Hi Susan,
that's an interesting one. As a separate problem from the fact that the
NH2 is tilted out of plane, according to this paper:
Godfrey, Peter D., Ronald D. Brown, and Andrew N. Hunter. "The shape of
urea." /Journal of molecular structure/ 413 (1997): 405-414.
http://dx.doi.org/10.1016/S0022-2860(97)00176-2
it looks like the nitrogen is planar in urea crystals, but pyramidal in
gas phase; this is the way the MMFF94 minimum energy geometry looks like.
The first of the conformers I get with pure ETKDG also seems to have a
bad geometry at the phenyl-substituted nitrogen:
As a workaround, you may either minimize the conformers with MMFF94 or
set the relevant dihedral to 0; see this Jupyter notebook for examples
of the two approaches (you'll need to run the notebook in your own
Jupyter instance to render Py3dMol objects):
https://gist.github.com/ptosco/aafc788d3b69b3fe585c93487a5c9972
Cheers,
p.
On 11/25/16 14:50, Susan Leung wrote:
I am using the ETKDG method for producing conformations for ureas and
thioureas.
The outputted conformers are planar for the substituted N but for the
terminal unsubstituted N, the conformation is wrong as the NH2 is not
planar to the C=O.
The code I am using is as follows:
urea = Chem.MolFromSmiles("NC(=O)NC1=CC=CC=C1")
h_urea = Chem.AddHs(urea)
AllChem.EmbedMultipleConfs(h_urea,numConfs=20,randomSeed=0xf00d,useExpTorsionAnglePrefs=True,\
useBasicKnowledge=True)
AllChem.AlignMolConformers(h_urea,h_urea.GetSubstructMatch(Chem.MolFromSmiles('C(=O)N')))
p = py3Dmol.view(width=400,height=400)
interact(drawit,
m=fixed(h_urea),p=fixed(p),confId=(0,h_urea.GetNumConformers()-1))
Many thanks,
Susan
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