ORGANIC COMPOUNDS II

RECALLING SOME FEATURES OF COVALENT BONDING

Carbon bonds covalently to other atoms. Although carbon – metal bonds have a highly
ionic character and there are compounds in which carbon forms stable cations, the
tetracovalency of carbon still holds for 99.9 % of the cases. You should recall that
“mixing” or hybridization of atomic orbitals lead to sp3, sp2 and sp combinations that
are properly oriented to accomplish with the geometrically most stable distribution of
the electron pairs (VEPReT).

Single bonds are formed by frontal interpenetration of the orbitals of the atoms forming
the bond: these are the σ (sigma) bonds. If there is a double or triple bond between two
atoms, then the first bond that holds the atoms together will be of the σ type but the
other (or others) will be formed by lateral overlapping of the orbitals located at right
angles of the σ bond axis. These are the π bonds in which the molecular orbitals have
two lobes lying above and below the plane that contains both nuclei.

The formation of σ bonds in ethane C2H6

The formation of a π bond in ethane C2H4

Sigma (σ) bonds

• Unlike pi (π) bonds allow free rotation around the axis joining the nuclei
• Are stronger than pi (π) bonds

LCAO

The mathematical approach to molecular orbitals uses an approximation called the

Linear Combination of Atomic Orbitals (LCAO) theory. According to this theory the
molecular orbitals can be fairly approximated as a new function that is obtained by
linear combination of the atomic functions involved in the bond:

Molecular orbital (MO) = Atomic Orbital (AO)1 ± Atomic Orbital (AO)2

Thus, the simplest combination of the AO’s gives two possible MO’s. Calculations
show that addition gives a MO with lower energy than each of the individual AO’s: it is
called a bonding MO and the electrons of the bond will occupy this level. On the other
hand subtraction gives a MO that is more energetic than the original AO’s. This one is
called the anti- bonding MO* and remains empty. If electrons were promoted to this
anti – bonding orbital, the bond would be unstable and eventually break down (that
happens when UV radiation is absorbed: DNA may break and tumours appear)

The hydrogen
molecule

Forming bonding and anti – bonding σ and π orbitals

DELOCALISED BONDS

An orbital model for the benzene structure

Benzene is built from hydrogen atoms (1s1) and carbon atoms (1s22s22px12py1).

Each carbon atom has to join to three other

atoms (one hydrogen and two carbons) and
doesn't have enough unpaired electrons to
form the required number of bonds, so it
needs to promote one of the 2s2 pair into the
empty 2pz orbital. This is exactly the same as happens whenever carbon forms bonds -
whatever else it ends up joined to.

Because each carbon is only joining to three other atoms, when the carbon atoms
hybridise their outer orbitals before forming bonds, they only need to hybridise three of
the orbitals rather than all four. They use the 2s electron and two of the 2p electrons, but
leave the other 2p electron unchanged.

The new orbitals formed are called sp2 hybrids, because they are made by an s orbital
and two p orbitals reorganising themselves. The three sp2
hybrid orbitals arrange themselves as far apart as possible -
which is at 120° to each other in a plane. The remaining p
orbital is at right angles to them.

Each carbon atom now looks like the diagram on the right.
This is all exactly the same as happens in ethene.

The difference in benzene is that each carbon atom is joined to two other similar carbon
atoms instead of just one. Each carbon atom uses the sp2 hybrids to form sigma bonds
with two other carbons and one hydrogen atom. The next diagram shows the sigma
bonds formed, but for the moment leaves the p orbitals alone (the two C atoms to the
front are not shown).

Notice that the p electron on each carbon atom is

overlapping with those on both sides of it. This
extensive sideways overlap produces a system of pi
bonds which are spread out over the whole carbon
ring. Because the electrons are no longer held
between just two carbon atoms, but are spread over
the whole ring, the electrons are said to be delocalised. The six delocalised electrons
go into three bonding molecular orbitals - two in each.

In common with the great majority of descriptions of the bonding in benzene, we are
only going to show one of these delocalised molecular orbitals for simplicity.

In the diagram, the sigma bonds have been shown as simple lines to make the diagram
less confusing. The two rings above and below the plane of the molecule represent one
molecular orbital. The two delocalised electrons can be found anywhere within those
rings. The other four delocalised electrons are in two similar (but not identical)
delocalised molecular orbitals.

