Week 15 Lecture: Isomerism, stereochemistry and conformation

Isomers can be structural isomers or stereoisomers.

Structural isomers have:

Same molecular formula

Different molecular structures

Structural isomers can be subdivided into;

1. Chain isomers (such as pentane and 2-methlybutane)
2. Position isomers (such as butan-1-ol and butan-2-ol)
3. Functional Group isomers (such as propanal, propanone, prop-2-en-1-ol
and oxetane)

Stereoisomers have:

Same molecular formula

Same functional groups but different arrangements in space

Stereoisomers can be further subdivided into conformational isomers and

configurational isomers (E/Z isomers and isomers with chiral centres).
A conformation is the 3D shape of the molecule that arises from the rotation of
bonds. A specific rotational arrangement that is stable is called a conformer.
In organic molecules, only single bonds from sp 3 carbons can rotate; so
conformers need sp3 hybridized carbons, which can only be found from alkane
structures.
For example, 2 conformers (conformational isomers) of ethane can arise from the
rotation around the C-C bond. NB: This also applies to all sp 3 carbon chains. The
two conformations are staggered and eclipsed. Staggered is when the
hydrogen atoms on both carbons are as far apart as possible and eclipsed is
when they are as close as possible (see CONFORMATIONAL ISOMERS OF ETHANE
DIAGRAM). As the C-C bond rotates, the ethane molecule passes through
eclipsed and staggered conformations. The eclipsed conformations have
hydrogen atoms closest, increasing atomic interactions and molecular energy.
When molecular energy increases, the conformer becomes less stable due to
more atomic interactions.
If you look at the molecules from the side (like a cross section), as the names
suggest the eclipsed conformers are where the functional/side groups
overlap/create an eclipse effect, whereas staggered conformers have gaps/are
staggered (SEE CONFORMATIONAL ISOMERS OF ETHANE DIAGRAM). This view is
called the NEWMAN PROJECTION.

If atoms in a conformer are brought too close that their electron clouds begin to
overlap, it creates electron repulsion and increase in molecular energy
(decreasing stability). This is called the steric effect. When steric effects are
extreme, it can prevent reactions from occurring, and is termed steric
hindrance/resistance.
Conformations can explain the stability of cyclohexane; there are no eclipsed
conformers in the chair form of cyclohexane.
6-carbon rings > 5-carbon rings (stability wise).
Cyclohexane can form 3 conformers: chair, half-chair and boat. The chair is the
most stable conformer and stabilities are due to steric effects. As the
cyclohexane interconverts between chair forms, the position of hydrogen atoms
also changes; the axial hydrogen atoms equatorial in another conformation and
vice versa. (Axial hydrogen atoms are in the plane of the y axis and equatorial
hydrogen atoms are in the plane of the x axis).
The above is configurational isomers of alkanes (remember only alkanes can
have sp3 bonds).

Stereosiome

Conformationa
l isomers
(alkanes)

E/Z isomers

Configurational
isomers (alkenes)

Isomers with
chiral centres

Unlike conformational isomers, configurational isomers cannot be interconverted

without breaking a bond (rotation is not possible).
Isomers with chiral centres are asymmetric molecules; such as amino acids. For a
molecule to be chiral, there must be at least one chiral atom (carbon) which has
4 different functional groups bonded to it. There can be multiple chiral centres in
a molecule.
Glycine is the only amino acid which is not chiral due to the central chiral carbon
having two hydrogen atoms bonded to it; it is said to be prochiral as it is one
step away from being chiral. This is noteworthy because it means in a prochiral
molecule, each hydrogen atom attached to the prochiral carbon centre in unique
and non-equivalent.
Optical isomers are called enantiomers. L/S isomers are when the priority of the
functional groups increases anti-clockwise, and D/R isomers are when the priority
increases clockwise.
As mentioned before, some molecules can have more than one chiral centre;
meaning it can more than two configurations. For example if a molecule has 2
chiral centres, it can have 4 possible configurations: 1 chiral = R or S, so 2 chiral
= RR or RS or SR or SS (FOR MORE DETAIL SEE THREONINE AND
DIASTEREOISOMERISM DIAGRAM).

A meso compound (or meso isomer) is a member of a set of stereoisomers and is

not optically active, but at least two members set are. For example, tartaric acid;
there is (2R,3R), (2R,3S), (2S,3R) and (2S,3S). (2R,3S) and (2S,3R) are not
enantiomers (are super imposable) and so are not optically active, and so ARE
THE SAME. This compound is known as meso-tartaric acid.
Enantiomers rotate polarised light because they have no axis/plane of symmetry,
but since meso compounds do have an axis/plane of symmetry they do not
rotate polarised light.