5.5 Applications of the Ab initio Method...................................
An extremely useful book by Hehre [ 39 ] discusses critically the merits of
various computational levels (ab initio and others) for calculating molecular prop-
erties, and contains a wealth of information, admonitory and tabular, on this general
subject.
5.5.1 Geometries.......................................................
It is probably the case that the two parameters most frequently sought from ab initio
calculations (and most semiempirical and DFT calculations too) are geometries
and (Section 5.5.2) energies, although this is not to say that other quantities, like
vibrational frequencies (Section 5.5.3) and parameters arising from electron distri-
bution (Section 5.5.4) are unimportant. Molecular geometries are important: they
can reveal subtle effects of theoretical importance, and in designing new materials
and, particularly, new drugs [ 109 ] the shapes of the candidates for particular roles
should be known with reasonable accuracy – for example, docking a putative drug
into the active site of an enzyme requires that we know the shape of the drug and
the active site. While the creation of new pharmaceuticals or materials can be
realized with the aid of molecular mechanics (Chapter 3) or semiempirical methods
(Chapter 6), the increasingly facile application of ab initio techniques to large
molecules makes it likely that this method will play a more important role in
such utilitarian pursuits. Novel molecules of theoretical interest can be studied
reliably only by ab initio methods, or possibly by density functional theory (Chapter 7),
which is closer in theoretical tenor to the ab initio, rather than semiempirical,
approach. The theory behind geometry optimizations was outlined in Section 2.4,
and some results of optimizations with different basis sets and electron correlation
methods have been given (Sections 5.3.3and5.4). Extensive discussions of the
virtues and shortcomings of various ab initio levels for calculating geometries can
be found in references [ 1 e, g, 39 ].
Molecular geometries or structures refer to the bond lengths, bond angles, and
dihedral angles that are defined by two, three and four, respectively,atomic nuclei.
In speaking of the distance, say, between two “atoms” we really mean theinternu-
cleardistance, unless we are considering nonbonded interactions, when we might
also wish to examine the separation of the van der Waals surfaces. In comparing
calculated and experimental structures we must remember that calculated geome-
tries correspond to a fictional frozen-nuclei molecule, one with no zero-point
energy, while experimental geometries are averaged over the amplitudes of the
various vibrations [ 110 ]. Furthermore, different methods measure somewhat dif-
ferent things. The most widely-used experimental methods for finding geometric
parameters are X-ray diffraction, electron diffraction and microwave spectroscopy.
X-ray diffraction determines geometries in a crystal lattice, where they may be
5.5 Applications of the Ab initio Method 281