blend, indicating that
the origin of reduced recombination may be much
more complex than originally though. Alternative
explanations will be presented.
1. N.S. Sariciftci, L. Smilowitz, A.J. Heeger and F. Wudl, Science
258 (1992) 1474.
2. C. J. Brabec, N. S. Sariciftci, and J. C. Hummelen, Adv. Funct.
Mater. 11 (2001) 11, 15
3. http://www.konarka.com/index.php/site/pressreleasedetail/
konarkas_power_plastic_achieves_world_record_83_
efficiency_certification_fr
4. T. M. Clarke and J. R. Durrant, Chem. Rev. 110 (2010) 6736.
5. A. Pivrikas, G. Juska, A. J. Mozer, M. Scharber, K. Arlauskas, N.
S. Sariciftci, H. Stubb, and R. Osterbacka, Phys. Rev. Lett. 94
(2005) 176806-1
6. T. M. Clarke, D. B. Rodovsky, A. A. Herzing, J. Peet, G. Dennler,
D. DeLongchamp, C. Lungenschmied, and A. J. Mozer, Adv.
Energy Mater. (2011), published online, DOI: 10.1002/
aenm.201100390
K.9 4:30pm – 5:00pm
Towards High-Efficiency Microalgae
Biofuel Systems
Ben Hankamer
Institute for Molecular Bioscience, The University of Queensland,
Brisbane, Qld 4072, Australia
Email : b.hankamer@imb.uq.edu.au, Tel : +61 7 334 62012, Fax :
+61 7 334 62103
Biography
PhD: Imperial College London (1990-1994)
Post Doc/Research lecturer: Imperial College
London (1994-2002)
Biographies and Abstracts
Monday 5 December - Session 4
Principle Investigator: Institute for Molecular
Bioscience, The University of Queensland
(2002-onwards)
Director: Solar Biofuels Consortium (www.
solarbiofuels.org) (2006-onwards)
Over the past 10 years, Ben Hankamer has
focused on the development of environmentally
friendly high-efficiency biofuel production systems.
This area represents a rapidly expanding
biotechnology. His specialization is in the structural
biology of the photosynthetic machinery, which
drives the conversion of solar energy into chemical
energy (fuels) and has published extensively on the
water splitting Photosystem II complex, its light
harvesting antenna system and V-type ATPase
(Nature, Nature Structural Biology, TIBS, PNAS).
Using this knowledge of the photosynthetic
machinery, he embarked on the targeted
engineering of the green alga Chlamydomonas
reinhardtii for high-efficiency biofuel production. To
facilitate the development of high efficiency biofuel
systems he founded the Solar Biofuels Consortium
(www.solarbiofuels.org) which he now directs. The
consortium includes eight international teams and
conducts economic analysis, bio-discovery,
marine biology, structural biology, molecular
biology, microbiology, genomics, metabolomics,
culture optimisation and bioreactor scale up within
a coordinated research program of parallel
research streams.
Abstract
The Stern Review (The Economics of Climate
Change) and the reports by the Intergovernmental
Panel on Climate Change have left little doubt that
concerted action is needed to develop CO2 free
energy technologies. Indeed to stabilize global
temperature increases below 2oC as agreed in the
United Nations Climate Change Conference in
Cancun has been reported to require CO2
emissions stabilization by 2010-2015.
The importance of CO2 neutral fuels in this
process is highlighted by the fact that fuels make
up ~80% of the global energy market. In contrast
global electricity demand accounts for only 17%.
Yet despite the importance of fuels, almost all CO2
free energy production systems under
development are designed to drive electricity
generation (e.g. clean-coal technology, nuclear,
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68
Biographies and Abstracts
Monday 5 December - Session 4
photovoltaic & wind). In contrast, and indeed
almost uniquely, bio-fuels target the much larger
fuel market and so in the future, have clear
potential to play an increasingly important role. The
presentation will provide an overview of the
physical constraints of photobiological biofuel
production in terms of area, solar energy and
nutrient requirements before presenting advances
made in terms of developing microalgal biofuel
systems.
Notes
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Session 5 – Theatre 2
5.1.1 10:30am – 10:45am
A novel Molecular Dynamics
approach for quantitative prediction
of adhesion and wettability:
application to responsive surfaces
George Yiapanis1 , David Henry2 , Evan
Evans3 , Irene Yarovsky1 1 Applied Sciences, RMIT University, GPO BOX 2476V, 3001,
Melbourne, Victoria
2 Chemical and Mathematical Sciences, Murdoch University,
Western Australia
3 BlueScope Steel Research, Port Kembla, NSW
Biographies and Abstracts
Tuesday 6 December - Session 5
Biography
George Yiapanis received his doctoral degree in
applied physics from RMIT University in Melbourne
in 2010. He is currently a postdoctoral fellow at
RMIT University, in the Materials Modelling
Simulation group, directed by Prof. Irene Yarovsky.
His research interest is exploring full atomistic
modelling of various organic and inorganic
surfaces and interfaces. Presently, he is working
on the design of responsive self-cleaning polymer
surfaces, and of self-assembled monolayers as
stable evaporation suppressants.
Abstract
Adhesion is an important property that dominates
a multitude of processes ranging from fouling to
nano-particle formation. For a two component
system, adhesion can be readily measured
through atomic force microscopy or contact angle
measurements.1,2 However, acquiring a
quantitative prediction of adhesion within a
three-component system, is not an easy task. An
example of a three-component system includes a
surface interacting with a dirt particle in a liquid
medium. Here, using atomistic Molecular Dynamic
modelling techniques, we developed an approach
to carry out this exact task, allowing us to predict
the dirt-shielding qualities of various responsive
polymeric brushes. The surface models have been
carefully designed to mimic the responsive
stay-clean behaviour of the Lady’s Mantle leaf,3
and include polyethylene glycol grafted organic
and inorganic substrates.
Our novel approach involves measuring the
contact-angle of nano-sized water droplets on soft
deformable surfaces (Figure 1a.). Using this new
approach together with our previously developed
in-silico force measurements4, we investigate the
adhesion of the carbon based contaminants5 onto
the adaptive surfaces in both dry and aqueous
environments. Our results show that polyethylene
glycol brushes impart dirt-shielding qualities
provided that the substrate is sufficiently
hydrophilic and robust (Figure 1b.). Analogous to
the flexible hairs of the Lady’s Mantle leaf, the
polyethylene glycol molecules provide a repulsive
energy barrier that prevents adhesion of
contaminants in water. Our new approach can be
applied to test wettability and adhesion of
essentially any material
Figure 1 a. Contact angle measurements using classical molecular
dynamics. b. Contour map of an adaptive surface which
comprises of PEG brushes on top of a robust silica substrate.
(1) Almazán-Almazán, M. C.; Paredes, J. I.; Pérez-Mendoza, M.; M.
Domingo-García a; López-Garzón, F. J.; Martínez-Alonso, A.;
Tascón, J. M. D. Journal of Colloid and Interface Science 2006,
293, 353.
(2) Lee, S. A.; Oh, S. H.; Lee, W. Journal of Colloid and Interface
Science 2009, 332, 461.(3) Otten, A.; Herminghaus, S.
Langmuir 2004, 20, 2405.
(4) Yiapanis, G.; Evans, E.; Henry, D. J.; Yarovsky, I. J Phys Chem C
2010, 114, 478.
(5) Yiapanis, G.; Henry, D. J.; Evans, E.; Yarovsky, I. In
Nanotechnology in Australia: Showcase of Early Career
Research in Australia; Kane, D. M., Micolich, A. P., Rabeau, J.
R., Eds.; Pan Stanford Publishing: 2011.
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70
Biographies and Abstracts
Tuesday 6 December - Session 5
5.1.2 10:45am – 11:00am
What can we learn from large-scale
ab initio calculations of ionic liquids?
Ekaterina I Izgorodina1 1 School of Chemistry, Monash University, Wellington Rd,
Clayton, VIC 3800, AUSTRALIA
Biography
Dr Ekaterina (Katya) Pas obtained her PhD from
the University of Muenster, in the field of
Theoretical Chemistry in 2004. Immediately after
her PhD Katya accepted a postdoctoral position
with Dr Michelle Coote at ANU to study free radical
and RAFT polymerisation. In 2006 she moved to
Monash University as a Research Fellow in the
Ionic Liquid group of Prof. Doug MacFarlane. In
2007 she was awarded an ARC APD Fellowship to
study ionic materials from the first principles and
appointed as a lecturer in the School of Chemistry.
Currently, Katya is a Senior Lecturer at Monash
Univeristy leading a research group that
specialises in fully ab initio calculations of ionic
liquids and liquid electrolytes.
Abstract
Large-scale calculations of archetypical ionic
liquids consisting up to eight ion pairs1 were
performed at the MP2 level of theory in
combination with a triple-ξ doubly polarised
Ahlrichs type basis set, TZVPP. These calculations
showed that dispersion interactions due to
electron correlation increased rapidly with
increasing number of ion pairs in the cluster. For
imidazolium-based ionic liquids the dispersion
contribution was up to 20% of the overall energy,
thus emphasising the importance of electron
correlation effects as cluster size increases. These
results also reflect the presence of all possible
inter-ion interactions, including like-ion dispersion
interactions such as inter-alkyl chains. Using the
Fragment Molecular Orbital approach in
combination with the MP2 level of theory2
three-body inter-ion interactions were established
to be necessary in describing Coulomb forces with
accuracy below 1 kJ mol-1, whereas two-body
corrections were already enough for dispersion
forces. A thorough analysis of charge transfer
between ions with increasing cluster size was
performed to understand its influence on the
Coulomb and induction forces in ionic systems. To
quantitatively evaluate the fundamental
components of the interaction energy such as
Coulomb, induction, repulsion, charge transfer and
dispersion, accurate energy decomposition
schemes are required. Currently available
schemes either cannot be used beyond a single
ion pair such as Symmetry-Adapted Perturbation
Theory (SAPT)3 or are not designed to treat
charged species such as Effective Fragment
Potential (EFP).4 Here we present a detailed
analysis of these two widely used decomposition
schemes in attempt to devise a new scheme for
decomposing interaction energies of ionic systems
into fundamental components.
5.1.3 11:00am – 11:15am
Formation of Radical Products From
Activation of Phospholipid Ozonides
Shane Ellis
University of Wollongong
Biography
Shane Ellis completed his degree in
Nanotechnology from the University of Wollongong
in 2008. He is currently in the 3rd year of his PhD
at the University of Wollongong looking at the
applications of surface ionization mass
spectrometry approaches for lipid analysis and
imaging. He spent 2 months at Professor Graham
Cooks Lab at Purdue University, Indiana, USA
looking at the distribution of lipids in the human
lens by desorption electrospray ionization mass
spectrometry imaging. His research is partly
funded by the Centre of Excellence for Free
Radical Chemistry and Biotechnology.
Abstract
Ozone is responsible for the oxidation of many
unsaturated organic compounds in the
atmosphere. These reactions can occur in the gas
phase or on surfaces such as those provided by
organic aerosols. Importantly, ozonolysis can give
rise to radical species (e.g. OH radicals) that are
able to propagate further oxidation, although the
precise mechanisms of radical formation are not
well understood. Using desorption electrospray

Biographies and Abstracts
Tuesday 6 December - Session 5
ionisation mass spectrometry we have observed
products arising from the reaction of ambient
ozone (present in laboratory air) with unsaturated
lipids. For example, analysis of the unsaturated
phosphatidylcholine (PC), PC (18:1n9/16:0) gives
rise to an abundant ion 48 Da above the [M+Na]+
ion of the parent lipid. Activation of the putative
ozonide ion, [M+Na+O3]+, by collision induced
dissociation (CID) on an ion-trap mass
spectrometer revealed ions corresponding to the
mass of aldehydes and carbonyl oxides (i.e.,
Criegee intermediates) although the structure of
the latter has not been determined. Such ions are
shown to be indicative of the double bond position
and have analytical utility in the structure
elucidation of naturally occurring unsaturated
lipids. In addition, dissociation of the ozonides
yields several product ions with masses
suggestive of odd–electron species. These radical
ions are proposed to form following homolytic
cleavage of the O-O bond of the secondary
ozonide and consistent with this, their mass is
observed to shift with the double bond position(s)
in the parent lipid. The structure of these radical
ions has been further probed using subsequent
fragmentation via CID (i.e., MSn) and ion-molecule
reactions with adventitious dioxygen present in the
ion-trap. Both approaches show behaviour
consistent with radical formation. These results
confirm the production of radicals directly from the
decomposition of activated secondary ozonides in
the gas phase and may have significance for
understanding the fate of long-lived ozonides in
the atmosphere. Finally the characteristic
fragmentation behaviour of secondary ozonides
(described above) will be compared to
[M+Na+O3]+adducts formed in gas phase
encounters between ozone and ionized,
unsaturated lipids [1] and may provide evidence for
the existence of the more elusive primary ozonide
in the latter experiment.
References
(1) Poad, B. L. J., Pham, H. T., Thomas, M. C., Nealon, J. R.,
Campbell, J. L., Mitchell, T. W., Blanksby, S. J., Ozone-Induced
Dissociation on a Modified Tandem Linear Ion-Trap: Observations
of Different Reactivity for Isomeric Lipids. J. Am. Soc. Mass
Spectrom. 2010, 21, 1989-1999.
5.1.4 11:15am – 11:30am
The Distal Effect of Electron-
Withdrawing Groups on the Stability
of Peptide Enolates and its
Exploitation in Synthesis
Junming Ho1 , Christopher J. Easton1 , Michelle
L. Coote1 1 ARC Centre of Excellence for Free Radical Chemistry and
Biotechnology, Research School of Chemistry, Australian
National University, Canberra, ACT 0200, Australia
Biography
Junming Ho is a post-doctoral fellow with Michelle
Coote at the ANU where he also recently
completed his PhD. His research involves the use
of computational and practical chemistry to
understand chemical reactivity and their
associated applications in synthesis and
biochemistry.
Abstract
Normally amides and esters exhibit much weaker
carbon acidities than ketones mainly as a result of
the effects of the various carbonyl carbon
substituents to attenuate resonance stabilisation of
the corresponding enolates. In a recent
computational study,1 we predicted that
N-electron-withdrawing substituents, hydrogen
bonding and protonation at amide nitrogen
selectively increase the acidity of a distal proton
adjacent to the amide carbonyl, to the extent that
the a-carbonyl acidity of some N-substituted
amides exceeds that of typical ketones. In this
contribution, the origin of the distal effect is
examined using high-level ab initio methods and
its relevance to certain enzymatic reactions is
highlighted. Using a combination of theory and
experiment, the synthetic utility of the effect is also
demonstrated through the controlled
stereochemical inversion of amino acid
derivatives.2
1. Ho, J.; Easton, C. J.; Coote, M. L. J. Am. Chem. Soc. 2010,
132,5515.
2. Ho, J.; Coote, M. L.; Easton, C. J. J. Org. Chem. 2011, 76,
5907.
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72
Biographies and Abstracts
Tuesday 6 December - Session 5
5.1.5 11:30am – 11:45am
Molecular magnetic properties:
benchmarking and applications
David J. Wilson1 , Trygve Helgaker 2 , Antonio
Rizzo3 1 La Trobe Institute for Molecular Science, La Trobe University,
Melbourne, Australia.
2 Centre for Theoretical and Computational Chemistry, University
of Oslo, Norway.
3 ICPF-CNR, UoS di Pisa, Area della Riccerca, via G. Moruzzi 1,
56124 Pisa, Italy.
Biography
David Wilson is a senior lecturer in the Dept of
Chemistry at La Trobe University, which he joined
in 2005. He completed a PhD under Prof Ellak von
Nagy-Felsobuki in Newcastle, before a
postdoctoral position at the University of Oslo with
Prof. Trygve Helgaker. Dr Wilson is a contributing
author to the Dalton program. His research
interests include theoretical development and
applications, which span from small molecules
(gas-phase chemistry) to ‘medium’ size (metal
chemistry) and very large molecules (biomolecular
modeling).
Abstract
We report benchmark studies of DFT and
CCSD(T) calculated magnetizabilities for a series
of 22 fluorine-containing molecules, systems for
which the calculation of magnetic properties is
particularly challenging. All calculations make use
of London atomic orbitals (the GIAO approach),
while basis sets up to aug-cc-pV6Z have been
employed. Statistical analysis of results provides
insight into the performance of various density
functionals in the calculation of magnetic
properties.
Several applications will be presented, with results
compared to available experimental data. This
includes the set of fluorine containing molecules,
for which the link with aromaticity will be explored.
An investigation of PF3 indicates unusually slow
basis set performance (up to aug-cc-pV6Z), and
the need to explicit core basis functions (up to
aug-cc-pCV5Z). Results for ferrocene will also be
presented. These coupled cluster results represent
the largest and likely most accurate calculations
ever reported for molecular properties of this
fascinating molecule.
5.1.6 11:45am – 12:00pm
Molecular Design Rules for
Frequency-Based, Universal
Quantum Computers
Laura K. McKemmish 1,2* , David J.
Kedziora3 , Graham R. White3 , Noel S. Hush4 ,
Jeffrey R. Reimers1 1 School of Chemistry, The University of Sydney, Sydney, NSW
2006 Australia
2 Research School of Chemistry, Australian National University,
Canberra, ACT 2601 Australia
3 School of Physics, The University of Sydney, Sydney, NSW
2006 Australia
4 School of Molecular Biosciences, The University of Sydney,
Sydney, NSW 2006 Australia
* laura.mckemmish@gmail.com
Biography
Laura McKemmish completed her Honours at the
University of Sydney in 2010, where her research
on frequency-based quantum computers and
quantifying the accuracy of adiabatic
approximations was inspired by the benefits that
considering theoretical chemistry and quantum
computation together. She has just started a PhD
at the Australian National University on developing
a method of quantifying the accuracy of
computational chemistry calculations. She has
researched a variety of topics, including
spectroscopy, biophysics, computational
chemistry (of the Creutz-Taube ion and aromatic
dimers), ionic liquids, quantum consciousness
and astronomy. She has chosen to specialise in
theoretical chemistry.
Abstract
NMR is a widely used technique through chemistry
and biochemistry, but the extensive experimental
equipment and nuclear-spin-manipulation
techniques that have been developed for these
applications can also be applied to allow
molecules to function as nuclear-spin-based
quantum registers for quantum computing
applications. Quantum computers and quantum
information processors (QIPs) present a promising

Biographies and Abstracts
Tuesday 6 December - Session 5
paradigm of computing, including exponential
speedup to computational simulation of quantum
systems [1]. Quantum registers differ from the
classical bits found in modern digital computers as
they do not need to exist only in eigenstates but
can also exist as an arbitrary linear combination of
eigenstates [2]; the simplest quantum register is a
qubit made from a quantum system that has two
discrete eigenstates, such as the spin of a 1H or
13C nucleus. In an NMR-based QIP (or other
molecular-based QIPs such as those built on
rotational, electronic, or vibrational spectroscopy),
systematically controlled electromagnetic pulses
applied to the whole system implement all gates to
allow computation[1]. Two types of gates are
required in a QIP, one-qubit gates which act on
single spins, and two-qubit gates which modify
one spin based on the state of another.
Over 46 molecules have been used in NMR-based
QIPs, the two largest molecules studied containing
7 and 12 qubits (independently controllable
nuclear spins). Some molecules function well,
others poorly. For example, histidine (12 qubits)
allows the spin of an initially polarized chin proton
to be passed to just 7 of other 11 qubits. We
provide the first explanation of why this is the case,
describing basic molecular design rules for NMR
(etc) quantum register design. We show how
standard GAUSSIAN calculations for the NMR (etc)
spectra properties can be used to make
quantitative predictions of functionality, as well as
a series of simplistic chemical structure rules for
qualitative prediction and analysis. Our analysis is
based on the effects that spectral congestion has
on inhibiting the operation of two-qubit gates.
The ability to scale NMR quantum computers to
larger sizes is severely limited because of many
factors. Our analysis of the two-qubit gates shows
that in general their construction becomes
exponentially more difficult as the register size
increases. By following our design rules, this
scaling can be reduced to linear or near-linear
scaling, thus enabling much larger registers to be
demonstrated. We use GAUSSIAN calculations
for an acetylene tetramer to show how a fully
functional 25-qubit register could be designed.
Session 5 – Main Theatre
5.2.1 10:30am – 10:45am
Single molecule fluorescence
microscopy: visualising DNA
replication and repair dynamics
within living E. coli cells
Andrew Robinson1 , Meghna Patel2 ,
Elizabeth A. Wood3 , Roger Woodgate 4 , Michael M.
Cox3 , Myron F. Goodman2 and Antoine M. van
Oijen1 1 Zernike Institute for Advanced Materials, University of
Groningen, Groningen 9747 AG, The Netherlands
2 Departments of Biological Sciences and Chemistry, University
of Southern California, Los Angeles CA 90089, USA
3 Department of Biochemistry, University of Wisconsin-Madison,
Madison, Wisconsin 53706, USA
4 Laboratory of Genomic Integrity, National Institute of Child
Health and Human Development, National Institutes of Health,
Bethesda, Maryland 20892-3371, USA
Biography
Andrew completed his PhD research in 2007 in
Bridget Mabbutt’s structural biology lab at
Macquarie University, Sydney. He then moved to
Wollongong to work as a postdoc in Nick Dixon’s
biochemistry lab, where he used xray
crystallography to study the proteins involved in
DNA replication in bacteria. Late 2010 he moved to
Antoine van Oijen’s single molecule biophysics lab
at the University of Groningen in The Netherlands,
where he is studying DNA replication and repair in
live bacterial cells.
Abstract
Decades of genetic studies and in vitro analyses
have painted a remarkably detailed picture of how
bacteria maintain their chromosomes. By carefully
coordinating the activities of individual DNA
replication and repair proteins, bacteria are
capable of faithfully maintaining their genetic
information whilst dividing rapidly and responding
to changing environmental conditions. Underlying
this ability are highly dynamic protein interaction
networks that are constantly remodelled in order
to facilitate discontinuous replication of the
chromosomal DNA and to allow any sites that
become damaged to be repaired. While these
networks and their players are now generally well
73

74
Biographies and Abstracts
Tuesday 6 December - Session 5
understood, how these processes are put into play
during the course of a cell cycle and how stressed
cells transition from DNA replication to repair
remain to be determined.
We are studying the coordination of DNA
replication and repair processes in living E. coli
cells using recently developed methods for
fluorescence microscopy with single molecule
level sensitivity. Such sensitivity is necessary as
most DNA replication and repair proteins are
maintained at very low copy number and are
active at only a few select sites within the cell. We
are using strains of E. coli in which subunits of
DNA pol III and DNA pol V are fused to bright
fluorescent proteins, allowing us to measure
cellular protein concentrations and quantify
proteins localised at replication and repair sites.
We have developed techniques that uniquely allow
us to make such measurements within rapidly
growing and dividing cells. By imaging cells within
flow devices, we can also introduce DNA
damaging agents and determine their effect on the
replication and repair processes. We are using
these techniques to characterise multi-fork
replication in rapidly dividing cells and to monitor
changes in the steady state concentration and
localisation of DNA pol V following UV-induced
DNA damage.
5.2.2 10:45am – 11:00am
Structured IlluminationMicroscopy
of Living Cells
Liisa M. Hirvonen, Trevor A. Smith
Ultrafast and Microspectroscopy Laboratories, ARC Centre of
Excellence for Coherent X-Ray Science, School of Chemistry,
University of Melbourne, Australia
email: liisah@unimelb.edu.au
Biography
Liisa did her BsC and Phd in King’s College
London. During her PhD, Liisa built one of the first
setups for structured illumination microscopy
under the supervision from Professor Rainer
Heintzmann. After completing her PhD, she took a
position as a post-doc in the School of Chemistry,
University of Melbourne, to develop superresolution
microscopy techniques in the Ultrafast
and Microspectroscopy Laboratories under the
direction of Associate Professor Trevor Smith.
Abstract
In recent years, several new techniques have been
proposed for surpassing the diffraction limit in
fluorescence microscopy [1]. One of these
techniques is structured illumination microscopy
(SIM) [2, 3], where a fine grating is
projected onto the sample, and the final image is
reconstructed froma set of images taken at
different grating positions. Although the resolution
improvement is limited to a factor of two, pulsed
lasers, scanning or special properties of the
fluorophores are not needed. It has been shown
that SIM is fast enough to image slowly moving
structures in living
cells [4, 5]. SIM is based on the projection of a fine
grating into the sample, and gathering information
in the form of Moir´e fringes. When two highfrequency,
i.e. high spatial resolution patterns are
multiplied (superimposed), Moir´e fringes appear.
These fringes carry information in low resolution
format, which is observable through a normal light
microscope. If the known grating pattern is then
removed computationally from the unknown
sample pattern, it is possible to restore previously
unobservable details about the sample. For the
restoration of the high resolution information a
minimum of three images are needed where the
grating pattern is moved between the images, and
a minimum of 3 grating directions are needed for
isotropic resolution improvement in the lateral
plane.
(a) (b) (c)
Figure 1: Moir´e fringes: If an unknown sample
pattern (a) is multiplied by a known illumination
pattern (b), Moir´e fringes appear
(c). If the illumination pattern is removed
computationally, previously unobservable details
can be restored. structured illumination provides a
cheap and relatively easily implementable method
for improving lateral resolution and reducing
out-of-focus blur in fluorescence microscopy. No
special properties are required from the
fluorophores, and pulsed lasers and scanning are
not needed. We are currently using this method to
image both living and fixed mammalian cell

samples, as well as living yeast cells, polymers for
solar cells, and botanical samples.
References
[1] L. M. Hirvonen, T. A. Smith, “Imaging on the nanoscale:
Super-resolution fluorescence microscopy,” Australian Journal of
Chemistry 64, 41-45 (2011).
[2] R. Heintzmann, C. Cremer, “Laterally modulated excitation
microscopy: Improvement of resolution by using a diffraction
grating,” Proceedings of SPIE 3568, 185-195 (1998).
[3] M. G. L. Gustafsson, “Surpassing the lateral resolution limit by a
factor of two using stuctured illumination microscopy,” Journal of
Microscopy 198, 82-87 (2000).
[4] P. Kner, B. B. Chhun, E. Griffis, L.Winoto, M. G. L. Gustafsson,
“Super-resolution video microscopy of live cells by structured
illumination,”Nature Methods 6, 339-342 (2009).
[5] L. M. Hirvonen, K. Wicker, O. Mandula, R. Heintzmann,
“Structured illumination microscopy of a living cell,” European
Biophysics Journal38, 807-812 (2009).
5.2.3 11:00am – 11:15am
Differential Dynamic Microscopy and
Dynamic Light Scattering studies of
Bacterial Motility
R. Nixon-Luke 1 , G. Bryant1 , C. Carnovale1 , V.
A. Martinez 2 , W.C.K Poon2 1 School of Applied Sciences, RMIT University, GPO Box 2476,
Melbourne, Victoria, 3000
2 SUPA and COSMIC, School of Physics & Astronomy, The
University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ,
United Kingdom
Biographies and Abstracts
Tuesday 6 December - Session 5
Biography
Reece complete a Bachelor of Applied Science
(Honours) at RMIT University and has commenced
his PhD. His research interests include
applications of light scattering techniques and
development of novel instrumentation
Abstract
Cell motility is an important characteristic of many
biological processes, and is ubiquitous in
unicellular organisms such as bacteria. The
bacterium Escherichia coli is a well studied model
system for understanding cell motility. These cells
execute random walks by alternating between
swimming (or ‘running’) at speeds of tens of
microns per second (for ~ 1 second), and then
tumbling (changing direction) for 0.1 s.
Dynamic Light Scattering (DLS) has long been
used for the measurement of Brownian motion in
colloids, proteins and macromolecules, and is a
routine technique for the determination of particle
size in such Brownian systems. Dynamic light
scattering can make accurate measurements over
a very short timescale, is non-invasive, requires
very little sample, and has a high sensitivity,
making it a perfect tool to investigate living
biological cells.
Early in the development of DLS, its potential for
studying bacterial motility was investigated [1];
however, these investigations were complicated by
a lack of understanding of the details of cell
motility, as well as equipment limitations, and were
never seriously pursued. Recently, a new
microscope technique has been developed based
on the principles of DLS. This technique, called
differential dynamic microscopy (DDM), has been
applied to the study of colloidal dispersions [2],
and found to be a suitable tool in the investigation
of bacterial motility [3].
We report on preliminary investigations of the
motility of E. Coli, and other motile bacteria, using
DDM and DLS. We observe that the correlation
functions exhibit two distinct decays: the faster
decay being due to the self-propelled velocity
(motility), and the second, slower decay being due
to the normal diffusive motion.
These functions were analysed using the model
proposed by Nossal, Chen and Lai [1] and revised
by Stock [4], which was found to provide good
agreement under most conditions. This analysis
yields the velocity distributions, the average
velocities and the fraction of non-motile cells. The
diffusion coefficients of the cells can be either an
input into the model, or a free parameter. We will
discuss the application of the techniques to other
motile systems.
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Biographies and Abstracts
Tuesday 6 December - Session 5
5.2.4 11:15am – 11:30am
Revisiting Boltzmann: disentangling
solid-state NMR measurements of
heterogeneous model membrane
systems
John D. Gehman1 , Marc-Antoine Sani1 ,
Frances Separovic1 , Anil K. Mehta2 1 School of Chemistry, Bio21 Institute, University of Melbourne,
VIC 3010 Australia; jgehman@unimelb.edu.au
2 Chemistry Department, Emory University, Atlanta, GA 30322
USA
Biography
After getting his undergraduate degree at Temple
University in Philadelphia, John worked for five
years at Merck in the Research Laboratories as a
biochemist in the Department of Antiviral
Enzymology. He moved next to Yale for his PhD,
where he shifted to more physical disciplines,
working and studying between the Biophysics
(MB&B) and (Physical) Chemistry departments.
After a short post-doc, also at Yale, John moved
again a bit further to Australia, where he is now an
Australian Research Council Future Fellow in
Chemistry at Melbourne University. He has two
beautiful daughters who stay up way too late,
especially when he’s in charge.
Abstract
On the one hand, solid-state NMR is ideal for
studying disordered materials that are difficult or
impossible to study by other means; on the other
hand, analysis of the resulting data is often
challenging, and requires iteration with extensive
modelling. We will discuss two examples:
heterogeneous distributions of chemical shift
tensor parameters, and distributions of
internuclear distances in rotational-echo doubleresonance
(REDOR) data. A method that uses an
adaptation of Boltzmann statistics maximum
entropy will be described, which provides for a
model-free approach to analysis of this type of
troublesome data.
In the case of REDOR data, the method can reveal
multiple distances with relatively few data points,
which is of particular benefit in application to
biological systems where relaxation limits signal
lifetimes. This reverses the practice of comparing
REDOR data to dephasing curves simulated for
several preconceived structural models, by
providing the information necessary to construct
models based on unbiased data analysis. In the
case of chemical shift tensor analysis, we apply
the method to arbitrarily complex phospholipid
mixtures as model membranes systems for
analysis of subtle perturbations, for example by
association with antimicrobial peptides.
The Boltzmann Statistics method also offers
intriguing philosophical implications, as it gives the
broadest, and perhaps most “honest” probability
distribution consistent with the data, but also helps
to determine which data points hold the greatest
information content, such that experimental time
can be focussed on gaining the best signal-tonoise
where it is likely to benefit most.
5.2.5 11:30am – 11:45am
Liposomes: Stable or Kinetically
Trapped?
Adam Mechler1 and Mubin S. Huda2 1 Department of Chemistry, La Trobe University, Bundoora
Campus, Bundoora, VIC 3086, a.mechler@latrobe.edu.au
2 Department of Chemistry, La Trobe University, Bundoora
Campus, Bundoora, VIC 3086, m.mubin@students.latrobe.edu.
au
Biography
Dr. Mechler has obtained his PhD at the University
of Szeged, Hungary, in physics/materials science.
His interest in biological nanostructures lead to 3
years of postdoctoral work at the University of
Califonia, Santa Barbara on the atomic force
microscopy of biomolecules, and then a research
fellowship at Monash University with a sharpening
focus on lipid membranes. He joined La Trobe
University as a senior lecturer in 2009.
Abstract
Liposomes: spherical vesicles of phospholipid
bilayers are among the most studied selfassembled
structures, largely due to their
relevance to biology through mimicking cell
membranes, and the potential applications in
biotechnology to support enzymatic processes in
vitro. From the physical chemistry point of view,

Biographies and Abstracts
Tuesday 6 December - Session 5
phospholipid self-assembly might be seen as a
spontaneous process, where the size and shape
of the liposomes is the result of a free energy
minimizing process. In this view the energy
increase inherent in the curvature tension is
compensated for in entropic terms, such as the
entropic advantage of a highly dispersed system
over the well ordered lamellar phase. Thus the
liposome suspension is in equilibrium; the
liposomes are thermodynamically stable. However,
the potential of liposomes for reaching an
equilibrium is frequently questioned. Calculations
of lipid residence time in the aggregate based on
critical micelle concentration predict that
liposomes would not change on an observable
timescale; they are kinetically trapped.
Controversially, in the literature several articles
empirically support the thermodynamic equilibrium
model.
Here we present the evidence of size evolution of
liposome suspensions from dynamical light
scattering measurements for three different
compositions: neat dimyristoyl phosphatidylcholine
(DMPC), DMPC:cholesterol 9:1 and
DMPC:DM phosphatidyl-glycerol 4:1. In all cases,
an initial broad and highly polydisperse population
evolved into a well defined, stable size distribution,
which was bimodal for DMPC and
DMPC:cholesterol 9:1. We used fluorescent
imaging to confirm that the reduction in
polydispersity was not caused by sedimentation.
We demonstrate that polydispersity can be
caused by the aggregation of small liposomes,
and that temperature alone is a sufficient, and
reversible, control of this aggregation. It is thus
unclear if the observed reduction in polydispersity
over time is the result of the slow separation of
liposomes from aggregates or an actual evolution
of the sizes of individual liposomes (or a mix of the
two); the final narrow size distributions however
confirm that in either case liposomes appear to
form with a size preference. These results suggest
that the balance between the adhesive van der
Waals and repulsive steric (protrusion, undulation,
peristaltic etc) forces has a strong effect on the
population homogeneity of liposome suspensions.
5.2.6 11:45am – 12:00pm
The Effect of Crystallization on
Protein Quaternary Structure
Donald G Vanselow 1
1 nativeproteins.blogspot.com 54 Greenways Rd., Glen Waverley
VIC 3150, Australia. dvanselow@hotmail.com
Biography
Dr Vanselow is a Thermodynamicist and
Biochemist interested in the interaction of these
fields throughout his career. He was a Lecturer at
the University of Melbourne from 1975 to 1978 and
Research Scientist in CSIRO from 1979 to 1983.
He then worked in private industry before joining
Monash University as a Scientific Manager in
Biochemistry in 1989. His interest in protein
structure and function began there. He left
Monash in 1998 and has continued his research
while engaged in school-teaching.
Abstract
Protein crystallization involves the conversion of a
liquid protein-in-water phase into a crystalline
water-in-protein phase. NMR studies support the
view that the tertiary structures of proteins are
usually very similar in both phases, but because of
the size limitation of NMR it has been impossible to
accurately measure differences, if any, in the
quaternary structures (arrangements of subunits).
For want of any counter-proposal in the early days
of x-ray crystallography, it is now widely assumed
that crystallization has little or no effect on
quaternary structure.
This presentation will show how the various
measurements of the surface energy of aqueous
interfaces can be combined to reveal the chemical
potential of water as a function of distance from an
interface. This will be a refinement of an earlier
model [1]. The extra chemical potential of water
near an interface is responsible for the
hydrophobic effect, which, in turn, is responsible
for the binding of proteins to each other. The other
significant effect at protein-protein interfaces is
electrostatic. Detailed modelling [2] has shown that
this is usually repulsive relative to opening the
77

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Biographies and Abstracts
Tuesday 6 December - Session 5
interface to water because of the affinity of water
for charges (solvation energy).
For a model protein it will be shown that the
crowding accompanying crystallization weakens
the hydrophobic effect. Repulsion due to solvation
energy then opens the original interfaces leading
to further crowding elsewhere because the system
cannot expand. Ultimately the parts of the protein
that can come into contact are those with minimal
solvation energy - the so-called hydrophobic
patches. This is what is observed in crystals.
An animation of the protein dihydrodipicolinate
synthase (DHDPS) transforming from its native
ovoid shape [3] into the torus seen in crystals will
be shown.
Mention will be made of the advances in
understanding the mechanisms of protein function
that result from reassembly of crystal structures
into physically and biologically realistic forms.
Refs:
[1] Vanselow, D. G. 2002. Role of constraint in catalysis and
high-affinity binding by proteins, Biophys. J. 82: 2293–2303.
[2] Hendsch, Z. S., B. Tidor. 1994. Do salt bridges stabilize
proteins? A continuum electrostatic analysis. Protein Sci. 3:
211-226.
[3] The data-base of native protein structures is at www.
nativeproteins.net76.net/gallery/index.htm
Papers describing the structures and discussing related issues
are at http://nativeproteins.blogspot.com
Both sites are maintained by the author.
Notes
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Session 6 – Theatre 2
6.1.1 1:15pm – 1:45pm
Anion Photoelectron Spectroscopy
of Ionic Complexes and Clusters
Duncan A. Wild, Kim M. Lapere, Stephen G.
Dale, Allan J. McKinley
Chemistry, School of Biomedical, Biomolecular, and Chemical
Sciences, The University of Western Australia,
M313 35 Stirling Hwy, Crawley, WA, 6009,
duncan.wild@uwa.edu.au
Biographies and Abstracts
Tuesday 6 December - Session 6
Biography
Dr Duncan Wild completed a Bachelor of Science
with Honours at the University of Melbourne,
where he also undertook a PhD researching
infrared spectroscopy of size-selected anion
complexes and clusters. In 2003 he received an
Alexander Von Humbolt Fellowship to undertake
research at the Max Planck Institute for
Biophysical Chemistry in Göttingen, Germany.
During this time he investigated the timescales for
energy relaxation of carotenoids, spectroscopy of
neutral stilbene-alkane gas phase complexes, and
assisted in the construction of a photoelectron
spectrometer. Dr Wild came to The University of
Western Australia in 2007 where he has
constructed a Time Of Flight Mass Spectrometer
coupled to a photoelectron Spectrometer in order
to study anion-molecule complexes of
atmospheric and astronomic interest.
Abstract
To understand the reactions that occur between
radicals and molecules one ultimately requires an
intimate knowledge of the potential energy surface
governing the reaction. Such surfaces are routinely
produced from ab initio calculations however their
accuracy requires critical assessment. This can be
achieved by applying spectroscopy to radicalmolecule
complexes which are features of the
reactive potential energy surface.
At the University of Western Australia we have
constructed an apparatus which allows us to
perform photoelectron spectroscopy of mass
selected anion-molecule complexes and clusters.
The TOF-PES consists of a time of flight (TOF)
mass spectrometer for selection of a specific
anion-molecule complex, and a photoelectron
spectrometer (PES) to monitor the photoelectrons
detached by UV radiation. As mass spectrometry
is applied it is possible to investigate larger clusters
of the form X-…Mn in a step wise fashion, thereby
bridging the gap between gas and bulk phase
contexts.
We complement our experiments with high level
ab initio calculations (up to CCSD(T)/aug-cc-pvtz).
We predict structures and energetics for the
anion-molecule and radical-molecule van der
Waals complexes, to aid in interpretation of the
spectra. We also produce multi-dimensional
potential energy surfaces. This contribution will
highlight our recent work we have undertaken on
the halogen anion-molecule complexes and
clusters.
6.1.2 1:45pm – 2:00pm
Ion Mobility Mass Spectrometry
Reveals New Insights into Structure
and Assembly of Protein Complexes
Tara Pukala1 , Antonio Calabrese1 , Danielle
Williams1 , Yanqin Liu1 1 School of Chemistry and Physics, University of Adelaide, North
Terrace, Adelaide, SA, 5005, tara.pukala@adelaide.edu.au
Biography
Dr Tara Pukala obtained a PhD from the University
of Adelaide (with J.H. Bowie) which was followed
by a postdoctoral role at the University of
Cambridge, UK (with C.V. Robinson). She returned
to a lectureship position at the University of
Adelaide in 2008, where she has established a
research group focussed on the development and
application of mass spectrometric and related
technologies for the investigation of biomolecular
systems.
Abstract
Protein-protein interactions play important roles in
controlling cellular processes, and offer new
targets for therapeutic intervention. However, the
structural variability and transient nature of
biological complexes means their architecture and
interactions can be difficult to characterise using
traditional methods. Mass spectrometry has
emerged as a powerful tool for the analysis of such
79

80
Biographies and Abstracts
Tuesday 6 December - Session 6
systems, due to its ability to investigate protein
assemblies at all levels of structural complexity. In
particular, ion mobility-mass spectrometry (IM-MS)
provides not only mass but shape information of
native protein assemblies, making it possible to
define protein complex identity, stoichiometry, size,
structural arrangement and subunit interactions in
a single experiment.
Here we describe the design and synthesis of
novel mass spectrometry amenable cross-linking
reagents, which can be used to stabilise proteinprotein
interactions by forming covalent bonds,
and if cross-linked sites are identified, can yield
clues about protein binding interfaces. In tandem
with an IM-MS based approach, we show that it is
possible to describe low-resolution models of
protein complexes of previously unknown
structure that are not amenable to traditional
structure biology approaches. We will discuss
current results from various systems under study
in our research group, including calciumcalmodulin-peptide
regulatory complexes, the 10
protein DNA transcription factor assembly TFIIH
and aggregation products of alpha synuclein
associated with Parkinson’s Disease.
6.1.3 2:00pm – 2:15pm
Nanomechanics of live bacterial cells
Michelle L Gee1 1 School of Chemistry, University of Melbourne, Parkville 3010
Australia, mlgee@unimelb.edu.au
Biography
Michelle Gee is a physical chemist with particular
interests in intermolecular and surface nano-scale
forces in cellular and biomimetic systems, and
nanostructures and molecular assemblies. She
received her PhD from the University of Melbourne
and subsequently held research fellowships at the
University of California Santa Barbara and
Princeton University. Michelle has held external
appointments that include visiting chairs in the
Departments of Physics and Chemical Engineering
at Carnegie Mellon University and at CNRS. She
currently serves on the editorial board of Soft
Materials and is an elected member of council to
the International Association of Colloid and
Interface Scientists. Michelle leads the Soft
Condensed matter Labs at the University of
Melbourne with expertise in lipid-peptide
interactions and the action antimicrobial peptides,
the biophysical properties of microbes, particularly
the bacterial glycocalyx and cell wall, and
self-assembled nanostructures for targeted drug
delivery, separations and high-density storage.
Recently her group has developed
multidimensional fluorescence spectroscopies and
direct nanomechanical force methodologies for
studying live cells.
Abstract
With the increased prevalence of superbugs,
pathogens resistant to antibiotics, research is
focussing on novel ways of interrogating the
behaviour of bacteria and the mechanisms by
which they protect themselves. It is thought that
bacterial surface polymers (fimbriae,
lipopolysaccharide and capsular glycocalyx) are
key components of cell survival. However, the
roles of these surface polymers and their
inter-relationships are not understood.
Here, we show how Atomic Force Microscopy
(AFM) can be used to measure the
nanomechanical properties of the surface of
individual, live bacterial cells, in situ, to give insights
into the biophysical behaviour of bacterial surface
polymers. Our results focus on Klebsiella
pneumoniae, an opportunistic pathogen that
causes diseases such as pneumonia, urinary tract
infections, surgical wound infections and infection
of the blood, known as bacteremia. We show for
the first time that AFM nanomechanical data for
wild type Klebsiella pneumoniae and its genetically
manipulated mutants give insights into the
biophysical structure and role of the cell capsule
and fimbriae in cell survival and cell adhesion.

