Lecture 2: Meet the Molecules

The Centipede was happy quite,

Until the Toad, in fun,

Said “Pray, which leg comes after which?”

This raised her doubts to such a pitch,

She fell exhausted in a ditch,

Not knowing how to run.

(1) The Macromolecule as a Collection of Atoms

The important thing to get on board is the difference between configuration and conformation.

Configuration refers to different ways of sticking the same atoms together. You cannot change the configuration of a molecule without breaking and remaking bonds.

Conformation refers to different ways of bending the same molecule, without breaking bonds.

Configuration (1)

An example of two very similar polymers: starch and cellulose.

This is representation of a glucose molecule. The molecule in nature consists of two anomeric configurations, which are easily switched round in nature. Some of you may have done the group project which involved making up solutions of glucose, and encountered this.

The plant can join up glucose in either of these ways to make starch (alpha) or cellulose (beta).

Cis-trans isomerism

One type of isomerism which is important in polymers is cis-trans isomerism, which refers to the configuration of groups around a C=C double bond. Here are two varieties of polyisoprene.

This is cis-polyisoprene, which is the form found in natural rubber. This polymer is molten even at 0°C, where it is a very viscous but elastic liquid. Note how the polymer backbone chain zig-zags up and down.

This is trans-polyisoprene, which is the form found in gutta-percha. This is a crystalline polymer which melts at over 40°C, and until the 1940s was used to insulate submarine cables. Note how the chain snakes up and down in a more complicated way than in natural rubber.

The C–C single bonds in the chain are somewhat longer than the C=C double bonds, but this effect is exaggerated in the diagrams.

Conformation (1)

The left hand picture shows the all-trans conformation of a polyethylene chain: this is the minimum energy conformation. This would be the equilibrium conformation at Absolute Zero. At T>0 deviations from the minimum-energy conformation are possible due to thermal motion. According to Boltzmann’s law the probability of realization of the conformation with the excess energy U over the minimum energy conformation is

and so with increasing temperature there is an increasing proportion of increasingly wriggly chains, as on the right. In fact, the perfectly extended chain is not achievable in normal practice for molecules longer than 100 carbon atoms, and is never found in the melt, only in the crystal. To get perfectly extended chains of about 1000 carbon atoms, the PE must be crystallized at high-pressure, a procedure much studied at Reading by Prof. David C. Bassett.

Configuration (2)

The most important configurational difference – tacticity.

This next picture shows two molecular models of PVC. Notice how, on the ‘I’ isotactic one, all the chlorine atoms stick out on one side, whereas on the ‘S’ syndiotactic chain they stick out on alternate sides. These are two different configurations, because you have to break and remake bonds to change one to the other/

Now imagine a polyethylene chain spread out in the all-trans, “concertina” conformation, as follows:

Here we show only the carbon atoms. (The hydrogens are ‘tiddlers’, and we do not show them.). We are looking down from above, so the zigzag moves towards and away from us. Each carbon atom has two hydrogens.

And here is the same chain with the zigzag viewed from the side.

Now imagine we are walking along the chain. Let us, on every second chain carbon atom, take off a hydrogen, and put a bigger group, perhaps a chlorine atom (PVC), or a methyl CH3 group (polypropylene) or a benzene ring-containing phenyl group C6H5 (polystyrene). If we put them all on the same side, we have an isotactic polymer:

But if we put them on alternate sides, we have a syndiotactic polymer.

Whereas if we put them on random sides we get an atactic polymer.

These are different polymers.

Isotactic / Syndiotactic / Atactic
Polypropylene / m.p. 160°C / m.p. somewhat lower / Gooey mess
Polystyrene / m.p. 240°C, opaque / m.p. 270°C, opaque / Common polystyrene, clear, softens about 110°C

Conformation (2)

Because of asymmetric distribution of side groups, isotactic polymers especially like to assume a helical conformation.

This three-fold helix is characteristic of isotactic polypropylene and isotactic polystyrene, but other polymers have different pitches of helix.

These two isotactic chains are not chemically different. If we were to rotate one 180° about a vertical axis, it would fit into the other.

But if we were to try to wind a helix, starting from left of page, one would form a right-handed helix and one would form a left. Without an actual 3D molecular model to play with, it is (to me at least) brain-boggling to try and work out which is which.

Note that this does NOT apply to amino-acid sequences as in peptides and proteins. The chain of the simplest peptide, polyglycine, goes one way:

–CH2–CO–NH–CH2–CO–NH–CH2–CO–NH–

and will always have to wind one way. The R groups always stick out on the same side:

R1 R3

–CH–CO–NH–CH–CO–NH–CH–CO–NH–CH–CO–NH–

R2 R4

If that is so, why have I drawn two up and two down?

Conformation (3)

Consider the two molecules, Ethane and Butane

Now look at the diagram below.

The middle stick represents the C—C bond under study.

If all the blobs are equal, they represent hydrogen atoms as in ethane

If the black blobs are methyl groups, we have butane

The black blobs could also be long chains, as in polyethylene.

Take Ethane first. At 0, 120, 240, 360°, the conformation is said to be staggered. At 60, 180, and 300°, the conformation is eclipsed. The hydrogen atoms are at their closest together, and experience a repulsion. This is called steric hindrance, which is Graeco-Roman for getting in the way. Therefore the staggered conformation has the lower energy.

Now look at Butane. The methyl groups are bulkier than the hydrogen atoms, and so experience more repulsion. There are three staggered conformations, called trans, gauche+, and gauche–. In the trans-conformation the methyl groups are furthest away, and this is the lowest energy configuration of all. This is why the all-trans conformation of the polyethylene chain has the lowest energy.

At room temperature, RT ~ 2.4 kJ.mole-1.

Now that we know how polymer chains become flexible, we can get more “physics-y” and treat:

 (2) The Macromolecule as a Physical Object

For this see the lecture notes to:

Introduction to polymer science by Prof. A.R.Khokhlov, (Moscow State University) Lecture 2

(3) How can we Observe Macromolecules?

Sometimes we can actually see them under the electron microscope. DNA is a good example of this.

/ Electron microscope picture of bacterial DNA partially released from its native shell. (Source: Dictionary of Science and Technology, Christopher Morris, ed. , San Diego, CA: AcademicPress, 1992.)

We can also observe them by scattering.

Light Scattering

If we dissolve polystyrene in a solvent, most likely the refractive index of the polystyrene molecule will be different from that of the solvent. This will cause scattering of light. In a dilute solution, the molecules will occupy a coil of size equal to their radius of gyration, and will scatter accordingly.

Neutron Scattering

That’s all very well, but can we observe molecules in ‘neat’ polymer? One approach is to mix two versions of the same polymer, for example ordinary polystyrene (h-PS) and deutero polystyrene (d-PS), in which the hydrogen has been replaced by its heavy isomer, deuterium. This is almost, but not quite, a perfect mixture. Deuterium and Carbon have practically the same (positive) scattering length, but that of hydrogen is negative (which means that the scattered neutrons invert their phase). So h-PS (C8H8)n and d-PS (C8D8)n will have different neutron refractive indices.

Atomic Nucleus / Scattering Length(fm)
1H / - 3.741
2D / + 6.671
C / + 6.646
N / + 9.362
O / + 5.803

Thus a small amount of one type of PS in the other are present as isolated coiled molecules which scatter neutrons.

Size exclusion chromatography.

This measures molecular size directly. Go to Macrogalleria Level 5 and click on the link.

MALDI Mass Spectroscopy.

This measures molecular mass directly. Go to Macrogalleria Level 5 and click on the link.