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Geometry Optimization -- An Overview
There are three different computational modes for geometry optimization.
Other properties of molecules can be computed as well.
 | Molecular mechanics follows classical
mechanics where atoms are treated as spheres and bonds as springs. Molecular
mechanics calculations will give you
information about the bond distances and angles in your compound.
You can also get information about the differences in steric energies associated with
different conformations of your molecule. Molecular mechanics calculations use
force fields to
describe the stretching, bending and twisting of bonds as well as
Van der Waals and hydrogen bonding interactions. Electrostatic interactions
are also considered. All of these
terms are summed together to give you a total steric energy for your molecule. This is the fastest method but
the resulting minimized structure may be at a local rather
than a global energy minimum. |
| MOPAC uses quantum mechanics to
solve the Schrödinger equation to determine bond strengths, atomic
hybridizations, partial charges and orbitals from the positions of the atoms
and the net charge. MOPAC is a semi-empirical method that will optimize the
geometry of your molecule and also give information concerning the location of
electron density within your system, the frontier molecular orbitals, electron
density distribution, partial charges, dipole moment, bond order, ionization
potentials, electron affinities and vibrational spectra. |
| Density Functional Theory (DFT) is an ab-initio
method although it is often considered an entirely separate class of
calculation. CAChe uses the DGauss program for DFT calculations.
You can use DGauss to compute optimum geometry, potential energy maps,
vibrational frequencies and spectra, transition states and reaction pathways,
molecule orbitals (and wavefunctions to generate density,
superdelocalizability and electrostatic potential surfaces), bond orders, atom
partial charges and NMR chemical shifts. |
| Quantum Mechanical Ab-Initio methods. Ab-Initio
is a Latin term for "from the beginning". In Ab-Initio
calculations everything is derived directly from theoretical principles.
Unlike semi-empirical methods, ab-initio
calculations do not include any existing experimental data. |
It is important to note that the different computation modes do not always
give the same result. The different parameters and assumptions for each
method are the reason for this.
In the first lesson you will use
Molecular Mechanics (MM3) to optimize the geometry of cyclohexanol.
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