I am trying to draw a structure of a polymer with a repeating unit of around 50-60 units, I am able to draw in ChemDraw ultra 12 and CheDraw18. The problem is that I am unable to get its 3D structure which I need to use for simulation. Any advice or suggestion is welcomed and appreciated. Thank you in advance.
which software are you using for simulation ?
chemdraw only draws 2D molecules, to draw 3D models you need another software. try Avogadro (its free) or ChemOffice suite they have a 3D software not sure what is its name.
anyhow, you can always draw 2D using ChemDraw export it as .mol format, then import to the software you are using.
To Oussama Kehireddine: Thank you for your reply. I am using ChemDraw 3D pro which is drawing molecules in 3D, however, when I draw the polymer (with n as repeating unit of 50-60 units), is not showing the 3D structure. I am using Gaussview 5.
If I have the structure in 2D and export it as .mol, then it is readable by Gaussview. I am afraid I am a novice in Gausse and in simulation in gneral.
I will check to see if this will work.
I am not sure if I can draw a polymer in its 3D in avogadro if the repating units are around 50-60 units. If Avogadros can do this, please confirm. Thank you for your effort and your advice.
Yeah, Avogadro does that
draw 2D of your polymer, save it as mol file and open it with avogadro, you will have your 3d view.
good luck
here are two polymers as mol files, i provide as examples try importing them to avogadro
they were created with ChemDraw 2D
@ Oussama: Thank you. It works, it shows the 3D in avogadro, now how I export to Gauss input of gif extension?
I figured it out. After having the mol imported to Avogadro, then we save it as mol2 extesion which then can be opened in Gaussview. Now it is still in 3D structure.
Thank you Oussama for your help.
You can export from Avogadro to one of the extension supported by Gauss, either
.gau
or
.gzmat
Adel Attia
you are welcome !
its was my pleasure helping you
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