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Physical and Theoretical Chemistry
Computational Quantum Chemistry
Professor Leo Radom
http://www.chem.usyd.edu.au/about/staff_radom.html
Chemistry is traditionally an
experimental science. However, recent advances in computer technology
and the development of highly efficient computer algorithms have
opened the way for a viable alternative approach to chemistry:
chemistry by computer. We use such computer calculations to
determine the structures of molecules and to help understand how
molecules react with one another. The procedure employed is called
ab initio molecular orbital theory, the term ab initio
signifying that the calculations are carried out from first
principles using the laws of quantum mechanics. No experimental data
other than values of fundamental physical constants are used. An
important feature is that the calculations can be carried out as
readily for reactive or hazardous species as for normal, stable
molecules. They are therefore particularly useful in cases where
experimental studies might be difficult or impossible. Properties
that may be examined include molecular structures and reaction
pathways, as well as many thermodynamic and spectroscopic properties.
During
the year, we enjoyed stimulating interaction with a number of
visitors. Thomas Büsgen, an undergraduate student from the
University of Applied Sciences, Bonn-Rhein-Sieg, spent five months in
the group, funded by the Studienstiftung des Deutschen Volkes. Ines
Corral, a visiting PhD student from the Autonoma University of
Madrid, joined the group for three months in September, on a
fellowship funded by the Ministerio de
Educación, Cultura y Deporte of Spain. Most recently,
Dr Maya Topf from the University of Oxford and Professor Uri Zoller
from the University of Haifa joined the group as Visiting Fellows in
October and November. In addition, Dr Rodolfo Gomez-Balderas joined
the group in February after having won a Fellowship funded by the
Consejo Nacional de Ciencia y Tecnologia of Mexico, while Dr Michelle
Coote took up an ARC Postdoctoral Fellowship in the group in June.
Enzyme-catalysed Reactions
Vitamin
B12 is one of nature's essential vitamins. We have used
ab initio calculations to model reactions mediated by coenzyme
B12. Although
these reactions have been extensively studied experimentally, there
is certainly no consensus as to how they proceed. We find that
protonation and/or deprotonation at appropriate sites facilitates the
reactions, and that reactions that are facilitated by protonation (or
deprotonation) are facilitated by the partial-proton-transfer that
enzymatic hydrogen bonding can provide. Our most recent studies have
been directed at the reaction catalysed by the enzyme ethanolamine
ammonia lyase where we find that interactions between the enzyme and
the migrating group of the substrate that afford an almost
fully-protonated migrating group will lead to the most efficient
catalysis. This and other recent examples
provide strong encouragement for the use of computer calculations in
a predictive manner in the study of enzyme reactions. (with
M.L. Coote, J.T. Bennett, and B.T. Golding [U. Newcastle upon Tyne],
D.M. Smith [Ludwig Maximilians U., Munich], S.D. Wetmore [Mount
Alison U., Canada])
Development of Improved Theoretical Procedures
The
ability to predict reliable thermochemistry represents a very
important application of ab initio molecular orbital theory.
We have recently been designing and assessing methods that are suited
for predicting accurate thermochemistry for free radicals because
these represent particular challenges for theoretical investigation.
Our latest work has been concerned with methods that we have
designated G3-RAD, G3X-RAD, G3(MP2)-RAD and G3X(MP2)-RAD. (with
D.J. Henry, M.B. Sullivan)
Free Radical Chemistry
Radicals
are ubiquitous in chemistry, biology, and polymer science. 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. We have been using theory to
determine radical stabilisation energies, with the important aim of
seeing how individual substituents stabilise or destabilise a radical
centre. We have also been examining the details of radical addition
reactions and radical abstraction reactions, both of which are very
important in biological chemistry and polymer chemistry. A
particularly important application is concerned with gaining a better
understanding of the RAFT polymerization process with the ultimate
aim of improved process control. (with M.L. Coote, D.J. Henry,
R. Gomez-Balderas, G.P.F. Wood, and H. Fischer [U. Zurich],
M.W. Wong [U. Singapore])
Oxidative Damage to Proteins
An
understanding of the oxidation of proteins by free radicals is
of great importance because of its implication in a number of human
disorders such as Alzheimer's disease, atherosclerosis, and diabetes,
as well as aging. We have been using ab initio molecular
orbital calculations to address the problem. Initial targets have
included the cleavage of the peptide backbone following radical
formation, and migration of the radical site within the peptide.
(with G.P.F. Wood, M.L. Coote, R. Jacob, C.J. Easton, and M.
Davies [Heart Research Inst., Sydney], R.A.J. O'Hair [U. Melbourne],
A. Rauk [U. Calgary, Canada])
Oxides and Hydroxides of Alkali and Alkaline Earth Metals
We have been examining the alkali metal oxides and hydroxides as a
preliminary to investigating their interesting acid and base
properties. Reliable experimental data are very sparse for these
molecules. Their theoretical description is not entirely
straightforward either and has necessitated incorporation of several
new features and the development of new basis sets. (with M.B.
Sullivan, A.P. Scott, T. Büsgen, and B.J. Smith [Walter and
Eliza Hall Inst., Melbourne], J.M.L. Martin [Weizmann Inst., Israel],
L.A. Curtiss [Argonne Nat. Lab., USA], S.R. Kass [U. Minnesota,
USA])
Hydrogen Bonding
Hydrogen
bonding is of great importance in chemical and biological systems.
Previous studies have mostly focused on hydrogen bonds involving
electronegative elements, e.g., O-H---N. We have examined
instead the weaker hydrogen bonds to carbon, e.g., C-H---N.
We have carried out systematic studies aimed at identifying which
types of systems will exhibit the strongest C-H---X hydrogen bonds.
The effect of electronegative substitution has been particularly
targeted. (with S.D. Wetmore [Mount Alison U., Canada])
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