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标题: Asking for help in the conformational search of an organic molecule [打印本页]

作者
Author: vitalys 时间: 2025-12-28 01:30
标题: Asking for help in the conformational search of an organic molecule
Hi everyone
I want to perform a conformational search for a flexible organic molecule (attached image). I am familiar with the wonderful tool "Gentor", but I am confused how to correctly handle rotatable bonds in the given molecule, since it has 4 rotatable bonds.
2- Synchronous rotations could be a good choise for this situation ???

Any guidance or suggestions would be greatly appreciated.

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作者
Author: sobereva 时间: 2025-12-28 07:10
You should use gentor (a component of molclus) to independently rotate the four bonds. Assume that rotating each bond by three times, then totally you will generate 3^4=81 initial conformers.

作者
Author: vitalys 时间: 2025-12-28 22:56

sobereva 发表于 2025-12-28 07:10
You should use gentor (a component of molclus) to independently rotate the four bonds. Assume that r ...

Thank you very much for your answer. Could you give me your opinion about chosen angles values for Gentor:
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作者
Author: sobereva 时间: 2025-12-30 14:45

vitalys 发表于 2025-12-28 22:56
Thank you very much for your answer. Could you give me your opinion about chosen angles values for ...

Rotating B4 by 180 degree is meaningless, because this results in exactly the same structure. Its stepsize should also be set to 120.

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