Introduction to Organic ChemistryOrganic chemistry is the chemistry of molecules that use carbon as a ‘skeleton’. Carbon is the only element that can form branching chains with itself. It can make covalent bonds with a wide variety of other elements and these properties allow carbon to make an uncountable variety of fascinating molecules with a huge diversity of properties.

alcohol (ethanol)glucose

penicillin G vitamin C

C

C C

C

O

CCOH

H

O

OOH H

H

O

H

H

H

C

CC

O

CC

C O

OHH

O

O

H

HO

H

H

H

H

H

HH

C

C

C C

C

C

C C

O

N

H

C

C N

C

O

S CC H

C

C C

O

O

HH

H

H H

H

H

H

H

HH

H

HH

H

C C O H

H

H

H

H

H

Why is Organic Chemistry Important?

C

C

C C

C

C

C

O

C

O

O C C O

H H

H H

H

H H

H

n

PET {poly (ethylene terephalate)}a modified nanotube

lysozyme (an enzyme)

All known life is based on organic chemistry.

Most modern materials are based on organic chemistry.

21st century technologies will be based on organic chemistry.

Drawing structuresFor simple, inorganic molecules like sulphuric acid (H2SO4), we can write chemical formulae with chemical symbols. But, in organic chemistry, the arrangement of the atoms is also important. We cannot easily represent this with only a formula so we usually use line drawings.

CH3CH3 C

H

H

H

C

H

H

H C C

H

H

H

H

H

H

H2O O

H

HO

H H

O

H H= = = =

CH2CH2 CH

HCH

H C C

H

H

H

H

H

H

H

H

C C

H

C

H

H

C

O

H

H

HH

H

H

1 2 3 4

H

H3CCH31

23

4OH

12

34

OH

Formula Lewis structure

Line drawing

=

=

=Line drawings are simple and let us draw complex structures easily. We always write in the heteroatoms (atoms which are not carbon or hydrogen). Sometimes we write the carbons, hydrogens and lone pairs if we think it is important. Always assume carbons fill their octet with bonds to hydrogen atoms unless a drawing explicitly shows otherwise (for instance with a positive charge on the carbon).

=

=

Line Drawings and 3D structureSometimes it is useful to show the 3D structure around a carbon using line drawings.

C

C

C C

C

C

C C

O

N

H

C

C N

C

O

S CC H

C

C C

O

O

HH

H

H H

H

H

H

H

HH

H

HH

H

benzylpenicillin

=>

H

ClCH3

F

H

C

HH

H

In the plane of the paper.

Behind the paper.

In front of the paper.

=H

H H

H You will learn on the next course that the 3D structure of this molecule is very important.

AlkanesAlkanes are compounds made of only carbon and hydrogen, joined by single bonds. It is important to study alkanes because they teach us about the basics of the carbon skeleton. An alkane is any compound with the formula CnH(2n+2) . Here are a few examples:

CH4 CH3CH3 CH3CH2CH3

CH3CH2CH2CH3

H3CCH3

CH3CH(CH3)2

CH3CH2CH2CH2CH3 CH3CH2CH(CH3)2 CH3C(CH3)2CH3

H3C CH3H3C

CH3

CH3

H3C

CH3

CH3

CH3

methaneethane propane

H3C CH3

H CH3

Constitutional Isomers

H3C CH3H3C

CH3

CH3

H3C CH3

H3CCH3

C5H12:iso-pentane, b.p. 27.7°C(2-methylbutane)

neopentane, b.p. 9.5°C(2,2-dimethylpropane)

n-pentane, b.p. 36°C

Note that single bonds in molecules can rotate. A rotation does not change the connections of the carbon skeleton and so rotations do not make constitutional isomers.

These compounds are constitutional isomers of pentane, C5H12. That means that the carbon skeleton is connected differently. Recognising constitutional isomers is a fundamental skill of organic chemistry because they have different physical and chemical properties.

