# Naming of asymmetric organic molecules with two nitroxides

When writing my diploma thesis I had to name my molecules following IUPAC nomenclature rules. There were several molecules like the following one, that contained two TEMPO groups, but were not symmetrical. The following is one example:

While I was able to find IUPAC recommendations on how to name radical organic molecules I could not find sufficient information for this case and ACD/Labs was no help either. I went ahead and replaced the two TEMPO groups with COOH, as this is a high ranking moiety, got a name for it and replaced the corresponding parts of the name with what I found (carboxy to ylooxy; carboxylic acid to oxidanyl) in the recommendations.

This was the name I came up with:

(4-(4'-((adamantan-1-yl)((1-ylooxy-2,2,6,6-tetramethylpiperidin-4-yl)carbamoyl)carbamoyl)-N-((adamantan-1-yl)carbamoyl)-[1,1'-biphenyl]-4-carboxamido)-2,2,6,6-tetramethylpiperidin-1-yl)oxidanyl

In the meantime, the results have been published but I always wondered, if this was correct. I checked on SciFinder (CAS No. 1947339-77-6) and an index name has still not yet been assigned.

Is there a more elegant way of finding a name for a molecule like this?

## 1 Answer

The structure can be redrawn somewhat more clearly:

Let's call the basic structure, where R1 = R2 = H, ‘the skeleton’.

If your name was, after fixing some enclosing parentheses to square or curly brackets, even the ‘preferred IUPAC name’, it's not a nice one, because it does not reflect the symmetry of the skeleton, and repeats the TEMPO and adamantane building block names.

(From now on, I'm gonna use the blockquote for IUPAC organic nomenclature rules 2013 generated names, or the book citations, if section name included.)

### "Almost preferred" IUPAC name, substituted carbamoyl biphenyl dicarboxamide

The skeleton is named

N4,N4′-dicarbamoyl[1,1′-biphenyl]-4,4′-dicarboxamide.

This preferred name is obviously based on the biphenyl dicarboxylic acid diamide

[1,1′-biphenyl]-4,4′-dicarboxamide

substituted with carbamoyl ($\ce{NH2-CO\bond{-}}$) groups at each nitrogen.

Simple monosubstituted derivatives of the skeleton (there are only two kinds of them initially) are named

N4,N4′-dicarbamoyl-N4-methyl[1,1′-biphenyl]-4,4′-dicarboxamide

and

N4-carbamoyl-N4′-(methylcarbamoyl)[1,1′-biphenyl]-4,4′-dicarboxamide.

R2 (“TEMPO-4-yl”) can be named,

2,2,6,6-tetramethyl-1-oxylpiperidine-4-yl (group)

according to the rules of making the radical to be prefix (e.g. when there is yet more prioritized radical):

P-71.5 Prefixes denoting radicals

(…)

Examples:

(…)

$\ce{-O^.}$

oxyl (preselected prefix)
ylooxidanyl
(not ylohydroxy)

(…)

P-71.7.d.1 (…)

(3-oxylbenzoyl)oxyl (PIN)
[3-(ylooxidanyl)benzoyl]oxidanyl

however the rules do not make a good distinction between residues (prefixes) and radicals.

So the resulting name would be
N4-(adamantan-1-yl)-N4′-[(adamantan-1-yl)carbamoyl]-N4′-(2,2,6,6-tetramethyl-1-oxylpiperidine-4-yl)-N4-[(2,2,6,6-tetramethyl-1-oxylpiperidine-4-yl)carbamoyl][1,1′-biphenyl]-4,4′-dicarboxamide. But it still redundantly repeats some building block names.

### Unfinished IUPAC name based on substituted "diallophanylated biphenyl"

P-66.1.6.1.1.4 Carboxylic acid derivatives of urea

Two carboxylic acids are related to urea; have been known as ‘allophanic acid’ for $\ce{H2N-CO—NH-COOH}$ and ‘hydantoic acid’ for $\ce{H2N-CO-NH-CH2-COOH}$. These names are no longer recommended. Preferred IUPAC names for these two acids and their derivatives are formed systematically.

