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getting the center of mass of each part of a molecule


On Monday, May 15, 2017 at 1:30:05 PM UTC-7, qasi... at gmail.com wrote:
> Hi,
> 
> I need to get the center of mass (COM) of each half of the ligand shown in the figure (https://i.stack.imgur.com/dtdul.png). I get the main COM all the ligand, lets say it is close to C1 atom. ...

I don't quite follow your terminology.  A ligand is typically something that hangs onto  something - usually a metal atom or some other larger molecule.

It looks like you want the center of mass of the styrene molecule.  Why not consider it as a benzene ring (C6H6) with the vinyl group (CH2CH) as a ligand?  

The benzene group will have its c.o.m. in the middle of the ring, by symmetry.  Make this the origin.  

The vinyl group's c.o.m can be calculated by the methods given in
http://hyperphysics.phy-astr.gsu.edu/hbase/cm.html

Then you can find the c.o.m of the whole molecule by considering it as two masses in a specific geometry.  This seems like the point of the exercise.

What may make this tricky is that the vinyl group can rotate at the point where it attaches to the benzene ring so the full molecule may not lie in a plane.