Should be able to do intramolecular bond breaking in reactions.

[acaly]

I'm using C++ interface.
Reaction: [O:4].[O:2]=[C:1][N:3]>>C:1[O:4].[N:3]
Reactants:
O
C1CCC(=O)NC1
Should give: NCCCCC(=O)O
But rdkit gives: CCCCC(=O)O + CCCCN

Also I want to know how to write a intra-molecule reaction in SMARTS. I tried
(C:1[OH].[N:3])>>[O:2]=[C:1][N:3] and succeeded. Is that right?

[greglandrum]

On Jul 3, 2013, at 3:53 PM, Wu Zhenwei notifications@github.com wrote:

I'm using C++ interface.
Reaction: [O:4].[O:2]=[C:1][N:3]>>C:1[O:4].[N:3]
Reactants:
O
C1CCC(=O)NC1
Should give: NCCCCC(=O)O
But rdkit gives: CCCCC(=O)O + CCCCN

Also I want to know how to write a intra-molecule reaction in SMARTS. I tried
(C:1[OH].[N:3])>>[O:2]=[C:1][N:3] and succeeded. Is that right?

The first C should be in square brackets, but otherwise that looks right to me.

[acaly]

Thanks for replying.
Oh that's a mistake. but rdkit still gives the wrong answer when i use
[O:2]=[C:1][N:3].[O:4]>>C:1[OH:4].[N:3]
as the reaction and C1CCC(=O)NC1 + O as the reactants:
CCCCC(=O)O + CCCCN.
I also tried [O:2]=[C:1][N:3].[O:4]>>(C:1[OH:4].[N:3]) which throws a exception when parsing.
so is there a way i can make the intro-molecule hydrolysis reaction working properly?

[greglandrum]

Problem 1:
You've got O:2 mapped in the reactants, but not in the products. This causes that atom to be removed when you run the reaction.

Problem 2:
You've told the code that you have two products, so you get two products. There's not currently a good way in reaction SMARTS to indicate that a bond is broken but that there may be one or more products.

[acaly]

I've checked my SMARTS this time. I think there's something wrong in the input box of github...
If there's no direct way, can I break the bond (firstly check if it's in a ring), add flags onto the two atoms and then use a rdkit reaction to change it to what i want?

[greglandrum]

On Thu, Jul 4, 2013 at 9:23 AM, Wu Zhenwei notifications@github.com wrote:

I've checked my SMARTS this time. I think there's something wrong in the
input box of github...
If there's no direct way, can I break the bond (firstly check if it's in a
ring), add flags onto the two atoms and then use a rdkit reaction to change
it to what i want?

re: text box
you might want to try either indenting the lines by four spaces or
surrounding them with triple quotes (''') so that github treats them as
code snippets.

For the intramolecular case: yes, you could find the bond using a
substructure search, break it (in an RWMol), and then add the O directly to
the RWMol. No need to use a reaction at all.

[greglandrum]

I'm changing the subject and marking this as an enhancement request: it should be possible to express intramolecular bond breaking reactions in reaction smarts.

One could imagine a syntax like this:
[O:2]=[C:1][N:3]>>([O:2]=[C:1]O.[N:3])

[acaly]

Thanks a lot.
My English is really poor

[NadineSchneider]

this was done in commit 8aac978