[nox]

spirochete: the confusion arose because we weren't sure if the peptide bond is being talked about or just FREE amino acids (ie a SINGLE, individual, standalone amino acid with NO peptide bonds)

the original email it clearly asks whether FREE amino acids were conjugated:

...The definition of conjugation would be the extra
stabilization provided by 3 parallel, overlapping, adjacent p orbitals.  I was
wondering then, would free amino acids count as "conjugated" molecules?  Namely the
carbonyl oxygen p orbital, the carbonyl carbon p orbital, and the alpha amino nitrogen p
orbital?

Response:  No, because the amino nitrogen lone pair is not adjacent to the carbonyl.

and the response is indeed correct, because in a FREE amino acid the amino group is separated from the carboxyl group by an sp3 hybridized central carbon, so conjugation would not be possible

[spirochete]

spirochete: the confusion arose because we weren't sure if the peptide bond is being talked about or just FREE amino acids (ie a SINGLE, individual, standalone amino acid with NO peptide bonds)

the original email it clearly asks whether FREE amino acids were conjugated:

...The definition of conjugation would be the extra
stabilization provided by 3 parallel, overlapping, adjacent p orbitals.  I was
wondering then, would free amino acids count as "conjugated" molecules?  Namely the
carbonyl oxygen p orbital, the carbonyl carbon p orbital, and the alpha amino nitrogen p
orbital?

Response:  No, because the amino nitrogen lone pair is not adjacent to the carbonyl.

and the response is indeed correct, because in a FREE amino acid the amino group is separated from the carboxyl group by an sp3 hybridized central carbon, so conjugation would not be possible

Yes you're right I should have read the entire thread more carefully.  The professor is correct there's no resonance in the free amino acid between the N terminus and the C terminus.

The professor was correct in his email.

[johnj7]

oh wow,  no i'm very sorry
i actually confused myself... what i meant to ask my prof in my email was not about a free AA at all, but a dipeptide...

so basically this whole time i was just confusing myself because i accidentally put "free AA" in the email!
wow that sucks

thank you nox, and spirochete,

"This is really a question of semantics.  You already understand that there's resonance there. The question is does it qualify as conjugation." ... that was exactly my problem, except i made it even worse  because i asked about the "free AA" in the email!

so one last question
nox implied this, and spirochete you said...
"Note that this lone pair has to be in a P orbital to be delocalized through resonance"
so just to make sure, the nitrogen is sp2 hybridized, with that lone pair in a single P orbital,
and the nitrogen is not sp3 hybridized.

so basically, bottom line -- according to  my professors definition of 3 parallel, adjacent, p orbitals constituting conjugation, the a dipeptide would be considered "conjugated" as nox showed.  but probabaly according to a more advanced definition (comment about cumulation), its really not considered conjugation.

would that be correct?

[nox]

so one last question
nox implied this, and spirochete you said...
"Note that this lone pair has to be in a P orbital to be delocalized through resonance"
so just to make sure, the nitrogen is sp2 hybridized, with that lone pair in a single P orbital,
and the nitrogen is not sp3 hybridized.

correct, the nitrogen in a peptide bond is sp2 hybridized an the lone pair sits in a non-hybridized p-orbital

same goes for one of the lone pairs on oxygen in carboxylic acids and esters

so basically, bottom line -- according to  my professors definition of 3 parallel, adjacent, p orbitals constituting conjugation, the a dipeptide would be considered "conjugated" as nox showed.  but probabaly according to a more advanced definition (comment about cumulation), its really not considered conjugation.

would that be correct?

yep, something like that

I guess the more technically correct term for the case of the peptide bond would be "delocalized bonding" since the 4 pi electrons (2 from the C=O pi bond and 2 from the nitrogen lone pair) are spread out over 3 atoms