I am trying to optimise an organic molecule using Avogadro software, and when I draw the molecule according to the correct sterochemistry (some bonds coming towards the screen and some going away from the screen) whenever I optimise the molecule using one of the forcefields the stereo chemistry starts to change and therefore some bonds face the wrong plane, is there a way to optimise the molecule without changing its stereochemistry in avogadro software?
Maybe you can try the restricted optimization. You will probably find the “restricted” option from one of the optimization types. And then you can freeze the particular bonds in question, and then start the optimization.
I hope it works.
Hi Wares,
This is very odd, and I have yet to experience such a problem. I guess that we are talking about point chirality where a carbon atom is a stereogenic center, and not axial or planar chirality? Could you share the molecule that you're talking about? Maybe that could give some insight into the issue.
Also, I would suggest you not to use molecular mechanics for the optimization (Avogadro offers only MM), but rather semiempirical methods or, even better, some DFT calculations. For semiempirical calculations, you could try ArgusLab software, it is free and fairly easy to use. It is getting a bit dated by now, but you'll get somewhat reasonable structures (for sure better than MM optimization). Also, MOPAC is a good software if you have some experience using it, but otherwise, I'd suggest using ArgusLab. However, DFT is the way to go if you need good structures. There are some free software packages (such as NWChem or GAMESS), and you could use Avogadro as a graphical interface.
Hope this helps.
Hi Wares,
Ya Basically Avogadro is old. When I Worked With it I also Faced Sometime This kind of Problem. To resolve This Problem You use Freezing tool that Freezes Particular bond Rotation And The selection of Basis Set that also Matter Specially in case of Organic Compound . If you Worked with Drug then select GAFF , If you Worked with Organic molecules Then Use MMFF94 or Ghemical. And i also Suggest You to Work With ArgusLab as Uros Stojiljkovic said..otherwise you also go through GaussView 5.0.
I Hope this helps You.
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