H3C CH3

12

3 45 5

C1 connected to C2, etc

C5 connected to C3

H3C

CH3

341 2

5

1 2 3

4 5

H3C CH3

H3CCH3

C5 and C4 connected to C2

H3CCH3

CH3

12 43

C1 connected to C2, etc

n-pentane

same molecule, not constitutional isomers

Functional Groups

By combining atoms that have different electronic properties, we can make different ‘functional groups’. These are parts that we can ‘clip onto’ a molecule to change what it can do. We can think of them like different parts of Lego. Here are just a few:

C C

double bond benzene ring

X

halide

spare electrons, no bond rotation

rigid, can easily add more functional groups

easy to change (X = halogen)

OH

alcohol

easy to change

O

ether

useful for connecting molecules

NH2

amine

useful Lewis base

N

O

O

nitro

strong electron withdrawing group

O

carbonyl

strong electron withdrawing group, spare electrons

OH

O

carboxylic acid

Useful acid, easily connects molecules

Building MoleculesOrganic chemistry is all about building and altering carbon-based molecules. We do this by connecting smaller molecules, disconnecting larger molecules and making interconversions between functional groups.

R R3 x ethene

ethene:H

H

H

Hpolyethylene fragment

But how do we know what reactions to do? It helps to know how functional groups work, how electrons move and which elements prefer which formal charges.

OH

O

OH

+O

O

O

O

O

OH

+O

OH

Osalicylic acid acetic anhydride

aspirin

acetic acid

‘R’ = any molecule, R is a radical (an atom or molecule with an unpaired electron).•

Functional Groups— Unsaturated Bonds

Unsaturated bonds do not rotate. This means that molecules with the same functional groups on different sides of the double bond are actually different configurational isomers with different physical and chemical properties.

H H

H H

HBr+

H H

H Br

H

H

An unsaturated bond is a bond that has spare electrons to donate to other atoms, i.e. double and triple bonds.

Because unsaturated bonds have spare electrons, it is easy to add new atoms and molecules to them. These reactions are called addition reactions.

CH3

H

H

Br

H

H

CH3

HH

Br

HH

CH3

H

H

Br

CH3

H

Br

H✕

same molecule

No rotation. These molecules are different configurational isomers.

rotation

HalogensHalogens form stable anions. This means that they can be detached from the parent molecules and replaced very easily. This is useful because we can easily replace halogens with other functional groups.

Halogens are also very electronegative. This means that they can pull electrons towards themselves by means of an inductive effect. Inductive effects have two main consequences: 1) they change the chemistry of the molecule, and 2) they change the polarity (and hence the solubility) of the molecule.

H

Cl

ClCl

∂+∂–

∂–

∂–

HO–Cl

ClCl

C

∂–

∂–

∂–HOH

H H

H Br

H

H

HO–

H H

HO H

H

H

Br–+

Replacing a halide with an alcohol.

Examples: 1) The hydrogen atoms in methane (CH4) are not acidic at all but the hydrogen atom in chloroform (CHCl3) has its electrons pulled away by the three chlorine atoms. This makes it weakly acidic and it can be removed by strong bases. 2) CHCl3 is a weakly polar molecule, making it a good solvent for weakly polar solutes (very many molecules in organic chemistry are weakly polar).

Cl

ClCl

∂+∂–

∂–

∂–

H

a non-polar solvent a weakly polar solvent

Amines and AlcoholsAmines are nitrogen atoms bonded to hydrogen or carbon. The nitrogen atom has a weakly held lone pair of electrons — this means amines are good bases:

Amines can also use their pair of electrons to form new chemical bonds. This makes amines good for linking molecules together.

NH2 BrNH

HBr

Alcohols look like amines but oxygen is more electronegative than nitrogen so it holds on to its lone pairs more strongly. This makes alcohols less reactive than amines.

OHHO

O

OH2–O

O

NH2HO

O

NH3–O

O

(Note the back reaction is stronger than the forward reaction)

Carbonyls are a carbon atom with a double bond to oxygen. They combine the spare electrons of double bonds with the electronegativity of oxygen. They can also use the lone pairs of oxygen as a weak base.

