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Stereochemistry ambiguity
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bobgr

Joined: 15 Jun 2004
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Link to postPosted: Mon Nov 15, 2004 8:26 pmPost subject: Stereochemistry ambiguity Reply with quote

Some of my students have been drawing structures in which there is a stereogenic C with one hashed or bold bond (indicating one configuration) and one squiggly bond (indicating two). It seems to me that the best way to handle such an ambiguity would be to underline the ambiguous C in red, as when the valence is incorrect. What do you think?

Here's an example of what they're doing:

Code:

<?xml version="1.0"?>
<MDocument>
  <MChemicalStruct>
    <molecule molID="m1">
      <atomArray
          atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9"
          elementType="C C C C C C C C O"
          x2="-5.133333206176758 -6.379199535193786 -5.903337117806563 -4.363329294546951 -3.88746687715973 -7.843832095766219 -6.62013411264671 -2.4228343165872976 -2.798529464975217"
          y2="2.243325592084533 1.3381089935725328 -0.12643844634735846 -0.12643844634735846 1.3381089935725328 1.8139781589016584 2.859144998862211 1.8139781589016593 0.24915751974787437"
          />
      <bondArray>
        <bond atomRefs2="a1 a2" order="1" />
        <bond atomRefs2="a1 a5" order="1" />
        <bond atomRefs2="a2 a3" order="1" />
        <bond atomRefs2="a3 a4" order="1" />
        <bond atomRefs2="a4 a5" order="1" />
        <bond atomRefs2="a2 a6" order="1" />
        <bond atomRefs2="a2 a7" order="1" />
        <bond atomRefs2="a5 a8" order="1">
          <bondStereo>H</bondStereo>
        </bond>
        <bond atomRefs2="a5 a9" order="1">
          <bondStereo convention="MDL" conventionValue="4" />
        </bond>
      </bondArray>
    </molecule>
  </MChemicalStruct>
</MDocument>
volfi
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Link to postPosted: Mon Nov 15, 2004 10:36 pmPost subject: Stereochemistry ambiguity Reply with quote

We can write a function in MolAtom which could check this.
isAmbiguousParity
If the atom has squiggly bond and an other hashed or bold bond starting from this atom then this function would return false.

I have to think about it because the graph invariants are also needed for this function. We need to check if the atom ligands' graph invariants are different.
bobgr

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Link to postPosted: Tue Nov 16, 2004 3:14 pmPost subject: Re: Stereochemistry ambiguity Reply with quote

volfi wrote:
We can write a function in MolAtom which could check this.
isAmbiguousParity
If the atom has squiggly bond and an other hashed or bold bond starting from this atom then this function would return false.

I have to think about it because the graph invariants are also needed for this function. We need to check if the atom ligands' graph invariants are different.
I do think the best way to handle it is at the MarvinSketch level, as incorrect valences are handled, rather than sending it to JChem to analyze. Alert the user to the "nonsense" of his representation before he even submits, just like you alert him to a pentavalent C.
volfi
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Link to postPosted: Tue Nov 16, 2004 7:09 pmPost subject: Re: Stereochemistry ambiguity Reply with quote

Quote:

I do think the best way to handle it is at the MarvinSketch level, as incorrect valences are handled, rather than sending it to JChem to analyze. Alert the user to the "nonsense" of his representation before he even submits, just like you alert him to a pentavalent C.
Yes sure!
It would be as you suggested. The skecther would recognize the problem.
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