Carbon Compounds

John Leaver

Organic Chemistry

• The vast majority of the compounds of the element carbon are called ‘Organic Compounds’ and their study is known as ‘Organic Chemistry’.

• Their large number is a consequence of the ability of carbon atoms to link together to form ‘chains’ and ‘rings’

Why ‘organic’ compounds?

• These substances are frequently found in living, or once living, matter – hence the name organic.

• It was once thought that they could only be created by ‘organic’ processes (i.e. from living material).

Note on Nomenclature

• The naming of organic compounds is an extensive subject with its own literature.

• This presentation is concerned more with giving an impression of the variety of organic compounds

• No attempt will be made in this session to teach the rules for naming organic compounds in a systematic way

• Although you are likely to ‘pick up’ some aspects of the topic

Hydrocarbons• The least complicated organic

compounds, with respect to their chemical behaviour, are those that contain only carbon and hydrogen atoms. These are called ‘hydrocarbons’.

• There are several classes of hydrocarbon – they differ with respect to the bonding present between carbon atoms.

Alkanes (old name ‘paraffins’)

• In alkanes there are only single bonds between carbon atoms.

• Each carbon atom is able to form four bonds in total

• In alkanes all ‘spare’ bonds are to hydrogen atoms

Alkanes – Example: Butane

CH3CH2

CH2

CH3

Butane C4H10 or CH3CH2CH2CH3 is a gas used as a fuel

A chain of Four carbonatoms joined by single bonds

All remaining bonds have hydrogen atoms attached, each carbon atom having four bonds in total

Note on the Representation of Organic Molecules

• It is important to be aware that in all but the most introductory of text books it is usual to assume the presence of most of the carbon and hydrogen atoms when depicting organic molecules

• Hence butane is more commonly shown as:

Representation of molecules - 2

You may also see 3D representations of molecules in ‘ball and stick’ form:

Representation of molecules - 3

• You may also encounter ‘space filling’ views that give an indication of the ‘surface’ of the molecule

General formula for Alkanes

• The molecular formulae of the series of straight chain alkanes may be represented by the following formula:

CnH2n+2

• The first fifteen are named on the next slide (notice that after the first four the name tells you how many carbon atoms are present).

Names of Alkanes• Methane (n=1)• Ethane (n=2)• Propane (n=3)• Butane (n=4)• Pentane (n=5)• Hexane (n=6)• Heptane (n=7)• Octane (n=8)

•Nonane (n=9)

•Decane (n=10)

•Undecane (n=11)

•Dodecane (n=12)

•Tridecane (n=13)

•Tetradecane (n=14)

•Pentadecane (n=15)As chain length increases physical properties change:

e.g. at room temp n=(1-4) gases, n=(5-16) liquids, n>16 solids

More complex alkane chains

• It is also possible to have branched alkane chains such as:

8-butyl-5,11-diethyl-pentadecane

This should help to indicate theenormous possibilities with respectto both size and complexity for alkanemolecules

Alkenes (old name ‘olefins’)

• Alkenes contain at least one example of a double bond between carbon atoms.

• As with alkanes, the remaining (non Carbon to Carbon) bonds are to hydrogen atoms.

• Alkenes are said to be ‘unsaturated’ i.e. there is scope for the addition of other atoms or radicals.

• They are therefore more chemically reactive than the ‘saturated’ alkanes.

Alkenes – Example: But-2-ene

CH3CH

CH

CH3

Double bond

The ‘2’ indicatesthe position ofthe bond

NB Alkenes have a higher percentage of carbon than do alkanes – they thereforeburn with a smokier flame

But-2-ene: other representations

The double bond on the ball and stick structure is represented by being shorter than the single bonds (more electrons are involved in forming the bond so thecarbon atoms are pulled closer together)

More complex alkenes

• Obviously hydrocarbon molecules may contain more than one double bond

• They are then ‘poly-unsaturated’:

CH3CH2

CHCH

CH3

CHCH

CH3

CH

CH

CH3

Alkynes (old name ‘acetylenes’)

• Alkynes are hydrocarbons containing at least one ‘triple bond’ between carbon atoms. They are rather reactive compounds.

