Posted by: Mark Foreman | February 4, 2014

Stereocentres

Dear Readers,

While some of you love stereochemistry I know that some of you are troubled by it, the diagrams on sheets of paper can be hard to see in 3D. I want to try and do something today to help you.

I suggest that you use the following to make a xyz file for ORTEP

8
XYZ file :   Halothane
C -0.687 -0.394 0.070
C 0.574 0.459 0.070
F -1.807 0.432 0.070
F -0.703 -1.197 -1.068
F -0.703 -1.198 1.206
Br 2.143 -0.698 0.070
Cl 0.596 1.495 -1.396
H 0.588 1.101 0.979

ORTEP can be downloaded and used for free for non commerical use from a very kind gentleman in Scotland named Louis Farrugia. In the tradition of crystalography he writes software for other crystalographers (and other people) and then he makes it avaiable for free to many people. This is a real deep and good service to the rest of the chemical community.

To use it you need to set some system variables in windows and then load the coordinates as XYZ files.

Now if you get the halothane coordinates into ORTEP (or some other viewing software) you can look at the arrangement of the atoms.

The key thing to do first is to work out which is the most heavy atom attached to the chiral centre, this is given the label 1, then the next heaviest is 2 etc etc until you do all four for a tetrahedral atom such as carbon.

What you also have to do is to rotate the molecule until the lightest atom is pointing away from you. For halothane here are four pictures taken as I turned it around. The bromine is brown, the chlorine is green and the fluorine is yellow/green.

First view of the molecule

First view of the molecule

Second view

Second view

Third view

Third view

Final view

Final view

You should see that the bromine is number 1, the chlorine is number 2 and the CF3 group is number 3. If you trace the path made by these atoms then it goes clockwise. Thus it is the R isomer.

You might want to try out some other files which I am showing below.

26

XYZ file : halogenated adamatane

C -3.965 -0.359 1.350
C -2.976 -0.544 0.187
C -4.872 -1.128 -1.348
C -5.872 -0.946 -0.193
C -3.660 -0.201 -1.148
C -4.142 1.260 -1.108
C -5.176 -1.285 1.136
C -5.139 1.455 0.049
C -6.342 0.519 -0.158
C -4.446 1.102 1.377
Br -7.403 -2.124 -0.455
Cl -2.498 -0.419 -2.500
I -5.806 3.497 0.096
F -3.341 -0.671 2.554
H -2.102 0.129 0.336
H -2.638 -1.604 0.161
H -4.526 -2.185 -1.372
H -5.373 -0.871 -2.308
H -3.268 1.932 -0.957
H -4.647 1.504 -2.069
H -5.896 -1.149 1.974
H -4.826 -2.341 1.105
H -7.062 0.654 0.680
H -6.835 0.767 -1.124
H -5.167 1.237 2.214
H -3.569 1.772 1.520

Here is another one a smaller molecule

5
XYZ file :   halon 1111
C 0 0 0
H 0.6 0.6 0.6
F 0.8 -0.8 -0.8
Cl -0.8 0.8 -0.8
Br -0.8 -0.8 0.8

And another one which is the other isomer of halon-1111

5
XYZ file :   halon 1111
C 0 0 0
H 0.6 0.6 0.6
F 0.8 -0.8 -0.8
Cl -0.8 -0.8 0.8
Br -0.8 0.8 -0.8

Well I hope that you have had fun with these molecules, my advice is “enjoy organic chemistry”.

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Responses

  1. Wait, clockwise makes the stereoisomer R (like rectus), not S.

    • Opps, I think I was typing too fast and pressed the wrong key. Thanks for spotting the error I am glad you are reading the blog.


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