6.1.4 2:15pm – 2:30pm
Gas-phase structures of two isomers
of deoxyguanosine radical cation:
experiments and theory
Linda Feketeová 1 , Bun Chan2 , George N.
Khairallah1 , Vincent Steinmetz 3 , Elizabeth Yuriev4 ,
Philippe Maitre3 , John D. Orbell5 , Leo Radom2 ,
Richard A.J. O’Hair1 1 ARC Centre of Excellence for Free Radical Chemistry and
Biotechnology, School of Chemistry and Bio21 Institute of
Molecular Science and Biotechnology, The University of
Melbourne, 30 Flemington Road, Parkville, VIC, 3010, Australia,
lfe@unimelb.edu.au
2 School of Chemistry, University of Sydney, NSW, 2006,
Australia, chan_b@chem.usyd.edu.au
3 Laboratoire de Chimie Physique, Université Paris Sud, 15,
avenue Jean PERRIN, Orsay Cedex, 91405, France, philippe.
maitre@u-psud.fr
4 Medicinal Chemistry and Drug Action, Monash Institute of
Pharmaceutical Sciences, Monash University, Parkville, VIC,
3052, Australia. Elizabeth.Yuriev@vcp.monash.edu.au
5 School of Engineering & Science, Victoria University, Werribee,
VIC, 3030, Australia, John.Orbell@vu.edu.au
Biography
Linda studied physics at the Comenius University
in Bratislava, Slovakia, where she specialized in
plasma physics. As an undergraduate, she visited
Leopold-Franzens University in Innsbruck, Austria,
several times, to study electron interactions with
nucleobases. Linda received her PhD in physics
from Leopold-Franzens University in 2006 with
focus on ion-surface interactions of charged
molecular ions. Afterwards she got awarded a
visiting fellowship to work at Queen�™s
University Belfast to build a new experimental
setup to study ion-molecule reactions in the gas
phase with well defined ion kinetic energies.
Afterwards she obtained European Science
Foundation fellowship, to work at Aarhus
University, Denmark, on electron scattering
experiments. After arriving in Australia, she joined
synchrotron group at Monash University before
she got awarded an ARC International Fellowship
with Prof. O�™Hair from The University of
Melbourne in 2008. In 2010 she was awarded an
ARC Postdoctoral Fellowship to study
biomolecules and biomolecular clusters.
Biographies and Abstracts
Tuesday 6 December - Session 6
Abstract
Electrospray ionisation (ESI) of methanolic
solutions containing a mixture of the nucleoside
deoxyguanosine, dG, incubated with Cu(NO 3 ) 2
resulted in the formation of a range of ions,
including doubly charged copper nucleoside
complexes [CuIIdGn]2+, with n ranging from 2 to
10. 1 Collision-induced dissociation (CID) of these
complexes proceeds via a number of different
pathways that depend on the size of the cluster, n.
When n = 3, monomeric radical cations are formed
via redox processes. When n = 4, dimeric radical
cations are formed. A key finding is that the radical
cations of dG have fragmentation patterns that
depend on the way they are formed. Thus, dG •+
formed directly in the ESI source or via CID of
[Cu II dG3] 2+ complex fragment in the same way,
giving the radical cation of the guanine base at m/z
151 via cleavage of the N-glycosidic bond. In
contrast, the CID spectra of radical cation formed
via the sequences [CuIIdG4] 2+ •+ •+ → dG → dG is
2
dominated by the loss of CH 2 O and further loss of
C 2 H 3 O 2 from the sugar moiety. In addition, infrared
(IR) fingerprint spectra of the two type of dG •+ ,
recorded using a Free Electron Laser coupled with
a quadrupole ion-trap, confirm that two different
isomers are obtained depending on the way they
are formed. These different fragmentation
reactions are attributed to different tautomeric
structures of the radical cations. MS/MS, quantum
chemical calculations, gas-phase IR spectroscopy,
and ion-molecule reactions were used to
determine the possible structures of these
tautomeric radical cations.
[1] Feketeová, L.; Yuriev, E.; Orbell, J. D.; Khairallah, G. N.; O’Hair,
R. A. J. Int. J. Mass Spectrom. 2010, 304, 74-82
81

82
Biographies and Abstracts
Tuesday 6 December - Session 6
6.1.5 2:30pm – 2:45pm
Attaching Molecular Hydrogen to
Atomic Ions
Evan Bieske 2 , Viktoras Dryza1 ,
1 School of Chemistry, University of Melbourne, Parkville 3010,
vdryza@unimelb.edu.au
2 School of Chemistry, University of Melbourne, Parkville 3010,
evanjb@unimelb.edu.au
Biography
Evan Bieske has been at the School of Chemistry,
University of Melbourne for 15 years. He is
primarily concerned with the spectroscopy of
molecular ions and ion clusters.
Abstract
This talk will focus on our laser spectroscopic
studies of small molecular complexes, in which
one or more hydrogen molecules is attached to an
atomic cation (Li+-H2, Na+-H2, Cr+-H2, B+-H2
and Ag+-H2) or anion (Cl--H2, Br--H2, I--H2).
These simple complexes serve as model systems
for understanding the bonding of dihydrogen to
charged sites in solid materials including zeolites
and metal organic frameworks which are currently
being investigated for hydrogen storage.3 The
infrared spectra, which feature full resolution of
rotational structure, are recorded by monitoring
charged photofragments, and deliver detailed
information on the manner in which H2 molecules
interact with metal cations and halide anions. In
some cases, the onset of dissociation at a
particular rovibrational level allows us to place
extremely narrow bounds on the dissociation
energy of the complex, providing a benchmark
against which current computational techniques
can be assessed. We will discuss the manner in
which the properties of the complexes, including
dissociation energy, vibrational band shift, and
intermolecular separation, depend on the
electronic structure of the atomic ion.
FIG. 1: Binding energies for M+-H2 complexes deduced through
thermochemical measurements. Infrared spectra have been
obtained for complexes with hatched bars, allowing extraction of
detailed structural information. The vibrational frequencies of H2
and D2 are marked on the right, indicating which complexes can
be studied using resonance enhanced photodissociation
spectroscopy.
6.1.6 2:45pm – 3:00pm
Which Density Functionals can be
reliably applied to Main Group
Thermochemistry?
Lars Goerigk1,2 , Stefan Grimme2 1 School of Chemistry, The University of Sydney, Sydney, New
South Wales 2006, Australia
2 Theoretical Organic Chemistry, Organisch-Chemisches Institut,
University of Münster, Corrensstr. 40, 48149 Münster, Germany
Biography
2003-2008: Studies in Chemistry, University of
Münster, Germany
2008-2011: PhD Thesis with Prof. Stefan Grimme,
University of Münster, Germany
Abstract
Which functional should I use? Many users of DFT
are regularly faced with this problem. We present
the results of a recent study, in which we tried to
answer this question and tried to shed some light
on the plethora of developed DFT methods.[1] Our
aim was to thoroughly investigate which
functionals are generally well applicable and
robust to describe the energetics of molecules.
Our study was based on the new GMTKN30
database for general main group thermochemistry,
kinetics and noncovalent interactions.[2,3] In total,
47 functionals were investigated: two LDAs, 14
GGAs, three meta-GGAs, 23 hybrids and five

double-hybrids. Besides the double-hybrids, also
other modern approaches, i.e., the M05 and M06
classes of functionals and range-separated
hybrids, were tested. The range of the properties
covered by GMTKN30 allowed us to give a reliable
answer to the question stated above.
Biographies and Abstracts
Tuesday 6 December - Session 6
Perdew’s metaphoric picture of Jacob’s Ladder for
the classification of density functionals’
performance could unbiasedly be confirmed with
GMTKN30. We also showed that there is no
statistical correlation between a functional’s
accuracy for atomization energies and the
performance for chemically more relevant reaction
energies.
For each rung on Jacob’s Ladder we recommend the functionals,
which we regard as the most robust ones in terms of accuracy,
reliability and robustness. The recommended methods are the
B97-D3 and revPBE GGAs, the oTPSS[2] meta-GAA, Truhlar’s
PW6B95 hybrid and the PWPB95[3] and DSD-BLYP doublehybrids.
The usage of an atom-pairwise London-dispersion
correction (DFT-D3) is shown to be crucial for accuracy.[4] We
discourage from regularly applying the B3LYP method, because
better alternatives are available. We hope that our
recommendations are helpful to the broad community of DFT
users.
[1] L. Goerigk, S. Grimme, Phys. Chem. Chem. Phys., 2011, 13,
6670.
[2] L. Goerigk, S. Grimme, J. Chem. Theory Comput. 2010, 6, 107.
[3] L. Goerigk, S. Grimme, J. Chem. Theory Comput. 2011, 7, 291.
[4] S. Grimme, J. Antony, S. Ehrlich, H. Krieg J. Chem. Phys. 2010,
132, 154104.
Session 6 - Main Theatre
6.2.1 1:15pm – 1:30pm
Polarization effects in ion channels
and bulk from ab initio MD
simulations
Serdar Kuyucak, Jeff Timko, Alexandra De
Castro,
School of Physics, University of Sydney, NSW 2006
Biography
2004-present: A/Prof. in Biophysics, University of
Sydney
1992-2003: Senior Fellow in Nuclear Physics and
Biophysics, ANU
1985-1991: Research Fellow in Nuclear Physics,
University of Melbourne
1983-1985: PDF in Nuclear Physics, University of
Tubingen
1982: PhD in Nuclear Physics from Yale University
Abstract
Classical force fields employed in molecular
dynamics (MD) simulations of biomolecules do not
include the polarization interaction explicitly.
Effects of polarization are taken into account in an
average way by boosting the partial charges on
atoms. Because this parametrization is done in
bulk solution, it may not work very well in a
different environment, e.g. membrane proteins, or
with higher charges such as Ca2+ ions. In
particular, polarization is expected to play an
important role in ion permeation across ion
channels. Indeed several calculations of the
potential of mean force (PMF) of K+ ions across
the gramicidin A channel have found a large
central energy barrier of height ~20 kT, which is
incompatible with the observed conductance of
K+ ions near the diffusion rate. Inclusion of the
polarization interaction has been shown to reduce
this barrier significantly.
Efforts are under way to construct polarizable
force fields to deal with such problems. However,
relying solely on experiments to constrain the
parameters of polarizable force fields is fraught
with difficulties. Ab initio calculations would be
83

84
Biographies and Abstracts
Tuesday 6 December - Session 6
very helpful in this regard by providing extensive
set of results for fitting the parameters and further
testing of the force fields. Towards this end, we
have performed ab initio MD simulations of ion
channels and bulk solution, and characterized
their polarization properties.
Salt solution is the main environment for
biomolecules and its correct description is
essential for their proper simulation. We have
constructed the PMF for the dissociation of Na-Cl
and Ca-Cl pairs in water from ab initio MD
simulations [1, 2]. Comparison of these ab initio
PMF’s to those obtained from the non-polarizable
force fields illustrates the significance of the
polarization. As one would expect the dipole
moments of the hydration waters differ significantly
between the ab ignition and classical results.
Analysis of the trajectory data further reveals that
the hydration numbers also differ and this has an
impact on the PMF’s.
Ion channels provide the most stringent tests for
the classical force fields. We have studied the
polarization effect in the gramicidin A and
potassium channels via ab inito MD simulations.
Our results indicate that presence of ions in the
channel has a significant effect on the dipole
moments carbonyl groups, boosting their dipole
moments appreciably compared to simulations
with water only [3]. This will help to lower the free
energy of ions in the channel and solve the
problems encountered in permeation of K+ ions
across the gramicidin A and potassium channels.
References
1. J. Timko, D. Bucher and S. Kuyucak. J. Chem. Phys. 132 (2010)
114510.
2. J. Timko, A. De Castro and S. Kuyucak, J. Chem. Phys. 134
(2011) 204510.
3. D. Bucher and S. Kuyucak, Chem. Phys. Lett.477 (2009) 207.
6.2.2 1:30pm – 1:45pm
A critical dual role for the pore helix
in hERG K channel inactivation
Matthew D Perry1 , Jamie I Vandenberg 1,2 ,
1 Molecular Cardiology and Biophysics Division, Victor Chang
Cardiac Research Institute, 405 Liverpool Street, Darlinghurst,
NSW 2010, Australia
2 St Vincent’s Clinical School, University of New South Wales,
NSW 2052, Australia
Biography
Matt Perry gained his PhD at the University of
Leeds in the UK, before undertaking post-doctoral
positions with John Mitcheson at University of
Leicester and subsequently with Mike Sanguinetti
at the University of Utah in Salt Lake City. He is
currently pursuing his interests in ion gating and
pharmacology at the Victor Chang Cardiac
Research Institute in Sydney with Jamie
Vandenberg.
Abstract
Human ether-a-go-go related gene (hERG)
potassium channels pass current (IKr) that plays
an important role in repolarization of the cardiac
ventricular action potential. Underlying the unique
hERG/IKr phenotype is a rapid, voltage-dependent
C-type inactivation gating mechanism.
Previously, we used ϕ-value analysis to determine
the temporal sequence of conformational changes
in the channel protein during the transition from
open to inactivated states (Wang et al, 2011; Nat
Struct & Mol Biol, 18: 35-42). After introducing a
point mutation, a ϕ-value is calculated by
comparing perturbations (versus WT) to the
energetics of the transition state, ∆log(k ), to that of
f
the stable end states, ∆log(K ). The ratio
eq
∆log(k )/∆log(K ) provides a ϕ-value between 0
f eq
and 1, where 0 indicates the last step in the
pathway and 1 indicates a change at the start of
the reaction. Such analysis revealed an initial loss
of potassium ions from the selectivity filter is
followed in turn by conformational changes in the
S5, S4, S4-S5 linker, S6 and pore helix. Finally, the
channel is rendered non-conducting through a
‘collapse’ of the selectivity filter. However, a key
question still to be answered is how loss of
potassium from the selectivity filter leads to

conformational changes in the S5 helix. We
hypothesized that the pore helix may play a dual
role, acting to couple the selectivity filter to the S5
helix (early) and to the S6 helix (late).
A mutagenesis scan identified two residues near
the base of the pore helix (Thr618 and Leu622)
where mutants resulted in sufficiently large
∆log(K ) values (>0.5) to permit accurate
eq
estimations of ϕ-values. Derived mean ϕ-values
for T618V and T618I were 0.87±0.03 (n=8) and
0.9±0.02 (n=7). The overall ϕ-value for Thr618
mutants (C, V, I, L, M, Q) was 0.89 (R2 =0.99).
Similarly, ϕ-value for L622V was 0.81±0.01 (n=7),
with an overall ϕ-value for Leu622 mutants (C, V,
M, I) of 0.85 (R2 =0.91). These results reveal that
during transition from open to inactivated states,
the base of the pore helix undergoes a
conformational change just after the exit of K+ ions
from the selectivity filter (ϕ ~1) and just prior to a
conformational change in the S5 domain (ϕ ~0.75).
Our study suggests that the pore helix plays a
critical dual role in C-type inactivation gating of
hERG channels, undergoing conformational
changes both early (coupling loss of K+ ions to S5
motion) and late (coupling S6 motion to selectivity
filter collapse) in the transition pathway.
6.2.3 1.45pm – 2.00pm
Bimodal Regulation of hERG Gating
by the N-Terminal Tail as Revealed
by Voltage Clamp Fluorometry
Peter S.P. Tan1 , Adam P. Hill1 , Chai Ann Ng1 ,
Matthew Perry1 , Jamie I. Vandenberg 1
1 Molecular Cardiology and Biophysics Division, Victor Chang
Cardiac Research Institute, Darlinghurst, New South Wales
Biography
Peter is a postdoctoral researcher at the Victor
Chang Cardiac Research Institute working with Dr
Adam Hill and Prof Jamie Vandenberg
Abstract
The cytoplasmic N-terminal domain of humanether-a-go-go
related gene (hERG) K+ channels
has been shown to modulate the unusually slow
deactivation of this channel. We have previously
Biographies and Abstracts
Tuesday 6 December - Session 6
solved the solution NMR structure of this region
showing it to contain a Per-Arnt-Sim (PAS) domain
(residues 26-135), an amphipathic α-helix (residues
13-23) and an unstructured tail segment (residues
2-9). Deletion of the tail and α-helical regions
(∆2-25) or the tail alone (∆2-9) both enhanced rates
of deactivation and slowed the rate of activation.
However, while ∆2-9 shifted the V0.5 of activation
in the depolarized direction, ∆2-25 did not,
suggesting a differential effect on the voltage
dependence of activation.
In this study we have used voltage clamp
fluorometry (VCF) to investigate the mechanism of
how these N-terminal deletions affect the
activation process. The fluorophore MTSR was
attached to position E518C in the voltage sensing
domain to track movement of this region during
activation in each of the N-terminal deletions. The
V0.5 of the fluorescent-voltage (FV) relationship for
∆2-9 was significantly shifted to more depolarized
potentials (18.2 ± 1.5 mV, n= 9) when compared to
control (0 ± 1.8 mV, n=12, one way ANOVA)
indicating that ∆2-9 affects activation gating by
shifting the voltage range over which the voltage
sensor moves. In contrast the V0.5 of ∆2-25 (1 ±
2.9 mV, n=7) was not significantly different from
control.
In contrast, both ∆2-9 and ∆2-25 have slow rates
of current activation (τ = 208 ± 9.6 ms and 169.2 ±
13.5 ms at 20kjmol-1 respectively, one-way
ANOVA) compared to control (τ = 90.5 ± 13.2 ms
at 20kjmol-1) with no observable effect on the
fluorescent report of the rate of voltage sensor
movement (τ = 89.6 ± 9.8 ms, 85.1 ± 7.2 ms and
81.8 ± 4.1 ms at 10kjmol-1for control, ∆2-9 and
∆2-25 respectively, one-way ANOVA). This data
shows that both ∆2-9 and ∆2-25 slowed rates of
activation independent of voltage sensor
movement. A likely explanation for these results is
that deletion of the N-terminal tail alters the rate of
opening/closing of the cytoplasmic activation gate
in the pore domain.
Our data suggests a bimodal regulation of
activation gating by the N-terminal domain of
hERG channels. While the α-helical region
modulates activation gating via an effect on
movement of the voltage sensor, the N-terminal tail
(residues 1-9) interact with the cytoplasmic
activation gate of the pore domain to regulate the
rates of opening and closing.
85

86
Biographies and Abstracts
Tuesday 6 December - Session 6
6.2.4 2:00pm – 2:15pm
Studies of Bacterial
Mechanosensitive (MS) Channels
under High Hydrostatic Pressure
Evgeny Petrov1 , Paul R Rohde1 and Boris
1, 2 Martinac
1 Victor Chang Cardiac Research Institute, Lowy-Packer Building,
405 Liverpool St, Darlinghurst, 2010.
2 St Vincent’s Clinical School, The University of New South
Wales, Victoria St, Darlinghurst, 2010 E.Petrov@victorchang.
edu..au; P.Rohde@victorchang.edu.au; B.martinac@
victorchang.edu.au
Biography
Senior Research Fellow, JAN2009 – Present
The Victor Chang Cardiac Research Institute, 405
Liverpool St, Darlinghurst, NSW 2010
Effect of high hydrostatic pressure on
mechanosensitive ion channels
Research Officer, JAN2005-DEC2008
School of Biomedical Sciences, Skerman Building
65, University of Queensland,
St Lucia, QLD 4067
Research Officer, SEP2004-DEC2004
Pharmacology Unit M510, School of Medicine and
Pharmacology, QEII Medical Centre,
The University of Western Australia, Crawley, WA
6009
Effect of static magnetic field on mechanosensitive
channels, reconstituted into phospholipids bilayer
Postdoctoral Fellow, SEP2001-MAR2003
University of California at Davis, Center for
Neuroscience, Dept. of Otolaryngology,
1544 Newton Ct., Davis, CA 95616 USA
Whole-cell Ca-current under membrane potential
oscillations in hair cells.
Ph.D., 1993-1995, Department of Biophysics,
SSMU, Russia.
Epithelium-derived relaxation in rat tracheal
smooth muscles mediated by second
messengers.
M.S., 1992-1993, Department of Biophysics,
SSMU, Russia.
Influence of aorta endothelium and trachea
epithelium on rats smooth muscle contractility
Abstract
High hydrostatic pressure (HHP) is present in
natural environments where it impacts on
biophysical properties of cell membranes and
protein quaternary structure [1, 2]. We have
investigated the effect of high hydrostatic pressure
on E. coli mechanosensitive (MS) channels of small
conductance MscS/MscK and G22E-MscL, a
spontaneously opening mutant of E. coli MscL.
Patch-clamp technique combined with a
flying-patch device and hydraulic setup allowed
the study of the effects of HHP up to 90 MPa on
both MS channels in situ from the channels
expressed in E. coli giant spheroplasts [3, 4, 5]. In
addition, the G22E-MscL mutant channels were
reconstituted into artificial liposome membranes
[6] and examined for the effects HHP on their
gating. Pressure affected MscS channel kinetics
but not conductance [3]. At negative pipette
voltages (corresponding to membrane
depolarization in the inside-out patch configuration
used in our experiments) the channel exhibited a
reversible reduction in activity with increasing
hydrostatic pressure between 0.1 and 90 MPa (1
and 900 atm) at room temperature (�230C). The
reduced activity was characterized by a significant
reduction in the channel opening probability
resulting from a shortening of the channel
openings with increasing pressure. Thus HHP
generally favoured channel closing in accordance
with thermodynamic predictions. In contrast,
against thermodynamic predictions, HHP in the
same range of 0.1–90 MPa increased G22E-MscL
channel open probability by favouring the open
state of the channel [5]. Furthermore, hydrostatic
pressure affected the channel kinetics, as
manifested by the propensity of the channel to
gate at subconducting levels with an increase in
pressure. In the MscS case we postulate that
lateral compression of the bilayer, under high
hydrostatic pressure, is responsible for reduction
in the channel open probability with increasing
hydrostatic pressure. In the G22-MscL case we
propose that the presence of water molecules
around the hydrophobic gate of the G22E-MscL
channel induce hydration of the hydrophobic lock
under HHP causing frequent channel openings
and preventing the channel closure in the absence
of membrane tension. In conclusion, our studies
indicate that HHP can be used as a valuable
experimental approach towards better
understanding of the gating mechanism in
complex channels such as MscS and MscL.

References:
[1] Macdonald, A. G. (1984) The effects of pressure on the
molecular structure and physio- logical functions of cell
membranes. Philos. Trans. R. Soc. Lond. B Biol. Sci. 304:47–68.
[2] Mozhaev, V. V., K. Heremans, J. Frank, P. Masson, and C.
Balny. (1996) High pressure effects on protein structure and
function. Proteins 24:81-91.
[3] Martinac, B., Buechner, M., Delcour, A.H.., Adler, J. and Kung,
C. (1987) Pressure-sensitive ion channel in Escherichia coli. Proc.
Natl. Acad. Sci. USA 84: 2297-2301.
[4] Macdonald, A.G. and Martinac, B. (2005) Effect of high
hydrostatic pressure on the bacterial mechanosensitive channel
MscS. Eur. Biophys. J. 34: 434-442.
[5] Petrov, E., Rohde, P.R. and Martinac, B. (2011) “Flying-patch”
patch-clamp study of G22E MscL mutant under high hydrostatic
pressure. Biophys. J. 100: 1635-1641. (Published as a Featured
Article in Research Highlights of the 2nd March issue of BJ.)
[6] Martinac, B., Rohde, P.R., Battle, A.R., Petrov, E., Pal, P., Fook
Weng Foo, A., Vásquez, V., Huynh, T. and Kloda, A. (2010)
Studying mechanosensitive ion channels using liposomes.
Methods Mol. Biol. 606: 31-53.
6.2.5 2:15pm – 2:30pm
SPontaneous Oscillatory
Contractions (SPOC): Assessing the
Contractile Performance of Human
Cardiomyopathies
Amy Li1 , James Wolfe2 , Eleanor Kable3 , Filip
Braet4 , Tatsuya Kagemoto 5 , Peter S Macdonald4 ,
Shinichi Ishiwata3 , Cristobal dos Remedios8 1 Department of Anatomy & Histology, The University of Sydney,
Sydney, NSW, 2006, amli7468@uni.sydney.edu.au
2 Department of Anatomy & Histology, The University of Sydney,
Sydney, NSW, 2006, jamesr@anatomy.usyd.edu.au
3 Australian Centre for Microscopy & Microanalysis, The
University of Sydney, Sydney, NSW, 2166, eleanor.kable@
sydney.edu.au
4 Australian Centre for Microscopy & Microanalysis, The
University of Sydney, Sydney, NSW, 2166, filip.braet@sydney.
edu.au
5 Department of Physics, School of Science & Engineering,
Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555,
Japan, yadara-fumia@ruri.waseda.jp
6 Heart & Lung Transplant Unit, St. Vincent’s Hospital,
Darlinghurst, NSW, pmacdonald@stvincents.com.au
7 Department of Physics, School of Science & Engineering,
Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555,
Japan, ishiwata@waseda.jp
8 Department of Anatomy & Histology, The University of Sydney,
Sydney, NSW, 2006, crisdos@anatomy.usyd.edu.au
Biography
Ms Li is currently completing her B.Sc. Honours
degree under the supervision of Professor Cris
Biographies and Abstracts
Tuesday 6 December - Session 6
dos Remedios. In her third year she completed a
double major in physiology and psychology and
has an excellent track record. Her supervisor in
confident she will be awarded first class honours
and it is her intention to continue in 2012 as a PhD
student.
Abstract
SPontaneous Oscillatory Contraction (SPOC) is a
novel state of muscle contraction that can be
observed in partially activated striated muscle
fibres. SPOC is characterised by auto-oscillations
between repetitive cycles of rapid lengthening and
slow shortening which correlates with diastole and
systole. There are two conditions by which
cardiomyocytes can be activated; ADP-induced
SPOC and Ca2+-induced SPOC. Ca-SPOC which
has been shown to highly correlate with heart beat
in a number of animal models.
This study aims to quantify the contractile
performance of cardiomyocytes isolated from
human dilated and hypertrophic cardiomyopathies
(some with known mutations) and compared with
aged matched non-failing donors. The parameters
of contractile performance include contraction and
relaxation velocities, period of contraction and
relaxation, SPOC velocity and SPOC period. We
will compare contractile changes between (1)
failing and non-failing hearts, (2) age-dependent
progression and (3) differences between ADP- and
Ca-SPOC in these hearts. These observations are
then related to their patient data (e.g. ejection
fraction, fractional shortening).
Interestingly, we were able to re-activate human
hearts that have been flash frozen at -200oC
within minutes of loss of coronary blood flow
(cross-clamping). Some samples have been stored
for more than twenty years. Cardiac muscle fibres
from the left atria and left ventricles, intraventricular
septa and papillary muscles were treated with a
series of washes prior to micro-dissection. These
samples were then measured and averaged at
very high spatial and temporal resolution using the
Leica SP5 multi-photon microscope.
Preliminary data so far have indicated that
measurable changes in contractile performance
were observed between non-failing and failing
hearts. Samples of hypertrophic cardiomyopathy
exhibited decreased rates of relaxation, consistent
87

88
Biographies and Abstracts
Tuesday 6 December - Session 6
with the clinically-described phenotype of diastolic
dysfunction. These observations reveal SPOC to
yield a range of functional parameters that can be
used to evaluate the functional state of human
heart muscle fibres. It may prove to provide a
valuable set of parameters that can objectively
assess the state of human heart failure.
6.2.6 2:30pm – 2:45pm
Does GLUT4 queue to get to the
plasma membrane?
Adelle C. F. Coster1 1 School of Mathematics & Statistics, University of New South
Wales, Sydney NSW and Garvan Institute for Medical Research,
Darlinghurst, NSW, A.Coster@unsw.edu.au
Biography
Adelle is an applied mathematician from UNSW
who, in collaboration with the Diabetes & Obesity
program at the Garvan Institute of Medical
Research, has been modelling the spatio-temporal
dynamics of the insulin signalling pathway and the
ultimate translocation of the glucose transporter
GLUT4 in response to differential levels of insulin.
In between this and trying to get mathematicians
into biology and biologists into mathematics she is
also the Treasurer of the Australian Society for
Biophysics.
Abstract
It is thought that the insulin-responsive glucose
transporter protein GLUT4, which is a membrane
embedded protein, recycles to the plasma
membrane (PM) via the endosomes but is also
sequestered in storage compartments. The
sequestered GLUT4 can then be released into the
recycling pathway in an insulin-dose dependent
manner.
The GLUT4 is exocytosed via small vesicles, which
fuse with the PM. The application of insulin to a
cell in the basal state causes an initial burst of
fusion events and then the rate returns to a steady
lower level, in some cases similar to that observed
in the basal case. It has been observed that the
total amount recycling to the PM in the presence of
insulin is higher than in the basal state. It is also
been observed that the endocytosis rate remains
relatively constant irrespective of the insulin dose.
Conversely, the transferrin receptor is thought to
recycle to the PM, but when endocytosed only
enters the early endosomes, being sorted away
from the GLUT4 which is sequestered. Thus the
transferrin receptor dynamics is controlled via
fusions of the recycling pathway alone.
Perturbation with insulin again causes an initial
burst of transferring receptor fusion events, which
then return to the near basal level.
So we have two types of burst phenomena, that
due to an additional entry of vesicles from a
sequestered store and that due to a change in the
recycling in an existing dynamic system.
One possible model that could characterise this
behaviour utilises queuing theory. This idea stems
from the presence of the microtubules that cross
the cytoplasm of the cells. Microtubules are
implicated in the sorting of different endocytic
vesicular contents and have well characterised
molecular motors which control the movement of
vesicles down their lengths.
Could these microtubules act as a scaffold for
vesicles, which would then form queues waiting
for fusion? The possible dynamics for such a
system are explored for GLUT4 and transferrin
receptor exocytosis in adipocytes.
6.2.7 2:45pm – 3:00pm
Dynamics of Protein Hydration Water
Kathleen Wood1 , Francois-Xavier Gallat2 ,
Douglas Tobias3 , Giuseppe Zaccai2 , Martin Weik4 1 Bragg Institute, Australian Nuclear Science and Technology
Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232,
kwo@ansto.gov.au
2 Institut Laue Langevin, Grenoble, France
3 University of California, Irvine, California, USA
4 Institut de Biologie Structurale, Grenoble, France
Biography
Katy Wood performed her PhD at the Institut Laue
Langevin, Grenoble, France, where she studied
protein and hydration water dynamics using
neutron spectroscopy. She then moved to the
Biological NMR group at the University of
Groningen in the Netherlands, studying intrinsically

Biographies and Abstracts
Tuesday 6 December - Session 6
unfolded proteins. She is currently jointly
responsible for the small angle neutron scattering
instrument at the Bragg Institute.
Katy Wood performed her PhD at the Institut Laue
Langevin, Grenoble, France, where she studied
protein and hydration water dynamics using
neutron spectroscopy. She then moved to the
Biological NMR group at the University of
Groningen in the Netherlands, studying intrinsically
unfolded proteins. She is currently jointly
responsible for the small angle neutron scattering
instrument at the Bragg Institute.
Abstract
Proteins are dynamical entities, interconverting
between different structures to perform their
functions. In a cellular context, the vast majority of
protein interactions are mediated by water, which
can be considered a biomolecule in its own right.
Here we characterise dynamics of proteins and
their surrounding hydration layer.
The influence of solvent dynamics on protein
dynamics is so important that some have used the
word ‘slaving’ to describe that water ‘imposes’ its
dynamics on proteins. Combining neutron
spectrosocpy with isotope labelling allowed us to
study separately the dynamics of water and
proteins in three systems: a soluble folded protein
[2], an intrinsically disordered protein [3] and a
membrane system [4]. We find a different
relationship between water and protein dynamics.
In the three systems.
The results presented are the work of all authors
on references [2-4].
1. Frauenfelder, H., P.W. Fenimore, G. Chen, and B.H. McMahon,
Protein folding is slaved to solvent motions. Proc Natl Acad Sci
U S A, 2006. 103(42): p. 15469-72.
2. Wood, K., A. Frolich, A. Paciaroni, M. Moulin, M. Hartlein, G.
Zaccai, D.J. Tobias, and M. Weik, Coincidence of Dynamical
Transitions in a Soluble Protein and Its Hydration Water: Direct
Measurements by Neutron Scattering and MD Simulations. J
Am Chem Soc, 2008. 130(14): p. 4586-4587.
3. Gallat, F.X., A. Laganowski, K. Wood, F. Gabel, L. van Eijk, J.
Wuttke, M. Moulin, M. Haertlein, D. Eisenberg, J-P. Colletier, G.
Zaccai, M. Weik, under review.
4. Wood, K., M. Plazanet, F. Gabel, B. Kessler, D. Oesterhelt, D.J.
Tobias, G. Zaccai, and M. Weik, Coupling of protein and
hydration-water dynamics in biological membranes. Proc Natl
Acad Sci U S A, 2007. 104(46): p. 18049-54.
Keynote Session - Main Theatre
K.10 4:20pm - 4:50pm
Dephosphorylation of the calcium
pump – an infrared spectroscopy
and density functional theory study
Andreas Barth1 , Maria Rudbeck1 , Margareta
Blomberg2 1 Department of Biochemistry and Biophysics, Stockholm
University, Arrhenius Laboratories, 10691 Stockholm, Sweden,
maria.rudbeck@gmail.com
2 Department of Physics, Albanova, Stockholm University,
Arrhenius Laboratories, 10691 Stockholm, Sweden, mb@fysik.
su.se
Biography
Andreas Barth is Professor in Experimental
Molecular Biophysics at the Department of
Biochemistry and Biophysics of Stockholm
University / Sweden. He is a trained physicist with
a Diploma degree from the Technical University of
Darmstadt / Germany. Courses and research
practice given by Hans-Joachim Galla made him
switch to biophysics for his PhD which he did at
the University of Freiburg /Germany with Werner
Mäntele. He became then Wellcome fellow at the
National Institute for Medical Research in London /
UK with Peter Bayley and moved via Erlangen to
Frankfurt am Main / Germany where he became
Assistant Professor. Since 2002 he has a position
at Stockholm University.
The common theme in his research has been the
application of spectroscopic techniques to the
study of proteins, with a particular focus on
infrared spectroscopy. Current topics are: the
mechanism of the Ca2+-ATPase, aggregation of
the Alzheimer’s peptide, membrane effects on
membrane proteins, infrared spectroscopy as a
tool for ligand binding studies and for analysing the
effect of poisons on marine organisms.
Abstract
The sarcoplasmic reticulum Ca2+-ATPase
(SERCA1a) actively pumps Ca2+ at the expense of
ATP hydrolysis, which leads to muscle relaxation.
During the pump cycle, ATP phosphorylates the
ATPase at Asp351 and the enzyme adopts two
phosphoenzyme intermediates Ca2E1P and E2P.
An important feature of E2P is its fast hydrolysis.
89

