[McSquared]

Hi all!

My text book states that a hydrogen bond is just an electromagnetic attractive interaction between two polar groups. Based on this you'd think that hydrogen bonding could occur in any kind of situation where you have polar groups, such as in a dipeptide. However, my teacher insists that there is no hydrogen bond in a dipeptide. He may very well be right, but based on the information in our text book, I don't see any reason why hydrogen bonding couldn't occur within a dipeptide.

 I mean, there is a negatively charged oxygen atom (in the -CO group) and a positively charged hydrogen atom (in the -NH group), so why wouldn't there be a hydrogen bond between the two, if a hydrogen bond is just an electromagnetic attractive interaction?

Any input will be greatly appreciated!

[Babcock_Hall]

A drawing would be helpful.  I never seen hydrogen bonding described as an electromagnetic attraction.  Also, one needs to differentiate between full positive charges attracting full negative charges (ionic attraction) and other kinds of attraction.

Hydrogen bonding can occur between groups that are ionic and also groups that are formally neutral.  It can be intramolecular or intermolecular.  Long polypeptide chains (proteins made of hundreds of amino acids) clearly do have intramolecular hydrogen bonds helping to hold them together.  A dipeptide might or might not, depending on which side chains are present and any geometrical constraints.

[McSquared]

Thanks for the quick response!

Yeah, I thought that was pretty strange way to put it. But anyways, a hydrogen bond is an electric attraction, if I'm not mistaken.

Sorry for being unclear. What I meant to say was if it's possible for a hydrogen bond to be present within a dipeptide under any circumstances. My teacher says that there are no hydrogen bonds in dipeptides, regardless of the amino acids involved. He's saying that (out of peptides) only helical polypeptide chains can have hydrogen bonds.

This was a question in an exam. The amino acids involved were not specified, so I guess it's about whether or not it's possible at all, under any circumstances.

[Arkcon]

I would not expect intermolecular bonds to form in a dipeptide.  I wight expect intramolecular bonds to form, and perhaps your book is referencing that.  Try to draw one out, for yourself, as Babcock_Hall: has suggested.  Draw a dipeptide, pick any two side chains as you think would be best, then draw the hydrogen bond between the two side chains.  That would be an intermolecular hydrogen bond.  Maybe a hydrogen bond would form with this peptide and another molecule, but that's not what you seem to be asking in your question.

[McSquared]

Thanks for the response, Arkcon!

What I'm asking here is whether or not there is a reason why a hydrogen bond could not be formed within a dipeptide, given that the there are polar groups present which would form a hydrogen bond in a helical polypeptide.

 My point of view is that if there are polar groups in neighboring amino acids in a dipeptide, there should be no reason why a hydrogen bond would not be formed. When I asked my teacher about this, he did not give a clear answer as to why there wouldn't be a hydrogen bond.

 He kept saying that hydrogen bonds can only be formed between polar groups in helical polypeptides. The thing that's confusing me with this explanation is the fact that according to him, the same polar groups that he's saying would not form hydrogen bonds in a dipeptide, would do so in a helical polypeptide. To my understanding the position of a charged atom in relation to another charged atom will not effect the existence of the attraction, only the its strength. What I mean is that if it is established that certain groups form a hydrogen bond, they will do so regardless of their positions in relation to one another (as long as the distance between them is roughly the same, the bond would of course be negligible if the distance was great enough.) But I don't exactly understand why it'd make any difference if the atoms in question were in neighboring amino acids in a dipeptide, or in "opposite" amino acids in a helical polypeptide. ( With "opposite" amino acids I refer to the amino acids that are opposite to each other in a helical structure)

And again, thanks for the responses, I really appreciate you helping me out!

[Babcock_Hall]

In the alpha helix, the residues that form the H-bonds are not adjacent in the sequence.  For example, the carbonyl oxygen of residue 1 accepts a H-bond from the N-H group of residue 5 in this drawing:  http://chemwiki.ucdavis.edu/Biological_Chemistry/Proteins/Protein_Structure

[Arkcon]

In a dipeptide, the hydrogen bonding groups are unlikely to be close enough.  Draw it and see.

[fledarmus]

Build models! For you to form an intermolecular hydrogen bond, you will need to have a geometry such that one hydrogen attached to either a nitrogen or oxygen would be able to interact with the lone pair of another nitrogen or oxygen without moving in space. if you can come up with such a structure, post it.

Usually when you make a dipeptide, the most stable rotamer of the molecule has the side chains going off in opposite directions from the backbone. Your geometry would have to be pretty good and your hydrogen bond pretty strong to that tendency.