# Why do amino acids hydrogen bond rather than ionic bond when they are forming secondary structures in proteins?

When peptide bonds are formed between amino acids, electron delocalisation causes the N to be more positive and the O to be more negative. As a result, why does 'hydrogen bonding' occur to form secondary structures such as alpha helices and beta pleated sheets, rather than 'ionic bonding'?

Is this simply a case of semantics, or is it the lack of transfer of an electron that makes the distinction between the two?

• This looks like a homework question. Perhaps you should look at the primary structure of polypetides before looking into the secondary structure. – VonBeche Oct 23 '16 at 18:38
• @D.J.Lawson please consider adding any relevant information to your question (which also shows that you did research to your question). As of now your query is likely to be closed/downvoted. – Ebbinghaus Oct 23 '16 at 18:58
• Why do you think there are ions here? – Zhe Oct 24 '16 at 13:49

For a proper ionic bond, you would need ions. However, the backbone of your peptide chain does not have ionic groups. While the resonance structure you drew is correct, note that it is only a resonance structure. It does a good job at explaining the lesser reactivity of an amide bond with respect to an ester or an acid chloride. And it also shows the partial negative charge of the oxygen. But nitrogen is not positively charged in an amide bond (it is slightly negatively charged). Thus, there is no positive counterion that your negative carbonyl oxygen could bond to.

A hydrogen bond is a very viable possibility, though. You may know that it requires three things:

• a hydrogen atom (check)

• bonded to an electronegative atom (typically $\ce{O, N, F}$ — check)

• and another electronegative atom that can receive (typically the same atoms — check)

So a hydrogen bond is possible where an ionic interaction is not.

Note that ionic interactions do happen in peptides. The side chains aspartate and glutamate are deprotonated (negatively charged) at ambient $\mathrm{pH}$ and the residues of lysine and arginine are positively charged. These can now form actual ionic interactions — although typically there will also be a significant hydrogen bonding component in these tertiary structure-creating bonds, too.

• So although the resonance structure depicts a positive charge on N, it retains its electronegative character and still has a partial negative charge? – D.J. Lawson Oct 24 '16 at 22:07
• @D.J.Lawson Yes. – Jan Oct 25 '16 at 13:10

(this should be a comment)
I think you are not quite understanding the concept of partial charged or charged. The N atom in the polypeptide chain (so the N in the peptide bond) is partially charged! to be in an ionic state it should have 4 bonds instead of 3.
The peptide bond which is formed(above) just contains a N atom which is bounded to three other atoms. The oxygen atom is also partially charged but not charged! read this about H-bonding and partial charge