Force Fields documentation page

Hi,

I was looking at the documentation at:

http://avogadro.openmolecules.net/wiki/Tutorials:Force_fields

Under Sulfones it states that the sulfone should be drawn with S-O single bonds rather than double bonds. Can anyone explain why this is the case? Is it that the calculated energy is too high, or is there a better explanation?

On a related matter, what is the default Force Field - MMFF94? I assume that the “Optimize Geometry” under the Extensions menu uses the Force Field that is selected through Extensions - Molecular Mechanics - Setup Force Field. Is this correct?

Thanks,

Steve


Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221

(517) 264-7657
swathen@sienaheights.edu

On Sun, Aug 9, 2009 at 8:12 PM, Steven WathenSWATHEN@sienaheights.edu wrote:

Hi,

I was looking at the documentation at:

http://avogadro.openmolecules.net/wiki/Tutorials:Force_fields

Under Sulfones it states that the sulfone should be drawn with S-O single bonds rather than double bonds. Can anyone explain why this is the case? Is it that the calculated energy is too high, or is there a better explanation?

The MMFF94 validation suite uses single bonds and the atom typing code
didn’t accept (or assign the wrong atom type resulting in wrong
energies) sulfone with double bonds. However, in recent versions both
accepted and if you use the adjust hydrogens feature while drawing,
using double bonds is easier (otherwise there will be an extra
hydrogen on the oxygen atoms). I’m not exactly sure which version of
Avogadro already has these changes (this also depends on the platform)
but if you draw both forms and compare the energies, they should be
the same.

On a related matter, what is the default Force Field - MMFF94? I assume that the “Optimize Geometry” under the Extensions menu uses the Force Field that is selected through Extensions - Molecular Mechanics - Setup Force Field. Is this correct?

Correct.

Thanks,

Steve


Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221

(517) 264-7657
swathen@sienaheights.edu

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