Dear Andrew,

You can find an chemical example there:

https://books.google.ch/books?id=IZInzn8Rsp8C&pg=PA49&lpg=PA49&dq=stereochemistry+sulfinamide+%5BS@@%5D&source=bl&ots=7AD1hUe0PJ&sig=037kY78v-qG6WRtSL6yJc-pCHn4&hl=fr&sa=X&ved=0ahUKEwiPv4aRuujKAhVHSBQKHTYDB7wQ6AEIHjAA#v=onepage&q=stereochemistry%20sulfinamide%20%5BS%40%40%5D&f=false


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Dr. Guillaume GODIN
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________________________________________
De : Andrew Dalke <da...@dalkescientific.com>
Envoyé : lundi 8 février 2016 16:05
À : rdkit-discuss@lists.sourceforge.net Discuss
Objet : [Rdkit-discuss] stereochemistry of S with degree 3

Hi!

  Could someone explain to this non-chemist what the chirality means in the 
following?

  CN[S@@](=O)C1=CC=CC=C1

It comes from PubChem id 12194260 at 
https://pubchem.ncbi.nlm.nih.gov/compound/12194260 .

Isn't this a symmetric structure, which can't have an orientation at that 
point? Even if it can have a chirality, which sort of chirality is it? The list 
at http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html says:

  Tetrahedral is the default class for degree four
  Allene-like is the default class for degree 2
  Square-planar is another class for degree four
  Trigonal-bipyramidal is the default class for degree five
  Octahedral is the default class for degree six

but says nothing about degree three. And RDKit agrees that this is degree 3:

  >>> mol = Chem.MolFromSmiles("CN[S@@](=O)C1=CC=CC=C1")
  >>> mol.GetAtomWithIdx(2).GetDegree()
  3


This came up while testing my algorithm to fragment a structure. I expect to 
get the same structure back.

I started with:

  >>> Chem.CanonSmiles("CN[S@@](=O)C1=CC=CC=C1")
  'CN[S@@](=O)c1ccccc1'

The fragmentation produces:

  >>> Chem.CanonSmiles("C*.N*.*[S@@](=O)C1=CC=CC=C1")
  '[*]C.[*]N.[*][S@@](=O)c1ccccc1'

I can manipulate this at the SMILES level to insert two closures and produce 
the reconnect-able SMILES

    C2.N23.[S@@]3(=O)C1=CC=CC=C1
     ^--^
         ^------^

When I process that, I get a flipped chirality:

  >>> Chem.CanonSmiles("C2.N23.[S@@]3(=O)C1=CC=CC=C1")
  'CN[S@](=O)c1ccccc1'

I did not expect this. The Daylight SMILES spec says:

  The chiral order of the ring closure bond is implied by the
  lexical order that the ring closure digit appears on the
  chiral atom (not in the lexical order of the "substituent" atom).

I expected the '*' of '*[S**]' and the '3' of '[S**]3' to have the same bond 
position so give the same chirality.

Finally, if I replace the '[S@@]' with a '[C@@]' or '[P@@]' I lose the 
chirality:

  >>> Chem.CanonSmiles("CN[C@@](=O)C1=CC=CC=C1")
  'CNC(=O)c1ccccc1'
  >>> Chem.CanonSmiles("CN[P@@](=O)C1=CC=CC=C1")
  'CN[P](=O)c1ccccc1'


At this point I can't tell if there's a problem with how I understand 
stereochemistry, how I understand SMILES, or how I understand RDKit.



                                Andrew
                                da...@dalkescientific.com



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