removing salts changes the structure and add bonds to heterocyclic compounds with nitrogen...

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removing salts changes the structure and add bonds to heterocyclic compounds with nitrogen...

e_vikeved
I use babel to remove salts from smiles and I have encountered that babel changes heterocyclic compounds with nitrogens, see example below.
Does anyone have any suggestions why this might happen?

input: C[C@H](CN1CCC(CC1)N2C(=O)Nc3cc(Cl)ccc23)NC(=O)c4cc5ccccc5[nH]4.OC(=O)C(F)(F)F

command: obabel -ismi file_in.smi -r -osmi -O file_out.smi

output: C[C@H](CN1CCC(CC1)n1c(=O)[nH]c2cc(Cl)ccc12)NC(=O)c1cc2ccccc2[nH]1

thanks!

Elisabet
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Re: removing salts changes the structure and add bonds to heterocyclic compounds with nitrogen...

Geoff Hutchison
I use babel to remove salts from smiles and I have encountered that babel
changes heterocyclic compounds with nitrogens, see example below.

This will trigger aromaticity perception, but the structure is unchanged.

input:
C[C@H](CN1CCC(CC1)N2C(=O)Nc3cc(Cl)ccc23)NC(=O)c4cc5ccccc5[nH]4.OC(=O)C(F)(F)F
vs.
output: C[C@H](CN1CCC(CC1)n1c(=O)[nH]c2cc(Cl)ccc12)NC(=O)c1cc2ccccc2[nH]1

If I depict these, e.g.
<a href="https://cactus.nci.nih.gov/chemical/structure/C[C@H](CN1CCC(CC1)N2C(=O)Nc3cc(Cl)ccc23)NC(=O)c4cc5ccccc5[nH]4.OC(=O)C(F)(F)F/image" class="">https://cactus.nci.nih.gov/chemical/structure/C%5BC@H%5D(CN1CCC(CC1)N2C(=O)Nc3cc(Cl)ccc23)NC(=O)c4cc5ccccc5%5BnH%5D4.OC(=O)C(F)(F)F/image
<a href="https://cactus.nci.nih.gov/chemical/structure/C[C@H](CN1CCC(CC1)n1c(=O)[nH]c2cc(Cl)ccc12)NC(=O)c1cc2ccccc2[nH]1/image" class="">https://cactus.nci.nih.gov/chemical/structure/C%5BC@H%5D(CN1CCC(CC1)n1c(=O)%5BnH%5Dc2cc(Cl)ccc12)NC(=O)c1cc2ccccc2%5BnH%5D1/image

There is no difference. What's happened is that in the Open Babel aromaticity model, the [nH]c(=O)n motif is aromatic. In your input, it's marked as aliphatic.

The bond orders are otherwise identical. What bonds are added?

-Geoff

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Re: removing salts changes the structure and add bonds to heterocyclic compounds with nitrogen...

Noel O'Boyle
Administrator
I note in passing that the development code has an option to preserve
the aromaticity as read in SMILES, but Geoff's point stands that the
structures are identicial and should be read identically by any
toolkit.

- Noel

On 7 June 2017 at 04:16, Geoffrey Hutchison <[hidden email]> wrote:

> I use babel to remove salts from smiles and I have encountered that babel
> changes heterocyclic compounds with nitrogens, see example below.
>
>
> This will trigger aromaticity perception, but the structure is unchanged.
>
> input:
> C[C@H](CN1CCC(CC1)N2C(=O)Nc3cc(Cl)ccc23)NC(=O)c4cc5ccccc5[nH]4.OC(=O)C(F)(F)F
>
> vs.
>
> output: C[C@H](CN1CCC(CC1)n1c(=O)[nH]c2cc(Cl)ccc12)NC(=O)c1cc2ccccc2[nH]1
>
>
> If I depict these, e.g.
> https://cactus.nci.nih.gov/chemical/structure/C%5BC@H%5D(CN1CCC(CC1)N2C(=O)Nc3cc(Cl)ccc23)NC(=O)c4cc5ccccc5%5BnH%5D4.OC(=O)C(F)(F)F/image
> https://cactus.nci.nih.gov/chemical/structure/C%5BC@H%5D(CN1CCC(CC1)n1c(=O)%5BnH%5Dc2cc(Cl)ccc12)NC(=O)c1cc2ccccc2%5BnH%5D1/image
>
> There is no difference. What's happened is that in the Open Babel
> aromaticity model, the [nH]c(=O)n motif is aromatic. In your input, it's
> marked as aliphatic.
>
> The bond orders are otherwise identical. What bonds are added?
>
> -Geoff
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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