RELATING THE ORBITAL MODEL TO THE PROPERTIES OF BENZENE

The shape of benzene

Benzene is a regular hexagon because all the bonds are identical. The delocalisation of
the electrons means that there aren't alternating double and single bonds.

The energetic stability of benzene

This is accounted for by the delocalisation. As a general principle, the more you can
spread electrons around - in other words, the more they are delocalised - the more stable
the molecule becomes. The extra stability of benzene is often referred to as
"delocalisation energy".

The reluctance of benzene to undergo addition reactions

With the delocalised electrons in place, benzene is about 150 kJ mol-1 more stable than
it would otherwise be. If you added other atoms to a benzene ring you would have to
use some of the delocalised electrons to join the new atoms to the ring. That would
disrupt the delocalisation and the system would become less stable.

Since about 150 kJ per mole of benzene would have to be supplied to break up the
delocalisation, this isn't going to be an easy thing to do.

The symbol for benzene

For most purposes we use the structure on the right. The hexagon shows
the ring of six carbon atoms, each of which has one hydrogen attached.
The circle represents the delocalised electrons. It is essential that you
include the circle.

AROMATICITY

This special stabilisation of benzene and related organic substances is called aromaticity
and the substances containing aromatic rings are called aromatic compounds. The
chemistry of aromatic compounds is different to the chemistry of non – aromatic (called
aliphatic) compounds. Aromatic compounds contain six membered rings with six
contiguous p electrons (there are other aromatic compounds beyond the scope of this
paper). The following structures show some simple aromatic compounds

HOW TO DRAW STRUCTURAL FORMULAE IN 3-DIMENSIONS

There are occasions when it is important to be able to show the precise 3-D arrangement
in parts of some molecules. To do this, the bonds are shown using conventional
symbols:

For example, you might want to show the 3-D arrangement of the groups around the
carbon which has the -OH group in butan-2-ol.

Butan-2-ol has the structural formula:

Using conventional bond notation, you could draw it as, for example:

Skeletal formulae

In a skeletal formula, all the hydrogen atoms are removed from carbon chains, leaving
just a carbon skeleton with functional groups attached to it.
For example, we've just been talking about butan-2-ol. The normal structural formula
and the skeletal formula look like this:

In a skeletal diagram of this sort

• there is a carbon atom at each junction between bonds in a chain and at the end
of each bond (unless there is something else there already - like the -OH group
in the example);
• there are enough hydrogen atoms attached to each carbon to make the total
number of bonds on that carbon up to 4.

Cyclohexane, C6H12, is a ring of carbon atoms each with two hydrogens attached. This
is what it looks like in both a structural formula and a skeletal formula.

And this is cyclohexene, which is similar but contains a double bond:

But the commonest of all is the benzene ring, C6H6, which has a special symbol of its
own as we have already seen.

WHAT IS STEREOISOMERISM?

You have learned what the terms “structural isomerism” means. Isomers are molecules
that have the same molecular formula, but have a different structure. In
stereoisomerism, the atoms making up the isomers are joined up in the same order, that
is, the structure of the isomers is the same but have a different configuration

Configuration of a structure is any of the different arrangements in space of its

atoms that can be isolated.
UNRESTRICTED ROTATION

Think about what happens in molecules where there is unrestricted rotation about
carbon bonds - in other words where the carbon-carbon bonds are all single. The next
diagram shows two possible space arrangements of 1,2-dichloroethane.

These two models represent exactly the same molecule. You can get from one to the
other just by twisting around the carbon-carbon single bond and at room temperature the
molecules have enough rotational energy to overcome low energy barriers. These
molecules are not isomers but conformers.

CONFORMATION

Conformation of a molecule is any of the infinite spatial arrangements of its

structure, obtained by rotation of any of its single (σ) bonds.

Conformations are easily interconverted and actually a molecule generally exists in

many of them simultaneously. Despite this apparent freedom, only two limiting
conformations are important: eclipsed conformation and staggered conformation.

The case of butane is

similar but somewhat
different: the methyl
groups can be eclipsed
either with a hydrogen
atom or with the other
methyl. This last conformation is the less stable and of the staggered conformations the
“anti” is more stable than any “gauche”
The energy barriers are low and do not hinder free rotation at room to moderately cold
temperatures. But nevertheless, these species can be detected as different entities at
temperatures below -100°C!!

