Molecule

An Introduction to
Organic Chemistry

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A beginners' guide to the chemistry of Carbon compounds


What is Organic Chemistry?

The word Organic is one of the most overused in the English language.

People use it as a derogatory term in phrases like Don't eat that; it's not organic. Of course, there is a precise scientific definition of the word. In science, Organic can be a biological or chemical term. In Biology it means any thing that is living or has lived. The opposite is Non-Organic. In Chemistry, an Organic compound is one containing Carbon atoms. The opposite term is Inorganic.

It's the Chemical meaning I want to explore in this essay.


Molecules

All substances are made up of molecules which are collections of atoms. All the molecules in existence are made up of about a hundred different kinds of atoms.

For example, a water molecule is composed of two atoms of Hydrogen and one atom of Oxygen. We write its formula as H2O.

A molecule of Sulphuric Acid contains two atoms of Hydrogen, one atom of Sulphur and four atoms of Oxygen. Its formula is H2SO4.

These are simple molecules containing only a few atoms. Most Inorganic molecules are small. Below are a few common inorganic substances with their formulas.

Name of Substance
Formula
Carbon Dioxide CO2
Salt NaCl
Nitric Acid HNO3
Laughing Gas N2O
Ammonia NH3
Saltpetre
(used in gunpowder)
KNO3
Carbon Monoxide CO
Potassium Permanganate
(used in labs)
KMnO4
Calcium Carbonate
(chalk)
CaCO3

All of these molecules have less than a dozen atoms.

The symbols Ca, K, Mn, Na and Cl stand for calcium, potassium, manganese, sodium and chlorine.


Molecules With Carbon

Most atoms are only capable of forming small molecules. However one or two can form larger molecules.

By far and away the best atom for making large molecules with is Carbon. Carbon can make molecules that have tens, hundreds, thousands even millions of atoms! The huge number of possible combinations means that there are more Carbon compounds that those of all the other elements put together!

A single Carbon atom is capable of combining with up to four other atoms. We say it has a valency of 4. Sometimes a Carbon atom will combine with fewer atoms.

The Carbon atom is one of the few that will combine with itself.
In other words Carbon combines with other Carbon atoms.

This means that Carbon atoms can form chains and rings onto which other atoms can be attached.

This leads to a huge number of different compounds. Organic Chemistry is essentially the chemistry of Carbon

Carbon compounds are classified according to how the Carbon atoms are arranged and what other groups of atoms are attached.


Hydrocarbons

The simplest Organic compounds are made up of only Carbon and Hydrogen atoms only. Even these run into thousands! Compounds of Carbon and Hydrogen only are called Hydrocarbons.

Please note that the molecule structure images below show the structure of three dimensional molecules in two dimensional format.

Alkanes

The simplest Hydrocarbon is methane, CH4. This is the simplest member of a series of hydrocarbons. Each successive member of the series has one more Carbon atom than the preceeding member. This is shown in the table below.

Formula
Structure
Name / Uses
CH4 Methane Methane - gas used for cooking.
C2H6 Ethane Ethane
C3H8 Propane Propane - heating fuel.
C4H10 Butane Butane - lighter / camping fuel.
C5H12 Pentane Pentane
C6H14 Hexane Hexane

As the reader can see, there is a series of these compounds with this general formula:

CnH2n+2

This series of compounds are called alkanes. The lighter ones are gases and used as fuels. The middle ones (7 Carbons to 12 Carbons) are liquids used in petrol (gasoline). The higher ones are waxy solids. Candle wax is a mixture of alkanes.

After Butane, the names of these compounds are from the Greek for the number of Carbon atoms followed by the suffix -ane. So, Decane would have the formula

C10H22.

Polythene is a very large alkane with millions of atoms in a single molecule. Apart from being flammable, alkanes are stable compounds found underground.

In the alkanes, all four of the Carbon valency bonds are taken up with links to different atoms. These types of bonds are called single bonds and are generally stable and resistant to attack by other chemicals. Alkanes contain the maximum number of Hydrogen atoms possible. They are said to be saturated.

The alkanes are not the only hydrocarbons.


Alkenes

Another series of compounds is called the alkenes. These have a general formula:

CnH2n.

