Biomedical Engineering Reference
In-Depth Information
such as exchange cannot be written as a simple, energy-independent potential,
the method is only capable of performing calculations within the SE and SEP
models.
6.3
Target calculations
The geometries of all DNA bases except uracil were determined using B3LYP/6-
31
G* density functional theory and Gaussian 03 [
24
]. Except for thymine,
the molecules were constrained to be in C
s
symmetry. The geometry of uracil
was optimised with the MP2 method and using a 6-31G* basis set as reported
previously [
52
].
There are various issues in choosing a suitable target wavefunction for use in
scattering calculations, which depend on what aspect of the problem is of interest.
For the SE and SEP models the use of Hartree-Fock wavefunctions is standard;
for CC calculations there is more choice. In particular these calculations usually
attempt to represent several low-lying states of the target. This can be difficult given
the constraints that all states must be represented by a single orbital set and that it
must be possible to use in a balanced and tractable scattering calculation.
Our favoured method is to represent CC target wavefunctions using a complete
active space (CAS) configuration interaction (CI) model. In the CAS-CI model,
core electrons are frozen in the self-consistent field (SCF) orbitals and the active
electrons are distributed amongst all the valence orbitals, subject only to the con-
straints of overall space-spin symmetry. This approach has significant advantages
in terms of performing a balanced treatment between the target and the scattering
wavefunction [
43
].
Even within the CAS-CI model there is considerable flexibility over the precise
choice of molecular orbitals used. Here we use CAS-SCF orbitals generated by
MOLPRO. Table
6.1
presents results for the bases considered. The calculations
were performed using cc-pVDZ Gaussian Type Orbital (GTO) basis sets and an
active space of 14 electrons in 10 orbitals for uracil, cytosine and thymine, 12
electrons in 10 orbitals for adenine and 12 electrons in 9 orbitals for guanine. Full
details, including the actual configurations used, are given in Table
6.2
. Besides the
calculated energies for the ground and 15 lowest excited states, the table gives our
calculated permanent dipole moment for each molecule. This property is important
since the long-range nature of this moment has a strong effect on the scattering.
C
6.4
Scattering calculations
In the scattering calculations the target basis set was augmented with sets of
GTOs with
(up to g-wave) to represent the continuum wavefunctions [
14
].
All calculations were performed for an R-matrix radius
` 4
a D 13
a
0
except those on
thymine which used
a D 15
a
0
.