GEOMETRIC (CIS / TRANS) ISOMERISM

How geometric isomers arise

When you have restricted rotation somewhere in a molecule, at that point the
conformers are no longer interchangeable at room temperature and appear as two
distinctly different substances: these are called cis-trans or geometric isomers.
Geometric isomerism is one form of stereoisomerism.

If you draw a structural formula instead of using models, you have to bear in mind the
possibility of this free rotation about single bonds. You must accept that these two
structures represent the same molecule:

But what happens if you have a carbon-carbon double bond - as in 1,2-dichloroethene?

These two molecules aren't the same. The carbon-carbon double bond won't rotate (π
bonds will break) and so you would have to take the models to pieces in order to
convert one structure into the other one. That is a simple test for isomers. If you have to
take a model to pieces to convert it into another one, then you've got isomers. If
you merely have to twist it a bit, then you haven't!

Drawing structural formulae for the last pair of models gives two possible isomers.

In one of them the two chlorine atoms are locked on opposite sides of the double bond.
This is known as the trans isomer. (trans: from Latin meaning "across").

In the other one the two chlorine atoms are locked on the same side of the double bond.
This is known as the cis isomer. (cis: from Latin meaning "on this side")
Another example of geometric isomers is the but-2-enes: in one case, the CH3 groups
are on opposite sides of the double bond, and in the other case they are on the same
side.

How to recognise the possibility of geometric isomerism

You obviously need to have restricted rotation somewhere in the molecule. Cycles and
double bonds are commonest cases. If you have a carbon-carbon double bond, then
think carefully about the possibility of geometric isomers.

What needs to be attached to the carbon-carbon double bond?

Think about this case:

Although we've swapped the right-hand groups around, these are still the same
molecule. To get from one to the other, all you would have to do is to turn the whole
model over.

You won't have geometric isomers if there are two groups the same on one end of the
bond - in this case, the two pink groups on the left-hand end.

So there must be two different groups on the left-hand carbon and two different groups
on the right-hand one. The cases we've been exploring earlier are like this:
PLANE POLARISED LIGHT

A simple analogy - "plane polarised string"

Imagine tying a piece of thick string to a hook in a wall, and then shaking the string
vigorously. The string will be vibrating in all possible directions - up-and-down, side-
to-side, and all the directions in-between - giving it a really complex overall motion.

Now, suppose you passed the string through a vertical

slit. The only vibrations still happening on the other
side of the slit will be vertical ones. All the others will
have been prevented by the slit.

What emerges from the slit could be described as "plane polarised string", because the
vibrations are only in a single (vertical) plane.

Now look at the possibility of putting a second slit on the

string. If it is aligned the same way as the first one, the
vibrations will still get through.

But if the second slit is at 90° to the first one, the string will stop vibrating entirely to
the right of the second slit. The second slit will only let through horizontal vibrations -
and there aren't any.
Plane polarised light

Light is also made up of vibrations - this time, electromagnetic ones. Some materials
have the ability to screen out all the vibrations apart from those in one plane and so
produce plane polarised light.

The most familiar example of this is the material that Polaroid sunglasses are made of.
If you wear one pair of Polaroid sunglasses and hold another pair up in front of them so
that the glasses are held vertically rather than horizontally, you'll find that no light gets
through - you will just see darkness. This is equivalent to the two slits at right angles in
the string analogy. The polaroids are described as being "crossed".

OPTICAL ISOMERISM

Optical isomers are named like this because of their effect on plane polarised light

An optically active substance is one which can rotate the plane of polarisation of
plane polarised light. If you shine a beam of polarised monochromatic light (light of
only a single frequency - in other words a single colour) through a solution of an
optically active substance, when the light emerges, its plane of polarisation is found to
have rotated.

The rotation may be either clockwise

or anti-clockwise. Assuming the
original plane of polarisation was
vertical, you might get either of these
results.

How can you tell that the plane of polarisation has been rotated? You use a
polarimeter. The polariser and analyser are both made of polaroid material.

The polarimeter is originally set up with

water in the tube. Water isn't optically
active - it has no effect on the plane of
polarisation. The analyser is rotated until
you can't see any light coming through the
instrument. The polaroids are then
"crossed". You will see no light.