• The simplest example is ethyne:

CH CH

Cyclic hydrocarbons

• As well as chains of carbon atoms it is also possible to have rings

• These are called cyclic compounds• The three sorts of hydrocarbon we

have seen so far can exist in rings and these are called cycloalkanes, cycloalkenes and cycloalkynes respectively (the latter are not commonly encountered)

Cycloalkanes and Cycloalkenes

• Some examples:

CH2CH

CH

CHCH

CH2CH2 CH2

CH2

CH2CH2

Cyclohexane

Cyclopenta-1,3-diene

CH2

CH

CH2

CH3

Methylcyclopropane

Aromatic compounds

• It might be supposed that a compound with this structure would be named cyclohexa-1,3,5-triene and would behave as though it had alternate single and double bonds

• However, when a ring of six carbon atoms, each attached to one hydrogen atom is made, it behaves as though all the carbon-carbon bonds are equivalent

CH

CHCH

CH

CHCH

Benzene

• In such a ring structure as on the previous slide the bonding electrons are able to spread around the ring (or ‘delocalise’) and the C6H6 ring is actually called benzene

• Compounds containing this structure are called ‘aromatic’ compounds

Representing benzene

• Sometimes it is convenient to represent benzene rings with alternate single and double bonds, like this:

• Alternatively they may also be represented by a hexagon containing a circle to indicate the delocalised electrons:

Other aromatic hydrocarbons

• It is possible for several benzene rings to join together to make larger molecules, such as:

anthracene phenanthrene

Heterocyclic Compounds• It is also possible for one or more of the

carbon atoms in a ring system to be replaced by another sort of atom (for example oxygen or nitrogen)

• Such compounds are called ‘heterocyclic’

• Many important biological molecules are heterocyclic (e.g. see sugars later)

Example of a Heterocyclic Compound

OHO

OH

OH

Deoxy-ribose

Functional Groups

• Organic chemicals often display characteristic properties as a consequence of the functional groups that they contain

• Functional groups are small groups of atoms that allow the molecule to react with other molecules in specific ways.

• Some examples will be found on the following few slides

Some Important Functional Groups

Class Formula Example Name

Alcohol -OH CH3OH Methanol

Aldehyde -CHO CH3CHO Ethanal

Amine -NH2 CH3NH2Methylamine

Carboxylic acid -COOH CH3COOH Ethanoic acid

Ester -COOR CH3COOCH3Methyl

methanoate

Ether -O- CH3OCH3Methoxymethane

Halogens -X CH3Br Methyl bromide

Ketone =CO CH3(CO)CH3Propanone

Functional Groups in more detail

• In the next few slides we will look at each of the functional groups from the table

• In particular we will consider:• Alternative names• Properties• Biological examples

Alcohols – the hydroxy group, -OH• Alcohols contain the hydroxy group, OH.

• E.g. CH3CH2OH ethanol or ethyl alcohol (a familiar compound to many)

cyclohexanol

OH OH

Phenol

The aromatic alcohols are known as phenols

Alcohols - 2

• Alcohols sometimes have a pleasant odour although the longer chain alcohols can have a rather ‘sickly’ smell. Aromatic alcohols have a sharper smell.

• Many alcohols are flammable.• Some liquid alcohols (those with

shorter chains and smaller rings) are also used as solvents and are miscible to some extent with water.

Alcohols - 3• The hydroxy group is common in biological

molecules and pharmaceutical compounds:

OH

OH

OH

OH

OOH

-D–glucose (a sugar)

OH

OH

CH2CH2NH2

Dopamine (a neural transmitterand sympathomimetic drug)

Aldehydes -CHO

• The simplest aldehyde is ‘formaldehyde’ HCHO (proper name, methanal,) used to preserve biological specimens.

• The aldehyde structure contains a ‘carbonyl’ group (C=O)

CH3

O

HEthanal

(old name, Acetaldehyde)

Aldehydes - 2

• Aldehydes are often rather pungent.