Alkenes have fewer hydrogen atoms than the alkanes. The extra valencies left over occur as double bonds between a pair of Carbon atoms. The double bonds are more reactive than single bonds making the alkenes chemically more reactive.

The simplest alkenes are listed in the table below:

Formula
Structure
Name / Uses
C2H4 Ethene Ethene - used as an industrial starter chemical.
C3H6 Propene Propene
C4H8 Butene Butene
C5H10 Pentene Pentene
C6H12 Hexene Hexene

These compounds are named in a similar manner to the alkanes except that the suffix is -ene.


Alkynes

A third series are the alkynes. These have the following formula:

CnH2n-2.

Alkynes have two carbon atoms joined by a tripple bond. This is highly reactive making these compounds unstable.

Examples of alkynes are:

Formula
Structure
Name / Uses
C2H2 Ethyne Ethyne - better known as acetylene which is used for welding underwater.
C3H4 Propyne Propyne
C4H6 Butyne Butyne
C5H8 Pentyne Pentyne
C6H10 Hexyne Hexyne

These highly reactive substances have many industrial uses.

Again the naming of these compounds is similar to the alkanes except that the suffix is -yne.


Carbon Rings

Alkanes, alkenes and alkynes all contain Carbon atoms in linear chains. There are also hydrocarbons arranged in rings. Some examples follow:

Formula
Structure
Name / Uses
C6H12 Cyclohexane Cyclohexane - a saturated hydrocarbon with the atoms arranged in a hexagonal ring. In organic chemistry, the presence of Hydrogen atoms is often assumed and this compund can be reprsented by a hexagonal ring:

Cyclohexane Ring
C6H6 Benzene Benzene - an industrial solvent.

The Benzene Ring is one of the most important structures in organic chemistry. In reality, its alternate double and single bonds are "spread around" the ring so that the molecule is symetrical. This structure is represented by a hexagon with a circle:

Benzene Ring
C7H8 Toluene Toluene - an important solvent and starter chemical.

Using the Benzene Ring, this molecule can also be depicted as:

Toluene Ring
C10H8 Naphthalene Naphthalene - used in moth balls.

This can be depicted as two fused Benzene Rings:

Naphthalene Ring

When rings are combined with chains, the number of hydrocarbons is virtually infinite.

And we are still using only two types of atoms (Carbon and Hydrogen). We will now add a third.


Carbon, Hydrogen and Oxygen

When Oxygen atoms are added, the variety of compounds grows enormously. In the table below, each row discusses a series of compounds.

General FormulaSeries NameDetails Examples
Structures
CnH2n+1OH Alcohols Alcohols have the OH (hydroxyl) group in the molecule.

A group of atoms that gives an organic series its distinctive character is called a functional group.

CH3OH
Methanol
wood alcohol

C2H5OH
Ethanol
drinking alcohol

C6H5OH
Phenol
carbolic acid - used as disinfectant

Methanol Ethanol
Phenol
(CnH2n+1)2O Ethers Ethers have an O atom attached to two hydrocarbon chains (or rings). (CH3)2O
Dimethyl Ether
a gas

(C2H5)2O
Diethyl Ether
a liquid used as an anaesthetic)

Dimethyl Ether Diethyl Ether
(CnH2n+1)2CO Ketones Ketones have a CO group attached to two hydrocarbon chains (or rings). CH3COCH3
Dimethyl Ketone
Also known as acetone: nail-varnish remover

Dimethyl Ketone
CnH2n+1CHO Aldehydes Aldehydes have a CHO group attached to a hydrocarbon chain (or ring). HCHO
Formaldehyde
preservative in labs

CH3CHO
Acetaldehyde

Formaldehyde Acetaldehyde
CnH2n+1CO2H Fatty Acids Fatty Acids contain the CO2H (or COOH) group attached to a hydrocarbon chain or ring. HCO2H
Formic Acid
in ant bites and stinging nettles

CH3CO2H
Acetic Acid
vinegar

C2H5CO2H
Butyric Acid
the rancid butter smell

Formic Acid Acetic Acid Butyric Acid
RCO2R'

(R, R' are Hydrocarbon chains or rings).

Esters Esters are similar to Fatty Acids except that the H in the COOH group is another hydrocarbon chain. They are usually very sweet smelling liquids used in perfumes. CH3CO2CH3
Methyl Methoate
essence of pear drops
Methyl Methoate

In the above examples, each molecule has a single functional group.