Now you put a solution of an optically active substance into the tube. It rotates the plane
of polarisation of the light, and so the analyser won't be at right-angles to it any longer
and some light will get through. You would have to rotate the analyser in order to cut
the light off again.

ENANTIOMERS

Simple substances which show optical isomerism exist as two isomers known as
enantiomers.
 • A solution of one enantiomer rotates the plane of polarisation in a clockwise
direction. This enantiomer is known as the (+) form.

• A solution of the other enantiomer rotates the plane of polarisation in an anti-

clockwise direction. This enantiomer is known as the (-) form.

When optically active substances are made in the lab, they often occur as a 50/50
mixture of the two enantiomers. This is known as a racemic mixture or racemate. It
has no effect on plane polarised light.

HOW OPTICAL ISOMERS ARISE

These two models each have the same groups joined to the central carbon atom, but still
manage to be different:

Obviously as they are drawn, the orange and blue groups aren't aligned the same way.
Could you get them to align by rotating one of the molecules? The next diagram shows
what happens if you rotate molecule B.

They still aren't the same - and there is no way that you can rotate them so that they look
exactly the same. These are optical isomers of each other.

They are described as being non-superimposable in the sense that (if you imagine
molecule B being turned into a ghostly version of itself) you couldn't slide one molecule
exactly over the other one. Something would always be pointing in the wrong direction.

What happens if two of the groups attached to the central carbon atom are the same?
The next diagram shows this possibility.
The two models are aligned exactly as before, but the orange group has been replaced
by another pink one.

Rotating molecule B this time shows that it is exactly the same as molecule A. You only
get optical isomers if all four groups attached to the central carbon are different.

CHIRAL AND ACHIRAL MOLECULES

The essential difference between the two examples we've looked at lies in the symmetry
of the molecules.

If there are two groups the same attached to the central carbon atom, the molecule has a
plane of symmetry. If you imagine slicing through the molecule, the left-hand side is an
exact reflection of the right-hand side.

Where there are four groups attached, there is no symmetry anywhere in the molecule.

An object which has no plane of symmetry is described as chiral. Such an object cannot
be superimposed to its mirror image. Think of your right hand. Its mirror image is your
left hand and they cannot be superimposed although they both have the same fingers
attached in the same position. Your hands are chiral objects. In fact chirality is a word
derived from the Greek word for hand (cheir). Chiromancy, chiropractic have the same
origin.

The carbon atom with the four different groups attached which causes this lack of
symmetry is described as a chiral centre or as an asymmetric carbon atom. The
molecule on the left above (with a plane of symmetry) is described as achiral. Only
chiral molecules have optical isomers.

THE RELATIONSHIP BETWEEN THE ENANTIOMERS

One of the enantiomers is simply a non-superimposable mirror image of the other

one. That is to say that molecules with a chiral centre, and consequently non
superimposable on their mirror images, will appear as two optically active enantiomers
In other words, if one isomer looked in a mirror, what it would see is the other one. The
two isomers (the original one and its mirror image) have a different spatial arrangement,
and so can't be superimposed on each other.

If an achiral molecule (one with a plane of symmetry) looked in a mirror, you would
always find that by rotating the image in space, you could make the two look identical.
It would be possible to superimpose the original molecule and its mirror image.

Except for the optical activity, enantiomers have exactly the same physical and
chemical properties as long as they do are not interacting or reacting with other
chiral species. To visualise this fact think of fitting any of your feet in a left shoe or
better any of your hands in a left glove. Results are really different!!!

TO FIND AN ASSYMMETRIC CARBON

To find an asymmetric centre is very simple: just inspect if there are any two equal
groups bonded to a C atom and repeat for all the atoms in the molecule. In drawings,
chiral carbons are often marked with a star. Some examples follow:

Butan-2-ol

It's extremely important to draw the isomers correctly. Draw one of

them using standard bond notation to show the 3-dimensional
arrangement around the asymmetric carbon atom.

Notice that you don't literally draw the mirror images of all the letters and numbers! It
is, however, quite useful to reverse large groups - look, for example, at the ethyl group
at the top of the diagram.

