A new 3D molecular structure representation using
quantum topology with application to structure-property
relationships
Chemometrics and Intelligent Laboratory Systems, 54 (2):
75--91 (2000)Abstract
We present a new 3D molecular structure representation
based on Richard F.W. Bader's quantum topological atoms
in molecules (AIM) theory for use in quantitative
structure-property/activity relationship (QSPR/QSAR)
modelling. Central to this structure representation
using quantum topology (StruQT) are critical points
located on the electron density distribution of the
molecules. Other gradient fields such as the Laplacian
of the electron density distribution can also be used.
The type of critical point of particular interest is
the bond critical point (BCP) which is here
characterised by using the following three parameters:
electron density rho, the Laplacian nabla2rho and
the ellipticity epsi. This representation has the
advantage that there is no need to probe a large number
of lattice points in 3D space to capture the important
parts of the 3D electronic structure as is necessary
in, e.g. comparative field analysis (CoMFA).We tested
the new structure representation by predicting the
wavelength of the lowest UV transition for a system of
18 anthocyanidins. Different quantitative
structure-property relationship (QSPR) models are
constructed using several chemometric/machine learning
methods such as standard partial least squares
regression (PLS), truncated PLS variable selection,
genetic algorithm-based variable selection and genetic
programming (GP). These models identified bonds that
either take part in decreasing or increasing the
dominant excitation wavelength. The models also
correctly emphasised on the involvement of the
conjugated pi system for predicting the wavelength
through flagging the BCP ellipticity parameters as
important for this particular data set.