[ghemical-devel] Fullerene calculations

[Tommi Hassinen]

You used molecular mechanics for the calculation, right?

The current molecular mechanics force fields in ghemical
are poor at detecting "resonance"-type effects in molecules
with aromatic nature, like in fullerenes. Currently the aromatic
bonds are just guessed to be like in benzene. This is the reason
for the result you got.

I suggest you should use a QM method to calculate precise
results for fullerenes, instead of molecular mechanics.

Please note that the geometry optimization algorithm itself is
the same for MM and QM calculations, it's just the energy
function that describes the molecule which is different.

Regards,
Tommi

________________________________________
From: Ulisses Leitao [ualeitao at yahoo.com]
Sent: Thursday, October 23, 2008 12:38 AM
To: Tommi Hassinen
Cc: ghemical-devel at bioinformatics.org
Subject: Fullerene calculations

Dear Tommi,

now  a scientific issue.

I used ghemical in order to optimize the fullerene chemical structure,
and found an interesting result.

The pdb file I had iniciate the calculations with had an
assimetrical hexagon, alternate with 1.45 nm and 1.37 nm long bonds.
The structure is basically some pentagons surrounded by hexagons,
making a carbon ball. The shorter bound distance was the frontier
of two pentagons.

The Energy calculation with ghemical gave in this case 3,084,7 kJ/mol.

After the optimization procedure with ghemical we found an energy of
1970,8 kJ/mol, with both side lengths approximately equals to 1.40 nm.

The question is: How precise is the ghemical in doing the geometry optimization?
What is the calculation method used?

Thanks a lot,

Ulisses