Examples:

$\ce{H2N-CO—NH-COOH}$
carbamoylcarbamic acid (PIN)
(aminocarbonyl)carbamic acid

$\ce{H2N-CO—NH-CO\bond{-}}$
carbamoylcarbamoyl (preferred prefix)
[(aminocarbonyl)amino]carbonyl

The allophanoyl- prefix can be found in the older IUPAC 1979 nomenclature, rule C-971.

The skeleton could be named

• 4,4′-diallophanoyl[1,1′-biphenyl], or
• 4,4′-bis(carbamoylcarbamoyl)[1,1′-biphenyl],

if you want.

But now we would have to repeat the two differently substituted allophanoyls in the name. Or derive a name from the symmetrical one, but how to number it?

### Urea based IUPAC name

Closer look at your structure reveals that it in fact is two N,N′ asymmetrically substituted urea

P-66.1.6.1.1 Urea and its substitutive derivatives

P-66.1.6.1.1.1 The compound $\ce{H2N-CO-NH2}$ has the retained named ‘urea’, Which is the preferred IUPAC name, With locants N and N′, as shown above the structure below. The systematic name is ‘carbonic diamide’. The locants 1, 2, and 3 have been used in the past and may be used in general nomenclature.

$$\begin{array}{ccc} \ce{H2\overset{N}{\underset{1}{N}}-\underset{2}{C}O-\overset{N'}{\underset{3}{N}}H2} & \hskip{3em} & \ce{H2\overset{N}{N}-CO-\overset{N'}{N}H2} \\ \text{urea (PIN)} & & \text{carbonic diamide} \end{array}$$

$$\bbox[0.5em,border:1px solid black]{\text{Numerical locants for urea are no longer used in the IUPAC preferred names.}}$$

molecules, N,the-other-one's-N′-interconnected with

[1,1′-biphenyl]-4,4′-diyldicarbonyl (group).

And that's a correct name, used e.g. in

2,2′-([1,1′-biphenyl]-4,4′-diyldicarbonyl)dipropanoic acid.

(If these propanoic acids were interconnected by different carbons, 2,3′ (there's no other option), such multiplicative name would be no longer a preferred one; see e.g. P-15.3.2.1.1. But never mind, we're making a nice one.)

The skeleton now can be named ([1,1′-biphenyl]-4,4′-diyldicarbonyl)diurea. (More precisely N,N′-([1,1′-biphenyl]-4,4′-diyldicarbonyl)diurea. Or N,N′′-…? And what about such multiplicative names of asymmetrical derivatives? There's no definitive answer, but this would be for another question.)

So we'll use the other urea numbering, the numerical, non-preferred one.

Now we get a nice name:
1,3′-([1,1′-biphenyl]-4,4′-diyldicarbonyl)bis[1-(adamantan-1-yl)-3-(2,2,6,6-tetramethyl-1-oxylpiperidine-4-yl)urea]

(But I would like similarly short and non-redundant name that would end like “…bis[(2,2,6,6-tetramethylpiperidin-1-yl)oxidanyl]” yet more.)

• This is a very comprehensive answer. I really like the concise urea name, as we described the products as urea derivatives. I'd just like to point out that the correct name of the oxygen-radicals (according to IUPAC RC-81.3.3.1) is supposed to be ylooxy. Generally, the prefix ylo should be used for radical bearing groups. See the following document for further reading: sbcs.qmul.ac.uk/iupac/ions/RC813.html#p331 – basseur Aug 13 '18 at 18:57
• @basseur Please note that I was mentioning that we are making the radical subtituent to be named by prefix. I have updated the 2013 rules citation with the example containing the "oxyl" preselected prefix (P-71,5). (I did not track consistency with previous version 1993 rules you linked.) – mykhal Aug 14 '18 at 9:16