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OK. I'm working in computational chemistry and the problem that bothers me is:

Given a molecule, I know that it has a central asymmetric atom with some parity which is either "Anticlockwise" or "AntiAntiClockwise" (or a really stupid way to say clockwise). I have the molecule drawn on a 2D canvas (they are in one plane).

For this example you could imagine 4 atoms. I have to specify which atoms lie in a different plane (3D perspective) and I can't seem to understand why is the parity important in that case? I'm using the SMILES O[C@@](F)(Cl)Br notation.

enter image description here

I'm really confused about this concept and it seems like the internet doesn't offer me a lot of information about it. So please tell me how is parity related to the plane the atom lies in? How can I map the edges and dashes to the SMILES of this structure?

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  • $\begingroup$ Maybe you should be more specific. What molecule is it? 4 total atoms or the central atom plus 4 more? $\endgroup$
    – DavePhD
    Commented Dec 15, 2014 at 16:01
  • $\begingroup$ @DavePhD a total of 4 atoms. $\endgroup$
    – Christo S. Christov
    Commented Dec 15, 2014 at 16:02
  • $\begingroup$ I really would like to be more specific but I have no idea how to explain this to myself. $\endgroup$
    – Christo S. Christov
    Commented Dec 15, 2014 at 16:03
  • $\begingroup$ so a central atom with 3 other atoms at vertices of equilateral triangle approximately? $\endgroup$
    – DavePhD
    Commented Dec 15, 2014 at 16:04
  • $\begingroup$ @DavePhD I hope this edit will help you udnerstand the problem $\endgroup$
    – Christo S. Christov
    Commented Dec 15, 2014 at 16:10

3 Answers 3

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This is really a cheminformatics problem. It's a reflection of the chirality or atomic stereochemistry about the atom you mention.

There are multiple ways of specifying chiral information in 2D and 3D.

As mentioned by Dave SMILES uses a clockwise and counter-clockwise from left to right in the string.

In 2D, we usually use wedge and hash notation. The problem is that some users use wedges and hashes for graphical appearance and not for stereochemical information (e.g., pseudo-3D look). So file formats also add atom parity to indicate the actual stereochemistry of atoms.

The "parity" idea has to do with the relationship between the atoms as they are ordered in the file, vs. the stereochemistry around the central atom. As indicated in the other answer, these are enantiomers, even though they use the same "@@" SMILES stereochemical indicator:

  • $\ce{O[C$@@$](F)(Cl)Br}$
  • $\ce{O[C$@@$](F)(Br)Cl}$

Note that the atom ordering is different, so the "parity" will be different. For your example, $\ce{O[C$@@$](F)(Cl)Br}$ I get "1" for the MDL parity.

From the MDL specification (Appendix A: Stereo Notes):

Number the atoms surrounding the stereo center with 1, 2, 3, and 4 in order of increasing atom number (position in the atom block) (a hydrogen atom should be considered the highest numbered atom, in this case atom 4). View the center from a position such that the bond connecting the highest-numbered atom (4) projects behind the plane formed by atoms 1, 2, and 3.

Sighting towards atom number 4 through the plane (123), you see that the three remaining atoms can be arranged in either a clockwise or counterclockwise direction in ascending numerical order.

enter image description here

For more details, you might want to look at the Open Babel documentation, OpenSMILES or the MDL specification.

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  • $\begingroup$ This anwser seems a lot better than mine. I only know about chirality, not parity. I could only think of gerade and ungerade. $\endgroup$
    – DavePhD
    Commented Dec 15, 2014 at 19:07
  • $\begingroup$ Definitely keep yours - it's short, succint, and correct. Anyone who wants the full-winded explanation can read mine. The main problem is that there are umpteen ways to specify chirality in 0D or 2D chemistry formats and people keep inventing new ones. :-) $\endgroup$
    – Geoff Hutchison
    Commented Dec 15, 2014 at 19:13
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In SMILES notation, the order of the remaining three atoms corresponds to clockwise order when viewed in the direction looking from the first listed atom toward the carbon center.

So you have written $\ce{O[C@@](F)(Cl)Br}$. Looking in the direction from the O atom toward the C atom, the clockwise order of the remaining atoms is F, Cl, Br.

You could write the other enantiomer as $\ce{O[C@@](F)(Br)Cl}$.

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The molecule is not 2 dimensional, it is 3 dimensional, in this case tetrahedral. Since the vertexes have different CI priorities, the molecule will spin one way in space, this is visualized by placing the lowest priority atom in the back and assigning priorities to the remaining. This spin causes rotation of polarized light and other effects. If you are familiar with chirality, which is an extension of Group Theory, it would seem to answer the questions you are having, unless I totally misunderstood what it is you are asking.

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