Dear fellows,
I am minimizing with MM a set of structures before QM (Gaussian) calculations.
Some of those contain an indoline ring (reduced indole on the 5 membered ring part). Thus the nitrogen is still conjugated to the benzyl ring, which remained aromatic.
Surprisingly for me, the minimization with all force fields (done in Avogadro) make the nitrogen behave like sp3, and then goes out of planarity. However, UFF force field preserves the planarity. I always read that MMFF94 is much better for small molecules than UFF, so I wonder what should I believe. Is the sp2/sp3 hybridization contained in those force fields ?
Hi Felix,
In place of MMFF94, try GAFF force field implemented in Avogadro, which is used for small molecules in doing molecular dynamics simulations using AMBER.
Hello Felix
The force fields basically behave better vs not so better on the basis of their atom type definition. So in this case UFF has the correct definition of the indoline N vs MMFF94. Just remember there are various FF for a large array of molecules. Its upto the user to determine the choice based on the structure.
Pansy
The Merck force field was developed to span a wide assortment of drug-like moieties. It knows sp2/sp3 only through the use of (improper) dihedral angle constraints. For your molecules, those parameters may not be present. It depends on how much they resemble the Merck training data.
I'm not sure that this is worth much of your time. The QM calculations will certainly converge to different structures than you are obtaining through the MM calculations. I can see that you might want to minimize the time your QM calculations take by starting "close" to an optimal structure, but the QM calculations will planarize aromatic bonds all by itself, even if the MM doesn't. Provided, of course, that you are using a suitably large basis set and reasonable quantum method.
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