It is possible to have two or more functional groups on a molecule. These can be the same group (as in Oxalic Acid - a poison found in rhubarb leaves - which has two fatty acid groups) or different (as in Hydroxymethanoic Acid - which has a hydroxyl group and a fatty acid group):

Oxalic Acid

(COOH)2 : Oxalic Acid

Hydroxymethanoic Acid
CH2OHCOOH : Hydroxymethanoic Acid

The most famous compounds containing Carbon, Hydrogen and Oxygen are the Carbohydrates. An example is the common sugar, Sucrose (C12H22O11).

This shows how varied and complex even simple organic compounds can be. Sucrose has a pair of rings: one hexaganol, the other pentaganol. Each ring contains an Oxygen atom. The rings are joined by an Oxygen (Ether) link. The entire compound contains several Hydroxyl (OH) groups.

Sucrose
Sucrose


Isomerism

An interesting phenomenon with organic molecules is called isomerism. Let us look at two compounds introduced earlier.

Dimethyl Ether: (CH3)2O and Ethanol: C2H5OH.

The first is a gas which will knock you out if inhaled. The second is common alcohol drunk in spirits. The two molecules are shown below.

Dimethyl Ether

Dimethyl Ether

Ethanol

Ethanol

Notice that both compounds contain 2 Carbon atoms, 6 Hydrogen atoms and 1 Oxygen atom.

Even though the atoms are the same, they are arranged differently. This yields two different compounds with the same number of atoms. These compounds are isomers and the phenomenon is called Isomerism.

In this example, the two molecules have different functional groups. They are structural isomers. Other types of isomers exist.

Isomerism increases the number of Organic compounds. The more Carbon atoms in a compound, the more ways of arranging the atoms and the larger number of isomers.


Adding Nitrogen

Many very important organic compounds contain Nitrogen. This produces more series of compounds.

General FormulaSeries NameDetails Examples
Structures
CnH2n+1NH2 Amines Amines have one or more of the Hydrogen atoms in Ammonia (NH3) replaced by a Hydrocarbon chain or ring.

Primary Amines have the formula RNH2

Secondary Amines have the formula RR'NH

Tertiary Amines have the formula RR'R''N.

(R, R', R'' are Hydrocarbon chains or rings).

CH3NH2
Methylamine
a pungent, water soluble gas
Methylamine
CnH2n+1CN Cyanides Cyanides have the CN group. CH3CN
Methyl Cyanide
Methyl Cyanide
CnH2nNH2COOH Amino Acids Amino Acids have two functional groups: the amine (NH2) group and the fatty acid (COOH) group.

Amino Acids combine together to form proteins which are an important component of living organisms.

CH2NH2COOH
Glycine
the simplest amino acid.
Glycine

A famous compound containing Nitrogen is Trinitro Toluene (C6H2CH3(NO2)3 - usually abbreviated to TNT). This is an artificially made explosive. Its structure is shown below:

Tri Nitro Toluene

Trinitro Toluene (TNT)

There are six isomers of this compound as the three NO2 groups can be placed in six different arrangements on the ring. These are known as positional isomers.


Other Atoms

The vast majority of organic compounds contain Carbon, Hydrogen, Oxygen and Nitrogen. Other types of atoms can be included to form even more compounds. These can contain atoms like Phosphorus, Sulphur (e.g. Thiamine, Vitamin B1), Magnesium (e.g. Chlorophyll) and Iron (e.g. Haemoglobin).

As can be imagined, these additions increase the number of compounds. Apart from the naturally occurring Organic compounds, millions more can be synthesised. These can include atoms like Chlorine (used in pesticides). Examples of organic compounds containing Chlorine are shown below.

There is no difference between the same substance extracted from living organisms and made in a laboratory.

Formula
Structure
Name / Uses
CHCl3 Chloroform Chloroform - a human-made anaesthetic.
C14H9Cl5 Dichloro Diphenyl Trichloro Methane Dichloro Diphenyl Trichloro Methane - DDT an insecticide.

I hope this introduction to Organic Chemistry indicates just how vast and interesting the subject is.

© 1998, 2005 KryssTal


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