Biological Chemistry - School of Physics and Astronomy - The ...

MAJOR
GRANTS
Mid-range Computer for Modelling in
Environmental Science, HEFCE, £532k.
Advanced Research Fellow in Molecular
Modelling, BNFL, £228k.
Tunnelling Contributions to Kinetic
Isotope Effects in Intramolecular Hydron
Transfers, EPSRC, £219k.
Modelling Redox Transformations of
Heavy Metals and Radionuclides at
Mineral Surfaces, NERC, £208k.
A Mid-Range Computer for Simulation
Studies in Chemistry, EPSRC, £203k.
New Theories of Chemical Reactions,
EPSRC, £190k.
Structure of Molecular Liquids and Liquid
Crystals-Hunting the Bridge Function,
EPSRC, £163k.
Electrochromic evacuated advanced
double glazing, EC, ELEVAG, £115k.
14
Theoretical Chemistry
N.A. Burton, J.N.L. Connor, I.H. Hillier, P.J. O’Malley,
J.J.W. McDouall, A.J. Masters, and P.L.A. Popelier
Computational and theoretical chemistry can now provide
important insights into, and predictions for, chemical systems
ranging from small gas phase molecules to large biological
molecules having thousands of atoms. This has been achieved
through a combination of fundamental theories using both
quantum and statistical mechanics coupled with modern
computational techniques, allowing these theories to be
applied to large and complex systems. Computational
chemistry is now recognized as an important discipline within
chemistry, which not only impinges on the three traditional
areas, but also makes important contributions in interdisciplinary
areas such as life sciences and materials.
The group at Manchester is at the forefront
of developing new methods and applying
them to current chemical problems.
Chemistry in the gas phase is the result of
collisions between atoms and molecules, and
in order to achieve a fundamental
understanding of gas-phase chemistry we
must understand how one atom or molecule
collides with a second atom or molecule.
Elegant and powerful theoretical methods 1
are being used to describe and predict stateof-the
art experimental results for different
types of collisions. 2
A major challenge of computational chemistry
is to model the chemical reactions of large
and complex molecules to chemical accuracy.
A range of new quantum mechanical
methods have been developed 3,4 which are
tailored to the size of the system being
investigated. These have been employed to
study complex problems in chemical structure
and reactivity, with important new chemical
concepts 5 emerging from the calculations.
These studies are important for understanding
a whole range of chemical reactivity, and
have allowed us to address problems in
biocatalysis, enzyme inhibition and
fundamental aspects of condensed phase
reactivity. Work in the latter area is of
particular relevance to atmospheric chemistry,
where, for example we have studied reactions
in water clusters involving the atmospherically
important molecules SO3 and ClONO2 6 . Many
of the applications have been focused on
biological problems 7-11 , involving, for example
the prediction of drug potency 11 and showing
the importance of extreme tunnelling in
enzyme catalysis. 9
Advances in understanding the structural and
electrical properties of important materials 12-15
such as liquid crystals 13 and polymers 14,15 have
been made, also using a variety of novel
methods. In the area of materials modelling
there is strong collaboration with the organic
materials innovation centre (OMIC), also in
the School of Chemistry, focusing in particular
on electro-optical devices.
a
b
Figure 1
Variation of energy of an electron at
different positions along the chains in a
sample of polyethylene. Orange denotes
the lowest energy and blue the highest.
Figure 2
Optimised active site for oxygen atom transfer
in dimethyl sulfoxide reductase: (a) reactant
complex and (b) transition structure.
1. R. Anni, J.N.L. Connor and C. Noli, Improved
nearside-farside method for elastic scattering
amplitudes. Phys. Rev. C, 66, 044610, 1-11
(2002).
2. G.C. Schatz, M. Hankel, T.W.J. Whiteley and
J.N.L. Connor, Influence of spin-orbit effects on
chemical reactions: Quantum scattering studies
of the Cl(2P) + HCI -> CIH + Cl(2P) reaction
using coupled ab initio potential energy surfaces.
J. Phys. Chem. A, 107, 7278-7289 (2003).
3. R.M. Nicoll, S.A. Hindle, G. MacKenzie, I.H.Hillier
and N.A. Burton, QM/MM methods and the
study of kinetic isotope effects: Modelling the
covalent junction region and application to the
enzyme Xylose Isomerase. Theor.Chem.Acc. 106,
105-112 (2001).
4. J.J.W. McDouall, Combining two-body density
functionals with multiconfigurational
wavefunctions: diatomic molecules. Mol. Phys.,
101, 361-371 (2003).
5. N.O.J. Malcolm and P.L.A. Popelier, In search of a
physical basis for the VSEPR model in terms of
the Laplacian of the electron density. Faraday
Discussions 124, 353-363 (2003).
6. E.V. Akhmastkaya, C.J. Apps, I.H. Hillier, A.J.
Masters, I.J. Palmer, N.E. Watt, M.A. Vincent and
J.C .Whitehead, The hydrolysis of SO3 and
ClONO2 in water clusters: A combined
experimental and theoretical study. J.Chem.Soc.,
Faraday Trans. 93, 2775-2779 (1997).
7. P.L.A. Popelier and L. Joubert, The elusive atomic
rationale for DNA base pair stability. J. Amer.
Chem. Soc., 124, 8725-8729 (2002).
8. P.J. O’Malley, The origin of the spin density
asymmetry at the QA binding site of type II
photosynthetic reaction centres. Chem. Phys.
Lett., 379, 277-281 (2003).
9. P.F. Faulder, G. Tresadern, K.K. Chohan, N.S.
Scrutton, M.J. Sutcliffe, I.H. Hillier and N.A.
Burton, QM/MM studies show substantial
tunnelling for the hydrogen-transfer reaction in
methylamine dehydrogenase. J. Amer. Chem.
Soc., 123, 8604-8605 (2001).
10. G. Tresadern, S. Nunez, P. Faulder, H. Wang, I.H.
Hillier and N.A. Burton, Direct dynamics
calculations of reaction rate and kinetic isotope
effects in enzyme catalyzed reactions. Faraday
Discussions, 122, 223-242 (2003).
11. M. P. Gleeson, N.A. Burton and I. H. Hillier,
Prediction of the potency of inhibitors of
adenosine deaminase by QM/MM calculations.
Chem. Commun., 2180-2181 (2003).
12. T. Khan, J.J.W. McDouall, E.J.L. McInnes, P.J.
Skabara, P. Frere, S.J. Coles and M.B.
Hursthouse, A combined substituent and
supramolecular approach for improving the
electron donor properties of 1,3-dithiole-2thione
derivatives. J. Mat. Chem., 13, 2490-
2498 (2003).
13. G. Germano, M.P. Allen and A.J. Masters,
Simultaneous calculation of the helical pitch and
the twist elastic constant in chiral liquid crystals
from intermolecular torques. J. Chem. Phys.,
116, 9422-9430 (2002).
14. M. Soutzidou, V.A. Glezakou, K. Viras, M.
Helliwell, A. J. Masters and M.A. Vincent, Low
frequency Raman spectroscopy of n-alcohols.
LAM vibration and crystal structure. J. Phys.
Chem. B, 106, 4405-4411 (2002).
15. A. Eilmes and R.W. Munn, Microscopic
calculation of the energetics of charged states in
amorphous polyethylene. J. Chem. Phys., 120,
7779-7783 (2004).
15