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Hydrogen bonds and resonance forms

Dear Reader,

My writing about organic solids has brought me onto the topic of hydrogen bonding; the hydrogen bond is a very important interaction between molecules or within a molecule. It is an interaction without which life as we know it would be impossible.

If we consider the boiling points of p block hydrides and other typical p block substances (such as CO2, CO and SiCl4) then it will be clear that water and hydrogen fluoride are abnormal. Almost which ever way we plot a graph of boiling point against something else these two compounds then the water and hydrogen fluoride (HF) come at a funny part of the graph. When we add some straight chain alcohols to the graph then this problem becomes clearer, the higher boiling points are associated with OH groups.

Boiling point vs molecular mass

You might ask what is special about an OH group, apart from the fact that if you write it the other way around it looks like the word which Santa keeps saying (Ho Ho Ho) at Christmas time.

The answer is that the important thing is that a hydrogen is bonded to an electronegative atom (oxygen) which also bears lone pairs. The electronegative nature of the oxygen induces a partial positive charge on the hydrogen atom.

Rather than these lone pairs being sigma bonds which go to nowhere the lone pairs can latch onto a hydrogen with a partial positive charge and then form a sigma bond. Thus we have a hydrogen bond.

The ability to form hydrogen bonds often increases the boiling point of a substance and makes it more soluble in water. Now rather than trying to hunt for hydrogen bonds by making measurements of boiling points or solubility. I know a better one, X-ray crystallography. Years ago I worked as a final year undergraduate for Henry Rzepa (He is still at Imperial College in London). I worked on a project associated with hydrogen bonding, in the project I had to make and crystallise a series of compounds which were related to an acetylene alcohol which had a rare hydrogen bond in its crystals.

One of the things which we found was that we could form cyclic oligomers of alcohols, here is an example of such a oligomer (From Henry’s group {M.B. Keller, H.S. Rzepa, A.J.P. White and D.J. Williams, First Electr.Conf.Trends in Org.Chem., 1995, page 50}).

Here is one view of the tetramer of alcohol groups.

Top view of the tetramer

While here is the side view of the tetramer.

Side view of the tetramer

The large group functions as a big fat thing which isolates the hydrogen bonding network from the outside world, here in the view of the space filling model you can see how the ring of alcohols is isolated from the outside world.

Spacefilling view

The fact that we have a tetramer tells us that the small effect of adding the chlorine to the acetylene (alkyne) stops the acetylene acting as a hydrogen bond acceptor. In the solid which lacks the chlorine atom the hydrogen bonding network is very different. For this see S.Y. Lin, Y. Okaya, D.M. Chiou and W.J. LeNoble, Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem., 1982, 38, 1669. This solid was reappraised by F.H. Allen, J.A.K. Howard, V.J. Hoy, G.R. Desiraju, D.S. Reddy and C.C. Wilson, Journal of the American Chemical Society, 1996, 118, 4081. In the 2-ethynyl-2-adamantanol the pi electron cloud of the acetylene acts as a source of electron density (hydrogen bond acceptor) for the bond. Here for your delight is a picture showing how the alcohol proton bonds to the acetylene.

The pi cloud of the acetylene acting as a hydrogen bond acceptor

We could continue with our hunt for interesting hydrogen bonds, the exotics are the sort of thing which puts a big fat smile on my face, but what students need to know first is the mundane day to day things. When looking for a hydrogen bond acceptor you need to look in a molecule for nitrogen and oxygen atoms which have lone pairs. The more electron rich nitrogen and oxygen atoms are more likely to be able to form hydrogen bonds than the more electron poor versions of the same groups.

One which you should keep your eyes open for is the amide oxygen, due to resonance the oxygen is more electron rich than the oxygen in a typical carbonyl compound. Before we get going on resonance I need to share a set of important rules. If you break any of these rules it is the chemical version of dragging your fingernails down a blackboard ! It is that bad !

The rules are

  1. Resonance can only move electrons, thus chemical bonds which are areas of electron density can be moved.

Thus we can make and break pi and even sigma bonds.

  1. Resonance can not move atomic nuclei, nuclei and electrons move about on different time scales.

We can not change the overall shape of a molecule. For goodness sake never try to suggest that a cis alkene is converted to a trans alkene through a change of one resonance form to another.

  1. Resonance can not alter the hybridization of an atom; if an atom is sp2 in one resonance form then it must be sp2 in all the others.

I have seen students draw things which suggest that a nitrogen in one resonance form of an amide is sp3 and in the other that it is sp2. For goodness sake do not do this ! It is just as silly as suggesting that a cat is a resonance form of a snake.

  1. The structure in real life is a combination of the resonance forms, it will be somewhere between the different resonance forms.
  2. Resonance forms with lots of charges tend to have very high energies, hence they make only a very small contribution to the overall structure.

For example we could draw a resonance form for benzene with alternate carbocation and carboanions, this would have the right hybridization of carbon atoms and all the atoms are in the right place. But the energy would be so jolly high that I suspect that this resonance form has almost a zero contribution to the real life structure of benzene.

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