atom naming for NMR assignments

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atom naming for NMR assignments

Eiso AB
hi,

I'm looking for some convenient standard atom naming scheme that I
could use for assigning (1H) NMR resonances on a large set of compounds.

Preferably, atoms that are topologically similar and/or are chemically
and or magnetically equivalent would have similar names (or root names),
for example the protons of a single methylgroup, equivalent protons
of rotating aromatic groups (like PHE/TYR HD/HE).

My initial thoughts run in this direction:

* generate cansmi (to be independent of how the input format is specified)

* name heavy atoms numerically or alphabetically following the smiles string or
   molecular tree from the start, preferably taking symmetries in the molecule
   into account (but how?).

* name the hydrogens after the attached heavyatom.

First and last point are trivial I guess, but the middle point seems to
be quite tricky. I'm probably not the first with this problem, so if anyone
knows software that does something similar or has suggestions how to approach
this, I would be very grateful.

kind regards - Eiso










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Re: atom naming for NMR assignments

Craig James-2
On 8/16/10 7:39 AM, eiso wrote:

> hi,
>
> I'm looking for some convenient standard atom naming scheme that I
> could use for assigning (1H) NMR resonances on a large set of compounds.
>
> Preferably, atoms that are topologically similar and/or are chemically
> and or magnetically equivalent would have similar names (or root names),
> for example the protons of a single methylgroup, equivalent protons
> of rotating aromatic groups (like PHE/TYR HD/HE).
>
> My initial thoughts run in this direction:
>
> * generate cansmi (to be independent of how the input format is specified)
>
> * name heavy atoms numerically or alphabetically following the smiles string or
>     molecular tree from the start, preferably taking symmetries in the molecule
>     into account (but how?).

When you generate a canonical SMILES, a string is created that lists the atoms' order in that SMILES.  The relevant code in smilesformat.cpp is this:

     if (canonical && !mol.HasData("Canonical Atom Order")) {
       OBPairData *canData = new OBPairData;
       canData->SetAttribute("Canonical Atom Order");
       canData->SetValue(m2s.GetOutputOrder());
       mol.SetData(canData);
     }

It is a space-separated string with the atom->GetIdx() value of each atom in canonical order.

> First and last point are trivial I guess, but the middle point seems to
> be quite tricky. I'm probably not the first with this problem, so if anyone
> knows software that does something similar or has suggestions how to approach
> this, I would be very grateful.

I hope this is what you are looking for.

Craig

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