N(delta)-acetyl... vs N(alpha)-acetyl

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


[N(alpha)-acetyl-ornithine](http://pubchem.ncbi.nlm.nih.gov/compound/907)


[N(delta)-acetyl-ornithine](http://pubchem.ncbi.nlm.nih.gov/compound/193343)


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?




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](https://pubchem.ncbi.nlm.nih.gov/compound/907#section=Identification) 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](https://pubchem.ncbi.nlm.nih.gov/compound/439232#section=Identification) 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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The difference does *not* lie in stereochemistry. Rather, *N*$^\alpha$-acetylornithine and *N*$^\delta$-acetylornithine are *regio*isomers 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](https://i.stack.imgur.com/zY4sd.png)


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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