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Molecular structures were optimized at the MP2/6-31G**++ level
with the help of the ab initio package
GAMESS (General Atomic
and Molecular Electronic Structure System)[Schmidt 93].
The computations were performed on clusters of Linux PC machines at ENSTA.
Geometry optimizations were performed for the following cations:
MethylOxonium; EthylOxonium; 1-PropylOxonium, 2-PropylOxonium
and 1-ButylOxonium, 2-ButylOxonium, IsoButylOxonium, TertButylOxonium.
Vibrational frequencies and ZPEs are computed,
and visual depictions of expected experimental IR spectra
are simulated with the help of Lorentzian functions.
MP2 Frequencies were not scaled.
Curves are displayed with the help of the
Xgraphic
software [Jouve 98].
With the help of the graphics package
MolDen, edition of Z-matrices and production of 2D images were performed
[Schaftenaar 97].
Since static 2D images are not often providing an easy way to understand
molecular structures,
optimized geometries are also displayed with the help of the freely available
ChemApp Java applet
written by John and George Purvis.
This did not appear obvious to us when our graphics were first created during the summer of 1999,
but the CAChe format is now linked to a proprietary product
distributed by Cache Software,
a Fujitsu subsidiary. Most regretfully, the original
ChemApp
page no longer exists.
We have nevertheless preserved an almost complete copy of
the original site that we have made available to our readers for convenience.
This did not appear obvious to us when our graphics were first created during the summer of 1999,
but the CAChe format is now linked to a proprietary product
distributed by Cache Software,
a Fujitsu subsidiary.
Since the ChemApp
applet reads only files in the
CAChe format,
we used the program
Babel
(A Molecular Structure Information Interchange Hub )
to convert GAMESS outputs into CAChe files.
There is now a Open Source successor to Babel : OpenBabel.
When the original
ChemApp
site was still online,
Dr. George Purvis
provided us a very kind help in order to diagnose a bug and find a way to avoid it.
It is interesting to notice that
the CAChe format allows also to display
Molecular Orbitals ( see eg Gaussian:
Viewing Molecular Orbitals with CAChe ). This feature has not been used in this article.
Below are listed a few commands that allow to interactively
manipulate a molecule with the help of
the ChemApp Java applet
| Click on Window |
Activation of the JAVA window |
| Right mouse button |
Applet menu display |
| r |
Molecule rotation with the mouse |
| t |
Molecule Translation with the mouse |
| % |
Magnification with the mouse
|
| x / y / z / w |
Rotation axis along X, Y , Z or W |
| space bar |
Toggle rotation |
| c |
Molecule at the center
|
| f |
Molecule comprised within the window |
| + or - |
Increase / Decrease rotation speed
|
| < or > |
Back and forth Zoom
|
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