90
Biographies and Abstracts
Tuesday 6 December - Session 6
To understand the underlying mechanism, we
performed an isotope exchange experiment which
identified the absorption of the phosphate group of
the phosphorylated intermediates [1]. Major bands
at 1194 and 1137 cm-1 are assigned to E2P, minor
bands at 1175 and 1115 cm-1 to Ca2E1P.
These data were evaluated by density functional
theory (DFT) calculations (B3LYP/6-31++G**,
6-311++G(3df, 3pd), where the aspartyl phosphate
of the ATPase was modeled by acetyl phosphate
and its interactions with the environment by HF
molecules. These were placed at several locations
and fixed distances with respect to acetyl
phosphate. For the various model environments, a
correlation was found between the average
antisymmetric P-O stretching vibration and the
bond length of the P-O bond that is cleaved during
dephosphorylation. However, the data points
scatter considerably and the models that most
closely reproduce the experimental wavenumbers
for acetyl phosphate in water and the ATPase
phosphoenzymes do not indicate a lengthening of
the scissile P-O bond due to the protein
environment.
Protein models of the catalytic site derived from
structural data were also analysed. They show that
the reactant state of the dephosphorylation
reaction is different from the E2P state adopted in
solution. The reactant state has a longer scissile
P-O bond but the expected wavenumbers of the
reactant state are not observed in the experimental
spectrum, indicating that the reactant state is
considerably higher in free energy than the E2P
ground state. The dephosphorylation reaction was
modeled and its mechanism will be presented.
Reference
[1] A. Barth, N. Bezlyepkina (2004), J. Biol. Chem. 279,
51888-51896
K.11 4:50pm – 5:10pm
Molecular Mechanisms of K+
Selectivity of the Na/K Pump
Haibo Yu1 1 School of Chemistry, University of Wollongong, NSW 2522,
Australia
Biography
Dr Haibo Yu joined the School of Chemistry at the
University of Wollongong in July 2011. He attended
the University of Science and Technology of China,
where he received his B.Sc. in 2000. In Dec 2004,
He completed his PhD in Chemistry at ETH Zurich,
Switzerland with Prof Wilfred F. van Gunsteren.
Afterwards, he worked with Prof Qiang Cui at the
University of Wisconsin-Madison and Prof Benoit
Roux at the University of Chicago in the USA. His
recent interests center on developing theoretical
and computational models to study complex
biomolecular systems.
Abstract
The sodium-potassium (Na/K) pump is a P-type
ATPase that generates Na+ and K+ concentration
gradients. For each ATP molecule, the pump
extrudes three Na+ and imports two K+ across the
cell membrane by alternating between outwardand
inward-facing conformations that preferentially
bind K+ or Na+, respectively. Remarkably, the
selective K+ and Na+ binding sites share several
residues, and how the pump is able to achieve the
different selectivities at the shared sites required
for the functional cycle is unclear. This talk will
present our latest findings on molecular
mechanisms of K+ selectivity of Na/K pump from
a joint computational and electrophysiological
study. Molecular simulations based on the crystal
structures of the Na/K pump in a K+-loaded state
reveal that protonation state of the acidic
side-chains involved in the binding sites is critical
to achieve the proper K+ selectivity. This prediction
is tested with electrophysiological experiments
showing that the selectivity of the E2P state for K+
over Na+ is affected by extracellular pH.
K.12 5:10pm – 5:30pm
Towards rational control of the
bacterial flagellar motor
Lawrence Lee
The Victor Chang Cardiac Research Institute
Biography
Lawrence Lee is a group leader at the Victor

Biographies and Abstracts
Tuesday 6 December - Session 6
Chang Cardiac Research Institute (VCCRI). He
received his PhD from the Faculty of Pharmacy at
the University of Sydney in 2008 and completed a
postdoctoral fellowship in the Structural and
Computational Biology Division of the VCCRI in
August 2011 before establishing a research group
in his current role. Using the bacterial flagellar
motor as a model system, his group uses an
interdisciplinary approach to determine molecular
mechanisms that are fundamental to biology and
to translate discovery into nano-technological
advance in biomimicry.
Abstract
The bacterial flagellar motor (BFM) is a reversible
biological nanorotor, which converts a flux of
cations into mechanical rotation. For over 30 years
the BFM has been a canonical system in molecular
and cellular biology as an example of a large,
sophisticated protein complex and the endpoint of
a well-studied sensory network that facilitates
bacterial chemotaxis. The latter has provided a
paradigm for sensory networks in general. The
BFM is also arguably the best in vivo-characterized
molecular machine. However, the complete lack of
high-resolution structural data of functional
subcomplexes hampers the BFMs promise to
provide enormous insight into molecular
processes that are fundamental to biology,
including biological energy conversion and
cooperative protein complex assembly and
function. We recently determined the structure of
the rotor protein most directly involved in torque
generation and rotational switching. This led to a
detailed molecular picture of both the BFM’s ~1.5
megadalton torque generating ring and a
cooperative mechanism of rotational switching[1].
Here, I describe some of our recent progress in
taking this molecular picture into live cells to
rationally probe the structure and function of the
BFM in vivo.
1. Lee LK, Ginsburg MA, Crovace C, Donohoe M, Stock D:
Structure of the torque ring of the flagellar motor and the
molecular basis for rotational switching. Nature (2010)
466(7309):996-1000.
Notes
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91

92
Poster Authors
P1 Melatonin and serotonin in characeae
Sabah Al Khazaaly 1 , Mary Jane Beilby 1 , Susan Murch 2 , Faisal Albisherawy 1
1 The University of NSW, School of Physics, Kensington, Sydney, NSW, 2052, m.j.beilby@unsw.edu.au
2 University of British Columbia, Okanagan , Kelowna, British Columbia, Canada, V1V 1V7 , susan.murch@ubc.ca
P2 Zn2+ inactivates H+/OH- channels of Chara australis
Sabah Al Khazaaly 1 , Mary Jane Beilby 1
1 The University of NSW, School of Physics, Kensington, Sydney, NSW, 2052, s.alkhazaaly@unsw.edu.au
1 The University of NSW, School of Physics, Kensington, Sydney, NSW, 2052, m.j.beilby@unsw.edu.au
P3 Phenol and p-Chorophenol Adsorption onto Alumina-Grafted Different
Polymers
Hadi S. Al-Lami 1 , Ammar H. Al-Dujiali 2 , Maha T. Sultan 3
1 Department of Chemistry, College of Science, University of Basra-Iraq
2,3 Department of Chemistry, College of Education/ Ibn Al-Haitham, University of Baghdad-Iraq.
P4 Experimental and Computational Investigations into Size Selected
Gold Clusters on Semiconductor Supports as Photoelectrochemical
Catalysts
Jason F. Alvino1 , Greg F. Metha2 1 The University of Adelaide, North Terrace Campus, SA, 5005, Jason.alvino@adelaide.edu.au
2 The University of Adelaide, North Terrace Campus, SA, 5005, greg.metha@adelaide.edu.au
P5 High-resolution FTIR spectroscopy of the ground state, v8, v7, v6 and
Coriolis “perturbation allowed” v12 and v10 modes of ketenimine.
M. K. Bane1 , C. D. Thompson1 , E. G. Robertson 2 , D. R. T. Appadoo3 , C. Medcraft1, D.
McNaughton1 .
1 School of Chemistry, Monash University, Victoria 3800 Australia
2 Department of Chemistry, La Trobe University, Victoria 3083 Australia
3 Australian Synchrotron, 800 Blackburn Rd, Clayton, 3168, Victoria. Australia
P6 An improved method, with theoretical analyses, for the simple
experimental measurement of liquid junction potentials
Peter H Barry1 , Trevor M Lewis1 , Andrew J Moorhouse1 1 Dept of Physiology, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia. Email:
p.barry@unsw.edu.au; t.lewis@unsw.edu.au; a.moorhouse@unsw.edu.au
P7 Computational and Experimental investigations into catalytic
applications of gas-phase gold-niobium bimetallic clusters
Trystan Bennett1 , Robert A. Hardy1 , Gregory F. Metha1 1. The University of Adelaide, North Terrace Campus, Adelaide SA 5005. Trystan.bennett@adelaide.edu.au

P8 Designing single-molecule assays to image the dynamics of molecular
chaperones
Quill Bowden1 and Till Böcking2 1 Centre for Vascular Research, UNSW, Sydney 2052, q.bowden@unsw.edu.au
2 Centre for Vascular Research, UNSW, Sydney 2052, till.boecking@unsw.edu.au
P9 In silico modeling of protein dynamics and drug design
Melissa J. Buskes1 , David J. D. Wilson2 , Belinda M. Abbott3 1 La Trobe Institute for Molecular Science, La Trobe University, Plenty Rd, Bundoora, VIC, 3086, M.Buskes@latrobe.edu.au
2 La Trobe Institute for Molecular Science, La Trobe University, Plenty Rd, Bundoora, VIC, 3086, David.Wilson@latrobe.edu.au
3 La Trobe Institute for Molecular Science, La Trobe University, Plenty Rd, Bundoora, VIC, 3086, B.Abbott@latrobe.edu.au
P10 Differential Dynamic Microscopy Studies of Bacterial Motility
C. Carnovale 1 , R. Nixon-Luke 1 , G. Bryant1 .
1 School of Applied Sciences, RMIT University, GPO Box 2476, Melbourne, Victoria, 3000
P11 Exciton Migration in Conjugated Polymer Dots
Scott N. Clafton 1 , Dr David M. Huang2 , Ming Chiu3 and Dr Tak W. Kee4 1 University of Adelaide, North Terrace Adelaide, South Australia, 5005, scott.clafton@adelaide.edu.au
2 University of Adelaide, North Terrace Adelaide, South Australia, 5005, david.huang@adelaide.edu.au
3 University of Adelaide, North Terrace Adelaide, South Australia, 5005, ming.chiu@adelaide.edu.au
4 University of Adelaide, North Terrace Adelaide, South Australia, 5005, tak.kee@adelaide.edu.au
P12 Species differences in the kinetics of the Na+,K+-ATPase
Ronald J. Clarke and Flemming Cornelius
School of Chemistry,University of Sydney, Sydney, NSW 2001, Australia, and Department of Physiology and Biophysics,
University of Aarhus, Aarhus, Denmark
Correspondence.: r.clarke@chem.usyd.edu.au
Poster Authors
P13 Cardiac troponin: a paramagnetic relaxation enhancement NMR study
Nicole M Cordina1 , C K Liew2 , D A Gell2 , J P Mackay2 , T M Logan3 , L J Brown1 1 Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia
2 School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
3 Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
P14 Unimolecular Reaction Chemistry of Atmospheric Peroxyl Radicals
Gabriel da Silva
Chemical and Biomolecular Engineering, The University of Melbourne, Parkville 3010, Australia
P15 Structural Analysis of Missense Mutations in the CLIC2 Chloride
Intracellular Ion Channel Protein
E L Daniel1 , J E Hare2 , S C Goodchild3 , N M Cordina4 , L J Brown5 1 Department of Chemistry and Biomolecular Science, Macquarie University, Sydney, New South Wales, 2109, elizabeth.
daniel@students.mq.edu.au
93

94
Poster Authors
P16 The Role of Spin in Triplet-Triplet Upconversion
A. Danos 1 , Y. Y. Cheng 1 , D. R. McCamey 2 , T. W. Schmidt 1
1 School of Chemistry, The University of Sydney, NSW 2006, Australia
2 School of Physics, The University of Sydney, NSW 2006, Australia
P18 Bonding between the uracil monomers of the cyclobutane pyrimidine
dimer radical anion by means of quantum chemical calculations
Linda Feketeová 2 , Andreas Mauracher1 ,David Gschliesser 1 , Peter Bartl1 , Violaine Vizcaino1 ,
Lukas An der Lan1 , Catrin Goeschen2 , Stephan Denifl1 , Richard A.J. O’Hair2 , T. D. Märk1 , P.
Scheier1 , U. Wille2 1 Institut für Ionenphysik und Angewandte Physik, Leopold-Franzens-Universität, Technikerstr. 25, Innsbruck, 6020, Austria,
andreas.mauracher@uibk.ac.at
2 ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, School of Chemistry and Bio21 Institute of
Molecular Science and Biotechnology, The University of Melbourne, 30 Flemington Road, Victoria, 3010, Australia, lfe@unimelb.
edu.au
P19 Structure and binding energies of the doubly charged zwitterionic
betaine clusters
Linda Feketeová 2 , Emilie Cauët1 , William A. Donald2 , Richard A.J. O’Hair2 ,
1 Service de Chimie Quantique et Photophysique, Université Libre de Bruxelles, avenue F.D. Roosevelt 50 CPi 160/09,
Brussels, 1050, Belgium, ecauet@ulb.ac.be
2 ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, School of Chemistry and Bio21 Institute of
Molecular Science and Biotechnology, The University of Melbourne, 30 Flemington Road, Victoria, 3010, Australia, lfe@unimelb.
edu.au
P20 Parametric Sensitivity Analyses of the Insulin Signalling Pathway
Catheryn Gray 1 , Adelle C. F. Coster 1,2
1 School of Mathematics & Statistics, University of New South Wales
2 Garvan Institute of Medical Research, Darlinghurst NSW
P21 Energy and Charge Transfer Interactions in a Mixed Porphyrin Cosensitized
TiO2 Electrode: A sub-ns Transient Absorption
Spectroscopy Study
M. J. Griffith, 1 A. J. Mozer, 1 P.Wagner, 1 G. G. Wallace, 1 D. L. Officer, 1 and R. Katoh 2,3
1. ARC Centre of Excellence for Electromaterials Science and Intelligent Polymer Research Institute, University of Wollongong,
Innovation Campus, Squires Way, North Wollongong, NSW, 2500, Australia.
Emails: mjg48@uow.edu, attila@uow.edu.au, pawel@uow.edu.au, gwallace@uow.edu.au, davido@uowmail.edu.au
2. National Institute of Advanced Industrial Science and Technology, Tsukuba Central 5, Tsukuba, Ibaraki, 305-8565, Japan.
3. Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Tamura, Koriyama,
Fukushima, 963-8642, Japan.
Email: rkatoh@chem.ce.nihon-u.ac.jp
P22 ACE I/D genotypes and their impact on heart rate variability: a limited
meta-analysis
Brett Hambly6 , Ethan Ng 1 , Yaxin Lu 2 , Slade Matthews3 , Herbert Jelinek4 , Craig McLachlan 5
1 Pathology, Univ of Sydney, NSW 2006, etng1324@uni.sydney.edu.au
2 Pathology, Univ of Sydney, NSW 2006, yalu4496@uni.sydney.edu.au
3 Pharmacology, Univ of Sydney, NSW 2006, sladem@med.usyd.edu.au

4 School of Community Health, Charles Sturt Univ, NSW 2640, HJelinek@csu.edu.au
5 Rural Clinical School, Univ of NSW, NSW, 2650, reperfusion@hotmail.com
6 Pathology, Univ of Sydney, NSW 2006, bretth@pathology.usyd.edu.au
Poster Authors
P23 UV-Vis Action Spectroscopy of Room Temperature Protonated
Aromatics
Christopher S. Hansen1 , Ben B. Kirk1 , Richard A.J. O’hair 2 , Stephen J. Blanksby1, Adam
J. Trevitt 1
1 School of Chemistry, University of Wollongong, NSW 2522 Australia
2 School of Chemistry, University of Melbourne, VIC 3010 Australia
P24 Stabilisation and Delivery of Medicinal Pigment Curcumin by
g-Cyclodextrin Dimers
Takaaki Harada1 , Duc-Truc Pham1 , Huy Tien Ngo1 , Tiffany Harris2 , Eleanor Need2 , Grant
Buchanan2 , Mandy Leung1 , Brendon Coventry, 3 Stephen F. Lincoln1 , Tak W. Kee1 1 School of Chemistry and Physics, The University of Adelaide, North Terrace Campus, Adelaide, SA, 5005, Australia, takaaki.
harada@adelaide.edu.au
2 Molecular Ageing Laboratory, School of Medicine, The University of Adelaide, Basil Hetzel Institute, The Queen Elizabeth
Hospital, 28 Woodville Road, Woodville South, SA, 5011, Australia
3 Discipline of Surgery, The University of Adelaide, Royal Adelaide Hospital, Adelaide, SA, 5005, Australia
P25 Effective Core Potential Benchmarking for Cerium Oxide Clusters
Using Density Functional Theory
Robert A. Hardy1 , Birte Reichers2 and Gregory F. Metha3 1 Department of Chemistry, The University of Adelaide, South Australia 5005, robert.hardy@adelaide.edu.au
2 Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany, birte.reichers@uni-bielefeld.de
3 Department of Chemistry, The University of Adelaide, South Australia 5005, gregory.metha@adelaide.edu.au
P26 Probing the Integral Membrane Form of Clic1 Using Fluorescence
Resonance Energy Transfer
Joanna E Hare1 , Sophia C Goodchild2, Louise J Brown3 1 Department of Chemistry and Biomolecular Science, Macquarie University, Sydney, New South Wales, 2109, joanna.hare@
students.mq.edu.au
2 Department of Chemistry and Biomolecular Science, Macquarie University, Sydney, New South Wales, 2109, sophia.
goodchild@mq.edu.au
3 Department of Chemistry and Biomolecular Science, Macquarie University, Sydney, New South Wales, 2109, louise.brown@
mq.edu.au
P27 Single Molecule Widefield Fluorescence Studies of Conjugated
Polymers
Emma N. Hooley1 , Toby D. M. Bell2 , Kenneth P. Ghiggino3 1 School of Chemistry, University of Melbourne, Victoria 3010, e.hooley@student.unimelb.edu.au
2 School of Chemistry, Monash University, Victoria, 3800, toby.bell@monash.edu
3 School of Chemistry, University of Melbourne, Victoria 3010, ghiggino@unimelb.edu.au
95

96
Poster Authors
P28 Potential role of forbidden disulfide motifs in Zn fingers.
Hulugalle D V K 1,3 , Haworth N L 2 , Ballouz S 1,4 , Jason Y. Liu 2 , Fan S W 1,3 , Wouters M A 2,3
1 Structural and Computational Biology Program, Victor Chang Cardiac Research Institute, Sydney, Australia.
2 School of Life and Environmental Sciences, Deakin University, Geelong, Australia
3 School of Medical Sciences, University of New South Wales, Sydney, Australia
4 School of Computer Science & Engineering, University of New South Wales, Sydney, Australia
P29 Cryopreservation – The Beginning of a DSC (Differential Scanning
Calorimetric) Understanding.
Taavi Hunt 1 , Anja Kaczmarczyk 2, 3 , Bryn Funnekotter 2, 3, Shane Turner 3, 4 , Eric Bunn 3, 4 , Gary
Bryant1 , Ricardo L. Mancera2 1 Applied Physics, School of Applied Sciences, RMIT University, Melbourne, VIC, Australia.
2 Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, Curtin University, Perth WA,
Australia.
3 Botanic Gardens and Parks Authority, Fraser Avenue, West Perth WA , Australia.
4 School of Plant Biology, Faculty of Natural and Agricultural Sciences, University of Western Australia, Crawley WA, Australia.
P30 A DNA-Based Assay for Chemical Toxicity in Wastewater and
Drinking Water
Vangelis George Kanellis1 , Amy Foreman1 , Leo Phillips1 , Cris dos Remedios1 , David
Hibbert2 , John Chapman3 , Moreno Julli3 , Ronald Patra3 1 Anatomy and Histology, The University of Sydney, Sydney, Anderson Stuart Building (F13), Sydney University, NSW, 2006,
Australia, cris.dosremedios@sydney.edu.au
2 School Chemistry , University of New South Wales, Sydney, Dalton Building, University of New South Wales, Kensington,
2052, b.hibbert@unsw.edu.au
3 New South Wales Government,
P31 Experimental and Computational Studies on Gas Phase Bimetallic
Holmium-Rhodium Clusters
Aidan M. Karayilan 1 , Gregory F. Metha1 1 University of Adelaide, North Terrace Campus Adelaide, SA, 5005, aidan.karayilan@adelaide.edu.au
2 University of Adelaide, North Terrace Campus Adelaide, SA, 5005, greg.metha@adelaide.edu.au
P32 Neutron membrane diffraction measurements of dehydrated DOPC
bilayers with introduced sugars
Ben Kent1 , Gary Bryant2 , Taavi Hunt2 and Christopher J. Garvey1 1 Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, Australia
2 Applied Physics, School of Applied Sciences, RMIT University, Melbourne, Australia
P33 •NO ejection from R• + •NO2. Does •NO2 add through N or O?
Benjamin B. Kirk1 , Adam J. Trevitt 1 , Stephen J. Blanksby1 1 School of Chemistry, University of Wollongong, NSW, 2522

P34 Non-Markovian Memory from Time-Local Stochastic Trajectories
Werner Koch 1 , Frank Grossmann 1
1 Research School of Chemistry, ANU, Canberra, ACT, 0200, Australia
2 Institut für Theoretische Physik, TU Dresden, 01062 Dresden, Germany
P35 Quantum Effects in H2-Li+-Benzene: A Model For Hydrogen Storage
Materials
Stephen J. Kolmann 1 , Meredith J. T. Jordan2 1 School of Chemistry, The University of Sydney, NSW, 2006. email: s.kolmann@chem.usyd.edu.au
2 School of Chemistry, The University of Sydney, NSW, 2006. email: m.jordan@chem.usyd.edu.au
P36 Anion photoelectron spectra of the halide-(N2)n and -(N2O)n clusters
Kim M. Lapere1 , Allan J. McKinley1 & Duncan A. Wild1 1 Chemistry, University of Western Australia, M313 35 Stirling Hwy Crawley, WA 6009, 20169424@student.uwa.edu.au
P37 Transient Absorption Spectroscopy of Curcumin-Copper Complex
Hei Man Mandy Leung1 , Dr Tak W. Kee2 1 School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia, 5005, Australia,
hei.leung@adelaide.edu.au
2 School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia, 5005, Australia, tak.kee@adelaide.edu.au
P38 Optimising the responsive behaviour of polymer surfaces using
Molecular Dynamics
Kamron Ley 1 , George Yiapanis 1 , Irene Yarovsky 1 , Evan Evans 2
1 Applied Sciences, RMIT University, GPO BOX 2476V, Victoria, 3001, Australia
2 BlueScope Steel Research, Port Kembla, NSW, Australia
Poster Authors
P39 Laser Spectroscopic Studies of Conformation in Neurotransmitters
Isabella Antony Lobo1 , David Wilson2 , Evan Bieske3 , Evan G Robertson 4
1 Department of Chemistry, La Trobe University, Bundoora, Victoria, 3086, ialobo@students.latrobe.edu.au
2 Department of Chemistry, La Trobe University, Bundoora, Victoria, 3086, david.wilson@latrobe.edu.au
3 School of Chemistry, University of Melbourne, Victoria, 3010, evanjb@unimelb.edu.au
4 Department of Chemistry, La Trobe University, Bundoora, Victoria, 3086, e.robertson@latrobe.edu.au
P40 Single Cell Membrane Analysis by TERS is Reaching Nanometer Scale
Christian Löbbe1 , Marc Richter2 , Heiko Haschke2 , Martin Hedegaard 3 , Tanja Deckert-
Gaudig4 , Peter Lampen5 , Volker Deckert 4,6
1 Scitech P/L, 4/72-74 Chifley Dr, Preston 3072, Australia
2 JPK Instruments AG, Bouchestr. 12, 12435 Berlin, Germany
3 Technical Faculty University of Southern Denmark, Institute of Sensors, Signals and Electrotechnics (SENSE), Campusvej 55,
5230 Odense M, Denmark
4 Institute of Photonic Technology (IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany
5 Leibnitz-Institut für Analytische Wissenschaften – ISAS e.V., Bunsen-Kirchhoff-Str. 11, Dortmund 44139, Germany
6 Friedrich-Schiller-Universität Jena, Institute of Physical Chemistry, Helmholzweg 4, 07743 Jena, Germany
97

98
Poster Authors
P41 Reinvestigating the 308 nm Photodissociation Dynamics of
Acetaldehyde: A Velocity Map Imaging Study Examining Two Distinct
Pathways Producing CO + CH4
Alan T. Maccarone 1 , Mitchell S. Quinn2 , Gabi de Wit3 , Scott A. Reid4 , B. Klaas Nauta5 ,
Scott H. Kable6 1 School of Chemistry, University of Sydney, New South Wales 2006, alanmac@uow.edu.au
2 School of Chemistry, University of Sydney, New South Wales 2006, mqui5334@uni.sydney.edu.au
3 School of Chemistry, University of Sydney, New South Wales 2006, g.dewit@chem.usyd.edu.au
4 Department of Chemistry, Marquette University, Milwaukee, WI, USA, scott.reid@marquette.edu
5 School of Chemistry, University of Sydney, New South Wales 2006, k.nauta@chem.usyd.edu.au
6 School of Chemistry, University of Sydney, New South Wales 2006, s.kable@chem.usyd.edu.au
P42 Understanding the immune interactions of an unstructured protein
antigen: the malaria surface protein MSP2
Christopher A. MacRaild1 , Marie Ø. Pedersen1 , Christopher G. Adda2 , Robin F. Anders2 and Raymond S. Norton1 1 Department of Medicinal Chemistry and Drug Action, Monash University, Melbourne, Australia.
2 Department of Biochemistry, La Trobe University, Melbourne, Australia
P43 Computational investigation of binding of kappa conotoxin to voltagegated
potassium channels
S. Mahdavi 1 and S. Kuyucak1 1-School of Physics, University of Sydney, NSW2006, Australia
P44 Ab initio and classical molecular dynamics study of the aggregation
propensities of amyloidogenic peptides in the presence of
nanomaterials
A.J. Makarucha 1 , N. Todorova1 , A. Mostofi 2 , I. Yarovsky 1
1 Health Innovations Research Institute, School of Applied Sciences, RMIT University, GPO Box 2476 V, Melbourne, VIC,
Australia.
2 Department of Material s & Physics, Imperial College London, London, U.K., SW7 2AZ
P45 Competitive N-O and O-C homolysis in TEMPO-based alkoxyamines
David L. Marshall 1 , Martin R. L. Paine1 , Ganna Gryn’ova2 , Philip J. Barker3, Michelle L.
Coote2 , Stephen J. Blanksby1 1 ARC Centre of Excellence for Free Radical Chemistry and Biotechnology & School of Chemistry, University of Wollongong,
NSW, 2522
2 ARC Centre of Excellence for Free Radical Chemistry and Biotechnology & Research School of Chemistry, Australian
National University, Canberra ACT, 0200
3 BlueScope Steel Research, P.O Box 202, Port Kembla, NSW, 2502
P46 Thermodynamics and Metabolomics integration into metabolic
Genome Scale Model to resolve metabolic flux directions
Veronica Martinez1 , Stefanie Dietmair1 , Lake-Ee Quek1 , Lars Keld Nielsen1 1 Australian Institute for Bioengineering and Nanotechnology, The University of Queensland Australia , Corner College and
Cooper Rds (Bldg 75) Brisbane, Qld, 4072

P47 Diagnostics for Orbital and Wavefunction Quality
Poster Authors
Laura K McKemmish 1 *, Jia Deng 1 and Peter Gill 1
1 Research School of Chemistry, Australian National University, Science Road, Acton 2601 ACT Australia
* laura.mckemmish@gmail.com
P48 Far-Infrared spectroscopy of water aerosols using synchrotron
radiation
Chris Medcraft1,2 , Evan G. Robertson 3 , Dominque R.T. Appadoo2 , Sigurd Bauerecker 4 and
Don McNaughton1 1 School of Chemistry, Monash University, Victoria 3800 Australia, chris.medcraft@monash.edu, don.mcnaughton@monash.
edu
2 Australian Synchrotron, 800 Blackburn Rd, Clayton, 3168, Victoria. Australia, dominque.appadoo@synchrotron.org.au
3 Department of Chemistry, La Trobe University, Victoria 3083 Australia, E.Robertson@latrobe.edu.au
4 Institut für Physikalische und Theoretische Chemie, Technische Universität Braunschweig, Hans-Sommer-Strasse 10,
D-38106 Braunschweig, Germany
P49 Quantum Chemical Studies of the Catalytic Mechanism of E3
Hydrolysis of Organophosphates in the Australian Sheep Blowfly L.
cuprina
Tamara Meirelles1 , Junming Ho1 , Michelle Coote1 , Colin Jackson1 *
1 Research School of Chemistry, Australian National University ACT 0200
*cjackson@rsc.anu.edu.au
P50 Ab Initio Folding of Helical Peptides Using Adaptive Hydrogen Bond-
Specific Charge Scheme
Siti Raudah Mohamed Lazim1 , Dawei Zhang2 Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological
University, 21 Nanyang Link, Singapore, 637371,
1 SITI13@e.ntu.edu.sg
2 zhangdw@ntu.edu.sg
P51 Amyloid-like fibrillization and the structure of glucagon in the presence
of anionic bicelles
Ayano Momose 1 , Izumi Yamane 1 , Hideki Fujita 1 , Eri Yoshimoto 1 , Izuru Kawamura1 ,
Marc-Antoine Sani2 , Frances Separovic2 , Akira Naito1 1 Graduate School of Engineering, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan naito@ynu.ac.jp
2 School of Chemistry, Bio21 Institute, University of Melbourne, VIC 3010
P52 Modelling Molecular Response in Anisotropic Electric Fields
Michael Morris1 , Meredith Jordan2 1 School of Chemistry, University of Sydney, NSW, 2006, morris_m@chem.usyd.edu.au
2 School of Chemistry, University of Sydney, NSW, 2006, mjtj@chem.usyd.edu.au
99

Poster Authors
P53 Examining the Electronic Interactions of Ligated Copper Nanoparticles
Generated by Laser Ablation Synthesis in Solution (LASiS)
Ashley Mulder1 , Mark Buntine1 , Aidon Slaney1 , Sean Long1 , Max Massi1 , Franca Jones1 ,
Mark Ogden1 1 Department of Chemistry, Curtin University, GPO BOX U1987, Perth WA 6845
P54 Patch Fluorimetry to Measure the Membrane Tension Required to Gate
Mechanosensitive Ion Channels
Takeshi Nomura1 , Charles Cranfield1,2 , Boris Martinac1,2 1 Victor Chang Cardiac Research Institute, Lowy-Packer Building, 405 Liverpool St, Darlinghurst, 2010.
2 St Vincent’s Clinical School, The University of New South Wales, de Lacy, Victoria St, Darlinghurst, 2010
T.nomura@victorchang.edu.au; C.cranfield@victorchang.edu.au; B.martinac@victorchang.edu.au
P55 Structural characterization of triacylglycerols by radical directed
dissociation
Huong T. Pham 1 , Stephen J. Blanksby 2 , Gavin E. Reid 3
1 School of Chemistry, University of Wollongong, Australia, thp658@uow.edu.au
2 School of Chemistry, University of Wollongong, Australia, blanksby@uow.edu.au
3 Department of Chemistry, Michigan State University, United States, reid@chemistry.msu.edu
P56 Organic Monolayers for Water Evaporation Suppression: A Molecular
Dynamic Study
Michael Plazzer, George Yiapanis, Irene Yarovsky1 1 Applied Physics, School of Applied Sciences, RMIT University, Melbourne 3000 irene.yarovsky@rmit.edu.au
P57 Langevin dynamics modelling of water diffusion in anisotropic
biophysical structures.
Sean Powell1 , Konstantin Momot1 1 Discipline of Physics, Queensland University of Technology, GPO Box 2434, Brisbane, QLD, 4001, sean.powell@qut.edu.au
P58 Photodissociation Dynamics of Acetaldehyde at 308 nm: A Comparison
of Experimental Studies and a Classical Trajectory Study of the
Transition State Mechanism
Mitchell S. Quinn1 , Gabi de Wit2 , Scott A. Reid3 , B. Klaas Nauta4 , Alan T. Maccarone 5 ,
Scott H. Kable6 , Meredith J. T. Jordan7 P59 Alanine scan of an immunosuppressive peptide: Surface plasmon
resonance analysis and structure-function relationships
Laura Raguine1 , Marina Ali1 , Veronika Bender1 , Eve Diefenbach2 , Nicholas Manolios1 1 Department of Rheumatology, Westmead Hospital, Westmead, NSW 2145, Australia.
2 Protein Production Facility, Westmead Millennium Institute, Westmead, NSW 2145, Australia.
100

P60 Affinity and selectivity of sea anemone toxin ShK for the Kv1.1, Kv1.2
and Kv1.3 channels from free energy simulations.
M.H. Rashid and S. Kuyucak
School of Physics, University of Sydney, NSW 2006, Australia,
harun@physics.usyd.edu.au, serdar@physics.usyd.edu.au.
P61 Large-scale fully ab initio calculations of ionic liquids using the
Fragment Molecular Orbital approach
Jason D. Rigby, Douglas R. MacFarlane, Ekaterina I. Izgorodina
School of Chemistry, Monash University, Wellington Road, Victoria, 3800, E-Mail: jason.rigby@monash.edu
P62 Structural studies of osmoregulatory ABC transporters
Stephanie J. Ruiz12 , , Maaike Jansen, and Bert Poolman
1 Department of Biochemistry, University of Groningen, The Netherlands
2 s.j.ruiz@rug.nl
P63 Determination of Threshold Dissociation Energies of Li+, Na+, K+ and
Cs+ Cationized Dimers of 3-Hydroxyflavone, 5-Hydroxyflavone and
5-Methoxyflavone by FTICR Mass Spectrometry and DFT Calculations
Chowdhury Hasan Sarowar 1 , Michael Guilhaus2 , Gary David Willett3 , Grainne Moran4 1 School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia, c.h.sarowar@unsw.edu.au
2 Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, NSW 2052, Australia
3 School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia, g.willett@unsw.edu.au
4 Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW 2052, Australia, g.moran@unsw.edu.
au
P64 The impact of the ab initio/DFT method used for geometry
optimisations on reaction enthalpies
D. L. A. Scarborough, C. D. Thompson, E. I. Izgorodina
School of Chemistry, Monash University, Victoria, Australia, 3800
Email: David.Scarborough@monash.edu
Poster Authors
P65 Spectroscopy of resonance-stabilized hydrocarbon radicals
Timothy W. Schmidt, Tyler P. Troy, Nahid Chalyavi, Zijun Ge, Gerard D. O’Connor,
Masakazi Nakajima, Neil J. Reilly, Damian L. Kokkin, Klaas Nauta, Scott H. Kable
School of Chemistry, The University of Sydney, NSW 2006, Australia
P66 Surface-enhanced Raman Spectroscopy of Isoflavones on Alternative
Substrates
Ryo Sekine1 , Evan G. Robertson, 2 Leone Spiccia3 , Richard A. Dluhy4 , Don McNaughton 5
1 Centre for Biospectroscopy, Monash University, Clayton, VIC, 3800, Australia, ryo.sekine@monash.edu
2 School of Molecular Sciences, La Trobe University, VIC, 3086, Australia, e.robertson@latrobe.edu.au
3 School of Chemistry, Monash University, Clayton, VIC, 3800, Australia, leone.spiccia@monash.edu
4 Department of Chemistry, The University of Georgia, Athens, GA, USA, dluhy@uga.edu
5 Centre for Biospectroscopy, Monash University, Clayton, VIC, 3800, Australia, don.mcnaughton@monash.edu
101

Poster Authors
P67 Dynamic Characterisation of Surfaces Using In-Silico Nano-
Indentation
102
Lachlan Shaw 1 , George Yiapanis 1 , David Henry 2 , Evan Evans 3 , Irene Yarovsky 2
1 School of Applied Sciences, RMIT University, GPO Box 2476, Vic, 3001
2 School of Chemical and Mathematical Sciences, Murdoch University, South Street, WA, 6150
3 BlueScope Steel Research Laboratories, Islands Rd, Port Kembla, NSW, 2505
P68 CyDNA: A versatile photoswitchable biopolymer for advanced
fluorescence microscopy applications.
Darren A. Smith 1,2 ,*, Philipp Holliger 3 , Cristina Flors 1 ,*
1 EaStChem School of Chemistry, University of Edinburgh, Edinburgh, EH9 3JJ, United Kingdom.
2 School of Chemistry, University of Melbourne, Melbourne, 3010, Australia.
3 MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom.
P69 Computational characterisation of an unusual metallacalix[4]arene
dinitrogen activator
Richard Terrett1 , Germán E. Cavigliasso1 , Rob Stranger1 , B.F. Yates 2
1 Research School of Chemistry, Australian National University, ACT, 0200, email: rterrett@rsc.anu.edu.au
2 School of Chemistry, University of Tasmania, Private Bag 75, Hobart, TAS 7001
P70 Recombination of photolytically generated iodine in single iodoalkane
microdroplets
Phillip J. Tracey1 , Bartholomew S. Vaughn1 , Adam J. Trevitt 1
1 School of Chemistry, University of Wollongong, NSW, 2522
pjt105@uowmail.edu.au
P71 Symmetry, Pseudo-symmetry and Evolution in Protein Structures
Donald G Vanselow 1
1 nativeproteins.blogspot.com 54 Greenways Rd., Glen Waverley VIC 3150, Australia. dvanselow@hotmail.com
P72 Single Microdroplet Laser Spectroscopy
Bartholomew S. Vaughn1 , Phillip J. Tracey 1 , Adam J. Trevitt 1 .
1 School of Chemistry, University of Wollongong, NSW 2522
bv703@uowmail.edu.au
P73 Molecular Dynamics of Curcumin and Linked Cyclodextrin Dimers
Samuel J. Wallace 1 , David M. Huang2 , Takaaki Harada, 3 Tak W. Kee4 1 University of Adelaide, North Terrace, South Australia, 5005, sam.wallace@adelaide.edu.au
2 University of Adelaide, North Terrace, South Australia, 5005, david.huang@adelaide.edu.au
3 University of Adelaide, North Terrace, South Australia, 5005, takaaki.harada@adelaide.edu.au
4 University of Adelaide, North Terrace, South Australia, 5005, tak.kee@adelaide.edu.au

