a detailed physical and mathematical affirmation of a trend that hitherto found its
boldest expression in the structural formulas of organic chemistry [ 5 ], and it is the
unequivocal negation of the till recently trendy assertion [ 6 ] that science is a kind of
game played with “paradigms” [ 7 ].
In computational chemistry we take the view that we are simulating the beha-
viour of real physical entities, albeit with the aid of intellectual models; and that as
our models improve they reflect more accurately the behavior of atoms and
molecules in the real world.
1.5 Summary...................................................................
Computational chemistry allows one to calculate molecular geometries, reactiv-
ities, spectra, and other properties. It employs:
Molecular mechanics – based on a ball-and-springs model of molecules
Ab initio methods – based on approximate solutions of the Schr€odinger equation
without appeal to fitting to experiment
Semiempirical methods – based on approximate solutions of the Schr€odinger
equation with appeal to fitting to experiment (i.e. using parameterization)
Density functional theory (DFT) methods – based on approximate solutions of the
Schr€odinger equation, bypassing the wavefunction that is a central feature of ab
initio and semiempirical methods
Molecular dynamics methods study molecules in motion.
Ab initio and the faster DFT enable novel molecules of theoretical interest to be
studied, provided they are not too big. Semiempirical methods, which are much
faster than ab initio or even DFT, can be applied to fairly large molecules (e.g.
cholesterol, C 27 H 46 O), while molecular mechanics will calculate geometries and
energies of very large molecules such as proteins and nucleic acids; however,
molecular mechanics does not give information on electronic properties. Computa-
tional chemistry is widely used in the pharmaceutical industry to explore the inter-
actions of potential drugs with biomolecules, for example by docking a candidate
drug into the active site of an enzyme. It is also used to investigate the properties of
solids (e.g. plastics) in materials science.
References.......................................................................
- Schaefer HF (2001) The cost-effectiveness of PCs. J. Mol. Struct. (Theochem) 573:129–137
- McKenna P (2006) The waste at the heart of the web. New Scientist 15 December (No. 2582)
- Environmental Industry News (2008) Old computer equipment can now be disposed in a way
that is safe to both human health and the environment thanks to a new initiative launched today
at a United Nations meeting on hazardous waste that wrapped up in Bali, Indonesia, 4 Nov 2008
References 5