CHOBenzaldehyde – is the constituent of almonds that

gives them their characteristic ‘marzipan’

smell

Aldehydes - 3

• The carbonyl group in aldehydes makes them somewhat reactive

• Under the right conditions aldehydes may be ‘reduced’ to alcohols or ‘oxidized’ to carboxylic acids

OHO

H

O

OHreduction oxidation

Aldehydes - 4• Examples of the aldehyde group in

biological/medicinal compounds

CHO

OH

CHO

OMe

Vanillin

Cinnamaldehyde

Amines – the amino group NH2

• Simple examples are:

NH2H

CH3NH2

methylamineor

aminomethane

NH2

cyclohexylamineor

aminocyclohexane

aminobenzeneor

aniline

Amines - 2• Amines often have a ‘fishy’ odour

and are associated with decomposition:

“Putrescine”(butane-1,4-diamine)

“Cadaverine”(pentane-1,5-diamine)

Both compounds are found in

decomposing corpses!

Amines - 3

• Examples of the amino group in biological/medicinal compounds

N

N

CHNHCHN

NH2

Adenine – one of the fivenucleic acid bases

NH2

Amphetamine – a CNSstimulant etc

Carboxylic acids -COOH

• Common example:

CH3

O

OH

Ethanoic acid (CH3COOH) – commonly known as ‘acetic acid’. The active ingredient of vinegar.

It forms when ethanol is oxidised, causing the vinegary taste of stale

wine.

Carboxylic acids - 2

• The smaller carboxylic acids tend to be pungent, corrosive liquids:

OH

O ‘Formic acid’ or methanoic acid (HCOOH) – a corrosive substance sprayed by ants

CH3 OH

O‘Butyric acid’ or butanoic acid

occurs in rancid butter and stale sweat

Carboxylic acids - 3

• Biological/medicinal examples of compounds containing -COOH

CH2

CH2

OH O

OH

O

OH

O OH

Citric acid – gives citrusfruits their sharp flavour

NH

O

OH

O OH

Kainic acid –

an anthelmintic

Esters –COOC-

• Esters form when carboxylic acids react with alcohols. They often have fruity odours:

CH3

O

O CH3

For example:Pineapples smellof ethyl propanoateCH3CH2COOCH2CH3

and other esters

‘Ester linkage’

Esters - 2

• Biological/medicinal examples

Dimethy phthalate (‘DIMP’)an insect repellent

benzocaine – a localanaesthetic

NH2O

O

Ethers: -O-• Ethers contain carbon atoms linked by

an oxygen atom• The oxygen atom may link chains or

rings, or be within a ring (cyclic ethers).

CH3CH2

OCH2

CH3

diethyl ether or ethoxyethanecommonly just called ‘ether’

O

O

O

O

O

O

A ‘crown’ ether –this one is 18-crown-6

Ethers - 2

• The smaller ethers are liquids with low boiling points, flammable and immiscible with water

• They are used as solvents• Ethers are generally rather un-reactive• Diethyl ether has been used as an

anaesthetic• Larger ethers with many ether links

may be water miscible

Ethers - 3

• Biological/medicinal examples

O

Cineole (1,3,3-trimethyl-2-oxabicyclo[2.2.2]octane) aconstituent of eucalyptus oil

O

O

O

Myristicin – a psychotropicconstituent of Nutmeg

Halogen compounds: -X

• The halogens fluorine (F), chlorine (Cl), bromine (Br) and iodine (I) may bind to carbon atoms in organic compounds

• The properties of these compounds are rather diverse as a consequence of the differences between the chemical properties of the halogens

• Some examples will be found on the next slide

Halogen compounds - 2Cl

Cl

Cl

H

trichloromethaneor ‘chloroform’ asolvent and anaesthetic

O

O

Br

‘Circladin’ ananticoagulant

F

OH

OOH

‘Capacin, athyroid inhibitor

O

OH O

I I

IO

NH

O

OHO

II

I O

NH

Myelotrast aradio-opaqueagent

Ketones: C=O

• Ketones contain a carbonyl group, C=O

• Smaller ketone molecules are liquids and are often good solvents for other organic compounds