It doesn't matter in the least in what order you draw the four groups around the central
carbon. As long as your mirror image is drawn accurately, you will automatically have
drawn the two isomers.

So which of these two isomers is (+) butan-2-ol and which is (-) butan-2-ol? There is no
simple way of telling that. The way to do this goes far beyond the scope of the course
2-hydroxypropanoic acid (lactic acid)

Once again the chiral centre is shown by a star.

The two enantiomers are:

2-aminopropanoic acid (alanine)

This is typical of naturally-occurring amino acids. Structurally, it is

just like the last example, except that the -OH group is replaced by
-NH2

The two enantiomers are:

Only one of these isomers occurs naturally: the (+) form. You can't tell just by looking
at the structures which this is.

It has, however, been possible to work out which of these structures is which. Naturally
occurring alanine is the right-hand structure, and the way the groups are arranged
around the central carbon atom is known as an L- configuration. Notice the use of the
capital L. The other configuration is known as D-. So you may well find alanine
described as L-(+) alanine. That means that it has this particular structure and rotates the
plane of polarisation clockwise.

Even if you know that a different compound has an arrangement of groups similar to
alanine, you still can't say which way it will rotate the plane of polarisation. The other
amino acids, for example, have the same arrangement of groups as alanine does (all that
changes is the CH3 group), but some are (+) forms and others are (-) forms.

It's quite common for natural systems to only work with one of the enantiomers of
an optically active substance. It isn't too difficult to see why that might be. Because
the molecules have different spatial arrangements of their various groups, only one
of them is likely to fit properly into the active sites on the enzymes they work with.
DIASTEREOMERS

Diastereoisomers also known as diastereomers are stereoisomers that are not

related as mirror images. They have different chemical and physical properties.
Molecules possessing more than one chiral centre also exhibit diastereoisomerism
because inverting one or more but not all of the centres, leads to structures which do
not have a mirror image relationship with the original. Inversion of a single chiral centre
gives a diastereomer of the original structure. Inversion of all chiral centres gives the
enantiomer. The figure below shows the four isomers for 2,3-dibromobutane: the
enantiomers above are diastereomers to the second enantiomeric pair.

Molecular symmetry may reduce the number of enantiomeric pairs

Cis-trans isomers are a case of enantiomeric pairs: two configurational isomers that are
not mirror images to each other.

PROBLEMS

1- The diagram shows a plant view (seen from above)

of the six polycentric (delocalised) π molecular orbitals of
benzene, their energies increasing from bottom to top. The two
colours mean that the orbital functions change sign. Below the
C – ring’s plane a symmetric figure would appear.
a- How many p electrons are involved in the
bond?
b- A nodal plane is a plane at which the
functions change sign. Trace the nodal planes (other than
the plane of the paper) for all six orbitals.
 c- According to your work is there any relationship between energy
and nodal planes?
d- Which orbitals are bonding and which are not bonding?
e- Accommodate the electrons in the orbitals
f-
2- Draw a diagram similar to the one that
appears in page 2 (see right) showing the relative
energies for the four molecular orbitals (bonding
and antibonding) that form between the C atoms
in ethane.
3- Does the rotational profile of 2,3-dichloroethane resemble that of ethane
or butane? Explain your choice.
4- Draw the following structures and decide whether they show or not
geometric isomerism:
a- propene
b- 1-chloropropene
c- 2-chloropropene
d- 1,2-dichlorocyclopentene
5- The table shows the boiling point of the
cis and trans isomers of 1,2-dichloroethene. Explain isomer B. point (°C)
the figures considering the relative electronegativity
of chlorine and carbon cis 60

trans 48

6- How can you tell if an unknown sample is optically active?

7- Use wedges, dotted lines etc. to draw the configuration of both enantiomers of

a- 2-aminobutane
b- propane-1,2-diol
c- 2-chloropropanal

8- The figure shows two molecules (geranial

and neral).
a- Suggest a reason for the ending of both names.
b- A challenge: write their systematic names
c- Write their molecular formula
d- What class of isomers are they?
e- Could they have other isomers of the same kind?
f- Are thy optically active?
g- In case they are active mark the chiral centre.
9- This other two molecules belong to the same
family of natural products: the terpenes.
a- Do you think there are any possibilities for cis trans
isomerism in them?
b- Are they optically active? In case they are mark the
chiral carbon