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In a different question, the task was to turn a wedge-and-dash representation into a Fischer projection. This involved rotation of a fairly complex molecule - either as a physical model or a mental model - to orient each chiral carbon in preparation for drawing the Fischer projection. How can you use free software to visualize this process?

enter image description here

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    $\begingroup$ This might be useful if kept in meta since most of formatting tricks are kept there.. +1 $\endgroup$
    – Safdar Faisal
    Jul 28, 2020 at 12:17
  • $\begingroup$ There is a lot of free 3d molecular viewers - Maestro for academics, VMD, Pymol, Avogadro... Some of them have option to optimize/clear structure $\endgroup$
    – XuMuK
    Jun 1, 2021 at 11:33

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I used Jmol to make the following animated GIF:

enter image description here

First I used NCBI's Pubchem Sketcher to get the SMILES code for the molecule: CC(C(C(C)F)(Br)F)O

Then, I loaded it into JSmol running here using the load molecule by name button. Internally, this triggers the command

load /*file*/"https://cactus.nci.nih.gov/chemical/structure/CC(C(C(C)F)(Br)F)O/file?format=sdf&get3d=true

I fixed the stereochemistry by clicking on the carbons with incorrect chirality after issuing the command "set picking INVERTSTEREO". To rotate around the bonds, I used "rotate branch @3 @2 180 180" and "rotate branch @3 @4 180 180". Finally, I chose the viewing orientations, displayed the orientationwith "show moveto" and issued the resulting moveto commands before and after rotating around the single bonds.

A more elaborate example with glucose (4 chiral centers) can be found on Proteopedia.

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