Understanding Molecular Conformation: The 3D World of Molecules

Dive into the fascinating world of molecular conformation. Discover how the 3D arrangement of atoms influences chemical properties and reactivity. Perfect for chemistry students and curious minds alike.

In this lesson, we will learn:

• To understand the difference between molecular configuration and conformation.
• To recall and draw different molecular conformations using a Newman projection.
• To correctly draw six-membered cyclic rings showing conformation.

• We've now been introduced to stereochemistry – the different possible 3d arrangements of a molecule, and (later) how they can affect chemical properties. The different types of isomerism we have seen are, so far, all about different configurations of a molecule.
Now it is time to briefly look at the conformation of a molecule. Using a stick figure analogy, the difference between configuration and conformation is shown below:

• A different configuration, has a different arrangement/connectivity, so in a molecule, bonds must break to change configuration.
• To change conformation, a molecule simply has to rotate around one or any number of its bonds. Bonds do not have to break to change conformation.
• The rotation of a single bond – or any chemical bond! – is a chemical process and like all chemical processes, bond rotation initially costs energy, so how often a bond rotates is related to the stability of the bond; the more stable, the less rotations per unit time, until the energy barrier is so large that rotations effectively do not happen (like in double bonds).
  In ethane, C₂H₆, the C-C single bond rotates very easily - let's look at two opposite conformations of ethane:
  
• There are two ways of drawing a molecule to show conformations:
• The side view, which you already use. When drawing a molecule in the plane of the paper, we use wedges and dashed lines to show the 3d shape.
• A Newman projection, which is viewing the molecule straight along a particular bond. In ethane here we are looking down the C-C bond. Here, using this is easier to see the difference between the two conformations. To draw a Newman projection, use the following guidelines:
• For the closer of the two carbons in the bond you're looking down, draw it like you would for skeletal formula. It should look like a trigonal planar center: see 'C atom in front', in the image above.
• For the further away of the two carbons, draw a large circle and the three attachments starting at the edge of the circle, see 'C atom at the back' in the image above.
• Ethane has two opposite conformations:
• Eclipsed: Where the three hydrogen atoms attached to each carbon atom are in line – in the same positions - relative to each other. Think eclipsed like a solar eclipse. We only draw eclipsed with the attachments slightly off of each other to show what is there: in the real molecule they are in line.
• Staggered: Where the three hydrogens attached to one carbon atom are rotated 1/6^th or around 60° of the way around, compared to the hydrogens on the other carbon. Think staggered as the 6 hydrogens across both carbon atoms are equally staggered, full circle.
Ethane is the simplest molecule with a C-C bond; with the six other atoms all hydrogen, there are three identical eclipsed conformations and three identical staggered conformations. In larger molecules, the attached groups are not all hydrogen so specific 'types' of staggered and eclipsed conformations exist. We'll see these later.
The staggered conformation of ethane is more stable than the eclipsed conformation, mostly due to repulsion between the electrons in the C-H bonds. These bonds are aligned when eclipsed, so maximum repulsion occurs, and are misaligned in the staggered conformation, so the minimum possible repulsion occurs.
In terms of potential energy then:
• The staggered conformations are troughs or minimum points (minima).
• The eclipsed conformations are peaks or 'minima' (maximum points).
• Only potential energy minima are considered true conformers because the maxima are unstable (like a transition state in a chemical reaction), and will rapidly return into a stable conformation with a potential energy minima.
This leaves us with three identical – or one unique – staggered conformation of ethane as a conformational isomer, or conformer.
• Conformation becomes more complicated in longer molecules such as butane. Compared to ethane, butane has two extra methyl groups around the 'central' C-C bond and these are much larger than a single hydrogen atom. See the diagram below - every panel is a different conformation made by rotating the central C-C bond by 60°:
  
  You should be able to see a few things:
  • There are two different staggered conformations (which are stable conformers):
  • Gauche (AKA synclinal), where the methyl groups are 'staggered near each other' and the dihedral angles are 60° and 300°. The dihedral angle is the angle between the groups, measured around the C-C bond from the view of the Newman projection. These two conformations (2 and 6) are mirror images of equal stability.
  • Anti-periplanar, where the methyl groups are staggered opposite each other. Periplanar means in the plane, while anti refers to them pointing in opposite directions. The dihedral angle is 180°.
  • There are two different eclipsed conformations which are unstable conformations:
  • Anticlinal, where the two methyl groups are 'eclipsed away from each other' and the dihedral angle is 120° or 240°. These two conformations (3 and 5) are mirror images of each other and are equally stable. Here, anti- is used to show that they are pointing in opposite directions.
  • Syn-periplanar, where the two methyl groups are eclipsing each other. The dihedral angle is 0°. Here, syn- means pointing together or in the same direction.
  Gauche, anticlinal and periplanar are commonly used terms when using Newman projections to deal with the relative positions of groups to each other.
• It is important you know how conformation applies to cyclic rings. Cyclic rings are very common in organic chemistry and so far, our skeletal formula is misleading because it makes it look like they are flat.
  Cyclic rings are not flat!
  Enthalpy data backs this claim up; aside from cyclopropane where it is impossible not to be planar, cyclic rings will twist out of plane to minimize repulsion between eclipsed C-H bonds - this is what we saw in ethane above! This creates 'ring strain' in many cyclic rings, but not in cyclohexane.
• Cyclohexane is the most stable of the small to medium-sized rings; there is almost no ring strain in this structure. This is why 6 membered rings are probably the most common cyclic rings in organic chemistry.
• It has two well-known conformations – the boat conformation and the chair conformation. Of these, only the chair conformation is a true conformer though – we can use a Newman projection to see why:
  
  The Newman projection of both conformations shows:
  • The boat conformation has 4 pairs of eclipsed C-H bonds on adjacent carbons, and one 'eclipsing' pair from the two 'ends' of the boat both pointing up.
  • The chair conformation has no eclipsing C-H bonds at all, so no repulsion of this sort occurs.
  This explains why the chair conformation is a stable conformer, and the boat conformation is just an unstable conformation. Cyclohexane also has a stable 'twist boat' conformer as well, but this is less stable than the chair conformer which cyclohexane is usually in.
This conformation creates two 'types' of protons: axial and equatorial. Each carbon in the ring has one of each but they alternate in positions (because they are all tetrahedral and the bonds don't eclipse!)