Carbonyls

Ketones are carbonyl groups joined to two carbon atoms. The electronegativity of oxygen is so powerful, the carbonyl carbon and the neighbouring carbons are both weakly positive and the neighbouring hydrogens are weakly acidic. The spare electrons allow addition reactions and strong acids can protonate the oxygen lone pairs.

Aldehydes are similar to ketones but they are at an end of the molecule. This makes it easier for reagents to react with the carbonyl group and aldehydes are more reactive than keytones.

O

R

R H

∂–∂+

∂+lone pairs are weakly basic

strong inductive effect

∂+ carbons

acidic hydrogens

Carboxylic acids have a hydroxyl (OH) group attached to the carbonyl. Resonance effects (discussed below) make the hydroxyl hydrogen very acidic.

R

HO

ROH

O

RO–

O

+ H+

Some Basic RulesThere are many kinds of reactions in organic chemistry. Once we understand some basic rules, however, it is easy to see common themes.

Electrons jump from lone pairs to adjacent bonds (to make double or triple bonds) or from unsaturated bonds to single bonds (which ‘moves’ the unsaturated bond) or onto atoms (to make lone pairs). They usually move as pairs. (Keep track of formal charges and always remember that period 2 atoms can never break the octet rule.)

Period 2 elements never expand the octet. H H

H

N

O ✗✗

NH3C

O✗

We use ‘curly arrows’ to show electrons moving. Electrons jump from atoms to adjacent bonds or vice versa. They usually move as pairs (but occasionally, single electrons can move in radicals).

N

O

N

O

+

–

ResonanceLone pair-single-double, or double-single-double bond patterns allow electrons to move especially easily. This is called resonance. Resonance makes molecules especially stable so it will always happen if possible. (Note resonance is not a chemical reaction, the real molecule is somewhere between the canonical forms. Resonance is shown by a special double-headed arrow.)

Base

H– –

resonance

Benzene is a particularly stable molecule. This is because the circular double-single-double pattern makes the resonance particularly strong (this is a simplified explanation, the real explanation needs a more detailed understanding of chemical bonding).

canonical form 1

canonical form 2

canonical form 1

canonical form 2

Resonance explains why carboxylic acids are acidic.

RO

OH

Base

RO

O

RO

O–

–

Formal ChargesMost elements in organic chemistry prefer to be neutral but is useful to develop an intuition about which elements prefer which formal charges.

Boron is on the left of the periodic table but it will take a negative formal charge to fill its octet. B + OH– B

OH–

Carbon will form cations or anions but they are always unstable and need to be stabilised by inductive effects or resonance.

–

Nitrogen easily forms cations by protonation or by making four covalent bonds. It can make anions but they are usually unstable unless stabilised by resonance.

NH3N

O

+

–

Oxygen easily, but only, forms cations by protonation. It also forms anions that are reasonably stable.

O+ H+

OH+

O– Na+

In organic molecules, halogens never form cations, except in resonance. They only, but easily, form anions when they leave a molecule.

Cl Cl

–

+

H H

H Br

H

H

HO–

H H

HO H

H

H

Br–+

H3C CH3

CH3

+

PolymersIf a molecule contains two functional groups for bond forming (e.g. unsaturated bonds or acid-base groups), there is the possibility to connect them into long chains. One such molecule is a monomer, two identical molecules connected together make a dimer, three make a trimer, and many –mers make a polymer.

We have already seen an example of the polymerisation of ethane:

Different monomers make polymers with different properties. For example polystyrene is stiffer than polyethylene because it contains rigid benzene rings. H2

C CH

n H2C CHn

Simple polymers can be recycled by melting and reforming them.

R H2C CH2 CH2

CH2

R

H2C CH2

R

H2C CH2 H2C CH2

R H2C CH2

H2C CH2

RH2C CH2 H2C CH2

× ~10 000 times

H2C

H2C

n

Polymers continuedIf a polymer still contains bond-forming functional groups after the initial polymerization, the polymer chains can be cross-linked to make the final material elastic or rigid. This cross-linking step is called ‘vulcanisation’ when making rubber. Cross-linked polymers cannot be recycled and decompose rather than melt.

