I have a problem while calculating molecular descriptors with Dragon 7. My structures are drawn in Avogadro and optimized with Gaussian. After this step, my structures look like the one I uploaded - the aromatic ring in imidazolium is no longer in form of two separate double bonds, the electrons are delocalized instead.
Unfortunatelly, it is not seen in Dragon (I upload the files in .mol2 format). The software warns me that one of C atoms (carbon between nitrogens) has unusual valence, 3 instead of 4 and no aromaticity is detected.
How can I fix this?
It seems that your molecule has quite unusual bonds. In order to not raise warnings when using your molecule in a chemoinformatic toolkit I suggest to modify the imidazolium as in: C1=C[NH+]=CN1. Replacing the two delocalized bonds with a single and a double bond and adding a + to the N with a double and two single bonds.
In order to check your molecule dataset I suggest to use alvaMolecule (https://bit.ly/2UtqSMJ).
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