Chemistry Reference
In-Depth Information
atomic coordinates. Force fields can be determined for atoms. These can be used
for simulations using molecular dynamics.
Semi-empirical methods use simplified version of equations from
ab
initio
methods. They can treat valence electrons explicitly and include parameters fitted
to experimental data. They are relatively computationally less expensive and can
handle larger systems. It may be however sometimes difficult to determine the
quality of the results.
From first principles,
ab initio
methods can solve numerically the quantum
mechanics Schrodinger (or Dirac) equation to calculate exact properties from only
the coordinates and species. This includes bond breaking/formation, chemical
reactions and ligand-protein binding. The method is however computationally
expensive and limited to small systems and fast processes. These calculations can
be up scaled by using elastic tensors, diffusivities. viscosities and force fields
determined for MD simulations. The
ab initio
methods can also be downscaled by
fitting electronic integrals in semi-empirical methods [644-712].
Density functional theory was well received because of the high
computational/scientific limiting demands of first-principle-based calculations. At
a more computationally affordable cost, density functional theory (DFT) opened
the way for more accurate calculations with larger models (more atoms).
The number of electrons or atoms determine the level of sophistication for the
calculation. Starting from the lower level, we have the empirical potentials (10
1
to
10
6
atoms). Tight binding calculation (10
4
atoms). Higher levels of calculations
includes self-consistent fields (SCF) Hartree Fock (HF), correlation perturbation
theory, configuration interaction and DFT. On the order of ~ 10
2
atoms are used
with SCF and DFT methods.
In the Born-Oppenheimer approximation, the electronic motion is decoupled from
that of the nuclei. The many-electron wave function is in 3N dimensional space
and the total energy is the expectation value of the Hamiltonian. Correlation is not
included and computationally more expensive methods (configuration interaction
and many body perturbation theories) had to be introduced.