Poster Authors
P74 De novo Structure prediction of Peptide Based Biomimetic
Carbohydrate Receptors
Mark Waller1 1 Organic Chemistry Institute, University of Münster, Corrensstraße 40, D-48149 Münster, Germany
P75 Modelling Cellulase Activity upon Cellulose Surfaces using Cellular
Automata
Andrew C. Warden1 , Bryce A. Little2 , Victoria S. Haritos1 1 CSIRO Ecosystem Sciences, Clunies Ross St, Acton, Canberra, ACT, 2601
2 CSIRO Livestock Industries, Queensland Biosciences Precinct, 306 Carmody Road, St. Lucia, QLD, 4067
P76 Lipid Composition Regulates the Conformation and Insertion of the
Antimicrobial Peptide Maculatin 1.1
Thomas Whitwell1 , Marc-Antoine Sani1 , Frances Separovic1 1 School of Chemistry, Bio21 Institute, University of Melbourne, VIC 3010
P77 The Quokka Small Angle Neutron Scattering Instrument at OPAL
K. Wood1 , C. J. Garvey1 , E. P. Gilbert1 1 Bragg Institute, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232,
Australia
P78 Structure, dynamics and interactions of malaria surface antigens
Tessa R. Young 1 , David K. Chalmers1 , Christopher A. MacRaild1 , Marie O. Pedersen1 , Robin
F. Anders2 , Raymond S. Norton1 1 Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Australia
2 Department of Biochemistry, La Trobe University, Bundoora, VIC 3086, Australia
P79 New insights into the chemical reactivity of the deazaflavin cofactor
F420 through quantum chemical calculations.
Peng Yuan1 , Junming Ho1 , Colin J. Jackson1 , Michelle L. Coote1 1 Research School of Chemistry, Australian National University, ACT, 0200, coote@rsc.anu.edu.au
P80 Utilization of Ambient Ozone for Determining Double Bond Positions in
Unsaturated Lipids
Shane R. Ellis1 , Marc in het Panhuis2 , Todd W. Mitchell3 , Stephen J. Blanksby1 ,
1 ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, School of Chemistry, University of Wollongong,
Wollongong, NSW, 2522
2 School of Chemistry, University of Wollongong, Wollongong, NSW, 2522
3 School of Health Sciences, University of Wollongong, Wollongong,
P81 Thioflavin T and its derivatives: Revealing their spectroscopic
properties in the absence and presence of insulin amyloid fibrils
Eric H.-L. Chen 1 , Jack C.-C. Hsu 1 , Frederick Y. Luh 1 , T.-S. Lim2 , Rita P.-Y. Chen1 1 Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
2 Department of Physics, Tunghai University, Taichung 407, Taiwan
103

Poster Presentations
Sunday 4 December - Session 1
P1
Melatonin and serotonin in
characeae
Sabah Al Khazaaly 1 , Mary Jane Beilby1 ,
Susan Murch2 , Faisal Albisherawy 1
1 The University of NSW, School of Physics, Kensington, Sydney,
NSW, 2052, m.j.beilby@unsw.edu.au
2 University of British Columbia, Okanagan , Kelowna, British
Columbia, Canada, V1V 1V7 , susan.murch@ubc.ca
Abstract
Neurohormone melatonin (N-acetyl-5methoxytryptamine)
is secreted principally by the
pineal gland of mammals including humans. The
concentration levels exhibits a circadian cycle with
a peak during the night. Other physiological
functions may depend on the melatonin signal,
such as immune antioxidative defences,
hemostasis and glucose regulation (Claustrat et al.
2005, Sleep Medicine Reviews 9: 11). Disturbed
melatonin secretion is likely to predispose the
organism to disease. Serotonin, which forms in the
same metabolic pathway as melatonin, functions
as a neurotransmitter in brains of animals.
Recent research found melatonin and serotonin in
higher plants (Murch and Saxena, 2002, In Vitro
Cellular & Developmental Biology - Plant, 38, 531;
Posmyk and Janas, 2009, Acta Physiologia
Plantarum 31: 1). Some medicinal plants, such as
St. John’s wort, contained up to gs per g of tissue.
The structure of melatonin and serotonin is closely
related to an important plant growth hormone
auxin. It appears that these ancient molecules are
highly conserved across biological kingdoms and
might also act in plants as growth hormones,
antioxidants and chronobiological substances.
The giant-celled characeae are extant relatives of
ancestors of all land plants and are used
extensively to model physiology and
electrophysiology of land plant cells. Thus the
presence or absence of melatonin and serotonin is
of interest. Preliminary experiments with salt
sensitive Chara australis and salt tolerant
Lamprothamnium succinctum yielded
comparatively high amounts of melatonin and
serotonin of up to 4 g/g and 50 g/g, respectively.
Melatonin and serotonin were extracted by
104
employing ethanol, purified by high performance
liquid chromatography (HPLC) and indentified by
mass spectrometry.
The effects of varying day-night regimes, light of
different wavelength and Ca2+ concentration on
the melatonin and serotonin levels will be tested at
single cell level. Later experiments will include
exogenously applied melatonin and inhibitors of
indoleamine metabolism, such as Ritalin and
Prozac.
P2
Zn2+ inactivates H+/OH- channels of
Chara australis
Sabah Al Khazaaly 1 , Mary Jane Beilby1 1 The University of NSW, School of Physics, Kensington, Sydney,
NSW, 2052, s.alkhazaaly@unsw.edu.au
1 The University of NSW, School of Physics, Kensington, Sydney,
NSW, 2052, m.j.beilby@unsw.edu.au
Abstract
Zn2+ inactivates many types of animal H+
channels by binding to histidine residues of the
channel proteins (DeCoursey, 2010, Physiology,
25: 27). Mercaptoethanol (ME) reverses this
inhibition by scavenging the zinc ions. Are plant H+
(or OH-) channels sufficiently similar to be affected
by Zn2+?
Giant-celled characeae, extant relatives to
ancestors of all land plants, exhibit acid and
alkaline banding with circulating external currents
between the zones (Spear et al 1969, Journal of
General Physiology, 54: 397; Walker and Smith,
1977, Journal of Experimental Botany, 28: 1190). In
the acid zone the proton pump exports H+ out of
the cell, while in the alkaline zone H+/OHchannels
facilitate either passive H+ influx or OHefflux.
Different schemes have been proposed
involving CO2 and HCO3- transport, but there is
agreement that banding facilitates carbon
assimilation in slightly alkaline ponds, where
freshwater characeae live. Cells transferred into a
medium of pH above 10.0 exhibit high
conductance and the membrane PD (potential
difference) behaves like a pH electrode: the whole
cell becomes an alkaline band (Bisson and Walker,
1980, Journal of Membrane Biology 56: 1). Upon

exposure to 1 mM ZnCl2, this high pH state is
abolished, but can be restored by exposure to 0.5
mM mercaptoethanol. Banding also disappears in
response to ZnCl2.
Beilby and Al Khazaaly (2009, Journal of
Membrane Biology, 230: 21) and Al Khazaaly et al
(2009, European Biophysics Journal 39: 167)
postulated that H+/OH- channels open transiently
at the onset of saline stress in salt sensitive Chara
australis, causing membrane PD noise; and remain
open in latter stages of saline stress, contributing
to cell deterioration. Zn2+ inhibited the saline noise
and the upwardly concave I/V characteristics
associated with the H+/OH- channel opening after
several hours of saline stress. Both these effects
could be reversed by ME. We will discuss the
similarity of plant and animal H+/OH- channels and
the increasing evidence for role of these channels
in plant salinity stress.
P3
Phenol and p-Chorophenol
Adsorption onto Alumina-Grafted
Different Polymers
Hadi S. Al-Lami 1 , Ammar H. Al-Dujiali 2 ,
Maha T. Sultan 3
1 Department of Chemistry, College of Science, University of
Basra-Iraq
2,3 Department of Chemistry, College of Education/ Ibn
Al-Haitham, University of Baghdad-Iraq.
Abstract
The ability of different alumina-grafted polymers
was examined for adsorption of phenol and
p-chlorophenol under different conditions (i.e.
concentrations and temperatures). Adsorption
behavior for standard alumina, alumina-graft
acrylic acid monomer and other three polymers (A,
B, C) in relation to adsorption of phenol and
p-chlorophenol showed that adsorption follows
Freundlich equation for phenol and p-chlorophenol
while substances behavior was different in this
process as the standard alumina adsorbed phenol
better than others while the adsorption of
p-chlorophenol onto alumina-graft acrylic acid
monomer and polymer A was better. Both
polymers B and C showed a good adsorption for
phenol and p-chlorophenol.
Poster Presentations
Sunday 4 December - Session 1
P4
Experimental and Computational
Investigations into Size Selected
Gold Clusters on Semiconductor
Supports as Photoelectrochemical
Catalysts
Jason F. Alvino1 , Greg F. Metha2 1 The University of Adelaide, North Terrace Campus, SA, 5005,
Jason.alvino@adelaide.edu.au
2 The University of Adelaide, North Terrace Campus, SA, 5005,
greg.metha@adelaide.edu.au
Abstract
For many years it has been known that
semiconductor surfaces or particles such as TiO2
can absorb light in order to directly drive the
processes required to generate H2. It has been
shown in recent years that doping TiO2 with
various noble metal nanoparticles such as Au or Pt
can promote H2 generation by acting as a
‘reservoir’ for photo-generated electrons.
Experimental studies are being developed to
investigate the photo-catalytic potential of various
configurations of size selected gold clusters on
semiconductor surfaces using an experimental
apparatus that can provide immediate feedback
on the gas composition of the reaction.
Computational studies have been performed on
various rutile (110) and anatase (101) TiO2 surface
models utilizing the ONIOM partitioning scheme.
This computational technique can model large
systems by defining two or three layers within the
structure that are treated with varying levels of
accuracy. In this work the high layer was treated
with density functional theory and the low layer
surrounding lattice structure was treated with
molecular mechanics methods. This has allowed
for the modelling of a large area of the TiO2
surface with minimal computational expense while
utilizing atomic centred basis sets for the
interaction site. Various types of defect sites were
modelled including but not limited to i) oxygen
vacancies, ii) smooth step-edges, and iii) rough
step edges. Au, Au2 and Au3 clusters were then
added to these defect sites to determine the
binding energy, reaction profiles, density of states
and morphological changes to the TiO2 surface.
105

Poster Presentations
Sunday 4 December - Session 1
The experimental apparatus and an explanation of
the computational procedure, including preliminary
results, will be presented in this poster.
P5
High-resolution FTIR spectroscopy
of the ground state, v8, v7, v6 and
Coriolis “perturbation allowed” v12
and v10 modes of ketenimine.
M. K. Bane1 , C. D. Thompson1 , E. G.
Robertson2 , D. R. T. Appadoo3 , C. Medcraft1, D.
McNaughton1 .
1 School of Chemistry, Monash University, Victoria 3800 Australia
2 Department of Chemistry, La Trobe University, Victoria 3083
Australia
3 Australian Synchrotron, 800 Blackburn Rd, Clayton, 3168,
Victoria. Australia
Abstract
Ketenimine (CH2CNH) is a transient molecule that
is of interest in interstellar chemistry and about
which little is known. This tautomer of acetonitrile
has been identified in the star forming region
Sagittarius B2(N) by observing microwave
emissions (1). In this study far- and mid-IR high
resolution spectra were recorded using a Bruker
HR125 coupled to the far-IR beam line of the
Australian synchrotron and both pure ground state
rotational transitions and ro-vibrational transitions
were recorded.
The excited vibrational states exhibit a complex
ro-vibrational structure, due primarily to strong
Coriolis interactions. As a consequence of this
coupling, some of these modes exhibit a novel
intensity sharing effect, with the relatively weak v10
and v12 (2) bands being analyzed completely
using perturbation allowed transitions, which
exhibit intensities independent of their own natural
dipole moment derivative.
The analysis of v7 (3), v10 and v6 (4) were also
complicated by the presence of local Fermi and
Coriolis resonances with the higher order
excitations of v12 and v8, which are themselves
strongly Coriolis coupled. Analysis of ground state
combination differences of v7 also uncovered
second order Coriolis interactions between the
106
ground state and both v12 and v8 at high Ka, and
a global fit including the ground state, v12, v8, v7,
2v12, v12 + v8, 2v8, v10 and v6 was achieved. The
combination and overtones are included in the fit
as dark-states, since they were too weak to be
observed.
1. F. J. Lovas, J. M. Hollis, A. J. Remijan and P. R. Jewell,
Astrophys. J., 2006, 645, L137
2. M. K. Bane, C. D. Thompson, E. G. Robertson, R. T. Appadoo
and D. McNaughton, Phys. Chem. Chem. Phys., 2011, 13, 6793
3. M. K. Bane, E. G. Robertson, C. D. Thompson, R. T. Appadoo,
C. Medcraft and D. McNaughton, J. Chem. Phys., 2011, 134,
234306
4. Analysis of v10 and v6 is currently unpublished
P6
An improved method, with
theoretical analyses, for the simple
experimental measurement of liquid
junction potentials
Peter H Barry1 , Trevor M Lewis1 , Andrew J
Moorhouse1 1 Dept of Physiology, School of Medical Sciences, University of
New South Wales, Sydney, NSW 2052, Australia. Email: p.
barry@unsw.edu.au; t.lewis@unsw.edu.au; a.moorhouse@
unsw.edu.au
Abstract
In electrophysiological experiments, accurate
potential measurements require corrections for
liquid junction potentials (LJPs). Under certain
conditions, as in patch clamp experiments and
dilution potential measurements, their magnitude
can often be ~5-10 mV or more. In most cases,
where the ion mobilities are known, LJP
corrections can be simply calculated. However, in
order to confirm such calculations, or if ion
mobilities are not known accurately, it is necessary
to measure LJPs experimentally. We describe here
an improved simple and accurate method for
doing this using a freshly-cut 3M KCl-agar

salt-bridge (in polyethylene tubing) as a reference
electrode. Critical to success, is cutting off at least
the last 5 mm of this KCl-agar salt-bridge just
before it is placed into a different test solution. This
ensures a fresh 3M KCl-agar surface in contact
with the test solution, and eliminates the major
history-dependent problem that normally arises
with 3M KCl reference salt-bridges (e.g., [1] and
[2]). The measured potentials also need to be
corrected for a small, well-defined and easily
calculable, shift in LJPs at this 3M KCl salt-bridge.
We directly demonstrate the extent of the
history-dependent problems and how the
freshly-cut tip eliminates them, supporting these
experiments with new theoretical analyses of NaCl
diffusing into a 3M KCl-agar salt bridge and the
KCl diffusing out of it, with diffusion coefficients
corrected for the 4% agar gel used in the
salt-bridges [3]. Using this improved technique, we
have measured LJPs for diluted solutions of NaCl
(with and without CaCl2), LiCl, KCl and CsCl and
for biionic combinations of the undiluted salts
(some earlier measurements are in [4, 5]). The
measured values give excellent agreement
(generally within expected errors of 0.1 mV) with
LJPs theoretically calculated with the Henderson
equation [6], and incorporated into a liquid junction
potential calculation program (JPCalc; [7]). We also
demonstrate that ion activities rather than
concentrations should be used for dilution LJP
calculations.
1. Barry, PH & Diamond, JM (1970) J Membrane Biol. 3: 393-122
2. Neher E (1992) Meth. Enzym. 207: 123-131
3. Slade AL, Cremers AE, Thomas HC (1966). J. Phys.Chem. 70:
2840-2844.
4. Sugiharto S, Carland JE, Lewis TM, Moorhouse AJ, Barry PH
(2010). Pflügers Archiv 460: 131-152.
5. Barry PH, Sugiharto S, Lewis TM, Moorhouse AJ. (2010)
Channels 4: 142-149
6. Barry PH, Lynch JW. (1991) J. Membrane Biol. 121: 101-117.
7. Barry, PH (1994) J. Neurosci. Meth. 51: 107-116
Poster Presentations
Sunday 4 December - Session 1
P7
Computational and Experimental
investigations into catalytic
applications of gas-phase goldniobium
bimetallic clusters
Trystan Bennett1 , Robert A. Hardy1 , Gregory
F. Metha1 1. The University of Adelaide, North Terrace Campus, Adelaide SA
5005. Trystan.bennett@adelaide.edu.au
Abstract
Mass Spectra of oxygen-poor bimetallic Au/Nb
clusters (AunNbxOy; n=0-2,x=1-5,y=0-3) were
recorded from clusters produced in the gas phase
using laser ablation, and ionised via multi-photon
ionisation with 220 nm light.
Computational studies were undertaken on all
species observed, using density functional theory
at the M06-L/SDD/aug-cc-pVTZ level of theory.
Gold atoms incorporated into these molecules
were found to attain δ- charge build-up, with
correlation between charge magnitude and the
oxidation state of the niobium atoms. Evidence of
gold substitution of both niobium and oxygen
atoms was found within predicted geometries.
Benchmarking of eleven density functionals was
undertaken across ionisation energies and
electron affinity calculations, with M06-L found to
be superior for calculations of niobium oxide
clusters.
This poster will present findings from the
benchmarking of eleven density functionals with
niobium oxide clusters, modelling both electron
affinities and ionisation energies. The functionals
benchmarked represent a wide array of
approaches, from pure DFT approaches such as
B97-D and M06-L, to hybrid DFT approaches
such as B3LYP, B3P86, and B98.
Further results are presented from the
experimental/computational application of the best
performing functional found during benchmarking,
M06-L. Structure calculations and Hirschfeld
charge investigations were performed upon 16
bimetallic gold-niobium oxide clusters, ranging in
size from 3 to 9 atoms. Examinations of electronic
structure, motif development and structure trends
107

Poster Presentations
Sunday 4 December - Session 1
trend are undertaken, with the end goal of
assessing the bimetallic clusters’ suitability for
further surface-deposition catalytic studies.
P8
Designing single-molecule assays to
image the dynamics of molecular
chaperones
Quill Bowden1 and Till Böcking2 1 Centre for Vascular Research, UNSW, Sydney 2052,
q.bowden@unsw.edu.au
2 Centre for Vascular Research, UNSW, Sydney 2052, till.
boecking@unsw.edu.au
Abstract
Molecular chaperones maintain protein
homeostasis in the cell by catalysing a wide variety
of processes throughout a protein’s life cycle. Their
functions include protein folding, remodelling of
protein assemblies, protection from denaturation
and resolubilisation of proteins from aggregates
that accumulate during cell stress. The aim of our
research is to elucidate the molecular mechanisms
of how chaperones from the Hsp70 family interact
with proteins that have assembled into oligomers
or are on the pathway towards aggregate
formation. Utilisation of single-molecule
fluorescence microscopy techniques will allow us
to observe individual molecules in the dynamic
chaperone-substrate interactions and thus resolve
reaction pathways that are obscured in traditional
ensemble approaches. Here we present our initial
results on developing strategies for protein
labelling and design of the fluorescence imaging
assay. This research has implications for a range
of neurodegenerative diseases that are
characterised by the accumulation of insoluble
protein aggregates (amyloid fibrils). Disease states
were previously attributed to the presence of these
amyloids in the neuronal regions, however current
research suggests that toxicity is actually exerted
by soluble pre-fibrillar species. A better
understanding of the interactions of chaperones
with assemblies of disease proteins will shed light
on the role of chaperones in modulating the
progression of these diseases.
108
P9
In silico modeling of protein
dynamics and drug design
Melissa J. Buskes1 , David J. D. Wilson2 ,
Belinda M. Abbott3 1 La Trobe Institute for Molecular Science, La Trobe University,
Plenty Rd, Bundoora, VIC, 3086, M.Buskes@latrobe.edu.au
2 La Trobe Institute for Molecular Science, La Trobe University,
Plenty Rd, Bundoora, VIC, 3086, David.Wilson@latrobe.edu.au
3 La Trobe Institute for Molecular Science, La Trobe University,
Plenty Rd, Bundoora, VIC, 3086, B.Abbott@latrobe.edu.au
Abstract
This presentation reports current results from an
ongoing study aimed at identifying selective and
potent inhibitors of target kinases through
molecular modeling – computer aided drug
design. The study of the interaction of small
molecules with proteins is a long held interest in
the Molecular Modeling group at La Trobe
University.
The work presented here builds on previous
studies designed to develop a potent inhibitor of
the target kinase, with a major focus on the issue
of selectivity of inhibitors. This was achieved by
modeling inhibitors through selected protein
kinases. Biological assay results of our lead series
of compounds highlight selectivity matters
between these particular kinases, and these
kinases were therefore selected for analysis. Our
goal was to optimize the lead compounds as a
result of modeling selectivity.
Results of molecular dynamics modeling of
inhibitors of the protein kinases will be presented.
In this work we have extensively used the AMBER
package in conjunction with the MM-PBSA and
MM-GBSA methods. Analysis of model
preparation, benchmarking and validation of
methodology, in comparison with experimental
data, was carried out in order to provide an
indication of accuracy, reproducibility and reliability
of this approach to the calculation of binding
energies.

P10
Differential Dynamic Microscopy
Studies of Bacterial Motility
C. Carnovale 1 , R. Nixon-Luke 1 , G. Bryant1 .
1 School of Applied Sciences, RMIT University, GPO Box 2476,
Melbourne, Victoria, 3000
Abstract
The importance of cell motility is apparent in many
facets of biology. It plays a fundamental role in the
process of internal fertilisation in vivo as well as
disease transmission and the spread of infection.
Used often as a model for understanding bacterial
motility, Escherichia coli generally exhibits random
walk movement in isotropic conditions.
Responsible for the motility of E. Coli, are
appendages called flagella which are arranged
laterally and distributed over the entire external cell
surface. This peritrichous arrangement of flagella
allow E. Coli to alternate forward motion driven by
counter clockwise flagella rotation for ~1 second
before reversal to clockwise movement for ~0.1
second which prompts a change in direction
through a brief tumbling motion [1].
The use of dynamic light scattering to analyse
bacterial motility has been explored for many
decades. In 1971 a seminal study performed by
Nossal, Chen & Lai [2] established one of the
earliest autocorrelation functions to interpret the
swimming speed distributions of E. Coli. While this
method of analysis provides accurate data for
diffusion rate and the fraction of non motile cells,
limitations of the model mean that non linear
movement such as tumbling cannot be accounted
for. Whilst using a low scattering angle (and
effectively a low scattering vector), lessens
undesirable contribution from the tumbling
motions, limitations in equipment capability
prevent this from being a possibility in most
laboratory settings.
Initially tested with colloidal suspensions [3],
differential dynamic microscopy (DDM) is a new
microscope technique based on the principles of
DLS which has recently been tested using
bacterial samples [4]. The main advantage over
DLS is that measurements can be taken using a
very small scattering vector which effectively
Poster Presentations
Sunday 4 December - Session 1
negates the contributions from the irregular
movement and tumbling motions of E.Coli.
In this abstract, we report on measurements of
bacterial motility through using DDM. We analyse a
number of strains of bacteria with different flagella
arrangements, and compare the results with
traditional methods.
We discuss the application to other motile
micro-organisms of varying sizes as well as future
generations of synthesised self motile molecules
1. Berg, H.C. and D.A. Brown, Chemotaxis in Escherichia coli
analyzed by three-dimensional tracking. Antibiotics and
chemotherapy, 1974. 19: p. 55-78.
2. Nossal, R., S.H. Chen, and C.C. Lai, Use of laser scattering for
quantitative determinations of bacterial motility. Optics
Communications, 1971. 4(1): p. 35-39.
3. Cerbino, R. and V. Trappe, Differential dynamic microscopy:
Probing wave vector dependent dynamics with a microscope.
Physical Review Letters, 2008. 100(18).
4. Wilson, L.G., et al., Differential Dynamic Microscopy of Bacterial
Motility. Physical Review Letters, 2011. 106(1).
P11
Exciton Migration in Conjugated
Polymer Dots
Scott N. Clafton 1 , Dr David M. Huang2 , Ming
Chiu3 and Dr Tak W. Kee4 1 University of Adelaide, North Terrace Adelaide, South Australia,
5005, scott.clafton@adelaide.edu.au
2 University of Adelaide, North Terrace Adelaide, South Australia,
5005, david.huang@adelaide.edu.au
3 University of Adelaide, North Terrace Adelaide, South Australia,
5005, ming.chiu@adelaide.edu.au
4 University of Adelaide, North Terrace Adelaide, South Australia,
5005, tak.kee@adelaide.edu.au
Abstract
Energy transfer dynamics of the conjugated
polymer poly[2-methoxy-5-(2-ethylhexyloxy)-1,4phenylene-vinylene]
(MEH-PPV) in two different
solvent environments have been investigated using
femtosecond fluorescence upconversion
spectroscopy. The two environments are that of a
reasonably good solvent (tetrahydrofuran) in which
MEH-PPV adopts a partially extended
conformation and a very poor solvent (water),
which drives the polymer chains into spherical and
highly compact nanoparticles (CPDots). Isotropic
fluorescence kinetic data show energy transfer
behaviour in both solvent environments that is
109

Poster Presentations
Sunday 4 December - Session 1
consistent with previous studies of conjugated
polymers. Time resolved fluorescence anisotropy
decay has previously been used to show that
energy transfer in partially extended polymer
conformations occurs both through space and
along the polymer backbone with approximate
time constants of 1.4 ps and 110 ps, respectively.
By comparing this result to the anisotropy decay of
CPDots it is clear that energy transfer in this
system occurs exclusively in a through space
manner. This is consistent with the hypothesis that
the compact structures of CPDots provide many
chromophores capable of participating in energy
transfer in close proximity to the excited
chromophore.
P12
Species differences in the kinetics of
the Na+,K+-ATPase
Ronald J. Clarke and Flemming Cornelius
School of Chemistry,University of Sydney, Sydney, NSW 2001,
Australia, and Department of Physiology and Biophysics,
University of Aarhus, Aarhus, Denmark
Correspondence.: r.clarke@chem.usyd.edu.au
Abstract
Crystal structures of the Na+,K+-ATPase from two
animal species (pig1 and shark2) have now been
resolved. The 3D structures are very similar and
the amino acid sequences of the alpha subunits of
the two enzymes display ~90% homology.
However, in spite of the similar structures,
stopped-flow investigations of the partial reactions
of the same preparations used for structure
determination have shown that the pig and shark
enzymes display significant differences in their
kinetics3,4. In the case of the pig enzyme, the
major rate-determining step of the reaction cycle
under saturating substrate conditions is the E2 →
E1 conformational transition associated with the
deocclusion of K+ ions and their release to the
cytoplasm. For the shark enzyme the major
rate-determining step appears to be the occlusion
of K+ ions from the extracellular medium by the
phosphorylated enzyme, E2P. These differences in
rate-determining step could have major
consequences for the physiology of the animals
concerned. For example, although both enzymes
110
have similar turnovers when all substrates are at
saturating concentrations, under physiological
conditions the turnovers could be quite different.
Furthermore, based on the different ratedetermining
steps, one would expect the turnover
of the shark enzyme to be much more sensitive to
the extracellular K+ concentration than that of the
pig. The apparent paradox of significantly different
kinetics in spite of very similar structures leads one
to ask what it is that really determines the kinetics
of the Na+,K+-ATPase. Are subtle differences in
the structure of the alpha-subunit sufficient to
explain the different kinetics? Could the kinetic
differences be due to differences in the structure
of the beta-subunit or the gamma (or FXYD)
subunit? Could their origin lie in different lipid
compositions of the surrounding membrane or be
associated with differences in protein-protein
interactions (i.e. between alpha-beta protomers)
within the membrane?
1. Morth JP et al (2007) Nature 450: 1043-5
2. Shinoda T et al (2009) Nature 459: 446-50
3. Khalid et al (2010) Biophys J 98: 2290-8
4. Myers et al (2011) Biophys J 100: 70-9
P13
Cardiac troponin: a paramagnetic
relaxation enhancement NMR study
Nicole M Cordina1 , C K Liew2 , D A Gell2 , J P
Mackay2 , T M Logan3 , L J Brown1 1 Department of Chemistry and Biomolecular Sciences,
Macquarie University, NSW 2109, Australia
2 School of Molecular and Microbial Biosciences, University of
Sydney, NSW 2006, Australia
3 Institute of Molecular Biophysics, Florida State University,
Tallahassee, FL 32306, USA
Abstract
Cardiac Troponin is a trimeric thin filament protein
complex that regulates muscle contraction.
Calcium (Ca2+) binding to the Troponin C (TnC)
subunit triggers the complex to undergo a large
conformational switch from the OFF state, where
acto-myosin interaction is sterically blocked, to the
ON state, where acto-myosin interaction, and thus
muscle contraction can occur. The 18 kDa
Ca2+-binding TnC subunit, which constitutes the
structural core of the troponin complex, has been
well characterized, however much less is known

about the 24 kDa inhibitory subunit, TnI. The
structure of troponin is of medical significance
since several mutations, which occur in all
subunits of the troponin complex, have been
linked to hypertrophic cardiomyopathy (HCM). We
have employed site-directed spin-labeling and
paramagnetic relaxation enhancement (PRE) NMR
spectroscopy to position key functional regions of
the TnI subunit with respect to the TnC subunit in
the binary TnC-TnI complex. The positioning of TnI
with respect to TnC was performed in both the
absence and presence of Ca2+to understand the
switch mechanism. Our strategy involves attaching
a nitroxide spin label to single cysteine mutants of
14N-TnI and reconstituting the spin-labeled TnI
with 15N-TnC. TROSY experiments were
performed in the paramagnetic and diamagnetic
states which enabled us to measure distances (10
- 25 Å) between the TnI spin label and assignable
TnC residues. We have spin labeled several key
structural and functional regions of TnI, including
the cardiac specific N-extension (TnI-28), the
N-terminal region (TnI-57), the inhibitory region
(TnI-137 and TnI-143), and the switch peptide
(TnI-151 and TnI-159). The two switch peptide
probe sites clearly show release of the switch
peptide from the hydrophobic pocket in the TnC
N-domain in the absence of Ca2+. The effect of
TnI phosphorylation on the conformation of the
binary troponin complex was also examined.
Phosphorylation of the TnI N-extension (S23, S24)
clearly perturbs interactions between the TnC
C-domain and the TnI N-extension. We have also
performed experiments to investigate the effect of
a recently identified TnC HCM mutation, A8V
(Landstrom et al, 2008, J Mol Cell Cardiol).
Structural consequences of this mutation were
observed in isolated TnC.
Poster Presentations
Sunday 4 December - Session 1
P14
Unimolecular Reaction Chemistry of
Atmospheric Peroxyl Radicals
Gabriel da Silva
Chemical and Biomolecular Engineering, The University of
Melbourne, Parkville 3010, Australia
Abstract
Volatile organic compounds (VOCs) and
oxygenated VOCs (OVOCs) play a key role in
determining the oxidative chemistry of the
atmosphere, particularly in the planetary boundary
layer in remote forested regions, where well-known
HOx (OH + HO2) radical cycles are involving ozone
and NOx are relatively inefficient. Numerous field
studies conducted over the last decade have
identified that OH radical levels are consistently
elevated over model predictions in forested areas,
particularly those with high levels of the biogenic
VOC isoprene and low levels of NOx. Unimolecular
decomposition reactions of peroxyl radicals
formed in the OH-initiated oxidation of isoprene
have been suggested as a mechanism for hydroxyl
radical regeneration in these environments. Using
computational chemistry and reaction rate
modelling, rate constants have been estimated for
isoprene peroxyl radical decomposition.
Furthermore, the potential for OH radical recycling
from the isoprene oxidation products
methacrolein, methyl vinyl ketone, and glyoxal is
also examined.
111

Poster Presentations
Sunday 4 December - Session 1
P15
Structural Analysis of Missense
Mutations in the CLIC2 Chloride
Intracellular Ion Channel Protein
E L Daniel1 , J E Hare2 , S C Goodchild3 , N M
Cordina4 , L J Brown5 1 Department of Chemistry and Biomolecular Science, Macquarie
University, Sydney, New South Wales, 2109, elizabeth.daniel@
students.mq.edu.au
Abstract
Chloride Intracellular Channels (CLIC proteins) are
GST homologues that are part of a conserved
protein family with dynamic properties. Members
of the CLIC protein family have been shown to
auto-insert into membranes, directly from the
cytosol, to create active ion channels. Recently,
five missense mutations (H101Q, S109C, P160A,
D161H & D161Y) in the CLIC2 protein have been
found in a large-scale next generation
resequencing of X chromosome genes. One of
these mutations, H101Q, was linked to X-linked
intellectual disability (XLID) with two male patients
exhibiting traits and features of XLID including
seizures, thumb position abnormality, large ears,
and large testes. The other four mutations were
also found in healthy individuals, suggesting that
the CLIC2 protein is fully functional despite the
mutations. An in silico modelling study proposed
that the structural stability, inherent flexibility and
membrane binding properties are affected by
these mutations (Witham et al., 2011). In particular,
the XLID linked H101Q mutation was suggested to
be more stable in solution but to exhibit reduced
plasticity necessary for binding and insertion into
the membrane bilayer. To confirm these modelled
observations, we will perform in vitro experiments
for each of these mutations to determine the
thermal stability and membrane binding properties
of the CLIC2 proteins. We have cloned CLIC2 and
introduced each of the five missense mutations.
We will express and purify the proteins for analysis
of their conformational stability by Circular
Dichroism spectroscopy. Additionally, we will use a
sucrose loaded vesicle sedimentation assay to
determine if membrane-binding properties are
impaired (Goodchild et al., 2009). The data will be
discussed in the context of the predicted effects
for each mutation.
112
References
Witham et al (2011) Proteins: Structure, Function, and
Bioinformatics 79: 2444-54.
Goodchild et al (2009) European Biophysics Journal 39: 129-38.
P16
The Role of Spin in Triplet-Triplet
Upconversion
A. Danos1 , Y. Y. Cheng1 , D. R. McCamey2 , T. W.
Schmidt1 1 School of Chemistry, The University of Sydney, NSW 2006,
Australia
2 School of Physics, The University of Sydney, NSW 2006,
Australia
Abstract
Triplet-Triplet Annihilation (TTA) Upconversion is a
class of photochemical reactions that combine the
energies of two or more photons into a single,
higher energy photon. Sunlight with energy below
the bandgap of a semiconductor photovoltaic
device, which normally is not absorbed, is thus
reclaimed.
Upconversion occurs when two molecules absorb
low energy photons and Inter-System Cross into
triplet excited states. Conservation of the
electrons’ spin allows for the molecules’ energies
to disproportionate, producing two singlet states
as a result. One of these is in the ground state, and
the other in a highly excited state. Fluorescence
from the excited singlet generates the upconverted
photon, which can then power a photovoltaic
device. Jablonski diagrams for these processes
are shown in Figure 1.
Figure 1: Jablonski diagrams of triplet formation (right), and TTA
(left) [1].
Although TTA upconversion has been
demonstrated within the School of Chemistry and
elsewhere, the spin mixing processes that result in
annihilation remain poorly understood [2]

Furthermore, no theoretical treatment has yet
accounted for the spin precession phase, nor
satisfactorily explained the non-uniform effects of
magnetic alignment upon upconversion rates [3].
Electron Paramagnetic Resonance (EPR) is an
ideal tool for examining the role of triplet spin in
TTA upconversion [4]. Our experiments involve
using microwaves to excite molecules between the
three degenerate triplet states, which correspond
to the three possible spin orientations. By altering
the populations of the triplet states and observing
the changes in upconversion intensity, we
investigate: the natural occupancy of the three spin
states following intersystem crossing, which of the
nine triplet pair configurations contribute to
upconversion, and which of these pair states
quench the reserve of excited molecules.
Key Words
Triplet, spin, upconversion, EPR, ESR, photovoltaics
1. Fückel, B., et al., Singlet Oxygen Mediated Photochemical
Upconversion of NIR Light. The Journal of Physical Chemistry
Letters, 2011. 2(9): p. 966-971.
2. Cheng, Y.Y., et al., Kinetic Analysis of Photochemical
Upconversion by Triplet−Triplet Annihilation: Beyond Any Spin
Statistical Limit. The Journal of Physical Chemistry Letters,
2010. 1(12): p. 1795-1799.
3. Mezyk, J., et al., Effect of an External Magnetic Field on the
Up-Conversion Photoluminescence of Organic Films: The Role
of Disorder in Triplet-Triplet Annihilation. Physical Review
Letters, 2009. 102(8): p. 087404.
4. Atherton, N.M., et al., Electron spin resonance. Vol. 14, A Review
of recent literature to 19931994, Cambridge: Royal Society of
Chemistry.
P18
Bonding between the uracil
monomers of the cyclobutane
pyrimidine dimer radical anion by
means of quantum chemical
calculations
Linda Feketeová 2 , Andreas
Mauracher1 ,David Gschliesser 1 , Peter Bartl1 ,
Violaine Vizcaino1 , Lukas An der Lan1 , Catrin
Goeschen2 , Stephan Denifl1 , Richard A.J. O’Hair2 ,
T. D. Märk1 , P. Scheier1 , U. Wille2 1 Institut für Ionenphysik und Angewandte Physik, Leopold-
Franzens-Universität, Technikerstr. 25, Innsbruck, 6020, Austria,
andreas.mauracher@uibk.ac.at
2 ARC Centre of Excellence for Free Radical Chemistry and
Biotechnology, School of Chemistry and Bio21 Institute of
Molecular Science and Biotechnology, The University of
Poster Presentations
Sunday 4 December - Session 1
Melbourne, 30 Flemington Road, Victoria, 3010, Australia, lfe@
unimelb.edu.au
Abstract
The major lesion in DNA caused by exposure to
ultraviolet radiation is formation of cyclobutane
pyrimidine dimers (CPD), namely cis,syn-thyminethymine
cyclobutane dimers (c,s-TT), resulting
from [2π+2π] cycloaddition of two adjacent bases
in the same oligonucleotide strand.1 This lesion
has serious biological consequences, such as
incorrect DNA replication, which could lead to
mutation, cancer or cell death.2 Whereas
placental mammals, including humans, remove
CPD lesions through nucleotide excision repair, in
prokaryotes, plants, and a variety of animals
dimerized pyrimidines are efficiently converted to
their monomeric form by the enzyme DNA
photolyase in a light-driven catalytic reductive
electron transfer cycle.3
A recent study4 revealed that the attachment of a
free electron to the cyclobutane pyrimidine dimers,
c,s-DMTDMT and c,a-DMTDMT, leads to the
formation of dimer radical anions, very likely
through dipole bound states.5 These radical
anions exhibit a lifetime of at least 80 μs, showing
that they are much more stable than previously
believed and that the splitting of the CPD radical
anion into the respective pyrimidine monomers is
associated with an activation barrier. This study
was extended to investigate the attachment of free
electrons to uracil cyclobutane pyrimidine dimers
(DMUDMU) with different geometry at the
cyclobutane ring. Along with these experiments,
we undertake theoretical approach to understand,
how the stereochemistry at the cyclobutane ring
affects the stability of the CPD radical anion, and
its dissociation. By means of quantum chemical
calculations we investigate the bonding between
the dimers of c,s-DMUDMU as well as
t,s-DMUDMU. We compare the results of
density functional theory to wave function based
approaches and post Hartree-Fock calculations.
In addition we look at the potential energy surface
for an approximate dissociation process of the
dimers.
[1] J. Cadet and P. Vigny, in Bioorganic Photochemistry:
Photochemistry and the Nucleic Acids, ed. H. Morrison, John
Wiley, New York, pp. 1–272 (1990)
[2] A. Dussy, E. Meggers and B. Giese, J. Am. Chem. Soc. 120
113

