User ac20ca0f01
09-08-2011 13:56:57
Hello,
I am using molconvert version 5.4.1.0 to generate 3D coordinated from isomeric SMILES. In the structure there are 2 chiral atoms and 3 sp3 Carbon atoms being part of a 6-membered ring. Therefore, this 6-membered ring can have different conformations. I have used the option -3:{fast} and -3:{fine} and both generated the same conformer. I have also used CORINA to generate the lowest energy connformer. It resulted in another structure which is supported by 1H-NMR coupling constants. I have attached the SMILES files and the generated MOL files.
Could you please give me a reference on the method used for the 3D structure generation? I would like to know why the two options in molconvert resulted in the same conformer which is not the lowest energy conformer for the structure.
I would highly appreciate any help for the generation of the correct conformer using molconvert.
kind regards,
Villy
ChemAxon 8b644e6bf4
11-08-2011 12:01:40
Dear Villy,
A brief description of the used method available at http://www.chemaxon.com/library/advanced-automatic-generation-of-3d-molecular-structures/ (see downloadable pdf file: http://www.chemaxon.com/conf/Advanced_automatic_generation_of_3D_molecular_structures.pdf ).
Generaly, fine build ( molconvert -3:S{fine} ) should be used instead of the "fast" ( molconvert -3:S{fast} ). As far as i know currently the fine build is the default selection ( molconvert -h thus probably wrong, it needs checkup ). For more option see help available by "molconvert -H3D"
To find low(est) energy conformer generating multiple conformers, using strict optimization limit and optionally using "hyperfine" filtering is advised.
The conformational analysis of the attached smiles structure seems to be incomplete: our code places the OH group only in axial position when generating up to 200 conformers; equatorial placement is missing. This needs further checkup from us.
Regards,
Gabor