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Can anyone tell me what the difference between these two compounds is:

N(alpha)-acetyl-ornithine

N(delta)-acetyl-ornithine

The only difference I can think of is the chiral properties of the nitrogen atom, i.e. nitrogen inversion.

If that is the case, does it make sense to differ between these to compounds, or will they be constantly interconverted?

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  • $\begingroup$ Welcome to chemistry.SE! If you had any questions about the policies of our community, you can ‎visit the help center or take a ‎‎tour of the website.‎ $\endgroup$ – M.A.R. Jun 11 '15 at 11:53
  • $\begingroup$ You did not link to *N*$^\delta$-acetylornithine but rather to a nonsymmetric version of *N*$^\alpha$-acetylornithine. I corrected your link (but it still needs to be peer reviewed). $\endgroup$ – Jan Jun 11 '15 at 12:39
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    $\begingroup$ Jan, "correcting" the link in a question like this changing the author's intent for the question. The link as it currently exists does list "N(delta)-acetylornithine" as a MeSH descriptor synonym for some weird reason. You should add the link to the right N(delta)-acetylornithine to your answer. BTW, how did you find that molecule? It did a pubchem structure search but it came up empty. $\endgroup$ – Curt F. Jun 11 '15 at 12:51
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    $\begingroup$ @CurtF. a search for acetylornithine did the trick. $\endgroup$ – Jan Jun 11 '15 at 13:19
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    $\begingroup$ Jan's edit has now been approved and as a result the accepted answer to the question (mine) now no longer makes any sense. The question originally linked to a Pubchem page which listed N(delta)-acetylornithine as a synonym for a structure that was not actually N(delta)-acetylornithine. That actually seems to have been the confusion experienced by the OP and it was what I tried to address in my question. With the link altered to point to the correct structure for N(delta)-acetylornithine, none of this is clear. $\endgroup$ – Curt F. Jun 11 '15 at 14:06
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Short answer: PubChem has an error.

Differences in structures as currently listed in PubChem

One other important difference is the stereochemistry of the sp3 carbon attached to the nitrogen atom, i.e., at carbon 2 of the 5-aminopetanoic acid chain.

  • N(alpha)-acetyl-ornithine has a computed IUPAC name in PubChem of 2-acetamido-5-aminopentanoic acid. The stereochemistry is not listed, which leads me to assume that it is a racemate.

  • The molecule/PubChem page that you called N(delta)-acetyl-ornithine has a computed IUPAC name in PubChem of (2S)-2-acetamido-5-aminopentanoic acid. The stereochemistry at the sp3 carbon bound to the nitrogen in this compound is clearly listed as S.

Inconsistencies between the structures and the names

  1. Confusingly, both compounds are called L-ornithines on those pubchem pages. But since carbon 2 is the α carbon, this is the position that should determine the L or D stereochemistry. Thus, I'm not sure why N(α)-acetyl-ornithine isn't just called N-acetyl-DL-ornithine and what you called "N(δ)-acetyl-ornithine" isn't just called N(α)-acetyl-L-ornithine.

  2. Secondly, there is the matter that the page you linked for "N(delta)-acetylornithine" lists a "main" name for the molecule of "N-acetylornithine" and "MESH descriptors" of "delta-N-acetylornithine". This use of "delta" is wrong because it is inconsistent with the listed structure. The α, β, γ, δ nomenclature exists to indicate which nitrogen atom is substituted. In ornithine carbons 2 and 5 of the core pentanoic acid chain have nitrogen atoms, these correspond to N(α) and N(δ). Thus, N(δ)-acetyl-L-ornithine should have the acetyl group substituting a different nitrogen atom than N(α)-acetyl-L-ornithine.

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    $\begingroup$ Thank you very much! Apparantly, I was confused by the inconsistency between the listed structure and the use of delta-N-acetylornithine as a MESH descriptor. $\endgroup$ – Anders Abildgaard Jun 11 '15 at 13:56
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    $\begingroup$ I should note that this answer addresses a previous version of the question, where the links to PubChem molecule pages were the ones provided by the OP, not by editors to the question. $\endgroup$ – Curt F. Jun 11 '15 at 14:07
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The difference does not lie in stereochemistry. Rather, N$^\alpha$-acetylornithine and N$^\delta$-acetylornithine are regioisomers of one another.

The superscript Greek letter denotes which nitrogen is substituted with an acetyl group. The lettering is relative to the carboxyl group as shown in the image below:

ornithine with Greek-letter labelled carbons

Note that:

  • The carboxyl group’s carbon does not get the $\alpha$, because it is considered part as the functional group from with the labelling begins

  • The $\alpha$ carbon is asymmetric. Both L- and D-compounds (or (S) and (R) according to CIP nomenclature) are possible for both N$^\alpha$- and N$^\delta$-acetylornithine.

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    $\begingroup$ This is a good answer, especially since Jan edited the original question. As a result of the edit, this answer now makes more sense than my own, but I'm not sure which version of the question (and answer) was more helpful to the OP. $\endgroup$ – Curt F. Jun 11 '15 at 14:10

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