Poster Presentations
Sunday 4 December - Session 1
7399 (1998)
[3] A. Sancar, Chem. Rev. 103 2203 (2003)
[4] A. Edtbauer, K. Russell, L. Feketeová, J. Taubitz, C.
Mitterdorfer, S. Denifl, R. A. J. O’Hair, T. D. Märk, P. Scheier and
U. Wille, Chem. Commun. 7291 (2009).
[5] A. Edtbauer, S. Denifl, V. Vizcaino, L. An der Lan, K. Russell, J.
Taubitz, U. Wille, L. Feketeová, R. A. J. O’Hair, T. D. Märk, E.
Illenberger and P. Scheier, Chem. Phys. Chem. 11 561 (2009)
P19
Structure and binding energies of
the doubly charged zwitterionic
betaine clusters
Linda Feketeová 2 , Emilie Cauët1 , William A.
Donald2 , Richard A.J. O’Hair2 ,
1 Service de Chimie Quantique et Photophysique, Université Libre
de Bruxelles, avenue F.D. Roosevelt 50 CPi 160/09, Brussels,
1050, Belgium, ecauet@ulb.ac.be
2 ARC Centre of Excellence for Free Radical Chemistry and
Biotechnology, School of Chemistry and Bio21 Institute of
Molecular Science and Biotechnology, The University of
Melbourne, 30 Flemington Road, Victoria, 3010, Australia, lfe@
unimelb.edu.au
Abstract
Ionic clusters are important species in a wide
variety of areas, none more obvious than biological
processes. The advent of electrospray ionisation
(ESI) has provided a new method for generating a
wide range of cluster ions, including ionic clusters
and biomolecular clusters. One of the fundamental
differences between amino acids in solution and in
the gas phase is the fact that they exist
predominantly in the zwitterionic form
(H3N+CH2CO2-) in solution but adopt the
nonzwitterionic form (H2NCH2CO2H) in the
gas-phase. Betaines (e.g. Glycine Betaine (GB) 1,
Dimethylsulfonioacetate (DMSA) 2) are particularly
interesting as a model of the fundamental gas
phase chemistry of the zwitterionic form of amino
acids, due to the presence of their permanent
fixed charges.
114
Since the discovery that the ESI of solution of
zwitterionic GB (1) leads to the formation of a
number of multiply protonated clusters [Mn+mH]
m+, where m = 1,...,4, with relatively high
abundance,1 we have studied the collisioninduced
dissociation (CID) and electron-induced
dissociation (EID) reactions of these clusters in
detail for one of the larger size [M21+2H]2+
clusters of GB,2 as well as clusters [M15+2H]2+ of
zwitterionic GB, and DMSA, that are close to the
stability limit, i.e. Coulomb repulsion of the charge
within the cluster competes with attractive forces
such as hydrogen bonding and charge-dipole
interactions.3 Multiply protonated clusters
fragment via competitive neutral loss and charge
separation.
Density functional theory (DFT) calculations on the
doubly charged dimer suggest that the doubly
charged clusters consist of a [M2+2H]2+ core
based on the hydrogen-bonded carboxylic acid
dimer.1 In the present study we investigate the
structure and stability of the larger clusters using
DFT calculations in order to gain additional insight.
[1] Feketeová, L.; O’Hair, R. A. J. Chem. Commun. 2008,
4942-4944.
[2] Feketeová, L.; O’Hair, R. A. J. Rapid Commun. Mass Spectrom.
2009, 23, 3259-3263.
[3] Yoo, E. J.-H.; Feketeová, L.; Khairallah, G. N.; O’Hair, R. A. J. J.
Phys. Chem. A. 2011, 115, 4179-4185.
P20
Parametric Sensitivity Analyses of
the Insulin Signalling Pathway
Catheryn Gray 1 , Adelle C. F. Coster 1,2
1 School of Mathematics & Statistics, University of New South
Wales
2 Garvan Institute of Medical Research, Darlinghurst NSW
Abstract
There is no comprehensive mathematical model of
the complex biological dynamics of insulin
signalling. The identification of the main nodes of
activity and the underlying mechanisms
connecting signal transduction to physical
translocation of glucose transporters is a
significant biological outcome as the metabolic
effects of insulin on glucose uptake are
fundamental to life. Given the ubiquitous nature of

this feedback and control system, quantitative
modelling is of widespread scientific interest. In the
longer term, understanding how this dynamic
system operates under normal conditions will be
vital to understanding its operation under
abnormal conditions.
Here we analyse the behaviour of an initial model
for the insulin signalling pathway, and identify the
key nodes controlling the regulation of the glucose
transporter protein GLUT4 at the cell surface. It is
known that this model has limitations and the
ramifications of these are explored, with a view to
modifying this to create a comprehensive,
validated model of insulin-stimulated metabolic
responses for fibroblasts, adipocytes and muscle
cells.
As in the cases of coupled mitogen-activated
protein kinase and phosphoinositide 3-kinase
(MAPK–PI3K) pathways related to cancers, we
make use of integrated and other sensitivity
measures to rank the key nodes in the insulin
network. The sensitivity of membrane GLUT4 with
respect to all parameters (rate constants and
non-zero initial concentrations) is explored.
P21
Energy and Charge Transfer
Interactions in a Mixed Porphyrin
Co-sensitized TiO2 Electrode: A
sub-ns Transient Absorption
Spectroscopy Study
M. J. Griffith, 1 A. J. Mozer, 1 P.Wagner, 1 G. G.
Wallace, 1 D. L. Officer, 1 and R. Katoh 2,3
1. ARC Centre of Excellence for Electromaterials Science and
Intelligent Polymer Research Institute, University of Wollongong,
Innovation Campus, Squires Way, North Wollongong, NSW,
2500, Australia.
Emails: mjg48@uow.edu, attila@uow.edu.au, pawel@uow.edu.au,
gwallace@uow.edu.au, davido@uowmail.edu.au
2. National Institute of Advanced Industrial Science and
Technology, Tsukuba Central 5, Tsukuba, Ibaraki, 305-8565,
Japan.
3. Department of Chemical Biology and Applied Chemistry,
College of Engineering, Nihon University, Tamura, Koriyama,
Fukushima, 963-8642, Japan.
Email: rkatoh@chem.ce.nihon-u.ac.jp
Abstract
Poster Presentations
Sunday 4 December - Session 1
Sensitisation of TiO2 with a wide variety of organic
and inorganic dyes has been extensively studied in
an attempt to synthesise highly efficient
photovoltaic devices. Given their efficacy in
photosynthesis, porphyrin molecules offer
immense potential in this regard.[1] However, there
have been very few reports of artificial porphyrin
devices which reproduce the constructive
intermolecular energy or charge transfer
processes so prevalent in photosynthetic systems.
[2]
In this study a mixed dye system with a potentially
high quantum yield for energy and charge transfer
has been created using two porphyrin
components; one a zinc porphyrin and the other a
free base porphyrin (Figure 1). The mixed system
shows superior solar cell performance when
compared to either of the individual
components,[3] a phenomenon which is
remarkable considering the similarity in the
absorption spectra of the two dyes.
Fig. 1 Chemical structures of porphyrin dyes employed in this
study.
The current study employs transient absorption
spectroscopy with 500 ps resolution to analyse
energy and charge transfer mechanisms by
monitoring formation of the dye cations formed
after excitation in the mixed dye system. Results
indicate that the electron injection yield
(proportional to the dye cation concentration) is
only amplified with respect to the individual dyes at
high dye surface coverages and small
intermolecular spacings (Fig 2a). This indicates
Forster type energy transfer is responsible for the
amplified injection yield. Furthermore, the free
base cation signal disappears on very fast time
scales in the mixture (Fig 2b), indicative of a charge
transfer mechanism which limits recombination.
115

Poster Presentations
Sunday 4 December - Session 1
Fig. 2 (a) Kinetics of dye cation creation in the mixed dye system
for different dye surface coverages. (b) Transient absorption
spectra of the mixed dye system at various time delays after
excitation
Keywords
Porphyrin, energy and charge transfer, sub-ns transient absorption
References
[1]. W.M. Campbell, A.K. Burrell, D.L. Officer, K.W Jolley; Coord.
Chem. Rev. 2004, 248, 1363.
[2]. A.J. Mozer, M.J. Griffith, G. Tsekouras, P. Wagner, G.G.
Wallace, S. Mori, K. Sunahara, M. Miyashita, J.C. Earles, K.C.
Gordon, L. Du, R. Katoh, A. Furube, D.L. Officer; J. Am. Chem.
Soc., 2009, 131, 15621.
[3]. M.J. Griffith, A.J. Mozer, G. Tsekouras, Y. Dong, P. Wagner, K.
Wagner, G.G. Wallace, S. Mori, D.L. Officer; App. Phys. Lett.,
2011, 98, 163502.
116
P22
ACE I/D genotypes and their impact
on heart rate variability: a limited
meta-analysis
Brett Hambly6 , Ethan Ng1 , Yaxin Lu 2 , Slade
Matthews3 , Herbert Jelinek4 , Craig McLachlan 5
1 Pathology, Univ of Sydney, NSW 2006, etng1324@uni.sydney.
edu.au
2 Pathology, Univ of Sydney, NSW 2006, yalu4496@uni.sydney.
edu.au
3 Pharmacology, Univ of Sydney, NSW 2006, sladem@med.usyd.
edu.au
4 School of Community Health, Charles Sturt Univ, NSW 2640,
HJelinek@csu.edu.au
5 Rural Clinical School, Univ of NSW, NSW, 2650, reperfusion@
hotmail.com
6 Pathology, Univ of Sydney, NSW 2006, bretth@pathology.usyd.
edu.au
Abstract
Heart rate variability (HRV) is a measure of
fluctuations in response to different stressors and
environmental changes. High HRV indicates the
ability to adapt to situations, while lower HRV
implies dysfunction and therefore a less healthy
individual. Genetic factors are capable of
substantial influence over HRV. A potential locus
for this is the angiotensin converting enzyme
(ACE), where polymorphisms may have an effect
on HRV. The ACE Insertion/Deletion (I/D)
genotypes are thought to influence HRV. The ACE
I/D polymorphism is the insertion of 287 bases into
intron 16 of the ACE gene. The D allele is
associated with higher levels of circulating ACE
and also with increased cardiovascular risk in a
number of studies of CVS disease states. Studies
investigating an association between HRV and
ACE I/D have been conducted in various normal
and diseased patient groups. These have
exhibited a lack of standardization in both
measurement and analysis of HRV, resulting in
apparently contradictory results. Consequently,
there remains much controversy surrounding the
ACE I/D polymorphism. We aimed to consolidate
and analyse these data using a meta-analysis. We
have reviewed published data to clarify some of
the uncertainty
regarding how ACE I/D polymorphisms affect HRV
and autonomic activity.

Secondly, this study has examined whether the
relevant genetic cohort studies are guided by the
HRV task force recommendations. Our initial
analysis shows that the ACE I/D polymorphism
correlates with HRV.
P23
UV-Vis Action Spectroscopy of Room
Temperature Protonated Aromatics
Christopher S. Hansen1 , Ben B. Kirk1 ,
Richard A.J. O’hair 2 , Stephen J. Blanksby1, Adam
J. Trevitt 1
1 School of Chemistry, University of Wollongong, NSW 2522
Australia
2 School of Chemistry, University of Melbourne, VIC 3010
Australia
Abstract
We have developed an instrumental setup for
investigating the UV-Vis photodissociation
efficiency of ions bringing together a mid-band
tunable OPO laser (220 nm – 2.5 μm) and a
modified, commercial stretched linear quadrupole
ion trap. Here we report preliminary
photodissociation studies of various protonated
aromatic compounds.
Briefly, ions are generated using electrospray
ionisation and focused into the linear ion trap
where the ion of interest is isolated. This trapped
ion population is then irradiated with a single OPO
laser pulse and scanned out of the trap for mass
spectrometric analysis. This allows us to examine
multiple fragmentation channels and infer their
relative photodissociation in a single experiment.
Our preliminary studies have focused on
protonated aromatic compounds, a significant
number of important compounds are aromatic or
contain aromatic units. An example of a
compound we have studied is the meta and para
isomers of aminophenol. Aminophenol exhibits
many fragmentation channels, mainly amine
hydrogen loss, alcohol hydrogen loss, ammonia
(NH3) loss and OH loss. This makes it a good
model compound for studying larger molecules
containing aromatic moieties with amine or alcohol
functionalisations.
Poster Presentations
Sunday 4 December - Session 1
Although the direct photoexcitation cross-sections
are typically weak, upon the population of a σ*
orbital aromatic moieties exhibit interesting
photofragmentation dynamics that are often
masked by optically bright π*π transitions. Insight
into these σ* excited states is necessary for
developing a thorough understanding of a
system’s electronic excited states and overall
photochemical behaviour. We present an effective
method for exploring such excited states and
compare our results to excited state calculations.
In this poster the experimental setup will be
explained in further detail and action spectra of
various protonated aromatics will be presented
and discussed.
P24
Stabilisation and Delivery of
Medicinal Pigment Curcumin by
g-Cyclodextrin Dimers
Takaaki Harada1 , Duc-Truc Pham1 , Huy Tien
Ngo1 , Tiffany Harris2 , Eleanor Need2 , Grant
Buchanan2 ,Mandy Leung1 , Stephen F. Lincoln1 ,
Tak W. Kee1 1 School of Chemistry and Physics, The University of Adelaide,
North Terrace Campus, Adelaide, SA, 5005, Australia, takaaki.
harada@adelaide.edu.au
2 Molecular Ageing Laboratory, School of Medicine, The
University of Adelaide, Basil Hetzel Institute, The Queen
Elizabeth Hospital, 28 Woodville Road, Woodville South, SA,
5011, Australia
Abstract
Curcumin is a polyphenol extracted from turmeric
which is known not only as a curry spice but also
as herbal medicine in India and other Asian
117

Poster Presentations
Sunday 4 December - Session 1
countries. This yellow molecule possesses variety
of therapeutic effects such as anti-cancer,
antioxidant and wound healing activities. However,
the poor aqueous solubility and stability of
curcumin limits its availability in biologically relevant
environment.
It is, therefore, important to encapsulate curcumin
with suitable delivery agents such as
g-cyclodextrin (g-CD). We have demonstrated that
this molecular self-assembly stabilises curcumin
moderately and it may potentially improve the
bioavailability of curcumin. In this poster, we
present the stabilisation and molecular delivery of
curcumin by diamide linked g-CD dimers, which
consist of two g-CDs that are connected with
either a succinamide or urea linker. They stabilize
curcumin highly effectively by strong cooperative
binding to form a 1:1 complex with curcumin under
physiological conditions. The half-life of curcumin
is extended by 180-780 times. In addition, we
demonstrate that curcumin delivered by both the
diamide linked g-CD dimers exhibits antiproliferative
effect on a metastatic prostate cancer
cell line (PC-3). Therefore, the diamide linked g-CD
dimers have great potential for delivery of
curcumin in cancer therapy.
P25
Effective Core Potential
Benchmarking for Cerium Oxide
Clusters Using Density Functional
Theory
Robert A. Hardy1 , Birte Reichers2 and
Gregory F. Metha3 1 Department of Chemistry, The University of Adelaide, South
Australia 5005, robert.hardy@adelaide.edu.au
2 Department of Chemistry, Bielefeld University, 33615 Bielefeld,
Germany, birte.reichers@uni-bielefeld.de
3 Department of Chemistry, The University of Adelaide, South
Australia 5005, gregory.metha@adelaide.edu.au
Abstract
Benchmark Density Functional Theory calculations
were performed on small cerium oxide clusters
(CemOn, m=2,3; n=0,1,…,m) to determine an
effective core potential (ECP) suitable for
calculations of cluster geometries and ionisation
118
energies. The ECPs selected for testing included
the 28 electron core Stuttgart Relativistic Small
Core (SRSC) with a valence shell configuration of
6s25d14f1, and the 47 electron core (4fn/Q11) and
48 electron core (4fn/Q10) MWB ECPs with
valence shell configurations of 5s25p66s25d1 and
5s25p66s2, respectively.
Our calculations show the 4fn/Q11 ECP performs
well with regard to providing similar ionisation
energies and cluster geometries to those
calculated using the well established SRSC
ECP1,2. This result, in consideration with the
greatly reduced computational expense
associated with the 4fn/Q11 ECP compared to the
SRSC ECP, makes the 4fn/Q11 ECP appropriate
for future calculations of our larger cluster systems.
The 4fn/Q10 ECP shows a poor comparison of
cluster geometries and ionisation energies to
those calculated using the SRSC ECP, particularly
in the case of the Cem bare metal clusters where
Ce-Ce bond lengths were calculated to be in
excess of 4 Å. The 4fn/Q10 ECP is therefore not
considered suitable for future calculations of
CemOn clusters. The comparison of the Ce
valence shell configurations for each of the ECPs
suggests that the Ce 4f electron is not imperative
in the formation of chemical bonds, whereas the
single 5d electron is crucial to bonding.
This poster will present comparisons of cluster
geometries and ionisation energies for structures
optimised with the SRSC, 4fn/Q11 and 4fn/Q10
ECPs. These results will be supported with a
comparison of vibrational frequencies calculated
for CeO and Ce2 dimers with published
experimental results3 to show the effectiveness of
the ECPs to model Ce-Ce and Ce-O bonding.
(1) Dolg, M.; Stoll, H.; Preuss, H. J. Chem. Phys. 1988, 90.
(2) Wu, X.-N.; Ding, X.-L.; Bai, S.-M.; Xu, B.; He, S.-G.; Shi, Q. The
Journal of Physical Chemistry C 2011, 115, 13329.
(3) Shen, X.; Fang, L.; Chen, X.; Lombardi, J. R. J. Chem. Phys.
2000, 113.

P26
Probing the Integral Membrane
Form of Clic1 Using Fluorescence
Resonance Energy Transfer
Joanna E Hare1 , Sophia C Goodchild2,
Louise J Brown3 1 Department of Chemistry and Biomolecular Science, Macquarie
University, Sydney, New South Wales, 2109, joanna.hare@
students.mq.edu.au
2 Department of Chemistry and Biomolecular Science, Macquarie
University, Sydney, New South Wales, 2109, sophia.goodchild@
mq.edu.au
3 Department of Chemistry and Biomolecular Science, Macquarie
University, Sydney, New South Wales, 2109, louise.brown@mq.
edu.au
Abstract
Chloride Intracellular Channel proteins (CLICs) are
controversial because they can adopt two
drastically different, yet stable conformations.
CLICs are expressed either as soluble, globular
proteins or integral membrane proteins.
Electrophysiological studies have shown that the
integral membrane form of the CLIC can function
as an ion channel. The controversy is raised as the
classic protein structure paradigm poses that the
unique amino acid sequence gives a protein a
single well defined three dimensional structure.
However, it is becoming increasingly apparent that
some proteins can adopt more than one stable
conformation. These proteins are referred to as
‘metamorphic’ proteins (Murzin, 2008).
Crystal structures have been solved for the soluble
form of several members of the CLIC family but
attempts to solve the integral membrane form
using traditional methods, such as NMR and
crystallography, have been largely unsuccessful.
Fluorescence Resonance Energy Transfer (FRET)
was therefore used to probe the transition of
CLIC1 as it interacts with the membrane bilayer.
FRET is a spectroscopic technique that is used to
measure distances and changes in distances that
may occur in a dynamic macromolecule. Two
chemical probes are attached to the
macromolecule(s) of interest. If the two probes are
in close proximity and the fluorescence emission
of the donor overlaps with the absorption profile of
the acceptor, then energy can be transferred via a
dipole-to-dipole interaction. The amount of energy
Poster Presentations
Sunday 4 December - Session 1
transfer is proportional to the distance between
the probes.
FRET is especially useful for investigation of the
CLIC structure as both the soluble form and the
integral membrane form can be probed
simultaneously under physiological conditions. In
this study, FRET was used to provide the first
structural evidence that CLIC1 interacts with the
bilayer. Two sets of probe pairs were used so that
a range of distances could be obtained. FRET was
measured from CLIC1 to a probe attached to the
head group of lipids incorporated into liposomes.
A strong FRET signal was detected between
CLIC1 and the bilayer. Environmental parameters
shown to affect channel activity, including pH and
redox, are now under investigation using the
established FRET assay to understand whether
they also promote membrane insertion of CLIC1.
Murzin, A., ‘Metamorphic Proteins’, Science, 2008. 320, p.
1725-1726
P27
Single Molecule Widefield
Fluorescence Studies of Conjugated
Polymers
Emma N. Hooley1 , Toby D. M. Bell2 , Kenneth
P. Ghiggino3 1 School of Chemistry, University of Melbourne, Victoria 3010,
e.hooley@student.unimelb.edu.au
2 School of Chemistry, Monash University, Victoria, 3800, toby.
bell@monash.edu
3 School of Chemistry, University of Melbourne, Victoria 3010,
ghiggino@unimelb.edu.au
Abstract
Conjugated polymers are finding increasing
application as materials for organic light emitting
diodes, photovoltaic devices and lasers. However,
polymers are inherently heterogeneous (e.g.
molecular weight distribution, conformation) and
understanding the light induced processes in
these materials remains a challenge.
Single molecule fluorescence spectroscopy (SMS)
allows isolated polymer chains to be studied,
removing the averaging inherent to bulk
fluorescence measurements. Intrachain relaxation
processes otherwise obscured can be identified
119

Poster Presentations
Sunday 4 December - Session 1
and characterised. SMS has been previously
applied to investigate the photophysics of
conjugated polymers and has yielded information
on triplet state dynamics, photo-oxidation and
charge-transfer mechanisms.
Widefield fluorescence microscopy is emerging as
a powerful single molecule spectroscopy
technique, as it allows a wide area to be
illuminated and the behaviour of the molecules to
be observed in real time. In addition, defocused
widefield images can provide information on the
properties and dynamics of the emission transition
dipole, thus allowing an insight into the molecular
orientation and diffusion properties of the polymer
chromophores.
Figure 1: a) Alt-co-MEH-PPV; b) F8BT
Derivatives of phenylene vinylene (PPV), especially
2-methoxy-5-(2’-ethyl-hexaloxy)-1,4-phenylene
vinylene (MEH-PPV) have been widely studied. We
have synthesised and investigated an alternating
co-polymer of PPV and MEH-PPV, (alt-co-MEH-
PPV) (Figure 1 a) and poly(9,9’-dioctylfluorenecobenzothiadiazole)
(F8BT) (Figure 1 b) and
applied SMS and defocused widefield techniques
to investigate the effects of structure on the
photophysical processes occurring in single
chains.
Single chains of alt-co-MEH-PPV and F8BT exhibit
fluorescence blinking on both short (submillisecond)
and long (seconds) time scales and
these results are interpreted in terms of
contributions by triplet state excursions, and
charge and energy transport processes. Widefield
fluorescence microscopy has provided additional
information on the nature and dynamics of the
emitting chromophores present in individual
polymer chains. Although the polymers consist of
a distribution of absorbing chromophores, in most
cases they behave as single fluorophore emitters.
120
P28
Potential role of forbidden disulfide
motifs in Zn fingers.
Hulugalle D V K 1,3 , Haworth N L 2 , Ballouz S
1,4 2 1,3 2,3
, Jason Y. Liu , Fan S W , Wouters M A
1 Structural and Computational Biology Program, Victor Chang
Cardiac Research Institute, Sydney, Australia.
2 School of Life and Environmental Sciences, Deakin University,
Geelong, Australia
3 School of Medical Sciences, University of New South Wales,
Sydney, Australia
4 School of Computer Science & Engineering, University of New
South Wales, Sydney, Australia
Abstract
Expulsion of Zn2+ from proteins following oxidation
of ligating Cysteine residues is an emerging area of
the oxidative stress response. During a recent data
mining survey of protein structures with pairs of
thiols in both reduced and oxidized (disulfide
bonded) states, we found two structural motifs
repeatedly associated with Zn2+ binding (1).
Forbidden disulfides are a canonical set of
disulfides with abnormal stereochemistry
associated with redox-activity. Here we show
through systematic analysis of Zinc finger
structures and sequences, that one of these
motifs is extremely prevalent in Zinc fingers. We
show that in around 50% of Zinc finger structures
two of the Zn2+-ligating thiols are embedded in a
secondary structure similar to an anti-parallel
β-diagonal disulfide-like motif (aBDD), located on
the β-hairpin structure known as a Zinc knuckle.
Formation of a disulfide by thiols of this motif has
recently been characterized in the molecular
chaperone Hsp33 and also demonstrated in
several other transcription factors (2). Although
other forbidden disulfide motifs are occasionally
present in Zinc fingers, none are as ubiquitous as
this aBDD-like motif. We show that the presence
of this motif and its position in the structure is
characteristic of different types of Zinc fingers,
suggesting a functional relationship. As Zinc
fingers comprise more than 17% of the human
genome, this motif is likely important in Zn2+
signalling.
1. Fan SW, George RA, Haworth NL, Feng LL, Liu JY, Wouters
MA. Conformational changes in redox pairs of protein
structures. Prot Sci 18: 1745-1765, 2009.

2. Ilbert M, Horst J, Ahrens S, Winter J, Graf PCF, Lilie H, Jakob U.
The redox-switch domain of Hsp33 functions as dual stress
sensor. Nat Struct Mol Biol 14: 556-563, 2007.
P29
Cryopreservation – The Beginning of
a DSC (Differential Scanning
Calorimetric) Understanding.
Taavi Hunt 1 , Anja Kaczmarczyk 2, 3 , Bryn
Funnekotter 2, 3, Shane Turner 3, 4 , Eric Bunn 3, 4 ,
Gary Bryant1 , Ricardo L. Mancera2 1 Applied Physics, School of Applied Sciences, RMIT University,
Melbourne, VIC, Australia.
2 Curtin Health Innovation Research Institute, Western Australian
Biomedical Research Institute, Curtin University, Perth WA,
Australia.
3 Botanic Gardens and Parks Authority, Fraser Avenue, West
Perth WA , Australia.
4 School of Plant Biology, Faculty of Natural and Agricultural
Sciences, University of Western Australia, Crawley WA,
Australia.
Abstract
A collaborative project between: RMIT University,
Curtin University, Botanical Gardens and Parks
Authority (WA) and Alcoa Australia. The major goal
of this collaboration is to understand the major
factors that determine the ability of various
recalcitrant plant species to survive cryogenic
storage, with particular relevance to post mining
restoration of bauxite mining activities in South
Western Australia. The Western Australian
endemic species Loxocarya Cinerea is a key
understory component of the Jarrah Forests of
South-West Western Australia, and hence is very
important in post-mining restoration. However it
rarely produces seeds and cannot be propagated
conventionally, therefore is produced via tissue
culture.
Cryopreservation refers to the storage of living
biological organisms at ultra low temperatures,
(Liquid Nitrogen, -196 °C), in such a way that they
can be revived and restored to their original living
state. This can be used as a long-term
conservation method and has been mainly applied
to agricultural plants requiring specific genotype
conservation [1], but this approach can also be
applied to endangered or recalcitrant plant
species.
Poster Presentations
Sunday 4 December - Session 1
From plant tissue culture, L. Cinerea shoot tips are
isolated, precultured, partial dehydrated then
cryoprotected. This process aims to avoid
intracellular ice formation that would otherwise
disrupt the cell membranes integrity, leading to
cellular death [2]. Dehydration and cryoprotection
are both critical steps; too much desiccation
results in over-exposure of the isolated shoot tips
to cryoprotective agents, this too can be
detrimental. Plant tissues can be successfully
cryogenically stored when intracellular water is
transformed into a vitrified glass during fast
cooling. [3]
Differential Scanning Calorimetry (DSC) measures
the energy released during a phase transition, i.e.
the formation of ice. DSC was performed on L.
Cinerea shoot tips to determine whether ice
formation takes place during LN cooling. DSC
results revealed zero or very little ice formation in
shoot tips treated with plant vitrification solution 2
(PVS2) for 30 min, indicating that L. cinerea shoot
tips are adequately cryoprotected with current
protocols. Therefore unsuccessful re-growth of
shoot tips after cryopreservation cannot be
explained by intracellular ice formation. Further
research on membrane components and oxidative
stress analysis during cryopreservation will help to
develop a successful protocol for this endemic
species.
[1] Kaczmarczyk A., (2008), CryoLetters 29(2), 145-156.
[2] Wolfe J., Bryant G., (1999), Cryobiology 39, 103-129.
[3] Turner S., Touchell D., (2001), CryoLetters 22(3), 163-174.
P30
A DNA-Based Assay for Chemical
Toxicity in Wastewater and Drinking
Water
Vangelis George Kanellis1 , Amy
Foreman1 , Leo Phillips1 , Cris dos Remedios1 , David
Hibbert2 , John Chapman3 , Moreno Julli3 , Ronald
Patra3 1 Anatomy and Histology, The University of Sydney, Sydney,
Anderson Stuart Building (F13), Sydney University, NSW, 2006,
Australia, cris.dosremedios@sydney.edu.au
2 School Chemistry , University of New South Wales, Sydney,
Dalton Building, University of New South Wales, Kensington,
2052, b.hibbert@unsw.edu.au
3 New South Wales Government,
121

Poster Presentations
Sunday 4 December - Session 1
Abstract
We describe a monitoring system employing DNA
as a biosensor of toxic chemicals. Metal ions and
other toxicants bind to DNA causing structural
changes that are detected by a fluorescent
reporter dye. Statistical analyses of test data using
48 wastewater samples indicate that the DNA-dye
assay compares favourably with C. dubia and
Microtox® bioassays as used by the Department
of the Environment Climate Change and Water
(DECCW). The DNA-dye system is simple,
operates within a sample pH range of 4-10, is
minute-long, has a 12-month use-by date, and
appears well suited as a field screening assay for
wastewater and drinking water. We found there is
a good correlation between the sample toxicity
and the heavy metal ion content as determined by
mass spectrometry (ICP-MS or ICP-OES).
However, it was also clear that some samples
were toxic despite the absence of heavy metals.
This suggests the DNA-dye system must have
sensed toxic organic compounds contained within
the samples. One of the main differences between
bioassays and mass spectroscopy is the former’s
synergistic or antagonistic toxic behaviours to
mixtures of metal ions in aqueous solutions.
Because environmental water samples rarely
contain only one types of metal ion, we examined
pairwise combinations of 16 metal ions (results
shown below). Similar to other studies, we also
noticed that some binary combinations of heavy
metal ions were more toxic than other binary
combinations. Two sources of genomic DNA were
investigated. One seems to be more suited to
testing the toxicity of wastewater, whilst the other
more sensitive DNA-dye was more suitable for
testing drinking water. Finally, we demonstrate
using high resolution NMR that Hg binding causes
a shift in the NMR spectrum consistent with it
binding to the aromatic base pairs of the genomic
DNA. We conclude the DNA-dye test is a
surrogate bioassay suitable for screening chemical
toxicity, particularly for toxic metal ions.
122
Observed toxicities for binary combinations of
metals ions using HAZ-1 DNA-dye. Open boxes
indicate metals that have additive toxicities (44%).
Boxes with vertical bars represent metals that,
when combined, are less toxic than their separate
additive effects; i.e., their effects are antagonistic
(35%). Lightly shaded boxes represent metals with
observed toxicities that are 50% greater than their
separate additive effects, that is, synergistic (21%).
The more darkly shaded boxes indicate metal
combinations for which the observed toxicities are
more than twice the toxicity predicted from their
separate (independent) effects, that is, very
synergistic (9%).
P31
Experimental and Computational
Studies on Gas Phase Bimetallic
Holmium-Rhodium Clusters
Aidan M. Karayilan 1 , Gregory F. Metha1 1 University of Adelaide, North Terrace Campus Adelaide, SA,
5005, aidan.karayilan@adelaide.edu.au
2 University of Adelaide, North Terrace Campus Adelaide, SA,
5005, greg.metha@adelaide.edu.au
Abstract
The adiabatic ionisation energies of six metal oxide
cluster series (Ho2Rh3On (n = 1,2), Ho3On (n =
1,2), Ho3RhOn (n = 0-4), Ho3Rh2On (n = 1-3),
Ho4On (n = 1-6) and Ho4RhOn (n=1-3)) have been
determined via photoionization efficiency
spectroscopy. Computational studies were
performed on three of the six metal oxide series
(Ho3On (n = 1,2), Ho3RhOn (n = 0-4), Ho4On (n =
1-6)) utilising DFT at the B3P86/SDD level of theory
to determine theoretical ionisation energies to
compare with experimental data. The
computational data was found to be complicated,
with many low lying isomers for each oxygen
containing cluster found to have ionisation
transitions correlating satisfactorily with
experiment. The incorporation of rhodium into the
holmium dominated oxide clusters was found to
induce a large charge separation, with the rhodium
atom attaining a δ- charge. The δ- charge on the
rhodium atom was found to decrease linearly with
oxidation level of the cluster.

