What are the implications of having different conformations?

Question

I have seen videos explaining what conformations are. I am curious about whether different conformations can give rise to slightly different properties. Particularly of interest is whether you can modify the smell of something by just rotating some bonds.

Answer 1

That's an interesting question. To start off, what Mith said in the comments is absolutely right. Let's say that two conformations of a molecule have different smells (which is in fact not an absurd proposition by any means). The problem is that, because there is a very low barrier to the interconversion of the conformations, the individual conformations do not really hang around long enough to be individually detected; you can only really detect a weighted average of the conformations.

To give you an example, you can devise di-substituted cyclohexanes that have two predominant chair conformations. These can be investigated by proton NMR spectroscopy, since axial-axial coupling constants are larger than equatorial-axial or equatorial-equatorial couplings. From the integrals of the relevant peaks you can determine the relative proportions of both conformations.

However, if you somehow managed to synthesise a sample of the pure diequatorial conformer (the one in blue) and put it into a NMR tube, some of it would have converted into the diaxial conformer (the one in red) before you could even run your NMR. In fact, there's probably no way you can synthesise a pure conformer to begin with.

Likewise, if you replace the NMR machine with your nose, there's no way you can open a bottle of a perfume X, with conformation X1, and smell something, then open a bottle of the same perfume X with conformation X2 and smell another thing. They would both smell the same because conformers aren't isolable. (Well, not unless you are working in an argon matrix at temperatures near absolute zero or something like that!)

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Mith then goes on to say that you can bind to a molecule to manipulate its conformation. That's the more interesting part, in my opinion at least! If you think about it, it's going to be very hard for us to devise some kind of surface that particularly favours one conformation over another. You'd need a very complex binding partner, with a very specific 3D shape, that "fits" with one conformation but not another conformation.

Does that ring a bell? It might, because nature has made those binding partners for us already. That previous paragraph is a perfect description of an enzyme: a protein that catalyses a biological reaction. Lysozyme is one of the most famous enzymes; it was the first enzyme whose structure was successfully solved by X-ray diffraction. It is also a great example of an enzyme that works by manipulating conformations.

Lysozyme binds to a series of carbohydrates in the peptidoglycan cell walls of some bacteria. Together with water, it hydrolyses the glycosidic bonds (a fancy name for an acetal) in these carbohydrates:

^{(image from Wikipedia)}

I'm not going to go into the full mechanism of this, but the striking thing is that upon binding to lysozyme, the "D ring" (which is the NAM residue on the left-hand side of the diagram above) is distorted from its usual chair conformation into a half-chair conformation. This is because it "fits" better into the exact 3D conformation of the enzyme (not shown in the diagrams):

^{(image modified from Wikipedia)}

This makes the ring more unstable and prone to hydrolysis (strictly speaking, more prone to nucleophilic attack by the aspartate-52 residue). Without this manipulation of the conformation, it's likely that the hydrolysis cannot proceed.

So, there you have it! One way in which the conformation of a molecule, upon binding to another molecule, affects its properties.