Halide Substitution on Aryl Bromides/Chlorides

User fd4af72735

05-12-2011 18:50:04

I'm trying to write a reaction in Reactor for a substitution for aryl halides, but am having trouble when it comes to reactants which have two in the same molecule. For instance, my reactant list has:


Ar-I


Ar-Br


Ar-Cl


Br-Ar-Cl


 


Of course, I'd like to react the Br part of the last one, but I can't figure quite figure out how to affect the selectivity. Thoughts?


 


Thanks in advance for any help


Jim

ChemAxon d76e6e95eb

05-12-2011 21:04:03

There are various ways for that. Your rank the sites in the SELECTIVITY rule. For example, if your aromatic carbon is mapped to 1 and the halogen 2, you can list explicitly the functional group ranking list in a matchFirst function:


matchFirst(ratom(1), { "[c:1]Cl", "[c:1]Br", "[c:1]I" }, 1)

Alternatively, you can refer to a property of the atom, for example, any of these should work as well (the negative sign is needed to put the lowest value to the top of the ranking list):


atno(ratom(2))

polarizability(ratom(2))

charge(ratom(2))

-charge(ratom(1))


In case of comparing floating pont values like charge and polarizability, it is advised to set the tolerance as well, for instance to 0.001.

User fd4af72735

05-12-2011 21:24:20

Thanks for the reply. I'm not familiar with the matchFirst function. I tried a direct copy of the first line you wrote


 




matchFirst(ratom(1), { "[c:1]Cl", "[c:1]Br", "[c:1]I" }, 1)

 


 


with ratom(2) to match my scheme, and got the attached error. It looks like some sort of syntax problem, but not being familiar with matchFirst, I wasn't sure where to turn.


 


Thanks

ChemAxon d76e6e95eb

05-12-2011 21:26:39

Please attach the reaction file as well.

User fd4af72735

05-12-2011 21:34:04

Certainly. It's extremely simple.

ChemAxon d76e6e95eb

05-12-2011 21:53:19

I have made some minor polishing, using ratom(2) in the rule according to your mapping in the scheme, mapping the leaving boron and oxigen atoms (don't rely on automapping) and adding aromatic properties to the carbons. Please see it attached, it seems OK here.


Which jchem version are you using?

User fd4af72735

05-12-2011 22:11:42

Still got the error. Strange.


 


Assuming I'm looking in the appropriate location (the About tab in Instant JChem), 5.2.5.1

ChemAxon d76e6e95eb

05-12-2011 22:19:15

I use version 5.6, the matchFirst function is relatively new, try then another rule. I would choose the one with atno, it seems the quickest. Please notice, that you need to refer to the map number of the halogen atoms in the reactant.


atno(ratom(3))

User fd4af72735

05-12-2011 22:31:36

The atno rule works. Going through this exercise, I have a much better understanding of how the selectivity rules work. Thanks for your help.


 


I'll talk to IT about upgrading to the latest JChem version, too

ChemAxon d76e6e95eb

05-12-2011 22:39:19

I am glad that we have found a solution. Have a nice day.