P32
Neutron membrane diffraction
measurements of dehydrated DOPC
bilayers with introduced sugars
Ben Kent1 , Gary Bryant2 , Taavi Hunt2 and
Christopher J. Garvey1 1 Bragg Institute, Australian Nuclear Science and Technology
Organisation, Lucas Heights, Australia
2 Applied Physics, School of Applied Sciences, RMIT University,
Melbourne, Australia
Abstract
Sugars play a key role in the prevention of damage
to natural cell membranes during desiccation or
slow freezing. Their accumulation is a known
natural defence against destabilisation of lipid
bilayer membranes during low water availability.
Dehydration causes the distance between bilayers
to be reduced, resulting in the onset of the
hydration force, which induces a compressive
stress in the plane of the membrane, reducing the
area per lipid headgroup and causing phase
transitions to occur. While sugars are known to
delay or prevent these transitions occurring, the
mechanisms of membrane stabilisation by sugars
are still under debate1 . Central to this debate is
whether the observed effects are attributable to
insertion of sugars between lipid headgroups
preventing reduction in the area per lipid during
compressive stress2 , or whether non-specific
effects of sugars – volumetric and osmotic,
combine to prevent close approach of membranes
during dehydration, thereby delaying the onset of
hydration forces3 .
Membrane diffraction is an established technique
for the study of the structure of lipid bilayers and
interaction with different molecules. Here we
report on the use of the technique to study the
interaction of a bilayer with a small solute
molecule, glucose. Scattering density profiles
obtained provide structural information across the
bilayers and information on the location of
introduced solutes. Due to the differences in
mechanisms between the competing membrane
preservation theories, the concentration profile of
sugars across the unit cell of the bilayer membrane
should differ according to the dominant effect. We
Poster Presentations
Sunday 4 December - Session 1
present results of neutron membrane diffraction
measurements designed to study the interaction of
glucose with partially dehydrated DOPC bilayers.
Concentration profiles of the sugars across the
unit cell are extracted, and the resulting
information on the interaction and location of the
sugars is discussed in terms of mechanisms of
membrane protection.
1. H. D. Andersen, C. Wang, L. Arleth, G. H. Peters and P. Westh,
Proceedings of the National Academy of Sciences, 2011, 108,
1874-1878.
2. L. M. Crowe, Comparative Biochemistry and Physiology - Part
A: Molecular & Integrative Physiology, 2002, 131, 505-513.
3. J. Wolfe and G. Bryant, Cryobiology, 1999, 39, 103-129.
P33
•NO ejection from R• + •NO2. Does
•NO2 add through N or O?
Benjamin B. Kirk1 , Adam J. Trevitt 1 , Stephen
J. Blanksby1 1 School of Chemistry, University of Wollongong, NSW, 2522
Abstract
Nitrogen dioxide (•NO2) is a free radical
tropospheric pollutant which contributes to the
brown colouration characteristic of photochemical
smog. •NO2 undergoes a variety of reactions in
the troposphere including radical-radical
combination with alkyl and alkoxyl radicals [1].
Recently, •NO2 was used as a radical trap to
probe carbon-centred radical intermediates
present during radical directed dissociation of
peptides in the gas phase [2]. Collision induced
dissociation (CID) of these reaction products in a
mass spectrometer resulted in ejection of •NO
suggesting that •NO2 may have added through an
oxygen. The ground state (2A1) of •NO2 formally
places the unpaired electron on the nitrogen, thus,
in order to add through oxygen, •NO2 must be
excited to its first excited state (2B2) where the
unpaired electron resides on oxygen. This
excitation requires considerable energy at 27.8
kcal mol-1 [3], suggesting that addition of •NO2
should not occur through nitrogen under ambient
conditions.
123

Poster Presentations
Sunday 4 December - Session 1
In this study we attempted to distinguish between
charge-tagged nitrobenzene and
nitrosoxybenzene analogues using CID. These
experiments were undertaken using an ion-trap
mass spectrometer modified to allow a fixed flow
of a neutral reagent (such as O2, •NO or •NO2) to
be seeded into the helium buffer gas of the mass
spectrometer. N,N,N-trimethylammonium
charge-tagged analogues of nitrobenzene (A)
generated by addition of •NO2 to a phenyl radical
(C6H5• + •NO2 → C6H5NO2) and
nitrosoxybenzene (B) generated by addition of
•NO to a phenoxyl radical (C6H5O• + •NO →
C6H5ONO), were subjected to CID and a
comparison made to the CID spectrum of
authentic N,N,N-trimethyl-4-nitrobenzaminium
cation (C). CID of A and C resulted in a major ion
due to neutral loss of •CH3 (Figure 1a). In contrast,
the major product generated during CID of B
occurred due to loss of •NO (Figure 1b). These
results suggest that •NO2 adds to phenyl radicals
via nitrogen and that loss of •NO observed during
CID of •NO2 adducts most likely occurs due to
isomerisation at the nitro substituent prior to
ejection of •NO.
[1] Atkinson, R.; Arey, J.; Chem. Rev., 2003, 103, 4605-4638
[2] Barlow, C.K.; Wright, A.; Easton, C.J.; O’Hair, R.A.J.; Org.
Biomol. Chem., 2011, 9, 3733–3745
[3] Weaver, A.; Metz, R.B.; Bradforth, S.E.; Neumark, D.M.; J.
Chem. Phys., 1989, 90, 2070–2071
124
P34
Non-Markovian Memory from
Time-Local Stochastic Trajectories
Werner Koch1 , Frank Grossmann1 1 Research School of Chemistry, ANU, Canberra, ACT, 0200,
Australia
2 Institut für Theoretische Physik, TU Dresden, 01062 Dresden,
Germany
Abstract
Markovian approximations for open quantum
systems have seen an impressive range of
applications for describing the dynamics of
molecules under the disturbing influence of an
environment. While in some special cases a
Markovian treatment is exact, it remains an
approximation for most others. In cases where the
strict ranges of applicability of a certain
approximation are transgressed, this does not
necessarily void the results obtained from such a
scheme. A comparison of such approximate
results with the full non-Markovian treatment can
identify the true limits for the (usually less arduous)
Markovian method and highlight the details of how
it fails. We present such an investigation for
trajectory based implementations of the non-
Markovian Stochastic Liouville-von-Neumann
method [1] and a finite difference implementation
of the Markovian Caldeira-Leggett master
equation [2].
[1] J. T. Stockburger, H. Grabert, Chem. Phys. 268 (2001) 249-256.
[2] F. Grossmann, W. Koch, J. Chem. Phys. 130 (3) (2009) 034105.
P35
Quantum Effects in H2-Li+-Benzene:
A Model For Hydrogen Storage
Materials
Stephen J. Kolmann 1 , Meredith J. T.
Jordan2 1 School of Chemistry, The University of Sydney, NSW, 2006.
email: s.kolmann@chem.usyd.edu.au
2 School of Chemistry, The University of Sydney, NSW, 2006.
email: m.jordan@chem.usyd.edu.au

Abstract
The interaction of H2 with a Li+-benzene
complex—a model for Li-doped MOF-5 and
Li-doped carbon based materials—is
characterised using Quantum Diffusion Monte
Carlo (QDMC) and Path Integral Monte Carlo
(PIMC) calculations on reduced- and fulldimensional
modified Shepard interpolated
potential energy surfaces, constructed using DFT.
The importance of quantum effects and
anharmonicity on the adsorption of H2 is
quantified by comparing these QDMC and PIMC
calculations to thermodynamic quantities obtained
from a harmonic oscillator normal mode analysis.
QDMC calculations suggest that the H2 ground
state nuclear wavefunction is completely
delocalised above the Li+-benzene complex, and
the PIMC calculations allow us to examine the
mobility of H2 with changing temperature. These
calculations together suggest simplifications that
can be used to model larger hydrogen storage
systems.
Recent modifications to the modified Shepard
interpolation scheme of Collins and co-workers1 to
interpolate systems of the size presented here will
also be discussed.
Figure 1. The H2-Li+-benzene minimum energy structure,
optimised at the M05-2X/6-311+G(2df,p) level of theory. The Li+
ion is sandwiched between the benzene ring and the H2 molecule.
The Li+ to H2 centre-of-mass distance is indicated.
1 M. A. Collins, Theor. Chem. Acc. 108, 313 (2002).
Poster Presentations
Sunday 4 December - Session 1
P36
Anion photoelectron spectra of the
halide-(N2)n and -(N2O)n clusters
Kim M. Lapere1 , Allan J. McKinley1 & Duncan
A. Wild1 1 Chemistry, University of Western Australia, M313 35 Stirling
Hwy Crawley, WA 6009, 20169424@student.uwa.edu.au
Abstract
We present recent work focusing on the anion
photoelectron spectra and ab initio calculations of
the X-···(N2)n and X-···(N2O)n clusters (X = Cl, Br
and I). Spectra of these species are recorded
using our newly-constructed Time-Of-Flight mass
spectrometer coupled to a PhotoElectron
Spectrometer (TOF-PES)[1].
We explore the radical X•···(N2)n and X•···(N2O)n
clusters via photodetachment of an electron from
the anion complexes. The work samples the
reaction potential energy surface for the dimer
complex, and follows the solvation upon increased
cluster size.
Fundamental data such as the electron affinities
(EA) and cluster stabilisation energies (Estab) of
the clusters are derived from experimental spectra
and compared with ab initio calculations for the
anion and neutral radical monomer species
employing MP2 and CCSD(T) methodologies. We
present geometries, vibrational frequencies and
energies for the Cl•···N2 and Br•···N2 clusters.
References:
Lapere, K. M.; LaMacchia, R. J.; Quak, L. H.; McKinley, A. J.; Wild,
D. A. Chemical Physics Letters 2011, 504, 13-19.
P37
Transient Absorption Spectroscopy
of Curcumin-Copper Complex
Hei Man Mandy Leung ,1 , Dr Tak W. Kee2 1 School of Chemistry and Physics, University of Adelaide,
Adelaide, South Australia, 5005, Australia,
hei.leung@adelaide.edu.au
2 School of Chemistry and Physics, University of Adelaide,
Adelaide, South Australia, 5005, Australia, tak.kee@adelaide.
edu.au
125

Poster Presentations
Sunday 4 December - Session 1
Abstract
Curcumin is the yellow pigment from turmeric
which exhibits anti-cancer and anti-amyloid
properties.
Studies have suggested that the anticancer and
anti-amyloid action of curcumin can be related to
its interaction with copper ions because there is an
elevated concentration of copper ions in tumours
and amyloid aggregates. In this work, ultrafast
transient absorption spectroscopy is used to study
the excited state of curcumin and curcumincopper
complex to elucidate the interactions
between curcumin and copper. Our results show
that the excited state lifetime of curcumin has
shortened when it is complexed in both the SDS
micellar solution and methanol. T his result
suggests that ligand-metal charge transfer (LMCT)
as a pathway for excited state relaxation.
P38
Optimising the responsive behaviour
of polymer surfaces using Molecular
Dynamics
Kamron Ley 1 , George Yiapanis 1 , Irene
Yarovsky 1 , Evan Evans 2
1 Applied Sciences, RMIT University, GPO BOX 2476V, Victoria,
3001, Australia
2 BlueScope Steel Research, Port Kembla, NSW, Australia
Abstract
Recent advancements made in polymer
modification have lead to a large demand for
responsive surfaces, particularly in the paintcoatings
industry. This is because responsive
systems have the potential to shed dirt by
reversibly switching between hydrophobic and
hydrophilic states with changing humidity.
In this study, we looked at utilising responsive
hydrophilic polymer brushes in the form of
polyethylene glycol (PEG) oligomers grafted on an
organic polyester based substrate1-4, with varying
levels of surface hydroxylation. By employing
force-field based molecular mechanics and
dynamics we were able to gain insight into the
responsive behaviour of these PEG modified
substrates under a variety of conditions and
126
environments, with particular interest in the
property of PEG expansion driven by
intermolecular hydrogen bonding with both the
substrate and other PEG chains.
Our initial research demonstrates that increasing
the grafting density results in interactions between
the grafted polymer segments. This in turn leads
different configurations being adopted by the PEG
chains, where they transition from a flat
configuration to a mushroom like configuration
(see figure below), which in turn leads to an
increased response displayed by the surfaces.
Typical MD configurations adopted by the PEG
chains; at lower grafting densities (flat), and higher
grafting densities (mushroom).
(1) Yarovsky, I.; Evans, E.; Polymer 2002, 43, 963
(2) Yiapanis, G.; Evans, E.; Henry, D. J.; Yarovsky, I. J Phys Chem C
2010, 114, 478.
(3) Yiapanis, G.; Henry, D. J.; Evans, E.; Yarovsky, I. J Phys Chem
C 2008, 112, 18141.
(4) Yiapanis, G.; Henry, D. J.; Evans, E.; Yarovsky, I. In
Nanotechnology in Australia: Showcase of Early Career
Research in Australia; Kane, D. M., Micolich, A. P., Rabeau, J.
R., Eds.; Pan Stanford Publishing: 2011.
P39
Laser Spectroscopic Studies of
Conformation in Neurotransmitters
Isabella Antony Lobo1 , David Wilson2 ,
Evan Bieske3 , Evan G Robertson 4
1 Department of Chemistry, La Trobe University, Bundoora,
Victoria, 3086, ialobo@students.latrobe.edu.au
2 Department of Chemistry, La Trobe University, Bundoora,
Victoria, 3086, david.wilson@latrobe.edu.au
3 School of Chemistry, University of Melbourne, Victoria, 3010,
evanjb@unimelb.edu.au
4 Department of Chemistry, La Trobe University, Bundoora,
Victoria, 3086, e.robertson@latrobe.edu.au
Abstract

Neurotransmitters are special class of biological
compounds controlling physical and mental
well-being. Probing the preferred conformational
structures of these biomolecules paves the way for
the development of drugs. The conformers of
amino-p-phenethylamine (APEA) were studied in a
jet-cooled environment by Resonance Enhanced
Two Photon Ionisation (R2PI) and IR-UV ion
depletion techniques. In this way conformerspecific
IR spectra were measured for four distinct
conformers of APEA. The experimental studies are
complimented by ab initio calculations conducted
at various levels of theory including g MP2/6-
311G+(d,p) and B3LYP/6-311G+(d,p). Comparison
of experimental and computed spectra allows the
two most populated conformers to be
unambiguously identified as those having a
gauche arrangement of the side chain which
facilitates an NH… type hydrogen bond. The other
two observed conformers are assigned to
structures with an anti side chain. The fifth gauche
conformer, predicted to be least stable, is not
observed. The above findings are in clear contrast
to a recent study on APEA, relying mainly on
ionisation energies as well as computational
methods, that identified an anti conformer as
being the most stable and heavily populated one.
Tranylcypromine (Parnate) is another subject for
these studies. It is a drug of the substituted
phenethylamine and amphetamine classes and
used in the treatment of mood and anxiety
disorders. Results for this compound will also be
presented.
Poster Presentations
Sunday 4 December - Session 1
Notes
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127

Poster Presentations
Monday 5 December - Session 2
P40
Single Cell Membrane Analysis by
TERS is Reaching Nanometer Scale
Christian Löbbe1 , Marc Richter2 , Heiko
Haschke2 , Martin Hedegaard 3 , Tanja Deckert-
Gaudig4 , Peter Lampen5 , Volker Deckert 4,6
1 Scitech P/L, 4/72-74 Chifley Dr, Preston 3072, Australia
2 JPK Instruments AG, Bouchestr. 12, 12435 Berlin, Germany
3 Technical Faculty University of Southern Denmark, Institute of
Sensors, Signals and Electrotechnics (SENSE), Campusvej 55,
5230 Odense M, Denmark
4 Institute of Photonic Technology (IPHT), Albert-Einstein-Straße
9, 07745 Jena, Germany
5 Leibnitz-Institut für Analytische Wissenschaften – ISAS e.V.,
Bunsen-Kirchhoff-Str. 11, Dortmund 44139, Germany
6 Friedrich-Schiller-Universität Jena, Institute of Physical
Chemistry, Helmholzweg 4, 07743 Jena, Germany
Abstract
It is known that cell surface glycoproteins are
acting as cell specific identifiers for cell-cell
interactions. Those macromolecules are often
important integral membrane proteins, where they
play a role as a receptor for active ingredients and
second messengers.
A common method to identify membrane proteins
is antibody labeling. Depending on the nature of
the markers it is possible to use fluorescence or
Raman spectroscopy as an analytical method.
Especially silver and gold-labeled antibodies
turned out to be very interesting as they can be
used to increase the sensitivity of Raman labels via
a plasmon enhancement1. However, the lateral
resolution capability with respect to the location of
specific protein arrangements of this method is
limited. Another disadvantage of labeling with
antibodies is the selectivity of the marker. Different
and specific markers must be chosen for each
protein of interest.
To provide spectroscopic information with high
spatial resolution tip-enhanced Raman scattering
(TERS) is the technique of choice2. The
combination of an atomic force microscope (AFM)
with a Raman microscope provides information on
the topography and the molecular structure of a
sample with high sensitivity.
We present results of TERS mapping
measurements on colon cancer cells. In particular,
128
an area of 90x90 nm was analyzed. Within this
area spectra were recorded on a square grid with
a spacing of 10 nm.
Based on hyperspectral unmixing algorithm
(N-FINDR), a band assignment of the spectrum of
each endmember was done. As expected, all the
TERS bands can be attributed to proteins or lipids,
the known components of the cell membrane.
Correlating the band assignment and the N-FINDR
results . a label-free localization of membrane
components could be achieved. We demonstrate
that the combination of high lateral resolution and
specificity of TERS potentially allows a direct
differentiation of membrane protein and lipid
regions3.
References
[1] J.Kneipp, H. Kneipp, K. Kneipp, Chem. Soc. Rev. 27 (2008),
1052–1060.
[2]E. Bailo, V. Deckert, Chem. Soc. Rev. 37 (2008), 921-930.
[3]M. Richter et al, Small 7 (2011), 209-214.
P41
Reinvestigating the 308 nm
Photodissociation Dynamics of
Acetaldehyde: A Velocity Map
Imaging Study Examining Two
Distinct Pathways Producing CO +
CH4
Alan T. Maccarone 1 , Mitchell S. Quinn2 ,
Gabi de Wit3 , Scott A. Reid4 , B. Klaas Nauta5 ,
Scott H. Kable6 1 School of Chemistry, University of Sydney, New South Wales
2006, alanmac@uow.edu.au
2 School of Chemistry, University of Sydney, New South Wales
2006, mqui5334@uni.sydney.edu.au
3 School of Chemistry, University of Sydney, New South Wales
2006, g.dewit@chem.usyd.edu.au
4 Department of Chemistry, Marquette University, Milwaukee, WI,
USA, scott.reid@marquette.edu
5 School of Chemistry, University of Sydney, New South Wales
2006, k.nauta@chem.usyd.edu.au
6 School of Chemistry, University of Sydney, New South Wales
2006, s.kable@chem.usyd.edu.au
Abstract
Since the discovery of the non-classical roaming
mechanism to form carbon monoxide and

molecular hydrogen in the photodissociation of
formaldehyde [1], similar pathways have been
discovered and postulated to exist in other
systems [2,3]. Notably acetaldehyde (CH3CHO)
has received much attention, with several studies
examining the dynamics and energy dependence
of the channels producing methane (CH4) and
carbon monoxide (CO) [4,5,6]. Despite many
thorough investigations, there are still
discrepancies in the branching ratio of the roaming
to transition state pathway.
In an experimental study, Velocity Map Images of
CO(v=0,J) photofragments from the 308 nm
photodissociation of acetaldehyde were BASEX
transformed to obtain CO speed distributions. The
distributions for J between 10 and 30 are clearly
bimodal and are well fit by two characteristic
temperatures. This bimodality reaffirms the
presence of two dynamically different mechanisms
to form CO + CH4, first proposed by Houston and
Kable using LIF and Doppler analysis [2]: one
produces CO with relatively little speed and
angular momentum, while the second makes fast
CO in high angular momentum states. When CH4
internal energy distributions are calculated directly
from the total kinetic energy distributions through
conservation of energy, the result is in good
agreement with the FT-IR results of Heazlewood
et. al. [5]. The branching ratio between the two
different pathways is seen to heavily favor the
mechanism which produces slow CO partnered
with highly internally excited CH4 fragments.
Theoretical work to describe these two different
mechanisms via direct dynamics calculations has
recently uncovered a few caveats. Experiments to
examine the competition between the two
pathways as a function of available energy could
help towards a more complete evaluation of the
dynamics in acetaldehyde photodissociation.
References:
[1] D. Townsend, S.A. Lahankar, S.K. Lee, S.D. Chambreau, A.G.
Suits, X. Zhang, J. Rheinecker, L.B. Harding, J.M. Bowman,
Science, 306, 1158 (2004).
[2] P.L. Houston, S.H. Kable, PNAS, 103, 16079 (2006).
[3] V. Goncharov, N. Herath, A.G. Suits, J. Phys. Chem. A, 112,
9423 (2008).
[4] B.F. Gherman, R.A. Friesner, T. Wong, Z. Min, R. Bersohn, J.
Chem. Phys., 114, 6128 (2001).
[5] B.R. Heazlewood, M.J.T. Jordan, S.H. Kable, T.M. Selby, D.L.
Osborn, B.C. Shepler, B.J. Braams, J.M. Bowman, PNAS, 105,
12719 (2008).
[6] L.B. Harding, Y. Georgievskii, S.J. Klippenstein, J. Phys. Chem.
A, 114, 765 (2010).
Poster Presentations
Monday 5 December - Session 2
P42
Understanding the immune
interactions of an unstructured
protein antigen: the malaria surface
protein MSP2
Christopher A. MacRaild1 , Marie Ø.
Pedersen1 , Christopher G. Adda2 , Robin F. Anders2 and Raymond S. Norton1 1 Department of Medicinal Chemistry and Drug Action, Monash
University, Melbourne, Australia.
2 Department of Biochemistry, La Trobe University, Melbourne,
Australia
Abstract
Merozoite surface protein 2 (MSP2) is one of the
most abundant proteins on the surface of the
merozoite stage of Plasmodium falciparum, and is
a clinically validated candidate for inclusion in a
malaria vaccine1. MSP2 is a GPI-anchored protein
consisting of conserved N- and C-terminal regions
and a variable central region of low sequence
complexity. Like many malaria antigens, MSP2 is
intrinsically unstructured, with few regions of
limited conformational restriction in solution2. The
central variable region appears to dominate natural
and protective immune responses; the mechanism
by which the conserved regions apparently evade
immune surveillance is unclear. More generally, the
structural basis and functional significance of
immune interactions with unstructured proteins is
poorly understood. We address these questions
by characterising the conformational behavior of
MSP2 under a range of solution conditions, and by
probing the interactions of a panel of monoclonal
antibodies against recombinant MSP2 in solution
and native MSP2 on the merozoite surface. These
antibodies recognise recombinant MSP2 but
possess variable abilities to recognise MSP2 on
the merozoite surface, consistent with patterns of
natural human immune responses. Understanding
the conformational basis of these cryptic epitopes
may aid the design of more effective vaccines
based on MSP2.
1. Genton, B., Betuela, I., Felger, I., Al-Yaman, F., Anders, R. F.,
Saul, A. et al. (2002). J. Infect. Dis. 185: 820–827.
2. Zhang, X., Perugini, M. A., Yao, S., Adda, C. G., Murphy, V. J.,
Low, A., Anders, R. F. and Norton, R. S. (2008). J. Mol. Biol.
379: 105-121.
129

Poster Presentations
Monday 5 December - Session 2
P43
Computational investigation of
binding of kappa conotoxin to
voltage-gated potassium channels
S. Mahdavi 1 and S. Kuyucak1 1-School of Physics, University of Sydney, NSW2006, Australia
Abstract
PVIIA is a member of the kappa conotoxin family
that inhibits the drosophila Shaker potassium
channel (Shaker). While Shaker is sensitive to this
toxin, the rat Kv1.1 channel is resistant to it. Here,
we study the interactions of PVIIA with the Shaker
and Kv1.1 channel to determine the molecular
interactions that give rise to this selectivity.
The 3D structure of Shaker and Kv1.1 are created
by structural homologies with Kv1.2 structure
(3LUT). We have docked PVIIA (ID:1AV3) on both
channels using HADDOCK. The best complex for
each channel is selected and embedded in a lipid
bilayer. They are equilibrated and ran for up to
20ns in MD simulations. From the trajectory data,
we have determined pair-residue interactions in
each channel-toxin complex.
In the Shaker-PVIIA complex, K7 enters the filter
and makes contact with the Y445 carbonyls. The
R2, K25, R22, N5 and N24 residues are also
responsible for electrostatic interactions and
hydrogen bonds through their contact with N423
and D447. There are several hydrophobic
interactions between I3, F9, L12, F23 and F425,
V451, which are stable throughout the simulation.
The Shaker-PVIIA structure yields results that are
in good agreement with experiments. We are now
performing free energy perturbation (FEP)
calculations to determine the changes in the
binding affinities when the toxin residues are
mutated. This will provide a more quantitative test
for the proposed complex and increase the
confidence in the computational model.
130
Figure1: Side view of two monomers of Shaker and PVIIA (in pink)
in Shaker-PVIIA complex . R2, K7 and N24 residues in toxin are
explicitly shown.
For Kv1.1-PVIIA complex, most charged and polar
residues of the toxin are in contact with E353 and
H355 . Consequently, electrostatic interactions
between Kv1.1and toxin are more probable.
However, these interactions are near the turret
region of the pore and fluctuate frequently. There
are no significant hydrophobic interactions as they
mostly mismatch.
In conclusion, in Shaker there are several stable
interactions of the toxin residues with the residues
near the selectivity filter and the turret region,
which generate a stable complex. In contrast, for
Kv1.1 most interactions are in the turret region
which are not very stable, and there is
considerable mismatch among the hydrophobic
residues.
P44
Ab initio and classical molecular
dynamics study of the aggregation
propensities of amyloidogenic
peptides in the presence of
nanomaterials
A.J. Makarucha 1 , N. Todorova1 , A. Mostofi 2 ,
I. Yarovsky 1
1 Health Innovations Research Institute, School of Applied
Sciences, RMIT University, GPO Box 2476 V, Melbourne, VIC,
Australia.
2 Department of Material s & Physics, Imperial College London,
London, U.K., SW7 2AZ

Abstract
As nanotechnology becomes more prevalent in
industrial, consumer and medical industries the
rate of exposure to nanomaterials increases and
the need to understand the effects that these
materials have on biological systems is paramount.
Computational studies have been conducted to
investigate the effects of nanomaterials on many of
these biological systems however few studies have
considered how surfaces and nanomaterials could
promote or inhibit peptide self-assembly of fibril
forming proteins 1.
Amyloidogenic proteins, which form insoluble
protein aggregates are involved in many
degenerative diseases, such as Parkinson’s,
Alzhiemer’s, Creutzfeld-Jacob disease, and
dialysis-related amyloidosis. It has been shown
that due to the large surface area of nanoparticles
the rate of protein fibrillation and thus aggregation
can be enhanced by decreasing the lag time for
nucleation 2. Apolipoprotein C-II (apoC-II) is a type
of plasma apolipoprotein known to aggregate in
lipid-depleted conditions, and its fibrils are a major
component in human atherosclerotic plaques 3. In
addition to the full-length protein, the peptide
fragments composed of residues 60 to 70
possess an inherent propensity for amyloid fibril
formation in solution. Comprehensive investigation
has been performed on the effects of mutation, pH
and lipid environment on the amyloidogenic
propensities of apoC-II(60-70)4-7.
Explicit solvent molecular dynamics was utilised to
investigate the aggregation propensities of
apoC-II(60-70) peptide in the presence of
carbonaceous nanomaterials, such as fullerene
(C60), single walled carbon nanotube and a
graphene sheet. The different shape of these
nanomaterials allowed for the effects of curvature
to be investigated on the fibril formation
propensities of the peptide. Simulations of
monomeric and dimeric apoC-II(60-70) were
performed. The results were compared with our
previous studies of apoC-II(60-70) peptides in
ambient conditions 5. We identified the
conformational changes in the peptide due to
curvature effects and surface-peptide interactions
that could affect the fibrillation propensities of
apoC-II(60-70).
Poster Presentations
Monday 5 December - Session 2
The linear-scaling DFT package, ONETEP, was
utilised to characterise the electronic structure and
binding energies of the previously identified
peptide – nanomaterial complexes using classical
MD. Geometry optimisation and binding energy
calculations were performed to characterise the
affinity of the peptide for individual nanomaterial.
We also identified the key residues in apoC-II(60-
70) that are responsible for association with
carbonaceous nanomaterials.
Chemistry B 113, 9447-53 (2009).
ApoC-II (60-70) adsorbed to carbon nanotube and
fullerene
1. Makarucha, A.J., Todorova, N. & Yarovsky, I. Nanomaterials in
biological environment: a review of computer modelling studies.
European Biophysics Journal 40, 103-115 (2010).
2. Linse, S. et al. Nucleation of protein fibrillation by nanoparticles.
Proc Natl Acad Sci U S A 104, 8691-8696 (2007).
3. Hatters, D.M., MacPhee, C.E., Lawrence, L.J., Sawyer, W.H. &
Howlett, G.J. Human apolipoprotein C-II forms twisted amyloid
ribbons and closed loops. Biochemistry 39, 8276-83 (2000).
4. Todorova, N. et al. Effects of mutation on the amyloidogenic
propensity of apolipoprotein C-II60–70 peptide. Physical
Chemistry Chemical Physics 12, 14762 (2010).
5. Hung, A., Griffin, M.D.W., Howlett, G.J. & Yarovsky, I. Effects of
oxidation, pH and lipids on amyloidogenic peptide structure:
implications for fibril formation? European Biophysics Journal
38, 99-110 (2008).
6. Todorova, N., Hung, A. & Yarovsky, I. Lipid concentration effects
on the amyloidogenic apoC-II(60-70) peptide: a computational
study. Journal of Physical Chemistry B 114, 7974-82 (2010).
7. Hung, A., Griffin, M.D., Howlett, G.J. & Yarovsky, I. Lipids
enhance apolipoprotein C-II-derived amyloidogenic peptide
oligomerization but inhibit fibril formation. Journal of Physical
131

Poster Presentations
Monday 5 December - Session 2
P45
Competitive N-O and O-C homolysis
in TEMPO-based alkoxyamines
David L. Marshall1 , Martin R. L. Paine1 ,
Ganna Gryn’ova2 , Philip J. Barker3, Michelle L.
Coote2 , Stephen J. Blanksby1 1 ARC Centre of Excellence for Free Radical Chemistry and
Biotechnology & School of Chemistry, University of Wollongong,
NSW, 2522
2 ARC Centre of Excellence for Free Radical Chemistry and
Biotechnology & Research School of Chemistry, Australian
National University, Canberra ACT, 0200
3 BlueScope Steel Research, P.O Box 202, Port Kembla, NSW,
2502
Abstract
2,2’,6,6’-tetramethylpiperidine-N-oxyl (TEMPO)
free radicals are highly stable radical scavengers.
As such, they find wide usage as the active form of
antioxidant hindered amine light stabilizers (HALS)
in surface coatings, including COLORBOND®
steel. The mechanism of action involves reversible
cycling between the nitroxyl radical and
alkoxyamine, the net result being the conversion of
deleterious alkyl and peroxyl radicals into inert
products, with the continual regeneration of the
active nitroxyl, as described by the “Denisov
Cycle”.
However, from empirical evidence it is clear that
HALS are inevitably chemically deactivated or
physically removed from the polymer; leading to
the eventual fading or discolouration of the
coating. We have previously demonstrated that
hydroxyl radicals decompose HALS into volatile
by-products, which would be readily lost by
evaporation during polymer cure, or in-service. An
increased abundance of secondary amines were
also detected upon exposure of TEMPO
derivatives to hydroxyl radicals, implying that N-H
amines (and by extension, aminyl radicals) may
play a greater role in the stabilization mechanisms
of HALS than previously considered. 1
Analysis of 4-carboxy-TEMPO based
alkoxyamines by negative ion electrosprayionization
mass spectrometry (ESI-MS) was
undertaken, with either collision induced
dissociation (CID) or photodissociation (PD)
tandem mass spectrometry (MS/MS). Herein, we
132
demonstrate a competition between nitrogenoxygen
and oxygen-carbon bond homolysis,
dependent on the structure of the captured radical
that forms the alkoxyamine. Moreover, for certain
alkoxyamine structures, the nitrogen-oxygen bond
is cleaved preferentially over the oxygen-carbon
bond.
The observed structure-dependent trends
correlate well with previous high level ab initio
calculations into relative free energies of homolysis
between the N-O and O-C bonds. For example,
heteroatoms in the α-position to the nitroxyl
oxygen stabilize the oxygen-carbon bond through
anomeric interactions, therefore promoting
nitrogen-oxygen homolysis. Conversely, a
neighbouring aromatic system greatly enhances
O-C homolysis through stabilization of the formed
benzyl radical. 2
The primary products of the undesirable N-O
cleavage are aminyl and alkoxyl radicals. If
repeated within surface coatings, the antioxidant
activity of the nitroxyl radical is lost, and moreover
the formed alkoxyl radicals may further propagate
polymer degradation. Indeed, an
oxidation product attributed to N-O homolysis has
already been observed after accelerated
weathering of a polymer coating containing a
commercially available alkoxyamine HALS. 3
Understanding the structure-activity relationship
between these two competing homolysis
processes will prove extremely useful, particularly
for assisting the selection of systems that promote
the desired O-C homolysis and/or resist the
unwanted N-O homolysis pathway.
1. Marshall DL, Christian ML, Gryn’ova G, Coote ML, Barker PJ,
Blanksby SJ. Organic & Biomolecular Chemistry 2011; 9: 4936.
2. Hodgson JL, Roskop LB, Gordon MS, Lin CY, Coote ML. J.
Phys. Chem. A 2010; 114: 10458.
3. Paine MRL, Barker PJ, Blanksby SJ. Analyst 2011; 136: 904.

P46
Thermodynamics and Metabolomics
integration into metabolic Genome
Scale Model to resolve metabolic
flux directions
Veronica Martinez1 , Stefanie Dietmair1 ,
Lake-Ee Quek1 , Lars Keld Nielsen1 1 Australian Institute for Bioengineering and Nanotechnology, The
University of Queensland Australia , Corner College and Cooper
Rds (Bldg 75) Brisbane, Qld, 4072
Abstract
The incorporation of the second law of
thermodynamics and the standard Gibbs energy
of formation with metabolomics data into
metabolic models can reveal the flux direction for a
subset of reversible reactions under a given
physiological condition. The flux solution space is
reduced when the direction of a reversible reaction
is fixed. This approach allows us to apply
metabolomics to better quantify cell metabolism.
For example, for parallel pathways that are found
in more than one compartment, it is possible to
distinguish between the degradation and the
synthesis routes if the reaction directions are
known. This will lead to a better understanding of
the possible functional states of the cell.
A software based on NET optimization was
developed to incorporate thermodynamic
constraints with metabolite concentrations. A
Human Genome Scale Model (GeM) was modified
to work with two compartments (cytoplasm and
mitochondria). Compartment properties (pH, ionic
strength, etc ) for mammalian cells were compiled
from literature together with thermodynamic data.
By applying only thermodynamic constraints to a
Human GeM 15 new irreversible reactions were
found. Nonetheless, there are still 1188 reversible
reactions that are not constrained. Accurate
metabolite concentrations are required to resolve
the direction of these reactions, but it is at present
not possible to determine the concentration of all
metabolites. Preliminary studies on HEK293 cells
revealed that no new reaction directions could be
determined despite measuring concentrations of
13 nucleotides. Therefore, targeted metabolomics
must be applied. In silico simulations based on the
Poster Presentations
Monday 5 December - Session 2
network topology and thermodynamic constraints
were realized to screen for potential metabolite
candidates. Briefly, the approach attempts to find
a set of reactions that, if each of their direction is
known, will fix the direction of other reversible
reactions; metabolites linked to these reactions are
therefore considered most useful to unravel the
directions of the initially reversible reactions.
In conclusion, thermodynamics can be
incorporated with a multi-compartment metabolic
network to identify new irreversibilities that are
essential to further constrain the metabolic model.
However, our simulations revealed that a large
number of metabolites still need to be measured,
possibly attributed to the fact that most metabolic
reactions can operate independently and are
highly redundant.
P47
Diagnostics for Orbital and
Wavefunction Quality
Laura K McKemmish 1 *, Jia Deng1 and
Peter Gill1 1 Research School of Chemistry, Australian National University,
Science Road, Acton 2601 ACT Australia
* laura.mckemmish@gmail.com
Abstract
As computer power increases, more chemistry is
done on computers, rather than in a laboratory,
because it is safer, cheaper and faster. Yet black
box approaches for computational chemistry are
limited by the lack of a universal method of
quantifying a wavefunction’s accuracy. Here, we
propose a paradigm for a diagnostic that
quantifies how well an approximate wavefunction
satisfies its Schrodinger equation (SE) independent
of any external input. This diagnostic is the angle in
Hilbert space, using some inner product metric,
between and ; an angle of zero implies that the
wavefunction satisfies its SE exactly, while higher
angles imply increasingly low quality
wavefunctions. A threshold, say 0.05, can be
selected for desired accuracy based on the
calculation’s purpose.
A useful functional intermediate step is to quantify
how well an orbital satisfies its Hartree-Fock
133

Poster Presentations
Monday 5 December - Session 2
equation[1]. We investigate the effect of different
inner product metrics (overlap, Coulomb and
Gaussian). We conclude that the inner product
metric is unsuitable due to its high sensitivity to
electron-nuclear cusp inaccuracies. Furthermore,
despite the relative ease of the required molecular
integrals for the Gaussian inner product metric,
this metric suffers from fatal errors in giving very
good scores to extremely bad orbitals for the
hydrogen-like atoms. Therefore, the most suitable
metric currently is the Coulomb metric. However,
some of the required molecular integrals have not
been found analytically due to the complicating
presence of two Coulomb operators; however,
one- and two-dimensional numeric integrals can
be found through a slight alteration of the method
presented in King[2].
In defining the wavefunction diagnostic, we make
slight alterations to the most obvious definition to
introduce size-intensivity to the diagnostic based
on a toy model. We then look at finding this
wavefunction quality diagnostic for the most
straightforward wavefunctions consisting of a sum
of Slater determinants in a Gaussian basis
function; this will allow Hartree-Fock (HF) and
CI-based wavefunctions to be analysed. In doing
so, we note that a four-dimensional numeric
integration is currently required. We present results
for a variety of small test cases and compare the
orbital and wavefunction diagnostic for HF results.
[1] Deng, J.; Gilbert, A. T. B.; Gill, P. M. W., Can. J. Chem., 2010,
88, 754-758
[2] Komornicki, A.; King, H. F., J. Chem. Phys., 2011, 134, 244115
P48
Far-Infrared spectroscopy of water
aerosols using synchrotron radiation
Chris Medcraft1,2 , Evan G. Robertson 3 ,
Dominque R.T. Appadoo2 , Sigurd Bauerecker 4 and
Don McNaughton1 1 School of Chemistry, Monash University, Victoria 3800
Australia, chris.medcraft@monash.edu, don.mcnaughton@
monash.edu
2 Australian Synchrotron, 800 Blackburn Rd, Clayton, 3168,
Victoria. Australia, dominque.appadoo@synchrotron.org.au
3 Department of Chemistry, La Trobe University, Victoria 3083
Australia, E.Robertson@latrobe.edu.au
4 Institut für Physikalische und Theoretische Chemie, Technische
Universität Braunschweig, Hans-Sommer-Strasse 10, D-38106
Braunschweig, Germany
134
Abstract
An Enclosive Flow Cooling (EFC) Cell has been
coupled to the Bruker IFS125HR spectrometer on
the High Resolution Infrared Beamline at the
Australian Synchrotron. This cell has been
modified from the design of Bauerecker[1] to
extend its optical range into the far-infrared where
the synchrotron source has the greatest
advantage over thermal sources. The coupling of
the EFC cell to a synchrotron source provides us
with a unique ability to perform a range of different
experiments in the gas and condensed phases
over a wide range of frequencies. We have used
this capability to probe the intermolecular
vibrations of water aerosols centred around 240
cm-1 over a wide range of particle formation
temperatures (see figure 1) and pressures (10-500
mbar). These bands are of great interest to
astronomers, providing an indication of both the
temperature of an observed ice feature, and
whether it arises from amorphous or crystalline ice
(which in turn has implications for solar system
formation). Significantly, we notice differences
between the band positions our aerosol spectra
and the previously published spectra of based on
thin films. We attribute these differences to the
absence of scattering (from the real part of the
refractive index of water ice) in our spectra.
Experiments were also performed in the midinfrared
as a means of comparison with previous
experiments.
References
[1] S. Bauerecker, M. Taraschewski, C. Weitkamp and H.K.
Cammenga, Rev. Sci. Instr., 2001, 72, 3946.
[2] C. Medcraft, E.G. Robertson, C.D. Thompson, S. Bauerecker
and D. McNaughton, PCCP, 2009, 11, 7848-7852
[3] E.G. Robertson, C. Medcraft, L. Puskar, R. Tuckermann, C.D.
Thompson, S. Bauerecker and D. McNaughton, PCCP, 2009,
11, 7853-7860

