When I calculate a 3D conformation of a molecule containing an amine group which is attached to a sp2 hybridized carbon (as in aniline or guanidium), this results in an tetrahedral nitrogen. Shouldn't this be planar?
Thanks for the report, it should be planar. This seems to be a force field bug; it will be fixed (with other force field related improvements) in 5.3.
can you give a statement about the release date of Marvin 5.3?
We use the conformer generation to prepare the input for virtual screening and QSAR analyses. As this kind of functional group appears frequently in bioactive molecules, an accurate molecular geometry is of critical importance for any activity prediction.
5.3 is planned to be released Q4 2009. Is this acceptable for you, or you need the 3D structure generation tool sooner?
this geometric issue is corrected and togedher with many forcefiled improvements will be released in marvin 5.3
Thank you for the report.
I am just testing out the pre-release version of Marvin 5.3. The geometry of anilin-related molecules seems correct now, but I wonder if the nitrogen in sulfonamides should be planar, too.
Unfortunately, I have no QM tool installed, so I cannot verify this one. CORINA produces a planar conformation.
I would say it depends.
The configuration of the nitrogen in case of the above molecule is sp3 like. A fast quantumchemical hf/6-31+g(d,p) geometry optimization was done to support this. Please see attached.
Although in the real life there is a wide range of sulfonamides containing sp2 or sp3 like nitrogen.
Even almost all intermediate geometries between the two hybridization states can be found.
There is a nice study on this issue:
http://www.dddc.ac.cn/embo04/lectures/920_martin.pdf from pg 51.
In Generate3D and in our Dreiding all these situations are treates as sp3.
I hope this helps.