• Acetone (propan-2-one) is a commonly used solvent:

CH3 CH3

O

Ketones - 2

• Biological/medicinal examples

O

Carvone – aconstituent of Carawayoil with carminative properties

O

O

‘Entobex’ ananti-amoebic

Bio-molecules

• The following few slides briefly outline some of the classes of bio-molecules that you may encounter:– Amino acids– Carbohydrates– Fatty acids– Peptides– Sugars– Vitamins

Amino acids• The molecules which combine to

make protein chains and polypeptides• They contain an amino group and a

carboxylic acid group:

Alanine Aspartic acid

Carbohydrates

• A group of compounds such as sugars, starches and celluloses that are found in plants and animals

• They have the general formula Cx(H2O)y

Fructose

Fatty acids

• A general term for saturated and unsaturated aliphatic carboxylic acids.

• The longer chain fatty acids are obtained from animal and vegetable fats.

Stearic oroctadecanoicacid – obtainedfrom animal fat

Peptides• Molecules composed of sequences of

amino acids joined by ‘peptide linkages’.• They may be just two amino acids

(dipeptides) or a few (oligopeptides) or many (polypeptides)

Phenylalanine

Aspartic acid A dipeptide

Peptidelink

Sugars

• Water soluble carbohydrate molecules occurring in plants and animals

O H

OHH

OH

H

OHH

OH O OH

OHOH

OH

Three different representations of the samesugar molecule

CH2OH

OHH

H OH

H OH

H

O

Vitamins

• The vitamins are a structurally heterogeneous group of compounds which are needed, usually in small amounts, for an organism to function

• Two examples follow, showing the lack of chemical similarity

Vitamin B12

N

Co+

N

N

N

NN

O

PN

OO

OONH

O

O

O

O

OH

O

O

O

C

C

C

CNH2

NH2

NH2

C

NH2

NH2

NH2

C C

C

OH

C

C

C

HHH

H

Vitamin C

Some more examples

• Organic compounds are used for a great variety of different purposes.

• Often a molecule will contain more than one of the functional groups (and others that have not been mentioned).

• The following few slides give some indication of the variety of organic compounds.

Aspirin

• Aspirin is:• 2-ethanoyloxybenzoic

acid

• It has been in use as an analgesic and anti-inflammatory drug for many years, having been introduced in 1899 by Baeyer.

O

O CH3

O

OH

Caffeine

• The stimulant that occurs in

tea, coffee and some

carbonated drinks N

NN

N

O

CH3

OCH3

CH3

1,3,7-trimethyl-3,7-dihydropurine-2,6,-dione

Camphor

• A compound used in some medicinal preparations such as liniments. It is obtained from the wood of a tropical tree.

CH3CH3

CH3O

1,7,7-trimethylbicyclo[2.2.1]heptan-2-one

Nicotine• An addictive

component of tobacco. It is addictive in small doses but highly toxic in larger doses and causes nausea, convulsions and death.

N

NCH3

Nicotine or 3-(1-methylpyrrolidin-2-

yl)pyridine

Quinine

• Anti-malarial extracted from bark of S. American tree

N

N

CH2

OH

OCH3

(6-methoxyquinoline-4-yl)-(5-vinyl-1-azabicyclo[2.2.2]oct-2-yl)-methanol

Saccharin

• Artificial sweetener

S

O

NH

O O

1,1-dioxo-1,2-dihydro-1lambda*6*-benzo[d]isothiazol-3-one

Xylocaine

• Local anaesthetic used in dentistry

CH3

CH3

NH

ONH+

Cl

[(2,6-dimethyl-phenylcarbonyl)-methyl]diphenylammonium chloride

Conclusion• The aims of this session were to:

– indicate the diversity of carbon compounds, especially in the context of biology and medicine

– allow you to gain some knowledge of the different functional groups

– indicate the complexity and vast number of carbon compounds you may encounter

– allow you to identify some of the broad classes of carbon compounds

– become more familiar with ways of representing organic molecules