P49
Quantum Chemical Studies of the
Catalytic Mechanism of E3
Hydrolysis of Organophosphates in
the Australian Sheep Blowfly L.
cuprina
Tamara Meirelles 1 , Junming Ho1 , Michelle
Coote1 , Colin Jackson1 *
1 Research School of Chemistry, Australian National University
ACT 0200
*cjackson@rsc.anu.edu.au
Abstract
Inhibition of acetylcholinesterase-catalyzed
acetylcholine hydrolysis at nerve synapses by
organophosphates has led to their use as
insecticides and chemical warfare agents.
Through a single point mutation, the sheep blowfly
Lucilia cuprina has evolved a new
organophosphate hydrolase, E3, from an existing
carboxylesterase. However, the exact mechanism
by which this active site mutation can confer this
change in activity is currently unknown. To
investigate the basis for the altered catalytic
mechanism of E3 in detail, we have performed
high-level quantum chemistry calculations on the
reaction mechanism as catalyzed by the original,
and mutant, enzymes. Our results suggest that a
Gly-Asp mutation within the active site introduces
a general base that can activate a water molecule
as part of a new catalytic mechanism. These
results provide a framework that can be used as
the basis for future work that will attempt to
identify further mutations to generate a more
efficient catalyst that can be used to detoxify
organophosphate in agricultural and medical
applications.
Poster Presentations
Monday 5 December - Session 2
P50
Ab Initio Folding of Helical Peptides
Using Adaptive Hydrogen Bond-
Specific Charge Scheme
Siti Raudah Mohamed Lazim1 , Dawei
Zhang2 Division of Chemistry and Biological Chemistry, School of Physical
and Mathematical Sciences, Nanyang Technological University, 21
Nanyang Link, Singapore, 637371,
1 SITI13@e.ntu.edu.sg
2 zhangdw@ntu.edu.sg
Abstract
Adaptive hydrogen bond-specific charge (HBC)
scheme is a newly developed on-the-fly charge
fitting that relays a relatively accurate electrostatic
polarization effect for hydrogen bonds established
during the theoretical folding of proteins.
Considering the inherent nature of protein folding
which necessitate continuous formation and
interruption of hydrogen bonds, on-the-fly charge
fitting of amino acids involved in hydrogen bonding
through fragment quantum mechanical
calculations offers an accurate description of the
electronic distribution of the protein during the
folding process. Here, we report the ab initio
folding of four different helical peptides viz. b30-82
domain of Subunit b of Escherichia Coli F1Fo
adenosine triphosphate synthase (2KHK),
transmembrane helix 6 of the human cannabinoid
receptor-2 (2KI9), N36 and C34 domain of gp41
from HIV-1 envelope glycoprotein through
conventional molecular dynamics simulation at
room temperature using implicit continuum
solvation model. Employing adaptive HBC
scheme, the effective folding of the four peptides
were observed with best Cα-RMSD with reference
to experimental structures determined to be 0.69
Å for 2KHK, 2.97 Å for 2KI9, 0.52 Å for N36 and
0.66 Å for C34. The folding pathways of the
proteins folded in this work were also elaborated
through detailed analyses encompassing
clustering, secondary structure assignment and
folding landscapes. These analyses showcased
the continuous growth of α-helix from the
nucleation sites formed along the peptide which
concurs with helix-coil transition model which
describes the first turn of helix as the nucleus
135

Poster Presentations
Monday 5 December - Session 2
acting as a stable infrastructure obliging the
development of consecutive turns to form a fully
compact α-helical protein.
P51
Amyloid-like fibrillization and the
structure of glucagon in the
presence of anionic bicelles
Ayano Momose 1 , Izumi Yamane 1 , Hideki
Fujita 1 , Eri Yoshimoto 1 , Izuru Kawamura1 ,
Marc-Antoine Sani2 , Frances Separovic2 , Akira
Naito1 1 Graduate School of Engineering, Yokohama National University,
Hodogaya-ku, Yokohama 240-8501, Japan naito@ynu.ac.jp
2 School of Chemistry, Bio21 Institute, University of Melbourne,
VIC 3010
Abstract
Glucagon is a 29-residue peptide hormone
secreted by α-cells of pancreatic islet cells when
blood glucose level is low and promotes resolution
of glycogen in liver to increase the level. Glucagon
easily dissolves in acidic solvent and forms
amyloid-like fibrils. In the case of amyloidogenic
proteins, when the monomers change to fibrils, the
secondary structure changes mainly from α-helix
to β-sheet. After glucagon changes to β-sheet
structure, it becomes cytotoxic. The detailed
structures and mechanism of fibrillization is not
well understood. In this study, the structure and
fibril formation of glucagon in acetic acid solution
(pH 3.3) and the effect of neutral and anionic
phospholipids (bicelles) was observed using high
resolution solid-state 13C NMR and TEM.
The fibrillization kinetics was revealed using a
two-step autocatalytic reaction model composed
of fibril nucleation (rate constant of k1) and fibril
extension reaction (rate constant of k2) by means
of 13C solid-state NMR. We observed signal
intensity change of glucagon fibrils under 5
different conditions: in solution, in presence of
neutral, 10%, 15% and 25% anionic bicelles. In the
presence of bicelles, the first reaction was faster
but the second reaction was slower than in
solution. It is conceivable that in the presence of
bicelles, peptides interacted and concentrated on
the surface and, therefore, the first reaction
136
(nucleation) was accelerated but the second
reaction (fibril elongation) was delayed. In addition,
the higher the concentration of negatively charged
lipids in the bicelles, the faster was the nucleation
and the slower the fibril elongation. This is due to
the electrostatic interaction between glucagon and
the negatively charged lipids. Glucagon has a
charge of +1 for the entire peptide and, under low
pH conditions, the positive charge is emphasized.
Thus we conclude that the bicelles accelerated the
nucleation and decelerated the fibril elongation of
glucagon. This tendency was strengthened by
increasing the ratio of negatively charged lipids in
the bicelles.
P52
Modelling Molecular Response in
Anisotropic Electric Fields
Michael Morris1 , Meredith Jordan2 1 School of Chemistry, University of Sydney, NSW, 2006,
morris_m@chem.usyd.edu.au
2 School of Chemistry, University of Sydney, NSW, 2006, mjtj@
chem.usyd.edu.au
Abstract
It has long been established that long-range
interactions play a key role in molecular processes.
For example, protein-ligand association is strongly
influenced by long-range interactions. Despite their
importance, it is often difficult to determine how
molecular structure is affected by changes in
these long-range interactions. In such
circumstances, it is useful to model the long-range
interaction using a classical power series
expanded in the field, F, and field gradient, ÑF, of
an interacting species, with coefficients
determined at zero-field. The accuracy and limits
of applicability of this expansion are investigated
for a small model system, ClH:NH3, which
undergoes significant spectroscopic and structural
change in typical atomic-scale fields. The ClH:NH3
structure and vibrational frequencies are
determined at first and second order in F and ÑF
for a variety of uniform and anisotropic external
fields. Spectroscopic and structural characteristics
are predicted, at first order in F and ÑF, to within
experimental error, with lower errors being
observed at second order. The accuracy of the

expansion is found to reduce as the magnitude of
F and ÑF increases or as the energy level
considered increases, although even at field
strengths large enough to cause dramatic
structural change in the complex, both the
structure and vibrational frequencies are effectively
quantitatively predicted using only terms linear in F
and ÑF. These results suggest that knowledge of
the zero-field molecular potential energy and
dipole and quadrupole moment surfaces may be
sufficient to accurately model long-range
interactions in a wide range of circumstances.
P53
Examining the Electronic
Interactions of Ligated Copper
Nanoparticles Generated by Laser
Ablation Synthesis in Solution
(LASiS)
Ashley Mulder1 , Mark Buntine1 , Aidon
Slaney1 , Sean Long1 , Max Massi1 , Franca Jones1 ,
Mark Ogden1 1 Department of Chemistry, Curtin University, GPO BOX U1987,
Perth WA 6845
Abstract
We have successfully created copper
nanoparticles (CuNP’s) in aqueous solutions using
the LASiS method (Laser Ablation Synthesis in
Solution). The fundamental frequency (1064 nm) of
a Nd:YAG laser was focused onto a copper plate in
a glass vial with approximately 15 mL of solution.
The copper plate was ablated for 30 minutes
during which time the solution took on a green/
yellow colour, characteristic of the CuNP surface
plasmon resonance (SPR) transition. Various
nitrogen containing ligands were added to the
solutions prior to laser ablation, to act as capping
ligands to protect the copper nanoparticles from
oxidation. All solutions were made up to 10-4
molar concentration and the ligands used were: (1)
1,10-phenanthroline, (2) 2,2’-bipyridine, (3)
4,4’-bipyridine, (4) 5-(2-pyridyl)-1H-tetrazole, (5)
5-(4-pyridyl)-1H-tetrazole, (6) 5-(2-pyridyl)-2-(tbutyl)-1H-tetrazole,
(7) 5-(4-pyridyl)-2-(t-butyl)-1Htetrazole,
(8) 5-phenyl-1H-tetrazole and (9)
5-methyl-1H-tetrazole. These solutions post
Poster Presentations
Monday 5 December - Session 2
ablation all took on a blue/green through to green/
yellow colour. These solutions were analysed by
TEM imaging to determine the particle size
distributions and by UV-Vis spectrometry to
ascertain the position of each solution’s SPR and
to study the kinetics of laser-based CuNP
formation and stability.
P54
Patch Fluorimetry to Measure the
Membrane Tension Required to Gate
Mechanosensitive Ion Channels
Takeshi Nomura1 , Charles Cranfield1,2 , Boris
Martinac1,2 1 Victor Chang Cardiac Research Institute, Lowy-Packer Building,
405 Liverpool St, Darlinghurst, 2010.
2 St Vincent’s Clinical School, The University of New South
Wales, de Lacy, Victoria St, Darlinghurst, 2010
T.nomura@victorchang.edu.au; C.cranfield@victorchang.edu.au;
B.martinac@victorchang.edu.au
Abstract
We report here the ability to measure the
membrane bilayer tension required to gate
mechanosensitive ion channels in a patch pipette
by using patch fluorimetry. By reconstituting
mechanosensitive ion channels in azolectin
liposomes that incorporate 0.1-1% 1,2-Dioleoyl-sn-
Glycero-3-Phosphoethanolamine-N-Lissamine
Rhodamine B Sulfonyl (PE-Rhod) it is possible to
visualise the patch in the pipette in situ using
fluorescence confocal microscopy. To open
mechanosensitive ion channels, such as the
bacterial mechanosensitive channels of large and
small conductance (MscL and MscS), a
measurable negative hydrostatic pressure is
applied to a patch. By a simple derivation of
Laplace’s law, the tension of the membrane at the
threshold pressure for channel opening can be
calculated according to the formula T=PR/2,
where T is the tension of the membrane (measured
in N/m), P is the pressure applied to stretch the
patch membrane (Pa) and R is the radius of the
curvature of the patch (m)[1]. The use of
fluorescence confocal microscopy enables a clear
visualisation and measurement of the radius of
curvature inside the patch when stretched. Here
we demonstrate how this patch fluorimetry has
137

Poster Presentations
Monday 5 December - Session 2
provided an accurate and quantifiable method to
measure the influence of amphipaths and other
lipophilic compounds on lipid-ion channel
interactions in situ.
[1] Sokabe, M., Sachs, F., and Jing, Z. Q., Quantitative video
microscopy of patch clamped membranes stress, strain,
capacitance, and stretch channel activation. Biophysical
Journal, 1991. 59(3): p. 722-728.
Supported by the NHMRC Grant 635525.
P55
Structural characterization of
triacylglycerols by radical directed
dissociation
Huong T. Pham 1 , Stephen J. Blanksby 2 ,
Gavin E. Reid 3
1 School of Chemistry, University of Wollongong, Australia,
thp658@uow.edu.au
2 School of Chemistry, University of Wollongong, Australia,
blanksby@uow.edu.au
3 Department of Chemistry, Michigan State University, United
States, reid@chemistry.msu.edu
Abstract
Deep-fat frying is one of the most common uses
for edible vegetable oils in the food industry. Oil
used for deep-fat frying is subjected to high
temperatures, moisture from foods, and migration
of other compounds from foods that can act as
pro-oxidants.[1] Unsaturated triacylglycerols are
the major components in such oils are likely
participating in dimerization and higher order
polymerization during this thermal procedure.
Such bio-polymerization processes are proposed
to occur via free radical mechanisms although
these are well understood due to the molecular
complexity of these species. Radical directed
dissociation (RDD) [2] is a mass spectrometric
technique that can be used to selectively initiate
and study radical reactions within isolated
molecules or simple ensembles within the gas
phase. In this approach a free radical initiator is
appended to an adducting agent (e.g.,
4-iodoaniline or 4-iodobenzoic acid) and
complexed with a lipid(s) by electrospray
ionisation. Such an approach was employed to
generate adduct ions of triacylglycerols (TAGs) in a
linear ion-trap mass spectrometer with
subsequent photoactivation of the mass-selected
138
complex at 266 nm (Nd:YAG, Continuum Minilite II)
leading to homolysis of the carbon-iodine bond.
Subsequent collision induced dissociation (CID) of
the nascent radical ions gives rise to a radical
directed dissociation mass spectrum that provides
a wealth of structurally informative fragmentation.
This methodology is complementary to
conventional approaches to structure elucidation
of complex lipids in mass spectrometry and will
assist in the characterisation of lipid dimers (and
higher polymers) arising from thermolysis of
vegetable oils. In addition, non-covalent
complexes of a single adducting agent with
multiple lipids have been generated with the
resulting RDD spectra providing evidence for
cross-linking of the lipids. Such spectra may
provide clues as to the chemical pathways
involved in free radical polymerisation of lipids.
[1] Winkler, J. K.; Warner, K. Eur. J. Lipid Sci. Technol. 2008, 110,
1068.
[2] Ly, T.; Julian, R. R. J. Am. Chem. Soc. 2008, 130, 351.
P56
Organic Monolayers for Water
Evaporation Suppression: A
Molecular Dynamic Study
Michael Plazzer, George Yiapanis, Irene
Yarovsky 1
1 Applied Physics, School of Applied Sciences, RMIT University,
Melbourne 3000 irene.yarovsky@rmit.edu.au
Abstract
Self assembled monolayers (SAM) have been of
interest to industry and medical science for their
novel properties of self-organisation, wetting and
selective permeation. The latter, is particularly
important for applications pertaining to chemical
and biological sensors1 , and to the facilitation of
gas transport2 and evaporation resistance.
However, when monolayers are used for external
applications, issues of stability and anchoring to
water have been shown to arise3 , affecting the
long-term functionality of the monolayers. To
elucidate the precise properties required for
long-term efficacy, one requires a thorough
understanding of the nature and strength of

interactions occurring at the monolayer / fluid
interface.
In this research, we use classical molecular
dynamics to investigate a range of amphiphilic
molecules forming monolayers on the surface of
water. The molecules comprise of alkyl chains of
18 carbons with different headgroups including
hydroxyl, glycol, methyl and ether groups. We
demonstrate how surface pressure isotherms can
be an indicator of the robustness of the
monolayers, that is, their ability to maintain stability
over a range of surface pressures. We show that
hydrogen bonding between the monolayer
headgroups and the interfacial water layer, as well
as between the headgroups themselves, play a
primary role in the anchoring and stability of the
monolayers, and that a balance between the two
leads to optimum water evaporation suppressing
performance. We conclude that the choice of
headgroup is the primary determining factor of the
monolayer’s performance.
1. N. Hambdi, J. Wang, H.G. Monbouquette, Journal of
Electroanalytical Chemistry 2005, 581, 2.
2. J.H. Kim, S.Y. Ha, S.Y. Nam, J.W. Rhim, K.H. Paek and Y.M.
Lee, J. Membr. Sci. 2001, 186
3 Solomon et al. Environmental Health. 2007, 7, 3.
Poster Presentations
Monday 5 December - Session 2
P57
Langevin dynamics modelling of
water diffusion in anisotropic
biophysical structures.
Sean Powell1 , Konstantin Momot1 1 Discipline of Physics, Queensland University of Technology, GPO
Box 2434, Brisbane, QLD, 4001, sean.powell@qut.edu.au
Abstract
Diffusion Tensor Imaging (DTI) is a form of
Magnetic Resonance Imaging (MRI) that measures
the anisotropic diffusion of water molecules. This
non-invasive imaging technique enjoys success in
medical research fields such as brain research [1,
2], studies of articular cartilage structure and
biomechanics [3], and clinical diagnosis of medical
conditions such as stroke, diffuse axonal injury,
multiple sclerosis, Alzheimer’s disease and
tumours. The utility of DTI for investigating the
microstructure of some ordered tissues is
presently constrained by the lack of models for
quantitative morphological interpretation of the
diffusion tensor.
In this study, we developed course-grained
molecular models of water dynamics in articular
cartilage. The aim was to relate diffusion
measurements to microstructural characteristics
such as collagen fibre volume fraction and fibre
alignment. In articular cartilage, the displacement
of diffusing water molecules is restricted in some
directions more than others by the collagen fibres.
DTI measures this RMS displacement anisotropy
to generate three-dimensional maps representing
the anisotropy of the average collagen alignment
on the length scale 50-200μm.
A c++ computer model was developed and
simulations of water diffusion in various articular
cartilage structures were performed. The degree
and direction of diffusion anisotropy was then
calculated for a range of collagen volume fractions
and fibre alignment angles. The simulations were
run on a 600 CPU SGI Altix supercomputer and
took around 3-5 days per structure to process.
Quantitative models were then built to relate the
diffusion tensor to articular cartilage
microstructure. This study is the first to quantify
the effects of different collagen fibre alignment
139

Poster Presentations
Monday 5 December - Session 2
angles on the diffusion tensor. The use of Langevin
dynamics enabled chemically realistic modelling of
the water-fibre interactions and allows for the
inclusion of proteoglycans.
The use of these models as an interpretive tool will
improve the utility of diffusion tensor imaging for
clinical diagnosis of diseases of articular cartilage
and assisting in the development of an improved
understanding of its biomechanical properties.
This research can be expanded to develop
quantitative models describing the diffusion of
water in a larger range of ordered biophysical
tissue such as tendons and muscle.
References
[1] Behrens TEJ, Berg HJ, Jbabdi S, Rushworth MFS, Woolrich
MW. Neuroimage 2007; 34:144-155
[2] Tournier JD, Yeh CH, Calamante F, Cho KH, Connelly A, Lin CP.
Neuroimage 2008; 42:617-625.
[3] de Visser SK, Bowden JC, Wentrup-Byrne E, Rintoul L,
Bostrom T, Pope JM, Momot KI. Osteoarthr Cartilage 2008;
16:689-697.
P58
Photodissociation Dynamics of
Acetaldehyde at 308 nm: A
Comparison of Experimental Studies
and a Classical Trajectory Study of
the Transition State Mechanism
Mitchell S. Quinn1 , Gabi de Wit2 , Scott A.
Reid3 , B. Klaas Nauta4 , Alan T. Maccarone 5 , Scott
H. Kable6 , Meredith J. T. Jordan7 1 School of Chemistry, University of Sydney, New South Wales
2006, m.quinn@chem.usyd.edu.au
2 School of Chemistry, University of Sydney, New South Wales
2006, g.dewit@chem.usyd.edu.au
3 Department of Chemistry, Marquette University, Milwaukee, WI,
USA, scott.reid@marquette.edu
4 School of Chemistry, University of Sydney, New South Wales
2006, k.nauta@chem.usyd.edu.au
5 School of Chemistry, University of Sydney, New South Wales
2006, alanmac@uow.edu.au
6 School of Chemistry, University of Sydney, New South Wales
2006, s.kable@chem.usyd.edu.au
7 School of Chemistry, University of Sydney, New South Wales
2006, mjtj@chem.usyd.edu.au
Abstract
The recent discovery of an alternate pathway to
molecular products, in a phenomenon known as
‘roaming’, has led to investigation of several
140
organic molecules that are thought to exhibit these
characteristics. The first two experimental systems
where the roaming mechanism was identified were
formaldehyde (H2CO) [1] and acetaldehyde
(CH3CHO) [2]. In these systems, the H atom or
CH3 group “roams” in the radical dissociation
channel and, in a self-abstraction process,
abstracts an H atom from the other moiety. The
products of a roaming mechanism are typically
rotationally and translationally cold, with high
vibrational excitation of the molecule that contains
the roaming fragment (i.e. H2 for H2CO and CH4
for CH3CHO). Molecular products formed from
more traditional “transition state” (TS) mechanisms
have a large amount of kinetic energy; that is, the
product molecules are translationally and
rotationally hot. Armed with this knowledge
chemists have since moved on to investigate
roaming in about a dozen other reactions.
This poster uses trajectories obtained on a
reaction path potential energy surface (PES) to
investigate the photodissociation of CH3CHO.
These trajectories were restricted to a section of
the PES consisting of only the traditional TS
mechanism. The trajectory results were compared
to recent experiments performed by the authors
(see the poster presented by Alan T. Maccarone)
as well as detailed trajectory calculations on a full
PES [3] and a reanalysis of previous experimental
results [2].
Furthermore the poster will outline the construction
of a zero point energy (ZPE) corrected PES for
H2CO. Due to the difficulty in including the ZPE in
classical and quasi-classical trajectories, and the
current impracticality of running full quantum
mechanical trajectories, we propose a method that
accounts for the ZPE when running classical
trajectories. A first order interpolated ZPE surface
is added to a second order modified Shepard
interpolated PES to create the corrected surface.
The surface allows for full classical trajectories to
include this important quantum mechanical
property through a well-defined and systematic
method.
References:
[1] D. Townsend, S. S. Lahankar, S. K. Lee, S. D. Chambreau, A.
G. Suits, X. Zang, J. Rheinecker, L. B. Harding, J. Bowman,
Science 306 1158 (2004)
[2] P. L. Houston, S. H. Kable, Proc. Natl. Acad. Sci. USA 103
16079 (2006)
[3] B. R. Heazlewood, M. J. T. Jordan, S. H. Kable, T. M. Selby, D.
L. Osborn, et al., Proc. Natl. Acad. Sci. USA 105 12719 (2008)

P59
Alanine scan of an
immunosuppressive peptide:
Surface plasmon resonance analysis
and structure-function relationships
Laura Raguine1 , Marina Ali1 , Veronika
Bender1 , Eve Diefenbach2 , Nicholas Manolios1 1 Department of Rheumatology, Westmead Hospital, Westmead,
NSW 2145, Australia.
2 Protein Production Facility, Westmead Millennium Institute,
Westmead, NSW 2145, Australia.
Abstract
T-cell mediated autoimmune diseases arise due to
the immune system’s inability to differentiate
between “self” and “non-self” antigens. This leads
to destruction and loss of function of the target
organ or tissue. T-cell mediated diseases include
rheumatoid arthritis and type I diabetes.
Immunosuppression is required to prevent such
diseases. Core peptide (CP) is an
immunosuppressive peptide that has the potential
to treat T-cell mediated diseases by inhibiting
autoreactive T-cell activation. By using an alanine
scan, the aim of this study was to examine the
structure versus function relationship of the
constituent amino acids within CP.
CP and CP analogues were synthesised using
solid phase peptide synthesis. CP analogues were
produced by substituting single amino acids with
alanine. Surface Plasmon Resonance (SPR) was
used to assess binding of CP and its analogues to
lipid membrane models. Antigen Presentation
Assays (APA) were used to assess CP and its
analogues ability to alter/inhibit cytokine
production. Briefly, CP was introduced to an
antigen specific T-cell culture (2B4 cells) in the
presence of antigen. Supernatant from these
activated T-cell cultures were collected after 24
hours and cytokine levels in the supernatant were
measured using a cytokine-dependent
proliferation assay and flow cytometry. Cytokine
levels were compared to a positive control.
CP and 10 of its analogues have been
synthesised, purified by high performance liquid
chromatography and characterised by mass
spectroscopy. Preliminary data using dimyristoyl
Poster Presentations
Monday 5 December - Session 2
phosphatidylglycerol (DMPG) liposomes suggest
the hydrophobic face between the two charged
amino acids (arginine and lysine) are important in
affecting binding affinity. A more complete
description of the biological and biophysical data
will be discussed at a later stage. Any correlations
between binding in SPR and cytokine production
in the APA will also be discussed.
P60
Affinity and selectivity of sea
anemone toxin ShK for the Kv1.1,
Kv1.2 and Kv1.3 channels from free
energy simulations.
M.H. Rashid and S. Kuyucak
School of Physics, University of Sydney, NSW 2006, Australia,
harun@physics.usyd.edu.au, serdar@physics.usyd.edu.au.
Abstract
The voltage gated potassium channel (Kv1.x) is an
attractive target for autoimmune diseases[1].
Potent and selective blockers of potassium
channels are potential therapeutics for treating
these diseases. Here we present molecular
dynamics (MD) studies for binding of the ShK toxin
from the sea anemone to the Kv1 channels, which
inhibits Kv1.1 and Kv1.3 potently and blocks Kv1.2
with a much lower affinity.
Based on crystal structure of voltage-gated
potassium channel Kv1.2 we have constructed a
homology model of Kv1.1 and Kv1.3. Haddock has
been used for the exploration of the
conformational space and the determination of
ligand/protein contacts. We have run the MD
simulation up to 10 ns for the channel-toxin
complex in a solvated lipid bilayer environment.
Several recognition and contact residues have
been identified from the MD simulations of the
complex. The most important is the K22 side
chain, which enters the filter and forms contacts
with the Y carbonyls in all Kv1 channels. Shk
interact with Kv1.1 channel by Lys18/Glu353(C),
Phe27/Gly376(A), Gln16/Glu353(B), Arg11/
Asp361(B), Arg29/Glu353(D), Ser20/Tyr379(D)
residue pairs, Kv1.2 channel by R29/E353(A), S19/
T383(C), M21/Gln357(D) residue pairs and Arg11/
141

Poster Presentations
Monday 5 December - Session 2
Asp402(A), Phe27/Gly401(C), Thr6/Asp402(D),
Arg1/Glu373(C), His19/Ser378(B), Ser20/Gly401(B)
Met21/Met403(C) residue pairs in Kv1.3 channel.
We calculate the potential of mean force (PMF) for
unbinding of ShK from the Kv1 channels using
umbrella sampling MD simulation. The absolute
binding energies determined form the PMF’s differ
by about 1 kcal/mol from the experimental
measurements [2].
P61
Large-scale fully ab initio
calculations of ionic liquids using the
Fragment Molecular Orbital
approach
Jason D. Rigby, Douglas R. MacFarlane,
Ekaterina I. Izgorodina
School of Chemistry, Monash University, Wellington Road, Victoria,
3800, E-Mail: jason.rigby@monash.edu
Abstract
Ionic liquids are a new class of liquids and solvent
based entirely on organic salts. They are finding a
wide range of applications, including in a number
of bio-science and biotechnology contexts. It has
been shown in previous studies1 that the interplay
between electrostatic and dispersion forces in
ionic liquids is an important factor when predicting
thermodynamic and transport properties.
However, the extent to which these components
impact on physical properties have not yet been
studied in detail using a fully ab initio method. The
main issue is that correlated levels of theory in
general scale poorly with molecular size, thereby
making the study of large clusters challenging.
Demands on disk and RAM become excessive
and typically extend beyond the capabilities of
most High Performance Computing clusters. The
Fragment Molecular Orbital (FMO) approach2,3 is
an attractive alternative, in which the system is
divided into molecular fragments, which are
relatively inexpensive to compute even at a
correlated level of theory. We explored the FMO
approach combined with the MP2 level of theory
for a series of four archetypical ionic liquids,
[NMe4][BF4], [C1mim][BF4], [C3mim][BF4] and
[C4mim][BF4], built into clusters of 1, 2, 4 and 8
142
ion-pairs. In these calculations, individual ions
were selected as fragments. The results were
compared with full MP2 and it was found that the
FMO-MP2 method produced excellent accuracy
within 0.2 kJ mol-1 when a three-body correction
was included. Significant improvements in
computational time were observed, thus paving
the way for fully ab initio large-scale calculations of
novel ionic liquids.
References
1. Bernard, U. L.; Izgorodina, E. I.; MacFarlane, D. R. The Journal
of Physical Chemistry C 2010, 114, 20472
2. Kitaura, L.; Ikeo, I.; Asada, T.; Nakano, T.; Uebayasi, M.
Chemical Physics Letters 1999, 313, 701
3. Fedorov, D.; Kitaura, K. The Journal of Chemical Physics 2004,
120, 6832
P62
Structural studies of osmoregulatory
ABC transporters
Stephanie J. Ruiz12 , , Maaike Jansen, and
Bert Poolman
1 Department of Biochemistry, University of Groningen, The
Netherlands
2 s.j.ruiz@rug.nl
Abstract
Osmoregulatory ABC transporters protect
bacterial cells against hyperosmotic stress by
accumulating small, osmotically active compounds
known as compatible solutes. Individual
transporters have been shown to influence
virulence in Staphylococcus aureus and Listeria
monocytogenes through their ability to specifically
import compatible solutes that are present at
higher concentrations in tissue.
OpuA from Lactococcus lactis is an
osmoregulatory transporter that has been
extensively studied due to its unusual architecture
(1,2). All ABC transporters contain two intracellular
ATP-binding domains (NBDs) and two multitransmembrane
domains (TMDs). In prokaryotic
ABC importers this core translocation complex, a
homodimer comprised of four separate
polypeptide chains, is joined by a substrate
binding protein (SBP) that provides the main
determinant of the transporter specificity. In most
studied systems, this SBP is either free in the

periplasm or anchored to the cell membrane via a
lipid moiety. In OpuA the TMD and SBP are fused,
resulting in a homodimeric complex that contains
two SBPs (or substrate-binding domains, SBDs)
per transporter. This has interesting implications
for the interactions between the various
subdomains of the transporter complex.
Lmo1421 and Lmo1422 from L. monocytogenes
are homologous to L. lactis OpuAA (NBD) and
OpuABC (TMD-SBD), respectively. They express
well and form a stable homodimeric complex in
various detergent solutions. Interestingly, despite
high levels of sequence similarity to OpuA and
other osmoregulatory ABC transporters,
Lmo1421/1422 has previously been identified as a
bile exclusion system (3).
The C-terminus of Lmo1422, containing the
putative substrate-binding domain, has been
expressed and purified in isolation. An X-ray
crystal structure of Lmo1422SBD was solved at a
resolution of 1.6 Å and reveals an overall fold
typical of class II substrate-binding proteins, with
the protein in the open conformation. A
comparison with homologous SBPs shows that
residues involved in binding a range of compatible
solutes are structurally conserved. Identification of
the Lmo1422SBD ligand(s) will aid in further
biochemical characterization of this unusual
transporter.
1. Biemans-Oldehinkel, H. et al. (2006) Proc. Natl. Acad. Sci. USA,
103, 10624-10629.
2. Karasawa, A. et al. (2011) J Biol Chem., 286, 37280-37291.
3. Sleator, R.D. et al. (2005) Mol. Microbiol., 55, 1183-1195.
P63
Determination of Threshold
Dissociation Energies of Li+, Na+, K+
and Cs+ Cationized Dimers of
3-Hydroxyflavone, 5-Hydroxyflavone
and 5-Methoxyflavone by FTICR
Mass Spectrometry and DFT
Calculations
Chowdhury Hasan Sarowar 1 , Michael
Guilhaus2 , Gary David Willett3 , Grainne Moran4 1 School of Chemistry, The University of New South Wales,
Sydney, NSW 2052, Australia, c.h.sarowar@unsw.edu.au
Poster Presentations
Monday 5 December - Session 2
2 Bioanalytical Mass Spectrometry Facility, The University of New
South Wales, Sydney, NSW 2052, Australia
3 School of Chemistry, The University of New South Wales,
Sydney, NSW 2052, Australia, g.willett@unsw.edu.au
4 Mark Wainwright Analytical Centre, The University of New South
Wales, Sydney, NSW 2052, Australia, g.moran@unsw.edu.au
Abstract
The threshold dissociation energies of alkali
metal-flavonoid complexes of the type [2L+M]+ are
determined in Fourier transform ion cyclotron
resonance mass spectrometry. The flavonoids (L)
examined are 3-hydroxyflavone, 5-hydroxyflavone
and 5-methoxyflavone and the alkali metal cation
(M) includes Li+, Na+, K+ and Cs+. The ions are
generated in a high pressure external ion source
and allowed to collide with target gas in the ion
cyclotron resonance cell. The threshold
dissociation energies for loss of one ligand from
[2L+M]+ of 5-methoxyflavone follow the order Li+
> Na+ > K+>>Cs+, and 3-hydroxyflavone and
5-hydroxyflavone follow the order Li+ > Na+. For
the same metal cation experiment, the
5-methoxyflavone complex has the highest
dissociation energy compared to 3-hydroxyflavone
and 5-hydroxyflavone. Density functional theory
calculations with a B3LYP functional and a
6-31G(d,p) basis set were used to obtain the
minimized energy geometric structures, vibrational
frequencies, and rotational constants for [L+M]+
and [2L+M]+ isomeric ions. The theoretical bond
dissociation energies are then calculated and
compared with the experimental bond dissociation
energies. The agreement between theory and
experiment is very good in all cases. This work has
been extended to determine the threshold
dissociation energies of Cu2+, Zn2+ and Pb2+
cationized flavone complexes.
143

Poster Presentations
Monday 5 December - Session 2
P64
The impact of the ab initio/DFT
method used for geometry
optimisations on reaction enthalpies
D. L. A. Scarborough, C. D. Thompson, E.
I. Izgorodina
School of Chemistry, Monash University, Victoria, Australia, 3800
Email: David.Scarborough@monash.edu
Abstract
Proton-Transfer-Reaction Mass-Spectrometry
(PTR MS), a technique that employs an ionmolecule
reaction as its ionisation method, is
becoming a common method for the online
detection of atmospheric pollutants. However,
molecular ion fragmentation can make the
identification and quantification of species difficult.
Quantum chemical calculations performed in the
gas phase, can provide great insight into the
reaction mechanisms, activation barriers and
reaction enthalpies of ion-molecule reactions. A
previous study by our group examined the
fragmentation pathways of small, atmospheric
pollutants such as ethanol and oxalic acid. As an
example a fragmentation pathway of ethanol in a
PTR MS system is shown below. It was found that
in some cases the level of theory used for
geometry optimisations affected the enthalpy
re-calculated at higher levels of theory such as
CCSD(T) and CBS-QB3 by up to 20 kJ mol-1
when compared to experiment. In the current work
the species involved in 30 ion-molecule reactions
were optimised using M06, B2PLYP, MP2 and
CCSD with the aug-cc-pVTZ basis set and B3LYP
with the 6-31+G(d) and 6-311G(d,p) basis sets to
determine which level of theory produces
structures that give the most accurate enthalpies
compared to CCSD(T) and CBS-QB3 calculations
and experimental results.
144
P65
Spectroscopy of resonancestabilized
hydrocarbon radicals
Tyler P. Troy, Nahid Chalyavi, Zijun Ge, Gerard
D. O’Connor, Masakazi Nakajima, Neil J. Reilly,
Damian L. Kokkin, Klaas Nauta, Scott H. Kable,
Timothy W. Schmidt
School of Chemistry, The University of Sydney, NSW 2006,
Australia
Abstract
Resonance-stabilized radicals such as
1-phenylpropargyl [1] and 1-vinylpropargyl [2] have
been identified to be prominent and ubiquitous
products of hydrocarbon discharges. The
identification of these radicals was made using a
synergy of resonant 2-colour 2-photon ionization
and 2-dimensional fluorescence spectroscopies.
We have since exploited the principle of resonance
stabilization to obtain the spectra of a library of
such radicals, including:
1-naphthylmethyl, 2-naphthylmethyl,
acenaphthenyl, 4-methylnaphth-1-ylmethyl, 5-
methylnaphth-1-ylmethyl, 4-phenylbenzyl,
4-(4’-methylphenyl)benzyl, 1,4-pentadienyl,
phenalenyl, indanyl, 2-hydroxyindan-1-yl,
2-methylindan-1-yl, 2-hydroxy-2-methylindan-1-yl,
inden-2-ylmethyl, 1-phenylallyl,[3] 2-ethylindan-1-yl,
2-ethyl-2-hydroxyindan-1-yl, 1-inden-2-ylethyl,
4,”,”-trimethylbenzyl and 4, “-dimethylbenzyl
radicals. The above species all display spectra in
the visible region of the spectrum, yet show a
variety of spectroscopic phenomena including

long Franck- Condon progressions, (pseudo)
Jahn- Teller effects, Fermi resonance and
Duschinsky mixing. The spectra will be discussed
in the context of the chemistry of combustion,
planetary atmospheres and interstellar space
References:
[1] Neil J. Reilly, Damian L. Kokkin, Masakazu Nakajima, Klaas
Nauta, Scott H. Kable, Timothy W.
Schmidt, J. Am. Chem. Soc. 130, 3137 (2008).
[2] Neil J. Reilly, Masakazu Nakajima, Tyler P. Troy, Nahid Chalyavi,
Kieran A. Duncan, Klaas Nauta,
Scott H. Kable, Timothy W. Schmidt, J. Am. Chem. Soc. 131,
13423-9 (2009).
[3] Tyler P. Troy, Nahid Chalyavi, Ambili S. Menon, Gerard D.
O'Connor, Burkhard Fückel,
Klaas Nauta, Leo Radom, and Timothy W. Schmidt, Chemical
Science, in press.
P66
Surface-enhanced Raman
Spectroscopy of Isoflavones on
Alternative Substrates
Ryo Sekine1 , Evan G. Robertson, 2 Leone
Spiccia3 , Richard A. Dluhy4 , Don McNaughton 5
1 Centre for Biospectroscopy, Monash University, Clayton, VIC,
3800, Australia, ryo.sekine@monash.edu
2 School of Molecular Sciences, La Trobe University, VIC, 3086,
Australia, e.robertson@latrobe.edu.au
3 School of Chemistry, Monash University, Clayton, VIC, 3800,
Australia, leone.spiccia@monash.edu
4 Department of Chemistry, The University of Georgia, Athens,
GA, USA, dluhy@uga.edu
5 Centre for Biospectroscopy, Monash University, Clayton, VIC,
3800, Australia, don.mcnaughton@monash.edu
Abstract
Isoflavones are naturally occurring chemicals with
a breadth of potential health effects. As an
anti-oxidant and phytoestrogen, it reduces the risk
of cardio-vascular diseases, cancer, osteoporosis
and various postmenopausal symptoms, while
adverse effects have also been found through its
action as an endocrine disruptor. 1 We have
recently investigated a series of isoflavones using
surface-enhanced Raman spectroscopy (SERS), a
technique capable of enormous Raman signal
enhancements and which overcome the low
sensitivity of normal Raman spectroscopy. SERS
is achieved by the adsorption of the analyte on
roughened metal surfaces or particles, where
Poster Presentations
Monday 5 December - Session 2
signals are enhanced by electromagnetic and
chemical mechanisms. SERS analysis of
isoflavones using citrate-reduced silver colloids
revealed that the deprotonation of hydroxyl groups
lead to their interaction with the metal surface, and
as a consequence, it is highly sensitive to the
hydroxyl substitution pattern of the isoflavones. 2
One of the key shortcomings of SERS precluding
its widespread use is the significant spectral
variability observed as a result of different
analyte-metal interactions. The technique relies
critically on the adsorption of the analyte on to the
metal, which is dependent on not only the analyte
and the metal, but also on the surrounding
environment. Furthermore, despite the intense
research in SERS, the preparation of reproducibly
effective, robust and reusable surfaces (substrates)
has been met with significant challenge. In the
interests of broadening the scope of SERS
applications in isoflavone research, we have
examined the spectra of isoflavones on alternative
substrates, selected on the basis of ease of
fabrication and reusability: oblique angle
deposition SERS substrates (OADs) 3,4 and sol gel
SERS substrates. 5 SERS from these substrates
are presented and compared to SERS on the Ag
colloids.
Figure 1. SERS of isoflavones daidzein and formononetin on Ag
colloids (black) and OADs (blue).
References
(1) Karahalil, B. Benefits and Risks of Phytoestrogens. In
Phytoestrogens in Functional Foods; Yildiz, F., Ed.; CRC Press:
Boca Raton, 2006.
(2) Sekine, R.; Vongsvivut, J.; Robertson, E. G.; Spiccia, L.;
McNaughton, D. J. Phys. Chem. B 2010, 114, 7104.
(3) Chaney, S. B.; Shanmukh, S.; Dluhy, R.; Zhao, Y.-P. Appl. Phys.
Lett. 2005, 87, 031908.
(4) Driskell, J. D.; Shanmukh, S.; Liu, Y.-J.; Chaney, S. B.; Tang,
X.-J.; Zhao, Y.-P.; Dluhy, R. A. J. Phys. Chem. C 2008, 112, 895.
(5) Lee, Y.-H.; Dai, S.; Young, J. P. J. Raman Spectrosc. 1997, 28,
635.
145

