User cbb759276f
30-10-2012 18:23:42
Hi,
I was looking at 3D visualisations of alpha-glucopyranose and beta-glucopyranose using MarvinView3D in MarvinSketch 5.3.7.
OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O
OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1O
When viewed in 3D, both molecules are presented with different ring conformations i.e. the anomeric -OH is equatorial in both alpha-glucopyranose and beta-glucopyranose
By contrast, the same molecules when viewed with Reaxys (also MarvinSketch 5.3.7) has the anomeric -OH axial in alpha-glucopyranose but it is equatorial in beta-glucopyranose (i.e. the same ring conformation in both).
Why does this happen? I have used the same settings/preferences for both. Also, is there a way of forcing my version of MarvinView3D to behave similar to Reaxys i.e. generate the same conformation for both anomers.
ChemAxon d51151248d
02-11-2012 11:02:51
Hi !
Thank you for reporting this issue. That is indeed a bug in the 3D structure generation of alpha-D-glucopyranose.
We have passed your question to the modeling group to correct the bug.
Daniel
ChemAxon 60613ab728
07-01-2013 07:38:42
Hi Tim,
We discussed your request in more details. In the 2D-3D conversion process (called clean3D), the position of the anomeric OHs are constrained only by the chirality. Further conformational constraints (apart from C/T isomerism), like the axial and equatorial positions, can't be specified in MarvinSketch.
There are two workarounds that can be applied:
1) Following the SMILES import, the Menu/Calculations/Conformation/Conformers plugin can be used to generate large number of conformers (500-1000 in this case). One of the low energy conformers will be the one that you look for, please find the attached screenshot. You can copy/paste the chosen molecule back into a MarvinSketch or into other applications.
We are aware of that the conformational analysis within 2D-3D conversion is not optimal on this structure: the desired low energy conformation is found only when generating >500 conformers.
2) You can use the current functionality of the Marvin Sketch in order to mimic a 3D builder. Draw a cyclohexane ring, add explicit H atoms. Clean it in 3D. Then replace the relevant hydrogen atoms to oxygen atoms. Use Clean3D/Gradient optimize to fix bond lengths. Thus you can obtain both the alpha and the beta isomers.
Please let us know if you have further questions.
Thank you,
Miklós