CH3

x y+ S8CH3CH3

CH3CH3

SS

CH3

SS

CH3

Monomers with different properties can be blended to make copolymers.

H2C CH2

CH3 +H2C

By combining the monomers in different ratios, we can get polymers with exactly the properties we require. Copolymers often cannot be recycled, however.

Graphite to BuckyballsGraphite has been known since ancient times. It is made of sheets of fused benzene rings

known as graphene sheets, stacked on top of each other.

The alternating double bonds

mean the electrons can move

along a sheet, because of

resonance, but there are no

direct bonds between the

sheets so the electrons cannot

move perpendicular to a sheet.

The sheets are only weakly

bound to each other. Graphene sheetGraphite

conduction

no

con

du

ction

In 1985, a research team investigating interstellar carbon

discovered a form of carbon closely related to graphite:

buckminster fullerene, C60. This discovery was significant

because it was the first 3-dimensional form of conductive

carbon. Since then, chemists have been able to make various

sizes of fullerenes, generally called ‘buckyballs’. The discovery

of C60 created a whole new field of organic chemistry.

Nanotubes and GrapheneChemists were soon able to adapt buckyball

manufacturing methods to make long tubes,

known as carbon nanotubes. Because the carbon

atoms are joined directly by double covalent

bonds, the nanotubes are extremely strong along

their length, much stronger than simple polymer

chains or an equivalent sized metal wire, and they

also conduct electricity. In addition, because they

are organic molecules, they can be modified with

functional groups.

In 2004, a physicist at Manchester University first

reported the isolation of a sample of graphite

only a few layers thick. By refining these

methods, researchers were soon able to isolate

individual graphene sheets. Graphene sheets are

stronger than diamond in 2-dimenions, conduct

electricity and can be functionalised by organic

chemistry. Functionalising graphene usually

begins by oxidation to produce graphene oxides.

O HO OH

OHO

OH

HO O

OH

O

A piece of a graphene oxide.

Introduction to MechanismsOrganic chemistry often seems confusing because there are so many different reactions.

Aldol reaction Michael reaction

OO+

O

–O

OH

O

O

Here are two examples, at first sight, they look very different and it is easy to think you will never be able to learn a hundred different reactions like these.

ONaOH

or H+

O OHO

+

However, when we look closely at the mechanism of the reaction, i.e. how the reaction happens, we can see that they are very closely related. By remembering only a few basic rules, we can easily remember thousands of different reactions, so let’s study the mechanisms of the aldol and Michael additions and look for common patterns.In both cases, inductive effects from the carbonyl group pull electron density from a neighbouring hydrogen, making it slightly acidic — we have seen this is a very common effect with carbonyl groups. A base can take the proton easily because the resulting anion is stabilised by resonance — we have also seen that this is a common property of carbonyl groups:

Aldol reaction Michael reaction

O

H H

H

O

H H

O

H

H

HO –

––

OO

HH

OO OO

O–

–

–

Introduction to Mechanisms 2

The anion then connects to a ∂+ part of the other molecule, which makes sense since we know that opposite charges attract. The ∂+ charge comes from different effects in the two reactions: inductive effects in the case of the aldol reaction and from resonance in the case of the Michael reaction.

Now we can see that these different-looking reactions are actually very similar. By learning a few rules and looking for patterns, organic chemistry becomes quite simple.

Note that it is always important to keep track of the octet rule and formal charges. This helps to check that you have written the mechanism correctly.

O

HH

–

O

∂+

∂–

O O–O O–

+

O

O

–

O–

O

O

Now we just add a little acid which adds a proton (H+) to the anion, giving us our final molecule.

O O–

H+O OH

O–

O

O

OH

O

O

H+

Quiz1. Which of the following molecules/ions are commonly thought of as organic molecules

C OO

C

CCC

CCC

CCC

H

CH

HC

N HH

H

H

C N–a. b. c. d.H

CHH

OC

H

HH

e.

2. How many hydrogens are attached to the indicated carbon atoms?

HN +a.

b.

c.

3. Which of the following diagrams shows a constitutional isomer of 3-methylhexane? 3-methylhexane

a. b. c. d. e. f.