Poster Presentations
Monday 5 December - Session 2
P67
Dynamic Characterisation of
Surfaces Using In-Silico Nano-
Indentation
Lachlan Shaw1 , George Yiapanis1 , David
Henry2 , Evan Evans3 , Irene Yarovsky2 1 School of Applied Sciences, RMIT University, GPO Box 2476,
Vic, 3001
2 School of Chemical and Mathematical Sciences, Murdoch
University, South Street, WA, 6150
3 BlueScope Steel Research Laboratories, Islands Rd, Port
Kembla, NSW, 2505
Abstract
Physical and chemical aspects of polymer
surfaces play an important role in interfacial
phenomena and dominate processes such as
adhesion and wettability. However, polymer
surfaces often display dynamic characteristics,
which depending on the intended application can
have a profound effect on the efficacy of the
materials performance. For example, studies have
shown that functionalized polymer surfaces tend
to recover their native state as a result of
ageing1-2. Here, using force-field Molecular
Dynamics we undertake in-silico nanoindentation3
to dynamically study the physical and
chemical properties of polymer surfaces and their
affects on adhesion. The indenter material chosen
represents a primary atmospheric contaminant
and the surface, a modified crosslinked polyester
paint coating. During nano-indentation we
calculated the adhesion between contaminant and
surface, and monitored dynamically, the surface
roughness, skewness and density of the polymer
layers (figure) by creation of surface contour maps.
This technique may be applied to any deformable
surface. Our results indicate that surface
crosslinking increases the roughness and rigidity
of the outer layer. In addition, crosslinking also
provides a stable platform for modifiers that would
otherwise migrate into the bulk material. However,
nano-indentation of regions with flexible subsurfaces
results in slip whereby crosslinkers shift
dramatically to the side of the incoming
contaminant resulting in both loss of rigidity and
envelopment of contaminant.
146
Adhesion and density obtained during nanoindentation.
Graph shows that variations in
interfacial adhesion are accompanied with
changes in the density of the indented material.
A. Oláh, H. Hillborg, G. J. Vancso, Applied Surface Science 239,
410 (2005).
G. Yiapanis, D. J. Henry, E. Evans, I. Yarovsky, The Journal of
Physical Chemistry C 111, 6465 (2007).
G. Yiapanis, D. J. Henry, E. Evans, I. Yarovsky, The Journal of
Physical Chemistry C 114, 478 (2009).
P68
CyDNA: A versatile photoswitchable
biopolymer for advanced
fluorescence microscopy
applications.
Darren A. Smith 1,2 ,*, Philipp Holliger 3 ,
Cristina Flors 1 ,*
1 EaStChem School of Chemistry, University of Edinburgh,
Edinburgh, EH9 3JJ, United Kingdom.
2 School of Chemistry, University of Melbourne, Melbourne, 3010,
Australia.
3 MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH,
United Kingdom.
Abstract
CyDNA is the product of the controlled synthesis
of a DNA fragment with a high density of Cy3 or
Cy5 dyes incorporated into its structure.[1] This
novel material can be up to 1kb and is constructed
by a modified DNA polymerase that allows
substitution of dC bases by their fluorescent
dye-labelled analogue, Cy3- or Cy5-dC. The
resulting biopolymer displays hundreds of
fluorophores and is brightly coloured and
fluorescent. The high dye content can, however,
result in dye-dye interactions that affect the overall

ightness of CyDNA. This may hinder the
application of this material in microarray and
microfluidic applications. We will present a bulk
and single-molecule photophysical study that
reveals several quenching mechanisms occurring
in CyDNA, namely, the formation of nonfluorescent
H-aggregates of the dyes as well as
energy hopping and transfer to lower energy,
non-fluorescent traps. We investigate the optimal
substitution patterns to enhance CyDNA
brightness.
Furthermore, it has previously been shown that, in
the presence of a thiol and an enzymatic oxygen
scavenging system, proximal Cy3 and Cy5
fluorophores form an optical switch.[2] We have
used this property to transform CyDNA into an
efficient photoswitchable biopolymer by
hybridizing complementary single stranded Cy3and
Cy5-substituted CyDNA. Photoswitching has
been applied in localization-based superresolution
fluorescence microscopy to study
CyDNA topology in nanoscale detail. Moreover, we
have used CyDNA photoswitching in Optical
Lock-in Detection imaging,[3] which is a technique
capable of greatly enhancing image contrast in
fluorescence microscopy. The combination of
CyDNA and the above techniques has enormous
potential in the study of the structure of
chromosomes at the nanoscale.[4]
This work was supported by a Universitas21 PhD
Scholarship and The Royal Society.
References:
[1] N. Ramsay et al., J. Am. Chem. Soc. 132 (2010) 5096.
[2] M. Bates et al., Phys. Rev. Lett. 94 (2005) 108101.
[3] G. Marriott et al., Proc. Natl. Acad. Sci. U.S.A. 105 (2008)
17789.
[4] C. Flors, Biopolymers 95 (2011) 290.
*Corresponding authors: E-mail: d.smith@student.unimelb.edu.au,
cristina.flors@ed.ac.uk
Poster Presentations
Monday 5 December - Session 2
P69
Computational characterisation of
an unusual metallacalix[4]arene
dinitrogen activator
Richard Terrett1 , Germán E. Cavigliasso1 ,
Rob Stranger1 , B.F. Yates 2
1 Research School of Chemistry, Australian National University,
ACT, 0200, email: rterrett@rsc.anu.edu.au
2 School of Chemistry, University of Tasmania, Private Bag 75,
Hobart, TAS 7001
Abstract
The calix[4]arene niobium(III) complex ([L]
Nb–N=N–Nb[L] where [L] = p-tert-butylcalix[4]
arene), reported to bind N2 in a μ2–linear dimeric
capacity and to activate the N–N triple bond to
1.39 Å, corresponding to the longest N–N bond
known in the end–on coordination mode, was
subjected to a computational investigation
involving both density functional and wavefunction
based methods to establish the basis for the
unprecedented level of activation. Replacement of
the calix[4]arene ligand with hydroxide or
methoxide ligands reveals that the organic
backbone structure of the calix[4]arene ligand
exerts negligible electronic influence over the metal
centre, serving only to geometrically constrain the
coordinating phenoxide groups. A fragment
bonding analysis shows that metal–to–dinitrogen
π* backbonding is the principal Nb–N interaction,
providing a strong electronic basis for analogy with
other well–characterised three– and four–
coordinate complexes which bind N2 end–on.
While the calculated structure of the metallacalix[4]
arene unit is reproduced with high accuracy, as is
also the Nb–Nb separation, the calculated
equilibrium geometry of the complex under a
variety of conditions consistently indicates against
a 1.39 Å activation of the N–N bond. Instead, the
calculated N–N distances fall within the range
1.26–1.28 Å, a result concordant with closely
related three– and four-coordinate μ2–N2
complexes as well as predictions derived from
trends in N–N stretching frequency for a number of
crystallographically characterized linear N2
activators. A number of potential causes for this
bond length discrepancy are explored.
147

Poster Presentations
Monday 5 December - Session 2
P70
Recombination of photolytically
generated iodine in single
iodoalkane microdroplets
Phillip J. Tracey1 , Bartholomew S. Vaughn1 ,
Adam J. Trevitt 1
1 School of Chemistry, University of Wollongong, NSW, 2522
pjt105@uowmail.edu.au
Abstract
Chemistry occurring at the liquid/air interface of
single microdroplets is important in chemical
systems such as fuel sprays and aerosols. To
explore this chemistry we have developed an
experimental setup probe physical and chemical
changes in single microdroplets by combining
optical cavity enhancement effects with Raman
spectroscopy. As a preliminary demonstration of
the instrumentations capabilities we have
investigated the recombination of iodine radicals
generated within single microdroplets using cavity
enhanced Raman spectroscopy (CERS).
The instrument consists of a three-laser setup and
a drop-on-demand droplet generator. Single
microdroplets are formed and free fall, first passing
through a CW He:Ne laser (λ = 632 nm) whose
scatter provides a trigger signal for the other two
lasers in the setup. A pulsed Nd:YAG UV laser (λ =
266 nm) irradiates the droplet to initiate photolysis.
Another pulsed Nd:YAG laser (λ = 532 nm) is used
to perform Raman spectroscopy, enhanced by
cavity resonance effects within the microdroplets.
UV laser photolysis of iodoalkanes results in the
liberation of iodine radicals, which subsequently
combine to form molecular iodine over the
timescale of hundreds of nanoseconds. Formation
of I2 within the droplets quenches the cavity
enhanced Raman, as the iodine population grows
until such a point that no signal is observed. By
controlling the delay between UV photolysis and
Raman acquisition, the decrease in Raman signal
148
can be plotted over time and the kinetics of iodine
radical recombination can be studied. The
experimental setup and findings from this study
will be presented in greater detail in this poster.
P71
Symmetry, Pseudo-symmetry and
Evolution in Protein Structures
Donald G Vanselow 1
1 nativeproteins.blogspot.com 54 Greenways Rd., Glen Waverley
VIC 3150, Australia. dvanselow@hotmail.com
Abstract
The principles of Evolution and Natural Selection
are applied to the existence of symmetry in
tetrameric proteins and the presence of pseudosymmetry
within protein subunits. The probability
that protein symmetry is shaped by these
principles is shown to be very useful in guiding the
computer-assisted assembly (docking) of the
subunits of tetrameric proteins. Without this
guidance the large number of degrees of freedom
involved in simultaneously docking four subunits
would render the docking process impossible. The
pseudo-symmetry of α and β barrels is helpful in
orientating them relative to the rest of the protein,
especially when the active site location is not
known. Examples will be shown from the
neuraminidases, galactose oxidase,
dihydrodipicolinate synthase (DHDPS), and
hemoglobin [1], where the tetramers [2] have been
assembled with help from symmetry and
pseudo-symmetry. In the case of hemoglobin,
pseudo-symmetry gives rise to possible
“quaternary isomers” which may explain the
mechanism of the pH dependence of oxygen
binding [1].
The shapes of these tetramers also conform with
the physics of catalysis and binding described in
2002 [3].
Refs:
[1] The data-base of native protein structures is at www.
nativeproteins.net76.net/gallery/index.htm
Papers describing the structures and discussing related issues are
at http://nativeproteins.blogspot.com
Both sites are maintained by the author.
[2] Vanselow, D. G. 2008. Haemoglobin Revisited. WATOC 2008
Poster No. 321. http://posters.f1000.com/P1181
[3] Vanselow, D. G. 2002. Role of constraint in catalysis and
high-affinity binding by proteins, Biophys. J. 82: 2293–2303.

P72
Single Microdroplet Laser
Spectroscopy
Bartholomew S. Vaughn1 , Phillip J.
Tracey1 , Adam J. Trevitt 1 .
1 School of Chemistry, University of Wollongong, NSW 2522
bv703@uowmail.edu.au
Abstract
The chemistry that occurs at the surface of single
microdroplets plays an important role in various
chemical systems, such as fuel sprays and
atmospheric aerosols. These surface processes
affect how these systems evolve chemically. This
poster will outline the development of a technique
that uses cavity enhanced Raman on single
microdroplets in order to probe the boundary
region of single microdroplets.
The experimental setup uses a piezo-activated
on-demand microdroplet generator to produce a
stable droplet stream – as we will demonstrate.
Once the droplets are formed they free-fall, where
they cross a continuous He:Ne laser. The light
scattered off the droplet is collected to trigger a
pulsed Nd:YAG laser operating at 532 nm, which
serves as the Raman probe laser. The scattered
light from the droplet is collected and focused into
a Czerny-Turner spectrometer equipped with a
CCD. In this way a single laser shot hits a single
droplet producing a one spectrum. The droplet
Raman spectra are dominated by cavity modes
that are dependent on the droplet size and
refractive index. Monitoring these peak positions in
the spectra allows us to sensitively track the
droplet size.
The setup was tested using water as a liquid to
master the techniques of reproducible droplet
generation, as well as optimising the optical
arrangement. This was extended to probe droplets
composed of squalane, squalene and biodiesel
fuels including methyl esters. The Raman spectra
contained C-H stretch vibrational band, as well as
C=C stretch in certain molecules. Interestingly the
C=O band was not observed in the methyl ester
droplets. This poster will discuss the experimental
configuration and findings in greater detail.
Poster Presentations
Monday 5 December - Session 2
P73
Molecular Dynamics of Curcumin
and Linked Cyclodextrin Dimers
Samuel J. Wallace 1 , David M. Huang2 ,
Takaaki Harada, 3 Tak W. Kee4 1 University of Adelaide, North Terrace, South Australia, 5005,
sam.wallace@adelaide.edu.au
2 University of Adelaide, North Terrace, South Australia, 5005,
david.huang@adelaide.edu.au
3 University of Adelaide, North Terrace, South Australia, 5005,
takaaki.harada@adelaide.edu.au
4 University of Adelaide, North Terrace, South Australia, 5005,
tak.kee@adelaide.edu.au
Abstract
Curcumin, which is a naturally occurring
compound known to have a wide range of
medicinal properties, including anti-cancer,
anti-oxidant and wound healing, is a biomolecule
of particular interest.1-3 The bioavailability of
curcumin however, is limited by its solubility and
stability in the aqueous environments.4 The
delivery of curcumin effectively in vivo requires
stabilisation in a host medium. Various strategies
to resolve the stabilisation issues have been
attempted with micelles, nanoparticles and
cyclodextrins.5-8 Cyclodextrins are cyclic
oligosaccharides with a hydrophobic interior and
hydrophilic exterior which provide an ideal
environment for the stabilisation of curcumin.
Recently, our group has used linked -cyclodextrin
dimers to enhance the stability of curcumin by a
factor of at least 700.6
The work presented here uses molecular
dynamics simulations running NAMD and using
the Generalised Amber Force Field to determine
149

Poster Presentations
Monday 5 December - Session 2
the binding constants and free energy of binding
of curcumin to linked -cyclodextrin dimers.9,10
The simulation results are compared with
experimental results.
(1) Masuda, T.; Jitoe, A.; Isobe, J.; Nakatani, N.; Yonemori, S.
Phytochemistry 1993, 32, 1557.
(2) Piper, J. T.; Singhal, S. S.; Salameh, M. S.; Torman, R. T.;
Awasthi, Y. C.; Awasthi, S. Int. J. Biochem. Cell Biol. 1998, 30,
445.
(3) Sidhu, G. S.; Manni, H.; Gaddipati, J. P.; Singh, A. K.; Seth, P.;
Banaudha, K. K.; Patnaik, G. K.; Maheshwari, R. K. Wound
Repair and Regeneration 1999, 7, 362.
(4) Wang, Y. J.; Pan, M. H.; Cheng, A. L.; Lin, L. I.; Ho, Y. S.; Hsieh,
C. Y.; Lin, J. K. J. Pharm. Biomed. Anal. 1997, 15, 1867.
(5) Aggarwal, B. B.; Anand, P.; Nair, H. B.; Sung, B. K.;
Kunnumakkara, A. B.; Yadav, V. R.; Tekmal, R. R. Biochem.
Pharmacol. 2010, 79, 330.
(6) Kee, T. W.; Harada, T.; Pham, D. T.; Leung, M. H. M.; Huy, T. N.;
Lincoln, S. F.; Easton, C. J. J. Phys. Chem. B 2011, 115, 1268.
(7) Kee, T. W.; Leung, M. H. M.; Colangelo, H. Langmuir 2008, 24,
5672.
(8) Tonnesen, H. H.; Masson, M.; Loftsson, T. Int. J. Pharm. 2002,
244, 127.
(9) Schulten, K.; Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.;
Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L. J.
Comput. Chem. 2005, 26, 1781.
(10) Wang, J. M.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case,
D. A. J. Comput. Chem. 2005, 26, 114.
P74
De novo Structure prediction of
Peptide Based Biomimetic
Carbohydrate Receptors
Mark Waller1 1 Organic Chemistry Institute, University of Münster,
Corrensstraße 40, D-48149 Münster, Germany
Abstract
Carbohydrate recognition poses a remarkable
challenge within host-guest chemistry. In a recent
study1 , cyclic oligopeptides consisting of two
Cys-His-Cys tripeptide fragments were found to
be able to selectively bind N-acetyl neuraminic
acid (NANA) with an unprecedented high binding
constant. Experimentally, a HisHis:NANA ratio of
1:2 was observed to exhibit strong cooperative
binding. Herein we applied a meta-optimization
strategy employing a multi-tiered SE, DFT and
QM/MM to elucidate possible candidate
structures. We carefully compare and contrast our
models to determine the origins of this cooperative
150
behaviour.
1 Ravoo et al. Angew. Chem. Int Ed. 2010, 49, 7340-7345
P75
Modelling Cellulase Activity upon
Cellulose Surfaces using Cellular
Automata
Andrew C. Warden1 , Bryce A. Little2 ,
Victoria S. Haritos1 1 CSIRO Ecosystem Sciences, Clunies Ross St, Acton, Canberra,
ACT, 2601
2 CSIRO Livestock Industries, Queensland Biosciences Precinct,
306 Carmody Road, St. Lucia, QLD, 4067
Abstract
With increasing emphasis on energy
independence and the growing concern over finite
petroleum reserves, attention has turned to
biomass as a potential feedstock with which to
produce a significant proportion of the world’s
liquid fuels. Lignocellulose is an abundant,
renewable raw material that contains cellulose, a
component that has the potential to replace oil as
a starting material for the production of transport
fuels.
The saccharification of cellulose, breaking the
polymer into monosaccharides, yields glucose
which can undergo microbial fermentation to
biofuels such as ethanol and butanol, or be used
as a feedstock for the production of lipids and
chemicals. Achieving efficient saccharification from
complex biomass is challenging, and one of the
main factors impeding the commercialisation of
the biochemical method of cellulosic fuels and
chemicals production.
Cellulase enzymes used to break down cellulose
into fermentable sugars are of several different
types (generally, cellobiohydrolase I,
cellobiohydrolase II, endoglucanase and
β-glucosidase) that perform different functions.
They form a complex, interacting network between
themselves, soluble hydrolysis product molecules
(both substrates and inhibitors) and the solid
cellulose substrate. Most models produced to date
use solution-phase kinetics to describe overall
cellulase activity. We have taken a 2-phase
approach whereby the solution chemistry is

modelled using traditional Michaelis-Menten
kinetics and the solid phase activity is described
using cellular automata.
Cellulase4D is a general purpose model with
which various behaviours of many individual
enzymes on the cellulose surface can be
examined. These include adsorption strength,
mobility on the surface, crowding or jamming and
adsorption probability. In addition, the model
incorporates solution phase behaviours described
with commonly used parameters such as kcat, Km
and Ki. We have incorporated a graphical user
interface with which the various parameters can
be altered, real-time plotting of the production of
hydrolysis products such as glucose, cellobiose
and higher polysaccharides, and a 3D
representation of the cellulose and enzymes that
can be manipulated by the user as the simulation
progresses.
We will present the results from simulations aimed
at unravelling the effects of crowding, adsorption
strength and reaction rates, and discuss the
possible implications for the tuning of properties of
the individual cellulase components through
enzyme engineering.
P76
Lipid Composition Regulates the
Conformation and Insertion of the
Antimicrobial Peptide Maculatin 1.1
Thomas Whitwell1 , Marc-Antoine Sani1 ,
Frances Separovic1 1 School of Chemistry, Bio21 Institute, University of Melbourne,
VIC 3010
Abstract
The effect of the lipid composition of biological
membranes on antimicrobial peptide (AMP)
structure needs to be understood to rationalise
AMP activity. The affinity of AMPs for anionic lipid
membranes is well reported, but this has often
been determined using dimyristoyl (tetradecyl)
chain phospholipid bilayers. In this study, we
highlight the importance of lipid chain length and
saturation on AMP secondary structure. Maculatin
1.1 is a 21 residue cationic AMP secreted from the
Poster Presentations
Monday 5 December - Session 2
skin of Australian tree frogs that acts against Gram
positive bacteria. The secondary structure of
maculatin 1.1 was determined by circular
dichroism spectroscopy in dispersions of
unilamellar vesicles and oriented bilayers using a
range of phospholipids. For neutral
phosphatidylcholine (PC), unlike anionic
phospholipids, the magnitude of the peptide
interactions was dependent on the constituent
acyl chain length and degree of saturation.
Oriented circular dichroism (OCD) data indicated
that helical structure was likely promoted by
peptide insertion into the hydrophobic core of PC
bilayers. The addition of cholesterol (30% mol/mol)
tended to decrease the membrane interaction of
the peptide. OCD spectra of maculatin 1.1 with
anionic lipid membranes, such as negatively
charge phosphatidylglycerol (PG), indicated that
the peptide was locked onto the membrane
surface due to electrostatic interactions.
Furthermore, increasing the membrane curvature
by using small unilamellar vesicles reduced the
proportion of helical structure in all systems by
~10%. Clearly, lipid chain length and saturation
strongly influenced the peptide interactions with
phospholipid membranes. Dye release
experiments are being performed to determine the
AMP mechanism and further experiments with
binary lipid mixtures are underway. Preliminary
data has indicated that increasing the proportions
of phosphatidylethanolamine (PE) in either PE/PC
or PE/PG consistently reduced the helical content
of maculatin 1.1 and may relate to the lack of
activity with Gram negative bacteria.
P77
The Quokka Small Angle Neutron
Scattering Instrument at OPAL
K. Wood1 , C. J. Garvey1 , E. P. Gilbert1 1 Bragg Institute, Australian Nuclear Science and Technology
Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232,
Australia
Abstract
Quokka is a 40 metre small angle neutron
scattering instrument installed on the cold source
of the OPAL research reactor operated by ANSTO.
Small angle scattering is a powerful technique for
151

Poster Presentations
Monday 5 December - Session 2
looking at the structures of objects on the
nanoscale (1-10nm), such as polymers, biomacromolecules,
ceramics, emulsions etc… Both
small angle neutron and x-ray scattering
instruments are accessible at the Bragg Institute
through a peer-reviewed proposal system. One of
the main advantages of neutrons over x-rays is the
possibility to design experiments making use of
the large difference in neutron scattering cross
section between hydrogen and its heavier isotope
deuterium.
In addition to the standard 20-position automatic
sample changer, a wide range of sample
environment equipment is available for use on the
beamline including a rheometer, rapid heat/
quench cell and a stop-flow mixing cell.
The capabilities and performance of Quokka will
be presented, along with highlights from recent
experiments.
Quokka will be available for beamtime requests in
March 2012 through the Bragg Institute portal
https://neutron.ansto.gov.au/Bragg/proposal/
index.jsp. It is also possible to submit proposals for
chemical and biological deuteration through the
same portal.
P78
Structure, dynamics and interactions
of malaria surface antigens
Tessa R. Young 1 , David K. Chalmers1 ,
Christopher A. MacRaild1 , Marie O. Pedersen1 ,
Robin F. Anders2 , Raymond S. Norton1 1 Monash Institute of Pharmaceutical Sciences, Monash
University, 381 Royal Parade, Parkville 3052, Australia
2 Department of Biochemistry, La Trobe University, Bundoora,
VIC 3086, Australia
Abstract
Merozoite surface protein 2 (MSP2) is one of the
most abundant antigens presented on the surface
of the blood stage malaria parasite, Plasmodium
falciparum, and thus a leading malaria vaccine
candidate. MSP2 is anchored to the parasite
membrane by a C-terminal
glycosylphosphatidylinositol (GPI) moiety, it is
highly disordered in solution and the conformation
152
of the protein on the surface of the merozoite is
unknown. Determination of this structure would
lead to a better understanding of the way in which
MSP2 interacts with the immune system.
Molecular dynamics simulations of the N-terminal
and C-terminal regions of MSP2 have been carried
out to determine the structures of N-terminal and
C-terminal regions of MSP2.
MSP2 contains conserved N-terminal and
C-terminal sequences flanking a central variable
region. Although highly polymorphic all MSP2
alleles can be grouped into two families, 3D7 and
FC27. Models of the first 31 residues, including the
full conserved N-terminal domain (25 residues) of
both 3D7 and FC27 MSP2 were built in an
alpha-helical conformation, as experimental
evidence suggests that the N-terminal regions
show a helical propensity (1). Molecular dynamics
simulations were carried out under a variety of
conditions: in solution, with micelles, and in a
membrane environment, to observe and compare
the helicity of the two peptides. Replica exchange
molecular dynamics simulations have also been
used, allowing the peptides to sample a larger
conformational space to aid in structure definition.
Molecular dynamics simulations of the GPIanchored
and free C-terminal region of MSP2
(MSP2193-228) in a membrane environment have
also been carried out evaluate if the GPI-anchor
modifies the conformation of this region of the
protein (2).
REFERENCES
1. Zhang, X., Perugini, M. A., Yao, S., Adda, C. G., Murphy, V. J.,
Low, A., Anders, R. F., and Norton, R. S. (2008) Solution
conformation, backbone dynamics and lipid interactions of the
intrinsically unstructured malaria surface protein MSP2., J Mol
Biol 379, 105-121.
2. Adda, C. G., Murphy, V. J., Sunde, M., Waddington, L. J.,
Schloegel, J., Talbo, G. H., Vingas, K., Kienzle, V., Masciantonio,
R., Howlett, G. J., Hodder, A. N., Foley, M., and Anders, R. F.
(2009) Plasmodium falciparum merozoite surface protein 2 is
unstructured and forms amyloid-like fibrils, Mol Biochem
Parasitol 166, 159-171.

P79
New insights into the chemical
reactivity of the deazaflavin cofactor
F420 through quantum chemical
calculations.
Peng Yuan1 , Junming Ho1 , Colin J. Jackson1 ,
Michelle L. Coote1 1 Research School of Chemistry, Australian National University,
ACT, 0200, coote@rsc.anu.edu.au
Abstract
The deazaflavin enzyme cofactor F420 is only
found in certain bacterial lineages, such as
Mycobacterium tuberculosis, and not in higher
organisms. Recent studies have shown it to be
involved in a range of redox reactions, including
the degradation of environmental toxins and the
activation of pro-drugs. However, we lack a
detailed understanding of its chemical reactivity
and its role in catalysis. To address this, we
describe the application of quantum chemistry
calculations to probe the reaction mechanism of
F420 and its substrates. This approach has the
potential to shed light on the role of this cofactor,
and the enzymes that utilize it, in a range of
important processes including detoxification and
drug metabolism.
P80
Utilization of Ambient Ozone for
Determining Double Bond Positions
in Unsaturated Lipids
Shane R. Ellis1 , Marc in het Panhuis2 , Todd
W. Mitchell3 , Stephen J. Blanksby1 ,
1 ARC Centre of Excellence for Free Radical Chemistry and
Biotechnology, School of Chemistry, University of Wollongong,
Wollongong, NSW, 2522
2 School of Chemistry, University of Wollongong, Wollongong,
NSW, 2522
3 School of Health Sciences, University of Wollongong,
Wollongong,
Abstract
Previously our group has reported the reaction of
ozone with ionized lipids within the confines of an
ion-trap mass spectrometer for the elucidation of
Poster Presentations
Monday 5 December - Session 2
double bond positions. [1]. While this has proven to
be a powerful analytical approach it requires an
expensive high-concentration ozone generator
and a specifically modified mass spectrometer.
Interestingly, ambient ozone - present in the
troposphere within urban environments - has
previously been identified as a source of oxidation
when samples are left in the ambient laboratory
environment [2] . In this study the surface analysis
technique Desorption Electrospray Ionization Mass
Spectrometry (DESI-MS) is used to investigate the
reaction of ambient ozone with unsaturated
phospholipids deposited onto Teflon and silica
TLC plates. Products originating from ozonolysis of
the deposited lipids can be observed after only 5
minutes following deposition and allow the
assignment of the double bond positions within
the parent lipid. This work describes the powerful
combination of DESI-MS and TLC in allowing both
the lipid composition and double bond positions
within lipids to be rapidly investigated simply by
exposing the sample to the ambient laboratory
environment prior to analysis, thus negating the
need for expensive ozone generators.
References
[1] Thomas, M. C., Mitchell, T. W., Harman, D. G., Deeley, J. M.,
Nealon, J. R., Blanksby, S. J. Ozone-Induced Dissociation:
Elucidation of Double Bond Position within Mass-Selected Lipid
Ions. Anal. Chem. 2007, 80, 303.
[2] Cohen, S. L. Ozone in Ambient Air as a Source of Adventitious
Oxidation. A Mass Spectrometric Study. Anal. Chem. 2006, 78,
4352.
P81
Thioflavin T and its derivatives:
Revealing their spectroscopic
properties in the absence and
presence of insulin amyloid fibrils
Eric H.-L. Chen 1 , Jack C.-C. Hsu 1 , Frederick
Y. Luh 1 , T.-S. Lim2 , Rita P.-Y. Chen1 1 Institute of Biological Chemistry, Academia Sinica, Taipei, 11529,
Taiwan
2 Department of Physics, Tunghai University, Taichung 407, Taiwan
Abstract
Thioflavin T (ThT) is a common tool for diagnostics
of the amyloid fibril formation. Pure ThT has a
strong absorption peak centered at 412 nm and
low fluorescence emission at 479 nm while excited
153

at 412 nm. While binding with amyloid fibrils, the
ThT/amyloid complex emits strong fluorescence at
487 nm while excited at 442 nm, making ThT
fluorescence assay is the most common and
sensitive technique in monitoring amyloid fibril
formation. Pervious researches suggested that the
strong fluorescence emission at 487 nm is
contributed from amyloids binding with ThT dimer
and that ThT monomer causes a weak absorption
at ~330 nm and an emission band at 450 nm while
excited at 330 nm. In this work, we found that ThT
is prone to be modified and three derivatives are
formed when ThT is dissolved in solution or upon
UV irradiation. These three derivatives are purified
by high performance liquid chromatography and
characterized by mass spectroscopy and nuclear
magnetic resonance. The spectroscopic
properties of pure ThT and its three derivatives
were carefully examined and compared. Our
results suggested that the emission peak at 450
nm which has been reported previously might be
resulted from one oxidized ThT derivative but not
ThT monomer.
Notes
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University of Wollongong
The University of Wollongong School of Chemistry has active research
programs in both pure and applied chemistry, with the recent ERA
assessment highlighting the quality and breadth of chemical research carried
out.
Major research areas include targeted drug discovery, design and synthesis,
biological chemistry, use of mass spectrometry to study both biological and
chemical systems, atmospheric chemistry, food chemistry, free radical
chemistry, laser chemistry, analytical and environmental chemistry,
nanomaterials and intelligent polymers.
Undergraduate programs include a Bachelor of Medicinal Chemistry and
Bachelor of Nanotechnology alongside the Bachelor of Science.
Whether you are interested in research, teaching and learning or just plain
curious about Chemistry, the School of Chemistry has something to offer.
ARC Centre of Excellence for Free Radical Chemistry and
Biotechnology
The ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
is home to over 140 researchers, drawing together a unique grouping of
fundamental chemists, medicinal chemists, biochemists, biologists and
materials scientists dedicated to the understanding and application of free
radical chemistry.
The Centre's research program is broad, encompassing aspects of free
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Its interdisciplinary approach has and will continue to provide significant
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Service to Science since 1972, BIOSCIENTIFIC PTY. LTD., provides Life Science
Researchers with a comprehensive range of specialty chemicals, antibodies,
stem cell products, cytokines, fluorescent reagents, radiolabelled products,
peptides and bio & organic chemicals.
BioScientific continues to source the best quality and guaranteed products.
www.biosci.com.au 1300 BIOSCI ( 246724 )
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Conference Sponsors
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eDAQ
eDAQ is a Sydney based company that manufactures and distributes a range of
electrochemical instrumentation including:
• high resolution INPHAZE electrical impedance spectrometers for surface and
membrane studies
• SDx Tethered Membrane systems for the examination of membrane ion
channels
• eDAQ potentiostats for voltammetric and similar experiments
• eDAQ contactless conductivity detectors for capillary electrophoresis and ion
chromatography
• low cost eDAQ isoPods for monitoring of pH, conductivity, dissolved oxygen,
amperometric sensors, etc.
as well as e-corder data acquisition systems for general purpose signal
monitoring.
eDAQ Pty Ltd
6 Doig Avenue, Denistone East, NSW 2112, Australia
Phone: +61 2 9807 8855 Fax: +61 2 9807 8844
Email: info@edaq.com http://www.edaq.com
GE Healthcare
GE Healthcare Life Sciences’ purpose is to help make the world healthier
through imaginative science. Our broad laboratory instrument portfolio offers
advanced technologies for protein purification, drug discovery, biomolecular
interaction, stability parameters and cellular analysis. Iconic brands as AKTA,
Biacore, Microcal, Fuji, Typhoon and IN-Cell ultimately enable researchers to gain
deeper insights into protein activity and function, cell biology and how potential
drugs work. With a host of consumables available through distribution partners,
your research needs are all consolidated at the one place. Our goal is to enable
Australian scientists to discover, develop and produce therapeutics to prevent,
diagnose, treat and cure disease.
For further information please contact:
GE Healthcare Australia Pty Limited
Phone: 1800 150 522 Fax: 1300 434 232
Email : sales.au@ge.com

Conference Sponsors
Lastek
Lastek’s scientific staff form a key group of experienced scientists representing a
broad range of companies offering state of the art equipment, and supporting
cutting edge technologies. Based on the Thebarton campus of Adelaide
University, Lastek has been supporting the Australian research market for the
past 23 years.
Areas of expertise extend from laser excitation sources through to photon
sensitive detectors for routine microscopy and complex spectroscopic
applications alike. Key installations include multi-photon and higher order
harmonic microscopes, Raman spectroscopy for the analysis of biological
samples, and time correlated single photon counting fluorescence spectroscopy.
http://www.lastek.com.au/
Mettler Toledo
Compliance, traceability, consistency, and reliability of measurement data are
primary concerns in the fields of academia and research. METTLER TOLEDO's
solutions cover the basic measurement needs in all scientific work, and can be
expanded into automated solutions. METTLER TOLEDO instruments are used in
research, scientific and quality control labs among many others, in the
pharmaceutical, chemical, food and cosmetics industries. Our scope of solutions
range from standard laboratory equipment such as balances, pipettes and pH
meters, through titrators, instruments for thermal analysis, melting point and
density meters, to solutions for the field of automated chemistry
www.mt.com
NewSpec specialises in the sales and service of high-end scientific research
equipment manufactured by leading international companies including:
• Bruker Nano (formerly Veeco Metrology products)
• Newport Corporation
• Spectra-Physics Lasers
• Fischer-Cripps Laboratories
NewSpec’s comprehensive product portfolio includes:
• Scanning Probe & Atomic Force Microscopes
• Surface Profilers; Confocal, Optical & Stylus models
• Nano Indentation Systems
• Desktop TEM/SEM systems
• Lasers, Solar Simulators & Light Sources
• Optical Tables & Vibration Isolation Systems
• Spectroscopy, Radiometers & Optical Measurement Systems
• Optics & Mechanics
• Motorised & Manual Positioning Systems
Contact details: Neil McMahon
Tel: 08 8463 1967 Fax: 08 8410 8816
sales@newspec.com.au www.newspec.com.au
134 Gilbert Street, Adelaide, South Australia, 5000
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Conference Sponsors
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Perkin Elmer
A healthier future starts with the work we do today
At PerkinElmer, we design, manufacture and deliver advanced technology
solutions that address the world's most critical health and safety concerns,
including maternal and fetal health, clean water and air, and safe food and toys.
Our expertise combines science, innovation and a culture of operational
excellence to offer our customers technology services and support that improve
the quality of people's lives worldwide.
Our work in environmental health improves the quality and sustainability of our
environment, and the security of people in the places where we live, work and
play. This includes providing the analytical instrumentation, and lighting and
sensor technologies and services that ensure clean air and water; safe food and
consumer products; and efficient, renewable energy - the essential components
of a healthier, safer today and tomorrow.
www.perkinelmer.com.au
Scitech
SciTech Pty Ltd established in 1989, offers a complete range of innovative
products in the fields of Nanotechnology, Spectroscopy, Imaging and
Microscopy.
Some of the latest key product developments include:
• The Nanowizard 3 from JPK Instruments; a high resolution and highly flexible
AFM designed for both Life Science and NanoScience applications.
• The JPK NanoTracker, an Optical Tweezer system which can track particles in
3D space and measure interactive forces between particles down to
picoNewtons.
• For Researchers with ideas larger than their budget we offer the new ultra low
cost “TT-AFM” Atomic force microscope.
• NanoIR combines AFM with IR spectroscopy and temperature measurement,
with a resolution of 100 nm!
• The Nanoink NLP2000 and DPN5000, DPN instruments for Nanofabrication
applications. Features include multiplexing capability, fast prototyping and the
ability to print a variety of protein inks with dot sizes from 100 nm – 10 um,
• CellZscope from NanoAnalytics measures the impedance of barrier-forming cell
cultures grown on permeable membranes.
• The Till iMic, a compact inverted DIGITAL microscope for high end microscopy
applications. The iMic is very compact, offers greater stability, versatility,
increased light throughput and faster operating speeds compared to a
conventional inverted microscope.

Conference Sponsors
• Featuring also the Andor range of CCD, EMCCD, InGas and sCMOS cameras
for spectroscopy and high end Microscopy, Super Resolution and confocal
applications. Andor also offers the Revolution XD and DSD spinning disk
confocal systems.
For Further information Contact
Christian Loebbe : 0400 440 426 christian@scitech.com.au
Con Sapounas: 0400 440 499 con@scitech.com.au
Lino Montuno: 0400 440 488 lino@scitech.com.au
Supporters
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