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Question:

I didn’t get the right geometry for phosphine (PCl5)after drawing it;. I got a flat molecule whereas the geometry is known to be bipiramidal. How can I get the correct geometry?

Answer:

While transferring the 2D information (i.e 2D ChemDraw structure information) to 3D, the 3D model of the structure generated based on defined atoms in Chem3D application (Atom types in the Parameter Tables). When it does not find one, it guesses and uses the closest one. So you have to check the missing element in the Chem3D application. The following links provide you some information regarding this.

http://www.cambridgesoft.com/support/DesktopSupport/KnowledgeBase/FAQ/details/Default.aspx?TechNote=581

http://www.cambridgesoft.com/support/DesktopSupport/KnowledgeBase/FAQ/details/Default.aspx?TechNote=397


Created on: 12/7/2017